scholarly journals Cell Tracking for Organoids: Lessons From Developmental Biology

Author(s):  
Max A. Betjes ◽  
Xuan Zheng ◽  
Rutger N. U. Kok ◽  
Jeroen S. van Zon ◽  
Sander J. Tans

Organoids have emerged as powerful model systems to study organ development and regeneration at the cellular level. Recently developed microscopy techniques that track individual cells through space and time hold great promise to elucidate the organizational principles of organs and organoids. Applied extensively in the past decade to embryo development and 2D cell cultures, cell tracking can reveal the cellular lineage trees, proliferation rates, and their spatial distributions, while fluorescent markers indicate differentiation events and other cellular processes. Here, we review a number of recent studies that exemplify the power of this approach, and illustrate its potential to organoid research. We will discuss promising future routes, and the key technical challenges that need to be overcome to apply cell tracking techniques to organoid biology.

2020 ◽  
Vol 1 ◽  
Author(s):  
Jonas Bertels ◽  
Gerrit T.S. Beemster

Abstract Growth is one of the most studied plant responses. At the cellular level, plant growth is driven by cell division and cell expansion. A means to quantify these two cellular processes is through kinematic analysis, a methodology that has been developed and perfected over the past decades, with in-depth descriptions of the methodology available. Unfortunately, after performing the lab work, researchers are required to perform time-consuming, repetitive and error-prone calculations. To lower the barrier towards this final step in the analysis and to aid researchers currently applying this technique, we have created leafkin, an R-package to perform all the calculations involved in the kinematic analysis of monocot leaves using only four functions. These functions support leaf elongation rate calculations, fitting of cell length profiles, extraction of fitted cell lengths and execution of kinematic equations. With the leafkin package, kinematic analysis of monocot leaves becomes more accessible than before.


2014 ◽  
Vol 5 ◽  
pp. 1193-1202 ◽  
Author(s):  
Dorothea Brüggemann ◽  
Johannes P Frohnmayer ◽  
Joachim P Spatz

Many cellular processes, such as migration, proliferation, wound healing and tumor progression are based on cell adhesion. Amongst different cell adhesion molecules, the integrin receptors play a very significant role. Over the past decades the function and signalling of various such integrins have been studied by incorporating the proteins into lipid membranes. These proteolipid structures lay the foundation for the development of artificial cells, which are able to adhere to substrates. To build biomimetic models for studying cell shape and spreading, actin networks can be incorporated into lipid vesicles, too. We here review the mechanisms of integrin-mediated cell adhesion and recent advances in the field of minimal cells towards synthetic adhesion. We focus on reconstituting integrins into lipid structures for mimicking cell adhesion and on the incorporation of actin networks and talin into model cells.


Biology ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 163
Author(s):  
Swapnil Gupta ◽  
Panpan You ◽  
Tanima SenGupta ◽  
Hilde Nilsen ◽  
Kulbhushan Sharma

Genomic integrity is maintained by DNA repair and the DNA damage response (DDR). Defects in certain DNA repair genes give rise to many rare progressive neurodegenerative diseases (NDDs), such as ocular motor ataxia, Huntington disease (HD), and spinocerebellar ataxias (SCA). Dysregulation or dysfunction of DDR is also proposed to contribute to more common NDDs, such as Parkinson’s disease (PD), Alzheimer’s disease (AD), and Amyotrophic Lateral Sclerosis (ALS). Here, we present mechanisms that link DDR with neurodegeneration in rare NDDs caused by defects in the DDR and discuss the relevance for more common age-related neurodegenerative diseases. Moreover, we highlight recent insight into the crosstalk between the DDR and other cellular processes known to be disturbed during NDDs. We compare the strengths and limitations of established model systems to model human NDDs, ranging from C. elegans and mouse models towards advanced stem cell-based 3D models.


2019 ◽  
Vol 48 (D1) ◽  
pp. D890-D895 ◽  
Author(s):  
Zhuang Xiong ◽  
Mengwei Li ◽  
Fei Yang ◽  
Yingke Ma ◽  
Jian Sang ◽  
...  

Abstract Epigenome-Wide Association Study (EWAS) has become an effective strategy to explore epigenetic basis of complex traits. Over the past decade, a large amount of epigenetic data, especially those sourced from DNA methylation array, has been accumulated as the result of numerous EWAS projects. We present EWAS Data Hub (https://bigd.big.ac.cn/ewas/datahub), a resource for collecting and normalizing DNA methylation array data as well as archiving associated metadata. The current release of EWAS Data Hub integrates a comprehensive collection of DNA methylation array data from 75 344 samples and employs an effective normalization method to remove batch effects among different datasets. Accordingly, taking advantages of both massive high-quality DNA methylation data and standardized metadata, EWAS Data Hub provides reference DNA methylation profiles under different contexts, involving 81 tissues/cell types (that contain 25 brain parts and 25 blood cell types), six ancestry categories, and 67 diseases (including 39 cancers). In summary, EWAS Data Hub bears great promise to aid the retrieval and discovery of methylation-based biomarkers for phenotype characterization, clinical treatment and health care.


1998 ◽  
Vol 111 (5) ◽  
pp. 541-547 ◽  
Author(s):  
M.S. Balda ◽  
K. Matter

Tight junctions are the most apical intercellular junctions of epithelial and endothelial cells and create a regulatable semipermeable diffusion barrier between individual cells. On a cellular level, they form an intramembrane diffusion fence that restricts the intermixing of apical and basolateral membrane components. In addition to these well defined functions, more recent evidence suggests that tight junctions are also involved in basic cellular processes like the regulation of cell growth and differentiation.


2002 ◽  
Vol 227 (9) ◽  
pp. 724-752 ◽  
Author(s):  
Corrine Welt ◽  
Yisrael Sidis ◽  
Henry Keutmann ◽  
Alan Schneyer

It has been 70 years since the name inhibin was used to describe a gonadal factor that negatively regulated pituitary hormone secretion. The majority of this period was required to achieve purification and definitive characterization of inhibin, an event closely followed by identification and characterization of activin and follistatin (FS). In contrast, the last 15–20 years saw a virtual explosion of information regarding the biochemistry, physiology, and biosynthesis of these proteins, as well as identification of activin receptors, and a unique mechanism for FS action—the nearly irreversible binding and neutralization of activin. Many of these discoveries have been previously summarized; therefore, this review will cover the period from the mid 1990s to present, with particular emphasis on emerging themes and recent advances. As the field has matured, recent efforts have focused more on human studies, so the endocrinology of inhibin, activin, and FS in the human is summarized first. Another area receiving significant recent attention is local actions of activin and its regulation by both FS and inhibin. Because activin and FS are produced in many tissues, we chose to focus on a few particular examples with the most extensive experimental support, the pituitary and the developing follicle, although nonreproductive actions of activin and FS are also discussed. At the cellular level, it now seems that activin acts largely as an autocrine and/or paracrine growth factor, similar to other members of the transforming growh factor β superfamily. As we discuss in the next section, its actions are regulated extracellularly by both inhibin and FS. In the final section, intracellular mediators and modulators of activin signaling are reviewed in detail. Many of these are shared with other transforming growh factor β superfamily members as well as unrelated molecules, and in a number of cases, their physiological relevance to activin signal propagation remains to be elucidated. Nevertheless, taken together, recent findings suggest that it may be more appropriate to consider a new paradigm for inhibin, activin, and FS in which activin signaling is regulated extracellularly by both inhibin and FS whereas a number of intracellular proteins act to modulate cellular responses to these activin signals. It is therefore the balance between activin and all of its modulators, rather than the actions of any one component, that determines the final biological outcome. As technology and model systems become more sophisticated in the next few years, it should become possible to test this concept directly to more clearly define the role of activin, inhibin, and FS in reproductive physiology.


2008 ◽  
Vol 36 (5) ◽  
pp. 868-873 ◽  
Author(s):  
Ana Talamillo ◽  
Jonatan Sánchez ◽  
Rosa Barrio

SUMOylation, a reversible process used as a ‘fine-tuning’ mechanism to regulate the role of multiple proteins, is conserved throughout evolution. This post-translational modification affects several cellular processes by the modulation of subcellular localization, activity or stability of a variety of substrates. A growing number of proteins have been identified as targets for SUMOylation, although, for many of them, the role of SUMO conjugation on their function is unknown. The use of model systems might facilitate the study of SUMOylation implications in vivo. In the present paper, we have compiled what is known about SUMOylation in Drosophila melanogaster, where the use of genetics provides new insights on SUMOylation's biological roles.


Photonics ◽  
2021 ◽  
Vol 8 (9) ◽  
pp. 383
Author(s):  
Mariana Potcoava ◽  
Jonathan Art ◽  
Simon Alford ◽  
Christopher Mann

Stimuli to excitable cells and various cellular processes can cause cell surface deformations; for example, when excitable cell membrane potentials are altered during action potentials. However, these cellular changes may be at or below the diffraction limit (in dendrites the structures measured are as small as 1 µm), and imaging by traditional methods is challenging. Using dual lenses incoherent holography lattice light-sheet (IHLLS-2L) detection with holographic phase imaging of selective fluorescent markers, we can extract the full-field cellular morphology or structural changes of the object’s phase in response to external stimulus. This approach will open many new possibilities in imaging neuronal activity and, overall, in light sheet imaging. In this paper, we present IHLLS-2L as a well-suited technique for quantifying cell membrane deformation in neurons without the actuation of a sample stage or detection microscope objective.


2015 ◽  
Vol 112 (40) ◽  
pp. E5543-E5551 ◽  
Author(s):  
Kamila Kalinowska ◽  
Marie-Kristin Nagel ◽  
Kaija Goodman ◽  
Laura Cuyas ◽  
Franziska Anzenberger ◽  
...  

Ubiquitination is a signal for various cellular processes, including for endocytic degradation of plasma membrane cargos. Ubiquitinating as well as deubiquitinating enzymes (DUBs) can regulate these processes by modifying the ubiquitination status of target protein. Although accumulating evidence points to the important regulatory role of DUBs, the molecular basis of their regulation is still not well understood. Associated molecule with the SH3 domain of signal transduction adaptor molecule (STAM) (AMSH) is a conserved metalloprotease DUB in eukaryotes. AMSH proteins interact with components of the endosomal sorting complex required for transport (ESCRT) and are implicated in intracellular trafficking. To investigate how the function of AMSH is regulated at the cellular level, we carried out an interaction screen for the Arabidopsis AMSH proteins and identified the Arabidopsis homolog of apoptosis-linked gene-2 interacting protein X (ALIX) as a protein interacting with AMSH3 in vitro and in vivo. Analysis of alix knockout mutants in Arabidopsis showed that ALIX is essential for plant growth and development and that ALIX is important for the biogenesis of the vacuole and multivesicular bodies (MVBs). Cell biological analysis revealed that ALIX and AMSH3 colocalize on late endosomes. Although ALIX did not stimulate AMSH3 activity in vitro, in the absence of ALIX, AMSH3 localization on endosomes was abolished. Taken together, our data indicate that ALIX could function as an important regulator for AMSH3 function at the late endosomes.


1995 ◽  
Vol 166 ◽  
pp. 273-282
Author(s):  
B.E. Westerlund

It is essential for our understanding of the evolution of the Magellanic System, comprising the Large and the Small Magellanic Cloud, the Intercloud or Bridge region and the Magellanic Stream, to know its motions in the past. The Clouds have a common envelope of neutral hydrogen; this indicates that they have been bound to each others for a long time. The Magellanic System moves in the gravitational potential of our Galaxy; it is exposed to ram pressure through its movement in the galactic halo. Both effects ought to be noticeable in their present structure and kinematics. It is generally assumed, but not definitely proven, that the Clouds have been bound to our Galaxy for at least the last 7 Gyr. Most models assume that the Clouds lead the Magellanic Stream. The interaction between the Clouds has influenced their structure and kinematics severely. The effects should be possible to trace in the motions of their stellar and gaseous components as pronounced disturbances. Recent astrometric contributions in this field show a great promise for the future if still higher accuracy can be achieved.


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