cell position
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2021 ◽  
Author(s):  
Oliver J Meacock ◽  
William M Durham

Most bacteria live attached to surfaces in densely-packed communities. While new experimental and imaging techniques are beginning to provide a window on the complex processes that play out in these communities, resolving the behaviour of individual cells through time and space remains a major challenge. Although a number of different software solutions have been developed to track microorganisms, these approaches typically rely on a large number of user-defined parameters that must be carefully tuned to effectively track cells. Testing a given parameter combination can take hours to days depending on the size of the dataset, making iterative optimisation impractical. To overcome these limitations, we have developed FAST, the Feature-Assisted Segmenter/Tracker, which uses unsupervised machine learning to optimise tracking while maintaining ease of use. Our approach, rooted in information theory, largely eliminates the need for users to iteratively adjust parameters manually and make qualitative assessments of the resulting cell trajectories. Instead, FAST measures multiple distinguishing "features" for each cell and then autonomously quantifies the amount of unique information each feature provides. We then use these measurements to determine how data from each feature should be combined to minimize tracking errors. Comparing our algorithm with a naïve approach that uses cell position alone revealed that FAST produced 4 to 10 times fewer tracking errors. The modular design of FAST combines our novel tracking method with tools for segmentation, extensive data visualisation, lineage assignment, and manual track correction. It is also highly extensible, allowing users to extract custom information from images and seamlessly integrate it into downstream analyses. FAST therefore enables high-throughput, data-rich analyses with minimal user input. It has been released for use in either Matlab or as a compiled stand-alone application, and is available at https://bit.ly/3vovDHn, along with extensive tutorials and detailed documentation.


Cancers ◽  
2021 ◽  
Vol 13 (23) ◽  
pp. 5910
Author(s):  
Maria Laura De Angelis ◽  
Federica Francescangeli ◽  
Ann Zeuner ◽  
Marta Baiocchi

Colorectal cancer (CRC) represents one of the most deadly cancers worldwide. Colorectal cancer stem cells (cCSCs) are the driving units of CRC initiation and development. After the concept of cCSC was first formulated in 2007, a huge bulk of research has contributed to expanding its definition, from a cell subpopulation defined by a fixed phenotype in a plastic entity modulated by complex interactions with the tumor microenvironment, in which cell position and niche-driven signals hold a prominent role. The wide development of cellular and molecular technologies recent years has been a main driver of advancements in cCSCs research. Here, we will give an overview of the parallel role of technological progress and of theoretical evolution in shaping the concept of cCSCs.


2021 ◽  
Author(s):  
Kaichi Watanabe ◽  
Yuhei Yasui ◽  
Yuta Kurose ◽  
Masashi Fujii ◽  
Takashi Yamamoto ◽  
...  

Abstract Gastrulation is a universal process in the morphogenesis of many animal embryos. In sea urchin embryos, it involves the invagination of a single-layered vegetal plate into the blastocoel. Although morphological and molecular events in gastrulation have been well studied, the mechanical driving forces and the regulatory mechanism underlying gastrulation is not fully understood. In this study, structural features and cytoskeletal distributions were studied in sea urchin embryos using an “exogastrulation” model induced by inhibiting the H+/K+ ion pump with omeprazole. The vegetal poles of the exogastrulating embryos showed reduced roundness indices, intracellular pH polarization, and intracellular F-actin polarization at the pre-early gastrulation stage compared with normal embryos. Gastrulation stopped when F-actin polymerization or degradation was inhibited via RhoA or YAP1 knockout, although pH distributions were independent of such a knockout. A mathematical model of sea urchin embryos at the early gastrulation reproduced the shapes of both normal and exogastrulating embryos using cell-dependent cytoskeletal features based on F-actin and pH distributions. Thus, gastrulation required appropriate cell position-dependent intracellular F-actin distributions regulated by the H+/K+ ion pump through pH control.


PLoS Biology ◽  
2021 ◽  
Vol 19 (7) ◽  
pp. e3001345
Author(s):  
Jessica E. Forsyth ◽  
Ali H. Al-Anbaki ◽  
Roberto de la Fuente ◽  
Nikkinder Modare ◽  
Diego Perez-Cortes ◽  
...  

Architectural changes at the cellular and organism level are integral and necessary to successful development and growth. During mammalian preimplantation development, cells reduce in size and the architecture of the embryo changes significantly. Such changes must be coordinated correctly to ensure continued development of the embryo and, ultimately, a successful pregnancy. However, the nature of such transformations is poorly defined during mammalian preimplantation development. In order to quantitatively describe changes in cell environment and organism architecture, we designed Internal Versus External Neighbourhood (IVEN). IVEN is a user-interactive, open-source pipeline that classifies cells into different populations based on their position and quantifies the number of neighbours of every cell within a dataset in a 3D environment. Through IVEN-driven analyses, we show how transformations in cell environment, defined here as changes in cell neighbourhood, are related to changes in embryo geometry and major developmental events during preimplantation mammalian development. Moreover, we demonstrate that modulation of the FGF pathway alters spatial relations of inner cells and neighbourhood distributions, leading to overall changes in embryo architecture. In conjunction with IVEN-driven analyses, we uncover differences in the dynamic of cell size changes over the preimplantation period and determine that cells within the mammalian embryo initiate growth phase only at the time of implantation.


2021 ◽  
Author(s):  
Reema Chaudhary ◽  
Swathi Kota ◽  
Hari S Misra

In rod shaped Gram-negative bacteria, FtsZ localization at mid cell position is regulated by the gradient of MinCDE complex across the poles. In round shaped bacteria, which lack predefined poles, the next plane of cell division is perpendicular to previous plane and the determination of site for FtsZ assembly is still intriguing. Deinococcus radiodurans, a coccus bacterium, is characterized by its extraordinary resistance to DNA damage. DivIVA, a putative component of Min system in this bacterium, interacts with cognate cell division and genome segregation proteins. Here, we report that deletion of chromosomal copy of DivIVA was possible only when wild type copy of DivIVA was expressed in trans on the plasmid. However, the deletion of C-terminal domain of DivIVA (CTD mutant) was possible but produced distinguishable phenotypes like smaller cells, slower growth and tilted septum orientation in D. radiodurans. In trans expression of DivIVA in CTD mutant could restore these features of wild type. Interestingly, the overexpression of DivIVA led to delayed separation of tetrad from octet state in both trans-complemented divIVA mutant and wild type cells. The CTD mutant showed upregulation of yggS-divIVAN operon. Both wild type and CTD mutant formed FtsZ foci, however unlike wild type, the position of foci in the mutant cells was found to be away from conjectural mid-cell position in cocci. Notably, DivIVA-RFP localizes to septum during cell division at the new division site. These results suggested that DivIVA is an essential protein in D. radiodurans and its C-terminal domain plays an important role in the regulation of its expression and orientation of new septal growth in this bacterium. Importance: In rod-shaped Gram-negative bacteria, the mid-cell position for binary fission is relatively easy to model. In cocci that do not have predefined poles, the plane of next cell division is shown to be perpendicular to the previous plane. However, the molecular basis of perpendicularity is not known in cocci. The DivIVA protein of Deinococcus radiodurans, a coccus bacterium, physically interacts with septum and establishes macromolecular interactions with genome segregation proteins through its N-terminal domain and with MinC through C-terminal domain. Here, we have brought forth some evidence to suggest that DivIVA is essential for growth, plays an important role in cell-polarity determination and its C-terminal domain plays a crucial role in the growth of new septum in correct orientation as well as regulation of its expression.


2021 ◽  
Author(s):  
John Isaac Murray ◽  
Elicia Preston ◽  
Jeremy P. Crawford ◽  
Jonathan D. Rumley ◽  
Prativa Amom ◽  
...  

AbstractHox transcription factors play a conserved role in specifying positional identity during animal development, with posterior Hox genes typically repressing the expression of more anterior Hox genes. Here, we dissect the regulation of the posterior Hox genes nob-1 and php-3 in the nematode C. elegans. We show that nob-1 and php-3 are co-expressed in gastrulation-stage embryos in cells that express the anterior Hox gene ceh-13. This expression is controlled by several partially redundant transcriptional enhancers. Surprisingly, these enhancers require ceh-13 for expression, providing an example of an anterior Hox gene positively regulating a posterior Hox gene. Several other regulators also act positively through nob-1/php-3 enhancers, including elt-1/GATA, ceh-20/ceh-40/Pbx, unc-62/Meis, pop-1/TCF, ceh-36/Otx and unc-30/Pitx. We identified defects in both cell position and cell division patterns in ceh-13 and nob-1;php-3 mutants, suggesting that these factors regulate lineage identity in addition to positional identity. Together, our results highlight the complexity and remarkable flexibility of Hox gene regulation and function.


Author(s):  
Shaoyuan Zhu ◽  
Zongwei Chen ◽  
Haoming Wang ◽  
Brian M. McDermott

Hair cells are heterogenous, enabling varied roles in sensory systems. An emerging hypothesis is that the transmembrane channel-like (Tmc) proteins of the hair cell’s mechanotransduction apparatus vary within and between organs to permit encoding of different mechanical stimuli. Five anatomical variables that may coincide with different Tmc use by a hair cell within the ear are the containing organ, cell morphology, cell position within an organ, axis of best sensitivity for the cell, and the hair bundle’s orientation within this axis. Here, we test this hypothesis in the organs of the zebrafish ear using a suite of genetic mutations. Transgenesis and quantitative measurements demonstrate two morphologically distinct hair cell types in the central thickness of a vestibular organ, the lateral crista: short and tall. In contrast to what has been observed, we find that tall hair cells that lack Tmc1 generally have substantial reductions in mechanosensitivity. In short hair cells that lack Tmc2 isoforms, mechanotransduction is largely abated. However, hair cell Tmc dependencies are not absolute, and an exceptional class of short hair cell that depends on Tmc1 is present, termed a short hair cell erratic. To further test anatomical variables that may influence Tmc use, we map Tmc1 function in the saccule of mutant larvae that depend just on this Tmc protein to hear. We demonstrate that hair cells that use Tmc1 are found in the posterior region of the saccule, within a single axis of best sensitivity, and hair bundles with opposite orientations retain function. Overall, we determine that Tmc reliance in the ear is dependent on the organ, subtype of hair cell, position within the ear, and axis of best sensitivity.


2021 ◽  
Vol 173 ◽  
pp. 102841
Author(s):  
Sakshi Popli ◽  
Rakesh Kumar Jha ◽  
Sanjeev Jain
Keyword(s):  

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