scholarly journals CyLaKS: the Cytoskeleton Lattice-based Kinetic Simulator

2021 ◽  
Author(s):  
Shane A. Fiorenza ◽  
Meredith D. Betterton ◽  
Daniel G. Steckhahn
Keyword(s):  
Cell Division ◽  
Detailed Balance ◽  
Cell Movement ◽  
Spatiotemporal Variation ◽  
Binding Kinetics ◽  
Self Organization ◽  
Simulation Framework ◽  
Cellular Processes ◽  
Associated Proteins ◽  
Cytoskeletal Networks

Interaction of cytoskeletal filaments, motor proteins, and crosslinkers drives important cellular processes including cell division and cell movement. Cytoskeletal networks also undergo nonequilibrium self-organization in reconstituted systems. An emerging problem in cytoskeletal modeling and simulation is spatiotemporal alteration of the dynamics of filaments, motors, and associated proteins. This can occur due to motor crowding and obstacles along filaments, motor interactions and direction switching, and changes, defects, and heterogeneity in the filament lattice. How such spatiotemporally varying cytoskeletal filaments and motor interactions affect their collective properties is not fully understood. We developed the Cytoskeleton Lattice-based Kinetic Simulator (CyLaKS) for problems with significant spatiotemporal variation of motor or filament properties. The simulation builds on previous work modeling motor mechanochemistry into a simulation with many interacting motors and/or associated proteins. CyLaKS also includes detailed-balance in binding kinetics and movement and lattice heterogeneity. The simulation framework is flexible and extensible for future modeling work. Here we illustrate use of CyLaKS to study long-range motor interactions, filament heterogeneity, motion of a heterodimeric motor, and how changing crosslinker number affects filament separation.

scholarly journals A novel landscape of nuclear human CDK2 substrates revealed by in situ phosphorylation

2020 ◽  
Vol 6 (16) ◽  
pp. eaaz9899
Author(s):  
Yong Chi ◽  
John H. Carter ◽  
Jherek Swanger ◽  
Alexander V. Mazin ◽  
Robert L. Moritz ◽  
...  
Keyword(s):  
Cell Division ◽  
Protein Complexes ◽  
Nuclear Architecture ◽  
Cyclin Dependent Kinase ◽  
Oncogenic Signaling ◽  
Cellular Processes ◽  
Validation Rate ◽  
Associated Proteins ◽  
Epigenetic Regulators

Cyclin-dependent kinase 2 (CDK2) controls cell division and is central to oncogenic signaling. We used an “in situ” approach to identify CDK2 substrates within nuclei isolated from cells expressing CDK2 engineered to use adenosine 5′-triphosphate analogs. We identified 117 candidate substrates, ~40% of which are known CDK substrates. Previously unknown candidates were validated to be CDK2 substrates, including LSD1, DOT1L, and Rad54. The identification of many chromatin-associated proteins may have been facilitated by labeling conditions that preserved nuclear architecture and physiologic CDK2 regulation by endogenous cyclins. Candidate substrates include proteins that regulate histone modifications, chromatin, transcription, and RNA/DNA metabolism. Many of these proteins also coexist in multi-protein complexes, including epigenetic regulators, that may provide new links between cell division and other cellular processes mediated by CDK2. In situ phosphorylation thus revealed candidate substrates with a high validation rate and should be readily applicable to other nuclear kinases.

scholarly journals ZapA tetramerization is required for midcell localization and ZapB interaction in Escherichia coli

2019 ◽  
Author(s):  
Nils Y. Meiresonne ◽  
Tanneke den Blaauwen
Keyword(s):  
Cell Division ◽  
Chromosome Segregation ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Bacterial Cell Division ◽  
Cellular Processes ◽  
Interaction Partners ◽  
Associated Proteins

AbstractBacterial cell division is guided by FtsZ treadmilling precisely at midcell. FtsZ itself is regulated by FtsZ associated proteins (Zaps) that couple it to different cellular processes. ZapA is known to enhance FtsZ bundling but also forms the synchronizing link with chromosome segregation through ZapB and matS bound MatP. ZapA exists as dimers and tetramers in the cell. Using the ZapAI83E mutant that only forms dimers, this paper investigates the effects of ZapA multimerization state on its interaction partners and cell division. By employing (fluorescence) microscopy and Förster Resonance Energy Transfer in vivo it is shown that; dimeric ZapA is unable to complement a zapA deletion strain and localizes diffusely through the cell but still interacts with FtsZ that is not part of the cell division machinery. Dimeric ZapA is unable to recruit ZapB, which localizes in its presence unipolarly in the cell. Interestingly, the localization profiles of the chromosome and unipolar ZapB anticorrelate. The work presented here confirms previously reported in vitro effects of ZapA multimerization in vivo and further places it in a broader context by revealing the strong implications for ZapB localization and ter linkage.

scholarly journals Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Paulo Caldas ◽  
Mar López-Pelegrín ◽  
Daniel J. G. Pearce ◽  
Nazmi Burak Budanur ◽  
Jan Brugués ◽  
...  
Keyword(s):  
Cell Division ◽  
Bacterial Cell ◽  
Large Scale ◽  
Bacterial Cell Division ◽  
Division Site ◽  
Associated Proteins ◽  
Z Ring ◽  
Cytoskeletal Networks ◽  
Cooperative Ordering

AbstractDuring bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This Z-ring not only organizes the division machinery, but treadmilling of FtsZ filaments was also found to play a key role in distributing proteins at the division site. What regulates the architecture, dynamics and stability of the Z-ring is currently unknown, but FtsZ-associated proteins are known to play an important role. Here, using an in vitro reconstitution approach, we studied how the well-conserved protein ZapA affects FtsZ treadmilling and filament organization into large-scale patterns. Using high-resolution fluorescence microscopy and quantitative image analysis, we found that ZapA cooperatively increases the spatial order of the filament network, but binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Together, our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a switch-like manner.

scholarly journals Tracking the Antibody Immunome in Sporadic Colorectal Cancer by Using Antigen Self-Assembled Protein Arrays

Cancers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2718
Author(s):  
María González-González ◽  
José María Sayagués ◽  
Luis Muñoz-Bellvís ◽  
Carlos Eduardo Pedreira ◽  
Marcello L. R. de Campos ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Clinical Utility ◽  
Genetic Alterations ◽  
Western World ◽  
Sporadic Colorectal Cancer ◽  
Protein Arrays ◽  
Humoral Immune ◽  
Cellular Processes ◽  
Healthy Donors ◽  
Associated Proteins

Sporadic Colorectal Cancer (sCRC) is the third leading cause of cancer death in the Western world, and the sCRC patients presenting with synchronic metastasis have the poorest prognosis. Genetic alterations accumulated in sCRC tumor cells translate into mutated proteins and/or abnormal protein expression levels, which contribute to the development of sCRC. Then, the tumor-associated proteins (TAAs) might induce the production of auto-antibodies (aAb) via humoral immune response. Here, Nucleic Acid Programmable Protein Arrays (NAPPArray) are employed to identify aAb in plasma samples from a set of 50 sCRC patients compared to seven healthy donors. Our goal was to establish a systematic workflow based on NAPPArray to define differential aAb profiles between healthy individuals and sCRC patients as well as between non-metastatic (n = 38) and metastatic (n = 12) sCRC, in order to gain insight into the role of the humoral immune system in controlling the development and progression of sCRC. Our results showed aAb profile based on 141 TAA including TAAs associated with biological cellular processes altered in genesis and progress of sCRC (e.g., FSCN1, VTI2 and RPS28) that discriminated healthy donors vs. sCRC patients. In addition, the potential capacity of discrimination (between non-metastatic vs. metastatic sCRC) of 7 TAAs (USP5, ML4, MARCKSL1, CKMT1B, HMOX2, VTI2, TP53) have been analyzed individually in an independent cohort of sCRC patients, where two of them (VTI2 and TP53) were validated (AUC ~75%). In turn, these findings provided novel insights into the immunome of sCRC, in combination with transcriptomics profiles and protein antigenicity characterizations, wich might lead to the identification of novel sCRC biomarkers that might be of clinical utility for early diagnosis of the tumor. These results explore the immunomic analysis as potent source for biomarkers with diagnostic and prognostic value in CRC. Additional prospective studies in larger series of patients are required to confirm the clinical utility of these novel sCRC immunomic biomarkers.

scholarly journals Data-driven modeling reveals cell behaviors controlling self-organization during Myxococcus xanthus development

2017 ◽  
Vol 114 (23) ◽  
pp. E4592-E4601 ◽  
Author(s):  
Christopher R. Cotter ◽  
Heinz-Bernd Schüttler ◽  
Oleg A. Igoshin ◽  
Lawrence J. Shimkets
Keyword(s):  
Cell Tracking ◽  
Myxococcus Xanthus ◽  
Cell Movement ◽  
Modeling Method ◽  
Data Driven ◽  
Self Organization ◽  
Emergent Properties ◽  
Developmental Cycle ◽  
Fluorescent Cell ◽  
Cell Behaviors

Collective cell movement is critical to the emergent properties of many multicellular systems, including microbial self-organization in biofilms, embryogenesis, wound healing, and cancer metastasis. However, even the best-studied systems lack a complete picture of how diverse physical and chemical cues act upon individual cells to ensure coordinated multicellular behavior. Known for its social developmental cycle, the bacterium Myxococcus xanthus uses coordinated movement to generate three-dimensional aggregates called fruiting bodies. Despite extensive progress in identifying genes controlling fruiting body development, cell behaviors and cell–cell communication mechanisms that mediate aggregation are largely unknown. We developed an approach to examine emergent behaviors that couples fluorescent cell tracking with data-driven models. A unique feature of this approach is the ability to identify cell behaviors affecting the observed aggregation dynamics without full knowledge of the underlying biological mechanisms. The fluorescent cell tracking revealed large deviations in the behavior of individual cells. Our modeling method indicated that decreased cell motility inside the aggregates, a biased walk toward aggregate centroids, and alignment among neighboring cells in a radial direction to the nearest aggregate are behaviors that enhance aggregation dynamics. Our modeling method also revealed that aggregation is generally robust to perturbations in these behaviors and identified possible compensatory mechanisms. The resulting approach of directly combining behavior quantification with data-driven simulations can be applied to more complex systems of collective cell movement without prior knowledge of the cellular machinery and behavioral cues.

The role of microtubules in chick blastoderm expansion—a quantitative study using colchicine

Development ◽  
1975 ◽  
Vol 34 (1) ◽  
pp. 265-277
Author(s):  
J. R. Downie
Keyword(s):  
Cell Division ◽  
Cell Shape ◽  
Shape Change ◽  
Cell Sheet ◽  
Cell Movement ◽  
Vitelline Membrane ◽  
General Context ◽  
Chick Blastoderm ◽  
Cell Shape Change ◽  
Cytoplasmic Microtubules

Since their discovery, cytoplasmic microtubules have been much studied in the context of cell movement and cell shape change. Much of the work has used drugs, particularly colchicine and its relatives, which break down microtubules — the so-called anti-tubulins. Colchicine inhibits the orientated movements of many cell types in vitro, and disrupts cell shape change in several morphogenetic situations. The investigation reported here used chick blastoderm expansion in New culture in an attempt to quantify the colchicine effect on orientated cell movement. However, although colchicine could halt blastoderm expansion entirely, a simple interpretation was not possible. (1) Colchicine at concentrations capable of blocking mitosis, and of disrupting all or most of the cytoplasmic microtubules of the cells studied, inhibited blastoderm expansion, often resulting in an overall retraction of the cell sheet. (2) Though blastoderm expansion does normally involve considerable cell proliferation, the colchicine effect could not be ascribed to a block on cell division since aminopterin, which stops cell division without affecting microtubules, did not inhibit expansion. (3) Blastoderm expansion is effected by the locomotion of a specialized band of edge cells at the blastoderm periphery. These are the only cells normally attached to the vitelline membrane — the substrate for expansion. When most of the blastoderm was excised, leaving the band of edge cells, and the cultures then treated with colchicine, expansion occurred normally. The colchicine effect on blastoderm expansion could not therefore be ascribed to a direct effect on the edge cells. (4) An alternative site of action of the drug is the remaining cells of the blastoderm. These normally become progressively flatter as expansion proceeds. If flattening in these cells is even partially dependent on their cytoplasmic microtubules, disruption of these microtubules might result in the inherent contractility of the cells resisting and eventually halting edge cell migration. That cell shape in these cells is dependent on microtubules was demonstrated by treating flat blastoderm fragments with colchicine. On incubation, the area occupied by these fragments decreased by 25–30 % more than controls. The significance of these results in the general context of orientated cell movements and cell shape determination is discussed, with particular emphasis on the analogous system of Fundulus epiboly.

Identification of putative Z-ring-associated proteins, involved in cell division in human pathogenic bacteriaHelicobacter pylori

FEBS Letters ◽  
2016 ◽  
Vol 590 (14) ◽  
pp. 2158-2171 ◽  
Author(s):  
Mohammad Kamran ◽  
Swati Sinha ◽  
Priyanka Dubey ◽  
Andrew M. Lynn ◽  
Suman K. Dhar
Keyword(s):  
Cell Division ◽  
Associated Proteins ◽  
Z Ring

Lipid Cell Biology: A Focus on Lipids in Cell Division

2018 ◽  
Vol 87 (1) ◽  
pp. 839-869 ◽  
Author(s):  
Elisabeth M. Storck ◽  
Cagakan Özbalci ◽  
Ulrike S. Eggert
Keyword(s):  
Mass Spectrometry ◽  
Cell Division ◽  
Cell Biology ◽  
Chemical Biology ◽  
Structural Integrity ◽  
Advanced Imaging ◽  
Functional Roles ◽  
Lipid Interactions ◽  
Cellular Processes ◽  
Alkyl Side Chains

Cells depend on hugely diverse lipidomes for many functions. The actions and structural integrity of the plasma membrane and most organelles also critically depend on membranes and their lipid components. Despite the biological importance of lipids, our understanding of lipid engagement, especially the roles of lipid hydrophobic alkyl side chains, in key cellular processes is still developing. Emerging research has begun to dissect the importance of lipids in intricate events such as cell division. This review discusses how these structurally diverse biomolecules are spatially and temporally regulated during cell division, with a focus on cytokinesis. We analyze how lipids facilitate changes in cellular morphology during division and how they participate in key signaling events. We identify which cytokinesis proteins are associated with membranes, suggesting lipid interactions. More broadly, we highlight key unaddressed questions in lipid cell biology and techniques, including mass spectrometry, advanced imaging, and chemical biology, which will help us gain insights into the functional roles of lipids.

The role of initial cells in maize anther morphogenesis

Development ◽  
1992 ◽  
Vol 116 (4) ◽  
pp. 1077-1085 ◽  
Author(s):  
R.K. Dawe ◽  
M. Freeling
Keyword(s):  
Cell Division ◽  
Small Groups ◽  
Cell Movement ◽  
Basic Structure ◽  
Early Growth ◽  
Structural Template ◽  
Axes Of Symmetry ◽  
The Relationship ◽  
Mature Anther

The near absence of cell movement in plants makes clonal analysis a particularly informative method for reconstructing the early events of organ formation. We traced the patterns of cell division during maize anther development by inducing sector boundaries that preceded the earliest events of anther initiation. In doing this, we were able to estimate the smallest number of cells that are fated to form an anther, characteristic cell division patterns that occur during anther morphogenesis, and the relationship between the pre-existing symmetry of the initial cells and the final symmetry of the mature anther. Four general conclusions are made: (1) anthers are initiated from small groups of 12 or fewer cells in each of two floral meristematic layers; (2) the early growth of the anther is more like a shoot than a glume or leaf; (3) cell ancestry does not dictate basic structure and (4) the orientation of initial cells predicts the orientation of the four pollen-containing microsporangia, which define the axes of symmetry on the mature anther. The final point is discussed with other data, and an explanation involving a ‘structural template’ is invoked. The idea is that the orientation of initial cells within the floral meristem establishes an architectural pattern into which anther cells are recruited without regard to their cellular lineages. The structural template hypothesis may prove to be generally applicable to problems of pattern formation in plants.

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