scholarly journals TISMorph: A tool to quantify texture, irregularity and spreading of single cells

2018 ◽  
Author(s):  
Elaheh Alizadeh ◽  
Wenlong Xu ◽  
Jordan Castle ◽  
Jacqueline Foss ◽  
Ashok Prasad
Keyword(s):  
Quantitative Analysis ◽  
Cell Shape ◽  
Single Cells ◽  
Physiological State ◽  
Biological Data ◽  
Osteosarcoma Cell ◽  
Cellular Processes ◽  
Classification Tasks ◽  
Insight Into ◽  
Cytoskeletal Drugs

AbstractA number of recent studies have shown that cell shape and cytoskeletal texture can be used as sensitive readouts of the physiological state of the cell. However, utilization of this information requires the development of quantitative measures that can describe relevant aspects of cell shape. In this paper we develop a toolbox, TISMorph, to calculate set of quantitative measures to address this need. Some of the measures introduced here are used previously and others are new and have desirable properties for shape and texture quantification of cells. These measures, broadly classifiable into the categories of textural, spreading and irregularity measures, are tested by using them to discriminate between osteosarcoma cell lines treated with different cytoskeletal drugs. We find that even though specific classification tasks often rely on a few measures, these are not the same between all classification tasks, thus requiring the use of the entire suite of measures for classification and discrimination. We provide detailed descriptions of the measures, well as TISMorph package to implement them. Image based quantitative analysis has the potential to become a new field of biological data (“image-omics”), providing quantitative insight into cellular processes.

Quantitative Analysis Of X-Ray Images From Geological Materials

1990 ◽  
Vol 48 (2) ◽  
pp. 244-245
Author(s):  
J. M. Paque ◽  
R. Browning ◽  
P. L. King ◽  
P. Pianetta
Keyword(s):  
Quantitative Analysis ◽  
Bulk Composition ◽  
Principal Component ◽  
Analytical Description ◽  
Bulk Sample ◽  
Geological Samples ◽  
X Ray ◽  
Software And Hardware ◽  
And Storage ◽  
Insight Into

Geological samples typically contain many minerals (phases) with multiple element compositions. A complete analytical description should give the number of phases present, the volume occupied by each phase in the bulk sample, the average and range of composition of each phase, and the bulk composition of the sample. A practical approach to providing such a complete description is from quantitative analysis of multi-elemental x-ray images.With the advances in recent years in the speed and storage capabilities of laboratory computers, large quantities of data can be efficiently manipulated. Commercial software and hardware presently available allow simultaneous collection of multiple x-ray images from a sample (up to 16 for the Kevex Delta system). Thus, high resolution x-ray images of the majority of the detectable elements in a sample can be collected. The use of statistical techniques, including principal component analysis (PCA), can provide insight into mineral phase composition and the distribution of minerals within a sample.

ABOUT SOME PECULIARITIES OF THE PHYSIOLOGICAL HETEROGENEITY OF THE POPULATION OF SCENEDESMUS QUADRICAUDA (TURP.) BREB. IN THE PRESENCE OF LOW CONCENTRATIONS OF METALS

2018 ◽  
pp. 34-43
Author(s):  
V. I. Ipatova ◽  
A. G. Dmitrieva ◽  
О. F. Filenko ◽  
T. V. Drozdenko
Keyword(s):  
Cell Division ◽  
Toxic Effect ◽  
Copper Chloride ◽  
Single Cells ◽  
Physiological State ◽  
Scenedesmus Quadricauda ◽  
Physiological Status ◽  
Lag Phase ◽  
Protective Mechanism ◽  
Low Concentrations

The structure of the laboratory population of green microalgae Scenedesmus quadricauda (Turp.) Breb (=Desmodesmus communis E. Hegew.) was studied at different stages of its growth (lag-phase, log-phase and stationary phase) at low concentrations of copper chloride and silver nitrate by the method microculture, allowing to monitor the state and development of single cells having different physiological status. The response of the culture of S. quadricauda - the change in the number of cells and the fractional composition (the fraction of dividing, «dormant» and dying cells) depended not only on the concentration of the toxicant in the medium, but also on the physiological state of the culture: the level of synchronization and the growth phase. Silver ions at low concentrations had a more pronounced toxic effect on the culture than copper ions at different phases of its development, especially at a concentration of 0.001 mg/l (10-9 M). The main mechanism of the toxic effect of metals is to inhibit the process of cell division. At low concentrations of toxicants, especially at a concentration of 0.001 mg/l, a «paradoxical» effect expressed in the predominance of the fraction of «dormant» cells was revealed. The temporary inhibition of the process of cell division can be regarded as a protective mechanism that allows preserving the integrity of the population and its ability to survive in a changing environment. The obtained data explain the effect of action of low concentrations of substances due to their inclusion in the cell, the subsequent accumulation in the cell and their low excretion.

New insight into the molecular switch mechanism of human Rho family proteins: shifting a paradigm

2013 ◽  
Vol 394 (1) ◽  
pp. 89-95 ◽  
Author(s):  
Mamta Jaiswal ◽  
Eyad Kalawy Fansa ◽  
Radovan Dvorsky ◽  
Mohammad Reza Ahmadian
Keyword(s):  
Quantitative Analysis ◽  
Bound State ◽  
Molecular Switch ◽  
Nucleotide Exchange ◽  
Gtp Binding ◽  
Switch Mechanism ◽  
Rho Family ◽  
Rho Family Proteins ◽  
Insight Into ◽  
Made In

Abstract Major advances have been made in understanding the structure, function and regulation of the small GTP-binding proteins of the Rho family and their involvement in multiple cellular process and disorders. However, intrinsic nucleotide exchange and hydrolysis reactions, which are known to be fundamental to Rho family proteins, have been partially investigated in the case of RhoA, Rac1 and Cdc42, but for others not at all. Here we present a comprehensive and quantitative analysis of the molecular switch functions of 15 members of the Rho family that enabled us to propose an active GTP-bound state for the rather uncharacterized isoforms RhoD and Rif under equilibrium and quiescent conditions.

scholarly journals Group I PAKs function downstream of Rac to promote podosome invasion during myoblast fusion in vivo

2012 ◽  
Vol 199 (1) ◽  
pp. 169-185 ◽  
Author(s):  
Rui Duan ◽  
Peng Jin ◽  
Fengbao Luo ◽  
Guofeng Zhang ◽  
Nathan Anderson ◽  
...  
Keyword(s):  
Cell Shape ◽  
Myoblast Fusion ◽  
Small Gtpase ◽  
Fusion Pore ◽  
Cellular Processes ◽  
Filament Assembly ◽  
Group I ◽  
Redundant Functions ◽  
Shape Changes

The p21-activated kinases (PAKs) play essential roles in diverse cellular processes and are required for cell proliferation, apoptosis, polarity establishment, migration, and cell shape changes. Here, we have identified a novel function for the group I PAKs in cell–cell fusion. We show that the two Drosophila group I PAKs, DPak3 and DPak1, have partially redundant functions in myoblast fusion in vivo, with DPak3 playing a major role. DPak3 is enriched at the site of fusion colocalizing with the F-actin focus within a podosome-like structure (PLS), and promotes actin filament assembly during PLS invasion. Although the small GTPase Rac is involved in DPak3 activation and recruitment to the PLS, the kinase activity of DPak3 is required for effective PLS invasion. We propose a model whereby group I PAKs act downstream of Rac to organize the actin filaments within the PLS into a dense focus, which in turn promotes PLS invasion and fusion pore initiation during myoblast fusion.

scholarly journals Molecular basis for Ras suppressor-1 recruitment to focal adhesions and stabilization of consensus adhesome complex

2021 ◽  
Author(s):  
Koichi Fukuda ◽  
Fan Lu ◽  
Jun Qin
Keyword(s):  
Cell Adhesion ◽  
Focal Adhesion ◽  
Specific Interaction ◽  
Tumor Development ◽  
Focal Adhesions ◽  
Adaptor Protein ◽  
Biological Data ◽  
Structural Basis ◽  
Lim Domain ◽  
Insight Into

AbstractRas suppressor-1 (Rsu-1) is a leucine-rich repeat (LRR)-containing protein that is crucial for regulating fundamental cell adhesion processes and tumor development. Rsu-1 interacts with a zinc-finger type multi LIM domain-containing adaptor protein PINCH-1 involved in the integrin-mediated consensus adhesome but not with highly homologous isoform PINCH-2. However, the structural basis for such specific interaction and regulatory mechanism remains unclear. Here, we determined the crystal structures of Rsu-1 and its complex with the PINCH-1 LIM4-5 domains. Rsu-1 displays an arc-shaped solenoid architecture with eight LRRs shielded by the N- and C-terminal capping modules. We show that a large conserved concave surface of the Rsu-1 LRR domain recognizes the PINCH-1 LIM5 domain, and that the C-terminal non-LIM region of PINCH-2 but not PINCH-1 sterically disfavors the Rsu-1 binding. We further show that Rsu-1 can be assembled, via PINCH-1-binding, into a tight hetero-pentamer complex comprising Rsu-1, PINCH-1, ILK, Parvin, and Kindlin-2 that constitute a major consensus integrin adhesome crucial for focal adhesion assembly. Consistently, our mutagenesis and cell biological data consolidate the significance of the Rsu-1/PINCH-1 interaction in focal adhesion assembly and cell spreading. Our results provide a crucial molecular insight into Rsu-1-mediated cell adhesion with implication on how it may regulate tumorigenic growth.

scholarly journals Quantifying exosome secretion from single cells reveals a modulatory role for GPCR signaling

2018 ◽  
Vol 217 (3) ◽  
pp. 1129-1142 ◽  
Author(s):  
Frederik Johannes Verweij ◽  
Maarten P. Bebelman ◽  
Connie R. Jimenez ◽  
Juan J. Garcia-Vallejo ◽  
Hans Janssen ◽  
...  
Keyword(s):  
Total Internal Reflection ◽  
Single Cells ◽  
Cell Communication ◽  
Exosome Biogenesis ◽  
Real Time Visualization ◽  
Target Membrane ◽  
Syntaxin 4 ◽  
Optical Reporters ◽  
Druggable Targets ◽  
Insight Into

Exosomes are small endosome-derived extracellular vesicles implicated in cell–cell communication and are secreted by living cells when multivesicular bodies (MVBs) fuse with the plasma membrane (PM). Current techniques to study exosome physiology are based on isolation procedures after secretion, precluding direct and dynamic insight into the mechanics of exosome biogenesis and the regulation of their release. In this study, we propose real-time visualization of MVB–PM fusion to overcome these limitations. We designed tetraspanin-based pH-sensitive optical reporters that detect MVB–PM fusion using live total internal reflection fluorescence and dynamic correlative light–electron microscopy. Quantitative analysis demonstrates that MVB–PM fusion frequency is reduced by depleting the target membrane SNAREs SNAP23 and syntaxin-4 but also can be induced in single cells by stimulation of the histamine H1 receptor (H1HR). Interestingly, activation of H1R1 in HeLa cells increases Ser110 phosphorylation of SNAP23, promoting MVB–PM fusion and the release of CD63-enriched exosomes. Using this single-cell resolution approach, we highlight the modulatory dynamics of MVB exocytosis that will help to increase our understanding of exosome physiology and identify druggable targets in exosome-associated pathologies.

Nutritional biomarkers and machine learning for personalized nutrition applications and health optimization

2021 ◽  
pp. 1-9
Author(s):  
Dimitrios P. Panagoulias ◽  
Dionisios N. Sotiropoulos ◽  
George A. Tsihrintzis
Keyword(s):  
Machine Learning ◽  
Physiological State ◽  
Prediction Method ◽  
Disease Diagnosis ◽  
Classification Model ◽  
Cell Physiology ◽  
Cellular Processes ◽  
General Evaluation ◽  
Model Training ◽  
The One

The doctrine of the “one size fits all” approach in the field of disease diagnosis and patient management is being replaced by a more per patient approach known as “personalized medicine”. In this spirit, biomarkers are key variables in the research and development of new methods for prognostic and classification model training based on advances in the field of artificial intelligence [1, 2, 3]. Metabolomics refers to the systematic study of the unique chemical fingerprints that cellular processes leave behind. The metabolic profile of a person can provide a snapshot of cell physiology and, by extension, metabolomics provide a direct “functional reading of the physiological state” of an organism. Via employing machine learning methodologies, a general evaluation chart of nutritional biomarkers is formulated and an optimised prediction method for body to mass index is investigated with the aim to discover dietary patterns.

Simplifying decision trees: A survey

1997 ◽  
Vol 12 (01) ◽  
pp. 1-40 ◽  
Author(s):  
LEONARD A. BRESLOW ◽  
DAVID W. AHA
Keyword(s):  
Decision Trees ◽  
Data Structures ◽  
Classification Accuracy ◽  
Case Based Reasoning ◽  
Reasoning Systems ◽  
Tree Generation ◽  
Good Classification ◽  
Classification Tasks ◽  
Insight Into ◽  
Case Based

Induced decision trees are an extensively-researched solution to classification tasks. For many practical tasks, the trees produced by tree-generation algorithms are not comprehensible to users due to their size and complexity. Although many tree induction algorithms have been shown to produce simpler, more comprehensible trees (or data structures derived from trees) with good classification accuracy, tree simplification has usually been of secondary concern relative to accuracy, and no attempt has been made to survey the literature from the perspective of simplification. We present a framework that organizes the approaches to tree simplification and summarize and critique the approaches within this framework. The purpose of this survey is to provide researchers and practitioners with a concise overview of tree-simplification approaches and insight into their relative capabilities. In our final discussion, we briefly describe some empirical findings and discuss the application of tree induction algorithms to case retrieval in case-based reasoning systems.

scholarly journals Mechanical stimulation of single cells by reversible host-guest interactions in 3D microscaffolds

2020 ◽  
Vol 6 (39) ◽  
pp. eabc2648
Author(s):  
Marc Hippler ◽  
Kai Weißenbruch ◽  
Kai Richler ◽  
Enrico D. Lemma ◽  
Masaki Nakahata ◽  
...  
Keyword(s):  
Single Cells ◽  
Three Dimensional ◽  
Stimuli Responsive ◽  
Traction Forces ◽  
Set Point ◽  
Cellular Processes ◽  
Laser Lithography ◽  
Cross Links ◽  
Tensional Homeostasis ◽  
Myosin Motors

Many essential cellular processes are regulated by mechanical properties of their microenvironment. Here, we introduce stimuli-responsive composite scaffolds fabricated by three-dimensional (3D) laser lithography to simultaneously stretch large numbers of single cells in tailored 3D microenvironments. The key material is a stimuli-responsive photoresist containing cross-links formed by noncovalent, directional interactions between β-cyclodextrin (host) and adamantane (guest). This allows reversible actuation under physiological conditions by application of soluble competitive guests. Cells adhering in these scaffolds build up initial traction forces of ~80 nN. After application of an equibiaxial stretch of up to 25%, cells remodel their actin cytoskeleton, double their traction forces, and equilibrate at a new dynamic set point within 30 min. When the stretch is released, traction forces gradually decrease until the initial set point is retrieved. Pharmacological inhibition or knockout of nonmuscle myosin 2A prevents these adjustments, suggesting that cellular tensional homeostasis strongly depends on functional myosin motors.

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