scholarly journals SHOT-R: A next generation algorithm for particle kinematics analysis

2021 ◽  
Author(s):  
Eloina Corradi ◽  
Walter Boscheri ◽  
Marie-Laure Baudet
Keyword(s):  
Numerical Method ◽  
Live Imaging ◽  
Single Particle Tracking ◽  
Kinematics Analysis ◽  
Cellular Mechanisms ◽  
Accurate Analysis ◽  
Imaging Experiment ◽  
Bona Fide ◽  
First Time ◽  
Polynomial Reconstruction

Analysis of live-imaging experiments is crucial to decipher a plethora of cellular mechanisms within physiological and pathological contexts. Kymograph, i.e. graphical representations of particle spatial position over time, and single particle tracking (SPT) are the currently available tools to extract information on particle transport and velocity. However, the spatiotemporal approximation applied in particle trajectory reconstruction with those methods intrinsically prevents an accurate analysis of particle kinematics and of instantaneous behaviours. Here, we present SHOT-R, a novel numerical method based on polynomial reconstruction of 4D (3D+time) particle trajectories. SHOT-R, contrary to other tools, computes bona fide instantaneous and directional velocity, and acceleration. Thanks to its high order continuous reconstruction it allows, for the first time, kinematics analysis of co-trafficked particles. Overall, SHOT-R is a novel, versatile, and physically reliable numerical method that achieves all-encompassing particle kinematics studies at unprecedented accuracy on any live-imaging experiment where the spatiotemporal coordinates can be retrieved.

The Pattern of Acetylation Defines the Priming Activity of Chitosan Tetramers

2019 ◽  
Author(s):  
Sven Basa ◽  
Malathi Nampally ◽  
Talita Honorato ◽  
Subha Narayan Das ◽  
Appa Rao Podile ◽  
...  
Keyword(s):  
Biological Activity ◽  
Degree Of Polymerization ◽  
Chitosan Oligosaccharides ◽  
Degree Of Acetylation ◽  
Bona Fide ◽  
First Time ◽  
Priming Activity

The biological activity of chitosans depends on their degree of polymerization (DP) and degree of acetylation (DA). However, information could also be carried by the pattern of acetylation (PA): the sequence of <i>β</i>-1,4-linked glucosamine (deacetylated/D) and <i>N</i>-acetylglucosamine (acetylated/A) units. To address this hypothesis, we prepared partially-acetylated chitosan oligosaccharides from a chitosan polymer (DA=35%, DP<sub>w</sub>=905) using recombinant chitosan hydrolases with distinct substrate and cleavage specificities. The mixtures were separated into fractions DP4–DP12, which were tested for elicitor and priming activities in rice cells. We confirmed that both activities were influenced by DP, <a>but also observed apparent DA-dependent priming activity, with the ADDD+DADD fraction proving remarkably effective</a>. We then compared all four mono-acetylated tetramers prepared using different chitin deacetylases and observed significant differences in priming activity. This demonstrates for the first time that PA influences the biological activity of chitosans, which can now be recognized as <i>bona fide</i> information-carrying molecules

The Pattern of Acetylation Defines the Priming Activity of Chitosan Tetramers

2019 ◽  
Author(s):  
Sven Basa ◽  
Malathi Nampally ◽  
Talita Honorato ◽  
Subha Narayan Das ◽  
Appa Rao Podile ◽  
...  
Keyword(s):  
Biological Activity ◽  
Degree Of Polymerization ◽  
Chitosan Oligosaccharides ◽  
Degree Of Acetylation ◽  
Bona Fide ◽  
First Time ◽  
Priming Activity

The biological activity of chitosans depends on their degree of polymerization (DP) and degree of acetylation (DA). However, information could also be carried by the pattern of acetylation (PA): the sequence of <i>β</i>-1,4-linked glucosamine (deacetylated/D) and <i>N</i>-acetylglucosamine (acetylated/A) units. To address this hypothesis, we prepared partially-acetylated chitosan oligosaccharides from a chitosan polymer (DA=35%, DP<sub>w</sub>=905) using recombinant chitosan hydrolases with distinct substrate and cleavage specificities. The mixtures were separated into fractions DP4–DP12, which were tested for elicitor and priming activities in rice cells. We confirmed that both activities were influenced by DP, <a>but also observed apparent DA-dependent priming activity, with the ADDD+DADD fraction proving remarkably effective</a>. We then compared all four mono-acetylated tetramers prepared using different chitin deacetylases and observed significant differences in priming activity. This demonstrates for the first time that PA influences the biological activity of chitosans, which can now be recognized as <i>bona fide</i> information-carrying molecules

scholarly journals Interactome Analysis of KIN (Kin17) Shows New Functions of This Protein

2021 ◽  
Vol 43 (2) ◽  
pp. 767-781
Author(s):  
Vanessa Pinatto Gaspar ◽  
Anelise Cardoso Ramos ◽  
Philippe Cloutier ◽  
José Renato Pattaro Junior ◽  
Francisco Ferreira Duarte Junior ◽  
...  
Keyword(s):  
Dna Replication ◽  
Protein Interactions ◽  
Ribosome Biogenesis ◽  
Cell Metabolism ◽  
Cell Types ◽  
Protein Protein Interactions ◽  
Cellular Mechanisms ◽  
Cancerous Cell ◽  
First Time

KIN (Kin17) protein is overexpressed in a number of cancerous cell lines, and is therefore considered a possible cancer biomarker. It is a well-conserved protein across eukaryotes and is ubiquitously expressed in all cell types studied, suggesting an important role in the maintenance of basic cellular function which is yet to be well determined. Early studies on KIN suggested that this nuclear protein plays a role in cellular mechanisms such as DNA replication and/or repair; however, its association with chromatin depends on its methylation state. In order to provide a better understanding of the cellular role of this protein, we investigated its interactome by proximity-dependent biotin identification coupled to mass spectrometry (BioID-MS), used for identification of protein–protein interactions. Our analyses detected interaction with a novel set of proteins and reinforced previous observations linking KIN to factors involved in RNA processing, notably pre-mRNA splicing and ribosome biogenesis. However, little evidence supports that this protein is directly coupled to DNA replication and/or repair processes, as previously suggested. Furthermore, a novel interaction was observed with PRMT7 (protein arginine methyltransferase 7) and we demonstrated that KIN is modified by this enzyme. This interactome analysis indicates that KIN is associated with several cell metabolism functions, and shows for the first time an association with ribosome biogenesis, suggesting that KIN is likely a moonlight protein.

scholarly journals Transcriptional landscape of cellular networks reveal interactions driving the dormancy mechanisms in cancer

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dilara Uzuner ◽  
Yunus Akkoç ◽  
Nesibe Peker ◽  
Pınar Pir ◽  
Devrim Gözüaçık ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Regulatory Networks ◽  
Metastatic Cancer ◽  
Interaction Network ◽  
Current Treatment ◽  
Cellular Mechanisms ◽  
Protein Protein Interaction ◽  
Cancer Dormancy ◽  
Protein Protein Interaction Networks ◽  
First Time

AbstractPrimary cancer cells exert unique capacity to disseminate and nestle in distant organs. Once seeded in secondary sites, cancer cells may enter a dormant state, becoming resistant to current treatment approaches, and they remain silent until they reactivate and cause overt metastases. To illuminate the complex mechanisms of cancer dormancy, 10 transcriptomic datasets from the literature enabling 21 dormancy–cancer comparisons were mapped on protein–protein interaction networks and gene-regulatory networks to extract subnetworks that are enriched in significantly deregulated genes. The genes appearing in the subnetworks and significantly upregulated in dormancy with respect to proliferative state were scored and filtered across all comparisons, leading to a dormancy–interaction network for the first time in the literature, which includes 139 genes and 1974 interactions. The dormancy interaction network will contribute to the elucidation of cellular mechanisms orchestrating cancer dormancy, paving the way for improvements in the diagnosis and treatment of metastatic cancer.

scholarly journals Watching a deep dive: Live imaging provides lessons about tooth invagination

2016 ◽  
Vol 214 (6) ◽  
pp. 645-647 ◽  
Author(s):  
Amnon Sharir ◽  
Ophir D. Klein
Keyword(s):  
Live Imaging ◽  
Cellular Mechanisms ◽  
Deep Dive ◽  
Critical Step ◽  
Organ Morphogenesis ◽  
Cell Biol ◽  
Mouse Incisor

Invagination of epithelium into the surrounding mesenchyme is a critical step that marks the developmental onset of many ectodermal organs. In this issue, Ahtiainen et al. (2016. J. Cell. Biol. http://dx.doi.org/10.1083/jcb.201512074) use the mouse incisor as a model to advance our understanding of the cellular mechanisms underlying ectodermal organ morphogenesis.

scholarly journals Phosphoregulation of the intracellular termini of K+-Cl− cotransporter 2 (KCC2) enables flexible control of its activity

2018 ◽  
Vol 293 (44) ◽  
pp. 16984-16993 ◽  
Author(s):  
Antje Cordshagen ◽  
Wiebke Busch ◽  
Michael Winklhofer ◽  
Hans Gerd Nothwang ◽  
Anna-Maria Hartmann
Keyword(s):  
Intrinsic Activity ◽  
Hek 293 ◽  
Flexible Control ◽  
Mediated Effects ◽  
293 Cells ◽  
Bona Fide ◽  
Graded Activity ◽  
First Time ◽  
Increased Activity

The pivotal role of K+-Cl− cotransporter 2 (KCC2) in inhibitory neurotransmission and severe human diseases fosters interest in understanding posttranslational regulatory mechanisms such as (de)phosphorylation. Here, the regulatory role of the five bona fide phosphosites Ser31, Thr34, Ser932, Thr999, and Thr1008 was investigated by the use of alanine and aspartate mutants. Tl+-based flux analyses in HEK-293 cells demonstrated increased transport activity for S932D (mimicking phosphorylation) and T1008A (mimicking dephosphorylation), albeit to a different extent. Increased activity was due to changes in intrinsic activity, as it was not caused by increased cell-surface abundance. Substitutions of Ser31, Thr34, or Thr999 had no effect. Additionally, we show that the indirect actions of the known KCC2 activators staurosporine and N-ethylmaleimide (NEM) involved multiple phosphosites. S31D, T34A, S932A/D, T999A, or T1008A/D abrogated staurosporine mediated stimulation, and S31A, T34D, or S932D abolished NEM-mediated stimulation. This demonstrates for the first time differential effects of staurosporine and NEM on KCC2. In addition, the staurosporine-mediated effects involved both KCC2 phosphorylation and dephosphorylation with Ser932 and Thr1008 being bona fide target sites. In summary, our data reveal a complex phosphoregulation of KCC2 that provides the transporter with a toolbox for graded activity and integration of different signaling pathways.

scholarly journals HSFs drive stress type-specific transcription of genes and enhancers

2021 ◽  
Author(s):  
Samu V Himanen ◽  
Mikael C Puustinen ◽  
Alejandro J Da Silva ◽  
Anniina Vihervaara ◽  
Lea Sistonen
Keyword(s):  
Oxidative Stress ◽  
Heat Shock ◽  
Rna Polymerase Ii ◽  
Molecular Mechanisms ◽  
Gene Promoters ◽  
Heat Shock Factors ◽  
Pol Ii ◽  
Bona Fide ◽  
Stressed Cells ◽  
First Time

Reprogramming of transcription is critical for the survival under cellular stress. Heat shock has provided an excellent model to investigate nascent transcription in stressed cells, but the molecular mechanisms orchestrating RNA synthesis during other types of stress are unknown. We utilized PRO-seq and ChIP-seq to study how Heat Shock Factors, HSF1 and HSF2, coordinate transcription at genes and enhancers upon oxidative stress and heat shock. We show that pause-release of RNA polymerase II (Pol II) is a universal mechanism regulating gene transcription in stressed cells, while enhancers are activated at the level of Pol II recruitment. Moreover, besides functioning as conventional promoter-binding transcription factors, HSF1 and HSF2 bind to stress-induced enhancers to trigger Pol II pause-release from poised gene promoters. Importantly, HSFs act at distinct genes and enhancers in a stress type-specific manner. HSF1 binds to many chaperone genes upon oxidative and heat stress but activates them only in heat-shocked cells. Under oxidative stress, HSF1 and HSF2 trans-activate genes independently of each other, demonstrating, for the first time, that HSF2 is a bona fide transcription factor. Taken together, we show that HSFs function as multi-stress-responsive factors that activate specific genes and enhancers when encountering changes in temperature and redox state.

scholarly journals Cephalopod Retinal Development Shows Vertebrate-like Mechanisms of Neurogenesis

2021 ◽  
Author(s):  
Francesca Napoli ◽  
Christina M Daly ◽  
Stephanie Neal ◽  
Kyle J McCulloch ◽  
Alexandra Zaloga ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Nervous System ◽  
Progenitor Cells ◽  
Cellular Proliferation ◽  
Imaging Techniques ◽  
Nuclear Migration ◽  
Live Imaging ◽  
Cellular Mechanisms ◽  
High Resolution Data ◽  
Interkinetic Nuclear Migration

Neurogenesis, the regulation of cellular proliferation and differentiation in the developing nervous system, is the process that underlies the diversity of size and cell type found in animal nervous systems. Our understanding of how this process has evolved is limited because of the lack of high resolution data and live-imaging methods across species. The retina is a classic model for the study of neurogenesis in vertebrates and live-imaging of the retina has shown that during development, progenitor cells are organized in a pseudostratified neuroepithelium and nuclei migrate in coordination with the cell cycle along the apicobasal axis of the cell, a process called interkinetic nuclear migration. Eventually cells delaminate and differentiate within the boundaries of the epithelium. This process has been considered unique to vertebrates and thought to be important in maintaining organization during the development of a complex nervous system. Coleoid cephalopods, including squid, cuttlefish and octopus, have the largest nervous system of any invertebrate and convergently-evolved camera-type eyes, making them a compelling comparative system to vertebrates. Here we have pioneered live-imaging techniques to show that the squid, Doryteuthis pealeii, displays cellular mechanisms during cephalopod retinal neurogenesis that are hallmarks of vertebrate processes. We find that retinal progenitor cells in the squid undergo interkinetic nuclear migration until they exit the cell cycle, we identify retinal organization corresponding to progenitor, post-mitotic and differentiated cells, and we find that Notch signaling regulates this process. With cephalopods and vertebrates having diverged 550 million years ago, these results suggest that mechanisms thought to be unique to vertebrates may be common to highly proliferative neurogenic primordia contributing to a large nervous system.

Kinematics Analysis and Numerical Method for Multi-Link Suspension

2011 ◽  
Vol 314-316 ◽  
pp. 810-814
Author(s):  
Mo Wu Lu ◽  
Wei Qiang Zhao
Keyword(s):  
Mathematical Model ◽  
Numerical Method ◽  
Matrix Method ◽  
Kinematics Analysis ◽  
Computer Based

This paper presents a numerical method for kinematics analysis of Multi-link suspension based on displacement matrix method. A mathematical model for kinematics analysis of multi-link suspension is established and the kinematical properties of multi-link suspension are analyzed using this method. The numerical method for solving this problem is discussed and the relevant program is developed. This method simplifies the solving process of kinematics properties analysis of multi-link suspension and is efficient especially for computer-based solving process.

scholarly journals Rapid Morphological and Cytoskeletal Response to Microgravity in Human Primary Macrophages

2019 ◽  
Vol 20 (10) ◽  
pp. 2402 ◽  
Author(s):  
Cora Sandra Thiel ◽  
Svantje Tauber ◽  
Beatrice Lauber ◽  
Jennifer Polzer ◽  
Christian Seebacher ◽  
...  
Keyword(s):  
Actin Cytoskeleton ◽  
Live Cell Imaging ◽  
Cell Imaging ◽  
Live Imaging ◽  
Live Cell ◽  
Cellular Structures ◽  
Microgravity Environment ◽  
Confocal Laser ◽  
Human Macrophages ◽  
Imaging Experiment

The FLUMIAS (Fluorescence-Microscopic Analyses System for Life-Cell-Imaging in Space) confocal laser spinning disk fluorescence microscope represents a new imaging capability for live cell imaging experiments on suborbital ballistic rocket missions. During the second pioneer mission of this microscope system on the TEXUS-54 suborbital rocket flight, we developed and performed a live imaging experiment with primary human macrophages. We simultaneously imaged four different cellular structures (nucleus, cytoplasm, lysosomes, actin cytoskeleton) by using four different live cell dyes (Nuclear Violet, Calcein, LysoBrite, SiR-actin) and laser wavelengths (405, 488, 561, and 642 nm), and investigated the cellular morphology in microgravity (10−4 to 10−5 g) over a period of about six minutes compared to 1 g controls. For live imaging of the cytoskeleton during spaceflight, we combined confocal laser microscopy with the SiR-actin probe, a fluorogenic silicon-rhodamine (SiR) conjugated jasplakinolide probe that binds to F-actin and displays minimal toxicity. We determined changes in 3D cell volume and surface, nuclear volume and in the actin cytoskeleton, which responded rapidly to the microgravity environment with a significant reduction of SiR-actin fluorescence after 4–19 s microgravity, and adapted subsequently until 126–151 s microgravity. We conclude that microgravity induces geometric cellular changes and rapid response and adaptation of the potential gravity-transducing cytoskeleton in primary human macrophages.

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