Fluorescence Recovery After Photobleaching (FRAP) in the Fission Yeast Nucleus

Delivani, Petrina; Chacón, Mariola R.; Schroth‐Diez, Britta; Tolic-Norrelykke, Iva M.

doi:10.21769/bioprotoc.941

Cited by 2 publications

(2 citation statements)

References 3 publications

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“…ROS levels in damaged cells were reported to be 3-45 times higher compared with those in normal cells. [2,33] In addition, H 2 O 2 has been popularly used for infection control at wound sites. [29] Therefore, an ROS-cleavable linker, TK, was used to conjugate EGFfr on NFs to facilitate the sustained release of EGFfr.…”

Section: Resultsmentioning

confidence: 99%

Reactive Oxygen Species (ROS)‐Assisted Nano‐Therapeutics Surface‐Decorated with Epidermal Growth Factor Fragments for Enhanced Wound Healing

Lee,

Bui,

Pham

et al. 2023

Macromolecular Bioscience

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In this study, stimuli‐responsive liberation of an epidermal growth factor fragment (EGFfr) is accomplished using nanofibrous meshes to improve wound healing effects. Electrospun nanofibers are fragmented by mechanical milling, followed by aminolysis to fabricate powdered nanofibrils (NFs). EGFfrs are covalently immobilized on NFs via thioketal linkers (EGFfr@TK@NF) for reactive oxygen species (ROS)–dependent liberation. EGFfr@TK@NF exhibits ROS‐responsive liberation of EGFfr from the matrix at hydrogen peroxide (H2O2) concentrations of 0–250 mm. Released EGFfr is confirmed to enhance the migration of HaCaT cell monolayers, and keratinocytic gene expression levels are significantly enhanced when H2O2 is added to obtain the released fraction of NFs. An in vivo study on the dorsal wounds of mice reveals that EGFfr‐immobilized NFs improve the expression levels of keratin1, 5, and 14 for 2 weeks when H2O2 is added to the wound sites, suggesting that the wounded skin is re‐epithelized with the original epidermis. Thus, EGFfrs‐immobilized NFs are anticipated to be potential nanotherapeutics for wound treatment in combination with the conventional disinfection process with H2O2.

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Section: Resultsmentioning

confidence: 99%

Reactive Oxygen Species (ROS)‐Assisted Nano‐Therapeutics Surface‐Decorated with Epidermal Growth Factor Fragments for Enhanced Wound Healing

Lee,

Bui,

Pham

et al. 2023

Macromolecular Bioscience

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“…Under the simplifying assumption that activation factors can dock anywhere on the surface of the two pre-RCs bound to each origin, we set the minimal value of the origin attraction sphere radius to 0.015 μm and explore higher values as well. To select plausible values of the particle diffusion coefficient, we considered that in the fission yeast nucleus the diffusion coefficient of GFP alone was reported to have a minimum value of ≈ 3 μm 2 /s [60], and sampled three realistic values in the range of [0, 3.5] μm 2 /s . The particle activation and binding probabilities were set to P act = P bind = 1.…”

Section: Model Variantsmentioning

confidence: 99%

A stochastic hybrid model of DNA replication incorporating 3D protein mobility dynamics

Windhager

Paine

Nathanailidou

et al. 2019

Preprint

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DNA replication is a complex process that ensures the maintenance of genetic information. Recently, advancements in chromatin conformation capture techniques have enabled the modeling of DNA replication as a spatio-temporal process. Here, we present a stochastic hybrid model for DNA replication that incorporates protein mobility dynamics and 3D chromatin structure. Performing simulations for three model variations and a broad range of parameter values, we collected about 300,000 in silico replication profiles for fission yeast and conducted a parameter sensitivity analysis. We find that the number of firing factors initiating replication is rate-limiting and dominates the time until completion of DNA replication. In support of recent work, we also find that explicitly modeling the recruitment of firing factors by the spindle pole body (SPB) best recapitulates published origin efficiencies, and independently validate these findings in vivo. Accounting for probabilistic effects in molecular interactions, we further investigated the replication kinetics inherent to the model and were able to capture known properties of DNA replication. Importantly, we confirm earlier observations that, without further assumptions, the characteristic shape of a function commonly used to describe replication kinetics arises from a rate-limiting number of firing factors in conjunction with their recycling upon replication fork collision. While the model faithfully recapitulates global spatial patterns of replication initiation, additional analysis of spatial concurrence and competition suggests that a uniform binding probability is too simplistic to capture local neighborhood effects in origin firing. In summary, our model provides a framework to realistically simulate DNA replication for a complete eukaryotic genome, and to investigate the relationship between three-dimensional chromatin conformation and DNA replication timing.Recent advancements in chromosome conformation capture techniques (e.g., 3C, Hi-C) have enabled the determination of DNA structure and nuclear organization. As a consequence, studies on various organisms have observed that DNA replication timing is highly correlated with chromatin folding and global nuclear architecture [34][35][36]. In mammalian cells, chromatin conformation maps agree with replication timing profiles

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Fluorescence Recovery After Photobleaching (FRAP) in the Fission Yeast Nucleus

Cited by 2 publications

References 3 publications

Reactive Oxygen Species (ROS)‐Assisted Nano‐Therapeutics Surface‐Decorated with Epidermal Growth Factor Fragments for Enhanced Wound Healing

Reactive Oxygen Species (ROS)‐Assisted Nano‐Therapeutics Surface‐Decorated with Epidermal Growth Factor Fragments for Enhanced Wound Healing

A stochastic hybrid model of DNA replication incorporating 3D protein mobility dynamics

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