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How the Timing of Biological Processes is Controlled and Modified...
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How the Timing of Biological Processes is Controlled and Modified at the Molecular and Cellular Level?

A special issue of Biology (ISSN 2079-7737).

Deadline for manuscript submissions: closed (31 May 2021) | Viewed by 13987

Special Issue Editors

Prof. Dr. Jacek Z. Kubiak

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Guest Editor
Dynamics and Mechanics of Epithelia Group, Faculty of Medicine, Institute of Genetics and Development of Rennes, University of Rennes, CNRS, UMR 6290, 35043 Rennes, France
Interests: embryo development; cell cycle; gene regulation; cancer; stem cells; gonads; genetic diseases
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Malgorzata Kloc

E-Mail Website
Guest Editor
Transplant Immunology, The Houston Methodist Research Institute, Houston, TX 77030, USA
Interests: macrophages; actin cytoskeleton; RhoA pathway; chronic rejection; transplantation; germ cells; stem cells; Xenopus laevis; development
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The correct timing of molecular and cellular events is critical for embryo development, cell/tissue homeostasis, and functions in all organisms. One of the examples is the temporal regulation of cell cycle events. The cell cycle has to proceed in a well-defined time frame to assure, for example, the coordination between cell proliferation and the embryo developmental program. The checkpoint mechanisms monitor if the necessary processes have been completed before starting the new ones. Thus, the precise timely coordination between molecular pathways and their specific regulation in different conditions allows the harmonious functioning of cells, tissues, and organs. Another example is a circadian rhythm, which refers to any biological process occurring with about 24 hours oscillation. Because all aspects of cell physiology require a precise time control the defects in this control may contribute to a number of diseases, including cancers, diabetes, and metabolic or behavioral disorders, and well beyond.
For this special issue, we invite research articles and review articles on all aspects of temporal regulation in cells and tissues, and particularly those, which contribute to our understanding of the role of the time-dependent coordination between molecular pathways in physiological vs. pathological conditions. We hope that the colleagues from many different fields of biology and medicine in which the “How the timing of biological processes is controlled and modified at the molecular and cellular level?” will contribute to this special issue. 

Prof. Dr. Jacek Z Kubiak
Prof. Dr. Malgorzata Kloc
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biology is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Timing regulation
  • molecular processes
  • cellular processes
  • cell cycle
  • circadian rhythm
  • embryo development
  • metabolism
  • cancer
  • diabetes

Related Special Issues

Published Papers (5 papers)

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Research

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15 pages, 1911 KiB  
Article
Intrauterine Infusion of TGF-β1 Prior to Insemination, Alike Seminal Plasma, Influences Endometrial Cytokine Responses but Does Not Impact the Timing of the Progression of Pre-Implantation Pig Embryo Development
by Cristina A. Martinez, Josep M. Cambra, Xiomara Lucas, Graça Ferreira-Dias, Heriberto Rodriguez-Martinez, Maria A. Gil, Emilio A. Martinez, Cristina Cuello and Inmaculada Parrilla
Biology 2021, 10(2), 159; https://doi.org/10.3390/biology10020159 - 17 Feb 2021
Cited by 4 | Viewed by 1969
Abstract
Seminal plasma (SP) in the female genital tract induces changes that affect multiple reproductive processes. One of the active components in SP is the transforming growth factor β1 (TGF-β1), which has major roles in embryo development and pregnancy. Embryo transfer (ET) technology is [...] Read more.
Seminal plasma (SP) in the female genital tract induces changes that affect multiple reproductive processes. One of the active components in SP is the transforming growth factor β1 (TGF-β1), which has major roles in embryo development and pregnancy. Embryo transfer (ET) technology is welcomed by the pig industry provided that embryo quality at embryo collection as well as the fertility and prolificacy of the recipients after the ET is increased. This study evaluated different intrauterine infusion treatments at estrus (40 mL of SP, TGF-β1 cytokine in the extender, or the extender alone (control)) by mimicking an ET scenario in so-called “donor” (inseminated) and “recipient” (uninseminated) sows. On day 6 (day 0—onset of estrus), all “donors” were laparotomized to determine their pregnancy status (presence and developmental stage of the embryos). In addition, endometrial explants were collected from pregnant “donors” and cyclic “recipients,” incubated for 24 h, and analyzed for cytokine production. SP infusions (unlike TGF-β1 infusions) positively influenced the developmental stage of day 6 embryos. Infusion treatments differentially influenced the endometrial cytokine production, mainly in donors. We concluded that SP infusions prior to AI not only impacted the porcine preimplantation embryo development but also influenced the endometrial cytokine production six days after treatment, both in donors and recipients. Full article
(This article belongs to the Special Issue How the Timing of Biological Processes is Controlled and Modified at the Molecular and Cellular Level?)
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16 pages, 1290 KiB  
Article
A Shorter Equilibration Period Improves Post-Warming Outcomes after Vitrification and in Straw Dilution of In Vitro-Produced Bovine Embryos
by Iris Martínez-Rodero, Tania García-Martínez, Erika Alina Ordóñez-León, Meritxell Vendrell-Flotats, Carlos Olegario Hidalgo, Joseba Esmoris, Xabier Mendibil, Sabino Azcarate, Manel López-Béjar, Marc Yeste and Teresa Mogas
Biology 2021, 10(2), 142; https://doi.org/10.3390/biology10020142 - 10 Feb 2021
Cited by 14 | Viewed by 2950
Abstract
This study was designed to the optimize vitrification and in-straw warming protocol of in vitro-produced bovine embryos by comparing two different equilibration periods, short equilibrium (SE: 3 min) and long equilibrium (LE: 12 min). Outcomes recorded in vitrified day seven (D7) and day [...] Read more.
This study was designed to the optimize vitrification and in-straw warming protocol of in vitro-produced bovine embryos by comparing two different equilibration periods, short equilibrium (SE: 3 min) and long equilibrium (LE: 12 min). Outcomes recorded in vitrified day seven (D7) and day eight (D8) expanded blastocysts were survival and hatching rates, cell counts, apoptosis rate, and gene expression. While survival rates at 3 and 24 h post-warming were reduced (p < 0.05) after vitrification, the hatching rates of D7 embryos vitrified after SE were similar to the rates recorded in fresh non-vitrified blastocysts. The hatching rates of vitrified D8 blastocysts were lower (p < 0.05) than of fresh controls regardless of treatment. Total cell count, and inner cell mass and trophectoderm cell counts were similar in hatched D7 blastocysts vitrified after SE and fresh blastocysts, while vitrified D8 blastocysts yielded lower values regardless of treatment. The apoptosis rate was significantly higher in both treatment groups compared to fresh controls, although rates were lower for SE than LE. No differences emerged in BAX, AQP3, CX43, and IFNτ gene expression between the treatments, whereas a significantly greater abundance of BCL2L1 and SOD1 transcripts was observed in blastocysts vitrified after SE. A shorter equilibration vitrification protocol was found to improve post-warming outcomes and time efficiency after in-straw warming/dilution. Full article
(This article belongs to the Special Issue How the Timing of Biological Processes is Controlled and Modified at the Molecular and Cellular Level?)
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11 pages, 4845 KiB  
Article
Identification and Spatiotemporal Expression of Adenosine Deaminases Acting on RNA (ADAR) during Earthworm Regeneration: Its Possible Implication in Muscle Redifferentiation
by Yoo Bin Yoon, Yun-Sang Yu, Beom Jun Park, Sung-Jin Cho and Soon Cheol Park
Biology 2020, 9(12), 448; https://doi.org/10.3390/biology9120448 - 05 Dec 2020
Cited by 3 | Viewed by 2148
Abstract
Adenosine deaminases acting on RNA (ADAR) catalyze the hydrolytic deamination of adenosine (A) to produce inosine (I) in double-stranded RNA substrates. A-to-I RNA editing has increasingly broad physiological significance in development, carcinogenesis, and environmental adaptation. Perionyx excavatus is an earthworm with potent regenerative [...] Read more.
Adenosine deaminases acting on RNA (ADAR) catalyze the hydrolytic deamination of adenosine (A) to produce inosine (I) in double-stranded RNA substrates. A-to-I RNA editing has increasingly broad physiological significance in development, carcinogenesis, and environmental adaptation. Perionyx excavatus is an earthworm with potent regenerative potential; it can regenerate the head and tail and is an advantageous model system to investigate the molecular mechanisms of regeneration. During RNA sequencing analysis of P. excavatus regenerates, we identified an ADAR homolog (Pex-ADAR), which led us to examine its spatial and temporal expression to comprehend how Pex-ADAR is linked to regeneration. At first, in domain analysis, we discovered that Pex-ADAR only has one double-stranded RNA-binding domain (dsRBD) and a deaminase domain without a Z-DNA-binding domain (ZBD). In addition, a comparison of the core deaminase domains of Pex-ADAR with those of other ADAR family members indicated that Pex-ADAR comprises the conserved three active-site motifs and a glutamate residue for catalytic activity. Pex-ADAR also shares 11 conserved residues, a characteristic of ADAR1, supporting that Pex-ADAR is a member of ADAR1 class. Its temporal expression was remarkably low in the early stages of regeneration before suddenly increasing at 10 days post amputation (dpa) when diverse cell types and tissues were being regenerated. In situ hybridization of Pex-ADAR messenger RNA (mRNA) indicated that the main expression was observed in regenerating muscle layers and related connective tissues. Taken together, the present results demonstrate that an RNA-editing enzyme, Pex-ADAR, is implicated in muscle redifferentiation during earthworm regeneration. Full article
(This article belongs to the Special Issue How the Timing of Biological Processes is Controlled and Modified at the Molecular and Cellular Level?)
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Review

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14 pages, 1176 KiB  
Review
Temporal Gradients Controlling Embryonic Cell Cycle
by Boyang Liu, Han Zhao, Keliang Wu and Jörg Großhans
Biology 2021, 10(6), 513; https://doi.org/10.3390/biology10060513 - 09 Jun 2021
Cited by 5 | Viewed by 2849
Abstract
Cell proliferation in early embryos by rapid cell cycles and its abrupt pause after a stereotypic number of divisions present an attractive system to study the timing mechanism in general and its coordination with developmental progression. In animals with large eggs, such as [...] Read more.
Cell proliferation in early embryos by rapid cell cycles and its abrupt pause after a stereotypic number of divisions present an attractive system to study the timing mechanism in general and its coordination with developmental progression. In animals with large eggs, such as Xenopus, zebrafish, or Drosophila, 11–13 very fast and synchronous cycles are followed by a pause or slowdown of the cell cycle. The stage when the cell cycle is remodeled falls together with changes in cell behavior and activation of the zygotic genome and is often referred to as mid-blastula transition. The number of fast embryonic cell cycles represents a clear and binary readout of timing. Several factors controlling the cell cycle undergo dynamics and gradual changes in activity or concentration and thus may serve as temporal gradients. Recent studies have revealed that the gradual loss of Cdc25 protein, gradual depletion of free deoxyribonucleotide metabolites, or gradual depletion of free histone proteins impinge on Cdk1 activity in a threshold-like manner. In this review, we will highlight with a focus on Drosophila studies our current understanding and recent findings on the generation and readout of these temporal gradients, as well as their position within the regulatory network of the embryonic cell cycle. Full article
(This article belongs to the Special Issue How the Timing of Biological Processes is Controlled and Modified at the Molecular and Cellular Level?)
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16 pages, 2983 KiB  
Review
RhoA- and Actin-Dependent Functions of Macrophages from the Rodent Cardiac Transplantation Model Perspective -Timing Is the Essence
by Malgorzata Kloc, Ahmed Uosef, Martha Villagran, Robert Zdanowski, Jacek Z. Kubiak, Jarek Wosik and Rafik M. Ghobrial
Biology 2021, 10(2), 70; https://doi.org/10.3390/biology10020070 - 20 Jan 2021
Cited by 9 | Viewed by 2958
Abstract
The small GTPase RhoA, and its down-stream effector ROCK kinase, and the interacting Rac1 and mTORC2 pathways, are the principal regulators of the actin cytoskeleton and actin-related functions in all eukaryotic cells, including the immune cells. As such, they also regulate the phenotypes [...] Read more.
The small GTPase RhoA, and its down-stream effector ROCK kinase, and the interacting Rac1 and mTORC2 pathways, are the principal regulators of the actin cytoskeleton and actin-related functions in all eukaryotic cells, including the immune cells. As such, they also regulate the phenotypes and functions of macrophages in the immune response and beyond. Here, we review the results of our and other’s studies on the role of the actin and RhoA pathway in shaping the macrophage functions in general and macrophage immune response during the development of chronic (long term) rejection of allografts in the rodent cardiac transplantation model. We focus on the importance of timing of the macrophage functions in chronic rejection and how the circadian rhythm may affect the anti-chronic rejection therapies. Full article
(This article belongs to the Special Issue How the Timing of Biological Processes is Controlled and Modified at the Molecular and Cellular Level?)
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