Feature Papers in Synthetic Biology and Systems Biology 2024

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Synthetic Biology and Systems Biology".

Deadline for manuscript submissions: 26 May 2025 | Viewed by 971

Special Issue Editor

Special Issue Information

Dear Colleagues,

We are pleased to announce a call for papers for our upcoming Special Issue “Feature Papers in Synthetic Biology and Systems Biology 2024” dedicated to the most exciting and relevant topics in these modern research fields. This Special Issue aims to showcase cutting-edge research, innovative methodologies, and transformative applications in these dynamic and interdisciplinary fields. We seek to highlight the latest advancements that push the boundaries of our understanding and capabilities in synthetic and systems biology. 

Researchers and practitioners are encouraged to submit their original work that demonstrates novel approaches, significant findings, and practical applications. 

Topics of interest include, but are not limited to, the design and construction of synthetic biological systems, computational modeling and simulation of biological processes, metabolic engineering, gene editing technologies, and systems biology approaches to understanding complex biological networks.

We welcome original research articles, comprehensive reviews, and insightful perspectives on a wide range of topics, including but not limited to the keywords listed below.

Dr. Pasquale Stano
Guest Editor

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. Life 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 2600 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

  • design and construction of synthetic biological systems
  • innovations in the creation of synthetic organisms, genetic circuits, and biomolecular devices
  • bottom-up synthetic biology
  • cell-free synthetic biology
  • tissue engineering and organoids
  • bioorthogonal parts, devices, systems
  • microcompartmentalized systems with soft or hard interfaces
  • theoretical considerations about synthetic biology
  • synthetic biology intersection with systems chemistry and bioorganic chemistry
  • computational modeling and simulation of biological processes
  • advances in computational tools and models that enhance our understanding of biological processes and systems
  • metabolic engineering and synthetic pathways
  • development of novel approaches for the production of biofuels, pharmaceuticals, and other valuable compounds
  • synthetic biology for approaching evolutionary problems
  • artificial evolution and in vitro evolution
  • optogenetics and related techniques
  • gene editing technologies, applications, and developments
  • education in synthetic and systems biology
  • cutting-edge techniques and applications of CRISPR and other gene editing tools
  • systems biology approaches to understanding complex biological networks
  • mathematical aspects of systems biology approaches
  • artificial photosynthesis
  • applications of synthetic biology in medicine, agriculture, and industry
  • practical applications of synthetic and systems biology in various sectors, including healthcare, agriculture, and industrial biotechnology
  • ethical, legal, and social implications of synthetic and systems biology
  • exploration of the broader implications of advancements in synthetic and systems biology, including ethical considerations and regulatory challenges and social implications

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Published Papers (1 paper)

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Research

27 pages, 5431 KiB  
Article
The plk1 Gene Regulatory Network Modeling Identifies Three Circuits for plk1-mediated Genomic Instability Leading to Neoplastic Transformation
by Jeison F. Suescum-Holguín, Diana Carolina Clavijo-Buriticá, Edward Fabian Carrillo-Borda and Mauricio Alberto Quimbaya
Life 2025, 15(5), 799; https://doi.org/10.3390/life15050799 - 17 May 2025
Viewed by 255
Abstract
Genomic instability has been increasingly recognized over the past decade as a fundamental driver of cancer initiation and progression, largely owing to its association with specific genes and cellular mechanisms that offer therapeutic potential. However, a comprehensive molecular framework that captures the interconnected [...] Read more.
Genomic instability has been increasingly recognized over the past decade as a fundamental driver of cancer initiation and progression, largely owing to its association with specific genes and cellular mechanisms that offer therapeutic potential. However, a comprehensive molecular framework that captures the interconnected processes underlying this phenomenon remains elusive. In this study, we focused on polo-like kinase 1 (PLK1), a key cell cycle regulator frequently overexpressed in diverse human tumors, to reconstruct a regulatory network that consolidates pre-existing biological knowledge exclusively related to pathways involved in genome stability maintenance and cancer. The resulting model integrates nine biological processes, 1030 reactions, and 716 molecular species to form a literature-supported network in which PLK1 serves as a central regulatory node. However, rather than depicting an isolated PLK1-centric system, this network reflects a broader and more complex architecture of interrelated genomic instability mechanisms. As expected, the simulations reproduced known behaviors associated with PLK1 dysregulation, reinforcing the well-established role of the kinase in genome destabilization. Importantly, this model also enables the exploration of additional, less-characterized dynamics, including the potential involvement of genes such as kif2c, incenp, and other regulators of chromosomal segregation and DNA repair, which appear to contribute to instability events downstream of PLK1. While these findings are grounded in mechanistic simulations and require further experimental validation, gene expression and survival analyses across tumor types support their clinical relevance by linking them to poor prognosis in specific cancers. Overall, the model provides a systemic and adaptable foundation for studying PLK1-related genomic instability, enabling both the reinforcement of known mechanisms and discovery of candidate genes and circuits that may drive tumorigenesis through compromised genome integrity across distinct cancer contexts. Full article
(This article belongs to the Special Issue Feature Papers in Synthetic Biology and Systems Biology 2024)
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