Special Issue "Trends and Outlooks in Synthetic Biology: A Special Issue for Celebrating 10 Years of Life and Its Landmarks"

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

Deadline for manuscript submissions: 18 June 2021.

Special Issue Editors

Prof. Dr. Pasquale Stano
E-Mail Website
Guest Editor
Dipartimento di Scienze e Tecnologie Biologiche e Ambientali (DiSTeBA), Università del Salento Campus Ecotekne, S. P. 6 Lecce-Monteroni, 73100 Lecce, Italy
Interests: origins of life; synthetic biology; artificial life; synthetic cells; drug delivery; bio-chem-ICTs; autopoiesis and cognition
Special Issues and Collections in MDPI journals
Prof. Dr. Norikazu Ichihashi
E-Mail Website
Guest Editor
Department of Life Science, Graduate School of Arts and Science, Komaba Institute of Science, the University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
Interests: in vitro synthetic biology; evolution; artificial cell; RNA replication; DNA replication; translation; ribosome
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

Since its inception in December 2011, the Editorial Board and Guest Editors of Life have been working hard to make Life an outstanding journal that receives the highest-quality submissions. One important goal was the inclusion of Life in the major databases in order to provide its authors with the visibility and impact that they desire. We are pleased to say that this goal has been met, as Life has been selected for inclusion in important databases such PubMed, Scopus, and the Science Citation Index Expanded (SCIE). Importantly, in 2020 Life has received its first Impact Factor (2.991), and will also reach a milestone by publishing its 10th volume. The Life Editorial Board and Editorial Office thank all who have contributed in the past, and welcome your contributions to Life in the years ahead.

Reaching these major milestones is quite relevant for a growing and dynamical journal, and it is worthy of celebration. Therefore we are launching a celebratory Special Issue on “Trends and Outlooks in Synthetic Biology” to further promote the improved recognition of Life as an outstanding journal in the field of synthetic biology. All researchers working in this field are invited to contribute to this Special Issue.

We would like to elicit the submission of articles (full articles, communications, reviews, etc.) related to the broad subject of Synthetic Biology, with a special focus on (but not limited to) bottom-up/cell-free approaches, artificial compartments (including microfluidics and microchambers), in vitro transcription and translation, in vitro evolution, and related topics. All types of approaches are welcome (experimental, theoretical, conceptual, numerical simulations, etc.).

We look forward to receiving your best contributions and assembling a high-quality Special Issue to celebrate the landmarks of Life.

Deadlines:

  • Early-bird deadline: 15 June 2021, with 200 CHF discount on APCs.

Prof. Dr. Pasquale Stano
Prof. Dr. Norikazu Ichihashi
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 papers will be 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 1600 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

  • synthetic biology
  • bottom-up
  • artificial cells
  • synthetic cells
  • protocells
  • microfluidics
  • microchamber
  • cell-free protein synthesis
  • transcription-translation
  • cell-free bioproduction
  • artificial compartments
  • multicompartment
  • reconstitution studies
  • artificial biodevices and biosystems
  • in vitro evolution
  • numerical simulations
  • stochastic simulations
  • high-throughput methods
  • cell-like biosensors
  • artificial life
  • synthetic life
  • non-standard amino acids
  • genetic networks

Published Papers (4 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Review

Open AccessArticle
Stability and Robustness of Unbalanced Genetic Toggle Switches in the Presence of Scarce Resources
Life 2021, 11(4), 271; https://doi.org/10.3390/life11040271 - 24 Mar 2021
Viewed by 380
Abstract
While the vision of synthetic biology is to create complex genetic systems in a rational fashion, system-level behaviors are often perplexing due to the context-dependent dynamics of modules. One major source of context-dependence emerges due to the limited availability of shared resources, coupling [...] Read more.
While the vision of synthetic biology is to create complex genetic systems in a rational fashion, system-level behaviors are often perplexing due to the context-dependent dynamics of modules. One major source of context-dependence emerges due to the limited availability of shared resources, coupling the behavior of disconnected components. Motivated by the ubiquitous role of toggle switches in genetic circuits ranging from controlling cell fate differentiation to optimizing cellular performance, here we reveal how their fundamental dynamic properties are affected by competition for scarce resources. Combining a mechanistic model with nullcline-based stability analysis and potential landscape-based robustness analysis, we uncover not only the detrimental impacts of resource competition, but also how the unbalancedness of the switch further exacerbates them. While in general both of these factors undermine the performance of the switch (by pushing the dynamics toward monostability and increased sensitivity to noise), we also demonstrate that some of the unwanted effects can be alleviated by strategically optimized resource competition. Our results provide explicit guidelines for the context-aware rational design of toggle switches to mitigate our reliance on lengthy and expensive trial-and-error processes, and can be seamlessly integrated into the computer-aided synthesis of complex genetic systems. Full article
Show Figures

Figure 1

Open AccessArticle
A Relationship between NTP and Cell Extract Concentration for Cell-Free Protein Expression
Life 2021, 11(3), 237; https://doi.org/10.3390/life11030237 - 13 Mar 2021
Viewed by 588
Abstract
The cell-free protein synthesis (CFPS) that synthesizes mRNA and protein from a template DNA has been featured as an important tool to emulate living systems in vitro. However, an obstacle to emulate living cells by CFPS is the loss of activity in the [...] Read more.
The cell-free protein synthesis (CFPS) that synthesizes mRNA and protein from a template DNA has been featured as an important tool to emulate living systems in vitro. However, an obstacle to emulate living cells by CFPS is the loss of activity in the case of usage of high concentration cell extracts. In this study, we found that a high concentration of NTP which inhibits in the case of lower concentration cell extract restored the loss of CFPS activity using high concentration cell extracts. The NTP restoration was independent of the energy regeneration system used, and NTP derivatives also restored the levels of CFPS using a high concentration cell extract. Experiments using dialysis mode of CFPS showed that continuous exchange of small molecule reduced levels of NTP requirement and improved reaction speed of CFPS using the high concentration of cell extract. These findings contribute to the development of a method to understand the condition of living cells by in vitro emulation, and are expected to lead to the achievement of the reconstitution of living cells from biomolecule mixtures. Full article
Show Figures

Figure 1

Open AccessArticle
Giant Vesicles Produced with Phosphatidylcholines (PCs) and Phosphatidylethanolamines (PEs) by Water-in-Oil Inverted Emulsions
Life 2021, 11(3), 223; https://doi.org/10.3390/life11030223 - 10 Mar 2021
Viewed by 502
Abstract
(1) Background: giant vesicles (GVs) are widely employed as models for studying physicochemical properties of bio-membranes and artificial cell construction due to their similarities to natural cell membranes. Considering the critical roles of GVs, various methods have been developed to prepare them. Notably, [...] Read more.
(1) Background: giant vesicles (GVs) are widely employed as models for studying physicochemical properties of bio-membranes and artificial cell construction due to their similarities to natural cell membranes. Considering the critical roles of GVs, various methods have been developed to prepare them. Notably, the water-in-oil (w/o) inverted emulsion-transfer method is reported to be the most promising, owning to the relatively higher productivity and better encapsulation efficiency of biomolecules. Previously, we successfully established an improved approach to acquire detailed information of 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)-derived GVs with imaging flow cytometry (IFC); (2) Methods: we prepared GVs with different lipid compositions, including phosphatidylcholines (PCs), phosphatidylethanolamines (PEs), and PC/PE mixtures by w/o inverted emulsion methods. We comprehensively compared the yield, purity, size, and encapsulation efficiency of the resulting vesicles; (3) Results: the relatively higher productivities of GVs could be obtained from POPC, 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-dilauroyl-sn-glycero-3-phosphoethanolamine (DLPE), DOPC: DLPE (7:3), and POPC: DLPE (6:4) pools. Furthermore, we also demonstrate that these GVs are stable during long term preservation in 4 °C. (4) Conclusions: our results will be useful for the analytical study of GVs and GV-based applications. Full article
Show Figures

Graphical abstract

Review

Jump to: Research

Open AccessReview
Primitive Compartmentalization for the Sustainable Replication of Genetic Molecules
Life 2021, 11(3), 191; https://doi.org/10.3390/life11030191 - 28 Feb 2021
Viewed by 897
Abstract
Sustainable replication and evolution of genetic molecules such as RNA are likely requisites for the emergence of life; however, these processes are easily affected by the appearance of parasitic molecules that replicate by relying on the function of other molecules, while not contributing [...] Read more.
Sustainable replication and evolution of genetic molecules such as RNA are likely requisites for the emergence of life; however, these processes are easily affected by the appearance of parasitic molecules that replicate by relying on the function of other molecules, while not contributing to their replication. A possible mechanism to repress parasite amplification is compartmentalization that segregates parasitic molecules and limits their access to functional genetic molecules. Although extent cells encapsulate genomes within lipid-based membranes, more primitive materials or simple geological processes could have provided compartmentalization on early Earth. In this review, we summarize the current understanding of the types and roles of primitive compartmentalization regarding sustainable replication of genetic molecules, especially from the perspective of the prevention of parasite replication. In addition, we also describe the ability of several environments to selectively accumulate longer genetic molecules, which could also have helped select functional genetic molecules rather than fast-replicating short parasitic molecules. Full article
Show Figures

Figure 1

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Confirmed

1. Dr. Katarzyna Adamala (University of Minnesota, USA)

2. Professor Cheemeng Tan (UC Davis, USA)

3. Dr. Melinda Bonnie Fagan;

4. Dr. Andras Gyorgy

5. Dr. Manish Kumar Gupta

6. Dr. Danielle Biscaro Pedrolli

Interested

1. Dr. DAVIES Jamie

2. Dr. Ali Shojaeian

3. Dr. Bhavisha Sheth

4. Dr. Jennifer Liu

 

 

Back to TopTop