Feature Paper Collection in Synthetic Biology

A special issue of SynBio (ISSN 2674-0583).

Deadline for manuscript submissions: 31 October 2024 | Viewed by 11555

Special Issue Editor


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Guest Editor
Department of Pharmacognosy, University of Vienna, Vienna, Austria
Interests: antibiotics; bioprospecting; secondary metabolites biosynthesis; bacterial genetics; metabolic engineering; synthetic biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

It is our pleasure to announce a new Special Issue entitled “Feature Papers in Synthetic Biology”. It aims to collect high-quality original research articles, communications, and review papers in the cutting-edge field of synthetic biology. We encourage Editorial Board Members of the SynBio (https://www.mdpi.com/journal/synbio/editors) and the prominent scholars invited by the Editorial Office and the Guest Editors to contribute feature papers reflecting the recent advance in their research field.

Prof. Dr. Sergey Zotchev
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. SynBio is an international peer-reviewed open access quarterly 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 1000 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.

Published Papers (6 papers)

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Editorial

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4 pages, 186 KiB  
Editorial
SynBio: A Journal for Advancing Solutions to Global Challenges
by Masahito Yamagata
SynBio 2023, 1(3), 190-193; https://doi.org/10.3390/synbio1030013 - 19 Oct 2023
Cited by 1 | Viewed by 882
Abstract
Synthetic biology is a science that uses engineering principles to design and build new biological systems [...] Full article
(This article belongs to the Special Issue Feature Paper Collection in Synthetic Biology)

Research

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10 pages, 2122 KiB  
Article
Exploring the Interactions between Human microRNAs and the Ilheus Virus Genome
by Joyhare Barbosa Souza and Samir Mansour Moraes Casseb
SynBio 2023, 1(3), 194-203; https://doi.org/10.3390/synbio1030014 - 26 Oct 2023
Viewed by 809
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that play a fundamental role in the regulation of gene expression in humans. There has been a growing interest in investigating the interactions between human miRNAs and viruses to better understand the underlying mechanisms of the [...] Read more.
MicroRNAs (miRNAs) are small non-coding RNA molecules that play a fundamental role in the regulation of gene expression in humans. There has been a growing interest in investigating the interactions between human miRNAs and viruses to better understand the underlying mechanisms of the immune response and viral pathogenesis. The Ilheus virus, an arbovirus transmitted by mosquitoes, is known to cause disease in humans, with symptoms ranging from mild fever to severe neurological complications. This scientific article aims to explore the potential role of human miRNAs in their association with the genome of the Ilheus virus. Previous research has indicated that miRNAs can affect viral replication and the host’s immune response, playing a critical role in modulating the virus–host interaction. Here, we will investigate the possible interactions between specific human miRNAs and regions of the Ilheus virus genome, focusing on identifying miRNAs that may impact viral replication or the host’s immune response. A search for potential human miRNAs associated with the viral genome of ILHV was conducted through database searches such as miRBase. For the elucidation of targets regulated by these miRNAs, the TargetScan program was adopted. Functional enrichment analysis, inferring the function of genes regulated by miRNAs, was provided by the DAVID software. To elucidate the secondary structure, tools hosted in the RNAFold repositories were employed. In summary, our research has identified miRNAs linked to crucial sections of the Ilheus virus genome. These miRNAs can potentially regulate genes associated with neurological and immune functions. This highlights the intricate interplay between human miRNAs and the Ilheus virus genome, suggesting a pivotal role for these molecules in the host’s response to viral infections. Full article
(This article belongs to the Special Issue Feature Paper Collection in Synthetic Biology)
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29 pages, 4521 KiB  
Article
Drug Discovery for Periodontitis Treatment Based on Big Data Mining, Systems Biology, and Deep Learning Methods
by Chun-Tse Wang and Bor-Sen Chen
SynBio 2023, 1(1), 116-143; https://doi.org/10.3390/synbio1010009 - 17 May 2023
Cited by 3 | Viewed by 2209
Abstract
Periodontitis, a chronic inflammatory oral condition triggered by bacteria, archaea, viruses, and eukaryotic organisms, is a well-known and widespread disease around the world. While there are effective treatments for periodontitis, there are also several shortcomings associated with its management, including limited treatment options, [...] Read more.
Periodontitis, a chronic inflammatory oral condition triggered by bacteria, archaea, viruses, and eukaryotic organisms, is a well-known and widespread disease around the world. While there are effective treatments for periodontitis, there are also several shortcomings associated with its management, including limited treatment options, the risk of recurrence, and the high cost of treatment. Our goal is to develop a more efficient, systematic drug design for periodontitis before clinical trials. We work on systems drug discovery and design for periodontitis treatment via systems biology and deep learning methods. We first applied big database mining to build a candidate genome-wide genetic and epigenetic network (GWGEN), which includes a protein-protein interaction network (PPIN) and a gene regulatory network (GRN) for periodontitis and healthy control. Next, based on the unhealthy and healthy microarray data, we applied system identification and system order detection methods to remove false positives in candidate GWGENs to obtain real GWGENs for periodontitis and healthy control, respectively. After the real GWGENs were obtained, we picked out the core GWGENs based on how significant the proteins and genes were via the principal network projection (PNP) method. Finally, referring to the annotation of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, we built up the core signaling pathways of periodontitis and healthy control. Consequently, we investigated the pathogenic mechanism of periodontitis by comparing their core signaling pathways. By checking up on the downstream core signaling pathway and the corresponding cellular dysfunctions of periodontitis, we identified the fos proto-oncogene, AP-1 Transcription Factor Subunit (FOS), TSC Complex Subunit 2 (TSC2), Forkhead Box O1 (FOXO1), and nuclear factor kappa-light chain enhancer of activated B cells (NF-κB) as significant biomarkers on which we could find candidate molecular drugs to target. To achieve our ultimate goal of designing a combination of molecular drugs for periodontitis treatment, a deep neural network (DNN)-based drug-target interaction (DTI) model was employed. The model is trained with the existing drug-target interaction databases for the prediction of candidate molecular drugs for significant biomarkers. Finally, we filter out brucine, disulfiram, verapamil, and PK-11195 as potential molecular drugs to be combined as a multiple-molecular drug to target the significant biomarkers based on drug design specifications, i.e., adequate drug regulation ability, high sensitivity, and low toxicity. In conclusion, we investigated the pathogenic mechanism of periodontitis by leveraging systems biology methods and thoroughly developed a therapeutic option for periodontitis treatment via the prediction of a DNN-based DTI model and drug design specifications. Full article
(This article belongs to the Special Issue Feature Paper Collection in Synthetic Biology)
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13 pages, 4924 KiB  
Article
Rapid Production of Cyclic Citrullinated Peptide Monoclonal Antibody in Nicotiana benthamiana for the Early Detection and Diagnosis of Rheumatoid Arthritis
by Van Giap Do
SynBio 2023, 1(1), 103-115; https://doi.org/10.3390/synbio1010008 - 25 Apr 2023
Cited by 2 | Viewed by 2537
Abstract
Rheumatoid arthritis (RA) is one of the most common autoimmune diseases, affecting 0.5% to 1% of the population. It could ultimately result in joint destruction, functional decline, work disability, and enhanced mortality. Cyclic citrullinated peptide antibodies (CCP Abs) are useful biomarkers for the [...] Read more.
Rheumatoid arthritis (RA) is one of the most common autoimmune diseases, affecting 0.5% to 1% of the population. It could ultimately result in joint destruction, functional decline, work disability, and enhanced mortality. Cyclic citrullinated peptide antibodies (CCP Abs) are useful biomarkers for the early detection and diagnosis of RA. In this study, we used plant viral-based expression vectors that produce rapidly large quantities of CCP-specific monoclonal antibodies. Heavy and light chain genes of a CCP monoclonal antibody (CCP mAb) were cloned from the hybridoma cell (12G1) and introduced into two separate plant viral-based expression vectors, TMV and PVX. A cyclic citrullinated peptide monoclonal antibody was produced in Nicotiana benthamiana through an Agrobacterium-mediated transient expression system. The expression of CCP mAb in tobacco plants was confirmed by dot blot, western blot analysis, and enzyme-linked immunosorbent assays (ELISA). It was shown that tobacco plants could accumulate CCP mAbs up to 0.35% of total soluble protein. Accumulated CCP mAb from infiltrated leaves was purified by protein G affinity chromatography. Immunoblot assays and ELISA showed plant-produced CCP mAbs successfully bound to a synthetic CCP peptide antigen. This system provides a fast strategy for the production of pharmaceutical CCP mAbs in tobacco plants. Full article
(This article belongs to the Special Issue Feature Paper Collection in Synthetic Biology)
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Review

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18 pages, 2623 KiB  
Review
Applications of Serine Integrases in Synthetic Biology over the Past Decade
by Fang Ba, Yufei Zhang, Luyao Wang, Wan-Qiu Liu and Jian Li
SynBio 2023, 1(2), 172-189; https://doi.org/10.3390/synbio1020012 - 11 Sep 2023
Cited by 1 | Viewed by 3648
Abstract
Serine integrases are emerging as one of the most powerful biological tools for biotechnology. Over the past decade, many research papers have been published on the use of serine integrases in synthetic biology. In this review, we aim to systematically summarize the various [...] Read more.
Serine integrases are emerging as one of the most powerful biological tools for biotechnology. Over the past decade, many research papers have been published on the use of serine integrases in synthetic biology. In this review, we aim to systematically summarize the various studies ranging from structure and the catalytic mechanism to genetic design and interdisciplinary applications. First, we introduce the classification, structure, and catalytic model of serine integrases. Second, we present a timeline with milestones that describes the representative achievements. Then, we summarize the applications of serine integrases in genome engineering, genetic design, and DNA assembly. Finally, we discuss the potential of serine integrases for advancing interdisciplinary research. We anticipate that serine integrases will be further expanded as a versatile genetic toolbox for synthetic biology applications. Full article
(This article belongs to the Special Issue Feature Paper Collection in Synthetic Biology)
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14 pages, 2332 KiB  
Review
Mechanism-of-Action-Based Development of New Cyclophosphamides
by Georg Voelcker
SynBio 2023, 1(2), 158-171; https://doi.org/10.3390/synbio1020011 - 24 Aug 2023
Viewed by 849
Abstract
Even more than 60 years after its introduction into the clinic, cyclophosphamide (CP), which belongs to the group of alkylating cytostatics, is indispensable for the treatment of cancer. This is despite the fact that its exact mechanism of action was unknown until a [...] Read more.
Even more than 60 years after its introduction into the clinic, cyclophosphamide (CP), which belongs to the group of alkylating cytostatics, is indispensable for the treatment of cancer. This is despite the fact that its exact mechanism of action was unknown until a few years ago, and therefore, all attempts to improve the effectiveness of CP failed. The reason for not knowing the mechanism of action was the uncritical transfer of the chemical processes that lead to the formation of the actual alkylating CP metabolite phosphoreamide mustard (PAM) in vitro to in vivo conditions. In vitro—e.g., in cell culture experiments—PAM is formed by β-elimination of acrolein from the pharmacologically active CP metabolite aldophosphamide (ALD). In vivo, on the other hand, it is formed by enzymatic cleavage of ALD by phosphodiesterases (PDE) with the formation of 3-hydroxypropanal (HPA). The discovery of HPA as a cyclophosphamide metabolite, together with the discovery that HPA is a proapoptotic aldehyde and the discovery that the cell death event in therapy with CP is DNA-alkylation-initiated p53-controlled apoptosis, led to the formulation of a mechanism of action of CP and other oxazaphosphorine cytostatics (OX). This mechanism of action is presented here and is confirmed by newly developed CP-like compounds with lower toxicity and an order of magnitude better effectiveness. Full article
(This article belongs to the Special Issue Feature Paper Collection in Synthetic Biology)
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