Analysis of the Innovation Trend in Cell-Free Synthetic Biology

Evaluation and Comparison of Academic Impact and Disruptive Innovation Level of Medical Journals: Bibliometric Analysis and Disruptive Evaluation

BACKGROUND

As an important platform for researchers to present their academic findings, medical journals have a close relationship between their evaluation orientation and the value orientation of their published research results. However, the differences between the academic impact and level of disruptive innovation of medical journals have not been examined by any study yet.

OBJECTIVE

This study aims to compare the relationships and differences between the academic impact, disruptive innovation levels, and peer review results of medical journals and published research papers. We also analyzed the similarities and differences in the impact evaluations, disruptive innovations, and peer reviews for different types of medical research papers and the underlying reasons.

METHODS

The general and internal medicine Science Citation Index Expanded (SCIE) journals in 2018 were chosen as the study object to explore the differences in the academic impact and level of disruptive innovation of medical journals based on the OpenCitations Index of PubMed open PMID-to-PMID citations (POCI) and H1Connect databases, respectively, and we compared them with the results of peer review.

RESULTS

First, the correlation coefficients of the Journal Disruption Index (JDI) with the Journal Cumulative Citation for 5 years (JCC5), Journal Impact Factor (JIF), and Journal Citation Indicator (JCI) were 0.677, 0.585, and 0.621, respectively. The correlation coefficient of the absolute disruption index (Dz) with the Cumulative Citation for 5 years (CC5) was 0.635. However, the average difference in the disruptive innovation and academic influence rankings of journals reached 20 places (about 17.5%). The average difference in the disruptive innovation and influence rankings of research papers reached about 2700 places (about 17.7%). The differences reflect the essential difference between the two evaluation systems. Second, the top 7 journals selected based on JDI, JCC5, JIF, and JCI were the same, and all of them were H-journals. Although 8 (8/15, 53%), 96 (96/150, 64%), and 880 (880/1500, 58.67%) of the top 0.1%, top 1%, and top 10% papers selected based on Dz and CC5, respectively, were the same. Third, research papers with the "changes clinical practice" tag showed only moderate innovation (4.96) and impact (241.67) levels but had high levels of peer-reviewed recognition (6.00) and attention (2.83).

CONCLUSIONS

The results of the study show that research evaluation based on innovative indicators is detached from the traditional impact evaluation system. The 3 evaluation systems (impact evaluation, disruptive innovation evaluation, and peer review) only have high consistency for authoritative journals and top papers. Neither a single impact indicator nor an innovative indicator can directly reflect the impact of medical research for clinical practice. How to establish an integrated, comprehensive, scientific, and reasonable journal evaluation system to improve the existing evaluation system of medical journals still needs further research.

Engineering cell-free systems by chemoproteomic-assisted phenotypic screening

Phenotypic screening is a valuable tool to both understand and engineer complex biological systems. We demonstrate the functionality of this approach in the development of cell-free protein synthesis (CFPS) technology. Phenotypic screening identified numerous compounds that enhanced protein production in yeast lysate CFPS reactions. Notably, many of these were competitive ATP kinase inhibitors, with the exploitation of their inherent substrate promiscuity redirecting ATP flux towards heterologous protein expression. Chemoproteomic-guided strain engineering partially phenocopied drug effects, with a 30% increase in protein yield observed upon deletion of the ATP-consuming SSA1 component of the HSP70 chaperone. Moreover, drug-mediated metabolic rewiring coupled with template optimization generated the highest protein yields in yeast CFPS to date using a hitherto less efficient, but more cost-effective glucose energy regeneration system. Our approach highlights the utility of target-agnostic phenotypic screening and target identification to deconvolute cell-lysate complexity, adding to the expanding repertoire of strategies for improving CFPS.

Exploration of the In Vitro Violacein Synthetic Pathway with Substrate Analogues

Evolution has gifted enzymes with the ability to synthesize an abundance of small molecules with incredible control over efficiency and selectivity. Central to an enzyme's role is the ability to selectively catalyze reactions in the milieu of chemicals within a cell. However, for chemists it is often desirable to extend the substrate scope of reactions to produce analogue(s) of a desired product and therefore some degree of enzyme promiscuity is often desired. Herein, we examine this dichotomy in the context of the violacein biosynthetic pathway. Importantly, we chose to interrogate this pathway with tryptophan analogues in vitro, to mitigate possible interference from cellular components and endogenous tryptophan. A total of nine tryptophan analogues were screened for by analyzing the substrate promiscuity of the initial enzyme, VioA, and compared to the substrate tryptophan. These results suggested that for VioA, substitutions at either the 2- or 4-position of tryptophan were not viable. The seven analogues that showed successful substrate conversion by VioA were then applied to the five enzyme cascade (VioABEDC) for the production of violacein, where l-tryptophan and 6-fluoro-l-tryptophan were the only substrates which were successfully converted to the corresponding violacein derivative(s). However, many of the other tryptophan analogues did convert to various substituted intermediaries. Overall, our results show substrate promiscuity with the initial enzyme, VioA, but much less for the full pathway. This work demonstrates the complexity involved when attempting to analyze substrate analogues within multienzymatic cascades, where each enzyme involved within the cascade possesses its own inherent promiscuity, which must be compatible with the remaining enzymes in the cascade for successful formation of a desired product.

Advancing reproducibility can ease the 'hard truths' of synthetic biology

Reproducibility has been identified as an outstanding challenge in science, and the field of synthetic biology is no exception. Meeting this challenge is critical to allow the transformative technological capabilities emerging from this field to reach their full potential to benefit the society. We discuss the current state of reproducibility in synthetic biology and how improvements can address some of the central shortcomings in the field. We argue that the successful adoption of reproducibility as a routine aspect of research and development requires commitment spanning researchers and relevant institutions via education, incentivization and investment in related infrastructure. The urgency of this topic pervades synthetic biology as it strives to advance fundamental insights and unlock new capabilities for safe, secure and scalable applications of biotechnology. Graphical Abstract.

A construction and empirical research of the journal disruption index based on open citation data

For many years, the journal evaluation system has been centered on impact indicators, resulting in evaluation results that do not reflect the academic innovation of journals. To solve this issue, this study attempts to construct the Journal Disruption Index (JDI) from the perspective of measuring the disruption of each journal article. In the actual study, we measured the disruption of articles of 22 selected virology journals based on the OpenCitations Index of Crossref open DOI-to-DOI citations (COCI) first. Then we calculated the JDI of 22 virology journals based on the absolute disruption index (D Z ) of the articles. Finally, we conducted an empirical study on the differences and correlations between the impact indicators and disruption indicators as well as the evaluation effect of the disruption index. The results of the study show: (1) There are large differences in the ranking of journals based on disruption indicators and impact indicators. Among the 22 journals, 12 are ranked higher by JDI than Cumulative Impact Factor for 5 years (CIF5), the Journal Index for PR6 (JIPR6) and average Percentile in Subject Area (aPSA). The ranking difference of 17 journals between the two kinds of indicators is greater than or equal to 5. (2) There is a medium correlation between disruption indicators and impact indicators at the level of journals and papers. JDI is moderately correlated with CIF5, JIPR6 and aPSA, with correlation coefficients of 0.486, 0.471 and - 0.448, respectively. D Z was also moderately correlated with Cumulative Citation (CC), Percentile Ranking with 6 Classifications (PR6) and Percentile in Subject Area (PSA) with correlation coefficients of 0.593, 0.575 and - 0.593, respectively. (3) Compared with traditional impact indicators, the results of journal disruption evaluation are more consistent with the evaluation results of experts' peer review. JDI reflects the innovation level of journals to a certain extent, which is helpful to promote the evaluation of innovation in sci-tech journals.

Opportunities to accelerate extracellular vesicle research with cell-free synthetic biology

Extracellular vesicles (EVs) are lipid-membrane nanoparticles that are shed or secreted by many different cell types. The EV research community has rapidly expanded in recent years and is leading efforts to deepen our understanding of EV biological functions in human physiology and pathology. These insights are also providing a foundation on which future EV-based diagnostics and therapeutics are poised to positively impact human health. However, current limitations in our understanding of EV heterogeneity, cargo loading mechanisms and the nascent development of EV metrology are all areas that have been identified as important scientific challenges. The field of synthetic biology is also contending with the challenge of understanding biological complexity as it seeks to combine multidisciplinary scientific knowledge with engineering principles, to build useful and robust biotechnologies in a responsible manner. Within this context, cell-free systems have emerged as a powerful suite of in vitro biotechnologies that can be employed to interrogate fundamental biological mechanisms, including the study of aspects of EV biogenesis, or to act as a platform technology for medical biosensors and therapeutic biomanufacturing. Cell-free gene expression (CFE) systems also enable in vitro protein production, including membrane proteins, and could conceivably be exploited to rationally engineer, or manufacture, EVs loaded with bespoke molecular cargoes for use in foundational or translational EV research. Our pilot data herein, also demonstrates the feasibility of cell-free EV engineering. In this perspective, we discuss the opportunities and challenges for accelerating EV research and healthcare applications with cell-free synthetic biology.

Streptomyces cell-free systems for natural product discovery and engineering

Streptomyces bacteria are a major microbial source of natural products, which are encoded within so-called biosynthetic gene clusters (BGCs). This highlight discusses the emergence of native Streptomyces cell-free systems as a new tool to accelerate the study of the fundamental chemistry and biology of natural product biosynthesis from these bacteria. Cell-free systems provide a prototyping platform to study plug-and-play reactions in microscale reactions. So far, Streptomyces cell-free systems have been used to rapidly characterise gene expression regulation, access secondary metabolite biosynthetic enzymes, and catalyse cell-free transcription, translation, and biosynthesis of example natural products. With further progress, we anticipate the development of more complex systems to complement existing experimental tools for the discovery and engineering of natural product biosynthesis from Streptomyces and related high G + C (%) bacteria.

A ubiquitous amino acid source for prokaryotic and eukaryotic cell-free transcription-translation systems

Cell-free gene expression (CFE) systems are an attractive tool for engineering within synthetic biology and for industrial production of high-value recombinant proteins. CFE reactions require a cell extract, energy system, amino acids, and DNA, to catalyse mRNA transcription and protein synthesis. To provide an amino acid source, CFE systems typically use a commercial standard, which is often proprietary. Herein we show that a range of common microbiology rich media (i.e., tryptone, peptone, yeast extract and casamino acids) unexpectedly provide an effective and low-cost amino acid source. We show that this approach is generalisable, by comparing batch variability and protein production in the following range of CFE systems: Escherichia coli (Rosetta^™ 2 (DE3), BL21(DE3)), Streptomyces venezuelae and Pichia pastoris. In all CFE systems, we show equivalent or increased protein synthesis capacity upon replacement of the commercial amino acid source. In conclusion, we suggest rich microbiology media provides a new amino acid source for CFE systems with potential broad use in synthetic biology and industrial biotechnology applications.