1,720,969 research outputs found
Design and Evaluation of Synthetic RNA-Based Incoherent Feed-forward Loop Circuits
No full textDe-novo-designed synthetic RNA regulators [1-3] have been utilized to construct complex RNA-based synthetic gene circuits in living cells. We constructed an RNA-only type 1 incoherent feedforward loop (IFFL) circuit in vivo using these regulators and explored their dynamic behaviors [4,5]. However, there were no significant timescale differences between direct activation and indirect inhibition, and no pulses were observed in the experiment. These results were confirmed by mathematical modeling and simulation results for a wide range of conditions. To increase the delay of the inhibitory pathway, we introduced a protein synthesis process into the circuit and designed an RNA-protein hybrid IFFL circuit using toehold switch (THS) and Tet repressor. Simulation results indicated that pulse generation could be achieved using this RNA-protein hybrid model, which was further validated by experimental realization in E. coli. This research demonstrates that RNA-based circuits can serve as modular and composable parts for synthetic biological circuits to achieve desired dynamics [6], and further suggests that previously unattainable transcription-only and translation-only RNA-based IFFL circuits could be implemented.2
Model-based investigation of the relationship between regulation level and pulse property of I1-FFL gene circuits
Get PDFMathematical models are powerful tools in guiding the construction of synthetic biological circuits, given their capability of accurately capturing and predicting circuit dynamics. Recent innovations in RNA technology have enabled the development of a variety of new tools for regulating gene expression at both the transcription and translation levels. However, the effects of different regulation levels on the circuit dynamics remain largely unexplored. In this study, we focus on the Type 1 incoherent feed-forward loop (I1-FFL) gene circuit with four different variations (TX, TL, HY-1, HY-2), to investigate how regulation at the transcription and translation levels affect the circuit dynamics. We develop a mechanistic model for each of the four circuits, and deploy sensitivity analysis to investigate the circuits’ dynamics in terms of pulse generation. Based on the analysis, we observe the repression regulation mechanism dominates the characteristics of the pulse as compared to the activation regulation mechanism, and find that the I1-FFL with transcription repression has a higher chance of generating a pulse meeting the desired criteria. The experimental results in E. coli also confirm our findings from the computational analysis. We expect our findings to facilitate future experimental construction of gene circuits with insights on the selection of appropriate transcription and translation regulation tools
Design and evaluation of synthetic RNA-based incoherent feed-forward loop circuits
Get PDFRNA-based regulators are promising tools for building synthetic biological systems that provide a powerful platform for achieving a complex regulation of transcription and translation. Recently, de novo-designed synthetic RNA regulators, such as the small transcriptional activating RNA (STAR), toehold switch (THS), and three-way junction (3WJ) repressor, have been utilized to construct RNA-based synthetic gene circuits in living cells. In this work, we utilized these regulators to construct type 1 incoherent feed-forward loop (IFFL) circuits in vivo and explored their dynamic behaviors. A combination of a STAR and 3WJ repressor was used to construct an RNA-only IFFL circuit. However, due to the fast kinetics of RNA–RNA interactions, there was no significant timescale difference between the direct activation and the indirect inhibition, that no pulse was observed in the experiments. These findings were confirmed with mechanistic modeling and simulation results for a wider range of conditions. To increase delay in the inhibition pathway, we introduced a protein synthesis process to the circuit and designed an RNA–protein hybrid IFFL circuit using THS and TetR protein. Simulation results indicated that pulse generation could be achieved with this RNA–protein hybrid model, and this was further verified with experimental realization in E. coli. Our findings demonstrate that while RNA-based regulators excel in speed as compared to protein-based regulators, the fast reaction kinetics of RNA-based regulators could also undermine the functionality of a circuit (e.g., lack of significant timescale difference). The agreement between experiments and simulations suggests that the mechanistic modeling can help debug issues and validate the hypothesis in designing a new circuit. Moreover, the applicability of the kinetic parameters extracted from the RNA-only circuit to the RNA–protein hybrid circuit also indicates the modularity of RNA-based regulators when used in a different context. We anticipate the findings of this work to guide the future design of gene circuits that rely heavily on the dynamics of RNA-based regulators, in terms of both modeling and experimental realization
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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