Relevant bibliographies by topics / RNA synthetic biology

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers

Academic literature on the topic 'RNA synthetic biology'

Author: Grafiati
Published: 4 June 2021
Last updated: 2 February 2022

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Journal articles on the topic "RNA synthetic biology"

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Isaacs, Farren J., Daniel J. Dwyer, and James J. Collins. "RNA synthetic biology." Nature Biotechnology 24, no. 5 (May 2006): 545–54. http://dx.doi.org/10.1038/nbt1208.

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Schmidt, Calvin M., and Christina D. Smolke. "RNA Switches for Synthetic Biology." Cold Spring Harbor Perspectives in Biology 11, no. 1 (January 2019): a032532. http://dx.doi.org/10.1101/cshperspect.a032532.

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Saito, Hirohide, and Tan Inoue. "Synthetic biology with RNA motifs." International Journal of Biochemistry & Cell Biology 41, no. 2 (February 2009): 398–404. http://dx.doi.org/10.1016/j.biocel.2008.08.017.

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Kim, Jongmin, and Elisa Franco. "RNA nanotechnology in synthetic biology." Current Opinion in Biotechnology 63 (June 2020): 135–41. http://dx.doi.org/10.1016/j.copbio.2019.12.016.

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O’Donoghue and Heinemann. "Synthetic DNA and RNA Programming." Genes 10, no. 7 (July 11, 2019): 523. http://dx.doi.org/10.3390/genes10070523.

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Synthetic biology is a broad and emerging discipline that capitalizes on recent advances in molecular biology, genetics, protein and RNA engineering as well as omics technologies. Together these technologies have transformed our ability to reveal the biology of the cell and the molecular basis of disease. This Special Issue on “Synthetic RNA and DNA Programming” features original research articles and reviews, highlighting novel aspects of basic molecular biology and the molecular mechanisms of disease that were uncovered by the application and development of novel synthetic biology-driven approaches.
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Green, Alexander A. "Synthetic bionanotechnology: synthetic biology finds a toehold in nanotechnology." Emerging Topics in Life Sciences 3, no. 5 (October 23, 2019): 507–16. http://dx.doi.org/10.1042/etls20190100.

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Enabled by its central role in the molecular networks that govern cell function, RNA has been widely used for constructing components used in biological circuits for synthetic biology. Nucleic acid nanotechnology, which exploits predictable nucleic acid interactions to implement programmable molecular systems, has seen remarkable advances in in vitro nanoscale self-assembly and molecular computation, enabling the production of complex nanostructures and DNA-based neural networks. Living cells genetically engineered to execute nucleic acid nanotechnology programs thus have outstanding potential to significantly extend the current limits of synthetic biology. This perspective discusses the recent developments and future challenges in the field of synthetic bionanotechnology. Thus far, researchers in this emerging area have implemented dozens of programmable RNA nanodevices that provide precise control over gene expression at the transcriptional and translational levels and through CRISPR/Cas effectors. Moreover, they have employed synthetic self-assembling RNA networks in engineered bacteria to carry out computations featuring up to a dozen inputs and to substantially enhance the rate of chemical synthesis. Continued advancement of the field will benefit from improved in vivo strategies for streamlining nucleic acid network synthesis and new approaches for enhancing network function. As the field matures and the complexity gap between in vitro and in vivo systems narrows, synthetic bionanotechnology promises to have diverse potential applications ranging from intracellular circuits that detect and treat disease to synthetic enzymatic pathways that efficiently produce novel drug molecules.
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Soll, Dieter. "A tRNA-guided research journey from synthetic chemistry to synthetic biology." RNA 21, no. 4 (March 16, 2015): 742–44. http://dx.doi.org/10.1261/rna.050625.115.

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Benenson, Yaakov. "Synthetic biology with RNA: progress report." Current Opinion in Chemical Biology 16, no. 3-4 (August 2012): 278–84. http://dx.doi.org/10.1016/j.cbpa.2012.05.192.

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Davidson, Eric A., and Andrew D. Ellington. "Synthetic RNA circuits." Nature Chemical Biology 3, no. 1 (December 15, 2006): 23–28. http://dx.doi.org/10.1038/nchembio846.

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Apura, Patrícia, Susana Domingues, Sandra C. Viegas, and Cecília M. Arraiano. "Reprogramming bacteria with RNA regulators." Biochemical Society Transactions 47, no. 5 (October 23, 2019): 1279–89. http://dx.doi.org/10.1042/bst20190173.

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Abstract The revolution of genomics and growth of systems biology urged the creation of synthetic biology, an engineering discipline aiming at recreating and reprogramming cellular functions for industrial needs. There has been a huge effort in synthetic biology to develop versatile and programmable genetic regulators that would enable the precise control of gene expression. Synthetic RNA components have emerged as a solution, offering a diverse range of programmable functions, including signal sensing, gene regulation and the modulation of molecular interactions. Owing to their compactness, structure and way of action, several types of RNA devices that act on DNA, RNA and protein have been characterized and applied in synthetic biology. RNA-based approaches are more ‘economical' for the cell, since they are generally not translated. These RNA-based strategies act on a much shorter time scale than transcription-based ones and can be more efficient than protein-based mechanisms. In this review, we explore these RNA components as building blocks in the RNA synthetic biology field, first by explaining their natural mode of action and secondly discussing how these RNA components have been exploited to rewire bacterial regulatory circuitry.
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Dissertations / Theses on the topic "RNA synthetic biology"

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Martin, Alarcon Daniel Alberto. "Tools for RNA and cell-free synthetic biology." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/104124.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, 2016.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 58-63).
Amid the myriad recent developments in synthetic biology, progress has been fastest in the areas with the most versatile tools for understanding and engineering biological systems. RNA synthetic biology and synthetic minimal cells are areas where design is limited by the availability of tools to observe, program, and manipulate the systems in question. In this work I present expanded toolsets to achieve these goals. The ability to monitor and perturb RNAs in living cells would benefit greatly from a modular, programmable protein architecture for targeting unmodified RNA sequences. I report that the RNA-binding protein PumHD (Pumilio homology domain), which has been widely used in native and modified form for targeting RNA, can be engineered to yield a set of four canonical protein modules, each of which targets one RNA base. These modules (which I call Pumby, for Pumilio-based assembly) can be concatenated in chains of varying composition and length, to bind desired target RNAs. I validate that the Pumby architecture can perform RNA-directed protein assembly and enhancement of translation of RNAs. I further demonstrate a new use of such RNA-binding proteins, measurement of RNA translation in living cells. Pumby may prove useful for many applications in the measurement, manipulation, and biotechnological utilization of unmodified RNAs in intact cells and systems. Genetic circuits are a fundamental tool in synthetic biology; an open question is how to maximize the modularity of their design, to facilitate their integrity, scalability, and flexibility. Liposome encapsulation enables chemical reactions to proceed in well-isolated environments. I here adapt liposome encapsulation to enable the modular, controlled compartmentalization of genetic circuits and cascades. I demonstrate that it is possible to engineer genetic circuit-containing synthetic minimal cells (synells) so that they contain multiple-part genetic cascades, that these cascades can be controlled by external as well as inter-liposomal communication without cross-talk, and that these cascades can also be fused in a controlled way so that the products of incompatible reactions can be brought together. Synells thus enable more modular creation of synthetic biology cascades, an essential step towards their ultimate programmability.
by Daniel Alberto Martin Alarcon.
Ph. D.
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Wesselhoeft, R. Alexander(Robert Alexander). "Synthetic circular RNA for protein expression." Thesis, Massachusetts Institute of Technology, 2019. https://hdl.handle.net/1721.1/122710.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2019
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 111-126).
Messenger RNA (mRNA) has broad potential for therapeutic and engineering applications. One fundamental limitation of mRNA is its relatively short half-life in biological systems, effected in part by rapid exonuclease-mediated degradation upon delivery. Circular RNA (circRNA), a type of single-stranded RNA with a contiguous structure that lacks the end motifs necessary for exonuclease recognition, may be resistant to this mechanism of degradation and therefore may exhibit superior stability. However, challenges in circularization, purification, and protein expression have impeded a thorough investigation of exogenous circRNA. By rationally designing ubiquitous accessory sequences to facilitate circularization, we engineered a permuted self-splicing intron that efficiently circularized RNAs up to 5kb in length in vitro.
With the addition of these accessory sequences, we were able to demonstrate nearly complete circularization of precursor RNAs containing an internal ribosome entry site (IRES) for translation initiation and a coding region such as erythropoietin or eGFP. We found that translation from optimized circRNA was robust, and circRNA protein expression stability far exceeded that of both unmodified and nucleoside modified linear mRNA in some cellular contexts. We monitored cytokine release and antiviral defense induction in sensitive cells transfected with circRNA purified by different methods and found that the immunogenicity and stability of circRNA preparations was dependent on the degree of purity, with small amounts of contaminating linear RNA leading to robust cellular immune responses.
In contrast to purified unmodified linear mRNA, purified unmodified circRNA was invisible to several RNA sensors including RIG-i and endosomai toil-like receptors (TLRs) and did not provoke a significant cytokine response upon transfection. Using purified circRNA, we finally provided the first demonstration to our knowledge of exogenous circRNA delivery and translation in vivo, and showed that the duration of circRNA translation was extended in adipose tissue in comparison to unmodified and uridine-modified linear mRNAs. In total, this work suggests that circRNA is a promising alternative to linear mRNA for therapeutic applications.
by R. Alexander Wesselhoeft.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Department of Biology
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DiAndreth, Breanna Elizabeth. "RNA sensing and programming platforms for mammalian synthetic Biology." Thesis, Massachusetts Institute of Technology, 2019. https://hdl.handle.net/1721.1/123058.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, 2019
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 153-173).
The field of synthetic biology aims to control cellular behavior using programmable gene circuits. Generally these gene circuits sense molecular biomarkers, process these inputs and execute a desired calculated response. This is especially relevant for gene and cell therapies where integrating multiple disease-related inputs and/or sophisticated control could lead to safer and more effective approaches. While mammalian synthetic biology has made great progress, few gene circuit-based therapies have entered the clinic. Regulatory issues aside, this lag may be due to several technical impediments. First, the computing part of circuits is often accomplished via transcriptional regulation, which presents challenges as we move toward the clinic. Second, the field relies on a limited set of sensors; the detection of other types of disease biomarkers will help robustly identify cell state.
Finally, the design cycle currently used to develop gene circuits is laborious and slow, which is not suitable for clinical development, especially applications in personalized medicine. In this thesis I describe how I address these three limitations. I develop a new posttranscriptional regulation platform based on RNA cleavage that I term "PERSIST" (Programmable Endonucleolytic RNA Scission-Induced Stability Tuning). CRISPR-specific endonucleases are adapted as RNA-level regulators for the platform and we demonstrate several genetic devices including cascades, feedback, logic functions and a bistable switch. I explore sensor designs for relevant biomolecules including mRNAs, miRNAs and proteins via the PERSIST and other platforms. Finally, I present a "poly-transfection" method, associated advanced data analysis pipelines, and computational models that make circuit engineering faster and more predictive.
Taken together, the expanded RNA toolkit that the PERSIST platform offers as well as advancements in sensing and circuit design will enable the more straightforward creation of robust gene circuits for gene and cell therapies.
by Breanna Elizabeth DiAndreth.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Department of Biological Engineering
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Matsuura, Satoshi. "Synthetic RNA-based logic computation in mammalian cells." Kyoto University, 2019. http://hdl.handle.net/2433/242426.

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Garcia, Martin Juan Antonio. "RNA inverse folding and synthetic design." Thesis, Boston College, 2016. http://hdl.handle.net/2345/bc-ir:106989.

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Thesis advisor: Welkin E. Johnson
Thesis advisor: Peter G. Clote
Synthetic biology currently is a rapidly emerging discipline, where innovative and interdisciplinary work has led to promising results. Synthetic design of RNA requires novel methods to study and analyze known functional molecules, as well as to generate design candidates that have a high likelihood of being functional. This thesis is primarily focused on the development of novel algorithms for the design of synthetic RNAs. Previous strategies, such as RNAinverse, NUPACK-DESIGN, etc. use heuristic methods, such as adaptive walk, ensemble defect optimization (a form of simulated annealing), genetic algorithms, etc. to generate sequences that minimize specific measures (probability of the target structure, ensemble defect). In contrast, our approach is to generate a large number of sequences whose minimum free energy structure is identical to the target design structure, and subsequently filter with respect to different criteria in order to select the most promising candidates for biochemical validation. In addition, our software must be made accessible and user-friendly, thus allowing researchers from different backgrounds to use our software in their work. Therefore, the work presented in this thesis concerns three areas: Create a potent, versatile and user friendly RNA inverse folding algorithm suitable for the specific requirements of each project, implement tools to analyze the properties that differentiate known functional RNA structures, and use these methods for synthetic design of de-novo functional RNA molecules
Thesis (PhD) — Boston College, 2016
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology
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Thomas, Gregory Stuart. "Targeting prostate cancer with synthetic RNA ligands." Diss., University of Iowa, 2012. https://ir.uiowa.edu/etd/1508.

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Prostate cancer represents a serious health concern as the most diagnosed form of cancer in men and the second leading cause of cancer death in the Western world. Current treatments for prostate cancer are non-targeted and result in a number of undesirable, non-specific effects, highlighting the need for novel, targeted therapeutics in the treatment of prostate cancer. Prostate Specific Membrane Antigen (PSMA) offers great promise in the targeting of prostate cancer for imaging and therapy. PSMA is a transmembrane carboxypeptidase with cell surface expression several orders of magnitude higher in cancerous prostatic epithelia than found in other tissue and PSMA is constitutively internalized into cells. The unique expression profile of PSMA and its constitutive internalization offer great value in the targeted delivery of therapeutics to prostate cancer cell. In 2002, two synthetic RNA ligands, aptamers, were selected for their ability to inhibit the enzymatic activity of PSMA. In 2006, the utility of these aptamers in the delivery of cytotoxic siRNA across the cell membrane was demonstrated in vivo using aptamer-siRNA chimeras. However, those experiments were performed by intratumoral injection, and systemic administration will be necessary for use in the clinic. In this thesis, we improve PSMA targeted chimeras to serve as more powerful therapeutics in the treatment of prostate cancer. We optimize existing aptamer-siRNA chimeras for increased potency and stability and improved pharmacokinetics to enable systemic administration. We truncate the PSMA binding aptamers for amenability to large-scale chemical synthesis. With emerging roles for PSMA enzymatic activity in the prostate cancer disease we identify aptamers that are suitable for chemical synthesis and retain inhibitory properties against PSMA. Finally, we assess the use of aptamers as synthetic ligands in the functional inhibition of PSMA mediated motility in prostate cancer. Our results demonstrate the ability of aptamer-siRNA chimeras to specifically kill PSMA-expressing cells with cytotoxic siRNA upon systemic injection. We confirm a newly reported role for PSMA in the promotion of cell motility and demonstrate the ability of aptamers to effectively neutralize PSMA-mediated motility. The results presented within argue strongly for the functional utility of aptamers in the treatment of prostate cancer.
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Harris, Andreas William Kisling. "The design of gene regulatory networks with feedback and small non-coding RNA." Thesis, University of Oxford, 2017. https://ora.ox.ac.uk/objects/uuid:e3a323b1-9067-415d-8728-6c70c1b6cf23.

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The objective of the field of Synthetic Biology is to implement novel functionalities in a biological context or redesign existing biological systems. To achieve this, it employs tried and tested engineering principles, such as standardisation and the design-build-test cycle. A crucial part of this process is the convergence of modelling and experiment. The aim of this thesis is to improve the design principles employed by Synthetic Biology in the context of Gene Regulatory Networks (GRNs). Small Ribonucleic Acids (sRNAs), in particular, are focussed on as a mechanism for post-transcriptional expression regulation, as they present great potential as a tool to be harnessed in GRNs. Modelling sRNA regulation and its interaction with its associated chaperone Host-Factor of Bacteriophage Qβ (Hfq) is investigated. Inclusion of Hfq is found to be necessary in stochastic models, but not in deterministic models. Secondly, feedback is core to the thesis, as it presents a means to scale-up designed systems. A linear design framework for GRNs is then presented, focussing on Transcription Factor (TF) interactions. Such frameworks are powerful as they facilitate the design of feedback. The framework supplies a block diagram methodology for visualisation and analysis of the designed circuit. In this context, phase lead and lag controllers, well-known in the context of Control Engineering, are presented as genetic motifs. A design example, employing the genetic phase lag controller, is then presented, demonstrating how the developed framework can be used to design a genetic circuit. The framework is then extended to include sRNA regulation. Four GRNs, demonstrating the simplest forms of genetic feedback, are then modelled and implemented. The feedback occurs at three different levels: autoregulation, through an sRNA and through another TF. The models of these GRNs are inspired by the implemented biological topologies, focussing on steady state behaviour and various setups. Both deterministic and stochastic models are studied. Dynamic responses of the circuits are also briefly compared. Data is presented, showing good qualitative agreement between models and experiment. Both culture level data and cell population data is presented. The latter of these is particularly useful as the moments of the distributions can be calculated and compared to results from stochastic simulation. The fit of a deterministic model to data is attempted, which results in a suggested extension of the model. The conclusion summarises the thesis, stating that modelling and experiment are in good qualitative agreement. The required next step is to be able to predict behaviour quantitatively.
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Klauser, Benedikt [Verfasser]. "RNA Synthetic Biology using the Hammerhead Ribozyme : Engineering of Artificial Genetic Switches / Benedikt Klauser." Konstanz : Bibliothek der Universität Konstanz, 2015. http://d-nb.info/1112745483/34.

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Cacan, Ercan. "Evolutionary synthetic biology: structure/function relationships within the protein translation system." Thesis, Georgia Institute of Technology, 2011. http://hdl.handle.net/1853/45838.

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Production of mutant biological molecules for understanding biological principles or as therapeutic agents has gained considerable interest recently. Synthetic genes are today being widely used for production of such molecules due to the substantial decrease in the costs associated with gene synthesis technology. Along one such line, we have engineered tRNA genes in order to dissect the effects of G:U base-pairs on the accuracy of the protein translation machinery. Our results provide greater detail into the thermodynamic interactions between tRNA molecules and an Elongation Factor protein (termed EF-Tu in bacteria and eEF1A in eukaryotes) and how these interactions influence the delivery of aminoacylated tRNAs to the ribosome. We anticipate that our studies not only shed light on the basic mechanisms of molecular machines but may also help us to develop therapeutic or novel proteins that contain unnatural amino acids. Further, the manipulation of the translation machinery holds promise for the development of new methods to understand the origins of life. Along another line, we have used the power of synthetic biology to experimentally validate an evolutionary model. We exploited the functional diversity contained within the EF-Tu/eEF1A gene family to experimentally validate the model of evolution termed ‘heterotachy’. Heterotachy refers to a switch in a site’s mutational rate class. For instance, a site in a protein sequence may be invariant across all bacterial homologs while that same site may be highly variable across eukaryotic homologs. Such patterns imply that the selective constraints acting on this site differs between bacteria and eukaryotes. Despite intense efforts and large interest in understanding these patterns, no studies have experimentally validated these concepts until now. In the present study, we analyzed EF-Tu/eEF1A gene family members between bacteria and eukaryotes to identify heterotachous patterns (also called Type-I functional divergence). We applied statistical tests to identify sites possibly responsible for biomolecular functional divergence between EF-Tu and eEF1A. We then synthesized protein variants in the laboratory to validate our computational predictions. The results demonstrate for the first time that the identification of heterotachous sites can be specifically implicated in functional divergence among homologous proteins. In total, this work supports an evolutionary synthetic biology paradigm that in one direction uses synthetic molecules to better understand the mechanisms and constraints governing biomolecular behavior while in another direction uses principles of molecular sequence evolution to generate novel biomolecules that have utility for industry and/or biomedicine.
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Wang, Qingqing. "Alternative Splicing Regulation in Programmed Cell Death and Neurological Disorders: A Systems Biology Approach." Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:10849.

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Alternative splicing (AS) is a major source of biological diversity and a crucial determinant of cell fate and identity. Characterizing the role of AS regulatory networks in physiological and pathological processes remains challenging. The work presented here addresses this challenge using systems biology analyses of AS regulatory networks in programmed cell death and neurological disorders. The first study describes a genome-wide screen based on splicing-sensitive reporters to identify factors that affect the AS of apoptosis regulators Bclx and Mcl1. The screen identified over 150 factors that affect apoptosis through modulating the pro- and anti-apoptotic splicing variants of these apoptosis regulators. This screen revealed a new functional connection between apoptosis regulation and cell-cycle control through an AS network. It also unearthed many disease-associated factors as AS effectors. The second study describes the functions of the Polyglutamine-binding protein 1 (PQBP1)-mediated AS regulatory network in neurological disorders. PQBP1 is a factor linked to intellectual disability and was unexpectedly identified as an AS effector from the screen described above. We found that PQBP1 influences the splicing of many mRNAs and is associated with a wide range of splicing factors. Depletion of PQBP1 in mouse primary cortical neurons caused defects in neurite outgrowth and altered AS of mRNAs enriched for functions in neuron projection regulation. Disease-mutants of PQBP1 lose associations with splicing factors and cannot complement the aberrant AS patterns and neuron morphology defects in PQBP1 depleted-neurons. This study revealed a novel function of PQBP1 in AS regulation associated with neurite outgrowth and indicated that aberrant AS underlies the pathology of PQBP1-related neurological disorders. A final study examines the dynamics of the Drosophila Sex-lethal AS regulation network using a combination of experimental tools and mathematical modeling. This study demonstrates that the features of Sxl AS regulation have great potentials in building synthetic memory circuits in mammalian cells to track cell fate. Collectively, this work describes the landscape of three diverse AS regulatory networks in various biological processes. The results and methods presented here contribute to our rapidly advancing knowledge of AS regulation in biology and human disease.
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Books on the topic "RNA synthetic biology"

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Ponchon, Luc. RNA scaffolds: Methods and protocols. New York: Humana Press, 2015.

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1949-, Müller S. C., ed. Synthetic peptides as antigens. Amsterdam: Elsevier, 1999.

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Cong he cheng dan bai zhi dao he cheng he suan: From protein synthesis to nucleic acid synthesis. Changsha Shi: Hunan jiao yu chu ban she, 2009.

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service), ScienceDirect (Online, ed. RNA turnover in eukaryotes: Nucleases, pathways and analysis of mRNA decay. San Diego, Calif: Academic, 2008.

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R, Fleischaker Gail, Colonna Stefano 1941-, Luisi P. L, North Atlantic Treaty Organization. Scientific Affairs Division., and NATO Advanced Research Workshop on Self-Production of Supramolecular Structures (1993 : Acquafredda di Maratea, Italy), eds. Self-production of supramolecular structures: From synthetic structures to models of minimal living systems. Dordrecht: Kluwer Academic Publishers, 1994.

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Van Regenmortel, M. H. V., ed. Synthetic polypeptides as antigens. Amsterdam: Elsevier, 1988.

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Synthetic Peptides as Antigens (Laboratory Techniques in Biochemistry and Molecular Biology). Elsevier Science, 1999.

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Muller, S., M. H. V. Van Regenmortel, J. P. Briand, and S. Plaue. Synthetic Polypeptides As Antigens (Laboratory Techniques in Biochemistry and Molecular Biology). Elsevier Science Publishing Company, 1988.

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Maquat, Lynne. Nonsense-Mediated mRNA Decay (Molecular Biology Intelligence Unit (Unnumbered).). Landes Bioscience, Inc., 2006.

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1947-, Witkowski J. A., ed. The inside story: DNA to RNA to protein. Woodbury, N.Y: Cold Spring Harbor Laboratory Press, 2005.

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Book chapters on the topic "RNA synthetic biology"

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Lee, Jaehyung, Andrew C. Keates, and Chiang J. Li. "Synthetic Biology and Bacteria-Based." In RNA Scaffolds, 267–80. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1499-0_19.

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Pitzer, Julia, Bob Van Hove, Aaron M. Love, Parayil Kumaran Ajikumar, Marjan De Mey, and Anton Glieder. "Novel DNA and RNA Elements." In Synthetic Biology, 65–99. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-22708-5_2.

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Sachdeva, Gairik, Cameron Myhrvold, Peng Yin, and Pamela A. Silver. "Synthetic RNA Scaffolds for Spatial Engineering in Cells." In Synthetic Biology, 261–78. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2018. http://dx.doi.org/10.1002/9783527688104.ch13.

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Kashida, Shunnichi, and Hirohide Saito. "Design of Ligand-Controlled Genetic Switches Based on RNA Interference." In Synthetic Biology, 169–79. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2018. http://dx.doi.org/10.1002/9783527688104.ch8.

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Shin, Jongoh, Namil Lee, Suhyung Cho, and Byung-Kwan Cho. "Targeted Genome Editing Using DNA-Free RNA-Guided Cas9 Ribonucleoprotein for CHO Cell Engineering." In Synthetic Biology, 151–69. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7795-6_8.

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Wang, Tingting, and Zhen Xie. "Construction and Integration of a Synthetic MicroRNA Cluster for Multiplex RNA Interference in Mammalian Cells." In Synthetic Biology, 347–59. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7795-6_19.

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Stark, Martha R., and Stephen D. Rader. "Efficient Splinted Ligation of Synthetic RNA Using RNA Ligase." In Methods in Molecular Biology, 137–49. Totowa, NJ: Humana Press, 2014. http://dx.doi.org/10.1007/978-1-62703-980-2_10.

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Yokobayashi, Yohei. "Small Molecule-Responsive RNA Switches (Bacteria): Important Element of Programming Gene Expression in Response to Environmental Signals in Bacteria." In Synthetic Biology, 181–88. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2018. http://dx.doi.org/10.1002/9783527688104.ch9.

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Rabinovich, Peter M., and Sherman M. Weissman. "Cell Engineering with Synthetic Messenger RNA." In Methods in Molecular Biology, 3–28. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-260-5_1.

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Villa, Jordan K., Yichi Su, Lydia M. Contreras, and Ming C. Hammond. "Synthetic Biology of Small RNAs and Riboswitches." In Regulating with RNA in Bacteria and Archaea, 527–45. Washington, DC, USA: ASM Press, 2018. http://dx.doi.org/10.1128/9781683670247.ch31.

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Conference papers on the topic "RNA synthetic biology"

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Rhee, Sungmin, Seokjun Seo, and Sun Kim. "Hybrid Approach of Relation Network and Localized Graph Convolutional Filtering for Breast Cancer Subtype Classification." In Twenty-Seventh International Joint Conference on Artificial Intelligence {IJCAI-18}. California: International Joint Conferences on Artificial Intelligence Organization, 2018. http://dx.doi.org/10.24963/ijcai.2018/490.

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Network biology has been successfully used to help reveal complex mechanisms of disease, especially cancer. On the other hand, network biology requires in-depth knowledge to construct disease-specific networks, but our current knowledge is very limited even with the recent advances in human cancer biology. Deep learning has shown an ability to address the problem like this. However, it conventionally used grid-like structured data, thus application of deep learning technologies to the human disease subtypes is yet to be explored. To overcome the issue, we propose a hybrid model, which integrates two key components 1) graph convolution neural network (graph CNN) and 2) relation network (RN). Experimental results on synthetic data and breast cancer data demonstrate that our proposed method shows better performances than existing methods.
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Thaiprasit, Jittrawan, Boonserm Kaewkamnerdpong, Dujduan Waraho, Supapon Cheevadhanarak, and Asawin Meechai. "Domain-based design platform of interacting RNAs: A promising tool in synthetic biology." In 2014 7th Biomedical Engineering International Conference (BMEiCON). IEEE, 2014. http://dx.doi.org/10.1109/bmeicon.2014.7017438.

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Blenis, John, Gina Lee, Jamie Dempsey, and Christina England. "Abstract IA03: mTORC1/S6K1: Regulation of RNA biogenesis, protein synthesis, and cell metabolism." In Abstracts: AACR Special Conference on Translational Control of Cancer: A New Frontier in Cancer Biology and Therapy; October 27-30, 2016; San Francisco, CA. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.transcontrol16-ia03.

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Rebello, Richard J., Eric Kusnadi, Don P. Cameron, Helen B. Pearson, Analia Lesmana, Jennifer R. Devlin, Denis Drygin, et al. "Abstract B23: Inhibition of ribosomal RNA synthesis as a new therapeutic approach to treat advanced prostate cancer." In Abstracts: AACR Special Conference on Translational Control of Cancer: A New Frontier in Cancer Biology and Therapy; October 27-30, 2016; San Francisco, CA. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.transcontrol16-b23.

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Smolke, Christina D. "Abstract IA5: Designing synthetic regulatory RNAs: New tools for temporal and spatial control in biological systems." In Proceedings: AACR Special Conference on Chemical Systems Biology: Assembling and Interrogating Computational Models of the Cancer Cell by Chemical Perturbations--Jun 27-30, 2012; Boston, MA. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.csb12-ia5.

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