scholarly journals Enzyme-free nucleic acid dynamical systems

2017 ◽  
Author(s):  
Niranjan Srinivas ◽  
James Parkin ◽  
Georg Seelig ◽  
Erik Winfree ◽  
David Soloveichik
Keyword(s):  
Dynamical Systems ◽  
Programming Languages ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Complex Dynamics ◽  
Molecular Systems ◽  
Synthetic Dna ◽  
Molecular Programming ◽  
And Control ◽  
Dna Components

Chemistries exhibiting complex dynamics—from inorganic oscillators to gene regulatory networks—have been long known but either cannot be reprogrammed at will, or rely on the sophisticated chemistry underlying the central dogma. Can simpler molecular mechanisms, designed from scratch, exhibit the same range of behaviors? Abstract coupled chemical reactions have been proposed as a programming language for complex dynamics, along with their systematic implementation using short synthetic DNA molecules. We developed this technology for dynamical systems, identifying critical design principles and codifying them into a compiler automating the design process. Using this approach, we built an oscillator containing only DNA components, establishing that Watson-Crick base pairing interactions alone suffice for arbitrarily complex dynamics. Our results argue that autonomous molecular systems that interact with and control their chemical environment can be designed via molecular programming languages.

scholarly journals Enzyme-free nucleic acid dynamical systems

Science ◽  
2017 ◽  
Vol 358 (6369) ◽  
pp. eaal2052 ◽  
Author(s):  
Niranjan Srinivas ◽  
James Parkin ◽  
Georg Seelig ◽  
Erik Winfree ◽  
David Soloveichik
Keyword(s):  
Dynamical Systems ◽  
Programming Languages ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Complex Dynamics ◽  
Molecular Systems ◽  
Synthetic Dna ◽  
Molecular Programming ◽  
Dna Components ◽  
At Will

Chemistries exhibiting complex dynamics—from inorganic oscillators to gene regulatory networks—have been long known but either cannot be reprogrammed at will or rely on the sophisticated enzyme chemistry underlying the central dogma. Can simpler molecular mechanisms, designed from scratch, exhibit the same range of behaviors? Abstract chemical reaction networks have been proposed as a programming language for complex dynamics, along with their systematic implementation using short synthetic DNA molecules. We developed this technology for dynamical systems by identifying critical design principles and codifying them into a compiler automating the design process. Using this approach, we built an oscillator containing only DNA components, establishing that Watson-Crick base-pairing interactions alone suffice for complex chemical dynamics and that autonomous molecular systems can be designed via molecular programming languages.

scholarly journals Integrated Bioinformatics Analysis of Potential mRNA and miRNA Regulatory Networks in Mice With Ischemic Stroke Treated by Electroacupuncture

2021 ◽  
Vol 12 ◽  
Author(s):  
Chunxiao Wu ◽  
Lijun Zhao ◽  
Xinrong Li ◽  
Yingshan Xu ◽  
Hongji Guo ◽  
...  
Keyword(s):  
Ischemic Stroke ◽  
Signaling Pathway ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Functional Enrichment ◽  
Neurological Deficits ◽  
Control Groups ◽  
Hub Genes ◽  
Key Genes ◽  
And Control

Background: The complicated molecular mechanisms underlying the therapeutic effect of electroacupuncture (EA) on ischemic stroke are still unclear. Recently, more evidence has revealed the essential role of the microRNA (miRNA)–mRNA networks in ischemic stroke. However, a systematic analysis of novel key genes, miRNAs, and miRNA–mRNA networks regulated by EA in ischemic stroke is still absent.Methods: We established a middle cerebral artery occlusion (MCAO) mouse model and performed EA therapy on ischemic stroke mice. Behavior tests and measurement of infarction area were applied to measure the effect of EA treatment. Then, we performed RNA sequencing to analyze differentially expressed genes (DEGs) and functional enrichment between the EA and control groups. In addition, a protein–protein interaction (PPI) network was built, and hub genes were screened by Cytoscape. Upstream miRNAs were predicted by miRTarBase. Then hub genes and predicted miRNAs were verified as key biomarkers by RT-qPCR. Finally, miRNA–mRNA networks were constructed to explore the potential mechanisms of EA in ischemic stroke.Results: Our analysis revealed that EA treatment could significantly alleviate neurological deficits in the affected limbs and reduce infarct area of the MCAO model mice. A total of 174 significant DEGs, including 53 upregulated genes and 121 downregulated genes, were identified between the EA and control groups. Functional enrichment analysis showed that these DEGs were associated with the FOXO signaling pathway, NF-kappa B signaling pathway, T-cell receptor signaling pathway, and other vital pathways. The top 10 genes with the highest degree scores were identified as hub genes based on the degree method, but only seven genes were verified as key genes according to RT-qPCR. Twelve upstream miRNAs were predicted to target the seven key genes. However, only four miRNAs were significantly upregulated and indicated favorable effects of EA treatment. Finally, comprehensive analysis of the results identified the miR-425-5p-Cdk1, mmu-miR-1186b-Prc1, mmu-miR-434-3p-Prc1, and mmu-miR-453-Prc1 miRNA–mRNA networks as key networks that are regulated by EA and linked to ischemic stroke. These networks might mainly take place in neuronal cells regulated by EA in ischemic stroke.Conclusion: In summary, our study identified key DEGs, miRNAs, and miRNA–mRNA regulatory networks that may help to facilitate the understanding of the molecular mechanism underlying the effect of EA treatment on ischemic stroke.

scholarly journals Analysis of single-cell gene pair coexpression landscapes by stochastic kinetic modeling reveals gene-pair interactions in development

2019 ◽  
Author(s):  
Cameron P. Gallivan ◽  
Honglei Ren ◽  
Elizabeth L. Read
Keyword(s):  
Single Cell ◽  
Gene Pair ◽  
Gene Network ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Complex Dynamics ◽  
Gene Interaction ◽  
State Transitions ◽  
Sequencing Data ◽  
Cell Gene

ABSTRACTSingle-cell transcriptomics is advancing discovery of the molecular determinants of cell identity, while spurring development of novel data analysis methods. Stochastic mathematical models of gene regulatory networks help unravel the dynamic, molecular mechanisms underlying cell-to-cell heterogeneity, and can thus aid interpretation of heterogeneous cell-states revealed by single-cell measurements. However, integrating stochastic gene network models with single cell data is challenging. Here, we present a method for analyzing single-cell gene-pair coexpression patterns, based on biophysical models of stochastic gene expression and interaction dynamics. We first developed a high-computational-throughput approach to stochastic modeling of gene-pair coexpression landscapes, based on numerical solution of gene network Master Equations. We then comprehensively catalogued coexpression patterns arising from tens of thousands of gene-gene interaction models with different biochemical kinetic parameters and regulatory interactions. From the computed landscapes, we obtain a low-dimensional “shape-space” describing distinct types of coexpression patterns. We applied the theoretical results to analysis of published single cell RNA sequencing data and uncovered complex dynamics of coexpression among gene pairs during embryonic development. Our approach provides a generalizable framework for inferring evolution of gene-gene interactions during critical cell-state transitions.

The Protective Effects of Green Tea Catechins in the Management of Neurodegenerative Diseases: A Review

2019 ◽  
Vol 16 (1) ◽  
pp. 57-65 ◽  
Author(s):  
Tahereh Farkhondeh ◽  
Hanieh Shaterzadeh Yazdi ◽  
Saeed Samarghandian
Keyword(s):  
Neurodegenerative Diseases ◽  
Signaling Pathways ◽  
Green Tea ◽  
Molecular Mechanisms ◽  
Main Role ◽  
Related Factor ◽  
Protective Effects ◽  
Tea Catechins ◽  
Green Tea Catechins ◽  
And Control

Background: The therapeutic strategies to manage neurodegenerative diseases remain limited and it is necessary to discover new agents for their prevention and control. Oxidative stress and inflammation play a main role in the pathogenesis of neurodegenerative diseases. The aim of this study is to review the effects of green tea catechins against the Neurodegenerative Diseases. Methods: In this study, we extensively reviewed all articles on the terms of Green tea, catechins, CNS disorders, and different diseases in PubMed, Science Direct, Scopus, and Google Scholar databases between the years 1990 and 2017. Results: The present study found that catechins, the major flavonoids in green tea, are powerful antioxidants and radical scavengers which possess the potential roles in the management of neurodegenerative diseases. Catechins modulate the cellular and molecular mechanisms through the inflammation-related NF-&amp;#954;B and the nuclear factor erythroid 2-related factor 2 (Nrf2) signaling pathways. Conclusion: The findings of the present review shows catechins could be effective against neurodegenerative diseases due to their antioxidation and anti-inflammation effects and the involved biochemical pathways including Nrf2 and NF-kB signaling pathways.<P&gt;

Radio-Susceptibility of Nasopharyngeal Carcinoma: Focus on Epstein- Barr Virus, MicroRNAs, Long Non-Coding RNAs and Circular RNAs

2020 ◽  
Vol 13 (3) ◽  
pp. 192-205 ◽  
Author(s):  
Fanghong Lei ◽  
Tongda Lei ◽  
Yun Huang ◽  
Mingxiu Yang ◽  
Mingchu Liao ◽  
...  
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Regulatory Networks ◽  
Epstein Barr Virus ◽  
Molecular Mechanisms ◽  
Acquired Resistance ◽  
Treatment Strategies ◽  
Circular Rnas ◽  
Barr Virus ◽  
Non Coding Rnas ◽  
Epstein Barr

Nasopharyngeal carcinoma (NPC) is a type of head and neck cancer. As a neoplastic disorder, NPC is a highly malignant squamous cell carcinoma that is derived from the nasopharyngeal epithelium. NPC is radiosensitive; radiotherapy or radiotherapy combining with chemotherapy are the main treatment strategies. However, both modalities are usually accompanied by complications and acquired resistance to radiotherapy is a significant impediment to effective NPC therapy. Therefore, there is an urgent need to discover effective radio-sensitization and radio-resistance biomarkers for NPC. Recent studies have shown that Epstein-Barr virus (EBV)-encoded products, microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), which share several common signaling pathways, can function in radio-related NPC cells or tissues. Understanding these interconnected regulatory networks will reveal the details of NPC radiation sensitivity and resistance. In this review, we discuss and summarize the specific molecular mechanisms of NPC radio-sensitization and radio-resistance, focusing on EBV-encoded products, miRNAs, lncRNAs and circRNAs. This will provide a foundation for the discovery of more accurate, effective and specific markers related to NPC radiotherapy. EBVencoded products, miRNAs, lncRNAs and circRNAs have emerged as crucial molecules mediating the radio-susceptibility of NPC. This understanding will improve the clinical application of markers and inform the development of novel therapeutics for NPC.

scholarly journals Thermochromic aggregation-induced dual phosphorescence via temperature-dependent sp3-linked donor-acceptor electronic coupling

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Tao Wang ◽  
Zhubin Hu ◽  
Xiancheng Nie ◽  
Linkun Huang ◽  
Miao Hui ◽  
...  
Keyword(s):  
Excited State ◽  
Room Temperature ◽  
Electronic Coupling ◽  
Temperature Dependent ◽  
Molecular Systems ◽  
Donor And Acceptor ◽  
Theoretical Investigations ◽  
Donor Acceptor ◽  
And Control ◽  
Two Temperature

AbstractAggregation-induced emission (AIE) has proven to be a viable strategy to achieve highly efficient room temperature phosphorescence (RTP) in bulk by restricting molecular motions. Here, we show that by utilizing triphenylamine (TPA) as an electronic donor that connects to an acceptor via an sp3 linker, six TPA-based AIE-active RTP luminophores were obtained. Distinct dual phosphorescence bands emitting from largely localized donor and acceptor triplet emitting states could be recorded at lowered temperatures; at room temperature, only a merged RTP band is present. Theoretical investigations reveal that the two temperature-dependent phosphorescence bands both originate from local/global minima from the lowest triplet excited state (T1). The reported molecular construct serves as an intermediary case between a fully conjugated donor-acceptor system and a donor/acceptor binary mix, which may provide important clues on the design and control of high-freedom molecular systems with complex excited-state dynamics.

scholarly journals Integrative Modelling of Gene Expression and Digital Phenotypes to Describe Senescence in Wheat

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 909
Author(s):  
Anyela Valentina Camargo Rodriguez
Keyword(s):  
Gene Expression ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Computational Modelling ◽  
Plant Morphology ◽  
Reproductive Organs ◽  
Biological Trait ◽  
Cereal Grain ◽  
Plant Level

Senescence is the final stage of leaf development and is critical for plants’ fitness as nutrient relocation from leaves to reproductive organs takes place. Although senescence is key in nutrient relocation and yield determination in cereal grain production, there is limited understanding of the genetic and molecular mechanisms that control it in major staple crops such as wheat. Senescence is a highly orchestrated continuum of interacting pathways throughout the lifecycle of a plant. Levels of gene expression, morphogenesis, and phenotypic development all play key roles. Yet, most studies focus on a short window immediately after anthesis. This approach clearly leaves out key components controlling the activation, development, and modulation of the senescence pathway before anthesis, as well as during the later developmental stages, during which grain development continues. Here, a computational multiscale modelling approach integrates multi-omics developmental data to attempt to simulate senescence at the molecular and plant level. To recreate the senescence process in wheat, core principles were borrowed from Arabidopsis Thaliana, a more widely researched plant model. The resulted model describes temporal gene regulatory networks and their effect on plant morphology leading to senescence. Digital phenotypes generated from images using a phenomics platform were used to capture the dynamics of plant development. This work provides the basis for the application of computational modelling to advance understanding of the complex biological trait senescence. This supports the development of a predictive framework enabling its prediction in changing or extreme environmental conditions, with a view to targeted selection for optimal lifecycle duration for improving resilience to climate change.

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