scholarly journals Transcriptional induction of nucleic acid sensors during coronavirus infection.

2020 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Nucleic Acid ◽  
Immune Responses ◽  
Dna And Rna ◽  
Coronavirus Infection ◽  
Molecular Patterns ◽  
Microarray Datasets ◽  
Transcriptional Induction ◽  
Acid Sensors

While adaptive immune responses involve antigen-specific responses, rapid innate immune responses involve detection of pathogen-associated molecular patterns such as the nucleic acids DNA and RNA (1). We mined five independent microarray datasets (2-6) to discover in an unbiased and systematic fashion pattern recognition receptors associated with coronavirus infection across a series of coronaviruses capable of infecting humans. We describe here the transcriptional induction of four nucleic acid and PAMP sensors following coronavirus infection in vitro and in vivo: Z-DNA-binding protein ZBP1, the DExH-box helicase DHX58 (LGP2), PYHIN1 and the Mediterannean Fever gene PYRIN as among the genes most differentially expressed following infection with coronaviruses. These data reveal unprecedented mobilization of nucleic acid sensors during coronavirus infection.

scholarly journals Nucleic Acid Computing and its Potential to Transform Silicon-Based Technology

2015 ◽  
Vol 2 (1) ◽  
Author(s):  
Seth G. Abels ◽  
Emil F. Khisamutdinov
Keyword(s):  
Nucleic Acid ◽  
Logic Gates ◽  
Rna Nanotechnology ◽  
Dna And Rna ◽  
Cellular Machinery ◽  
Living Organisms ◽  
Silicon Based ◽  
Molecular Computers

AbstractMolecular computers have existed on our planet for more than 3.5 billion years. Molecular computing devices, composed of biological substances such as nucleic acids, are responsible for the logical processing of a variety of inputs, creating viable outputs that are key components of the cellular machinery of all living organisms. We have begun to adopt some of the structural and functional knowledge of the cellular apparatus in order to fabricate nucleic-acid-based molecular computers in vitro and in vivo. Nucleic acid computing is directly dependent on advances in DNA and RNA nanotechnology. The field is still emerging and a number of challenges persist. Perhaps the most salient among these is how to translate a variety of nucleic-acid-based logic gates, developed by numerous research laboratories, into the realm of silicon-based computing. This mini-review provides some basic information on the advances in nucleic-acid-based computing and its potential to serve as an alternative that can revolutionize silicon-based technology.

scholarly journals Convolutional models of RNA energetics

2018 ◽  
Author(s):  
Michelle J. Wu
Keyword(s):  
Nucleic Acid ◽  
Network Architecture ◽  
Nearest Neighbor ◽  
Current Model ◽  
Mrna Translation ◽  
Large Space ◽  
Dna And Rna ◽  
Nucleic Acid Interactions

AbstractNucleic acid molecular biology and synthetic biology are undergoing rapid advances with the emergence of designer riboswitches controlling living cells, CRISPR/Cas9-based genome editing, high-throughput RNA-based silencing, and reengineering of mRNA translation. Many of these efforts require the design of nucleic acid interactions, which relies on accurate models for DNA and RNA energetics. Existing models utilize nearest neighbor rules, which were parameterized through careful optical melting measurements. However, these relatively simple rules often fail to quantitatively account for the biophysical behavior of molecules even in vitro, let alone in vivo. This is due to the limited experimental throughput of optical melting experiments and the infinitely large space of possible motifs that can be formed. Here, we present a convolutional neural network architecture to model the energies of nucleic acid motifs, allowing for learning of representations of physical interactions that generalize to arbitrary unmeasured motifs. First, we used existing parameterizations of motif energies to train the model and demonstrate that our model is expressive enough to recapitulate the current model. Then, through training on optical melting datasets from the literature, we have shown that the model can accurately predict the thermodynamics of hairpins containing unmeasured motifs. This work demonstrates the utility of convolutional models for capturing the thermodynamic parameters that underlie nucleic acid interactions.

scholarly journals Phosphatase PP2C6 negatively regulates phosphorylation status of Pti1b kinase, a regulator of flagellin-triggered immunity in tomato

2019 ◽  
Author(s):  
Fabian Giska ◽  
Gregory B. Martin
Keyword(s):  
Immune Responses ◽  
Plant Immunity ◽  
Active Form ◽  
Control Plant ◽  
Negative Regulator ◽  
Response To Treatment ◽  
Positive Regulators ◽  
Molecular Patterns

AbstractPlant immune responses, including the production of reactive oxygen species (ROS), are triggered when pattern recognition receptors (PRR) become activated upon detection of microbe-associated molecular patterns (MAMPs). Receptor-like cytoplasmic kinases are key components of PRR-dependent signaling pathways. In tomato two such kinases, Pti1a and Pti1b, are important positive regulators of the plant immune response. However, it is unknown how these kinases control plant immunity at the molecular level, and how their activity is regulated. To investigate these issues, we used mass spectrometry to search for interactors of Pti1b in Nicotiana benthamiana leaves and identified a protein phosphatase, PP2C6. An in vitro pull-down assay and in vivo split luciferase complementation assay verified this interaction. Pti1b was found to autophosphorylate on threonine-233 and this phosphorylation was abolished in the presence of PP2C6. An arginine-to-cysteine substitution at position 240 in the Arabidopsis MARIS kinase was previously reported to convert it into a constitutive-active form. The analogous substitution in Pti1b made it resistant to PP2C6 phosphatase activity, although it still interacted with PP2C6. Treatment of N. benthamiana leaves with the MAMP flg22 induced threonine phosphorylation of Pti1b. Expression of PP2C6, but not a phosphatase-inactive variant of this protein, in N. benthamiana leaves greatly reduced ROS production in response to treatment with MAMPs flg22 or csp22. The results indicate that PP2C6 acts as a negative regulator by dephosphorylating the Pti1b kinase, thereby interfering with its ability to activate plant immune responses.

scholarly journals Development of a novel TLR8 agonist for cancer immunotherapy

2020 ◽  
Vol 1 (1) ◽  
Author(s):  
Yuxun Wang ◽  
Heping Yang ◽  
Huanping Li ◽  
Shuda Zhao ◽  
Yikun Zeng ◽  
...  
Keyword(s):  
Immune Responses ◽  
Drug Targets ◽  
Ex Vivo ◽  
Phase 1 ◽  
Single Agent ◽  
Cancer Drug ◽  
Favorable Safety ◽  
Molecular Patterns

Abstract Toll-like receptors (TLRs) are a family of proteins that recognize pathogen associated molecular patterns (PAMPs). Their primary function is to activate innate immune responses while also involved in facilitating adaptive immune responses. Different TLRs exert distinct functions by activating varied immune cascades. Several TLRs are being pursued as cancer drug targets. We discovered a novel, highly potent and selective small molecule TLR8 agonist DN052. DN052 exhibited strong in vitro cellular activity with EC50 at 6.7 nM and was highly selective for TLR8 over other TLRs including TLR4, 7 and 9. DN052 displayed excellent in vitro ADMET and in vivo PK profiles. DN052 potently inhibited tumor growth as a single agent. Moreover, combination of DN052 with the immune checkpoint inhibitor, selected targeted therapeutics or chemotherapeutic drugs further enhanced efficacy of single agents. Mechanistically, treatment with DN052 resulted in strong induction of pro-inflammatory cytokines in ex vivo human PBMC assay and in vivo monkey study. GLP toxicity studies in rats and monkeys demonstrated favorable safety profile. This led to the advancement of DN052 into phase 1 clinical trials.

scholarly journals PP2C phosphatase Pic1 negatively regulates the phosphorylation status of Pti1b kinase, a regulator of flagellin-triggered immunity in tomato

2019 ◽  
Vol 476 (11) ◽  
pp. 1621-1635 ◽  
Author(s):  
Fabian Giska ◽  
Gregory B. Martin
Keyword(s):  
Immune Responses ◽  
Plant Immunity ◽  
Active Form ◽  
Control Plant ◽  
Negative Regulator ◽  
Response To Treatment ◽  
Positive Regulators ◽  
Molecular Patterns

Abstract Plant immune responses, including the production of reactive oxygen species (ROS), are triggered when pattern recognition receptors (PRRs) become activated upon detection of microbe-associated molecular patterns (MAMPs). Receptor-like cytoplasmic kinases are key components of PRR-dependent signaling pathways. In tomato, two such kinases, Pti1a and Pti1b, are important positive regulators of the plant immune response. However, it is unknown how these kinases control plant immunity at the molecular level and how their activity is regulated. To investigate these issues, we used mass spectrometry to search for interactors of Pti1b in Nicotiana benthamiana leaves and identified a PP2C protein phosphatase, referred to as Pic1. An in vitro pull-down assay and in vivo split-luciferase complementation assay verified this interaction. Pti1b was found to autophosphorylate on threonine-233, and this phosphorylation was abolished in the presence of Pic1. An arginine-to-cysteine substitution at position 240 in the Arabidopsis MARIS kinase was previously reported to convert it into a constitutive-active form. The analogous substitution in Pti1b made it resistant to Pic1 phosphatase activity, although it still interacted with Pic1. Treatment of N. benthamiana leaves with the MAMP flg22 induced threonine phosphorylation of Pti1b. The expression of Pic1, but not a phosphatase-inactive variant of this protein, in N. benthamiana leaves greatly reduced ROS production in response to treatment with MAMPs flg22 or csp22. The results indicate that Pic1 acts as a negative regulator by dephosphorylating the Pti1b kinase, thereby interfering with its ability to activate plant immune responses.

scholarly journals TLR5 participates in the TLR4 receptor complex and promotes MyD88-dependent signaling in environmental lung injury

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Salik Hussain ◽  
Collin G Johnson ◽  
Joseph Sciurba ◽  
Xianglin Meng ◽  
Vandy P Stober ◽  
...  
Keyword(s):  
Immune Responses ◽  
Ex Vivo ◽  
Dominant Negative ◽  
Tlr4 Signaling ◽  
In Vivo Animal Models ◽  
Molecular Patterns ◽  
Myd88 Pathway ◽  
Tlr4 Receptor

Lung disease causes significant morbidity and mortality, and is exacerbated by environmental injury, for example through lipopolysaccharide (LPS) or ozone (O3). Toll-like receptors (TLRs) orchestrate immune responses to injury by recognizing pathogen- or danger-associated molecular patterns. TLR4, the prototypic receptor for LPS, also mediates inflammation after O3, triggered by endogenous hyaluronan. Regulation of TLR4 signaling is incompletely understood. TLR5, the flagellin receptor, is expressed in alveolar macrophages, and regulates immune responses to environmental injury. Using in vivo animal models of TLR4-mediated inflammations (LPS, O3, hyaluronan), we show that TLR5 impacts the in vivo response to LPS, hyaluronan and O3. We demonstrate that immune cells of human carriers of a dominant negative TLR5 allele have decreased inflammatory response to O3 exposure ex vivo and LPS exposure in vitro. Using primary murine macrophages, we find that TLR5 physically associates with TLR4 and biases TLR4 signaling towards the MyD88 pathway. Our results suggest an updated paradigm for TLR4/TLR5 signaling.

scholarly journals Induction of methyl-CpG-binding domain proteins in coronavirus infection.

2020 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Microarray Data ◽  
Binding Proteins ◽  
Significant Differential Expression ◽  
Coronavirus Infection ◽  
Human Coronaviruses ◽  
Vitro Analysis ◽  
Transcriptional Induction ◽  
In Vitro Analysis

Coronavirus SARS-CoV-2 (“COVID-19”) has infected close to 20,000,000 people worldwide (1, 2). We mined published and public microarray data (3-8) to determine in an unbiased fashion genes most transcriptionally perturbed in the host following coronavirus infection with a series of human coronaviruses, including SARS-CoV-1, MERS-CoV and HCoV-229E. We observed significant transcriptional induction of the methyl-CpG-binding proteins MBD5 and MeCP2 following infection with two genetically distinct MERS-CoV isolates in human cells in vitro. Analysis of independent microarray data revealed less significant differential expression of MBD5 and MeCP2 in the lungs of mice following infection with SARS-CoV-1 in vivo. Epigenetic mechanisms involving methyl-CpG-binding proteins may be important to establishment of coronavirus infection in the human host.

scholarly journals TLR5 participates in the TLR4 receptor complex and biases towards MyD88-dependent signaling in environmental lung injury

2019 ◽  
Author(s):  
Salik Hussain ◽  
Collin G Johnson ◽  
Joseph Sciurba ◽  
Xianglin Meng ◽  
Vandy P Stober ◽  
...  
Keyword(s):  
Immune Responses ◽  
Ex Vivo ◽  
Dominant Negative ◽  
Receptor Complex ◽  
Tlr4 Signaling ◽  
Molecular Patterns ◽  
Myd88 Pathway ◽  
Tlr4 Receptor

AbstractLung disease causes significant morbidity and mortality, and is exacerbated by environmental injury, e.g. through lipopolysaccharide (LPS) or ozone (O3). Toll-like receptors (TLRs) orchestrate immune responses to injury by recognizing pathogen- or danger-associated molecular patterns. TLR4, the prototypic receptor for LPS, also mediates inflammation after O3, triggered by endogenous hyaluronan. Regulation of TLR4 signaling is incompletely understood. TLR5, the flagellin receptor, is expressed in alveolar macrophages, and regulates immune responses to environmental injury. Using in vivo animal models of TLR4-mediated inflammations (LPS, O3, hyaluronan), we show that TLR5 impacts the in vivo response to LPS, hyaluronan and O3. We demonstrate that immune cells of human carriers of a dominant negative TLR5 allele have decreased inflammatory response to O3 exposure ex vivo and LPS exposure in vitro. Using primary murine macrophages, we find that TLR5 physically associates with TLR4 and biases TLR4 signaling towards the MyD88 pathway. Our results suggest an updated paradigm for TLR4/TLR5 signaling.

scholarly journals Abnormal Nucleic Acid Metabolism of Lymphocytes in Plasma Cell Myeloma and Macroglobulinemia

Blood ◽  
1969 ◽  
Vol 33 (2) ◽  
pp. 300-312 ◽  
Author(s):  
SYDNEY E. SALMON ◽  
H. HUGH FUDENBERG
Keyword(s):  
Nucleic Acid ◽  
Dna Synthesis ◽  
Past History ◽  
Acid Synthesis ◽  
Nucleic Acid Metabolism ◽  
Lymphocyte Function ◽  
Dna And Rna ◽  
Lymphocyte Dna Synthesis

Abstract Twenty-six patients with multiple myeloma and macroglobulinemia of Waldenström were studied clinically and immunologically with characterization of their paraproteins and normal immunoglobulins, as well as by in vitro culture of their peripheral lymphocytes for evaluation of DNA and RNA synthesis after phytohemagglutinin stimulation. The lymphocytes of the patients were found to be significantly deficient in response to PHA as compared to normals and patients with benign hypergammaglobulinemia. Levels of normal immunoglobulins were reduced in almost all of the paraproteinemic patients, but there was not a direct correlation between lymphocyte unresponsiveness and immunoglobulin deficiency. The defect in lymphocyte function appeared to be cellular inasmuch as normal lymphocytes had normal DNA synthesis when cultured in myeloma plasma. The decrease in lymphocyte nucleic acid synthesis appeared to be unrelated to immunoglobulin class, quantitative levels or antigenic characteristics of the patients’ paraproteins. Untreated myeloma patients with a past history of infection had lower levels of lymphocyte DNA synthesis than those patients who lacked such a history, suggesting a relationship between the in vitro lymphocyte response to PHA and the in vivo response to the antigenic challenge of bacterial infection.

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