scholarly journals Inhibition of SARS-CoV-2 polymerase by nucleotide analogs from a single-molecule perspective

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Mona Seifert ◽  
Subhas C Bera ◽  
Pauline van Nies ◽  
Robert N Kirchdoerfer ◽  
Ashleigh Shannon ◽  
...  
Keyword(s):  
Single Molecule ◽  
Rna Synthesis ◽  
Vaccine Development ◽  
Magnetic Tweezers ◽  
Experimental Paradigm ◽  
Antiviral Protein ◽  
Nucleotide Analogs ◽  
Poor Understanding ◽  
The Impact ◽  
Near Future

The absence of ‘shovel-ready’ anti-coronavirus drugs during vaccine development has exceedingly worsened the SARS-CoV-2 pandemic. Furthermore, new vaccine-resistant variants and coronavirus outbreaks may occur in the near future, and we must be ready to face this possibility. However, efficient antiviral drugs are still lacking to this day, due to our poor understanding of the mode of incorporation and mechanism of action of nucleotides analogs that target the coronavirus polymerase to impair its essential activity. Here, we characterize the impact of remdesivir (RDV, the only FDA-approved anti-coronavirus drug) and other nucleotide analogs (NAs) on RNA synthesis by the coronavirus polymerase using a high-throughput, single-molecule, magnetic-tweezers platform. We reveal that the location of the modification in the ribose or in the base dictates the catalytic pathway(s) used for its incorporation. We show that RDV incorporation does not terminate viral RNA synthesis, but leads the polymerase into backtrack as far as 30 nt, which may appear as termination in traditional ensemble assays. SARS-CoV-2 is able to evade the endogenously synthesized product of the viperin antiviral protein, ddhCTP, though the polymerase incorporates this NA well. This experimental paradigm is essential to the discovery and development of therapeutics targeting viral polymerases.

scholarly journals Signatures and mechanisms of efficacious therapeutic ribonucleotides against SARS-CoV-2 revealed by analysis of its replicase using magnetic tweezers

2020 ◽  
Author(s):  
Mona Seifert ◽  
Subhas Chandra Bera ◽  
Pauline van Nies ◽  
Robert N. Kirchdoerfer ◽  
Ashleigh Shannon ◽  
...  
Keyword(s):  
Single Molecule ◽  
Magnetic Tweezers ◽  
Therapeutic Strategies ◽  
High Fidelity ◽  
Experimental Paradigm ◽  
Nucleotide Analogs ◽  
The Third ◽  
Nucleotide Addition ◽  
A Chain ◽  
Chain Terminator

SummaryCoronavirus Disease 2019 (COVID-19) results from an infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the third coronavirus outbreak to plague humanity this century. Currently, the most efficacious therapeutic against SARS-CoV-2 infection is the Remdesivir (RDV), an adenine-like ribonucleotide analogue that is very efficiently incorporated by the SARS-CoV-2 replicase. Understanding why RDV is so well incorporated will facilitate development of even more effective therapeutics. Here, we have applied a high-throughput, single-molecule, magnetic-tweezers platform to study thousands of cycles of nucleotide addition by the SARS-CoV-2 replicase in the absence and presence of RDV, a Favipiravir-related analog (T-1106), and the endogenously produced ddhCTP. Our data are consistent with two parallel catalytic pathways of the replicase: a high-fidelity catalytic (HFC) state and a low-fidelity catalytic (LFC) state, the latter allowing the slow incorporation of both cognate and non-cognate nucleotides. ddhCTP accesses HFC, T-1106 accesses LFC as a non-cognate nucleotide, while RDV efficiently accesses both LFC pathway. In contrast to previous reports, we provide unequivocal evidence against RDV functioning as a chain terminator. We show that RDV incorporation transiently stalls the replicase, only appearing as termination events when traditional, gel-based assays are used. The efficiency of ddhCTP utilization by the SARS-CoV-2 replicase suggests suppression of its synthesis during infection, inspiring new therapeutic strategies. Use of this experimental paradigm will be essential to the development of therapeutic nucleotide analogs targeting polymerases.

scholarly journals On Mautner-Type Probability of Capture of Intergalactic Meteor Particles by Habitable Exoplanets

Sci ◽  
2019 ◽  
Vol 1 (3) ◽  
pp. 61
Author(s):  
Andjelka B. Kovačević
Keyword(s):  
Single Molecule ◽  
Rare Events ◽  
Birth And Death Processes ◽  
Habitable Zones ◽  
Source Populations ◽  
Dynamical Description ◽  
The Impact ◽  
Near Future ◽  
Host Stars ◽  
Information Metrics

Both macro and microprojectiles (e.g., interplanetary, interstellar and even intergalactic material) are seen as important vehicles for the exchange of potential (bio)material within our solar system as well as between stellar systems in our Galaxy. Accordingly, this requires estimates of the impact probabilities for different source populations of projectiles, including for intergalactic meteor particles which have received relatively little attention since considered as rare events (discrete occurrences that are statistically improbable due to their very infrequent appearance). We employ the simple but comprehensive model of intergalactic microprojectile capture by the gravity of exoplanets which enables us to estimate the map of collisional probabilities for an available sample of exoplanets in habitable zones around host stars. The model includes a dynamical description of the capture adopted from Mautner model of interstellar exchange of microparticles and changed for our purposes. We use statistical and information metrics to calculate probability map of intergalactic meteorite particle capture. Moreover, by calculating the entropy index map we estimate the concentration of these rare events. We further adopted a model from immigration theory, to show that the time dependent distribution of single molecule immigration of material indicates high survivability of the immigrated material taking into account birth and death processes on our planet. At present immigration of material can not be observationally constrained but it seems reasonable to think that it will be possible in the near future, and to use it along other proposed parameters for life sustainability on some planet.

Manipulating and probing enzymatic conformational fluctuations and enzyme–substrate interactions by single-molecule FRET-magnetic tweezers microscopy

2014 ◽  
Vol 16 (26) ◽  
pp. 13052-13058 ◽  
Author(s):  
Qing Guo ◽  
Yufan He ◽  
H. Peter Lu
Keyword(s):  
Single Molecule ◽  
Critical Role ◽  
Magnetic Tweezers ◽  
Enzymatic Reactions ◽  
Substrate Interactions ◽  
Single Molecule Level ◽  
Single Molecule Fret ◽  
Enzyme Substrate ◽  
The Impact ◽  
Enzyme Substrate Interactions

To investigate the critical role of the enzyme–substrate interactions in enzymatic reactions, the enzymatic conformation and enzyme–substrate interaction at a single-molecule level are manipulated by magnetic tweezers, and the impact of the manipulation on enzyme–substrate interactions are simultaneously probed by single-molecule FRET spectroscopy.

scholarly journals Interrogating the activities of conformational deformed enzyme by single-molecule fluorescence-magnetic tweezers microscopy

2015 ◽  
Vol 112 (45) ◽  
pp. 13904-13909 ◽  
Author(s):  
Qing Guo ◽  
Yufan He ◽  
H. Peter Lu
Keyword(s):  
Enzymatic Activity ◽  
Single Molecule ◽  
Total Internal Reflection ◽  
Enzymatic Reaction ◽  
Magnetic Tweezers ◽  
Amplex Red ◽  
Enzyme Substrate ◽  
Conformational Fluctuation ◽  
Function Relationship ◽  
The Impact

Characterizing the impact of fluctuating enzyme conformation on enzymatic activity is critical in understanding the structure–function relationship and enzymatic reaction dynamics. Different from studying enzyme conformations under a denaturing condition, it is highly informative to manipulate the conformation of an enzyme under an enzymatic reaction condition while monitoring the real-time enzymatic activity changes simultaneously. By perturbing conformation of horseradish peroxidase (HRP) molecules using our home-developed single-molecule total internal reflection magnetic tweezers, we successfully manipulated the enzymatic conformation and probed the enzymatic activity changes of HRP in a catalyzed H2O2–amplex red reaction. We also observed a significant tolerance of the enzyme activity to the enzyme conformational perturbation. Our results provide a further understanding of the relation between enzyme behavior and enzymatic conformational fluctuation, enzyme–substrate interactions, enzyme–substrate active complex formation, and protein folding–binding interactions.

Syrian Crisis and Migration

2015 ◽  
Vol 12 (3) ◽  
pp. 181-192 ◽  
Author(s):  
Pinar Yazgan ◽  
Deniz Eroglu Utku ◽  
Ibrahim Sirkeci
Keyword(s):  
Human Mobility ◽  
Special Issue ◽  
Host Countries ◽  
Syrian Crisis ◽  
Mass Migration ◽  
Large Numbers ◽  
And Migration ◽  
Europe Today ◽  
The Impact ◽  
Near Future

With the growing insurrections in Syria in 2011, an exodus in large numbers have emerged. The turmoil and violence have caused mass migration to destinations both within the region and beyond. The current "refugee crisis" has escalated sharply and its impact is widening from neighbouring countries toward Europe. Today, the Syrian crisis is the major cause for an increase in displacement and the resultant dire humanitarian situation in the region. Since the conflict shows no signs of abating in the near future, there is a constant increase in the number of Syrians fleeing their homes. However, questions on the future impact of the Syrian crisis on the scope and scale of this human mobility are still to be answered. As the impact of the Syrian crisis on host countries increases, so does the demand for the analyses of the needs for development and protection in these countries. In this special issue, we aim to bring together a number of studies examining and discussing human mobility in relation to the Syrian crisis.

Mechanically-Tunable Quantum Interference in Ferrocene-Based Single-Molecule Junctions

2020 ◽  
Author(s):  
María Camarasa-Gómez ◽  
Daniel Hernangómez-Pérez ◽  
Michael S. Inkpen ◽  
Giacomo Lovat ◽  
E-Dean Fung ◽  
...  
Keyword(s):  
Single Molecule ◽  
Quantum Interference ◽  
Degrees Of Freedom ◽  
Building Blocks ◽  
Ferrocene Derivative ◽  
Single Molecule Junctions ◽  
Molecule Junction ◽  
Single Molecule Junction ◽  
The Impact ◽  
D Orbitals

Ferrocenes are ubiquitous organometallic building blocks that comprise a Fe atom sandwiched between two cyclopentadienyl (Cp) rings that rotate freely at room temperature. Of widespread interest in fundamental studies and real-world applications, they have also attracted<br>some interest as functional elements of molecular-scale devices. Here we investigate the impact of<br>the configurational degrees of freedom of a ferrocene derivative on its single-molecule junction<br>conductance. Measurements indicate that the conductance of the ferrocene derivative, which is<br>suppressed by two orders of magnitude as compared to a fully conjugated analog, can be modulated<br>by altering the junction configuration. Ab initio transport calculations show that the low conductance is a consequence of destructive quantum interference effects that arise from the hybridization of metal-based d-orbitals and the ligand-based π-system. By rotating the Cp rings, the hybridization, and thus the quantum interference, can be mechanically controlled, resulting in a conductance modulation that is seen experimentally.<br>

Monitoring the Structural Dynamics of U2 snRNA Via Single-Molecule Förster Resonance Energy Transfer

2018 ◽  
Author(s):  
Alexander Carl DeHaven
Keyword(s):  
Energy Transfer ◽  
Structural Dynamics ◽  
Single Molecule ◽  
Conformational Dynamics ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Förster Resonance Energy Transfer ◽  
U2 Snrna ◽  
Folding Dynamics ◽  
The Impact

This thesis contains four topic areas: a review of single-molecule microscropy methods and splicing, conformational dynamics of stem II of the U2 snRNA, the impact of post-transcriptional modifications on U2 snRNA folding dynamics, and preliminary findings on Mango aptamer folding dynamics.

The Supply-Demand Research of Cultural and Tourism Industries Policies in China with the Impact of COVID-19

2020 ◽  
Vol 11 (1) ◽  
pp. 24-24
Author(s):  
Dr. Jianfei Yang
Keyword(s):  
Tourism Industry ◽  
Chinese Government ◽  
Cultural Industries ◽  
Real Situation ◽  
The Real ◽  
The World ◽  
The Impact ◽  
Near Future ◽  
Post Period

COVID-19 has made a bad influence on economic and society including cultural and tourism industry in China，2020.The industry has received a huge loss in the first quarter of the year and the situation is getting worse in the near future. It is believed that there will be a long impact for the country even the world. In order to recover the industry, Chinese government has published series of policies to support the enterprises and clusters to reduce the bad influence of COVID-19. This paper mainly uses filed survey and documentary research to map the real situation of the industry. It tries to find the policy demand of the industries and then analyze the policies published by government to conquer COVID-19. Meanwhile it will focus on whether the supply meet the demand and give suggestions on how to promote the policy efficiency in the post period of COVID-19 in China. Keywords: Evaluation; Cultural Industries; Policy; Park; Pandemic

scholarly journals Using Satellite Data for CBRN (Chemical, Biological, Radiological, and Nuclear) Threat Detection, Monitoring, and Modelling

2021 ◽  
Author(s):  
Gary Sutlieff ◽  
Lucy Berthoud ◽  
Mark Stinchcombe
Keyword(s):  
Satellite Data ◽  
Meteorological Data ◽  
Atmospheric Composition ◽  
Chemical Detection ◽  
List Type ◽  
Data Types ◽  
Wide Range ◽  
Future Technologies ◽  
The Impact ◽  
Near Future

Abstract CBRN (Chemical, Biological, Radiological, and Nuclear) threats are becoming more prevalent, as more entities gain access to modern weapons and industrial technologies and chemicals. This has produced a need for improvements to modelling, detection, and monitoring of these events. While there are currently no dedicated satellites for CBRN purposes, there are a wide range of possibilities for satellite data to contribute to this field, from atmospheric composition and chemical detection to cloud cover, land mapping, and surface property measurements. This study looks at currently available satellite data, including meteorological data such as wind and cloud profiles, surface properties like temperature and humidity, chemical detection, and sounding. Results of this survey revealed several gaps in the available data, particularly concerning biological and radiological detection. The results also suggest that publicly available satellite data largely does not meet the requirements of spatial resolution, coverage, and latency that CBRN detection requires, outside of providing terrain use and building height data for constructing models. Lastly, the study evaluates upcoming instruments, platforms, and satellite technologies to gauge the impact these developments will have in the near future. Improvements in spatial and temporal resolution as well as latency are already becoming possible, and new instruments will fill in the gaps in detection by imaging a wider range of chemicals and other agents and by collecting new data types. This study shows that with developments coming within the next decade, satellites should begin to provide valuable augmentations to CBRN event detection and monitoring. Article Highlights There is a wide range of existing satellite data in fields that are of interest to CBRN detection and monitoring. The data is mostly of insufficient quality (resolution or latency) for the demanding requirements of CBRN modelling for incident control. Future technologies and platforms will improve resolution and latency, making satellite data more viable in the CBRN management field

scholarly journals A Low-Cost Assistive Robot for Children with Neurodevelopmental Disorders to Aid in Daily Living Activities

2021 ◽  
Vol 18 (8) ◽  
pp. 3974
Author(s):  
Roberto J. López-Sastre ◽  
Marcos Baptista-Ríos ◽  
Francisco Javier Acevedo-Rodríguez ◽  
Soraya Pacheco-da-Costa ◽  
Saturnino Maldonado-Bascón ◽  
...  
Keyword(s):  
Neurodevelopmental Disorders ◽  
Low Cost ◽  
Children And Youth ◽  
Proof Of Concept ◽  
Robotic Platform ◽  
Assistive Robot ◽  
Technical Details ◽  
The Impact ◽  
Near Future ◽  
Everyday Living

In this paper, we present a new low-cost robotic platform that has been explicitly developed to increase children with neurodevelopmental disorders’ involvement in the environment during everyday living activities. In order to support the children and youth with both the sequencing and learning of everyday living tasks, our robotic platform incorporates a sophisticated online action detection module that is capable of monitoring the acts performed by users. We explain all the technical details that allow many applications to be introduced to support individuals with functional diversity. We present this work as a proof of concept, which will enable an assessment of the impact that the developed technology may have on the collective of children and youth with neurodevelopmental disorders in the near future.

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