scholarly journals In vivo structure and dynamics of the SARS-CoV-2 RNA genome

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yan Zhang ◽  
Kun Huang ◽  
Dejian Xie ◽  
Jian You Lau ◽  
Wenlong Shen ◽  
...  
Keyword(s):  
Life Cycle ◽  
Rna Structure ◽  
Structural Basis ◽  
Long Distance ◽  
Alternative Structures ◽  
Translational Frameshifting ◽  
Functional Relevance ◽  
Discontinuous Transcription ◽  
Whole Life Cycle

AbstractThe dynamics of SARS-CoV-2 RNA structure and their functional relevance are largely unknown. Here we develop a simplified SPLASH assay and comprehensively map the in vivo RNA-RNA interactome of SARS-CoV-2 genome across viral life cycle. We report canonical and alternative structures including 5′-UTR and 3′-UTR, frameshifting element (FSE) pseudoknot and genome cyclization in both cells and virions. We provide direct evidence of interactions between Transcription Regulating Sequences, which facilitate discontinuous transcription. In addition, we reveal alternative short and long distance arches around FSE. More importantly, we find that within virions, while SARS-CoV-2 genome RNA undergoes intensive compaction, genome domains remain stable but with strengthened demarcation of local domains and weakened global cyclization. Taken together, our analysis reveals the structural basis for the regulation of replication, discontinuous transcription and translational frameshifting, the alternative conformations and the maintenance of global genome organization during the whole life cycle of SARS-CoV-2, which we anticipate will help develop better antiviral strategies.

scholarly journals In vivo structure and dynamics of the RNA genome of SARS-Cov-2

2021 ◽  
Author(s):  
Yan Zhang ◽  
Kun Huang ◽  
Dejian Xie ◽  
Jian You Lau ◽  
Wenlong Shen ◽  
...  
Keyword(s):  
Life Cycle ◽  
Structural Basis ◽  
Rna Structures ◽  
Long Distance ◽  
Alternative Structures ◽  
Translational Frameshifting ◽  
Ribosome Stalling ◽  
Positive Strand Rna ◽  
Discontinuous Transcription

AbstractThe SARS-CoV-2 coronavirus, which causes the COVID-19 pandemic, is one of the largest positive strand RNA viruses. Here we developed a simplified SPLASH assay and comprehensively mapped the in vivo RNA-RNA interactome of SARS-CoV-2 RNA during the viral life cycle. We observed canonical and alternative structures including 3’-UTR and 5’-UTR, frameshifting element (FSE) pseudoknot and genome cyclization in cells and in virions. We provide direct evidence of interactions between Transcription Regulating Sequences (TRS-L and TRS-Bs), which facilitate discontinuous transcription. In addition, we reveal alternative short and long distance arches around FSE, forming a “high-order pseudoknot” embedding FSE, which might help ribosome stalling at frameshift sites. More importantly, we found that within virions, while SARS-CoV-2 genome RNA undergoes intensive compaction, genome cyclization is weakened and genome domains remain stable. Our data provides a structural basis for the regulation of replication, discontinuous transcription and translational frameshifting, describes dynamics of RNA structures during life cycle of SARS-CoV-2, and will help to develop antiviral strategies.

scholarly journals The short- and long-range RNA-RNA Interactome of SARS-CoV-2

2020 ◽  
Author(s):  
Omer Ziv ◽  
Jonathan Price ◽  
Lyudmila Shalamova ◽  
Tsveta Kamenova ◽  
Ian Goodfellow ◽  
...  
Keyword(s):  
Long Range ◽  
Rna Structure ◽  
Purifying Selection ◽  
Etiologic Agent ◽  
Long Distance ◽  
Rna Interaction ◽  
Positive Strand Rna ◽  
Discontinuous Transcription ◽  
Transcription And Replication

SUMMARYThe Coronaviridae is a family of positive-strand RNA viruses that includes SARS-CoV-2, the etiologic agent of the COVID-19 pandemic. Bearing the largest single-stranded RNA genomes in nature, coronaviruses are critically dependent on long-distance RNA-RNA interactions to regulate the viral transcription and replication pathways. Here we experimentally mapped the in vivo RNA-RNA interactome of the full-length SARS-CoV-2 genome and subgenomic mRNAs. We uncovered a network of RNA-RNA interactions spanning tens of thousands of nucleotides. These interactions reveal that the viral genome and subgenomes adopt alternative topologies inside cells, and engage in different interactions with host RNAs. Notably, we discovered a long-range RNA-RNA interaction - the FSE-arch - that encircles the programmed ribosomal frameshifting element. The FSE-arch is conserved in the related MERS-CoV and is under purifying selection. Our findings illuminate RNA structure based mechanisms governing replication, discontinuous transcription, and translation of coronaviruses, and will aid future efforts to develop antiviral strategies.

The illustrated life cycle of Microbotryum on the host plant Silene latifolia

Botany ◽  
2010 ◽  
Vol 88 (10) ◽  
pp. 875-885 ◽  
Author(s):  
Angela Maria Schäfer ◽  
Martin Kemler ◽  
Robert Bauer ◽  
Dominik Begerow
Keyword(s):  
Life Cycle ◽  
Light And Electron Microscopy ◽  
Laboratory Data ◽  
Infection Process ◽  
Host Cells ◽  
Silene Latifolia ◽  
Long Distance ◽  
Biological Studies ◽  
Plant Parasitic

The plant-parasitic genus Microbotryum (Pucciniomycotina) has been used as a model for various biological studies, but fundamental aspects of its life history have not been documented in detail. The smut fungus is characterized by a dimorphic life cycle with a haploid saprophytic yeast-like stage and a dikaryotic plant-parasitic stage, which bears the teliospores as dispersal agents. In this study, seedlings and flowers of Silene latifolia Poir. (Caryophyllaceae) were inoculated with teliospores or sporidial cells of Microbotryum lychnidis-dioicae (DC. ex Liro) G. Deml & Oberw. and the germination of teliospores, the infection process, and the proliferation in the host tissue were documented in vivo using light and electron microscopy. Although germination of the teliospore is crucial for the establishment of Microbotryum, basidium development is variable under natural conditions. In flowers, where the amount of nutrients is thought to be high, the fungus propagates as sporidia, and mating of compatible cells takes place only when flowers are withering and nutrients are decreasing. On cotyledons (i.e., nutrient-depleted conditions), conjugation occurs shortly after teliospore germination, often via intrapromycelial mating. After formation of an infectious hypha with an appressorium, the invasion of the host occurs by direct penetration of the epidermis. While the growth in the plant is typically intercellular, long distance proliferation seems mediated through xylem tracheary elements. At the beginning of the vegetation period, fungal cells were found between meristematic shoot host cells, indicating a dormant phase inside the plant. By using different microscopy techniques, many life stages of Microbotryum are illustrated for the first time, thereby allowing new interpretations of laboratory data.

scholarly journals The Mite-Gallery Unit: A New Concept for Describing Scabies through Entodermoscopy

2019 ◽  
Vol 4 (1) ◽  
pp. 48 ◽  
Author(s):  
Gaetano Scanni
Keyword(s):  
Life Cycle ◽  
The Elderly ◽  
Sarcoptes Scabiei ◽  
Optical Microscope ◽  
Functional Explanation ◽  
Diagnostic Challenge ◽  
Local Skin ◽  
Whole Life Cycle

Scabies has always represented a diagnostic challenge for dermatologists, especially in subclinical cases or in atypical ones due to the coexistence of other diseases. Fortunately, dermatoscopy has enabled easier and faster in situ diagnosis. The aim of this study is to examine old and new dermatoscopic signs that Sarcoptes scabiei produces on the skin during its whole life cycle through entodermoscopy (dermatoscopy with an entomological focus) which, unlike traditional optical microscope examination, allows the local micro-environment to be preserved intact. Patients were enrolled during outbreaks of scabies from hospitals or nursing homes for the elderly in Bari (Italy). The study was performed applying both immersion and polarized dry dermatoscopy. The systematic use of dermatoscopy highlighted the morphological complexity of the Sarcoptes tunnel that had been described previously as a simple unitary structure. On the contrary, it is possible to distinguish three separate segments of the burrow that introduce a new anatomo-functional concept called the Mite-Gallery Unit (MGU). This approach, based on the mite life cycle and local skin turnover (the latter usually being ignored), allows the dermatologist to recognize not only Sarcoptes using the gallery, but also new descriptors including tunnels without Sarcoptes, those with acari alone, and those with associated signs of inflammation. The diagnosis of scabies using optical microscopy until recently has always involved demonstrating the mite and its products outside the human body (on a glass slide) without taking into account exactly what happens within the epidermis. Entodermoscopy is a term used to encapsulate both the presence of the parasite, the usual target of microscopy, and the changes produced in the superficial layers of the epidermis in situ. Thus, the scabies tunnel or burrow can be shown to be composed of three parts, the Head, Body, and Tail, in which different events affecting both mite and host develop. The Mite-Gallery Unit provides a new anatomical and functional explanation of scabies because it provides a more comprehensive in vivo and in situ dermatoscopic diagnosis. In this respect, dermatoscopy takes into account the behavior of the mite in addition to its interaction with its habitat, the human skin.

scholarly journals Integrative analysis of Zika virus genome RNA structure reveals critical determinants of viral infectivity

2018 ◽  
Author(s):  
Pan Li ◽  
Yifan Wei ◽  
Miao Mei ◽  
Lei Tang ◽  
Lei Sun ◽  
...  
Keyword(s):  
Zika Virus ◽  
Rna Structure ◽  
Intramolecular Interaction ◽  
Virus Genome ◽  
Structural Basis ◽  
Viral Infectivity ◽  
Structural Elements ◽  
Zikv Infection ◽  
Neurological Conditions

SUMMARYSince its outbreak in 2007, Zika virus (ZIKV) has become a global health threat that causes severe neurological conditions. Here we perform a comparativein vivostructural analysis of the RNA genomes of two ZIKV strains to decipher the regulation of their infection at the RNA level. Our analysis identified both known and novel functional RNA structural elements. We discovered a functional long-range intramolecular interaction specific for the Asian epidemic strains, which contributes to their infectivity. Our findings illuminate the structural basis of ZIKV regulation and provide a rich resource for the discovery of RNA structural elements that are important for ZIKV infection.

scholarly journals RNA structure probing reveals the structural basis of Dicer binding and cleavage

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Qing-Jun Luo ◽  
Jinsong Zhang ◽  
Pan Li ◽  
Qing Wang ◽  
Yue Zhang ◽  
...  
Keyword(s):  
Rna Structure ◽  
Structural Data ◽  
Spatial Distance ◽  
Structural Basis ◽  
Rna Structures ◽  
Structure Information ◽  
Functional Sites ◽  
Structure Probing ◽  
Rna Immunoprecipitation

AbstractIt is known that an RNA’s structure determines its biological function, yet current RNA structure probing methods only capture partial structure information. The ability to measure intact (i.e., full length) RNA structures will facilitate investigations of the functions and regulation mechanisms of small RNAs and identify short fragments of functional sites. Here, we present icSHAPE-MaP, an approach combining in vivo selective 2′-hydroxyl acylation and mutational profiling to probe intact RNA structures. We further showcase the RNA structural landscape of substrates bound by human Dicer based on the combination of RNA immunoprecipitation pull-down and icSHAPE-MaP small RNA structural profiling. We discover distinct structural categories of Dicer substrates in correlation to both their binding affinity and cleavage efficiency. And by tertiary structural modeling constrained by icSHAPE-MaP RNA structural data, we find the spatial distance measuring as an influential parameter for Dicer cleavage-site selection.

scholarly journals Construction of exchange integrated information chain management model leading by information nurse for large instrument and equipment in operating room

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jinghua Dai ◽  
Xiaoqiang Ren ◽  
Peng Wu ◽  
Xiangdong Wang ◽  
Jiang Li ◽  
...  
Keyword(s):  
Life Cycle ◽  
Life Cycle Management ◽  
Management Model ◽  
Control Group ◽  
Equipment Management ◽  
Observation Group ◽  
Chain Management ◽  
Information Chain ◽  
Whole Life Cycle ◽  
Running Mode

Abstract Background This study aims to explore the information chain management model of large instrument and equipment inter-working in the operating room (OR) led by information nurses. Methods Through the chain management process of large instruments and equipment in the OR, which was based on information nurses, the management model of inter-working and integrating information chain was established, the key links were controlled, and the whole life cycle management of instruments and equipment from expected procurement to scrapping treatment was realized. Using the cluster sampling method, 1562 surgical patients were selected. Among these patients, 749 patients were assigned to the control group before the running mode, and 813 patients were assigned to the observation group after the running mode. The related indexes for large instrument and equipment management in the department before and after the running mode were compared. Results In the observation group, the average time of equipment registration was (22.05 ± 2.36), the cost was reduced by 2220 yuan/year, and the satisfaction rate of the nursing staff was 97.62%. These were significantly better, when compared to the control group (P < 0.05). Furthermore, the awareness rate of the whole staff for equipment repair application was 95.12%, and the arrival time of maintenance personnel and the examination and approval time of equipment management were greatly shortened (P < 0.05). Conclusion The integrated management model of large instrument and equipment interworking in the OR based on chain flow realizes the whole life cycle management of instruments and equipment, which is essential to improve management efficiency.

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