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Mechanical Fractionation of Cultured Neuronal Cells into Cell Body and Neurite Fractions

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Colorimetric RT-LAMP and LAMP-sequencing for Detecting SARS-CoV-2 RNA in Clinical Samples

Authors: Konrad Herbst, Matthias Meurer, Daniel Kirrmaier, Simon Anders, Michael Knop and Viet Loan Dao Thi, date: 03/20/2021, view: 1141, Q&A: 0

[Abstract]

During pandemics, such as the one caused by SARS-CoV-2 coronavirus, simple methods to rapidly test large numbers of people are needed. As a faster and less resource-demanding alternative to detect viral RNA by conventional qPCR, we used reverse transcription loop-mediated isothermal amplification (RT-LAMP). We previously established colorimetric

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RI-SEC-seq: Comprehensive Profiling of Nonvesicular Extracellular RNAs with Different Stabilities

Authors: Juan Pablo Tosar, Fabiana Gámbaro, Mauricio Castellano and Alfonso Cayota, date: 02/20/2021, view: 1198, Q&A: 0

[Abstract]

Exosomes and other extracellular vesicles (EVs) are considered the main vehicles transporting RNAs in extracellular samples, including human bodily fluids. However, a major proportion of extracellular RNAs (exRNAs) do not copurify with EVs and remain in ultracentrifugation supernatants of cell-conditioned medium or blood serum. We have observed

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Colorimetric RT-LAMP Methods to Detect Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Authors: Gun-Soo Park, Seung-Hwa Baek, Keunbon Ku, Seong Jun Kim, Seung Il Kim, Bum-Tae Kim and Jin-Soo Maeng, date: 11/05/2020, view: 1904, Q&A: 0

[Abstract] Standard diagnostic methods of Coronavirus Disease 2019 (COVID-19) rely on RT-qPCR technique which have limited point-of-care test (POCT) potential due to necessity of dedicated equipment and specialized personnel. LAMP, an isothermal nucleic acid amplification test (NAAT), is a promising technique that may substitute RT-qPCR for POCT of genomic ...

A Protocol for Simple, Rapid, and Direct Detection of SARS-CoV-2 from clinical samples, using Reverse Transcribed Loop-Mediated Isothermal Amplification (RT-LAMP)

Authors: Rawi Naddaf, Nadav Ben-Assa, Tal Gefen, Tal Capucha, Haitham Hajjo, Noa Mandelbaum, Lilach Elbaum, Shai Kaplan, Assaf Rotem, Michal Chowers, Moran Szwarcwort-Cohen, Mical Paul and Naama Geva-Zatorsky, date: 10/20/2020, view: 1712, Q&A: 0

[Abstract] SARS-CoV-2 has quickly spread all around the globe causing illness and wide damages. Most countries were unprepared for such a rapid spread and crisis. This led to various strategies for effective control of the new pandemic. A key aspect in all countries was to effectively test the population for the virus. Most countries chose a lockdown ...

Using RNA Sequencing and Spike-in RNAs to Measure Intracellular Abundance of lncRNAs and mRNAs

Authors: Megan D. Schertzer, McKenzie M. Murvin and J. Mauro Calabrese, date: 10/05/2020, view: 1412, Q&A: 0

[Abstract] Long noncoding RNAs (lncRNAs) play essential roles in normal physiology and in disease but their mechanisms of action can be challenging to identify. For mechanistic studies, it is often useful to know a lncRNA’s intracellular abundance, i.e., approximately how many molecules of the lncRNA are present in a typical cell of a cell-type of ...

Screening Method for CRISPR/Cas9 Inhibition of a Human DNA Virus: Herpes Simplex Virus

Authors: Werner M. Neuhausser, Hyung S. Oh, Pierce Eggan, Magdalena Angelova, Rory Kirchner, Kevin C. Eggan and David M. Knipe, date: 09/05/2020, view: 2617, Q&A: 0

[Abstract] The efficiency of cleavage of individual CRISPR/Cas9-sgRNAs remains difficult to predict based on the CRISPR target sequence alone. Different intracellular environments (dependent on cell type or cell cycle state for example) may affect sgRNA efficiency by altering accessibility of genomic DNA through DNA modifications such as epigenetic marks and ...

Paper Lateral Flow Biosensor for Nodavirus Reverse Transcribed RNA Detection

Authors: Dimitra K. Toubanaki and Evdokia Karagouni, date: 08/05/2020, view: 1226, Q&A: 0

[Abstract] Paper nanobiosensors have been established as an excellent platform for analysis of veterinary and human pathogens causing various diseases. Especially, lateral flow assays or biosensors ideal for sensitive, rapid, robust and accurate analysis in laboratory setups and on-site analysis. Viral RNA detection is of great importance for public health ...

Confocal and Super-resolution Imaging of RNA in Live Bacteria Using a Fluorogenic Silicon Rhodamine-binding Aptamer

Authors: Regina Wirth, Peng Gao, G. Ulrich Nienhaus, Murat Sunbul and Andres Jäschke, date: 05/05/2020, view: 4051, Q&A: 0

[Abstract] Genetically encoded light-up RNA aptamers have been shown to be promising tools for the visualization of RNAs in living cells, helping us to advance our understanding of the broad and complex life of RNA. Although a handful of light-up aptamers spanning the visible wavelength region have been developed, none of them have yet been reported to be ...

Viral Double-Stranded RNA Detection by DNase I and Nuclease S1 digestions in Leishmania parasites

Authors: Nathalie Isorce and Nicolas Fasel, date: 05/05/2020, view: 1721, Q&A: 0

[Abstract] Many RNA viruses are found in protozoan parasites. They can be responsible for more serious pathology or treatment failure. For the detection of viral double-stranded RNA (dsRNA), sequence-dependent and -independent methods are available, such as quantitative real-time PCR and immunofluorescence, dot blot, ELISA or sequencing. The technique ...

Real-time Fluorescence Measurement of Enterovirus Uncoating

Authors: Visa Ruokolainen, Mira Laajala and Varpu Marjomäki, date: 04/05/2020, view: 1587, Q&A: 0

[Abstract] Viruses need to open, i.e., uncoat, in order to release their genomes for efficient replication and translation. Especially for non-enveloped viruses, such as enteroviruses, the cues leading to uncoating are less well known. The status of the virus has previously been observed mainly by transmission electron microscopy using negative ...

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