Although the in vitro ligation approach allows rapid preparation of mutant and reporter viruses, the requirement to assemble and transcribe genome-length RNA requires technical expertise. Alternative coronavirus reverse genetic systems have used bacterial artificial chromosomes, a vaccinia virus, and a yeast recombination-based assembly11 (link),19 (link). These alternate systems offer less assembly requirements, but are more prone to potential off-target mutations due to the use of larger size of viral cDNA and the need for amplification in host cells. Besides our SARS-CoV-2 infectious cDNA clone3 (link), a yeast-based platform and a similar multiple plasmid approach have been shown to produce recombinant SARS-CoV-219 (link),23 (link). The yeast platform required screening of several clones to identify virus equivalent to the original clinical isolate19 (link). In contrast, both of the cDNA-fragment-based approaches yielded production of recombinant SARS-CoV-2 equivalent to the clinical isolate. These results are consistent with the previously characterized phenotypes of the epidemic SARS-CoV and MERS-CoV isolates as compared to their recombinant versions5 (link),15 (link). The fidelity to the clinical isolate of SARS-CoV-2 is an important advantage of these multiple plasmid infectious clone systems.
Vaccinia virus
It is commonly used as a vaccine to prevent smallpox, a serious and contagious disease.
Vaccinia virus has a wide host range and can infect a variety of mammalian cells, making it a valuable tool for research into viral replication, host-pathogen interactions, and the development of new therapies.
Researchers can leverage PubCompare.ai's powerful features to optimize their Vaccinia virus studies, including identifying the most effective protocols and products from the literature, preprints, and patents.
This AI-driven comparison tool can enhance the reproducibilty and accuaracy of Vaccinia virus research, helping scientists make more informed decisions and advance the field.
Most cited protocols related to «Vaccinia virus»
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To identify predicted binders, all possible 9-mer peptides in vaccinia WR sequences were scored using the matrix values, where the final score for each peptide represents the product of the matrix value for the corresponding residue at each position. Algorithms derived by combining positional scanning combinatorial library and individual peptide data sets were generated using the stabilized matrix method (SMM) approach, as previously described [56 (link)].
Most recents protocols related to «Vaccinia virus»
Example 5
To determine whether cytotoxicity of OTS-412 was maintained despite the inhibition of OTS-412 virus replication by GCV, the cytotoxicity between the following groups was compared: groups treated with the wild type HSV1-TK-expressing vaccinia virus, alone or in combination with GCV, and groups treated with OTS-412, alone or in combination with GCV. Specifically, HCT-116 cancer cells were treated with 0.05 MOI (0.05 pfu/cell) of wild type HSV1-TK-expressing vaccinia virus or OTS-412, alone or in combination with GCV (50 μg). The resulting cells were cultured for 72 hours and analyzed for cytotoxicity using CCK8 (Cell Counting Kit 8).
As a result, the cytotoxicity of OTS-412 and GCV combined treatment was maintained at 95% or more of OTS-412 single treated group whereas the vaccinia virus expressing wild-type HSV1-TK showed almost no cytotoxicity (
Example 2
A Flag tagged p27 encoding plasmids can be engineered to facilitate in vitro transcription of p27 encoding mRNA (
To reduce innate immune responses and toxicity and at the same time maximize the efficiency and duration of expression of the mRNA encoding p27 described in
Example 3
To confirm the introduction of the HSV1-TKmut gene expression in OTS-412, wild type vaccinia virus and OTS-412 were identified by restriction enzyme mapping. After respectively infecting the wild-type vaccinia virus and OTS-412 into human osteosarcoma cells, the viruses were isolated and viral genomic DNAs were extracted to obtain a negative control (Wild type-VV) and a positive control (OTS-412).
The obtained viral DNAs were digested with HindIII restriction enzyme (10 units/2.5 μg) and separated by size using a DNA electrophoresis apparatus (
Example 4
Capping of a polynucleotide can be performed with a mixture includes: IVT RNA μg-180 μg and dH2O up to 72 μl. The mixture can be incubated at 65° C. for 5 minutes to denature RNA, and then can be transferred immediately to ice.
The protocol can then involve the mixing of 10× Capping Buffer (0.5 M Tris-HCl (pH 8.0), 60 mM KCl, 12.5 mM MgCl2) (10.0 IA); 20 mM GTP (5.0 IA); 20 mM S-Adenosyl Methionine (2.5 μl); RNase Inhibitor (100 U); 2′-O-Methyltransferase (400U); Vaccinia capping enzyme (Guanylyl transferase) (40 U); dH2O (Up to 28 μl); and incubation at 37° C. for 30 minutes for 60 μg RNA or up to 2 hours for 180 μg of RNA.
The polynucleotide can then be purified using Ambion's MEGACLEAR™ Kit (Austin, TX) following the manufacturer's instructions. Following the cleanup, the RNA can be quantified using the NANODROP™ (ThermoFisher, Waltham, MA) and analyzed by agarose gel electrophoresis to confirm the RNA is the proper size and that no degradation of the RNA has occurred. The RNA product can also be sequenced by running a reverse-transcription-PCR to generate the cDNA for sequencing.
Example 5
Capping of a RNA polynucleotide is performed as follows where the mixture includes: IVT RNA 60 μg-180 μg and dH2O up to 72 μl. The mixture is incubated at 65° C. for 5 minutes to denature RNA, and then is transferred immediately to ice.
The protocol then involves the mixing of 10× Capping Buffer (0.5 M Tris-HCl (pH 8.0), 60 mM KCl, 12.5 mM MgCl2) (10.0 μl); 20 mM GTP (5.0 μl); 20 mM S-Adenosyl Methionine (2.5 μl); RNase Inhibitor (100 U); 2′-O-Methyltransferase (400U); Vaccinia capping enzyme (Guanylyl transferase) (40 U); dH2O (Up to 28 μl); and incubation at 37° C. for 30 minutes for 60 μg RNA or up to 2 hours for 180 μg of RNA.
The RNA polynucleotide may then be purified using Ambion's MEGACLEAR™ Kit (Austin, TX) following the manufacturer's instructions. Following the cleanup, the RNA may be quantified using the NANODROP™ (ThermoFisher, Waltham, MA) and analyzed by agarose gel electrophoresis to confirm the RNA polynucleotide is the proper size and that no degradation of the RNA has occurred. The RNA polynucleotide product may also be sequenced by running a reverse-transcription-PCR to generate the cDNA for sequencing.
Top products related to «Vaccinia virus»
More about "Vaccinia virus"
Also known as smallpox vaccine, it is commonly used as a preventative measure against the serious and highly contagious smallpox disease.
This versatile virus has a wide host range, allowing it to infect a variety of mammalian cells, making it a valuable tool for researchers studying viral replication, host-pathogen interactions, and the development of new therapies.
Researchers can leverage the powerful features of PubCompare.ai to optimize their Vaccinia virus studies.
This AI-driven comparison tool can help identify the most effective protocols and products from the literature, preprints, and patents, enhancing the reproducibility and accuracy of Vaccinia virus research.
By comparing and analyzing data from various sources, scientists can make more informed decisions and advance the field.
Key aspects of Vaccinia virus research include the Vaccinia Capping System, which is used to cap the 5' end of mRNA, ensuring proper processing and translation.
The MEGACLEAR™ Kit can be used for high-yield purification of Vaccinia virus from cell culture.
The NanoDrop spectrophotometer is a common tool for quantifying the concentration of Vaccinia virus DNA or RNA samples.
Fetal Bovine Serum (FBS) and Dulbecco's Modified Eagle Medium (DMEM) are often used as culture media for Vaccinia virus propagation.
The Vaccinia Capping Enzyme is a crucial component in the Vaccinia Capping System, while T7 RNA polymerase is used to transcribe Vaccinia virus genes in in vitro systems.
Lipofectamine 2000 is a transfection reagent that can be used to introduce Vaccinia virus genetic material into host cells.
The Ab35219 antibody is a specific marker for Vaccinia virus infection.
Researchers may also utilize E. coli Poly(A) Polymerase to add poly(A) tails to Vaccinia virus mRNA transcripts.
By integrating these key aspects of Vaccinia virus research, scientists can leverage the power of PubCompare.ai to optimize their studies, leading to more reproducible and accurate findings that advance our understanding of this important virus and its potential applications.