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Vaccinia virus

Vaccinia virus is a large, complex DNA virus that belongs to the Orthopoxvirus genus.
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»

Our seven-cDNA-fragment approach has several key advantages over alternative methods, including bacterial artificial chromosomes, a vaccinia virus, and a yeast recombination-based assembly11 (link),19 (link) (See details below). First, it permits rapid generation of mutant and reporter viruses by manipulation of a smaller plasmid (i.e., the plasmid that contains the targeted mutation fragment), reducing the risk of off-target mutations or deletions being inadvertently incorporated into the recombinant virus. Second, this approach allows simultaneous manipulation of multiple mutations from different cDNA fragments. More than one mutation from different cDNA fragments can be engineered in parallel to make combinatory mutant viruses. Such flexibility is important when characterizing a combinatory effect of multiple viral elements on host immune response or developing a live-attenuated vaccine platform, which often requires multiple mutation sites to be investigated at the same time20 (link),21 (link). In addition, the seven-fragment system allows quick insertion of mutations that arise from sequencing of new clinical isolates or swapping of regions from related coronaviruses found in animals13 (link),22 (link). Collectively, the reverse genetic system offers a wealth of opportunities to explore and study SARS-CoV-2 infection and pathogenesis.
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.
Publication 2021
Bacterial Artificial Chromosomes Clone Cells Coronavirus COVID 19 DNA, Complementary Epidemics Gene Deletion Genitalia Genome Insertion Mutation Ligation Middle East Respiratory Syndrome Coronavirus Mutagenesis, Site-Directed Mutation pathogenesis Phenotype Plasmids Recombination, Genetic Response, Immune Saccharomyces cerevisiae SARS-CoV-2 Sepsis Severe acute respiratory syndrome-related coronavirus Vaccines, Attenuated Vaccinia virus Viral Components Virus

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Publication 2007
bacteriophage T7 RNA polymerase Centrifugation cesium chloride Chick Embryo Fibroblasts HeLa Cells L Cells Methionine Reoviridae Strains Vaccinia virus Virion Virus

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Publication 2009
Animals Biological Assay CD8-Positive T-Lymphocytes Cells Chimera Clone Cells Epitopes GZMB protein, human Institutional Animal Care and Use Committees Lymphocytic choriomeningitis virus Lymphoid Progenitor Cells Mus PRDM1 protein, human RAG-1 Gene Senile Plaques Strains Vaccinia virus
IC50 nM values for each mixture were standardized as a ratio to the geometric mean IC50 nM value of the entire set of 180 mixtures, and then normalized at each position as previously described [17 (link),18 (link)] so that the value associated with the optimal value at each position corresponds to 1. For each position, an average (geometric) relative binding affinity (ARB) was calculated, and then the ratio of the ARB for the entire library to the ARB for each position was derived. We have denominated this ratio, which describes the factor by which the normalized geometric average binding affinity associated with all 20 residues at a specified position differs from that of the average affinity of the entire library, as the specificity factor (SF). As calculated, positions with the highest specificity will have the highest SF value. Primary anchor positions were then defined as those associated with an SF > 2.4. This criterion identifies positions where the majority of residues are associated with significant decreases in binding capacity. Secondary anchors were identified based on the standard deviation of residue specific values at each position.
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)].
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Publication 2008
cDNA Library Peptides Vaccinia virus
A sequence-optimized mRNA encoding prefusion-stabilized SARS-CoV-2 S-2P protein was synthesized in vitro using an optimized T7 RNA polymerase-mediated transcription reaction with complete replacement of uridine by N1m-pseudouridine34 . The reaction included a DNA template containing the immunogen open-reading frame flanked by 5’ UTR and 3’ UTR sequences and was terminated by an encoded polyA tail. After transcription, the Cap 1 structure was added to the 5’ end using Vaccinia capping enzyme (New England Biolabs) and Vaccinia 2’O-methyltransferase (New England Biolabs). The mRNA was purified by oligo-dT affinity purification, buffer exchanged by tangential flow filtration into sodium acetate, pH 5.0, sterile filtered, and kept frozen at −20 °C until further use.
The mRNA was encapsulated in a lipid nanoparticle through a modified ethanol-drop nanoprecipitation process described previously20 (link). Briefly, ionizable, structural, helper, and PEG lipids were mixed with mRNA in acetate buffer, pH 5.0, at a ratio of 2.5:1 (lipids:mRNA). The mixture was neutralized with Tris-Cl, pH 7.5, sucrose was added as a cryoprotectant, and the final solution was sterile filtered. Vials were filled with formulated LNP and stored frozen at −70 °C until further use. The drug product underwent analytical characterization, which included the determination of particle size and polydispersity, encapsulation, mRNA purity, double stranded RNA content, osmolality, pH, endotoxin, and bioburden, and the material was deemed acceptable for in vivo study.
Publication 2020
3' Untranslated Regions Acetate Antigens bacteriophage T7 RNA polymerase Buffers Chromatography, Affinity Cryoprotective Agents DNA, A-Form Endotoxins Enzymes Ethanol Filtration Freezing Lipid Nanoparticles Lipids Methyltransferase oligo (dT) Pharmaceutical Preparations Poly(A) Tail Proteins RNA, Double-Stranded RNA, Messenger SARS-CoV-2 Sodium Acetate Strains Sucrose TRAF3 protein, human Transcription, Genetic Tromethamine Uridine Vaccinia virus

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 (FIG. 8). It was confirmed that the vaccinia virus expressing wild-type HSV1-TK had higher sensitivity to GCV than HSV1-TKmut inserted in OTS-412 and that the cancer cell killing effect was hardly observed due to the complete inhibition of viral replication.

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Patent 2024
Cells Cytotoxin HCT116 Cells Human Herpesvirus 1 Hypersensitivity Malignant Neoplasms Psychological Inhibition Vaccinia virus Virus Replication
Not available on PMC !

Example 2

A Flag tagged p27 encoding plasmids can be engineered to facilitate in vitro transcription of p27 encoding mRNA (FIG. 17): A) Flag-tagged p27); B) Flag-tagged p27 followed by two 2 fully complementary target sequences for the mature miR-126-3p strand at its 3′-UTR (p27-2x126TS). A Flag-tag can be incorporated to distinguish between endogenous and exogenous p27 expression.

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 FIG. 17, the following modified nucleotide substitutions or combinations thereof can be used: 1) Pseudouridine; 2) N-1-methylpseudouridine; 3) 5-methoxy-U; 4) 5-hydroxymethyl-C; 5) 5-methyl-C and 6) combination of Pseudouridine and 5-methyl-C. mRNAs can be in vitro transcribed using T7 RNA polymerase followed by 5′ capping and poly(A) tail addition using a Vaccinia Capping Enzyme and E. coli Poly(A)Polymerase (New England BioLabs Inc.), respectively.

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Patent 2024
bacteriophage T7 RNA polymerase Cells Enzymes Escherichia coli Genes, Duplicate Immunity, Innate Nucleotides Obstetric Delivery Plasmids Poly(A) Tail Polynucleotide Adenylyltransferase Pseudouridine RNA, Messenger Transcription, Genetic Vaccinia virus

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 (FIG. 5). As a result, when comparing the negative control group and the positive control group, four corresponding bands (arrows) and one mismatching band (dotted arrow) between 4 kb and 8 kb were identified. The mismatching band had a large gene size, which showed that the HSV1-TKmut gene and the firefly luciferase gene were inserted into the TK region of vaccinia virus. It was confirmed as a unique band pattern of OTS-412 different from that of the wild-type vaccinia virus. When the wild-type vaccinia virus and OTS-412 after several passages were compared with the control groups, the same band patterns as those of the respective control groups were observed, confirming that the HSV1-TKmut gene in OTS-412 had genetic stability.

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Patent 2024
Cells Deoxyribonuclease HindIII DNA DNA, A-Form DNA, Viral Electrophoresis Gene Expression Genes Genome Homo sapiens Human Herpesvirus 1 Luciferases, Firefly Osteosarcoma Reproduction Vaccinia virus Viral Genome Virus
Not available on PMC !

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.

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Patent 2024
austin Buffers DNA, Complementary Electrophoresis, Agar Gel Endoribonucleases Enzymes Magnesium Chloride Methyltransferase Polynucleotides Reverse Transcription RNA Degradation S-Adenosylmethionine Transferase Tromethamine Vaccinia virus
Not available on PMC !

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.

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Patent 2024
austin Buffers DNA, Complementary Electrophoresis, Agar Gel Endoribonucleases Enzymes Magnesium Chloride Methyltransferase Polynucleotides Reverse Transcription RNA Caps RNA Degradation S-Adenosylmethionine Transferase Tromethamine Vaccinia virus

Top products related to «Vaccinia virus»

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The Vaccinia Capping System is a laboratory tool used to add a 5' cap structure to RNA, a process known as capping. Capping is a crucial step in the synthesis of mRNA and helps protect the RNA from degradation and enhance translation efficiency. The system utilizes enzymes derived from the vaccinia virus to perform the capping reaction.
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The MEGACLEAR™ Kit is a nucleic acid purification system designed for the efficient extraction and purification of DNA, RNA, and other nucleic acids from a variety of sample types. The kit utilizes a simple, spin-column-based protocol to facilitate rapid and reliable purification of nucleic acids.
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The NanoDrop is a spectrophotometer designed for the quantification and analysis of small volume samples. It measures the absorbance of a sample and provides accurate results for DNA, RNA, and protein concentration measurements.
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Fetal Bovine Serum (FBS) is a cell culture supplement derived from the blood of bovine fetuses. FBS provides a source of proteins, growth factors, and other components that support the growth and maintenance of various cell types in in vitro cell culture applications.
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DMEM (Dulbecco's Modified Eagle's Medium) is a cell culture medium formulated to support the growth and maintenance of a variety of cell types, including mammalian cells. It provides essential nutrients, amino acids, vitamins, and other components necessary for cell proliferation and survival in an in vitro environment.
The Vaccinia Capping Enzyme is a recombinant enzyme that catalyzes the addition of a guanine nucleotide cap structure to the 5' end of mRNA transcripts. This enzyme is derived from the vaccinia virus and plays a crucial role in the viral mRNA capping process.
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T7 RNA polymerase is an enzyme that initiates and catalyzes the transcription of DNA to RNA. It is derived from the T7 bacteriophage and is commonly used in in vitro transcription systems to produce RNA from a DNA template.
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Lipofectamine 2000 is a cationic lipid-based transfection reagent designed for efficient and reliable delivery of nucleic acids, such as plasmid DNA and small interfering RNA (siRNA), into a wide range of eukaryotic cell types. It facilitates the formation of complexes between the nucleic acid and the lipid components, which can then be introduced into cells to enable gene expression or gene silencing studies.
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Ab35219 is a product offered by Abcam. It is a lab equipment item, but a detailed description of its core function cannot be provided while maintaining an unbiased and factual approach. Additional information about the intended use or interpretation of this product is not available.
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E. coli Poly(A) Polymerase is an enzyme isolated from Escherichia coli that catalyzes the addition of a poly(A) tail to the 3' end of RNA molecules.

More about "Vaccinia virus"

Vaccinia virus is a large, complex DNA virus that belongs to the Orthopoxvirus genus.
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.