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TypeBlog Post...Brenner, M. (2004). Expression specificity of GFAP transgenes. Neurochemical Research, 29(11 SPEC. ISS.), 2075...
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Antibodies 101: Multiplex Immunofluorescence
TypeBlog Post...interpret. Check out (Jambor et al., 2021) for more guidelines for creating clear and informative figures. Pro-tip... -
A Control for All Seasons
TypeBlog Post...Western blotting When comparing samples in different lanes in a western blot, you’ll need to include a loading... -
Plasmids 101: Restriction Cloning
TypeBlog Post... comb, run the gel on the slower side, and skip lanes between samples. In addition to a DNA ladder standard... -
9 tips for a successful postdoctoral experience
TypeBlog Post...of these decisions is complex, here are a few guidelines to help you evaluate projects: If all of your... -
Fluorescent Proteins 101: Monitoring Cell Mobility Using Fluorescent Proteins
TypeBlog Post...constructs have facilitated the creation of mouse lines that can be used in fate mapping experiments. Immune... -
Selecting Your Plasmid Purification Kit
TypeBlog Post...plasmid purification is always an option, let’s be honest — kits are quick, easy, and don’t involve phenol-chloroform... -
Optogenetics + CRISPR, Using Light to Control Genome Editing
TypeBlog Post...article). The group first tested photocaging various lysines in Cas9 to determine which best deactivated the... -
Lentiviral Vector Guide
TypeGuide...strand of RNA contains packaging genes, regulatory genes, accessory genes, and the long-terminal repeats...replicate. This feature can be harnessed for stable delivery of various genes, mutations, or treatments into...complex genomes, containing packaging genes and accessory genes specific to each virus type, while retroviruses...require the regulatory genes tat and rev , along with virus-specific accessory genes (for example, vif , ...Packaging plasmid — contains packaging genes gag and pol , and regulatory genes tat and rev ; separated into two... tools. Stable Cell Lines Lentiviral vectors can be used to make stable cell lines due to their integration...survive can be expanded to create stable cell lines. The cell lines will have the lentiviral genome and the ... -
Gamma-Retroviral Vector Guide
TypeGuide...replicate. This feature can be harnessed for stable delivery of various genes, mutations, or treatments into...the necessary packaging genes, while lentiviruses also contain accessory genes specific to each virus ...common packaging genes gag , pol , and env . The LTRs flank all of these required genes, and anything in...Packaging Cell Lines Gamma-retroviral vectors can be packaged using helper-free cell lines (Figure 3B). ...transgene. Stable Cell Lines Gamma-retroviral vectors are often used to make stable cell lines. Like their popular...survive can be expanded to create stable cell lines. The cell lines will have the gamma-retroviral genome and...proto-oncogenes. As with most experiments, infection risks occur with contact to mucous membranes or broken... -
Adenovirus Guide
TypeGuide... developed where more adenoviral genes have been removed. These genes are now supplied in trans , via ... the potential for insertional mutagenesis and the risk of oncogenesis. However, random integration events...Chimpanzee adenoviral vectors as vaccines for outbreak pathogens . Human Vaccines & Immunotherapeutics, 13 (...2015). Adenovirus-vectored Ebola vaccines . Expert Review of Vaccines, 14 (10), 1347–1357. https://doi.org...two inverted terminal repeats (ITRs). Adenoviral genes are divided into early (E1A, E1B, E2, E3, E4) and... Figure 1: Wild-type adenovirus and its genome. Genes over or under the line are in forward or reverse...related. AAVs require the presence of adenoviral genes E1, E4, E2a and VA for replication. For more information... -
CRISPR Guide
TypeGuide...repress, visualize, and isolate genes. Activation or Repression of Target Genes Figure 9: Overview of CRISPRi... and a user-defined ∼20-nucleotide spacer that defines the genomic target to be modified. You can therefore...CRISPR was originally employed to knock out target genes in various cell types and organisms, but modifications... ability to selectively activate/repress target genes, purify specific regions of DNA, image DNA in live...Multiplexing applications include editing multiple genes at once; using dual nickases to generate a knockout... used to knock out, activate, or repress target genes when paired with the appropriate Cas enzyme. Specific...CRISPR specificity. SpCas9 (from Streptococcus pyogenes ) is the most popular Cas endonuclease, with many... -
Adeno-associated virus (AAV) Guide
TypeGuide...related. AAVs require the presence of adenoviral genes E1, E4, E2a and VA for replication. For more information...capsids. Helper plasmid — containing adenoviral genes not present in the AAV genome required for viral...Additional production systems based on other human cell lines, such as HeLa and A549 cells, and even insect Sf9...purified for their use as viral vectors to deliver genes to cells in in vivo models. For more detailed protocols...vector production, rAAV vectors do not carry the genes to express Rep78 and Rep 68 proteins and are therefore...transgene expression and the expression of neighboring genes. rAAV episomes can develop chromatin-like organization...non-pathogenicity, ability to efficiently deliver genes to a wide range of tissues with minimal immune response... -
Molecular Biology Reference
TypeGuide...Protocols Origins of Molecular Genetics The concept of genes as carriers of phenotypic information was introduced...significant discoveries lead to the conclusions that genes encode proteins and reside on chromosomes, which...fragments of double-stranded DNA that typically carry genes and can replicate independently from chromosomal...used to study DNA fragments of interest, such as genes. Creation of recombinant DNA Molecular Cloning Plasmids...optimized for their use of studying and manipulating genes. For instance, most plasmids are replicated in E...information as the parental cell, and are thus termed clones of the original cell. The plasmid DNA is similarly...scientists to break chromosomes down to study their genes, marking the birth of molecular genetics. Today,... -
Antibody Guide
TypeGuide...performs a chemiluminescent reaction in the presence of several different substrates. The luminescence produced...Recombinant antibodies are created by cloning antibody genes from specific hybridoma cells into plasmids. Plasmids...region is a stable part of the antibody, which determines the isotype of the antibody. B cells, the immune...tears, saliva, mucus) where it protects mucosal membranes Dimer with a valency of 4 IgA1; IgA2 IgD Coexpressed... epitope, or polyclonal, meaning there are many clones that are specific to multiple epitopes on one antigen...Sodium azide, an antimicrobial agent, can block some amines needed for conjugation reactions and should be ... tubulin (sometimes referred to as housekeeping genes). This allows for relative comparison of expression... -
Guide to Using Pooled Libraries
TypeGuide... multiple genes at once. A well-designed screen can help you begin to understand what genes are important...genetic screening, or identifying previously unknown genes that contribute to a phenotype. At their simplest... backbone, but they express or target different genes. Some libraries cover the majority of the genome... if they are designed to cover only a subset of genes, or very large (e.g. the Toronto KnockOut (TKO) ...Sequence those cells that pass (“win”) Get a list of genes involved in the selection NEGATIVE screen: Apply...generally very robust, and tens of thousands of genes that were initially present may be narrowed down...screen, negative screens are often used to identify genes that are essential for growth/survival under certain... -
Promoters
TypeGuide...general transcription factor proteins and histones can bind. Histones are proteins found in eukaryotic cells...transcription of genes. There are three types of RNA polymerases that all transcribe different genes. RNA polymerase...like operons. Operons are a cluster of different genes that are controlled by a single promoter and operator...repressor or activator can bind, and the structural genes that are transcribed together. Operon regulation...polymerase I transcribes genes encoding ribosomal RNA (rRNA) which is a main component of a cell’s ribosome...translation of a protein. RNA polymerase III transcribes genes encoding transfer RNAs (tRNA), the adaptor molecules... -
Plan Your Experiment
TypeGuide...more effective than dCas9 alone for mammalian cell lines. Activate (CRISPRa) Increase expression of an endogenous...cells, or selection marker to generate stable cell lines (for details, see Plasmids 101: Mammalian Vectors...and/or gRNA in a wide variety of mammalian cell lines Useful for difficult to transfect cell types, can...Protocol for genomic deletions in mammalian cell lines Select Your Target Sequence and Design Your gRNA...subcloning into a plasmid, and screening individual clones. PCR amplification and next-generation sequencing... -
Chemogenetics Guide
TypeGuide... PSAM plasmids ! LMOs Luminopsins (LMOs), or luminescent opsins, are opto-chemogenetic fusion proteins... LMOs a versatile option. Coupling brighter bioluminescent modules, such as luciferase-fluorescent protein... a single molecule driven by FRET-modified bioluminescence. Neurophotonics. 11:021005. PMID: 38450294 ...Manipulation for Ameliorating Huntington's Disease Pathogenesis. iScience , in press. Magnus CJ, Lee PH, Atasoy...Inhibitory luminopsins: genetically-encoded bioluminescent opsins for versatile, scalable, and hardware-independent... -
Optogenetics Guide
TypeGuide... chimera 470 ChIEF, ChEF, ChD Engineered by chimeragenesis of ChR1 and ChR2 450-470 C1V1 ChR1-VChR1 chimera...injection site. Optical Switches Researchers have harnessed plant and bacterial photoreceptors to create protein...improve upon previous tools through directed mutagenesis - use Addgene's Optical Switch Plasmid Table ... sequester and release proteins from cellular membranes using light. light-induced protein dissociation...