HomeZebrafish Gene Editing Glossary

Zebrafish Gene Editing Glossary

In Vivo

Studies which are conducted in biological specimens such as cell culture or animals
models. An important experimental tool for disease research, drug discovery, and
understanding of animal development. Learn more about using zebrafish as an in vivo model.

Toxicity Studies

The testing of compounds or substances to determine their safety profile in living
organisms. Learn more about Toxicity Testing using zebrafish.

Fluorescent Tagging

Fluorescent tagging is used to aid in visualization of spatiotemporal dynamics of a given gene's protein product in live (and sometimes fixed) cells or whole animals. Zebrafish are an excellent model system for visualization of fluorescent proteins due to their clear tissues during early development. Learn about our fluorescent tagging services.

Model Organism

Non-human species whose genetics and development are well understood,  and can be maintained in laboratory settings. Zebrafish is an increasingly  popular model organism  because of its genetic similarity to humans and ease of breeding and maintenance. HERE is a quick overview of the zebrafish model. Learn about comparisons between other model organisms.

Transgenic Zebrafish

Transgenic zebrafish contain targeted DNA that has been introduced into their genome by genetic engineering techniques such as Tol2 or CRISPR.

Zebrafish CRISPR Injection Mix

CRISPR is a powerful technique that has revolutionized  genome editing across species. An easy way to get started using CRISPR reagents in zebrafish is through a pre-assembled injection mix containing all the desired components. Learn more about our services.

Genomic Data

The genome is an organism's DNA including all of its genes.  Genomic data refers to sequenced DNA from a human or model organism. To find specific zebrafish gene orthologs, visit the HElio search tool.

DNA Extraction

The procedure to extract DNA from cells or tissues for further analysis such as sequencing or PCR. The ZEG instrument is a new technology that allows for rapid extraction of DNA from live zebrafish embryos.

Proteins

Proteins are large biomolecules or macromolecules that are comprised of individual  amino acids. Zebrafish proteins can be distinguished starting from embryo stages with special tools.

Antibodies

Antibodies are specialized proteins  that  help fight viral or bacterial  infections. They are also very useful to study biological processes because they allow for visualization of protein location and dynamics in fixed tissues or cells. For proteins where no antibody exists CRISPR techniques present a visualization solution. Learn more about gene editing technologies to introduce epitope tags and fluorescent markers on proteins of interest.

Tol2 Transposon System

A technique used to create insertions in the zebrafish genome, especially large cargo. There are advantages and disadvantages of both the Tol2 system and CRISPR for gene editing.

Zebrafish genome comparison to humans

Zebrafish share 70% of human genes. Due to the similarity of organ development and function, they are widely used to model human diseases. Learn more about recent zebrafish discoveries.

Services

We offer a variety of o  zebrafish genome editing services utilizing the Tol2 system and CRISPR. Learn more.

Zebrafish Facts

Some key facts regarding zebrafish as a disease model:

  1. The sequencing of the zebrafish genome began in 2001.
  2. The current zebrafish reference genome assembly is GRCz11.
  3. The zebrafish is among the leading models to study developmental biology, cancer, toxicology, drug discovery, and molecular genetics.

Disease models

Animal disease models are often preferred for disease research because of their unlimited supply and ease of experimental manipulation. Zebrafish are well accepted as a tool to  study diseases and drive the discovery of therapeutics.

Knockout

Gene knockouts are a commonly used tool for scientists to understand gene function by the removal or alteration of a particular sequence of DNA. . These changes in the DNA can be created permanently in model systems and maintained through breeding schemes. Learn more about how to create a knockout zebrafish.

Microinjection

A technique to inject very small volumes of liquid via a fine glass needle into cells or tissues. Microinjection is a common technique used to create transgenic zebrafish lines. Learn more about our zebrafish services and capabilities.

Neurodegenerative disease zebrafish model

The zebrafish is a powerful model system to study diseases of the nervous system. It is now possible to create zebrafish containing specific patient genetic variants that are associated with disease.

CRISPR

Stands for Clustered Regularly Interspaced Short Palindromic Repeats. It is a simple and very powerful way to introduce precise changes in a genome of interest.

CRISPR Pros and Cons

There are many reasons to choose a CRISPR approach to gene editing, and you might be wondering about the strengths and weaknesses. Learn more about the CRISPR toolbox. Learn more if you want to evaluate a CRISPR approach to the zebrafish genome editing.

CRISPR Screening

CRISPR screening is a experimental approach designed to find the cells or animals in a population that are carrying the desired genetic edit.

CRISPR Edits

CRISPR technology can be used to create a wide range of genetic edits. These include knockouts, precise knock-ins, and protein tag knock-ins. Learn more.

CRISPR Off Target

Off target effects are nonspecific and unintended genetic modifications caused by CRISPR or other genetic engineering techniques.  To learn about how zebrafish can help eulcidate CRISPR off target activity, read this article.

Cas9

A critical component of the CRISPR engineering system. The Cas9 enzyme cuts the DNA at the targeted location effectively opening the genome up to either disrupt the region of interest, or create the location for the insertion of the precise repair template of interest. CRISPR genetic editing has been widely adopted by  zebrafish researchers to create precise models.

Endogenous tagging

Endogenous tagging enables a protein of interest to be visualized through fluorescence or an epitope marker. Creation of models with endogenous tags is possible using CRISPR gene editing.

Point mutation

A point mutation is a genetic mutation where a single nucleotide base is deleted, inserted or otherwise changed in DNA. Learn more about creation of point mutations in zebrafish.

LoxP

One of the more difficult aspects of biology is how to perform loss-of-function studies of essential genes. Using conditional mutagenesis by insertion of loxP sites creates "floxed" genes which are deletions of sequence in targeted loci. Learn more about Loxp in zebrafish and Loxp injection services.

GFP tagging

GFP (green fluorescent protein), is used to aid in visualization of spatiotemporal dynamics of a given gene's protein product in live (and sometimes fixed) animals.

CRO

Contract Research Organization.

sgRNA Validation

sgRNA stands for single guide RNA. sgRNA complexes with Cas9 protein to make double stranded cuts in target DNA sequences. Learn more about the our CRISPR Injection Mix with sgRNA validation.

PAM

Stands for the protospacer adjacent motif. It is a short DNA sequence of about 2-6 base pairs. adjacent to the DNA region targeted for cleavage by CRISPR-Cas9. Niemann Pick Type can slowly progressing lysosomal disorder characterized by the inability of cells to metabolize cholesterol and other lipids. It is caused by mutations in NCP1. Studies of Zebrafish NCP1 morphants display abnormal brain morphology and increased cell death.

ZEG Zebrafish Embryonic Genotyper

This instrument quickly and gently extracts genetic material from live zebrafish embryos in order to rapidly genotype individuals at early stages of development. Learn about this product and/or to purchase, click here:

Alagille syndrome zebrafish

Alagille syndrome is characterized as bile abnormally collecting in the liver leading to liver damage. New research on this disease has utilized zebrafish models to because of the high degree of genetic conservation with humans, and the ease of manipulation of the liver and associated organs.

Transgenesis

Transgenesis is the process of introducing a gene (also referred to as a transgene) from one organism into the genome of another organism. Learm more about zebrafish transgenesis services, check:

Zebrafish Plasmids

A small, extrachromosomal circular DNA molecule that can be introduced into cells. They typically carry specific cargo and often include antibiotic resistance genes and other markers. Tol2 plasmids in particular are useful for for zebrafish genetic engineering. Learn more about our services utilizing plasmid builds to create zebrafish transgenics , check out:

PCR master mix

A premixed concentrated solution of a regular PCR reaction. A master mix is an efficient way to set up multiple reactions at once. To purchase or learn more about PCR master mixes.

zGrad

A nanobody based system that inactivates proteins in zebrafish. (https://elifesciences.org/articles/43125)

Epitope Tagging

A technique in which a characterized epitope is fused to a protein of interest. By tagging a protein in this way it is possible to detect proteins for which no antibody is available. Learn about our Epitope Tagging services.

PCR Genotyping

A technique to identify the genotype of an organism by utilizing PCR to amplify a gene or region of interest. See PCR and its comparison with HRMA.

Knock-In

Insertion of a specific sequence into the genome. The location can be highly specific within a genetic locus. Learn more about our Knock-In services.

Stxbp1 Disorder

A disorder causing abnormal brain function and intellectual disability. Explore zebrafish stxbp1 models HERE.

Embryotoxicity

When a substance is introduced to an organism during embryonic stages, causing abnormal development or death. Learn more about a study involving zebrafish and rat embryotoxic.

Floxed Gene

Is the process of placing a specific DNA sequences between two LoxP sites, therefore positioning the sequences to be removed when Cre recombinase is expressed. Learn about zebrafish floxed services.

Gene Finder

An ortholog database tool using public data from Wormbase (C. elegans)  and ZFIN (D. rerio). Using CRISPR and other genome editing methods, we can create genetically engineered animal models for better understanding genetic mutations and disease biology discovery.

Cre recombinase

Promotes recombination of two loxP sites resulting in removal of the target region in the genome. Learn more about our services in zebrafish.

ssODN

Single-stranded oligo donors. It is utilized by CRISPR. Learn about the challenges of CRISPR in zebrafish.

Zebrafish Mutagenesis

Occurs when zebrafish DNA is altered by a genetic mutation either in the lab or by random occurrences in the environment. Learn about direct mutagenesis services for zebrafish.

Arginine

Is a specific amino acid related to pathogenicity. To learn more about arginine and its effects on models such as zebrafish.

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