In Vivo

Studies performed within a living organism, such as cell cultures, animal models, or whole organisms. Zebrafish, as an in vivo model, offer unparalleled opportunities for disease research, drug discovery, and understanding developmental biology due to their transparency and rapid development. Learn more about zebrafish’s in vivo applications.

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. 

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.

Zebrafish Facts

Some key facts regarding zebrafish as a disease model:

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

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.

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.

HDR (Homology Directed Repair)

A precise DNA repair mechanism used by cells to fix double-strand breaks by using a homologous DNA template. In zebrafish gene editing, HDR is employed to introduce specific genetic changes, such as knockins, point mutations, or fluorescent tags. HDR is highly efficient during early embryonic stages when cells are actively dividing.

NHEJ (Non-Homologous End Joining)

A DNA repair pathway that fixes double-strand breaks without requiring a homologous template. NHEJ is faster but less precise than HDR, often leading to small insertions or deletions (indels) at the repair site. In zebrafish research, NHEJ is commonly used for creating gene knockouts by disrupting gene function.

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.

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.

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.

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.

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.

sgRNA

sgRNA stands for single guide RNA. sgRNA complexes with Cas9 protein to make double stranded cuts in target DNA sequences. 

CRISPR/Cas9

CRISPR/Cas9 technology can be used to create a wide range of genetic edits. These include knockouts, precise knockins, and protein tag knockins. Learn more.

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.

Knockin

Insertion of a specific sequence into the genome. The location can be highly specific within a genetic locus.

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.

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 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.

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.

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.

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.

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.

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.

Transgenesis

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

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 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. 

Transgenic Zebrafish

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

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.

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. 

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.

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.

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.

PCR Genotyping

A technique to identify the genotype of an organism by utilizing PCR to amplify a gene or region of interest. 

Zebrafish Knockdown

A genetic technique used to temporarily reduce the expression of a gene, often achieved through morpholinos or RNA interference.

Morpholino Oligonucleotides

Synthetic molecules used to block the translation of specific mRNA sequences in zebrafish, enabling gene function studies.