• Proteins
  • Mouse models carrying mutations for the nine Usher-associated genes have splayed stereocilia, and some show delayed maturation of ribbon synapses suggesting these proteins may play different roles in terminal differentiation of auditory hair cells. (biomedsearch.com)
  • This gene encodes a member of the fascin family of actin-binding proteins. (cancerindex.org)
  • The expression of odontogenesis-related genes, and the calcification of the mDE6 cells were reduced by the inhibition of phosphorylated Smad1/5 (p-Smad1/5) and phosphorylated Akt (p-Akt) proteins. (nih.gov)
  • The expression of bone morphogenetic proteins (BMPs) bmp2b (Figure 4C and D) and bmp4 (Figure 4G and H) were similar in both def6 morphants and wild-type siblings, indicating that knockdown of def6 did not affect ventral cell fate specification. (nih.gov)
  • Proteins called 'CRISPR-associated genes' (cas genes) encode cellular machinery that cuts exogenous DNA into small fragments and inserts them into a CRISPR repeat locus. (wikipedia.org)
  • This makes them a particularly attractive system for testing the ectopic activity of gene products and loss-of-function experiments using antagonizing reagents such as morpholinos, dominant-negatives and neomorphic proteins. (wikipedia.org)
  • Coregulator - Transcription coregulators are proteins that work with transcription factors to regulate gene expression. (wikipedia.org)
  • RNA has been largely investigated within its role as an intermediary in the translation of genes into proteins. (wikipedia.org)
  • In 1987, Plant Genetic Systems (Ghent, Belgium), founded by Marc Van Montagu and Jeff Schell, was the first company to genetically engineer insect-resistant (tobacco) plants by incorporating genes that produced insecticidal proteins from Bacillus thuringiensis (Bt). (wikipedia.org)
  • While RNA interference relies on cellular components for efficacy (e.g. the Dicer proteins, the RISC complex) a simple alternative for gene knockdown is Morpholino antisense oligos. (wikipedia.org)
  • These recruited proteins are then responsible for the subsequent activation of other downstream proteins, including protein kinases (IKKi, IRAK1, IRAK4, and TBK1) that further amplify the signal and ultimately lead to the upregulation or suppression of genes that orchestrate inflammatory responses and other transcriptional events. (wikipedia.org)
  • genetics
  • While the name "behavioural genetics" connotes a focus on genetic influences, the field broadly investigates genetic and environmental influences, using research designs that allow removal of the confounding of genes and environment. (wikipedia.org)
  • Do not confuse with the genetics definition of Candidate gene. (wikipedia.org)
  • Morpholinos are used as research tools for reverse genetics by knocking down gene function. (wikipedia.org)
  • Inferring a gene's function by applying genetic perturbations to knock down or knock out a gene and studying the resulting phenotype is known as reverse genetics. (wikipedia.org)
  • Perturb-seq is a reverse genetics approach that allows for the investigation of phenotypes at the level of the transcriptome, to elucidate gene functions in many cells, in a massively parallel fashion. (wikipedia.org)
  • Reverse genetics is a method that is used to help understand the function of a gene by analyzing the phenotypic effects of specific engineered gene sequences. (wikipedia.org)
  • There are several different methods of reverse genetics: Site-directed mutagenesis is a sophisticated technique that can either change regulatory regions in the promoter of a gene or make subtle codon changes in the open reading frame to identify important amino residues for protein function. (wikipedia.org)
  • specific genes
  • Another technology made possible by prokaryotic genome manipulation is the use of transcription activator-like effector nucleases (TALENs) to target specific genes. (wikipedia.org)
  • RNAi is a valuable research tool, both in cell culture and in living organisms, because synthetic dsRNA introduced into cells can selectively and robustly induce suppression of specific genes of interest. (wikipedia.org)
  • It interferes with the expression of specific genes with complementary nucleotide sequences by degrading mRNA after transcription, preventing translation. (wikipedia.org)
  • The Perturb-seq protocol uses CRISPR technology to inactivate specific genes and DNA barcoding of each guide RNA to allow for all perturbations to be pooled together and later deconvoluted, with assignment of each phenotype to a specific guide RNA. (wikipedia.org)
  • siRNA
  • The contributions of each system were investigated by a knockdown approach utilizing siRNA injections. (biomedsearch.com)
  • Small interfering RNA (siRNA) technique was performed to silence fascin1. (cancerindex.org)
  • Currently, the most common technique for performing gene knockdown is small interfering RNA (siRNA). (broadinstitute.org)
  • This suggests C2c2 could represent an alternate approach to siRNA, complementing the specificity and simplicity of CRISPR-based DNA editing and offering researchers adjustable gene "knockdown" capability using RNA. (broadinstitute.org)
  • Binding can occur either through the blocking of transcription (in the case of gene-binding), the degradation of the mRNA transcript (e.g. by small interfering RNA (siRNA)) or RNase-H dependent antisense), or through the blocking of either mRNA translation, pre-mRNA splicing sites, or nuclease cleavage sites used for maturation of other functional RNAs, including miRNA (e.g. by morpholino oligos or other RNase-H independent antisense). (wikipedia.org)
  • Gene knockdown by this method is achieved by introducing small double-stranded interfering RNAs (siRNA) into the cytoplasm. (wikipedia.org)
  • Morpholinos are synthetic oligonucleotides that can be used to inhibit nuclear RNA splicing or mRNA translation and are the common gene inhibition reagent in Xenopus as neither siRNA or miRNA have yet been shown to reproducibly function in frog embryos. (wikipedia.org)
  • Since in principle any gene can be knocked down by a synthetic siRNA with a complementary sequence, siRNAs are an important tool for validating gene function and drug targeting in the post-genomic era. (wikipedia.org)
  • siRNA is also similar to miRNA, however, miRNAs are derived from shorter stemloop RNA products, typically silence genes by repression of translation, and have broader specificity of action, while siRNAs typically work by cleaving the mRNA before translation, and have 100% complementarity, thus very tight target specificity. (wikipedia.org)
  • Gene knockdown by transfection of exogenous siRNA is often unsatisfactory because the effect is only transient, especially in rapidly dividing cells. (wikipedia.org)
  • Polymerase Chain Re
  • Commonly made in the laboratory by solid-phase chemical synthesis, these small bits of nucleic acids can be manufactured as single-stranded molecules with any user-specified sequence, and so are vital for artificial gene synthesis, polymerase chain reaction (PCR), DNA sequencing, library construction and as molecular probes. (wikipedia.org)
  • Tumor
  • Microarray of frataxin-deficient Schwann cells demonstrated strong activations of inflammatory and cell death genes including interleukin-6 and Tumor Necrosis Factor which were confirmed at the mRNA and protein levels. (biomedsearch.com)
  • Furthermore, angiogenesis was detected in 27% of zebrafish injected with control cells, whereas only 12.5% of fish receiving knockdown cells showed the formation of new vessels, suggesting a role for calpain 2 in tumor cell angiogenesis. (zfin.org)
  • oligos
  • Morpholino oligos were conceived by Summerton (Gene Tools) at AntiVirals Inc. (now Sarepta Therapeutics) and originally developed in collaboration with Weller. (wikipedia.org)
  • phenotypic
  • First, we analyze a medium scale dataset that looks at perturbation effects of the pluripotency regulator Nanog in murine embryonic stem cells.We also show how phenotypic patterning allows for extensive comparison and identification of high impact knockdown targets.The novel functionality implemented in Arena3D enables effective understanding and comparison of temporal patterns within morphological layers, to help with the system-wide analysis of dynamic processes. (nih.gov)
  • Gene expression levels or other measures can be loaded and visualized at different time points and phenotypic comparison is facilitated through clustering and correlation display or highlighting of impacting changes through time. (nih.gov)
  • We also show how phenotypic patterning allows for extensive comparison and identification of high impact knockdown targets. (nih.gov)
  • A form of gene action, epistasis can either be additive or multiplicative in its effects on specific phenotypic traits. (wikipedia.org)
  • RNAs
  • RNAs are the direct products of genes, and these small RNAs can bind to other specific messenger RNA (mRNA) molecules and either increase or decrease their activity, for example by preventing an mRNA from being translated into a protein. (wikipedia.org)
  • Techniques for targeting Morpholinos to RNAs and delivering Morpholinos into cells have recently been reviewed in a journal article and in book form. (wikipedia.org)
  • double-stranded
  • Knockout libraries perturb genes through double stranded breaks that prompt the error prone non-homologous end joining repair pathway to introduce disruptive insertions or deletions. (wikipedia.org)
  • phenotype
  • A line chart of timeline evolution of knockdown values for each phenotype can be obtained by clicking on a particular node of interest, as shown for genes incenp and ranbp3, both of which display increasingly higher signal for the phenotype 'polylobed' (green line) throughout the time course. (nih.gov)
  • The ability to analyze the loss-of-function phenotype allows analysis of gene function when there is no access to mutant alleles. (wikipedia.org)
  • The resulting phenotype may reflect the normal function of the gene. (wikipedia.org)
  • Morpholino
  • A Morpholino, also known as a Morpholino oligomer and as a phosphorodiamidate Morpholino oligomer (PMO), is a type of oligomer molecule (colloquially, an oligo) used in molecular biology to modify gene expression. (wikipedia.org)
  • Deletion
  • This might entail 'knocking in' recombinase sites (such as lox or frt sites) that will cause a deletion at the gene of interest when a specific recombinase (such as CRE, FLP) is induced. (wikipedia.org)
  • Complementary
  • A complementary technology uses catalytically dead Cas9 (usually denoted dead Cas9 or dCas9) lacking endonuclease activity to regulate genes in an RNA-guided manner. (wikipedia.org)
  • knockout
  • Unique among plants, in Physcomitrella patens, gene knockout via homologous recombination to create knockout moss (see figure) is nearly as efficient as in yeast. (wikipedia.org)
  • mutations
  • Mutations in the frataxin gene cause dorsal root ganglion demyelination and neurodegeneration, which leads to Friedreich's ataxia. (biomedsearch.com)
  • Cis-dominant - mutations (e.g., of an operator) that alter the functioning of genes on that same piece of DNA. (wikipedia.org)
  • This is accomplished by introducing point mutations in the two catalytic residues (D10A and H840A) of the gene encoding Cas9. (wikipedia.org)
  • This is a method that combines a standard and efficient technique of mutagenesis with a chemical mutagen such as ethyl methanesulfonate (EMS) with a sensitive DNA-screening technique that identifies point mutations in a target gene. (wikipedia.org)
  • transcripts
  • The microarray assay indicates that transcripts of genes with functions related to immunity and reduction-oxidation (redox) reactions are up-regulated in Ae. (biomedsearch.com)
  • The primary transcripts from such genes are first processed to form the characteristic stem-loop structure of pre-miRNA in the nucleus, then exported to the cytoplasm. (wikipedia.org)
  • perturbation
  • Baseline - a measure of the gene expression level of a gene or genes prior to a perturbation in an experiment, as in a negative control. (wikipedia.org)
  • Upon completion of the protocol, bioinformatics analyses are conducted to associate each specific cell and perturbation with a transcriptomic profile that characterizes the consequences of inactivating each gene. (wikipedia.org)
  • silence
  • In particular, methods used to silence genes are being increasingly used to produce therapeutics to combat cancer and diseases, such as infectious diseases and neurodegenerative disorders. (wikipedia.org)
  • induce
  • Tb4 may increase RUNX2 expression to induce the expression of odontogenesis-related genes in the mDE6 cells. (nih.gov)
  • However, little is known as to whether upregulated Tb4 can induce the expression of odontogenesis-related genes, such as Amelx, Ambn and Enam, without the expression of Runx2, and of the association between Tb4 and other signaling pathways upstream of Runx2 expression. (nih.gov)
  • encodes
  • It arises because the operator represents a site on the DNA rather than a gene that encodes a product. (wikipedia.org)
  • promoter
  • In this study we found that Slug-silenced cells changed in morphology, decreased in their migration ability, increased Sox9 and Sox5 and decreased Sox6 and STAT1 expression.On the contrary, the effect of Slug depletion on Runx2 was influenced by cell type.Interestingly, we demonstrated a direct in vivo regulatory action of Slug by chromatin immunoprecipitation, showing a specific recruitment of this TF in the promoter of Runx2 and Sox9 genes. (nih.gov)
  • The sgRNA expression vector design will depend largely on the experiment performed but requires the following central components: Promoter Restriction sites Primer Binding Sites sgRNA Guide Barcode Reporter gene: Fluorescent gene: vectors are often constructed to include a gene encoding a fluorescent protein, such that successfully transduced cells can be visually and quantitatively assessed by their expression. (wikipedia.org)
  • Transcription
  • Corepressor - A protein that reduces (represses) the expression of genes by binding to and activating a repressor transcription factor. (wikipedia.org)
  • Gene expression - the transcription of DNA into messenger RNA by RNA polymerase. (wikipedia.org)
  • For example, the well-studied Krüppel associated box (KRAB) domain can be fused to dCas9 to repress transcription of the target gene up to 99% in human cells. (wikipedia.org)
  • Identification of the transcription start site of a target gene and considering the preferences of sgRNA improves efficiency, as does the presence of accessible chromatin at the target site. (wikipedia.org)
  • Nodes
  • Nodes correspond to gene knockdown events and are colored according to the scoring scale, as indicated (white-dark red, low-high). (nih.gov)
  • The vertices (nodes) are represented by various regulatory elements and gene products while the edges (links) are represented by their interactions. (wikipedia.org)
  • cells
  • The EVL knockdown cells impaired RAD51 assembly onto damaged DNA after ionizing radiation or mitomycin C treatment. (biomedsearch.com)
  • Expression of this gene is also a marker for Reed-Sternberg cells in Hodgkin's lymphoma. (cancerindex.org)
  • The mDE6 cells expressed odontogenesis-related genes, such as Runx2, Amelx, Ambn and Enam, and formed calcified matrices upon the induction of calcification, thus showing characteristics of odontogenic epithelial cells. (nih.gov)
  • Knockdown of calpain 2 resulted in a 2.9-fold decrease in the invasion of human glioblastoma cells in zebrafish brain. (zfin.org)
  • Control cells diffusely migrated up to 450 µm from the site of injection, whereas knockdown cells remained confined in clusters. (zfin.org)
  • The invasion study was repeated in organotypic mouse brain tissues, and calpain 2 knockdown cells demonstrated a 2.3-fold lower area of dispersal compared with control cells. (zfin.org)
  • This technique of fate mapping is used to study cells as they differentiate into their final cell fates. (wikipedia.org)
  • Gene knockdown is achieved by preventing cells from making a targeted protein. (wikipedia.org)
  • Droplet-based microfluidics platforms (or other cell sorting and separating techniques) are used to isolate individual cells, and then scRNA-seq is performed to generate gene expression profiles for each cell. (wikipedia.org)
  • Antibiotic resistance gene: similar to fluorescent markers, antibiotic resistance genes are often incorporated into vectors to allow for selection of successfully transduced cells. (wikipedia.org)
  • Selection for successfully transduced cells is then performed using a fluorescence assay or an antibiotic assay, depending on the reporter gene used in the expression vector. (wikipedia.org)