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  • 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)
  • PRPF8 mutations are generally missense and scattered throughout the gene (Figure 1A,D). The high level of conservation between the yeast Prp8 and human PRPF8 proteins allows for precise mapping of homologous mutations (Figure 1D). (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)
  • Protein
  • 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)
  • One of the affected genes, PRPF8, encodes the most evolutionarily conserved spliceosomal protein. (nih.gov)
  • A further analysis of a cohort of 447 cases of MDS and related conditions showed that 20% contain mutations in various spliceosomal protein genes, including SF3B1, SRSF2, U2AF1, ZRSR2 and LUC7L2 (Supplementary Figure 1B). (nih.gov)
  • The single-cell-cloned CSCs treated with the different tumor cell/tissue-derived conditioned culture medium, which is a mimic of carcinoma microenvironment, could differentiate into corresponding tumor cells and express specific markers of the respective type of tumor cells at the gene, protein and cell levels, respectively. (nih.gov)
  • 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)
  • Therefore, the addition of molecular manipulation techniques, including gene and protein knock downs, knock outs and overexpression, along with live cell imaging techniques has been transformational in understanding what mechanisms are involved with cell fate determination. (wikipedia.org)
  • Corepressor - A protein that reduces (represses) the expression of genes by binding to and activating a repressor transcription factor. (wikipedia.org)
  • Gene knockdown is achieved by preventing cells from making a targeted protein. (wikipedia.org)
  • it is the process by which the information in a gene, encoded as a sequence of bases in DNA, is converted into the structure of a protein. (wikipedia.org)
  • The technology uses a catalytically-dead Cas9 (usually denoted as dCas9) protein lacking endonuclease activity to regulate genes in an RNA-guided manner. (wikipedia.org)
  • 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)
  • For example, over-expression of a mutant gene may result in high levels of a non-functional protein resulting in a dominant negative interaction with the wildtype protein. (wikipedia.org)
  • They received their name from their similarity to the protein coded by the toll gene identified in Drosophila in 1985 by Christiane Nüsslein-Volhard. (wikipedia.org)
  • siRNA
  • The contributions of each system were investigated by a knockdown approach utilizing siRNA injections. (biomedsearch.com)
  • When Bcl-2 was knocked down with siRNA or inhibited with HA 14-1 or ABT-737, serum starvation induced profound cell death and enhanced autophagic flux under nutrition deprivation conditions, while knockdown of autophagic gene Beclin1 or autophagy inhibitors (bafilomycin A1 and E64D), rescued cell death. (nih.gov)
  • 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)
  • tumor
  • Metabolite-by-metabolite comparison, tumor immunoreactivity, and gene expression analyses showed that CYP epoxygenases and arachidonic acid-epoxygenation products, EET metabolites, are strongly associated with TNBC metastasis. (springer.com)
  • 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)
  • In sum, the exploration of clinical and functional consequences suggests that PRPF8 is a novel leukemogenic gene in myeloid neoplasms with a distinct phenotype likely manifested through aberrant splicing. (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)
  • Mutations
  • Mutations in the fused in sarcoma/translated in liposarcoma gene (FUS/TLS, FUS) have been identified in sporadic and familial forms of amyotrophic lateral sclerosis (ALS). (isharonline.org)
  • Mutations in the frataxin gene cause dorsal root ganglion demyelination and neurodegeneration, which leads to Friedreich's ataxia. (biomedsearch.com)
  • MIR155 suppresses target-gene expression by directly interacting with their 3' untranslated regions (UTRs), mutations of the binding sites abolish their MIR155 responsiveness.Furthermore, by downregulating MTOR signaling, MIR155 also attenuates cell proliferation and induces G 1/S cell cycle arrest.Collectively, these data present a new role for MIR155 as a key regulator of autophagy via dysregulation of MTOR pathway. (nih.gov)
  • MIR155 suppresses target-gene expression by directly interacting with their 3' untranslated regions (UTRs), mutations of the binding sites abolish their MIR155 responsiveness. (nih.gov)
  • 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)
  • 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)
  • Transcription
  • Interestingly, this multilineage differentiation potential of single-cell-cloned liver CSCs sharply declined after the specific knockdown of octamer-binding transcription factor 4 (Oct4) alone, even though they were under the same induction conditions (carcinoma microenvironments). (nih.gov)
  • 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)
  • RNAs
  • 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)
  • transgenic
  • Stable transgenic knockdown of RACB reduced the ability of barley to accommodate haustoria of B. graminis in intact epidermal leaf cells and to form hairs on the root epidermis, suggesting that RACB is a common element of root hair outgrowth and ingrowth of haustoria in leaf epidermal cells. (tum.de)
  • 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)
  • 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)
  • 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)
  • 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)
  • cell
  • In the present study, SIRT1 re-expression or knockdown was induced in hepatoma cell lines and liver normal cell lines. (isharonline.org)
  • Here, we show that single-cell-cloned CSCs, accidentally obtained from a human liver cancer microvascular endothelial cells, express classic stem cell markers, genes associated with self-renewal and pluripotent factors and possess colony-forming ability in vitro and the ability of serial transplantation in vivo. (nih.gov)
  • Experiment: Gurdon used a technique known as nuclear transfer to replace the killed-off nucleus of a frog (Xenopus) egg with a nucleus from a mature cell (intestinal epithelial). (wikipedia.org)
  • This technique of fate mapping is used to study cells as they differentiate into their final cell fates. (wikipedia.org)
  • The gene knockdown efficiency can also be improved by using cell squeezing. (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)
  • In the December 2016 issue of the Cell journal, two companion papers were published that each introduced and described this technique. (wikipedia.org)
  • Plant
  • In the case of the plant model system huge mutant libraries have been created based on gene disruption constructs. (wikipedia.org)
  • genome
  • Second, we investigate a large scale dataset consisting of genome-wide knockdown screens for human genes essential in the mitotic process. (nih.gov)
  • Genome browser BLAST Expression Search and Clone Search (search by gene symbol, gene name, or Affymetrix id) Gene nomenclature guidelines Literature search: Textpresso- uses an algorithm to match your search to specific criteria or section of a paper. (wikipedia.org)
  • The initiating dsRNA can also be endogenous (originating in the cell), as in pre-microRNAs expressed from RNA-coding genes in the genome. (wikipedia.org)
  • Techniques such as fragment-based design, virtual screening and genome sequencing have helped generate drug leads. (wikipedia.org)
  • In contrast, when genes are knocked out, they are completely erased from the organism's genome and, thus, have no expression. (wikipedia.org)
  • To the extent it is useful to craft a distinction between these related concepts, RNA silencing may be thought of as referring to the broader scheme of small RNA related controls involved in gene expression and the protection of the genome against mobile repetitive DNA sequences, retroelements, and transposons to the extent that these can induce mutations. (wikipedia.org)
  • Its plasmid collection contains plasmids used for functions such as genome engineering (including CRISPRS), gene expression, shRNA knockdown, viral-mediated gene delivery, detection of miRNA and promoter activity. (wikipedia.org)
  • In the case of the yeast model system directed deletions have been created in every non-essential gene in the yeast genome. (wikipedia.org)