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Gene knockdown - Wikipedia, the free encyclopedia Also known as knockdown organisms or simply knockdowns, their most direct use is for learning about a gene that has been sequenced, but has an unknown or incompletely known function, an experimental approach known as reverse genetics. Knockdown is also the process of creating such an organism or using such a reagent, as in "knocking down a gene." Popular reagent-based methods of knocking down the expression of a gene include suppression of translation using small interfering RNA (siRNA) or Morpholino oligos. en.wikipedia.org /wiki/Knockdown   (139 words)

CSHL - Researchers Achieve Germline Transmission of RNAi 'Gene Knockdown' in Mice To adapt RNAi for the study of gene function in mice, Thomas Rosenquist of Stony Brook University and Greg Hannon of Cold Spring Harbor Laboratory used genetic engineering to create mouse embryonic stem cells in which RNAi was targeted to a particular gene. Such a reduction in gene expression is called a "gene knockdown" to distinguish it from traditional methods that involve "gene knockouts" or the complete deletion of a DNA segment from a chromosome. Although the current study targeted a gene thought to be involved in DNA repair, any gene would have sufficed as a target to demonstrate proof of principle as this study has done. www.cshl.edu /public/releases/press011903.html   (314 words)

RNA interference - Wikipedia, the free encyclopedia The machinery is however also used by the cell itself to regulate gene activity: certain parts of the genome are transcribed into microRNA, short RNA molecules that fold back on themselves in a hairpin shape to create a double strand. Repressing a gene from being expressed allows for testing of the protein and its role in the life of a cell or larger organism. Since RNAi may not totally abolish expression of a gene, using it against a gene is sometimes referred as a "knockdown", to distinguish it from procedures in which the DNA sequence encoding a gene is removed. en.wikipedia.org /wiki/RNA_interference   (1194 words)

Atugen - Discovery platform --> Gene silencing tools   (Site not responding. Last check: 2007-10-12) Gene function is elucidated by correlating reduction in gene expression (mRNA and/or protein knockdown) with changes in phenotype. The knockdown of gene function is transient, and therefore different from the classical gene knockout technology which is more time consuming and irreversible. The gene silencing technology allows the observation of subtle, acute changes even in short and transient time periods such as for example during cell cycle progression. www.atugen.com /genetools.htm   (260 words)

Genetic Methods and Protocols Neurochemical and behavioral consequences of widespread gene knockdown in the adult mouse brain by using nonviral RNA interference Gene knockdown with intrathecal siRNA of NMDA receptor NR2B subunit reduces formalin-induced nociception in the rat In vivo knockdown of gene expression in brain cancer with intravenous RNAi in adult rats www.ihcworld.com /neuroscience/genetic.htm   (339 words)

Morpholino-based gene knockdown screen of novel genes with developmental function in Ciona intestinalis -- Yamada et ... or palps of the adhesive organ in the knockdown larvae. 3-5% of the genes encoded in the genome Early embryonic expression of FGF4/6/9 gene and its role in the induction of mesenchyme and notochord in Ciona savignyi embryos. dev.biologists.org /cgi/content/full/130/26/6485   (6370 words)

Biocompare - Product Literature Center RNA interference is a powerful technique for gene knockdown experiments in academic research and an important tool for target identification and target validation in therapeutic research. A growing number of different cell lines are used for gene knockdown experiments, and in many cases protocols for transfection do not exist. The housekeeping genes G6PDH and HPRT can be used as a positive control for gene knockdown experiments when siRNA transfection conditions have to be optimized. www.biocompare.com /techart.asp?id=856   (621 words)

Reversibly-Sterile Fish Via Transgenesis - 12/3 ISB News Report However GnRH genes in fish are not without their problems in that multiple copies are present in the genome. Three possible approaches to gene knockdown are RNA interference (RNAi), ribozyme, or antisense. It is clear that the efficiency with which knockdown of the specific gene expression is achieved will depend both on the quality of message made and the amount of antisense made. www.fass.org /fasstrack/news_item.asp?news_id=1714   (1360 words)

Local gene knockdown in the brain using viral-mediated RNA interference - Nature Medicine Notably, the average weights of the Th knockdown mice were not significantly different from those of control mice after targeting both the substantia nigra compacta (AAV-shTH mice, 26.2 g; AAV-shSCR mice, 25.5 g) and the VTA (AAV-shTH mice, 25.6 g; AAV-shSCR mice, 24.9 g), suggesting that overall health was not affected by the gene knockdown. The persistant expression of genes delivered by AAV allows animals to be evaluated for long-term effects of gene knockdown, and should provide stability to disease models. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. www.nature.com /cgi-taf/DynaPage.taf?file=/nm/journal/v9/n12/full/nm964.html   (3869 words)

OligoEngine   (Site not responding. Last check: 2007-10-12) However, the knockdown effect of siRNA is typically limited to 7-10 days, making them unsuitable for use in long-term knockdown experiments either in cells or in vivo. It provides the means to analyze gene function over a long period through stable inhibition, essential when studying inducible processes such as UV or other irradiation damage response, host-pathogen interactions, or cell differentiation. Furthermore, because RNAi produces a range of levels of gene knockdown it is possible to model the effect of drugs more accurately than with traditional gene knockout technologies such as dominant negative mutation and homologous recombination. www.oligoengine.com /Home/mid_prodPSUPER.html   (1969 words)

Stable Suppression of Gene Expression in Murine Embryonic Stem Cells by RNAi Directed from DNA Vector-Based Short ... gene knockdown effect is both specific and persistent. RNAi gene knockdown effect in ES cells was achieved [23]. Characterisation of Wnt gene expression during the differentiation of murine embryonic stem cells in vitro: role of Wnt3 in enhancing haematopoietic differentiation. stemcells.alphamedpress.org /cgi/content/full/22/1/93   (3300 words)

Using siRNA Technique to Generate Transgenic Animals with Spatiotemporal and Conditional Gene Knockdown -- Chang et al. ... The phenotype and symptoms of ABCA1 gene knockdown mice. McManus MT, Sharp PA: Gene silencing in mammals by small interfering RNAs. Zuo J: Transgenic and gene targeting studies of hair cell function in mouse inner ear. ajp.amjpathol.org /cgi/content/full/165/5/1535   (4107 words)

Clontechniques Jan 2004 - BD™ Knockout RNAi System and BD QZyme™ qPCR Assays: A Complete System for ...   (Site not responding. Last check: 2007-10-12) The complete sequencing of the human genome makes amplification-based analysis the most attractive and fastest method to evaluate gene silencing, especially in cases where a specific antibody is unavailable or a functional test for a novel gene has not been developed. Cotransfection of p53-EGFP and the p53 shRNA, or NF B-EGFP and the NF B shRNA, resulted in markedly reduced gene expression at the protein level, as determined by flow cytometry (data not shown) and epifluorescence microscopy (Figure 2). Expression levels of the target gene and ribosomal protein L15 (RPLO, an endogenous control) were simultaneously determined using first-strand cDNA from cotransfected cells. www.clontech.com /clontech/archive/JAN04UPD/TechNote_Knockout.shtml   (1114 words)

Leukemogenesis Caused by Incapacitated GATA-1 Function -- Shimizu et al. 24 (24): 10814 -- Molecular and Cellular ... The gross morphological appearance of livers and spleens of the recipient nude mice is similar to that of the donors (Fig. The neo gene was detected in both spleen (Sp) and lymph node (LN) DNAs of recipient nude mice (lanes 6 and 7). GATA-1 and GATA-2 gene expression is related to the severity of dysplasia in myelodysplastic syndrome. mcb.asm.org /cgi/content/full/24/24/10814   (6854 words)

Specificity of short interfering RNA determined through gene expression signatures -- Semizarov et al. 100 (11): 6347 ...   (Site not responding. Last check: 2007-10-12) Each color patch in the matrix represents the expression fold change of the associated gene relative to the untreated control: red indicates up-regulation and blue indicates down-regulation, as shown by the color bar. genes represented in the plot, with the exception of a few outliers. Inhibition of MDR1 gene expression by chimeric HNA antisense oligonucleotides www.pnas.org /cgi/content/full/100/11/6347   (4778 words)

Discovery Genomics, Inc. - Gene Discovery: Morphant Technology   (Site not responding. Last check: 2007-10-12) Morphant Technology is thus a method for inhibiting expression of targeted genes in order to determine their function in the development and health of zebrafish. Relevance to humans – 90% of the human genes are in the zebrafish genome. DGI has discovered 15 genes and partially validated and filed patents on six genes related to angiogenesis and bone and cartilage formation. www.discoverygenomics.net /morphant.phtml   (590 words)

A ribozyme-mediated, gene "knockdown" strategy for the identification of gene function in zebrafish -- Xie et al. 94 ... A ribozyme-mediated, gene "knockdown" strategy for the identification of gene function in zebrafish -- Xie et al. A ribozyme-mediated, gene "knockdown" strategy for the identification of gene function in zebrafish gene in the developing zebrafish embryo has been developed. www.pnas.org /cgi/content/abstract/94/25/13777   (401 words)

A ribozyme-mediated, gene "knockdown" strategy for the identification of gene function in zebrafish -- Xie et al. 94 ... gene is not destroyed or disrupted as in a knockout experiment, gene do not form a tail (25) and this phenotype is easily observable The mRNA sequence of the ntl gene (9) was analyzed with the www.pnas.org /cgi/content/full/94/25/13777   (3204 words)

shRNA vectors   (Site not responding. Last check: 2007-10-12) And by using expression constructs instead of oligo injection, it is possible to perform multi-generational studies of gene knockdown because the vector can become a permanent fixture in the cell line. Or, combine the TranSignal p53 Target Gene Array with the TranSilent p53 shRNA Vector to assess the effect of p53 suppression on 146 human or 122 mouse p53-rgulated genes in your experimental model. Gene expression was reduced 80-90% in shRNA-transfected cells versus control cells. panomics.multipath.net /SR1000.cfm   (988 words)

siRNA-mediated gene silencing: a global genome view -- Semizarov et al. 32 (13): 3836 -- Nucleic Acids Research the consequences of gene silencing on a genome-wide scale (9). The Gene Ontology nodes strongly affected by the Rb1 silencing are shown, along with the number of genes affected, number of genes present on the chip (in the affected/present format), and the Z-score, which indicates the relatedness of the gene expression signature to the process. Ohtani,K., Iwanaga,R., Nakamura,M., Ikeda,M., Yabuta,N., Tsuruga,H. and Nojima,H. ((1999)) Cell growth-regulated expression of mammalian MCM5 and MCM6 genes mediated by the transcription factor E2F. nar.oxfordjournals.org /cgi/content/full/32/13/3836   (4177 words)

Single copy shRNA configuration for ubiquitous gene knockdown in mice -- Seibler et al. 33 (7): e67 -- Nucleic Acids ... Genes encoding the Renilla (Rluc) and firefly luciferases (Fluc) along with an adenovirus splice acceptor sequence and a polyadenylation signal (pA) were placed downstream of the endogenous promoter of rosa26. Homologous recombination at the rosa26 locus is detectable using EcoRV-digested genomic DNA and probe 1, resulting in a 11.7 kb band for the wild type (wt) and a 2.5 kb band for the targeted alleles. The efficiency of luciferase knockdown appeared not to be influenced by the age of the animal. nar.oxfordjournals.org /cgi/content/full/33/7/e67   (4658 words)

RNAi FAQ   (Site not responding. Last check: 2007-10-12) This is because RNAi-mediated gene silencing, though highly efficient, relies on translational inhibition to disrupt gene expression. Thus, even though some genes can be reduced to less than 10% of wild-type levels, there will always be some “leaky” expression of mRNA that escapes the RISC complex and is translated. A true null allele is possible only through traditional methods that knockout the gene at the DNA level. www.clarifyrnai.com /faq_1.asp   (184 words)

Lentivirus-delivered stable gene silencing by RNAi in primary cells -- STEWART et al. 9 (4): 493 -- RNA Lentivirus-delivered stable gene silencing by RNAi in primary cells -- STEWART et al. Sequence-specific knockdown of GFP expression by retrovirus-delivered GFP hairpin RNA expression. genes with a neutral or growth-promoting phenotype, it is possible www.rnajournal.org /cgi/content/full/9/4/493   (4453 words)

RNA interference: from model organisms towards therapy for neural and neuromuscular disorders -- Buckingham et al. 13 ... RNAi knockdown of genes in Drosophila and C. inhibiting a gene associated with a polyglutamine disorder (110). Caplen, N.J., Fleenor, J., Fire, A. and Morgan, R.A. (2000) dsRNA-mediated gene silencing in cultured Drosophila cells: a tissue culture model for the analysis of RNA interference. hmg.oxfordjournals.org /cgi/content/full/13/suppl_2/R275   (6343 words)

Effective targeted gene 'knockdown' in zebrafish - Nature Genetics   (Site not responding. Last check: 2007-10-12) The sequencing of the zebrafish genome should be completed by the end of 2002. Direct assignment of function on the basis of this information would be facilitated by the development of a rapid, targeted 'knockdown' technology in this model vertebrate. We generated phenocopies of mutations of the genes no tail (ref. 2), chordin (ref. 3), one-eyed-pinhead (ref. 4), nacre (ref. 5) and sparse (ref. 6), removing gene function from maternal through post-segmentation and organogenesis developmental stages. nature.com /ng/journal/v26/n2/abs/ng1000_216.html;jsessionid=5B755C4...   (246 words)

siRNA Announcement   (Site not responding. Last check: 2007-10-12) Transfect with high efficiency to study the cellular and functional consequences of gene knockdown. One key component in the study of gene knockdown is the effective delivery of siRNA as a prerequisite for meaningful results. Figure 1: Effective and specific knockdown of EGFP expression in HEK 293 cells, co-transfected with an EGFP expression plasmid, and either a GPF-specific siRNA or a luciferase-specific siRNA (negative control). www.roche-applied-science.com /announcements/sirna/sirna.htm   (334 words)

A Practical Vector for Efficient Knockdown of Gene Expression in Rice (Oryza sativa L.)   (Site not responding. Last check: 2007-10-12) Based on its principle, a new generation of vectors containing an inverted target sequence separated by an intron as a loop, developing simplifications to the procedure of RNAi construction are required to improve the efficiency of gene inactivation techniques. With this vector, only 1 PCR product amplified by a single pair of primers and 2 ligation reactions were needed to create an RNAi construct, which shortened the time span before being transformed into the plant. Therefore, the RNAi vector pTCK303 based on the homology-dependent gene-silencing mechanisms facilitated the inhibition of endogenous genes in a monocot and was proven to be a practical and efficient platform for silencing a rice gene. pubs.nrc-cnrc.gc.ca /ispmb/r05-008.html   (349 words)

BD Clontech RNAi Products   (Site not responding. Last check: 2007-10-12) I know which gene I'd like to knockdown. I need to screen a large number of potential knockdown sequences. I'm not seeing good knockdown with the oligos or vector constructs that I'm using. www.clarifyrnai.com   (232 words)

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