Genomes and Genes
Summary: Synthetic transcripts of a specific DNA molecule or fragment, made by an in vitro transcription system. This cRNA can be labeled with radioactive uracil and then used as a probe. (King & Stansfield, A Dictionary of Genetics, 4th ed)
- Vester B, Wengel J. LNA (locked nucleic acid): high-affinity targeting of complementary RNA and DNA. Biochemistry. 2004;43:13233-41 pubmed..The wide applicability of LNA oligonucleotides for gene silencing and their use for research and diagnostic purposes are documented in a number of recent reports, some of which are described herein. ..
- Barker C, Griffin C, Dolganov G, Hanspers K, Yang J, Erle D. Increased DNA microarray hybridization specificity using sscDNA targets. BMC Genomics. 2005;6:57 pubmed..microarray analysis of gene expression uses T7 RNA polymerase-driven in vitro transcription (IVT) to produce complementary RNA (cRNA) that can be hybridized to arrays...
- Hegeman C, Halter C, Owens T, Hanson M. Expression of complementary RNA from chloroplast transgenes affects editing efficiency of transgene and endogenous chloroplast transcripts. Nucleic Acids Res. 2005;33:1454-64 pubmed..While complementary RNA that guides nucleotides for alteration has been detected in other RNA modification systems, it is not known ..
- Evans S, Datson N, Kabbaj M, Thompson R, Vreugdenhil E, de Kloet E, et al. Evaluation of Affymetrix Gene Chip sensitivity in rat hippocampal tissue using SAGE analysis. Serial Analysis of Gene Expression. Eur J Neurosci. 2002;16:409-13 pubmed..This report provides the first broad evaluation of Affymetrix Gene Chip sensitivity relevant to studying the brain. ..
- Yang L, Tran D, Wang X. BADGE, Beads Array for the Detection of Gene Expression, a high-throughput diagnostic bioassay. Genome Res. 2001;11:1888-98 pubmed..The changes in expression profiles were very similar. Our study showed that the BADGE assay was capable of profiling expression of multiple genes at affordable cost and rapid speed. ..
- Tchurikov N, Chistyakova L, Zavilgelsky G, Manukhov I, Chernov B, Golova Y. Gene-specific silencing by expression of parallel complementary RNA in Escherichia coli. J Biol Chem. 2000;275:26523-9 pubmed..Together with in vitro nuclease protection studies these results indicate that a parallel RNA duplex might be formed in vivo and both types of duplexes, antiparallel or parallel, can induce gene-specific silencing by similar mechanisms. ..
- Cox L, Larman M, Saunders C, Hashimoto K, Swann K, Lai F. Sperm phospholipase Czeta from humans and cynomolgus monkeys triggers Ca2+ oscillations, activation and development of mouse oocytes. Reproduction. 2002;124:611-23 pubmed..Microinjection of complementary RNA for both human and cynomolgus monkey PLCzeta elicits Ca(2+) oscillations in mouse oocytes equivalent to ..
- Luzzi V, Mahadevappa M, Raja R, Warrington J, Watson M. Accurate and reproducible gene expression profiles from laser capture microdissection, transcript amplification, and high density oligonucleotide microarray analysis. J Mol Diagn. 2003;5:9-14 pubmed..The accuracy and technical reproducibility of the method suggests that expression profiling using transcript amplification and high density oligonucleotide microarrays can be used on a routine basis. ..
- Sijen T, Steiner F, Thijssen K, Plasterk R. Secondary siRNAs result from unprimed RNA synthesis and form a distinct class. Science. 2007;315:244-7 pubmed..Therefore, secondary siRNAs represent a distinct class of small RNAs. Their biogenesis depends on RdRPs, and we propose that each secondary siRNA is an individual RdRP product. ..
- Craig I, Mill J, Craig G, Loat C, Schalkwyk L. Application of microarrays to the analysis of the inactivation status of human X-linked genes expressed in lymphocytes. Eur J Hum Genet. 2004;12:639-46 pubmed..Six of the targets were represented by more than one probe set, which gave independent support for the conclusions reached. ..
- Maiti M, Nauwelaerts K, Lescrinier E, Schuit F, Herdewijn P. Self-complementary sequence context in mature miRNAs. Biochem Biophys Res Commun. 2010;392:572-6 pubmed publisher..The self-complementarity of mature miRNAs can provide a mechanistic tuning and a regulatory sophistication to the process of miRNA mediated gene regulation. ..
- Paul A, Yechoor V, Raja R, Li L, Chan L. Microarray gene profiling of laser-captured cells: a new tool to study atherosclerosis in mice. Atherosclerosis. 2008;200:257-63 pubmed publisher..We believe that this method represents a useful new tool for the unbiased analysis of global gene expression of specific sub-regions in atherosclerotic lesions in different rodent models. ..
- Xiao P, Tang A, Yu Z, Gui Y, Cai Z. Gene expression profile of 2058 spermatogenesis-related genes in mice. Biol Pharm Bull. 2008;31:201-6 pubmed..This study provides a molecular basis for the identity of spermatogenesis-related gene in mouse testis and leads to the elucidation of the molecular events underlying mammalian male reproduction. ..
- Albaek N, Petersen M, Nielsen P. Two carbocyclic locked nucleic acid analogues give structural information about the role of hydration in A-type duplexes. Nucleosides Nucleotides Nucleic Acids. 2007;26:1529-32 pubmed..Strongly stabilized duplexes with complementary RNA and slightly destabilized duplexes with complementary DNA are observed...
- Doddareddy M, Choo H, Cho Y, Rhim H, Koh H, Lee J, et al. 3D pharmacophore based virtual screening of T-type calcium channel blockers. Bioorg Med Chem. 2007;15:1091-105 pubmed..This result shows a successful example of ligand based drug discovery of potent T-type calcium channel blockers. ..
- Krutzfeldt J, Rajewsky N, Braich R, Rajeev K, Tuschl T, Manoharan M, et al. Silencing of microRNAs in vivo with 'antagomirs'. Nature. 2005;438:685-9 pubmed..Our findings show that antagomirs are powerful tools to silence specific miRNAs in vivo and may represent a therapeutic strategy for silencing miRNAs in disease. ..
- Ruan H, Zarnowski M, Cushman S, Lodish H. Standard isolation of primary adipose cells from mouse epididymal fat pads induces inflammatory mediators and down-regulates adipocyte genes. J Biol Chem. 2003;278:47585-93 pubmed
- Bleasby K, Hall L, Perry J, Mohrenweiser H, Pritchard J. Functional consequences of single nucleotide polymorphisms in the human organic anion transporter hOAT1 (SLC22A6). J Pharmacol Exp Ther. 2005;314:923-31 pubmed
- Kobayashi Y, Sakai R, Ohshiro N, Ohbayashi M, Kohyama N, Yamamoto T. Possible involvement of organic anion transporter 2 on the interaction of theophylline with erythromycin in the human liver. Drug Metab Dispos. 2005;33:619-22 pubmed..Our present findings suggest that hOat2 may, at least in part, be involved in the theophylline-erythromycin interaction in the human liver. ..
- Chandran U, Dhir R, Ma C, Michalopoulos G, Becich M, Gilbertson J. Differences in gene expression in prostate cancer, normal appearing prostate tissue adjacent to cancer and prostate tissue from cancer free organ donors. BMC Cancer. 2005;5:45 pubmed..A possible field effect surrounding prostate cancers and the implications of these findings for characterizing gene expression changes in prostate tumors are discussed. ..
- Jutabha P, Kanai Y, Hosoyamada M, Chairoungdua A, Kim D, Iribe Y, et al. Identification of a novel voltage-driven organic anion transporter present at apical membrane of renal proximal tubule. J Biol Chem. 2003;278:27930-8 pubmed..Therefore, it is proposed that OATV1 plays an important role to excrete drugs, xenobiotics, and their metabolites driven by membrane voltage through the apical membrane of the tubular epithelial cells into the urine. ..
- Wilson H, O Neill H. Preparation of label from small cell numbers for microarray screening. OMICS. 2004;8:190-6 pubmed..Adoption of this approach can be used to give an accurate profile of genes expressed in the specific cell subset of interest. Published methods and successful variations applied to these are discussed here. ..
- Eguchi Y, Ihara M, Ochi E, Shibata Y, Matsuda K, Fushiki S, et al. Functional characterization of Musca glutamate- and GABA-gated chloride channels expressed independently and coexpressed in Xenopus oocytes. Insect Mol Biol. 2006;15:773-83 pubmed publisher..These results suggest that MdGluCl-alpha assists in the expression of MdRdl when the two are coexpressed...
- Zhu J, Qiu Y, Valobra M, Qiu S, Majumdar S, Matin D, et al. Plasma cells and IL-4 in chronic bronchitis and chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2007;175:1125-33 pubmed..Inflammatory cells are increased in bronchial submucosal glands and mucosa of large airways in smokers with CB. Gland-associated plasma cells express IL-4, and these likely promote mucus hypersecretion. ..
- Worthington R, Bell N, Wong R, Micklefield J. RNA-selective cross-pairing of backbone-extended pyrrolidine-amide oligonucleotide mimics (bePOMs). Org Biomol Chem. 2008;6:92-103 pubmed..bePOM I and II oligomers were synthesised using solid-phase peptide chemistry. Interestingly, UV thermal denaturation and circular dichroism studies reveals bePOM I and II can hybridise with complementary RNA, but not DNA.
- Caelers A, Berishvili G, Meli M, Eppler E, Reinecke M. Establishment of a real-time RT-PCR for the determination of absolute amounts of IGF-I and IGF-II gene expression in liver and extrahepatic sites of the tilapia. Gen Comp Endocrinol. 2004;137:196-204 pubmed..Therefore, it will be helpful when investigating gene expression in any species and tissue whenever absolute levels are of concern. ..
- Joshi P, Suryanarayanan A, Schulte M. A vertical flow chamber for Xenopus oocyte electrophysiology and automated drug screening. J Neurosci Methods. 2004;132:69-79 pubmed..Such a system can easily satisfy need for automated oocyte electrophysiology in academic settings, especially small to medium sized laboratories. ..
- Ben Ami H, Yassin L, Farah H, Michaeli A, Eshel M, Treinin M. RIC-3 affects properties and quantity of nicotinic acetylcholine receptors via a mechanism that does not require the coiled-coil domains. J Biol Chem. 2005;280:28053-60 pubmed..Together our results suggest that subunit-specific interactions of RIC-3 with nAChR subunits, mediated by the transmembrane domains, are sufficient for the effects of RIC-3 on nAChR quantity and quality. ..
- Murthy M, Pedemonte N, MacVinish L, Galietta L, Cuthbert A. 4-Chlorobenzo[F]isoquinoline (CBIQ), a novel activator of CFTR and DeltaF508 CFTR. Eur J Pharmacol. 2005;516:118-24 pubmed..As activation of CFTR and KCNN4 work in unison to promote epithelial chloride secretion, CBIQ is a new chemical scaffold for developing agents that may be useful in cystic fibrosis. ..
- Zhang L, Lee J, John S, Uozumi N, Kodama I. Mechanosensitivity of GIRK channels is mediated by protein kinase C-dependent channel-phosphatidylinositol 4,5-bisphosphate interaction. J Biol Chem. 2004;279:7037-47 pubmed..These results suggest that the mechanosensitivity of GIRK channels is mediated primarily by channel-PIP2 interaction, with PKC playing an important role in modulating the interaction probably through PIP2 hydrolysis. ..
- Crow M, Deng T, Addley M, Brownlee G. Mutational analysis of the influenza virus cRNA promoter and identification of nucleotides critical for replication. J Virol. 2004;78:6263-70 pubmed..Overall, our results suggest that the corkscrew secondary-structure model is required for authentic cRNA promoter activity in vivo, although the precise role of the 3' hairpin loop remains unknown. ..
- Miska E, Alvarez Saavedra E, Townsend M, Yoshii A, Sestan N, Rakic P, et al. Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol. 2004;5:R68 pubmed..We used this method to determine the microRNA expression profile during mouse brain development and observed a temporal wave of gene expression of sequential classes of microRNAs. ..
- Shcheynikov N, Kim K, Kim K, Dorwart M, Ko S, Goto H, et al. Dynamic control of cystic fibrosis transmembrane conductance regulator Cl(-)/HCO3(-) selectivity by external Cl(-). J Biol Chem. 2004;279:21857-65 pubmed..The physiological significance of these finding is discussed in the context of HCO(3)(-) secretion by tissues such as the pancreas and salivary glands. ..
- Carvacho I, Gonzalez W, Torres Y, Brauchi S, Alvarez O, Gonzalez Nilo F, et al. Intrinsic electrostatic potential in the BK channel pore: role in determining single channel conductance and block. J Gen Physiol. 2008;131:147-61 pubmed publisher..The model explains the experimental results adequately and, in particular, gives an economical explanation to the differential effect on the conductance of the neutralization of charges D326 and E329. ..
- Sheng S, Perry C, Kashlan O, Kleyman T. Side chain orientation of residues lining the selectivity filter of epithelial Na+ channels. J Biol Chem. 2005;280:8513-22 pubmed
- Van Lommel L, Janssens K, Quintens R, Tsukamoto K, Vander Mierde D, Lemaire K, et al. Probe-independent and direct quantification of insulin mRNA and growth hormone mRNA in enriched cell preparations. Diabetes. 2006;55:3214-20 pubmed..It is anticipated that other examples exist in which measurement of very abundant mRNAs in dedicated cells will help to understand biological processes, monitor disease states, or assist biotechnological manufacturing procedures. ..
- Xiao G, Mochly Rosen D, Boutjdir M. PKC isozyme selective regulation of cloned human cardiac delayed slow rectifier K current. Biochem Biophys Res Commun. 2003;306:1019-25 pubmed..Identification of the particular isozyme(s) that mediates the regulation of I(Ks) channels is of importance for the understanding of the mechanism of ion channel regulation and the development of new therapeutic agents. ..
- Zhou Y, Kanner B. Transporter-associated currents in the gamma-aminobutyric acid transporter GAT-1 are conditionally impaired by mutations of a conserved glycine residue. J Biol Chem. 2005;280:20316-24 pubmed..Our results can be explained by a model invoking two outward-facing states of the empty transporter and a defective transition between these states in the glycine 80 mutants. ..
- Shojaiefard M, Lang F. Stimulation of the intestinal phosphate transporter SLC34A2 by the protein kinase mTOR. Biochem Biophys Res Commun. 2006;345:1611-4 pubmed..In conclusion, mTOR and SGK1 cooperate in the stimulation of the intestinal phosphate transporter SLC34A2. ..
- Cope G, Murthy M, Golbang A, Hamad A, Liu C, Cuthbert A, et al. WNK1 affects surface expression of the ROMK potassium channel independent of WNK4. J Am Soc Nephrol. 2006;17:1867-74 pubmed..Together, these findings emphasize that the molecular mechanisms that underpin WNK1 regulation of ROMK expression are distinct from those that affect NCCT expression. ..
- Himmelreich U, Aime S, Hieronymus T, Justicia C, Uggeri F, Zenke M, et al. A responsive MRI contrast agent to monitor functional cell status. Neuroimage. 2006;32:1142-9 pubmed..The chelate can easily be modified to be targeted by enzymes expressed during specific change of cell status like activation or differentiation. Such a system is suitable for functional cellular in vivo MR imaging. ..
- Darby I, Bisucci T, Desmouliere A, Hewitson T. In situ hybridization using cRNA probes: isotopic and nonisotopic detection methods. Methods Mol Biol. 2006;326:17-31 pubmed..Finally, it can be shown that low-level mRNA expression is easier to detect in frozen sections than in paraffin-embedded material, with a consequent loss in quality of morphology. ..
- Kaiya H, Tsukada T, Yuge S, Mondo H, Kangawa K, Takei Y. Identification of eel ghrelin in plasma and stomach by radioimmunoassay and histochemistry. Gen Comp Endocrinol. 2006;148:375-82 pubmed..The present results suggest that ghrelin may participate in osmoregulation in eels. ..
- Mercer T, Dinger M, Sunkin S, Mehler M, Mattick J. Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A. 2008;105:716-21 pubmed publisher..Our results show that the majority of ncRNAs are expressed in the brain and provide strong evidence that the majority of processed transcripts with no protein-coding capacity function intrinsically as RNAs. ..
- Sax J, El Deiry W. Identification and characterization of the cytoplasmic protein TRAF4 as a p53-regulated proapoptotic gene. J Biol Chem. 2003;278:36435-44 pubmed..These data suggest a correlation that the orphan adaptor protein TRAF4 may play a role in p53-mediated proapoptotic signaling in the response to cellular stress. ..
- Westover K, Bushnell D, Kornberg R. Structural basis of transcription: separation of RNA from DNA by RNA polymerase II. Science. 2004;303:1014-6 pubmed..This separation of nucleic acid strands is brought about by interaction with a set of proteins loops in a strand/loop network. Formation of the network must occur in the transition from abortive initiation to promoter escape. ..
- Kang H, Park J, Jeong S, Kim J, Moon H, Perez Reyes E, et al. A molecular determinant of nickel inhibition in Cav3.2 T-type calcium channels. J Biol Chem. 2006;281:4823-30 pubmed..1. These findings indicate that His-191 in the S3-S4 loop is a critical residue conferring nickel block to Ca(v)3.2 and reveal a novel role for the S3-S4 loop to control ion permeation through T-type Ca2+ channels. ..
- Wijchers P, Hoekman M, Burbach J, Smidt M. Identification of forkhead transcription factors in cortical and dopaminergic areas of the adult murine brain. Brain Res. 2006;1068:23-33 pubmed..These forkhead transcription factors may play a role in maintenance and survival of developing and adult neurons. ..
- Patzel V. In silico selection of functional RNA molecules. Curr Opin Drug Discov Devel. 2004;7:360-9 pubmed..The success of these significant but costly processes depends upon intelligent functional RNA design and the development of high-throughput compatible in silico selection tools and filters. ..
- Li C, Crambert G, Thuillard D, Roy S, Schaer D, Geering K. Role of the transmembrane domain of FXYD7 in structural and functional interactions with Na,K-ATPase. J Biol Chem. 2005;280:42738-43 pubmed..These amino acids act in a synergistic way. These results highlight the important structural and functional role of the TM domain of FXYD7 and delineate the determinants that mediate the complex interactions of FXYD7 with Na,K-ATPase. ..
- Zheng L, Gibbs M, Rodoni B. Quantitative PCR measurements of the effects of introducing inosines into primers provides guidelines for improved degenerate primer design. J Virol Methods. 2008;153:97-103 pubmed publisher..Greater declines in the rate of amplification were observed with RNA templates, suggesting that reverse transcription suffers more than PCR amplification when inosine is included in the reverse primer. ..
- Papke R, McCormack T, Jack B, Wang D, Bugaj Gaweda B, Schiff H, et al. Rhesus monkey alpha7 nicotinic acetylcholine receptors: comparisons to human alpha7 receptors expressed in Xenopus oocytes. Eur J Pharmacol. 2005;524:11-8 pubmed..They also point to the potential importance of a newly identified sequence element for modeling the specific amino acids involved with receptor activation. ..
- Levandoski M, Piket B, Chang J. The anthelmintic levamisole is an allosteric modulator of human neuronal nicotinic acetylcholine receptors. Eur J Pharmacol. 2003;471:9-20 pubmed..Several results led us to conclude that levamisole potentiation occurs through noncompetitive binding to the receptor. We propose pseudo-site binding for noncompetitive potentiation by levamisole. ..