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RNA Transcripts (rna + transcript)
Kinds of RNA Transcripts Selected AbstractsInfluenza virus assays based on virus-inducible reporter cell linesINFLUENZA AND OTHER RESPIRATORY VIRUSES, Issue 5 2009Yunsheng Li Background, Virus-inducible reporter genes have been used as the basis of virus detection and quantitation assays for a number of viruses. A strategy for influenza A virus-induction of a reporter gene was recently described. In this report, we describe the extension of this strategy to influenza B virus, the generation of stable cell lines with influenza A and B virus-inducible reporter genes, and the use of these cells in various clinically relevant viral assays. Each of the cell lines described herein constitutively express an RNA transcript that contains a reporter gene coding region flanked by viral 5,- and 3,-untranslated regions (UTR) and therefore mimics an influenza virus genomic segment. Upon infection of the cells with influenza virus the virus-inducible reporter gene segment (VIRGS) is replicated and transcribed by the viral polymerase complex resulting in reporter gene expression. Findings, Reporter gene induction occurs after infection with a number of laboratory strains and clinical isolates of influenza virus including several H5N1 strains. The induction is dose-dependent and highly specific for influenza A or influenza B viruses. Conclusions, These cell lines provide the basis of simple, rapid, and objective assays that involve virus quantitation such as determination of viral titer, assessment of antiviral susceptibility, and determination of antibody neutralization titer. These cell lines could be very useful for influenza virus researchers and vaccine manufacturers. [source] Time-dependent expression of myostatin RNA transcript and protein in gastrocnemius muscle of mice after sciatic nerve resectionMICROSURGERY, Issue 5 2007Chenxin Shao M.D. Myostatin, a member of the transforming growth factor-, (TGF-,) superfamily, has been identified as a negative regulator of skeletal muscle mass. To provide more data on the role of myostatin in denervation-induced muscle atrophy, we examined the time-dependent changes in myostatin mRNA and protein as well as Smad2 and phospho-Smad2 protein levels in the denervated gastrocnemius muscle of mice after sciatic neurectomy, using quantitative real-time RT-PCR and Western blotting, respectively. We conducted morphometric analyses to measure the wet weight ratio of the denervated muscle (the operated side/contralateral nonoperated side) and the cross-sectional area of muscle fibers, and observed the morphology of denervated muscle. The experimental results showed that in the early stage of denervation, the levels of myostatin mRNA and protein in the denervated gastrocnemius muscle increased instantly, reaching a peak at day 3 and day 7 after sciatic neurectomy, respectively, when compared with the normal values. In addition, the phospho-Smad2 protein was observed to have a similar expression profile to that of the myostatin mRNA. The present study perhaps opens a new window into myostatin modulation in muscle atrophy due to denervation. © 2007 Wiley-Liss, Inc. Microsurgery, 2007. [source] Systematic mutagenesis of the thymidine tract of the pyrBI attenuator and its effects on intrinsic transcription termination in Escherichia coliMOLECULAR MICROBIOLOGY, Issue 1 2007Katalin Sipos Summary The pyrBI attenuator of Escherichia coli is an intrinsic transcription terminator composed of DNA with a hyphenated dyad symmetry and an adjacent 8 bp T:A tract (T-tract). These elements specify a G+C-rich terminator hairpin followed by a run of eight uridine residues (U-tract) in the RNA transcript. In this study, we examined the effects on in vivo transcription termination of systematic base substitutions in the T/U-tract of the pyrBI attenuator. We found that these substitutions diminished transcription termination efficiency to varying extents, depending on the nature and position of the substitution. In general, substitutions closer to the dyad symmetry/terminator hairpin exhibited the most significant effects. Additionally, we examined the effects on in vivo transcription termination of mutations that insert from 1 to 4 bases between the terminator hairpin and U-tract specified by the pyrBI attenuator. Our results show an inverse relationship between termination efficiency and the number of bases inserted. The effects of the substitution and insertion mutations on termination efficiency at the pyrBI attenuator were also measured in vitro, which corroborated the in vivo results. Our results are discussed in terms of the current models for intrinsic transcription termination and estimating termination efficiencies at intrinsic terminators of other bacteria. [source] Translational read-through of a nonsense mutation in ATP7A impacts treatment outcome in Menkes disease,ANNALS OF NEUROLOGY, Issue 1 2009Stephen G. Kaler MPH Protein translation ends when a stop codon in a gene's messenger RNA transcript enters the ribosomal A site. Mutations that create premature stop codons (nonsense mutations) typically cause premature translation termination. An alternative outcome, read-through translation (or nonsense suppression), is well known in prokaryotic, viral, and yeast genes but has not been clearly documented in humans except in the context of pharmacological manipulations. Here, we identify and characterize native read-through of a nonsense mutation (R201X) in the human copper transport gene, ATP7A. Western blotting, in vitro expression analyses, immunohistochemistry, and yeast complementation assays using cultured fibroblasts from a classic Menkes disease patient all indicated small amounts of native ATP7AR201X read-through and were associated with a dramatic clinical response to early copper treatment. Ann Neurol 2009;65:108,113 [source] Trans -splicing in DrosophilaBIOESSAYS, Issue 11 2002Vincenzo Pirrotta Splicing is an efficient and precise mechanism that removes noncoding regions from a single primary RNA transcript. Cutting and rejoining of the segments occurs on nascent RNA. Trans -splicing between small specialized RNAs and a primary transcript has been known in some organisms but recent papers show that trans -splicing between two RNA molecules containing different coding regions is the normal mode in a Drosophila gene.1,3 The mod(mdg4) gene produces 26 different mRNAs encoding as many protein isoforms. The differences lie in alternative 3, exons encoded by different transcriptional units and spliced to the 5, common region by a surprising trans -splicing mechanism. BioEssays 24:988,991, 2002. © 2002 Wiley-Periodicals, Inc. [source] The effect of hfq on global gene expression and virulence in Neisseria gonorrhoeaeFEBS JOURNAL, Issue 19 2009Manuela Dietrich Hfq is an RNA chaperone that functions as a pleiotropic regulator for RNA metabolism in bacteria. In several pathogenic bacteria, Hfq contributes indirectly to virulence by binding to riboregulators that modulate the stability or translation efficiency of RNA transcripts. To characterize the role of Hfq in the pathogenicity of Neisseria gonorrhoeae, we generated an N. gonorrhoeae hfq mutant. Infectivity and global changes in gene expression caused by the hfq mutation in N. gonorrhoeae strain MS11 were analyzed. Transcriptional analysis using a custom-made N. gonorrhoeae microarray revealed that 369 ORFs were differentially regulated in the hfq mutant, MS11hfq, in comparison with the wild-type strain (202 were upregulated, and 167 were downregulated). The loss-of-function mutation in hfq led to pleiotropic phenotypic effects, including an altered bacterial growth rate and reduced adherence to epithelial cells. Twitching motility and microcolony formation were not affected. Hfq also appears to play a minor role in inducing the inflammatory response of infected human epithelial cells. Interleukin-8 production was slightly decreased, and activation of c-Jun N-terminal kinase, a mitogen-activated protein kinase, was reduced in MS11hfq- infected epithelial cells in comparison with wild type-infected cells. However, activation of nuclear factor kappa B, extracellular signal-regulated kinase 1/2 and p38 remained unchanged. The data presented suggest that Hfq plays an important role as a post-transcriptional regulator in N. gonorrhoeae strain MS11 but does not contribute significantly to its virulence in cell culture models. [source] A tumour-associated DEAD-box protein, rck/p54 exhibits RNA unwinding activity toward c-myc RNAs in vitroGENES TO CELLS, Issue 8 2003Yukihiro Akao Background:, The rck/p54 protein of 473 amino acids belongs to the family of DEAD-box/putative RNA helicase proteins. DEAD-box proteins have been implicated in a wide variety of cellular processes ranging from the initiation of protein synthesis and ribosome biosynthesis to premRNA splicing by means of modifying the RNA structure. Our previous data suggested that rck/p54 positively affected the translation initiation of c-myc mRNA. Results:, The data obtained from morphological studies and surface plasmon resonance assays clearly indicated that the protein specifically bound to c-myc RNA transcripts (RNAs) and exhibited RNA unwinding activity toward c-myc RNAs in the presence of ATP in vitro. Experiments using a deletion mutant of rck/p54 retaining only its N-terminal 289 amino acids demonstrated that the deleted C-terminal 184 amino acid domain is involved in the RNA unwinding activity. Conclusion:, These findings strongly suggest that rck/p54 may play an important role in translation initiation by restructuring mRNAs even in the cell and contribute to carcinogenesis. [source] Detection of elafin as a candidate biomarker for ulcerative colitis by whole-genome microarray screeningINFLAMMATORY BOWEL DISEASES, Issue 9 2006Carl-Fredrik Flach PhD Abstract The cause of ulcerative colitis (UC) is largely unknown. Microarray studies are an efficient way of investigating the various genes involved. Here, we have used whole-genome microarrays to clarify the clinical picture and to identify new biomarkers for improved diagnosis. Rectal biopsies were taken from five UC patients and five matched controls, and RNA transcripts were prepared. After labeling, each sample was individually applied to the microarray chips. All transcripts that were more than 10-fold up-regulated in all five patients were analyzed further in seven additional patients and seven controls using quantitative polymerase chain reaction. Of 47,000 transcripts examined, 4 were highly up-regulated in all patients: those encoding elafin, a secreted protease inhibitor, the ion and amino acid transporter B0,+ (SLC6A14), and the metabolic enzyme aldolase B, as well as a recently identified transcript named similar to numb-interacting homolog. The up-regulation of these transcripts appears to follow the progression of the disease because elevated expression was detected in the proximal part of the colon in patients with total colitis but not in patients with left-sided colitis. Immunohistologic examination showed very distinct differences in the expression of elafin. Extensive expression was detected in enterocytes and goblet cells of the affected mucosa, whereas there was no detectable expression in unaffected mucosa and in healthy controls. The results implicate four transcripts and proteins of special interest as possible targets for pharmacologic interference and as biomarkers in UC. Of these, elafin may be of special interest because it is a secreted protein that may be measured in body fluids. [source] Microarray-based DNA profiling to study genomic aberrations,IUBMB LIFE, Issue 7 2008Nic Waddell Abstract High throughput microarrays were initially developed to analyse the expression of many RNA transcripts in parallel. The technology has since been adapted to a variety of applications, one of which is the analysis of the genome to study DNA dosage and sequence content. Advances in microarray fabrication and completion of large-scale genome sequencing projects have enabled the rapid development of affordable array-based methods for high-resolution genome-wide assessment of DNA alterations. This review will describe the evolution of microarray assays to study genomic aberrations and will highlight how they have enabled researchers to gain insight into the biology of human diseases and how they will benefit research in the future. © 2008 IUBMB IUBMB Life, 60(7): 437,440, 2008 [source] Absence of detectable measles virus genome sequence in blood of autistic children who have had their MMR vaccination during the routine childhood immunization schedule of UKJOURNAL OF MEDICAL VIROLOGY, Issue 5 2006M.A. Afzal Abstract Leukocyte preparations from children with documented evidence of MMR vaccination and confirmed diagnosis of autism were examined by several assays designed to target multiple regions of the measles virus genome sequence. No sample was found positive by any method. The assays applied were highly sensitive, specific and robust in nature, and were based on the amplification of measles virus RNA transcripts by real-time quantitative RT-PCR (QRT-PCR) as well as by conventional RT-PCR-nested PCR. The assays applied were potentially able to detect measles virus RNA down to single figure copy numbers per reaction. The amount of total nucleic acid extract of leukocytes subjected to various measles virus-specific investigations was several fold higher than minimally required of a sample where measles virus persistence is well documented. This study failed to substantiate reports of the persistence of measles virus in autistic children with development regression. J. Med. Virol. 78:623,630, 2006. © 2006 Wiley-Liss, Inc. [source] Novel putative nonprotein-coding RNA gene from 11q14 displays decreased expression in brains of patients with schizophreniaJOURNAL OF NEUROSCIENCE RESEARCH, Issue 1 2003Oxana O. Polesskaya Abstract A modified method of differential display was employed to identify a novel gene (named PSZA11q14), the expression of which was reduced in brains from patients with schizophrenia. Decreased expression of PSZA11q14 was identified initially in Brodmann's area (BA) 21 from a small group of patients with schizophrenia (n = 4) and normal controls (n = 6) and was confirmed subsequently using independent RT-PCR assay in BA 21, 22, and 9, and in hippocampus from a larger group of patients with schizophrenia (n = 36) and controls (n = 35). PSZA11q14 is located on chromosome 11q14, an area shown previously to co-segregate with schizophrenia and related disorders in several families. Decreased expression of PSZA11q14 in patients with schizophrenia and its location on 11q14 provide converging lines of evidence indicating that PSZA11q14 may be involved in at least some cases of schizophrenia. PSZA11q14 shows no significant homology with any known gene. It has no introns and produces two RNA transcripts of ,4.5 and ,7.0 kb. The largest open reading frame (ORF) in the PSZA11q14 transcripts may potentially encode for a short polypeptide of 71 amino acids. High frequency of rare codons, the short size of this ORF, and low homology with mouse sequences, however, indicate that PSZA11q14 may instead represent a novel member of a family of nonprotein-coding RNA genes that are not translated and that function at the RNA level. PSZA11q14 is located within the first intron of the DLG-2 gene and transcribed in the opposite direction to DLG-2. These results suggest that PSZA11q14 may be considered a candidate gene for schizophrenia acting as an antisense regulator of DLG-2, which controls assembling functional N -methyl- D -aspartate (NMDA) receptors. © 2003 Wiley-Liss, Inc. [source] Cholangiocytes as immune modulators in rotavirus-induced murine biliary atresiaLIVER INTERNATIONAL, Issue 8 2009Barrett H. Barnes Abstract Background/Aims: Biliary atresia (BA) is a progressive disease characterized by bile duct inflammation and fibrosis. The aetiology is unknown and may be due to a virus-induced, autoimmune-mediated injury of cholangiocytes. Cholangiocytes are not only targets of injury but may also modulate hepatic inflammation. The aim of this study was to determine the immune profile of murine cholangiocytes and the ability to function as antigen-presenting cells (APCs) in culture with Rhesus rotavirus (RRV), poly I:C (viral mimic) or interferon-,/tumour necrosis factor-,. Methods/Results: Both the cholangiocyte cell line (long-term culture) and fresh, ex vivo cholangiocytes expressed APC surface markers major histocompatibility complex (MHC)-class I and II and CD40, while only the cultured cell line expressed costimulatory molecules B7-1 and B7-2. Despite APC expression, cultured cholangiocytes were unable to function as competent APCs in T-cell proliferation assays. Furthermore, both cultured and ex vivo cholangiocytes expressed RNA transcripts for many pro-inflammatory cytokines and chemokines. Conclusions: Although cholangiocytes contain APC molecules, they are incompetent at antigen presentation and cannot elicit effective T-cell activation. Upregulation of MHC-class I and II found in BA mice may serve to prime the cholangiocyte as a target for immune-mediated injury. Cholangiocytes produced many pro-inflammatory cytokines and chemokines in the setting of RRV infection and T-helper type 1 cytokine milieu, suggesting a role of cholangiocytes as immune modulators promoting the ongoing inflammation that exists in RRV-induced BA. [source] A microarray's view of life in the desert: adding a powerful evolutionary genomics tool to the packrat's middenMOLECULAR ECOLOGY, Issue 11 2009MARJORIE D MATOCQ Identifying the genetic architecture of adaptive traits is fundamental to understanding how organisms respond to their environment, over both ecological and evolutionary timeframes. Microarray technology that allows us to capture the simultaneous expression of thousands of genes provides unparalleled insight into how organisms cope with their environment at the transcriptional level. Recent studies in Molecular Ecology demonstrate how microarrays can rapidly identify which genes and pathways allow organisms to face some of the most fundamental physiological challenges posed by the environment, including compensation for the hypoxic and thermal stress of high-altitudes (Cheviron et al. 2008) and, in this issue, the biotransformation of toxic plant secondary compounds by mammals (Magnanou et al. 2009). Microarrays (Ekins et al. 1989; Fodor et al. 1991) are glass slides affixed with hundreds to thousands of oligonucleotide or cDNA sequences (probes). Messenger RNA transcripts (typically reverse transcribed to cDNA) are isolated from a tissue/sample of interest and hybridized to the array. Binding to specific probes indicates that a particular gene was transcriptionally active at or near the time of sampling and thus provides a potentially comprehensive measure of gene expression. Although a tremendously powerful tool, commercially produced oligonucleotide arrays are only available for a handful of model organisms. Nonetheless, evolutionary ecologists have exploited this resource by using a cross-species hybridization approach (e.g. Saetre et al. 2004), that is, hybridizing a model organism array with a nonmodel sample (Bar-Or et al. 2007). Magnanou et al. (2009) present a novel example of using a model muroid microarray (Agilent Technologies, Rattus) to study physiological response in a wild, nonmodel muroid, Neotoma. [source] Multiple copies of cytochrome oxidase 1 in species of the fungal genus FusariumMOLECULAR ECOLOGY RESOURCES, Issue 2009SCOTT R. GILMORE Abstract Using data from published mitochondrial or complete genomes, we developed and tested primers for amplification and sequencing of the barcode region of cytochrome oxidase 1 (COX1) of the fungal genus Fusarium, related genera of the order Hypocreales, and degenerate primers for fungi in the subdivision Pezizomycotina. The primers were successful for amplifying and sequencing COX1 barcodes from 13 genera of Hypocreales (Acremonium, Beauveria, Clonostachys, Emericellopsis, Fusarium, Gliocladium, Hypocrea, Lanatonectria, Lecanicillium, Metarhizium, Monocillium, Neonectria and Stilbella), 22 taxa of Fusarium, and two genera in other orders (Arthrosporium, Monilochaetes). Parologous copies of COX1 occurred in several strains of Fusarium. In some, copies of the same length were detected either by heterozygous bases in otherwise clean sequences or in different replicates of amplification and sequencing events; this may indicate multiple transcribed copies. Other strains included one or two introns. Two intron insertion sites had at least two nonhomologous intron sequences among Fusarium species. Irrespective of whether the multiple copy issue could be resolved by sequencing RNA transcripts, developing a precise COX1 -based barcoding system for Fusarium may not be feasible. The overall divergence among homologous COX1 sequences obtained so far is rather low, with many species sharing identical sequences. [source] Expression of receptor activator of nuclear factor-,B ligand by B cells in response to oral bacteriaMOLECULAR ORAL MICROBIOLOGY, Issue 3 2009X. Han Introduction:, We investigated receptor activator of nuclear factor-,B ligand (RANKL) expression by B lymphocytes during early and late aspects of the immune response to Aggregatibacter actinomycetemcomitans, a gram-negative, anaerobic bacterium associated with aggressive periodontal disease. Methods:, Expression of messenger RNA transcripts (tumor necrosis factor-,, Toll-like receptors 4 and 9, interleukins 4 and 10, and RANKL) involved in early (1-day) and late (10-day) responses in cultured rat splenocytes was examined by reverse transcription,polymerase chain reaction (RT-PCR). The immune cell distribution (T, B, and natural killer cells and macrophages) in cultured rat splenocytes and RANKL expression in B cells were determined by flow cytometric analyses. B-cell capacity for induction of osteoclast differentiation was evaluated by coculture with RAW 264.7 cells followed by a tartrate-resistant acid phosphatase (TRAP) activity assay. Results:, The expression levels of interleukins 4 and 10 in cultured cells were not changed in the presence of A. actinomycetemcomitans until cultured for 3 days, and peaked after 7 days. After culture for 10 days, the percentages of B and T cells, the overall RANKL messenger RNA transcripts, and the percentage of RANKL-expressing immunoglobulin G-positive cells were significantly increased in the presence of A. actinomycetemcomitans. These increases were considerably greater in cells isolated from A. actinomycetemcomitans -immunized animals than from non-immunized animals. RAW 264.7 cells demonstrated significantly increased TRAP activity when cocultured with B cells from A. actinomycetemcomitans -immunized animals. The addition of human osteoprotegerin-Fc to the culture significantly diminished such increases. Conclusion:, This study suggests that B-lymphocyte involvement in the immune response to A. actinomycetemcomitans through upregulation of RANKL expression potentially contribute to bone resorption in periodontal disease. [source] Revealing frequent alternative polyadenylation and widespread low-level transcription read-through of novel plant transcription terminatorsPLANT BIOTECHNOLOGY JOURNAL, Issue 7 2010Aiqiu Xing Summary Plant genetic engineering can create transgenic crops with improved characteristics by introducing trait genes through transformation. Appropriate regulatory elements such as promoters and terminators have to be present in certain configurations for the transgenes to be properly expressed. Five terminators native to soybean genes-encoding a MYB family transcription factor (MYB2), a Kunitz trypsin inhibitor (KTI1), a plasma membrane intrinsic protein (PIP1), a translation elongation factor (EF1A2) and a metallothionein protein (MTH1) were cloned and tested for their ability to enable transgene expression, mRNA polyadenylation and transcription termination. The terminators are as good as a control terminator of the potato proteinase inhibitor II gene (PINII) in conferring proper transgene expression, leading to mRNAs with various polyadenylation sites and terminating mRNA transcripts. RNA transcription read-through was detected in all transgenic plants and was quantified by qRT-PCR to be <1% at positions ,1 kb downstream of the 5, ends of different terminators. The detection of read-through RNA transcripts of the corresponding endogenous genes up to approximately 1 kb beyond the polyadenylation sites suggests that limited RNA transcription read-through is a normal phenomenon of gene expression. The study also provided more choices of terminators for plant genetic engineering when constructing DNA constructs containing multiple gene expression cassettes. [source] Quantitative RT-PCR analysis of estrogen receptor gene expression in laser microdissected prostate cancer tissueTHE PROSTATE, Issue 8 2009Thomas J. Walton Abstract BACKGROUND Real-time quantitative RT-PCR analysis of laser microdissected tissue is considered the most accurate technique for determining tissue gene expression. The discovery of estrogen receptor beta (ER,) has focussed renewed interest on the role of estrogen receptors in prostate cancer, yet few studies have utilized the technique to analyze estrogen receptor gene expression in prostate cancer. METHODS Fresh tissue was obtained from 11 radical prostatectomy specimens and from 6 patients with benign prostate hyperplasia. Pure populations of benign and malignant prostate epithelium were laser microdissected, followed by RNA isolation and electrophoresis. Quantitative RT-PCR was performed using primers for androgen receptor (AR), estrogen receptor beta (ER,), estrogen receptor alpha (ER,), progesterone receptor (PGR) and prostate specific antigen (PSA), with normalization to two housekeeping genes. Differences in gene expression were analyzed using the Mann,Whitney U -test. Correlation coefficients were analyzed using Spearman's test. RESULTS Significant positive correlations were seen when AR and AR-dependent PSA, and ER, and ER,-dependent PGR were compared, indicating a representative population of RNA transcripts. ER, gene expression was significantly over-expressed in the cancer group compared with benign controls (P,<,0.01). In contrast, PGR expression was significantly down-regulated in the cancer group (P,<,0.05). There were no significant differences in AR, ER, or PSA expression between the groups. This study represents the first to show an upregulation of ER, gene expression in laser microdissected prostate cancer specimens. CONCLUSIONS In concert with recent studies the findings suggest differential production of ER, splice variants, which may play important roles in the genesis of prostate cancer. Prostate 69: 810,819, 2009. © 2009 Wiley-Liss, Inc. [source] RNA editing: a driving force for adaptive evolution?BIOESSAYS, Issue 10 2009Willemijn M. Gommans Abstract Genetic variability is considered a key to the evolvability of species. The conversion of an adenosine (A) to inosine (I) in primary RNA transcripts can result in an amino acid change in the encoded protein, a change in secondary structure of the RNA, creation or destruction of a splice consensus site, or otherwise alter RNA fate. Substantial transcriptome and proteome variability is generated by A-to-I RNA editing through site-selective post-transcriptional recoding of single nucleotides. We posit that this epigenetic source of phenotypic variation is an unrecognized mechanism of adaptive evolution. The genetic variation introduced through editing occurs at low evolutionary cost since predominant production of the wild-type protein is retained. This property even allows exploration of sequence space that is inaccessible through mutation, leading to increased phenotypic plasticity and provides an evolutionary advantage for acclimatization as well as long-term adaptation. Furthermore, continuous probing for novel RNA editing sites throughout the transcriptome is an intrinsic property of the editing machinery and represents the molecular basis for increased adaptability. We propose that higher organisms have therefore evolved to systems with increasing RNA editing activity and, as a result, to more complex systems. [source] Nonsense-mediated RNA decay: A molecular system micromanaging individual gene activities and suppressing genomic noiseBIOESSAYS, Issue 5 2005Claudio R. Alonso Nonsense-mediated RNA decay (NMD) is an evolutionary conserved system of RNA surveillance that detects and degrades RNA transcripts containing nonsense mutations. Given that these mutations arise at a relatively low frequency, are there any as yet unknown substrates of NMD in a wild-type cell? With this question in mind, Mendell et al.1 have used a microarray assay to identify those human genes under NMD regulation. Their results show that, in human cells, NMD regulates hundreds of physiologic transcripts and not just those containing nonsense mutations. Among the NMD targets are a number of non-functional RNAs expressed from vestigial sequences derived from retroviral and transposable elements. These findings support the notion that NMD is a high profile post-transcriptional mechanism micromanaging the activity of multiple gene batteries and suppressing the expression of genetic remnants. BioEssays 27:463,466, 2005. © 2005 Wiley Periodicals, Inc. [source] Multiple P2Y receptor subtypes in the apical membranes of polarized epithelial cellsBRITISH JOURNAL OF PHARMACOLOGY, Issue 8 2000H L McAlroy Apical ATP, ATP, UTP and UDP evoked transient increases in short circuit current (ISC, a direct measure of transepithelial ion transport) in confluent Caco-2 cells grown on permeable supports. These responses were mediated by a population of at least three pharmacologically distinct receptors. Experiments using cells grown on glass coverslips showed that ATP and UTP consistently increased intracellular free calcium ([Ca2+]i) whilst sensitivity to UDP was variable. Cross desensitization experiments suggested that the responses to UTP and ATP were mediated by a common receptor population. Messenger RNA transcripts corresponding to the P2Y2, P2Y4 and P2Y6 receptors genes were detected in cells grown on Transwell membranes by the reverse transcriptase,polymerase chain reaction. Identical results were obtained for cells grown on glass. Experiments in which ISC and [Ca2+]i were monitored simultaneously in cells on Transwell membranes, confirmed that apical ATP and UTP increased both parameters and showed that the UDP-evoked increase in ISC was accompanied by a [Ca2+]i -signal. Ionomycin consistently increased [Ca2+]i in such polarized cells but caused no discernible change in ISC. However, subsequent application of apical ATP or UTP evoked a small rise in ISC but no rise in [Ca2+]i. UDP evoked no such response. As well as evoking increases in [Ca2+]i, the ATP/UTP-sensitive receptors present in Caco-2 cells thus allow direct control over ion channels in the apical membrane. The UDP-sensitive receptors, however, appear to simply evoke a rise in [Ca2+]i. British Journal of Pharmacology (2000) 131, 1651,1658; doi:10.1038/sj.bjp.0703743 [source] ORMDL3 , guilt by association?CLINICAL & EXPERIMENTAL ALLERGY, Issue 10 2008M. Wjst Summary A recent British,German study described ORMDL3 as a new asthma gene. Although the association with chromosome 17q12 marker is plausible from earlier linkage data, it is far from being clear which gene caused the association signal, as it is derived from a large linkage disequilibrium (LD) block. Not only Aiolos and GSDML but also distant genes that are regulated by this site may be relevant. There may be even unidentified RNA transcripts requiring a much more detailed genetic and functional analysis before finding ORMDL3 guilty by association. [source] | |||||||||||||||||||||||||