Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “RNA extraction”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,459 records · Page 81Linked to original sources
PubMedDate not supplied

Cardiac mRNA levels during the development and growth of the rat.

Developmental variations of RNA content and of total mRNA activity were examined in fetal, neonatal and adult rats. The amount of cardiac RNA extractable with the LiCl urea extraction procedure decreased from 3 mg/g tissue in the 18-day-old fetal heart to 1 mg/g in the 30-day-old heart and then to 0.5 mg/g in 100-day-old animals. Translations in the reticulocyte lysate translation system showed a similar pattern for total mRNA activity. It is shown that over this entire period both RNA content and mRNA activity vary as an exponential function of the growth rate of the heart and an explanation for this relationship is proposed. An examination of the translation products of the abundant mRNAs shows that the development of the heart is characterized by a general reduction in all mRNAs.

Aging↗
PubMed1979

Suppression of the accumulation of steroid-inducible glutamine synthetase mRNA on embryonic chick retinal polysomes by interferon preparation.

The suppression mechanism of glutamine synthetase [EC 6.3.1.2] induction mediated by chick interferon preparation was investigated in embryonic chick neural retina cell cultures. A translational assay was used to measure the level of mRNA coding for the enzyme. RNA extracted from the retinal polysomes was chromatographed on oligo(dT)-cellulose and translated in a cell-free protein synthesizing system derived from wheat germ. The newly synthesized enzyme was isolated by immunoprecipitation with anti-enzyme gamma-globulin and identified using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Neither polysomal profiles nor total protein synthesis directed by the RNA preparations was affected by interferon treatment. Comparing the amount of glutamine synthetase synthesized in vitro by equal amounts of mRNA fraction from retinas treated with or without interferon indicated that the suppression was associated with reduced level of the enzyme mRNA on polysomes.

Animals↗
PubMed1993

Mitochondrial RNA abundance in differentiating human colonic epithelial tumor cells estimated through use of a mitochondrial genome map.

We describe a procedure for quantification of mitochondrial (mt) RNA present in total RNA extracts of HT-29 human colonic adenocarcinoma cells grown under conditions for rapid growth (25 mM glucose) or differentiation (25 mM trehalose or 5 mM butyrate). Purified mt DNA was fragmented into specific coding regions using restriction endonuclease sites predicted from HeLa cell mt DNA sequence and probed with either 32P-labelled mt DNA or cDNA made from total RNA of HT-29 or HeLa cells. The amounts of probe that hybridized to various gene-encoded mt DNA fragments or RNA were quantified by laser densitometry. Use of 13 restriction endonucleases revealed that most if not all the mt DNA of HT-29 and K562 leukemic cells was comparable in size to that of HeLa cells. Relative levels of mt RNA from rapidly growing HT-29 and HeLa cells were lower than those measured for differentiated HT-29 cells induced by either trehalose or butyrate. In rapidly growing HT-29 cells and HeLa cells, the highest levels of specific mt RNAs were those encoded by mt DNA sequences immediately flanking the nested promoters and the heavy-strand replication origin (OH). Expression patterns of specific mt RNAs from HT-29 cells treated with butyrate and with trehalose were similar, but not identical. In either case, the mt RNAs that increased the most were those coded by mt DNA sequences located downstream from the light-strand replication origin (OL), suggesting a novel pattern of expression not seen before.

Butyrates↗
PubMed2002

Putative protein digestion in a sap-sucking homopteran plant pest (rice brown plant hopper; Nilaparvata lugens: Delphacidae)--identification of trypsin-like and cathepsin B-like proteases.

Sap-sucking phytophagous insect species of the order Hemiptera have been assumed not to carry out digestive proteolysis, but instead to rely on free amino acids in the phloem and xylem saps for their nutritional requirements. Extracts prepared from isolated guts of rice brown planthopper (Nilaparvata lugens), a homopteran crop pest, were shown to contain protease activity, with hydrolysis of both protein and synthetic peptide substrates being observed. Assays with specific inhibitors suggested that a trypsin-like serine protease was responsible for most of hydrolytic activity against synthetic substrates. A cDNA library was prepared from RNA extracted from N. lugens gut tissue, and screened for protease-encoding sequences. cDNAs for a cathepsin B-like protease and a trypsin-like protease were isolated and fully characterised; the latter exhibits a novel C-terminal region and an unusual activation mechanism, and represents a small gene family. Soya bean Kunitz trypsin inhibitor (SKTI) is an effective inhibitor of protein hydrolysis by N. lugens gut extracts in vitro, explaining why transgenic rice plants expressing this protein are partially resistant to the insect (Mol. Breed. 5 (1999) 1). It is suggested that digestive proteolysis may be widespread in sap-sucking homoptera, and can make a significant contribution to nutrition.

Amino Acid Sequence↗
PubMed1999

A novel family of plant splicing factors with a Zn knuckle motif: examination of RNA binding and splicing activities.

An important group of splicing factors involved in constitutive and alternative splicing contain an arginine/serine (RS)-rich domain. We have previously demonstrated the existence of such factors in plants and report now on a new family of splicing factors (termed the RSZ family) from Arabidopsis thaliana which additionally harbor a Zn knuckle motif similar to the human splicing factor 9G8. Although only around 20 kDa in size, members of this family possess a multi-domain structure. In addition to the N-terminal RNA recognition motif (RRM), a Zn finger motif of the CCHC-type is inserted in an RGG-rich region; all three motifs are known to contribute to RNA binding. The C-terminal domain has a characteristic repeated structure which is very arginine-rich and centered around an SP dipeptide. One member of this family, atRSZp22, has been shown to be a phosphoprotein with properties similar to SR proteins. Furthermore, atRSZp22 was able to complement efficiently splicing deficient mammalian S100 as well as h9G8-depleted extracts. RNA binding assays to selected RNA sequences indicate an RNA binding specificity similar to the human splicing factors 9G8 and SRp20. Taken together, these result show that atRSZp22 is a true plant splicing factor which combines structural and functional features of both h9G8 and hSRp20.

Alternative Splicing↗
PubMed2007

Hepatitis C virus productive infection in mononuclear cells from patients with cryoglobulinaemia.

The relationship between the occurrence of cryoglobulins and hepatitis C virus (HCV) productive infection in peripheral blood and bone marrow-derived lymphocytes was explored. HCV minus strand RNA, the viral replicative intermediate, was searched for by a polyA(+) tract strand-specific Tth-based reverse transcriptase-polymerase chain reaction (RT-PCR) in lymphoid cells of 46 patients with acute and chronic infection. The HCV minus strand was demonstrated in RNA extracted from six (13%) and five (11%) peripheral blood and bone marrow-derived lymphocytes, respectively. The HCV replicating form in lymphoid cells was associated strictly with mixed cryoglobulinaemia (MCG), in that it was found in six of 13 (46%) MCG patients, including two with B cell non-Hodgkin's lymphoma (NHL). No traces of HCV-negative strand RNA were found in four patients with acute hepatitis C, in 15 with chronic active hepatitis without extrahepatic disorders, in seven with monoclonal gammopathy of undetermined significance, and in seven with B-NHL without MCG. These results emphasize the direct role of the virus in the pathogenesis of MCG and support the contention that HCV is not specifically lymphotropic, its entry and replication in lymphoid cells being determined largely by selective interactions.

Acute Disease↗
PubMed2006

Preparation of His-tagged armored RNA phage particles as a control for real-time reverse transcription-PCR detection of severe acute respiratory syndrome coronavirus.

Armored RNA has been increasingly used as both an external and internal positive control in nucleic acid-based assays for RNA virus. In order to facilitate armored RNA purification, a His6 tag was introduced into the loop region of the MS2 coat protein, which allows the exposure of multiple His tags on the surface during armored RNA assembly. The His-tagged armored RNA particles were purified to homogeneity and verified to be free of DNA contamination in a single run of affinity chromatography. A fragment of severe acute respiratory syndrome coronavirus (SARS-CoV) genome targeted for SARS-CoV detection was chosen for an external positive control preparation. A plant-specific gene sequence was chosen for a universal noncompetitive internal positive control preparation. Both controls were purified by Co2+ affinity chromatography and were included in a real-time reverse transcription-PCR assay for SARS-CoV. The noncompetitive internal positive control can be added to clinical samples before RNA extraction and enables the identification of potential inhibitive effects without interfering with target amplification. The external control could be used for the quantification of viral loads in clinical samples.

Histidine↗
PubMed1976

Size, subunit composition, and secondary structure of the Friend virus genome.

Electron microscope and gel electrophoresis studies show that the high-molecular-weight (50 to 70S) RNA extract from Friend virus (FV) is a dimer with the same basic structure previously observed for the RNAs from RD-114 virus, baboon virus, and woolly monkey virus. This observation greatly strengthens the inference that the dimer structure is a general characteristic of the RNAs of all mammalian type C viruses. The FV dimer is slightly less stable than the RNA dimer of woolly monkey virus, which is, in turn, much less stable than those of RD-114 and baboon virus. There are three FV monomer components, small (S), medium (M), and large (L), with molecular lengths of 6.7 +/- 0.6, 7.7 +/- 0.6, and 9.5 +/- 0.6 kilobases, respectively. There are approximately equal amounts of the S and M components and much less of the L component. Most of the dimers are homodimers (SS, MM, and LL). The frequency of heterodimers (SM, SL, ML) is much less than expected for a random assortment model.

Friend murine leukemia virus↗
PubMed2005

Detection of API2-MALT1 fusion transcripts in cytologic specimens of patients with pulmonary mucosa-associated lymphoid tissue lymphoma.

Mucosa-associated lymphoid tissue (MALT) lymphoma constitutes up to 90% of primary pulmonary lymphomas, but its diagnosis is often difficult. API2-MALT1 fusion is specific to MALT lymphoma and is detected in nearly half of the pulmonary cases. Cytologic examinations have played a pivotal role in the diagnosis of pulmonary tumors; however, cytologic specimens have only infrequently been used for molecular studies. In this study, we performed a multiplex reverse transcription-polymerase chain reaction (RT-PCR) assay to detect the API2-MALT1 fusion transcript in archival cytologic specimens used as RNA sources. We studied 3 pulmonary MALT lymphoma cases that were positive for the fusion gene as detected with RNA extracted from diagnostic histologic specimens. In 1 case, a conventional PCR clonality assay for the immunoglobulin heavy chain gene rearrangement failed to detect the monoclonality. In all 3 cases, the fusion transcript was successfully detected in the cytologic specimens of sputum, bronchoalveolar lavage fluid, bone marrow smears, and pleural effusions. This finding suggests that such specimens can be used as RNA sources in multiplex RT-PCR assays for the API2-MALT1 fusion transcript. The detection of API2-MALT1 fusion as carried out with these specimens would be useful as an ancillary assay for the diagnosis, staging, and follow-up of pulmonary MALT lymphoma.

Aged↗
PubMed1993

Presence of subgenomic mRNAs in virions of coronavirus IBV.

The presence of subgenomic mRNAs in virions of IBV was examined by probing Northern blots of RNA extracted from virions using as a probe a cDNA of the 3'-terminal nucleocapsid protein (N) gene. This detects all five mRNAs because of the 3'-coterminal, nested-set arrangement of coronavirus mRNAs. The mRNAs were readily detected even after extensive purification of virions and after RNase A treatment of virions. In sucrose gradients the peaks of virus particles, genomic RNA (gRNA), and mRNAs were coincident. Cellular mRNA was not detected in virions. The molar ratio of gRNA to each mRNA ranged from about 10 to 30 for IBV-Beaudette and 25 to 800 for IBV-M41. The molar ratio of genomic to intracellular viral mRNAs was also determined. From this it was estimated that the efficiency of incorporation of gRNA into virions was at least 20- to 100-fold greater, depending on the mRNA species, for IBV-Beaudette and 100- to 500-fold for IBV-M41. It is concluded that most virions contain only gRNA or contain only one species of mRNA on average in addition to gRNA.

Animals↗
PubMed2006

Real-time RT-PCR detection of Bovine Viral Diarrhoea virus in whole blood using an external RNA reference.

A novel two-step real-time RT-PCR assay using SYBR Green I was developed for the detection of acute Bovine Viral Diarrhoea virus (BVDV) infection in whole blood from cattle. During infection animals experience a characteristic transient leucopenia and the number of cells per volume of blood changes over time; so quantitation of viral load by reference to a cellular housekeeping gene is not ideal as this may hide significant animal to animal variation. Therefore, to facilitate comparison of different samples, an external RNA reference was used for normalisation whereby each sample was spiked with the RNA virus, Canine Enteric Coronavirus (CECov), prior to RNA extraction, for comparative purposes. Real-time RT-PCR was carried out with two primer sets designed to amplify either a 156 bp region of the BVDV 5'-UTR or a 280 bp region of the CECov nucleocapsid protein gene. Linearity and efficiency of the assay was established and the method assessed using samples from BVDV-challenged calves. Viral RNA was quantified on days 6 and 14 post-challenge by real-time RT-PCR. Infectious virus isolation by traditional cell culture was negative after day 7. This study demonstrates encouraging results for rapid, sensitive and reliable detection of acute BVDV infection and provides an alternative real-time RT-PCR method for use on whole blood samples or samples where suitable housekeeping genes are not available.

5' Untranslated Regions↗
PubMed1969

Analysis of the ribonucleic acid of murine leukemia virus.

Cells producing the Rauscher strain of murine leukemia virus (MLV) were exposed to (3)H-uridine, and labeled virus was collected at hourly intervals. Ribonucleic acid (RNA) extracted from virions (vRNA) had a characteristic single peak when analyzed by electrophoresis in polyacrylamide-agarose composite gels. Exposure of vRNA to dimethyl sulfoxide, urea, formaldehyde, or heat altered the mobility to a faster moving form (vRNA'). This vRNA' sedimented more slowly than native vRNA in sucrose gradients. Incubation of labeled virions at 37 C resulted in fragmentation of viral RNA which was detectable only after denaturation. Also, large differences in the temperature required for the change from vRNA to vRNA' were seen with alterations in NaCl concentration. These experiments demonstrate that the vRNA of MLV is held in a specific conformation by hydrogen bonds distributed over a large part of the molecule. The possibility that an undefined factor is associated with viral RNA is discussed.

Centrifugation, Density Gradient↗
PubMed2000

Optimized rapid amplification of cDNA ends (RACE) for mapping bacterial mRNA transcripts.

A simple, efficient and sensitive RACE-based procedure was developed for the determination of unknown 5' regions from bacterial cDNA. A number of critical modifications were made to the standard RACE method, including the optimization of the RNA extraction, reverse transcription and PCR conditions. This procedure was used to accurately determine the site of transcript initiation and structure of the promoter region of the Helicobacter pylori aspartate carbamoyltransferase gene (pyrB). The technique avoids many of the difficulties associated with established bacterial transcript mapping protocols and can be performed in two days starting with less than 1 microgram of total RNA. The modifications described here have significant potential for the identification of transcript start sites of bacterial genes and non-polyadenylated eukaryotic RNA.

DNA, Complementary↗
PubMed1999

Failure to demonstrate Borna disease virus genome in peripheral blood mononuclear cells from psychiatric patients in Korea.

RNA, extracted from peripheral blood mononuclear cells (PBMC) obtained from 81 Korean psychiatric patients (39 with schizophrenia, 33 with bipolar affective disorders and nine with major depression), was analyzed for a 391-nucleotide, highly conserved region of the p24 protein-encoding ORF II of Borna disease virus (BDV), using nested reverse transcription-polymerase chain reaction (RT-PCR). BDV genomic RNA was not detected in PBMC from any of the 81 Korean psychiatric patients. These data do not support an etiologic association between BDV infection and neuropsychiatric disorders in humans.

Adult↗
PubMed2005

Bones, teeth, and genes: a genomic homage to Harry Sicher's "Axial Movement of Teeth".

AIM: The model of the unopposed rodent molar was used to study the morphologic and genetic mechanisms of tooth eruption. METHODS: Left maxillary molar teeth of 12-day-old Swiss-Webster mice were extracted under anesthesia, and mandibular molars were allowed to supererupt. To trace areas of tissue remodeling and to determine areas of new tissue formation, mice were injected with fluorescent dyes, tetracycline, alizarin red, and calcein blue. Subsequent to sacrifice, mandibular tissue blocks were prepared for ultrathin ground sections, fluorescent microscopy, and von Kossa's mineral detection procedure. A second set of specimens was prepared for RNA extraction and microarray analysis. RESULTS: The data established significant eruption of first and second mandibular mouse molars 12 days after complete extraction of antagonists, exceeding the control side by 0.13 mm. Labeled tissue sections revealed significant amounts of new bone and cementum apposition on the unopposed side compared to the control side, as revealed by fluorescent markers and ultrathin ground sections. Microarray transcript level comparisons between the experimental and the control groups demonstrated significant (more than twofold) increase in gene expression of elastin and tenascin C extracellular matrix proteins; brevican, lumican, and biglycan proteoglycans; as well as fibroblast growth factor 9. CONCLUSION: In this study, the authors have established the unopposed mouse molar as a model to study tissue dynamics during the axial movement of teeth. The data indicated significant new formation of bone and cementum in tandem with increased expression of extracellular matrix-related genes.

Animals↗
PubMed1990

Development and characterization of nucleic acid probes to infectious bursal disease viruses.

Radiolabeled cDNA probes were prepared using both segments of double-stranded genomic infectious bursal disease virus (IBDV) RNA as template. The probes were synthesized and labeled with 32P using random primers and reverse transcriptase. Probes were prepared to the genomic RNA extracted from a pathogenic serotype 1 virus (ST-C) and from an attenuated serotype 1 vaccine virus (D-78) which is commercially available. These probes were determined to range in size from approximately 200 to 1500 nucleotides in length using a 6% denaturing polyacrylamide gel. The probes were used in a dot hybridization assay and detected approximately 10 ng of IBDV RNA. In addition, they detected genomic RNA from five different subtypes of IBDV serotype 1 and from two serotype 2 viruses. The probes appeared to be specific for viral RNA since hybridization to cell culture nucleic acid was not detected.

Animals↗
PubMed2001

Regulation of gonadotropin subunit transcription after ovariectomy in the rat: measurement of subunit primary transcripts reveals differential roles of GnRH and inhibin.

The aim of this study was to determine if the changes in gonadotropin subunit gene expression following ovariectomy reflect transcriptional and/or posttranscriptional regulation by GnRH or inhibin. Subunit transcription rates were determined by recently developed quantitative RT-PCR for subunit primary transcripts (as an indicator of gene transcription), which allow us to measure both mRNA and PT from RNA extracted from a single pituitary. Following ovariectomy, LHbeta PT concentrations increased 2- to 3-fold between 72 h and 7 d, paralleling changes in serum LH and LHbeta mRNA. In contrast, serum FSH, FSHbeta mRNA, and FSHbeta PT concentrations were 6- to 9-fold greater 12-24 h after ovariectomy followed by an additional 2.5-fold increase at 72 h. Although alpha RNA was elevated at 72 h after ovariectomy, alpha-primary transcript did not change. GnRH antagonist prevented the increase in LHbeta-PT at 72 h, but had no effect on the increase in FSHbetaPT at 12 h and was only partially effective at 72 h. The acute GnRH-independent increase in FSHbeta-primary transcript after ovariectomy could be duplicated by the administration of inhibin antiserum to intact rats; inhibin-alpha antiserum did not affect LHbeta-primary transcript, but increased FSHbeta-primary transcript concentrations 8- to 11-fold. The half-disappearance rates of LHbeta and FSHbeta primary transcripts were measured after GnRH blockade or administration of recombinant human inhibin A. The half-disappearance times for LHbeta and FSHbeta primary transcripts following GnRH blockade were 13 and 17 min, respectively; the mRNAs did not change. The effects of inhibin were specific for FSHbeta; 60 min after inhibin FSHbeta-primary transcript was undetectable with a half-disappearance time of 19 min, additionally FSHbeta mRNA levels also fell with a half-life of 94 min. In conclusion, these data support previous evidence that GnRH regulates gonadotropin gene expression primarily at the level of transcription. However, the acute increase in FSHbeta-primary transcript after ovariectomy or immunoneutralization of inhibin-alpha, and the rapid fall in FSHbeta-primary transcript following rh inhibin, provide novel evidence that inhibin suppresses FSHbeta gene transcription in addition to its action in regulating FSHbeta mRNA stability.

Animals↗
PubMed1999

Localization of interferon regulatory factor-1 (IRF-1) in nonpregnant human endometrium: expression of IRF-1 is up-regulated by prolactin during the secretory phase of the menstrual cycle.

PRL expression in the human uterus is up-regulated during the mid to late secretory phase of the menstrual cycle. This coincides with up-regulation of the expression of the PRL receptor, which is localized primarily to the endometrial glandular epithelial cells. Recent data have demonstrated activation of the Jak (Janus kinase)/Stat (signal transducer and activator of transcription) signaling pathway in the secretory endometrium after stimulation with exogenous PRL. However, the target genes for the action of PRL on the endometrial epithelial cells have not been elucidated. In this study we have investigated the pattern/site of expression of the transcription factor interferon regulatory factor-1 (IRF-1) as well as the effect of exogenous PRL on the transcription of IRF-1 in the human endometrium during the mid to late secretory phase of the menstrual cycle. Expression of the IRF-1 gene was confirmed by RNase protection assays using a 260-bp homologous [alpha-32P]UTP-labeled IRF-1 complementary ribonucleic acid (RNA) probe and 10 microg total RNA extracted from human endometrium (n = 5) collected between days 19 and 26 of the menstrual cycle. Northern and Western blot analyses were conducted on secretory phase human endometrium (n = 3) using human [alpha-32P]dCTP-labeled IRF-1 complementary DNA and antihuman IRF-1 antibody. Expression of the IRF-1 gene in the secretory phase endometrium was encoded by a RNA transcript of approximately 2.1 kb and a protein of 48 kDa. Furthermore, expression of the IRF-1 gene in the secretory phase endometrium was localized by immunohistochemistry predominantly to the glandular epithelial cells as has been shown previously for the PRL receptor. To investigate the effect of PRL on expression of IRF-1, human endometrial biopsies (n = 3) collected between days 24-26 of the menstrual cycle were cultured in the presence of cycloheximide with or without 100 ng/mL human PRL for 2 and 4 h. Culture of endometrial tissue with PRL for 2 and 4 h resulted in 2.9 +/- 0.3-fold (P < 0.01) and 1.7 +/- 0.1-fold induction of expression of the IRF-1 gene, respectively. These data demonstrate the expression of the transcription factor IRF-1 in the glandular epithelium of the endometrium and its regulation by PRL during the secretory phase of the menstrual cycle. Previous observations of the temporal up-regulation of expression of both PRL and PRL receptors in the secretory human endometrium and their localization to the stromal and glandular compartments, respectively, suggest that endometrial PRL mediates transcription of the IRF-1 gene in a paracrine fashion.

Blotting, Northern↗