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PubMed1990

Differential expression of TGF beta isoforms in murine palatogenesis.

We have studied the expression of genes encoding transforming growth factors (TGFs) beta 1, beta 2 and beta 3 during development of the secondary palate in the mouse from 11.5 to 15.5 days postcoitum using in situ hybridisation. The RNA detected at the earliest developmental stage is TGF beta 3, which is localised in the epithelial component of the vertical palatal shelf. This expression continues in the horizontal palatal shelf, predominantly in the medial edge epithelium, and is lost as the epithelial seam disrupts, soon after palatal shelf fusion. TGF beta 1 RNA is expressed with the same epithelial pattern as TGF beta 3, but is not detectable until the horizontal palatal shelf stage. TGF beta 2 RNA is localised to the palatal mesenchyme underlying the medial edge epithelia in the horizontal shelves and in the early postfusion palate. The temporal and spatial distribution of TGF beta 1, beta 2 and beta 3 RNAs in the developing palate, together with a knowledge of in vitro TGF beta biological activities, suggests an important role for TGF beta isoforms in this developmental process.

Animals↗

PubMed2006

[An epidemiological investigation of bats carrying SARS-CoV in Guangzhou and its vicinity].

OBJECTIVE: To detect serve acute respiratory syndrome-associated coronavirus (SARS-CoV) and SARS-like-CoV in fruit bats captured in Guangzhou and its vicinity. METHODS: Totally 927 bats of 9 species (Cynopterus sphinx, Rousettus leschenaulti, Miniopterus schreibersi, Hipposideros pratti, Rhinolophusasinicus, Scotophilusakuhlii, Hipposideros Pomona, Rhinolophus affinis, and Rhinolophus pusillus) captured in Guangzhou and its vicinity from September 2004 to November 2005 were available for this investigation, from which 3,043 samples (813 throat swasb, 524 sera, 853 lung tissues and 853 colorectal tissue specimens) were obtained. SARS-Cov and SARS-like-CoV were detected in these specimens using diagnostic kit for novel coronavirus N protein (ELISA), SARS-CoV Virus RNA detection kit, fluorescence PCR, Genchip, RT-PCR and cell isolation culture methods. RESULTS AND CONCLUSION: No SARS-CoV and SARS-like-CoV were detected in the 3043 samples, indicating the current absence of SARS-CoV and SARS-like-CoV in the bats captured in Guangzhou and its vicinity.

Animals↗

PubMed1991

Detection of polyadenylated RNA in hepatitis B virus-infected peripheral blood mononuclear cells by polymerase chain reaction.

Polymerase chain reaction (PCR) with a reverse transcriptase step characterized a specific transcription activity in hepatitis B virus (HBV)-infected peripheral blood mononuclear cells (PBMC) in two patients (1 and 2) with chronic hepatitis positive for antibody to hepatitis B core antigen (HBc). Patient 1 was also coinfected with human hepatitis delta virus. A patient who cleared HBV replication after antiviral treatment with vidarabine served as negative control. HBV-specific RNA poly A sequences were detected by PCR in PBMC of patients 1 and 2 even without detectable HBV DNA (patient 2) as shown by dot blot and PCR assays. RNA sequences were found in both the nucleus and cytoplasm. The demonstration of HBV mRNA sequences within PBMC suggests the transcription of viral DNA, in agreement with the findings of HBV surface antigen in PBMC. The results in patient 1 demonstrated HBV mRNA sequences in leukocytes even without PCR-detectable HBV DNA sequences, likely due to ongoing hepatitis delta virus replication.

Base Sequence↗

PubMed2000

The ribosomal RNA processing machinery is recruited to the nucleolar domain before RNA polymerase I during Xenopus laevis development.

Transcription and splicing of messenger RNAs are temporally and spatially coordinated through the recruitment by RNA polymerase II of processing factors. We questioned whether RNA polymerase I plays a role in the recruitment of the ribosomal RNA (rRNA) processing machinery. During Xenopus laevis embryogenesis, recruitment of the rRNA processing machinery to the nucleolar domain occurs in two steps: two types of precursor structures called prenucleolar bodies (PNBs) form independently throughout the nucleoplasm; and components of PNBs I (fibrillarin, nucleolin, and the U3 and U8 small nucleolar RNAs) fuse to the nucleolar domain before components of PNBs II (B23/NO38). This fusion process is independent of RNA polymerase I activity, as shown by actinomycin D treatment of embryos and by the lack of detectable RNA polymerase I at ribosomal gene loci during fusion. Instead, this process is concomitant with the targeting of maternally derived pre-rRNAs to the nucleolar domain. Absence of fusion was correlated with absence of these pre-rRNAs in nuclei where RNA polymerase II and III are inhibited. Therefore, during X. laevis embryogenesis, the recruitment of the rRNA processing machinery to the nucleolar domain could be dependent on the presence of pre-rRNAs, but is independent of either zygotic RNA polymerase I transcription or the presence of RNA polymerase I itself.

Animals↗

PubMed1994

[Tv1--a new family of Drosophila virilis retrotransposons].

A new method for isolation and cloning of functionally active retrotransposons was proposed and tested. The method is based on the hypothesis about the universal character of retrotransposition through reverse transcription. A new retrotransposon family (Tvl) was coned from the Drosophila virilis genome. A full-length Tvl copy was 7 kb. The cell line under consideration contained 500-1000 Tvl copies per cell, i.e., it accounted for 0.3% of the genome. Tvl RNA, detected in the cell culture, was almost absent in cells of adult flies. A 7-kb polyadenylated RNA was the main transcript of Tvl. Extrachromosomal circular and linear Tvl copies were cloned and characterized. The following features of Tvl structural organization were studied: (1) element was flanked by perfect direct repeats of 453 bp size (long terminal repeats, LTRs); (2) element sequences adjacent to the LTRs were homologous to binding sites of primer serine tRNA and the polypurine blocks of retrotransposons 17.6 and 297; and (3) expected transcription of LTRs occurred as for known retrotransposons, --producing RNA with a direct terminal repeat.

Animals↗

PubMed1971

Nucleic Acid Metabolism in Germinating Onion: I. Changes in Root Tip Nucleic Acid during Germination.

Nucleic acid synthesis in the G(1) cell population of the 1-millimeter apex of the Allium cepa embryo was studied during the initial 73 hours of germination. Quantitative data indicate that the total amount of RNA per cell began to increase after 18 hours of germination while the initial DNA per cell increase did not occur until some 20 hours later. Polyacrylamide gel electrophoresis patterns of (3)H-uridine-labeled total nucleic acid samples indicated that synthesis of all detectable RNA fractions present in the pre-emergent 1-millimeter apex (i.e., cytoplasmic and "chloroplast-like" RNA) began at approximately the same time (18 hours). Synthesis of the various cytoplasmic RNA fractions continued throughout the germination period. Data indicating synthesis of the "chloroplast-like" RNA were obtained only for the initial 36 hours of germination. Specific radioactivity of (3)H-uridine-labeled total nucleic acid increased during the first 41.5 hours of germination but then decreased while the accumulation of RNA per cell continued to increase throughout the 73-hour period. In addition, a method is described which reduced the bacterial contamination of Allium seed to a level not detectable by incorporation of radioactive precursors into bacterial ribosomal RNA.

Journal Article↗

PubMed1993

Detection of hepatitis C viral RNA in sporadic acute non-A, non-B hepatitis by polymerase chain reaction. Its usefulness for the early diagnosis of seronegative infection.

To determine the prevalence of hepatitis C viral infection in patients with sporadic non-A, non-B (NANB) acute hepatitis, hepatitis C viral RNA was studied in the plasma of 15 patients by reverse transcription-polymerase chain reaction assay. Plasma samples were sequentially obtained from 15 patients, and polymerase chain reaction was performed with two nested pairs of primers deduced from the 5'-non-coding region of hepatitis C viral sequences. Anti-C100 and anti-GOR antibodies were also measured with an enzyme-linked immunosorbent assay system. Plasma hepatitis C viral RNA was detected transiently in 7 of 15 patients (47%) at an early phase of the clinical course, while anti-C100 antibodies were detectable in only 2 (29%) of hepatitis C viral RNA-positive patients, and in 1 (13%) of the negative patients. Of 7 patients that were positive for plasma hepatitis C viral RNA, 4 (57%) had relapsing or protracted courses. In contrast, in all patients with undetectable hepatitis C viral RNA, hepatitis C viral RNA recovered and remained normal for at least 1 year. Thus, hepatitis C viral infection represents almost half the patients with acute sporadic NANB hepatitis, and detection of hepatitis C viral RNA in an early clinical phase is superior to anti-C100 measurement for diagnosing acute sporadic hepatitis C viral infection.

Adult↗

PubMed2002

Low expression of insulin in the thymus of non-obese diabetic mice.

Insulin is a predominant autoantigen in IDDM in man and the NOD mouse. Failure of negative selection of diabetogenic T cells in thymus may be an important pre-disposing cause of the disease. To obtain insight into negative selection against such T-cell clones the thymic expression of insulin was studied in NOD and Balb/c mice by quantitative competitive RT-PCR. We detected RNA for insulin in the thymus of 3-week-old Balb/c mice as well as in NOD mice. However, the NOD mice expressed only half as many insulin transcripts as the Balb/c mice. Also, insulin protein was detected in the thymic medulla of both Balb/c and NOD mice. Furthermore, thymic RNA preparations were investigated for the presence of insulin transcription factors. None of the known pancreatic transcription factors for insulin; Pdx-1, Pax6 or Nkx6.1 were detectable in the thymus of Balb/c mice. These results support the idea that low insulin expression in the thymus may be a predisposing cause for development of diabetes in NOD mice analogous with what has been found in humans with the disease-disposing IDDM2 allele. Furthermore, our results suggest that insulin expression in the thymus may be regulated by different principles from those in the pancreas.

Aging↗

PubMed2004

Analysis of HCV co-infection with occult hepatitis B virus in patients undergoing IFN therapy.

BACKGROUND/AIM: Occult hepatitis B virus (HBV) infection is characterized by the presence of HBV DNA in the absence of hepatitis B surface antigen (HBsAg) in the patient serum. Although such infections have been identified in patients with chronic hepatitis C, the clinical significance of those co-infections is still not understood. Our aim was, therefore, to assess the prevalence and clinical consequences of occult HBV infection in chronic hepatitis C patients undergoing antiviral therapy. METHODS: The study population consisted of 53 HBsAg-negative patients with chronic hepatitis C treated with IFN/ribavirin or IFN/ribavirin/amantadine. Nine patients experienced a viral breakthrough (BT), 30 were non-responders (NR) and 14 were responders (R). HBV-DNA detection by PCR was performed using primers specific for the S region of the HBV genome and HCV-RNA detection by PCR with primers localised in both the 5'NC and core region of HCV genome, before, during and after treatment. Viral genome sequences were also studied. RESULTS: Occult HBV genomes were found in the serum of four of 53 (7.5%) patients, unrelated to anti-HBc status. No significant differences in biochemical, virological, or histological markers, age, duration of infection, were observed in patients with or without HBV DNA. There was an inverse correlation in the evolution of HBV DNA and HCV RNA levels. Direct sequencing showed that S gene of occult HBV presented mutations in the "a" determinant while no specific mutation in the core region of HCV was observed. None of the four patients co-infected with HBV and HCV were responders to anti-HCV therapy. CONCLUSION: In our clinical setting, the prevalence of occult HBV co-infection among patients with chronic hepatitis C was low and independent of the presence of markers of previous HBV infection. Further studies in larger cohort of patients are warranted to determine if occult HBV co-infection may be involved in HCV resistance to combination therapy.

Adult↗

PubMed2004

Retrospective differentiation of canine distemper virus and phocine distemper virus in phocids.

Formalin-fixed paraffin-embedded tissues from one Caspian seal (Phoca caspica), one harp seal (Phoca groenlandica), one hooded seal (Cystophora cristata), and one harbor seal (Phoca vitulina vitulina) were used to compare the utility of immunohistochemistry (IHC) versus that of a novel seminested reverse transcriptase polymerase chain reaction (RT-PCR) to detect and differentiate canine distemper virus (CDV) and phocine distemper virus (PDV). Four antibodies made against PDV were able to detect both viruses. Two antibodies made against cetacean morbillivirus (CMV) did not label antigens from either CDV or PDV. A third anti-CMV antibody inconsistently stained CDV antigens but did not label PDV antigens. The seminested RT-PCR was able to detect RNA of the phosphoprotein gene in all positive cases. Nucleotide sequence analyses of seminested RT-PCR products were used to differentiate CDV RNA from PDV RNA. From these data, it was determined that IHC using antibodies generated against PDV provided a rapid means of detection for both CDV and PDV antigens; however, differentiation between CDV and PDV was achieved only with the RT-PCR assay.

Animals↗

PubMed1983

Bluegill virus is a ribovirus of positive-strand polarity.

RNA was extracted from purified Bluegill virus (BGV) and fractionated onto a poly (U)-Sepharose-4 B column. More than 70 per cent of this RNA became bound and could be subsequently eluted from the column. By polynucleotide phosphorylase digestion, the poly (A) sequences were located at the 3'-terminus of the RNA. This RNA and purified BGV RNA were infectious as shown by plaque assay titration of the virus produced. Furthermore, we were unable to detect RNA polymerase activity in preparations of BGV. These results indicate that the genome in the BGV particle is a positive-strand RNA.

Animals↗

PubMedDate not supplied

The use of competitive affinity chromatography for the isolation of proteins which promote transcription.

A method is described for isolating proteins which bind preferentially to specific sequences of DNA and is used to enrich preparations in proteins promoting eukaryotic gene transcription. An ion-exchange fraction which promotes the transcription of the ovalbumin gene in in vitro runoff assays was isolated from the oviducts of diethylstilbesterol-stimulated chicks. This fraction was recirculated between two coupled columns, one containing random sequences of prokaryotic DNA and the other a specific cloned DNA fragment from the 5' region of the ovalbumin gene. Recirculation was performed in the presence of a decreasing salt gradient, after which columns were disconnected and separately eluted. The eluate obtained from the column containing cloned DNA showed a preference for binding to DNA fragments derived from the ovalbumin gene when examined in nitrocellulose filter binding assays. This fraction retained the ability of its precursor to promote gene transcription in a concentration-dependent manner. Active preparations were also examined in assays measuring total RNA synthesis from native DNA templates. Although the fraction isolated from the column of specific DNA had no detectable RNA polymerase activity itself, it enhanced the activity of calf thymus RNA polymerase II. The method presented should find general application in the purification of factors which regulate biological processes by binding to specific sequences of DNA.

Animals↗

PubMed2003

Incorporation of reporter molecule-labeled nucleotides by DNA polymerases. II. High-density labeling of natural DNA.

The modification of nucleic acids using nucleotides linked to detectable reporter or functional groups is an important experimental tool in modern molecular biology. This enhances DNA or RNA detection as well as expanding the catalytic repertoire of nucleic acids. Here we present the evaluation of a broad range of modified deoxyribonucleoside 5'-triphosphates (dNTPs) covering all four naturally occurring nucleobases for potential use in DNA modification. A total of 30 modified dNTPs with either fluorescent or non-fluorescent reporter group attachments were systematically evaluated individually and in combinations for high-density incorporation using different model and natural DNA templates. Furthermore, we show a side-by-side comparison of the incorporation efficiencies of a family A (Taq) and B (Vent(R) exo-) type DNA polymerase using the differently modified dNTP substrates. Our results show superior performance by a family B-type DNA polymerase, Vent(R) exo-, which is able to fully synthesize a 300 bp DNA product when all natural dNTPs are completely replaced by their biotin-labeled dNTP analogs. Moreover, we present systematic testing of various combinations of fluorescent dye-modified dNTPs enabling the simultaneous labeling of DNA with up to four differently modified dNTPs.

Base Sequence↗

PubMed2005

RNA template-directed photoligation via 5-carboxyvinyl-2'-deoxyuridine.

An efficient RNA template-directed photoligation of oligodeoxynucleotides (ODNs) via 5-carboxyvinyl-2'-deoxyuridine ((CV)U) was described. When ODN containing (CV)U at the 5' end was photoirradiated with ODN containing a pyrimidine base at the 3' end in the presence of template RNA, an efficient photoligation was observed. RNA template-directed photoligation of ODNs should provide a useful technique for sensitive and accurate RNA detection.

Deoxyuridine↗

PubMedDate not supplied

A contribution to the incidence of nucleoli in normal human blood monocytes.

BACKGROUND AND OBJECTIVE: Normal blood monocytes were studied in blood donors to provide more information on the presence of nucleoli and nucleolar types in these cells. METHODS: Nucleoli in monocytes were visualized using cytochemical procedures that detect RNA and characteristic nucleolar proteins, i.e. nucleophosmin, nucleolin, fibrillarin and AgNOR proteins, in peripheral blood smears. RESULTS: Nucleoli were detected in all blood monocytes. The nucleolar coefficient (number of nucleoli per cell) was 2.6 and no differences were found between men and women. Concerning the incidence of nucleolar types, monocytes from both male and female blood donors possessed mainly only inactive micronucleoli characteristic of mature or advanced maturation stages of blood cells; however, 16-20% of monocytes also contained functionally dominant ring-shaped nucleoli, which reflect a reversible decrease of rRNA transcription and in blood cells are intermediate stages between actively transcribing large nucleoli in highly immature cells and inactive micronucleoli in terminal nucleolated maturation stages. Monocytes containing large nucleoli with a relatively uniform distribution of RNA characteristic of immature or stimulated blood cells were rare (< 2%). INTERPRETATION AND CONCLUSIONS: Nucleoli are present in all normal blood monocytes. The incidence of the main nucleolar types represents a very convenient complementary marker for evaluating the maturation and possibly the stimulated state of these cells.

Cell Nucleolus↗

PubMed2005

Isolation and detection of enterovirus RNA from large-volume water samples by using the NucliSens miniMAG system and real-time nucleic acid sequence-based amplification.

Concentration of water samples is a prerequisite for the detection of the low virus levels that are present in water and may present a public health hazard. The aim of this study was to develop a rapid, standardized molecular method for the detection of enteroviruses in large-volume surface water samples, using a concentration method suitable for the detection of infectious viruses as well as virus RNA. Concentration of water was achieved by a conventional filter adsorption-elution method and ultrafiltration, resulting in a 10,000-fold concentration of the sample. Isolation of virus RNA by a silica-based RNA extraction method was compared with the nonmagnetic and magnetic NucliSens RNA isolation methods. By using the silica-based RNA extraction method in two out of five samples, enterovirus RNA was detected, whereas four out of five samples were positive following RNA isolation with magnetic silica beads. Moreover, estimated RNA levels increased at least 100 to 500 times. Furthermore, we compared enterovirus detection by an in-house reverse transcription (RT)-PCR with a novel commercially available real-time nucleic acid sequence-based amplification (NASBA) assay. We found that the rapid real-time NASBA assay was slightly less sensitive than our in-house RT-PCR. The advantages, however, of a commercial real-time NASBA assay, like the presence of an internal control RNA, standardization, and enormous decrease in turnaround time, makes it an attractive alternative to RT-PCR.

Animals↗

PubMed1995

Abnormal glucocorticoid receptor-activator protein 1 interaction in steroid-resistant asthma.

Glucocorticosteroids are a very effective treatment for asthma and other chronic inflammatory diseases. However, a small proportion of patients is resistant to the therapeutic effects of glucocorticoids. Pharmacokinetic and ligand binding studies suggest that the molecular abnormality in steroid resistance lies distal to nuclear translocation. We have previously reported that there is a decreased ability of glucocorticoid receptors (GR) to bind to the DNA-binding site in peripheral blood mononuclear cells (PBMC) after dexamethasone treatment. This reduced DNA binding was due to a decrease in the number of receptors available rather than an alteration in affinity for DNA. To study this reduced DNA binding, we examined the ability of the nuclear translocated transcription factors activator protein 1 (AP-1), nuclear factor kappa B (NF-kappa B) and cyclic AMP response element-binding protein (CREB) to bind to their DNA-binding sites and to interact with GR in PBMC from patients with steroid-sensitive and steroid-resistant asthma. There was a significant reduction in the interaction between GR and AP-1 in these steroid-resistant patients, although interaction with other transcription factors activated in inflammation (NF-kappa B and CREB) was unaffected. An increase in the basal levels of AP-1 DNA binding was also detected in the nuclei from steroid-resistant asthmatic patients. There were no differences in the amount of messenger RNA detected for the components of AP-1, c-Fos and c-Jun, nor in the sequences of these messenger RNAs. These results suggest either that the ability of the GR to bind to glucocorticoid response elements and AP-1 is altered in steroid-resistant patients or that increased levels of AP-1 prevent GR DNA binding, and that this may be the molecular basis of resistance to the antiinflammatory effect of steroids in these cells.

Asthma↗

PubMed2025

Integrating Enzyme-DNA Complex and CRISPR/Cas12a for Robust Norovirus Detection.

Human norovirus (NoV) is a primary cause of acute gastroenteritis in children, making accurate and rapid detection essential for effective disease prevention and control. In this study, we developed a sensitive and efficient platform for pathogen nucleic acid detection by integrating asymmetric nucleic acid sequence-based amplification (asymmetric NASBA), enzyme-DNA molecular complex, and the clustered regularly interspaced short palindromic repeats (CRISPR) system, namely an A-enDMC platform. The target recognition capability of the enzyme-DNA complex operates independently from the signal amplification function of the CRISPR system. By decoupling the CRISPR reaction from the dependence on specific target sequences, the platform's universality and modularity are enhanced. The assay is fast (< 1.5 h), highly sensitive (< 5 copies/µL), and demonstrates no cross-reactivity with other common viruses. Compared to the widely used RT-qPCR method, the platform demonstrates high consistency in detection results, with the detection coincidence rate of 96.77% and a kappa value of 0.87. This platform provides a versatile technological tool for highly sensitive and specific RNA detection, demonstrating its extensive potential in real sample analysis.

Norovirus↗