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[Effect of non-histone chromatin proteins on the transcription of globin genes].

Globin gene transcription was studied in vitro using chromatin of normal and Rauscher virus-transformed erythroid cells. For this purpose the reconstituted chromatin was obtained and used as a template for RNA synthesis. The RNA-transcript was then analysed for the presence of globin mRNA sequences. When chromatin was reconstituted using DNA from Rauscher-transformed erythroblasts and reticulocyte nonhistone proteins they enhanced transcription. Most of the globin gene activation was due to the nonhistone protein fraction eluted from hydroxylapatite in 0.05 M Na-phosphate and the RNA-transcript in this case contained the largest quantity of globin sequences.

Animals↗

Effects of estrogen on gene expression in the chick oviduct. IV. Initiation of RNA synthesis on DNA and chromatin.

The interaction of Escherichia coli RNA polymerase (ribonucleoside triphosphate:RNA nucleotidyltransferase, EC 2.7.7.6.) with chick oviduct DNA and chromatin has been studied in order to quantify the RNA polymerase binding sites and rifampicin-resistant initiation sites. The number of high affinity binding sites at saturation was calculated from the number of molecules of enzyme bound to DNA or to chromatin. The number of rifampicin-resistant initiation sites was calculated from the total quantity and the number average chain length of RNA synthesized under the conditions in which only RNA polymerase already in a stable preinitiation complex could avoid inhibition by the drug. Using an assessment of the temperature requirement for the information of this preinitiation complex, we were able to differentiate initiations at single-stranded or nicked DNA regions from initiations at double-stranded DNA regions. This method enabled us to rule out the possibility that RNA chain initiation on chromatin was due to initiation at nicked or end regions of DNA. In addition, we also demonstrated that not all RNA polymerase molecules bound to DNA or chromatin are located at a site at which RNA chain initiation can immediately begin. This methodological approach should allow investigators to monitor the individual reactions and factors involved in in vitro transcription of eukaryotic DNA and chromatin.

Animals↗

Interleukin (IL)-1 and Porphyromonas gingivalis lipopolysaccharide stimulation of IL-6 production by fibroblasts derived from healthy or periodontally diseased human gingival tissue.

BACKGROUND: Human gingival fibroblasts (HGF) play a key role in tissue repair and destruction. These cells express low levels of interleukin (IL)-6 constitutively and increased levels after stimulation with lipopolysaccharide (LPS) or the cytokines IL-1 and tumor necrosis factor-alpha (TNF-alpha). However, little information is available on IL-6 production by fibroblasts derived from diseased tissue. The present study compared constitutive and induced IL-6 production by human gingival fibroblasts (HGF) derived from healthy and diseased periodontal tissue. We also evaluated whether IL-1 acted in a synergistic manner with LPS in inducing IL-6 production by HGF and whether LPS acted via CD14. METHODS: HGF derived from healthy and diseased tissue and foreskin fibroblasts were grown to confluency, photographed, and counted, and their constitutive IL-6 production was quantitated by ELISA. Healthy and diseased HGF were also pretreated with IL-1alpha, followed by incubation with Porphyromonas gingivalis or Escherichia coli LPS. Culture supernatants were assessed for IL-6 protein by ELISA and cell lysates for mRNA by reverse transcription-polymerase chain reaction (RT-PCR). In order to determine if LPS stimulation was mediated through the LPS receptor, CD14, surface receptors on HGF were assessed by flow cytometry and the total RNA CD14 mRNA was assessed. RESULTS: Higher quantities of IL-6 were produced by the diseased HGF before and after stimulation than by the healthy HGF. Pretreatment with IL-1alpha followed by LPS stimulation of the healthy and diseased HGF cell lines resulted in an additive effect on IL-6 production. Pretreatment with IL-1alpha followed by a second incubation with the same stimulant produced higher amounts of IL-6 than cultures incubated with LPS alone or following IL-1alpha pretreatment. Similar amounts of IL-6 mRNA were present in unstimulated HGF from either diseased or healthy tissue and in those incubated with IL-1alpha only. After incubation with IL-1alpha and LPS, diseased HGF produced slightly more mRNA than healthy HGF. CD14 was not expressed by healthy or diseased HGF even after stimulation with either P. gingivalis or E. coli LPS. CD14 message was also undetectable. CONCLUSIONS: Taken together, these results indicate heterogeneity among gingival fibroblasts and an additive effect of IL-1 and P. gingivalis LPS on IL-6 production by HGF. Furthermore, the LPS effect on HGF was not mediated by CD14.

Cell Count↗

Rapid lysis technique for mycobacterial species.

The lysis of mycobacterial cells typically has been difficult and time-consuming. We report a method for the physical rupture of Mycobacterium paratuberculosis and several other members of the family Mycobacteriaceae using a Mini-Beadbeater cell disrupter (Biospec Products; Bartlesville, Okla.) and zirconium beads, a process which yields DNA and RNA of high molecular weight and in greater quantity than that obtained by rupture in a Ribi pressure cell.

Animals↗

Brain-specific expression of MAP2 detected using a cloned cDNA probe.

We describe the isolation of a set of overlapping cDNAs encoding mouse microtubule associated protein 2 (MAP2), using an anti-MAP antiserum to screen a mouse brain cDNA expression library cloned in bacteriophage lambda gt11. The authenticity of these clones was established by the following criteria: (a) three non-identical clones each expressing a MAP2 immunoreactive fusion protein were independently isolated from the expression library; each of these clones cross-hybridized at the nucleic acid level; (b) anti-MAP antiserum was affinity purified using nitrocellulose-bound fusion protein; these antibodies detected only MAP2 in an immunoblot experiment of whole brain microtubule protein; (c) a series of cDNA "walking" experiments was done so as to obtain a non-overlapping cloned fragment corresponding to a different part of the same mRNA molecule. Upon subcloning this non-overlapping fragment into plasmid expression vectors, a fusion protein was synthesized that was immunoreactive with an anti-MAP2 specific antiserum. Thus, a single contiguous cloned mRNA molecule encodes at least two MAP2-specific epitopes; (d) the cloned cDNA probes detect an mRNA species in mouse brain that is of a size (approximately 9 kb) consistent with the coding capacity required by a 250,000-D protein. The MAP2-specific cloned cDNA probes were used in RNA blot transfer experiments to assay for the presence of MAP2 mRNA in a variety of mouse tissues. Though brain contained abundant quantities of MAP2 mRNA, no corresponding sequences were detectable in RNA prepared from liver, kidney, spleen, stomach, or thymus. We conclude that the expression of MAP2 is brain-specific. Use of the MAP2 specific cDNA probes in genomic Southern blot transfer experiments showed the presence of a single gene encoding MAP2 in mouse. The microheterogeneity of MAP2 is therefore ascribable either to alternative splicing within a single gene, or to posttranslational modification(s), or both. Under conditions of low stringency, the mouse MAP2 cDNA probe cross-hybridizes with genomic sequences from rat, human, and (weakly) chicken, but not with sequences in frog, Drosophila, or sea urchin DNA. Thus, there is significant interspecies divergence of MAP2 sequences. The implications of the above observations are discussed in relationship to the potential biological function of MAP2.

Animals↗

Quantitative analysis of RNA cleavage during RNA-directed DNA synthesis by human immunodeficiency and avian myeloblastosis virus reverse transcriptases.

We have determined the extent of RNA cleavage carried out during DNA synthesis by either human immunodeficiency virus (HIV) or avian myeloblastosis virus (AMV) reverse transcriptases (RTs). Conditions were chosen that allowed the analysis of the cleavage and synthesis performed by the RT during one binding event on a given template-primer. The maximum quantity of ribonuclease H (RNase H) sensitive template RNA left after synthesis by the RTs was determined by treatment with Escherichia coli RNase H. RNA cleavage products that were expected to be too short to remain hybridized, less than 13 nucleotides in length, were quantitated. Results showed that HIV- and AMV-RT degraded about 80% and less than 20%, respectively, of the potentially degradable RNA to these short products. Survival of longer, hybridized RNA was not a result of synthesis by a population of RTs that had selectively lost RNase H activity. Using an assay that evaluated the proportion of primers extended versus RNA templates cleaved during primer-extension by the RTs, we determined that essentially each molecule of HIV- and AMV-RT with polymerase also has RNase H activity. The results indicate that although both HIV- and AMV-RTs cleave the RNA template during synthesis, the number of cleavages per nucleotide addition with HIV-RT is much greater. They also suggest that some hybridized RNA segments remain right after the passage of the RT making the first DNA strand. In vivo, these segments would have to be cleaved or displaced in later reactions before second strand DNA synthesis could be completed.

Avian Myeloblastosis Virus↗

Quantification of newly synthesized virus RNA in moloney murine leukaemia virus-infected cells.

A technique for the isolation and characterization of newly transcribed murine leukaemia virus RNA in chronically infected cells has been developed. Cellular RNA was pulse labelled with 3H-uridine and virus-specific sequences were annealed with an excess of mercurated complementary DNA. Based on the affinity between mercurated cDNA and sulphydryl-Sepharose, the hybrid was specifically selected by affinity column chromatography. The specificity of this method was dependent on the purity of the cDNA and it was necessary to remove non-viral sequences from the cDNA in order to isolate virus-specific RNA. Between 0.5 and 0.8% of the labelled RNA in Moloney MuLV-infected rat cells and 1.5% of the labelled RNA in Moloney MuLV-infected NIH Swiss mouse cells were virus-specific. Using this methodology, the effect of the cell cycle on the transcriptional activity of proviral genes was investigated. Cultures of Moloney MuLV-infected rat cells arrested in Go phase of the cell cycle released reduced quantities of virus, but continued to synthesize virus RNA. The pools of virus RNA and p30 antigen in the Go-arrested cells equalled the pools in actively dividing cells. These results suggested that post-transcriptional events controlled virus production in the Go-arrested cells.

Animals↗

Mechanism of interferon action: further evidence for transcription as the primary site of action in simian virus 40 infection.

Interferon inhibits the replication of simian virus 40 (SV40) in monkey cells and reduces markedly the formation of both early virus protein (i.e. SV40 T antigen) and early SV40 RNA. This suggests that in SV40 infection interferon acts primarily by inhibiting transcription. To test this conclusion further, we examined alternative mechanisms which might explain these results and made the following observations. (1) The quantity of input SV40 DNA in the nucleus 24 h post infection (p.i.) was the same in interferon-treated and control cells. Thus interferon does not appear to diminish the quantity of SV40 DNA template available for transcription. (2) Chemical inhibitors of protein synthesis did not mimic the selective inhibition of early SV40 RNA formation induced by interferon, indicating that the transcription of early SV40 RNA is not dependent upon the prior synthesis of any virus-induced protein. Thus a block in translation cannot readily explain the reduced formation of early SV40 RNA in interferon-treated cells. (3) Fractionation of SV40 infected cells after a one-hour labelling period showed that interferon produced a comparable reduction in the quantity of early SV40 RNA in the nucleus and the cytoplasm. Thus the observed inhibition of early SV40 RNA is not due solely (if at all) to enhanced cytoplasmic degradation. These results indicate that the primary effect of interferon in SV40 infected monkey cells is either to inhibit the transcription of early virus RNA or to enhance its turnover in the nucleus.

Cell Line↗

Schistosoma mansoni: influence of infection on levels of translatable mRNA and on polypeptide synthesis in the ovotestis and albumen gland of Biomphalaria glabrata.

Larval trematode infection causes a disruption of normal reproductive activity in the molluscan intermediate host. Because relatively little is known about the dynamics of this host-parasite interaction, the effect of Schistosoma mansoni infection on translatable mRNA pools and on polypeptide synthesis was examined in the ovotestis (OT) and albumen gland (AG) of Biomphalaria glabrata. Total RNA was isolated from OTs and AGs from uninfected control snails and snails at 14, 21, and 28 days postinfection (pi) with 20 S. mansoni miracidia and subjected to a rabbit reticulocyte in vitro translation system. Quantitative densitometry of autofluorograms of one-dimensional SDS-PAGE slab gels revealed reductions in quantities of total proteins synthesized in vitro from RNA isolated from infected OTs at 21 and 28 days pi, but not at Day 14 pi. Similar reductions were seen in 10 individual polypeptides selected for a more detailed analysis. In contrast to the OT, Day 14 pi-infected AGs exhibited an initial increase in total protein synthesized in the in vitro translation system utilized, followed by significant reductions at 21 and 28 days pi. Selective modulation of labeled polypeptides was evident in 11 polypeptides chosen for a more detailed analysis. This general pattern of parasite inhibitory effects was also seen in parallel pulse-chase studies using [35S]methionine metabolic labeling of in vitro-cultured OTs and AGs. In these experiments, significant reductions in the amounts of labeled polypeptides found in culture supernatants at 14, 21, and 28 days pi were evident. Total polypeptide synthesis also was solubilized AGs from infected snails at 21 and 28 days pi. Results indicate that larval trematode infection induced a generalized disruption of polypeptide metabolism in OTs and AGs of B. glabrata. Such inhibition may occur at both the transcriptional and the translational levels and is initially manifested early in infection, during the time that daughter sporocysts begin to migrate and colonize the digestive gland and OT.

Animals↗

Characterization of the poly(adenylic acid) sequences in RNA synthesized in vitro by mouse myeloma nuclei.

The size and quantity of poly(A)sequences made by mouse myeloma nuclei in vitro are dependent on the concentration of KCI, ATP, other ribonucleoside triphosphates, as well as the nature of the divalent cation in the reaction medium. Reduction of the KC1 concentration from 120 mM to 5 mM, for example, stimulates poly(A) synthesis 10- to 20-fold. These poly (A) sequences are similar in size to cellular nuclear poly(A), but the RNA molecules to which they are attached are much shorter than poly(A) containing RNA molecules made at 120 mM KC1. Presence of Mn2+ in the medium led to a much more heterogenous population of poly(A) sequences. From such observations we have found reaction conditions in which nuclei synthesize molecules that resemble native nuclear poly(A) + RNA. Not only are the lengths and amounts of the poly(A) sequences similar, but they also undergo a terminal turnover like that of the poly(A) in hnRNA. An oligo(A) sequence that resembles the oligo(A) found in non-poly(A) containing hnRNA of mouse myeloma and HeLa cells is also synthesized in vitro. These observations suggest that some processing functions are retained during the in vitro incubation of these nuclei.

Base Sequence↗

[Analysis of the activity of matrix DNA synthesis in the lymphocytes of patients after kidney transplantation and the role of the processes of degradation of DNA-dependent RNA polymerases in the overall cellular nucleolytic activity].

The activity and quantity of deoxyribonucleases in T and B lymphocyte cells isolated from peripheral blood of patients with transplanted kidney were investigated. Twenty three patients with transplanted organ, aged 35 +/- 9.7, treated with cyclosporin A and thirteen individuals after renal transplantation in age 34.8 +/- 6.3 treated conservatively were studied. The enzyme activity was defined as resting DNase activity (DNase 0). Where specifiel the reaction mixture was supplied either with 5 mM MgCl2 (DNaseMg2+) or 1 mM MnCl2 (DNase1 x Mn2+) or 2 mM MnCl2 (DNase2 x Mn2+). Two enzyme groups with molecular mass 32 kDa and 14 to 18 kDa were analyzed. It was evidenced that the nuclease activity in B lymphocyte isolated from patients treated with cyclosporin A after organ transplantation was quite close to the control subjects. On the contrary, the nucleases activity and quantity increased in T lymphocyte of the same patients and increasing in enzymes activity was depending upon haemodialysis period of time prior to organ transplantation. Enzymes activity correlate with clinical parameters typical for kidney transplant rejection. The activity and quantity of nucleases was slightly reduced in both T and B lymphocytes isolated from patients treated conservatively after organ transplantation. The useful of nuclease assay for monitoring of kidney transplant rejection is discussed.

Adult↗

Processing of ribosomal RNA in a temperature sensitive mutant of BHK cells.

The processing of ribosomal RNA has been studied in a temperature sensitive mutant of the Syrian hamster cell line BHK 21. At 39 degrees C, these cells are unable to synthesize 28S RNA, and 60S ribosomal subunits, while 18S RNA, and 40S subunits are produced at both temperatures. At 39 degrees C the 45S RNA precursor is transcribed and processed as in wild type cells. The processing of the RNA precursors becomes defective after the cleavage of the 41S RNA, and the separation of the 18S and 28S RNAs sequences in two different RNA molecules. The 36S RNA precursor, which is always present in very small quantity in the nucleoli of wild type cells and of the mutant at 33 degrees C, is found in very large amounts in the mutant at 39 degrees C. The 36S RNA can be, however, slowly processed to 32S RNA. The 32S RNA cannot be processed at 39 degrees C, and it is degraded soon after its formation. Only a small proportion accumulates in the nucleoli. The 32S RNA synthesized at 39 degrees C cannot be processed to 28S RNA upon shift to the permissive temperature, even when the processing of the newly synthesized rRNA has returned to normal. The data suggest that the 36S and 32S RNAs are contained in aberrant ribonucleoprotein particles, leading to a defective processing of the particles as a whole.

Cell Line↗

Correlates between autoantibodies to nucleolar antigens and clinical features in patients with systemic sclerosis (scleroderma).

Immunofluorescence on rat liver sections was used to select high-titer antinucleolar antibodies (ANoA) in the sera of patients with systemic sclerosis (scleroderma). In 646 patients, 53 ANoA sera (8%) were identified, and of these, 46 were available in sufficient quantities for further analysis. The complex of RNA polymerase I was immunoprecipitated by 7 sera (15%), which uniformly produced punctate nucleolar staining. The PM-Scl antigen, a particle consisting of 11 polypeptides, was immunoprecipitated by 8 sera (17%), all of which displayed homogeneous nucleolar staining. A 34-kd nucleolar protein (fibrillarin) of the U3 RNP complex was positive in immunoblotting of 22 sera (48%), which characteristically produced clumpy nucleolar staining. Antibodies against RNA polymerase I were associated with diffuse scleroderma of short duration, which was characterized by a high prevalence of internal organ involvement, including renal crisis. Anti-U3 RNP antibodies had a high prevalence in men with significantly less joint involvement, compared with ANoA-negative patients. Anti-PM-Scl antibodies identified a group of scleroderma patients with a high prevalence of concomitant myositis and renal involvement.

Antibodies, Antinuclear↗

Multiplex reverse transcription-polymerase chain reaction combined with on-chip electrophoresis as a rapid screening tool for candidate gene sets.

Combining multiplex reverse transcription-polymerase chain reaction (mRT-PCR) with microfluidic amplicon analysis, we developed an assay for the rapid and reliable semiquantitative expression screening of 11 candidate genes for drug resistance in human malignant melanoma. The functionality of this approach was demonstrated by low interexperimental variations of amplicon quantities after endpoint analysis. When applied to RNA samples derived from drug-sensitive and -resistant melanoma cell lines, mRT-PCR delivered results qualitatively concordant with data obtained from Northern blot and array analyses. The screening of additional melanoma cell lines resulted in distinct expression patterns for ten candidate genes. Our approach reveals a rapid and easy-to-handle alternative for candidate gene set evaluation from limited amounts of RNA.

Cell Line, Tumor↗

Histophysiological studies on the corpus allatum during prepupal diapause in Monema flavescens (Lepidoptera).

The appearance of the corpus allatum, the central endocrine gland of diapause, was examined histologically in the slug moth prepupae, Monema flavescens (Lepidoptera). Before beginning of diapause, the secretory cells of the corpus allatum increase in size with the enrichment of the cytoplasm in quantity and in number of orgenelles, while RNA synthesis also starts. As diapause progresses, the secretory cells have many large unstained vacuoles in the cytoplasm, which were demonstrated to contain some substances of lipoidal nature. It is not clear that the substance is juvenile hormone itself or a material related to juvenile hormone. Agranular ER is the most characteristic organelle connected with mitochondria and situated around the vacuoles during diapause. Electron micrographs show that agranular ER and mitochondria have an essential role for the production of juvenile hormone. The function of the corpus allatum during diapause and the relationship between juvenile hormone and diapause are discussed.

Animals↗

A revised strategy for cloning antibody gene fragments in bacteria.

The ability to clone and overexpress genes encoding mouse Fab (antigen-binding fragment) proteins in bacteria led to the development of a methodology which has the potential to replace traditional hybridoma technology [Huse et al., Science 246 (1989) 1275-1281]; however, several observations have suggested that clones with desirable chemical properties may be missed in immunoscreens of large combinatorial libraries due to low levels of functional Ab protein. To increase the efficiency of cloning and characterization of Ab gene fragments, we have reconsidered several features of the original cloning vehicles. These studies show that at the present time a unique expression system cannot adequately accommodate the requirements of plaque-lift immunoassays for clonal selection and biochemical assays for further characterization in vitro. A monocistronic arrangement of heavy- and light-chain-encoding genes using two lacP promoters produces sufficient amounts of functional Ab protein for clonal selection from phage lambda libraries and minimizes interference with the lytic cycle of recombinant vectors. In liquid culture, a strong coliphage promoter and a relatively abundant RNA polymerase can be used to produce quantities of Ab protein sufficient for further characterization in vitro. A rapid purification protocol obviates the need for fusing heavy-chain protein to a decapeptide sequence, an affinity-tail sequence which slows the folding and assembly of the Ig heterodimer. These results have been used to formulate a new strategy for cloning and characterization of Ab gene fragments in bacteria.

Amino Acid Sequence↗

A SICAvar switching event in Plasmodium knowlesi is associated with the DNA rearrangement of conserved 3' non-coding sequences.

Plasmodium knowlesi variant antigens are expressed at the surface of infected erythrocytes and are encoded by the Schizont Infected Cell Agglutination variant antigen (SICAvar) multigene family. The 3' region of the SICAvar gene locus encoding the 205 kDa variant antigen expressed in the Pk1(B+)1+ parasites was found to be altered compared to the Pk1(A+) parental clone. Here we report that this alteration is the result of a DNA rearrangement and that the original and altered 205 SICAvar alleles appear to encode bona fide variant antigens. Importantly, 205A and 205B SICAvar RNA sequences are detectable in similar apparent quantities as determined by quantitative real-time reverse-transcription polymerase chain reaction (qRT-PCR) amplification experiments. However, expression of the 205 kDa SICA protein at the surface of the infected erythrocyte is not characteristic of the Pk1(A+) parasites and the 205 SICAvar transcript has not been detected in Pk1(A+) parasites by northern blot analysis. Furthermore, we report that many distinct SICAvar transcripts were detected in P. knowlesi Pk1(B+)1+ cDNA library hybridization screens. Of special interest, in light of these data, distinctive differences at the 3' end of the 205A and 205B alleles are observed, which may be of functional importance. An analysis of the 3' untranslated region (UTR) of SICAvar genes in more than 100 sequences revealed a surprising common sequence pattern characterized by blocks of imperfect, GT-rich, heptad repeated motifs (Block I), followed by A and T rich homopolymers (Block II) and in a large number of genes, GC-rich segments (Block III). We show that this region undergoes extensive recombination and that the preferential stability of the 205 SICAvar transcript in Pk1(B+)1+ parasites may be associated with the presence of its specific Block III sequences. We speculate that the conserved yet polymorphic SICAvar 3'UTR sequences, and comparable regions in P. falciparum var genes, function in the stage-specific and developmentally regulated post-transcriptional gene silencing (PTGS) of variant antigen transcripts.

3' Untranslated Regions↗

Epithelioid sarcoma producing granulocyte colony-stimulating factor.

An epithelioid sarcoma of the perineum of a 60-year-old man with widespread metastases produced leukocytosis, myeloid hyperplasia of the bone marrow, and splenomegaly. High titers of granulocyte colony-stimulating factor (G-CSF) were found in the patient's serum and primary culture medium of the tumor tissue. The tumor tissue extract contained m-RNA for G-CSF in large quantities, proving that the tumor was the source of this cytokine.

Granulocyte Colony-Stimulating Factor↗