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PubMed1992

Development of a sensitive reverse transcriptase PCR assay, RT-RPCR, utilizing rapid cycle times.

We describe a procedure to analyze rare gene transcripts quantitatively using a reverse transcriptase-polymerase chain (RT-PCR) reaction. RNA purified from cells and tissues is reverse-transcribed using random hexamer primers and is amplified using very short cycle times. The products are trace-labeled with [32P[dCTP, which allows for the quantitation of the products by gel electrophoresis and excision of bands. The quantity of the PCR product is directly proportional to the quantity of cDNA added and is reproducible from a single cDNA preparation or from samples derived from separate preparations. Because cDNA synthesis is primed with random oligonucleotides, the same cDNA sample preparation can be examined for many different gene products.

Animals↗
PubMed2006

Recombinant Thermus aquaticus RNA polymerase for structural studies.

Advances in the structural biology of bacterial transcription have come from studies of RNA polymerases (RNAPs) from the thermophilic eubacteria Thermus aquaticus (Taq) and Thermus thermophilus (Tth). These structural studies have been limited by the fact that only endogenous Taq or Tth RNAP, laboriously purified from large quantities of Taq or Tth cell paste and offering few options for genetic modification, is suitable for structural studies. Recombinant systems for the preparation of Taq RNAP by co-overexpression and assembly in the heterologous host, Escherichia coli, have been described, but these did not yield enzyme suitable for crystallographic studies. Here we describe recombinant systems for the preparation of Taq RNAP harboring full or partial deletions of the Taq beta' non-conserved domain (NCD), yielding enzyme suitable for crystallographic studies. This opens the way for structural studies of genetically manipulated enzymes, allowing the preparation of more crystallizable enzymes and facilitating detailed structure/function analysis. Characterization of the Taqbeta'NCD deletion mutants generated in this study showed that the beta'NCD is important for the efficient binding of the sigma subunit, confirming previous hypotheses. Finally, preliminary structural analysis (at 4.1Angstroms resolution) of one of the recombinant mutants revealed a previously unobserved conformation of the beta-flap, further defining the range of conformations accessible to this flexible structural element.

Bacterial Proteins↗
PubMed2001

Quantitative analyses of messenger RNA of human endogenous retrovirus in patients with systemic lupus erythematosus.

OBJECTIVE: Human endogenous retrovirus (HERV) has emerged as a possible causative agent of systemic lupus erythematosus (SLE). To investigate the role of HERV in the etiology of SLE, we performed quantitative analyses of messenger RNA (mRNA) of the HERV clone 4-1 in patients with SLE. METHODS: Reverse transcriptase (RT)-polymerase chain reaction (PCR) and real-time quantitative PCR (RQ-PCR; TaqMan methodology) were used in this experiment. RESULTS: The quantities of mRNA of the HERV clone 4-1 gag region in patients with SLE were significantly higher than in healthy controls, and the amounts of such mRNA in the patients were decreased by steroid treatment. CONCLUSION: These phenomena may be related to the production of viral components derived from HERV clone 4-1 and contribute to the pathogenesis of SLE; studies using a larger number of patients are required to confirm these points.

Adult↗
PubMed2006

Molecular architecture and conformational flexibility of human RNA polymerase II.

Transcription by RNA polymerase II (RNAPII) is a central process in eukaryotic gene regulation. While atomic details exist for the yeast RNAPII, characterization of the human complex lags behind, mostly due to the inability to obtain large quantities of purified material. Although the complexes have the same protein composition and high sequence similarity, understanding of transcription and of transcription-coupled DNA repair (TCR) in humans will require the use of human proteins in structural studies. We have used cryo-electron microscopy, image reconstruction, and variance analysis to characterize the structure and dynamics of human RNAPII (hRNAPII). Our studies show that hRNAPII in solution parallels the conformational flexibility of the yeast structures crystallized in different states but also illustrate a more extensive conformational range with potential biological significance. This hRNAPII study will serve as a structural platform to build up higher-order transcription and TCR complexes and to gain information that may be unique to the human RNAPII system.

Cryoelectron Microscopy↗
PubMed2004

Intraperitoneal nitric oxide production in patients treated by continuous ambulatory peritonal dialysis.

BACKGROUND: Nitric oxide (NO) generation within the peritoneum could potentially affect peritoneal transport by increasing capillary vasodilatation, and increase peritoneal permeability during episodes of bacterial peritonitis. As peritoneal mesothelial cells have a common embryological derivation with endothelial cells, then mesothelial cells could potentially be a major source of locally produced NO. METHODS: NO was measured using the Griess reaction in fresh and spent dialysate effluent (SPDE) from uninfected CAPD patients, and from those during episodes of bacterial peritonitis. Human peritoneal mesothelial cells (HPMC) were cultured and NO production determined in the presence of SPDE and the effect of a potential NO substrate, L-arginine, and NO synthase inhibitor, L-NMMA. NO production by peritoneal macrophages (MØ), obtained from SPDE and the effect of staphylococci was also determined. RNA for inducible nitric oxide synthase (iNOS) was sought using Northern blotting technique following combination stimulation with lipopolysaccharide and cytokines (IL-1beta, TNF-alpha and gamma-INF, and/or spent dialysate from patients with bacterial peritonitis). RESULTS: Whereas fresh CAPD dialysate was nitrite-free, SPDE from the day time exchange contained 41 +/- 3 microM (nitrite and nitrate), and that from the overnight dwell 91 +/- 8 microM. During CAPD peritonitis, dialysate nitrite and nitrate increased from 9.3 +/-0.8 to 17.5 +/- 2.4 microM/l x h, for the first CAPD bag at presentation, and 15.2 +/- 1.8 for the second and 16.2 +/- 2.4 for the third exchange (p < 0.01 compared to non-infected control). By the second day, levels had returned to baseline, 7.3 +/- 0.9 microM/l x h. HPMC produced 261 nmol nitrate and nitrite/mg cell protein, and this increased in a dose-dependent manner with the addition of spent uninfected CAPD dialysate, to 365 nmol/mg with 1:10 dilution and 655 nmol/mg with 1:2 dilution, p < 0.001. The addition of the substrate, L-arginine, resulted in a 10% increase in nitrite and nitrate production, whereas the addition of L-NMMA produced a 10% reduction. Peritoneal MØ obtained from SPDE produced similar quantities of nitrite and nitrate to peritoneal mesothelial cells, and cultures of Staphylococcus aureus resulted in a reduction in nitrite and nitrate levels, as they were used as a growth requirement. However, we could not demonstrate RNA production for iNOS by HPMC following cytokine or SPDE stimulation. CONCLUSIONS: This suggests that HPMC may be an important source of locally generated NO within the peritoneal cavity under basal conditions, but as they do not contain iNOS, the increased NO produced during episodes of acute bacterial peritonitis is more likely due to a combination of increased NO production by peritoneal endothelial cells and transmigrating macrophages.

Arginine↗
PubMed1978

Role of prolactin and glucocorticoids in the expression of casein genes in rabbit mammary gland organ culture. Quantification of casein mRNA.

Milk synthesis is initiated solely by prolactin in the pseudopregnant rabbit and glucocorticoids potentiate this action of prolactin. In organ culture, prolactin, in the presence or in the absence of insulin, enhances casein synthesis and cortisol (inactive alone) amplifies this action. Measurements of casein mRNA concentration in total cellular RNA, by hybridization with DNA complementary to casein mRNA, revealed that the stimulation of casein synthesis by the glucocorticoid is accompanied by an increase in the amount of casein mRNA. A systematic comparison of variations of these two parameters indicated that the major effect of glucocorticoids on lactogenesis in the rabbit at this stage of mammary gland development is mediated through an increase in the quantity of casein mRNA available for translation. No simultaneous control of casein mRNA translation by cortisol was observed.

Animals↗
PubMed1977

Histochemical reactions of liver cells in cholesterol-fed rabbits.

The liver cells of 8 rabbits fed for 12 to 16 weeks with a cholesterol diet showed a decrease of RNA and a stronger reactivity for acid phosphatase and beta-glucuronidase. The non-specific esterase showed a weaker reactivity in the cells with a larger amount of cholesterol and a stronger reaction in the cells with a smaller quantity of this substance. Several enzymes such as: diaphorases, those of the pentose shunt and respiratory cycle as well as those related to the metabolism of lipids, proteins and mucopolysaccharides showed a unconspicuous reactivity. The glycogen was found in a lesser amont in 6 out of 8 rabbits but with a higher concentration in 2 of them. The reactivity of UDPG-GT, active phosphorylase, F-1,6-PA, F-1,6-P Ald, LDH and ADH was stronger in the last 2 animals but weaker in the 6 others. In this 8 rabbit group the total phosphorylase and G-6-PA showed respectively always a stronger and a weaker reactivity than their controls. In the liver of 2 cholesterol-fed for 20 weeks rabbits it was observed a centrolobular fibrosis, a smaller amount of RNA and glycogen as well as a global decrease of the enzymatic reactivity.

Animals↗
PubMed1999

Simultaneous extraction of hepatitis C virus (HCV), hepatitis B virus, and HIV-1 from plasma and detection of HCV RNA by a reverse transcriptase-polymerase chain reaction assay designed for screening pooled units of donated blood.

BACKGROUND: Testing for viral nucleic acids should reduce the residual risk of transmitting viral infections by transfusion of blood components. The AmpliScreen Hepatitis C (HCV) Test, Version 2.0, was designed for screening pools composed of samples from individual units of blood or plasma. STUDY DESIGN AND METHODS: An ultracentrifugation step during sample processing simultaneously extracts and concentrates HCV, HIV type 1, and hepatitis B virus particles from plasma. An HCV internal control RNA serves as an extraction and amplification control for each processed sample. Processed samples are amplified by reverse transcriptase polymerase chain reaction and detected by hybridization of the amplified products to HCV- and internal-control-specific oligonucleotide probes. Plasma samples containing known quantities of HCV were used to evaluate analytical sensitivity and precision. RESULTS: The analytical sensitivity of the test was 25 IU of HCV per mL of pooled plasma; all HCV genotypes were detected with similar efficiency. The test did not react with other blood-borne viruses. The within-run and total coefficients of variation were 1.3-13.0 percent and 1.7-22.0 percent, respectively, with low copy samples producing the more variable results. The test performed well using plasma collected in either EDTA, ACD, or PPT Vacutainer tubes. Plasma samples containing elevated levels of hemoglobin, albumin, triglycerides, or bilirubin did not interfere with the test. The test detected HCV RNA 23 to 32 days prior to seroconversion for four of the five seroconversion panels tested. CONCLUSION: The AmpliScreen HCV Test, Version 2.0 provides a reproducible and specific method for screening pooled blood units for HCV. Theoretically, this test has sufficient sensitivity to detect a single infected unit containing 2.4 x 10(3) IU of HCV per mL in a pool with 95 uninfected units and should reduce the window period by at least 20 to 30 days.

Blood↗
PubMed1978

Sequential changes of T- and B-cells, virus antigen expression and primary histologic tumor diagnosis in virus-induced lymphomagenesis of mice.

T- and B-cell counts, estimation of Ig receptor fluidity, and expression of virus-coded antigens were correlated with histological findings during the development of virus-induced mouse lymphoma. Tested were BALB/c mice after infection with the strongly oncogenic Moloney leukemia virus (MLV), the moderately oncogenic (in BALB/c mice) Gross passage A virus (GLV-A), and the essentially non-oncogenic Gross 3T3 tissue culture virus (GLV-T). Methods included immunofluorescence microscopy with antisera against T-cells, B-cells and MLV intact virus, routine histology, and electron microscopy. Following time sequence of changes was observed in mice with oncogenic MLV- and GLV-A infection but not in GLV-T infection: Significant decrease of Ig receptor fluidity and expression of virus antigen were observed already at the initial investigation, i.e. 2 weeks post virus infection. This was followed by significant decreases in percent T-cells 5--8 weeks later, accompanied by histologic atrophy of the thymus and of thymus-dependent regions of lymphatic tissues. Another 2--8 weeks after the decrease in percent T-cells occurred, the first lymphomatous foci became obvious in the thymus. Clinically overt and generalized lymphoma was diagnosed at 20--30 weeks post virus infection. Ultrastructurally, some changes in the arrangement and quantity of cytoplasmic microfilaments were noted in proliferating lymphoblasts and in lymphoma cells. It is concluded, that the described changes were related to the oncogenic potential of mouse C-type RNA viruses and not just to virus infection per se.

AKR murine leukemia virus↗
PubMed1978

Large scale isolation of nuclei and nucleoli from vitellogenic oocytes of Xenopus laevis.

A new method is described which allows the purification of large quantities of nuclei (germinal vesicles) from Xenopus laevis vitellogenic oocytes of different developmental stages. From the isolated nuclei, purified nucleoli were obtained. The isolated germinal vesicles are transcriptionally active showing endogenous RNA polymerase activity as well as a high level of activity with an exogenously added template.

Animals↗
PubMed1991

Mutational analysis of the DNA polymerase and ribonuclease H activities of human immunodeficiency virus type 2 reverse transcriptase expressed in Escherichia coli.

We have constructed a plasmid that, when introduced into Escherichia coli, induces the synthesis of large quantities of a polypeptide with an apparent molecular weight of 68 kDa. The HIV-2 reverse transcriptase (RT) made in E. coli is soluble in bacterial extracts and possesses both RNA-dependent DNA polymerase and ribonuclease H (RNase H) activities typical of retroviral RTs. The HIV-2 RT expression clone was used to generate mutations in HIV-2 RT. There is a strong correlation between the effects of individual mutations on the DNA polymerase and RNase H activities. Mutations that profoundly affect the two catalytic functions are not clustered in any particular region of the polypeptide. Those few mutations that selectively affect either the RNase H or the DNA polymerase suggest that, like other retroviral RTs, the DNA polymerase is associated with the amino-terminal portion of HIV-2 RT and the RNase H with the carboxy-terminal portion. Genetically, the HIV-2 RT resembles the HIV-1 RT more closely than it resembles Moloney murine leukemia virus RT. The two catalytic functions of Moloney murine leukemia virus RT can be separately expressed in active form by molecular cloning; those of HIV-1 and HIV-2 RT cannot.

Amino Acid Sequence↗
PubMed1991

A system, using neural cell lines, to characterize HSV-1 vectors containing genes which affect neuronal physiology, or neuronal promoters.

Among the potential uses of defective herpes simplex virus (HSV-1) vectors are to study neuronal physiology, neuronal gene regulation, and to perform gene therapy of neuronal diseases. The prototype HSV-1 vector, pHSVlac, stably expresses Escherichia coli beta-galactosidase from the HSV-1 immediate early (IE) 4/5 promoter in cultured rat peripheral and CNS neurons, and in neurons in the adult rat brain. The LacZ gene and the IE 4/5 promoter in pHSVlac can be replaced with genes which affect neuronal physiology or cellular promoters, respectively. A system is required to characterize these HSV-1 vectors; cultured neurons, a mixture of different kinds of neurons and glia, cannot be used. In contrast, neural cell lines represent a homogenous population of neural cells available in virtually unlimited quantities. A system, using neural cell lines, to characterize HSV-1 vectors carrying other genes or promoters is now reported: First, 4 assays are described to detect HSV-1 vector DNA, RNA transcribed from the vector, and to quantitate beta-galactosidase expression. Second, 8 cell lines derived from rodents, primates, and humans were infected with pHSVlac virus and shown to express beta-galactosidase. The cell lines tested included adrenergic and cholinergic mouse neuroblastoma cells, rat pheochromocytoma cells, rodent pituicytes, and human neuroblastoma cells. Infection of these cell lines should prove useful for characterizing HSV-1 vectors with molecular and biochemical assays. Third, differentiated rat pheochromocytoma and mouse neuroblastoma cells, which resemble neurons, were infected with pHSVlac virus and shown to stably express beta-galactosidase. Infection of these cells should be useful for determining the effect of various HSV-1 vectors on neuronal physiology. Thus, HSV-1 vectors containing various genes or promoters can be characterized using the system described in this study.

Animals↗
PubMed2002

Optimised SEREX technique for the identification of leukaemia-associated antigens.

The serological analysis of antigens by recombinant expression cloning (SEREX) has been used by many laboratories to immunoscreen lambda phage cDNA libraries produced from a range of tumour cell types. We and others have found it difficult to extract an optimal quality and quantity of mRNA for the preparation of cDNA libraries which represent the genes transcribed in haematological samples. The difficulty is believed to be due to residual haem groups in the isolated RNA sample which inhibit the activity of reverse transcriptase used in the later production of cDNA. During our preparation of a cDNA library for SEREX studies, we optimised the isolation of mRNA from samples from patients with haematological malignancies. We compared the efficacy of different methods of mRNA extraction using a range of haematological sample sizes and describe the most efficient techniques to maximise mRNA yield and quality for cDNA library production. The phage library we prepared contained a range of cDNA insert sizes, including high molecular weight sequences which, following immunoscreening with autologous patient sera, led to the isolation of 17 novel antigens. Using the methodology described, we have shown SEREX to be effective for the isolation of leukaemia-associated antigens, which may act as targets for immunotherapy.

Aged↗
PubMed2006

Adipocyte differentiation-related protein promotes fatty acid storage in cytosolic triglycerides and inhibits secretion of very low-density lipoproteins.

OBJECTIVE: We investigated the role of adipocyte differentiation-related protein (ADRP) in triglyceride turnover and in the secretion of very low-density lipoprotein (VLDL) from McA-RH7777 cells and primary rat hepatocytes. METHODS AND RESULTS: An increase in the expression of ADRP increased triglyceride accumulation in cytosolic lipid droplets and prevented the incorporation of fatty acids into secretable triglycerides, thereby reducing the secretion of triglycerides as well as of apolipoprotein B-100 (apoB-100) and apoB-48 VLDL. The ability of ADRP to block the secretion of apoB-100 VLDL1 decreased with increasing quantities of fatty acids in the medium, indicating a saturable process and emphasizing the importance of sequestering of fatty acids for the effect of ADRP on VLDL secretion. Knockdown (small interfering RNA) of ADRP decreased the pool of cytosolic lipid droplets but increased only the secretion of apoB-48 VLDL1. Additionally, there was an increased flow of fatty acids into beta-oxidation. CONCLUSIONS: ADRP is essential for the accumulation of triglycerides in cytosolic lipid droplets. An increase in ADRP prevents the formation of VLDL by diverting fatty acids from the VLDL assembly pathway into cytosolic triglycerides, whereas a decrease of the protein increases the sorting of fatty acids to beta-oxidation and promotes the secretion of apoB-48 VLDL1.

Animals↗
PubMed2003

Difference of gene expression profiles between esophageal carcinoma and its pericancerous epithelium by gene chip.

AIM: To study the difference of gene expression between esophageal carcinoma and its pericancerous epithelium and to screen novel associated genes in the early stage of esophageal carcinogenesis by cDNA microarray. METHODS: Total RNA was extracted with the original single step way from esophageal carcinoma, its pericancerous epithelial tissue and normal esophageal epithelium far from the tumor. The cDNA retro-transcribed from equal quantity of mRNA was labeled with Cy5 and Cy3 fluorescence functioning as probes. The mixed probes were hybridized with two pieces of BioDoor 4 096 double dot human whole gene chip. Fluorescence signals were scanned by ScanArray 3 000 laser scanner and farther analyzed by ImaGene 3.0 software with the digital computer. RESULTS: (1) A total of 135 genes were screened out, in which 85 and 50 genes whose the gene expression levels (fluorescence intensity) in esophageal carcinoma were more than 2 times and less than 0.5 times respectively compared with the normal esophageal epithelium. (2) There were also total 31 genes, among then 27 and 4 whose expressions in pericancerous tissue were 2-fold up-regulated and 0.5-fold down-regulated respectively compared with normal esophageal epithelium. (3) There were 13 genes appeared simultaneously in both pericancerous epithelium and esophageal carcinoma, while another 18 genes existed in pericancerous epithelium only. CONCLUSION: With the parallel comparison among these three gene profiles, it was shown that (1). A total of 135 genes, Whose expression difference manifested as fluorescence intensity were more than 2 times between esophageal carcinoma and normal esophageal epithelium, were probably related to the occurrence and development of the esophageal carcinoma. (2). The 31 genes showing expression difference more than 2 times between pericancerous and normal esophageal epithelium might be relate to the promotion of esophageal pericancerosis and its progress. The present study illustrated that by using the gene chip to detect the difference of gene expression profiles might be of benefit to the gene diagnosis, treatment and prevention of esophageal carcinoma.

Carcinoma↗
PubMed2001

[Protein synthesis in kidneys of merino sheep in postnatal ontogenesis].

By evaluating parameters of activity of the nucleolar organizers (AgNORs), patterns of protein synthesis in cells of the right and left kidneys of merino sheep were examined in dependence of their age, sex, and the organ position. Depending on these parameters, the number of AgNORs in the kidney of merino sheep varies from 2 to 7. The total area of AgNORs in cells was within 0.50 +/- 0.03-2.22 +/- 0.05 mcm2. In different structure of nephrons, regions of nuclear organizers differ in both the quantity and total area. The obtained data testify that in kidney of 3 month old males and females of merino sheep the synthesis of 18S- and 28S-classes of ribosomal RNA and, accordingly, proteins occurs most actively.

Aging↗
PubMed1989

IgM secreted by human T lymphoma virus-I-infected and transformed human B cell clones recognize a 66-kilodalton host-encoded protein.

It has previously been determined that transformed human B cells may be infected by and retain integrated human T cell lymphotropic virus, type I (HTLV-I). Although HTLV-I is primarily associated with transformation of human T lymphocytes, immortalized B cell populations have arisen after cocultivation of normal B cells and irradiated HTLV-I-infected T cells. To test whether HTLV-I infection might be involved in this B cell transformation process, we characterized five independent HTLV-I-infected and -immortalized human B cell clones. All five clones contained clonal HTLV-I integrations, expressed cell surface IgM, and secreted IgM in quantities varying from 0.1 to 4.0 micrograms/ml. Immunoblotting and immunoprecipitation of metabolically labeled cell lysates failed to detect synthesis of HTLV-I gag, env, or tat gene products, and cellular RNA dot blot analysis detected varying levels of HTLV-I gene transcripts in only three of the five clones. The secreted IgM from culture supernatants were affinity purified, and were found to selectively immunoprecipitate an acidic protein (isoelectric point = 5.0) of 66,000 m.w. (p66) from purified radioiodinated HTLV-I virions. This p66 copurified with metabolically labelled HTLV-I-infected B cell IgM from HKA-3 cells. Although HTLV-I RNA transcripts were present at low levels, the absence of HTLV-I proteins in HKA-3 cells made it unlikely that p66 was related to the major HTLV-I envelope glycoprotein, gp62. Anti-idiotypic mAb directed against the IgM produced by one B cell clone (HKA-3), as well as purified HTLV-I virions (containing p66), stimulated HKA-3 cell proliferation. Preincubating the anti-Id antibody or HTLV-I with excess HKA-3 IgM abolished the binding of either to HKA-3 cells. These data suggest that HTLV-I infected cells produce a cellular protein (p66), which is incorporated into and copurifies with HTLV-I virions, and which in at least one case (HKA-3) may act as a mitogenic stimulus, potentially contributing to the HTLV-I mediated transformation process.

Antibodies, Anti-Idiotypic↗
PubMed1986

Vimentin gene: expression in human lymphocytes and in Burkitt's lymphoma cells.

We have isolated a human genomic clone for the intermediate filament subunit vimentin with a DNA probe encoding chicken vimentin. We show that the gene for this protein exists as a single copy in the haploid human genome and is transcribed into one mature RNA species of 2 kb. In vitro translation of poly(A)+ mRNA in a rabbit reticulocyte cell-free system showed that vimentin is a major product of RNA from normal lymphocytes but not of RNA extracted from Burkitt cells. 2-kb vimentin mRNA can be detected with a DNA probe in normal lymphocytes and in fibroblasts, but not in cell lines derived from Burkitt's lymphoma (JI, JBL2, BJAB, DAUDI). The abundance of vimentin mRNA is correlated with the quantity of vimentin present in the cells, suggesting that the level of expression is regulated by the abundance of mRNA. The half-lives of vimentin mRNA were found identical in both fibroblasts and lymphocytes and belong to the class of stable mRNA.

Animals↗