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PubMed1995

A rapid method for the preparation of plasmid DNA.

A rapid method was developed to prepare plasmid DNA to be used for in vitro transcription, subcloning and sequencing. Clean plasmid DNA can be prepared within 90 min using this method and the quality of the plasmid DNA was found to be suitable for sequencing, preparation of in vitro RNA transcript and electroporation. Using this method plasmid DNA can be prepared from 2 ml to 100 ml culture. The yield of the recombinant plasmids was found to be in the range of 50-100 micrograms from 10 ml culture depending on the low and high copy number plasmids. The advantage of this method is that one can easily and rapidly prepare large quantities of plasmid DNA of high quality to be used for various purposes.

DNA↗
PubMed1978

Drusen of the optic nerve head.

Fifty-two eyes with drusen of the optic nerve head from the autopsy and surgical files of the Eye Pathology Laboratory of the Wilmer Institute from January 1967 through December 1975 were reviewed, and histochemical and electron microscopic studies performed. Histopathologic associations with the drusen included 19 eyes with associated optic nerve atrophy, 16 eyes with peripapillary crowding, one case involving prominent dilated vessels pushed aside by the drusen, and one eye with central retinal vein occlusion. Drusen appear to be composed predominantly of a mucoprotein matrix with significant quantities of acid mucopolysaccharides along with small quantities of ribonucleic acid and, occasionally, iron. The literature is reviewed and various correlations and pathogenetic theories are discussed.

Adult↗
PubMed1985

Screening of lambda library for differentially expressed genes using in vitro transcripts.

We present an improved approach to the screening of eucaryotic libraries for differential gene expression. Previous techniques have generated probe via the harvesting of cellular poly(A)+ RNA and synthesizing labeled cDNA probe using reverse transcriptase. In our approach we prepare labeled RNA probe via in vitro transcription. Unlike cDNA preparation, in vitro transcription (i) directly reflects the ongoing rate of gene expression, and (ii) allows one to assess expression of genes whose transcripts are not polyadenylated. To make this approach practical for the screening of a large library, we modified and optimized existing in vitro transcription techniques, enhancing manyfold the [alpha-32P]UTP incorporation into mRNA, while almost completely suppressing rRNA incorporation. In addition, we developed a simple procedure for making precise replicate dot blots of very large quantities of lambda-phage library DNA. By combining our techniques of in vitro transcription and replicate blotting, we are able to approach detection of a twofold difference in gene expression over a greater than 1000-fold range in overall expression. Our single-clone amplification and dot-blotting technique resulted in nearly the same number of lambda-phage DNA copies per dot for all members of the library. This feature allows us to assign genes to different expression classes, as well as to detect any alterations in expression. We demonstrate our approach by screening the drosophila genomic DNA library with in vitro transcripts from drosophila tissue culture cells. Screening of the entire drosophila genomic library at the 99% probability level is readily achieved.

Animals↗
PubMed2004

One-Step RT-PCR protocols improve the rate of dengue diagnosis compared to Two-Step RT-PCR approaches.

Dengue is the most important arboviral disease transmitted to humans. In our laboratory, we have been working on the standardization of the polymerase chain reaction (PCR) diagnosis of this disease. In this work, we compared five commercial kits regularly used on reverse-transcription polymerase chain reaction (RT-PCR) protocols: two Two-Step kits (SuperScript II RT/Super Mix kit and reverse transcription system/Taq DNA polymerase) and three One-Step kits (ready-to-go RT-PCR Beads kit, QIAGEN One-Step RT-PCR kit, and AcessQuick RT-PCR system). Thirty-one serum samples of patients with clinical diagnosis of dengue fever (DF) were analyzed by RT-PCR and serology. RNA extraction was done with the QIAamp Viral RNA kit, and cDNA synthesis and PCR done according to the manufacturer's protocol for the five kits. Out of the 31 serum samples collected from patients suspected of having dengue, 27 were IgM-positive, confirming the dengue diagnosis. Out of those, 24 were positive by the ready-to-go RT-PCR Beads kit, 25 were positive by AcessQuick RT-PCR system and 27 were positive by QIAGEN One-Step RT-PCR kit. On the other hand, only six samples were positive by the SuperScript II RT/Super Mix kits and 10 were positive by reverse transcription system/Taq DNA polymerase kit. The best performance observed with the One-Step kits was confirmed in spiked samples with known quantities of dengue-1 virus since they detected up 1 x 10(2) PFU/ml, while the most sensitive Two-Step kit detected up 1 x 10(4) PFU/ml. These data show that One-Step RT-PCR kits yielded a higher rate of dengue virus detection than the Two-Step kits and correlated well with the serological diagnosis.

DNA, Complementary↗
PubMed1985

Abnormal expression of the myelin-associated glycoprotein in the central nervous system of dysmyelinating mutant mice.

Total cytoplasmic brain RNA was isolated at two different ages from three neurological mutant mice (qk/qk, jp/Y, and shi/shi) and their apparently normal littermates. This RNA was translated in vitro in a rabbit reticulocyte lysate system. Myelin-associated glycoprotein (MAG)-related polypeptides were immunoprecipitated from equal amounts of total translation products derived from mRNA of mutant animals, normal littermates, or control animals. The developmentally regulated synthesis of MAG polypeptides was compared among the mutants and normal animals. mRNA from qk/qk brains synthesized an overabundance of p67MAG (five- to sevenfold) which may be compensation for a decreased synthesis of p72MAG. mRNA from jp/Y brains synthesized less than 10% of normal amounts of both MAG polypeptides. The quantity of MAG synthesized by 15-day shi/shi brain mRNA was slightly decreased compared with normal brain mRNA but the quantity of MAG synthesized by adult shi/shi brain mRNA was normal. No apparent differences were detected in the sizes of the MAG polypeptides synthesized by any of the mutants studied. The data suggest that the genetic defect in qk/qk mutants directly or indirectly affects the coordinated developmental regulation of MAG polypeptide synthesis leading to an overabundance of the MAG polypeptide that is normally found in older animals. The jp/Y mutation appears to affect general myelin protein synthesis. Finally, shi/shi mutants may have a delayed synthesis of MAG. The data are discussed in the light of recent observations concerning the synthesis of myelin proteins and their proposed role in myelin assembly.

Animals↗
PubMed1997

The synovial expression and serum levels of interleukin-6, interleukin-11, leukemia inhibitory factor, and oncostatin M in rheumatoid arthritis.

OBJECTIVE: To determine the expression of interleukin-6 (IL-6), IL-11, leukemia inhibitory factor (LIF), and oncostatin M (OSM) and their major cellular sources in the joints of rheumatoid arthritis (RA) patients, as well as the correlation of circulating levels of these IL-6-type cytokines and C-reactive protein (CRP). METHODS: Messenger RNA (mRNA) and protein levels for IL-6, IL-11, LIF, and OSM were determined by using reverse transcription-polymerase chain reaction and enzyme-linked immunosorbent assay, respectively. RESULTS: Cells isolated from the synovium of RA patients expressed mRNA for IL-6, IL-11, LIF, and OSM at higher levels than did synovial cells from osteoarthritis (OA) patients, and spontaneously released greater quantities of these proteins in culture. Fibroblast cell lines derived from RA synovium were able to produce IL-6, IL-11, and LIF, but not OSM, when stimulated with IL-1 and tumor necrosis factor alpha. OSM was found to be produced spontaneously by synovial tissue macrophages. IL-6, IL-11, LIF, and OSM were present in synovial fluid from the RA patients; levels of IL-6, LIF, and OSM were present in significantly greater quantities in RA patients than in OA patients. However, only IL-6 was significantly elevated in the serum of RA patients and correlated with the serum CRP level, while other IL-6-type cytokines were not detected. CONCLUSION: IL-6, IL-11, LIF, and OSM are all produced in large amounts at the site of disease activity, but IL-6 derived from synovial fibroblasts may be the major hormone-like mediator that induces the hepatic synthesis of acute-phase proteins in RA.

Adult↗
PubMed1988

Growth factor production by a human megakaryocytic tumor cell line.

A recently described human megakaryocytic tumor cell line was analyzed for the presence of growth factor activity and was found to produce large quantities of transforming growth factor beta-like (TGF-beta) and basic fibroblast growth factor-like (bFGF) activities. Growth factor activities were identified using a radioreceptor assay for the TGF-beta-like activity, a heparin-binding assay for the b-FGF-like activity, and a demonstration of distinct biological activities for each type of factor. Tumor poly-A+ RNA revealed strong signals when probed with complementary DNA corresponding to bovine basic FGF and human TGF-beta and weak signals when probed with cDNA corresponding to epidermal growth factor (EGF) and TGF-alpha. The levels of EGF and TGF-alpha produced in the tumor line were too low to be detected by radioreceptor assays. Relative levels of messenger RNA encoding each of the growth factors reflected the relative levels of each of the respective factors tested. These data represent the first definitive identification of FGF-like activities in megakaryocytic-like cell lines. Interestingly, the line displayed little activity similar to platelet-derived growth factor (PDGF) when assayed either biochemically or by poly-A+ RNA analysis.

Animals↗
PubMed1988

Phenol emulsion-enhanced DNA-driven subtractive cDNA cloning: isolation of low-abundance monkey cortex-specific mRNAs.

To isolate cDNA clones of low-abundance mRNAs expressed in monkey cerebral cortex but absent from cerebellum, we developed an improved subtractive cDNA cloning procedure that requires only modest quantities of mRNA. Plasmid DNA from a monkey cerebellum cDNA library was hybridized in large excess to radiolabeled monkey cortex cDNA in a phenol emulsion-enhanced reaction. The unhybridized cortex cDNA was isolated by chromatography on hydroxyapatite and used to probe colonies from a monkey cortex cDNA library. Of 60,000 colonies screened, 163 clones were isolated and confirmed by colony hybridization or RNA blotting to represent mRNAs, ranging from 0.001% to 0.1% abundance, specific to or highly enriched in cerebral cortex relative to cerebellum. Clones of one medium-abundance mRNA were recovered almost quantitatively. Two of the lower-abundance mRNAs were expressed at levels reduced by a factor of 10 in Alzheimer disease relative to normal human cortex. One of these was identified as the monkey preprosomatostatin I mRNA.

Amino Acid Sequence↗
PubMed2006

Ghrelin and cholecystokinin in term and preterm human breast milk.

AIM: To determine whether ghrelin and cholecystokinin (CCK) are present in significant quantities in term and preterm human breast milk, and to identify their source. METHODS: Samples were collected from 10 mothers who delivered term infants and 10 mothers who delivered preterm infants. Estimated fat content was measured. Ghrelin and CCK levels were measured in whole and skim breast milk samples using radioimmunoassays (RIA). Reverse transcriptase-polymerase chain reaction (RT-PCR) was performed using RNA from human mammary epithelial cells (hMECs) and mammary gland with primers specific to ghrelin. RESULTS: The median ghrelin level in whole breast milk was 2125 pg/ml, which is significantly higher than normal plasma levels. There was a direct correlation between whole milk ghrelin levels and estimated milk fat content (r=0.84, p<0.001). Both the mammary gland and hMECs produced ghrelin. While CCK was detected in some samples, levels were insignificant. Infant gestational age, birthweight, maternal age, and maternal pre-pregnancy body mass index did not significantly affect the results. CONCLUSION: Ghrelin, but not CCK, is present in breast milk. Since the mammary gland produces ghrelin message, and ghrelin levels in breast milk are higher than those found in plasma, we conclude that ghrelin is produced and secreted by the breast.

Adult↗
PubMed1999

Comprehensive transcript analysis in small quantities of mRNA by SAGE-lite.

Serial analysis of gene expression (SAGE) is a powerful technique that can be used for global analysis of gene expression. Its chief advantage over other methods is that SAGE does not require prior knowledge of the genes of interest and provides quantitative and qualitative data of potentially every transcribed sequence in a particular tissue or cell type. Furthermore, SAGE can quantify low-abundance transcripts and reliably detect relatively small differences in transcript abundance between cell populations. However, SAGE demands high input levels of mRNA which are often unavailable, particularly when studying human disease. To overcome this limitation, we have developed a modification of SAGE that allows detailed global analysis of gene expression in extremely small quantities of tissue or cultured cells. We have called this approach 'SAGE-Lite'. This technique was used for the global analysis of transcription in samples of normal and pathological human cerebrovasculature to study the molecular pathology of intracranial aneurysms. These samples, which are obtained during operative surgical repair, are typically no bigger than 1 or 2 mm and yield <100 ng of total RNA. In addition, we show that SAGE-Lite allows simple and rapid isolation of long cDNAs from short (15 bp) SAGE sequence tags.

Cell Line↗
PubMed1989

Purification and analysis of RNA polymerase II transcription factors by using wheat germ agglutinin affinity chromatography.

We recently found that many RNA polymerase II transcription factors are modified with N-acetylglucosamine residues. These sugar moieties confer upon transcription factors an ability to bind the lectin wheat germ agglutinin. We have taken advantage of this interaction to devise a purification procedure for the "GC-box" binding transcription factor Sp1. Crude nuclear extracts are first subjected to wheat germ agglutinin affinity chromatography and then subjected to sequence-specific DNA affinity chromatography. The Sp1 protein purified by this procedure is at least 95% pure, and the overall recovery is greater than 80%. In addition to yielding larger quantities of Sp1 than conventional schemes, the new purification procedure is also simpler and more rapid. We show that wheat germ agglutinin affinity chromatography can also be used to purify the glycosylated forms of the CCAAT-binding transcription factor. Thus, wheat germ agglutinin affinity chromatography may aid the purification of other transcription factors that bear N-acetylglucosamine residues. Furthermore, the ability to separate glycosylated forms of transcription factors from their unglycosylated counterparts by wheat germ agglutinin affinity chromatography should facilitate investigations into the role of N-acetylglucosamine residues in the functioning of transcription factor proteins.

Acetylglucosamine↗
PubMed2002

A Bayesian approach to parameter estimation in HIV dynamical models.

In the context of a mathematical model describing HIV infection, we discuss a Bayesian modelling approach to a non-linear random effects estimation problem. The model and the data exhibit a number of features that make the use of an ordinary non-linear mixed effects model intractable: (i) the data are from two compartments fitted simultaneously against the implicit numerical solution of a system of ordinary differential equations; (ii) data from one compartment are subject to censoring; (iii) random effects for one variable are assumed to be from a beta distribution. We show how the Bayesian framework can be exploited by incorporating prior knowledge on some of the parameters, and by combining the posterior distributions of the parameters to obtain estimates of quantities of interest that follow from the postulated model.

Bayes Theorem↗
PubMed2002

A novel sensitive microarray approach for differential screening using probes labelled with two different radioelements.

We have developed a novel microarray approach for differential screening using probes labelled with two different radioelements. The complementary DNAs from the reverse transcription of mRNAs from two different biological samples were labelled with radioelements of significantly different energies (3H and 35S or 33P). Radioactive images corresponding to the expressed genes were acquired with a MicroImager, a real time, high resolution digital autoradiography system. An algorithm was used to process the data such that the initially acquired radioactive image was filtered into two subimages, each representative of the hybridisation result specific for one probe. The simultaneous screening of gene expression in two different biological samples requires <100 ng mRNA without any amplification. In such conditions, the technique is sensitive enough to directly quantify the amount of mRNA even when present in small amounts: 10(7) molecules in the probe as assessed with an added control sequence and 2 x 10(5) molecules with an endogenous tyrosine hydroxylase mRNA. This novel technique of double radioactive labelling on a microarray is thus suitable for the comparison of gene expression in two different biological samples available in only small quantities. Consequently, it has great potential for various biological fields, such as neuroscience.

Animals↗
PubMed2005

Regulation of the immunoexpression of aquaporin 9 by ovarian hormones in the rat oviductal epithelium.

The volume of oviductal fluid fluctuates during the estrous cycle, suggesting that water availability is under hormonal control. It has been postulated that sex-steroid hormones may regulate aquaporin (AQP) channels involved in water movement across cell membranes. Using a functional assay (oocytes of Xenopus laevis), we demonstrated that the rat oviductal epithelium contains mRNAs coding for water channels, and we identified by RT-PCR the mRNAs for AQP5, -8, and -9, but not for AQP2 and -3. The immunoreactivity for AQP5, -8, and -9 was localized only in epithelial cells of the oviduct. The distribution of AQP5 and -8 was mainly cytoplasmic, whereas we confirmed, by confocal microscopy, that AQP9 localized to the apical plasma membrane. Staining of AQP5, -8, and -9 was lost after ovariectomy, and only AQP9 immunoreactivity was restored after estradiol and/or progesterone treatments. The recovery of AQP9 reactivity after ovariectomy correlated with increased mRNA and protein levels after treatment with estradiol alone or progesterone administration after estradiol priming. Interestingly, progesterone administration after progesterone priming also induced AQP9 expression but without a change in mRNA levels. Levels of AQP9 varied along the estrous cycle with their highest levels during proestrus and estrus. These results indicate that steroid hormones regulate AQP9 expression at the mRNA and protein level and that other ovarian signals are involved in the expression of AQP5 and -8. Thus hormonal regulation of the type and quantity of water channels in this epithelium might control water transport in the oviductal lumen.

Animals↗
PubMedDate not supplied

A comparative kinetic RT/-PCR strategy for the quantitation of mRNAs in microdissected human renal biopsy specimens.

Molecular biology techniques, to be applicable to a diagnostic renal biopsy specimen, should (1) be highly sensitive to be performed on a very small quantity of tissue; (2) be quantitative because they have to analyze genes normally expressed in the tissue and (3) allow the analysis of as large a number of genes as possible. Among different methods, only the reverse-transcriptase polymerase chain reaction (RT/-PCR) might comply with previous requisites, but the few RT/-PCR examples on renal biopsies in the literature do not allow starting RNA quantification and quality control; furthermore they have the drawback of analyzing only few genes. In an ongoing study to assess the expression of a number of genes in glomeruli and in tubulointerstitium of patients with different nephropathies, we developed a comparative RT/-PCR kinetic strategy based on the purification and quantification of total glomerular and tubulointerstitial RNA and on the use of an internal standard, the housekeeping gene G3PDH. We demonstrate that in microdissected diagnostic renal biopsies (1) glomerular and interstitial starting RNA can be quantified; (2) the G3PDH gene may be used both as an internal standard and as an indirect marker of RNA integrity; (3) as low as 28 ng of total RNA is sufficient to obtain PCR products of eight genes, and (4) it is worth to operate on microdissected biopsy specimens because of the different expression of genes in the two renal compartments.

Actins↗
PubMed2004

Expression and purification of heterologous proteins in plant tissue using a geminivirus vector system.

In the past, plant molecular biologists have relied on Escherichia coli, baculovirus and other expression systems to produce plant proteins to quantities sufficient for biochemical analysis. However, such expression systems often result in the production of proteins which possess improper posttranslational modifications. Here, we present a plant virus-based expression system superior to those currently available. We demonstrate that bean yellow dwarf geminivirus (BeYDV) replicates and expresses foreign proteins at high levels in tobacco, Arabidopsis, and other dicotyledonous plants, making it more universal than plant RNA viruses with restricted host ranges which are currently used as expression systems. The DNA-based nature of the BeYDV genome renders it stable for the incorporation of large plant open reading frames, and gives it an advantage over other plant virus-based expression systems which possess insert size restrictions. Using this expression system, the rapid accumulation of a novel Arabidopsis-derived mitogen-activated protein kinase to levels sufficient for standard biochemical analysis is demonstrated.

Arabidopsis↗
PubMed1990

Pregnancy-specific beta 1-glycoprotein messenger ribonucleic acid and immunoreactive protein in the rat testis.

Human pregnancy-specific beta 1-glycoprotein (PS beta G) is synthesized in large quantities by syncytiotrophoblasts of the placenta. Recent studies using a partial cDNA of PS beta G isolated from human term placenta detected the presence of mRNA highly homologous to placental PS beta G in a number of extraplacental tissues, including human and rat testis. The present study determined in the rat that the amount of PS beta G mRNA based on percentage of total tissue RNA was greatest in the testis of mature rats, followed by senescent and prepubertal rats. In experiments using rats with testicular feminization syndrome (Tfm) which exhibit end-organ insensitivity to androgen stimulation, slot blot analysis of testicular RNA showed reduced levels of PS beta G mRNA in Tfm rats compared to normal rats. Northern blot analysis of rat testicular RNA probed with a human placental PS beta G cDNA demonstrated the presence of a single mRNA species of 1.65 kilobases. Subsequent studies investigated whether proteins immunologically similar to PS beta G were present in the testes from normal and Tfm rats. The rat testes were perfused with fixative, and sections from paraffin-embedded tissues were treated with rabbit anti-human PS beta G, followed by the avidin-biotin-peroxidase complex. Testes from the normal rat showed intense immunostaining in late spermatids (steps 16, 17, 18, and 19 of spermiogenesis), residual bodies, as well as cytoplasm of Leydig cells. Spermatozoa within the epididymis also demonstrated intense immunolabeling. Paraffin sections of the testes from the Tfm rat showed light diffuse cytoplasmic immunostaining in cells of the seminiferous tubules. Since spermiogenesis does not proceed normally, and no spermatids were seen, it was not possible to accurately stage the seminiferous tubules of the Tfm rat. The Leydig cells of the Tfm testes stained intensely, however, as was observed in the testes of the normal rat. These data suggest that the rat may provide an animal model for the investigation of the biological function and regulation of PS beta G in the testis.

Animals↗
PubMedDate not supplied

Autoantibodies and autoantigens in the urine of SLE patients.

Autoantibodies against RNA polymerase I (RNAPI), DNA, La and ribosomal P proteins were detected in the urine of systemic lupus erythematosus (SLE) patients, many with normal protein excretion rates. In a number of cases, the antibodies were detectable in the urine but not the serum sample of the same patient. The presence and relative concentrations of the urinary autoantibodies correlated with disease activity. RNAPI antigens were detected in the urine of SLE patients by radioimmunoassay and immunoblotting using rabbit antisera prepared against the purified holoenzyme. Immunoaffinity purification of the rabbit anti-RNAPI with SLE urine proteins resulted in antibodies directed primarily against the largest RNAPI subunit (S1; 194 kDa). Antibodies prepared against recombinant fusion proteins representing the DNA binding regions of human RNAPI(S1) reacted with a 35 kDa SLE urinary protein, a putative fragment of RNAPI(S1). Ribosomal protein P0 was detected in SLE patients' urine by immunoblotting, using rabbit antiserum prepared against recombinant human P1 fusion protein. The relative quantities of urinary P0 correlated with disease status. Analysis of urinary autoantibodies and corresponding antigens in conjunction with analysis of serum autoantibodies may be of value for the purpose of monitoring disease activity.

Autoantibodies↗

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