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Laser-capture microdissection, a tool for the global analysis of gene expression in specific plant cell types: identification of genes expressed differentially in epidermal cells or vascular tissues of maize.

Laser-capture microdissection (LCM) allows for the one-step procurement of large homogeneous populations of cells from tissue sections. In mammals, LCM has been used to conduct cDNA microarray and proteomics studies on specific cell types. However, LCM has not been applied to plant cells, most likely because plant cell walls make it difficult to separate target cells from surrounding cells and because ice crystals can form in the air spaces between cells when preparing frozen sections. By fixing tissues, using a cryoprotectant before freezing, and using an adhesive-coated slide system, it was possible to capture large numbers (>10,000) of epidermal cells and vascular tissues (vascular bundles and bundle sheath cells) from ethanol:acetic acid-fixed coleoptiles of maize. RNA extracted from these cells was amplified with T7 RNA polymerase and used to hybridize a microarray containing approximately 8800 maize cDNAs. Approximately 250 of these were expressed preferentially in epidermal cells or vascular tissues. These results demonstrate that the combination of LCM and microarrays makes it feasible to conduct high-resolution global gene expression analyses of plants. This approach has the potential to enhance our understanding of diverse plant cell type-specific biological processes.

Aquaporins↗

Identification and mapping of human papillomavirus type 1 RNA transcripts recovered from plantar warts and infected epithelial cell cultures.

Multiple spliced transcripts of human papillomavirus type 1 were detected by electron microscopic analysis of R-loops formed with total RNA extracted from plantar warts and with poly(A)+ RNA isolated from cultured keratinocytes infected with human papillomavirus type 1. The 5' ends of the RNAs were mapped to sites in the E7 open reading frame (ORF), just upstream of the E6 ORF and in the upstream regulatory region. Species with 5' ends in E7 accounted for over 95% of all transcripts seen. Two polyadenylation sites were used, one at the end of the early (E) region of the viral DNA, the other at the end of the late (L) region. The most abundant species had a short 5' exon of approximately 100 nucleotides spanning the junction of the E7 and E1 ORFs spliced to a 3' exon of 800 nucleotides in the region with overlapping E2 and E4 ORFs; it was polyadenylated at the end of the E region. This species probably encodes the abundant E4 protein found in plantar warts (F. Breitburd, O. Croissant, and G. Orth, Cancer Cells, vol. 5, in press; J. Doorbar, D. Campbell, R. J. A. Grand, and P. H. Gallimore, EMBO J. 5:355-362, 1986). Other transcripts had exons spanning the E6-E7 ORFs, the E4-E5-L2-L1 ORFs, or the L1 ORF. The infrequent L1 transcript, probably the mRNA coding for the major capsid protein, had the same 5' exon in E7 as the abundant mRNA spliced from E1 and E4 ORFs, suggesting genetic regulation via the choice of the alternative polyadenylation sites or mRNA processing.

Base Sequence↗

CD40 expression by human peripheral blood eosinophils.

In this study, we have investigated CD40 expression in human peripheral blood eosinophils and in human chronically inflamed nasal tissues, i.e., nasal polyps. We show by both reverse transcriptase-PCR and Northern blot analysis that eosinophils from allergic subjects express human CD40 mRNA. We also show that constitutive CD40 mRNA expression in eosinophils could be upregulated by exposure to IgA immune complexes and downregulated by IL-10 and the synthetic steroid budesonide. In addition, we demonstrate that eosinophils express CD40 protein by flow cytometry. Such expression is biologically functional as cross-linking CD40 with CD40 mAbs enhances eosinophil survival in a dose-dependent fashion; in addition, CD40 ligation stimulates eosinophils to release GM-CSF. CD40-mediated eosinophil survival was largely inhibited by an anti-GM-CSF neutralizing antibody suggesting GM-CSF involvement in the survival enhancing mechanism. CD40 mRNA was also detected in total RNA extracted from nasal polyp tissues but not in RNA isolated from normal nasal mucosa (inferior turbinate); by immunohistochemistry, we were able to detect immunoreactive CD40 protein in a variety of cell types in the polyp stroma, but primarily in eosinophils. These observations suggest previously unforeseen interactions between eosinophils and cells expressing the CD40 ligand and, thus, novel pathways by which eosinophils may contribute to the regulation of airway inflammation.

Antibodies, Monoclonal↗

The prevalence of different African horsesickness virus serotypes in the Onderstepoort area near Pretoria, during an outbreak of African horsesickness in South Africa in 1995/1996.

During 1995/1996 parts of South Africa experienced exceptionally high rainfall. Large numbers of Culicoides midges were seen and an outbreak of African horsesickness (AHS) followed. In the Onderstepoort area, near Pretoria in Gauteng, a number of horses died of suspected AHS. Virus isolation and typing was done from blood and/or organ samples of 21 suspected cases as well as from five zebra which were kept in the area. Virus was isolated from 14 of the 21 suspected cases but not from the zebra. The neutralizing antibody response of the zebra to the nine different African horsesickness virus (AHSV) serotypes was determined. Results indicated the highest prevalence of serotypes 2 and 4 followed by serotypes 1, 6 and 9. Reverse transcription polymerase chain reaction (RT-PCR) was performed on total RNA extracted from blood samples of the zebra. AHSV RNA was indicated in three of five zebra by agarose gel electrophoresis analysis of amplicons and in four of five zebra after Southern blot hybridization using a 32P-labelled probe. RT-PCR can be used together with serological techniques in studies of AHS to further clarify the epizootiology of the disease.

African Horse Sickness↗

[Study of viral specific RNA synthesis in FHM and RTG-2 cells infected with infectious pancreatic necrosis (IPN) virus (author's transl)].

In FHM and RTG-2 cells infected with IPN virus two types of viral directed RNAs where isolated in the presence of 0.5 mug/ml actinomycin D. One type, sedimenting at 14-15 S in sucrose gradients, was shown to be resistant to digestion by pancreatic RNase and did not precipitate in presence of lithium chloride 2 M. Furthermore the molecules sedimented in the same way as the double stranded RNA extracted from purified virions. The second type of RNA, sedimenting at 23-24 S, was sensitive to RNase and was precipitable by LiCl, indicating that it was single-stranded. Additionally it was shown by polyacrylamide gel electrophoresis that this type of RNA resolved into four peaks. The single stranded 23-24 S RNA was detectable in cells from the third hour following infection; it represents the major portion of total viral directed RNA that was synthesized during a cycle of replication. The synthesis of both single stranded and double stranded RNA increased exponentionally until the 7th hour post-infection and began to decrease at about 10 hours.

Animals↗

Presence of HCV RNA in hepatic tissue and effectiveness of treatment with interferon and ribavirin.

BACKGROUND: The aim of the study was to assess the prognostic value of HCV RNA detection in hepatic tissue for the response to treatment with interferon alfa (IFN) and ribavirin (RIB) in patients with chronic hepatitis C. PATIENTS AND METHODS: A group of 55 patients infected with HCV was examined before the commencement of treatment with IFN and RIB. In all of them HCV RNA was detected in the serum. The presence of HCV RNA in hepatic tissue was confirmed using a technique combining a new method of HCV RNA extraction from hepatic tissue and detection of HCV RNA with RT-PCR Cobas Amplicor Roche tests. The group of 55 patients received IFN (3-6 MU, 3 times a week) and RIB (800-1200 mg daily) for 6 to 12 months. The response to treatment was assessed 6 months after completion of the therapy. Sustained response (SR) was defined as absence of HCV RNA in the serum and normalization of ALT levels. RESULTS: The presence of HCV RNA in hepatic tissue was confirmed in 48 patients (group A), and in 7 (group B) HCV RNA was not detected in the liver. SR was observed in 17 patients from group A and 6 from group B. Significant correlation (p < 0.05) was found between detection of HCV RNA in hepatic tissue and response to IFN + RIB therapy. CONCLUSIONS: As it follows from our results, the detection of HCV RNA in the hepatic tissue of a patient with chronic hepatitis C may be a negative prognostic factor for the patient's response to IFN + RIB therapy.

Adolescent↗

[Detection of HCV-RNA in liver tissue does not correlate with inflammatory process and fibrosis activity in chronic hepatitis C].

The significance of HCV-RNA presence in the liver tissue in chronic hepatitis C activity or prognosis has not yet been clearly explained. Therefore, we have examined the relationship between the presence of HCV-RNA in the liver and selected parameters of disease activity and liver damage. A group of 48 chronically HCV infected patients (7-63 years old, mean 39 years) was evaluated. In the patients we assessed the activity of transaminases (ALT, AST), gammaglutamyltransferase (GGTP), and alkaline phosphatase (ALP). The patients underwent routine liver biopsies and the liver tissue was examined histopathologically and in order to detect the presence of HCV-RNA, by means of a combined procedure joining a new method of HCV-RNA extraction from the liver tissue and HCV-RNA detection with RT-PCR automatic Cobas Amplicor Hepatitis C ver. 2.0 assay (Roche Diagnostics). At the time of the liver biopsy, 44 of the patients were identified as having detectable serum HCV-RNA (as examined by means of Cobas Amplicor Hepatitis C ver. 2.0 assay), 3 patients were negative, and 1 was not tested. The presence of HCV-RNA in the liver tissues was detected in 39 cases (81.2%). In the parameters examined we have not found any significant differences between currently liver HCV-RNA positive and negative patients. Presence of the detectable HCV-RNA in the liver bioptats from chronic hepatitis C patients does not correlate with disease activity or level of liver damage.

Adolescent↗

Co-ordinate induction of collagen type I and biglycan expression in keloids.

Proteoglycans are macromolecules displaying structural roles as well as regulatory functions in the maintenance of the extracellular matrix. Biglycan/PG-I and decorin/PG-II are two small proteoglycans that are structurally related but differ considerably in their localization in vivo and behaviour in vitro. Decorin and, to a minor extent, biglycan, can be located at the surface of type I collagen fibrils and have been shown to influence collagen fibrillogenesis. However, the physiological role of biglycan in the dermis is not known. Biopsies obtained from keloids were bisected and processed for total RNA extraction and immunohistochemistry. Northern blot analysis of total RNA obtained from keloids with high growth tendency in vivo showed a marked induction of biglycan and collagen alpha 1(I)mRNA expression in comparison with total RNA obtained from normal skin or keloids with little growth tendency. In contrast, decorin mRNA expression remained largely unaltered. Studying these biopsies by immunohistochemistry, decorin expression in the dermis was unaltered comparing normal and keloid tissue, whereas a markedly increased staining for biglycan was observed in the keloid tissue, which was most pronounced in the nodular formations, and was a characteristic feature of keloids. The altered expression of biglycan in keloid tissue might be involved in the abnormal regulation of extracellular matrix deposition either through the binding of growth factors or by influencing the three-dimensional organization of collagen fibres or associated molecules.

Biglycan↗

Rescue of infectious classical swine fever and foot-and-mouth disease virus by RNA transfection and virus detection by RT-PCR after extended storage of samples in Trizol.

A method for storing samples containing classical swine fever virus (CSFV) or foot-and-mouth disease virus (FMDV), respectively, was developed, which abolishes the infectivity of both plus strand RNA viruses, and allows storage of samples above 0 degrees C for an extended time, yet preserves the viral RNA in a state which allows its detection by reverse transcription-polymerase chain reaction (RT-PCR), and even rescue of infectious virus after transfection of the extracted RNA into susceptible cells. Supernatants from infected cell cultures as well as organs from diseased animals were stored in Trizol(R) for 1-4 weeks at -20 degrees C, 4 degrees C, room temperature, or 37 degrees C. RNA was then extracted and used subsequently for RT-PCR, as well as transfection into susceptible cells to initiate the replication of progeny virus. Formaldehyde-fixed samples were also included in this study. Storage up to 4 weeks at 37 degrees C in Trizol(R) still yielded positive RT-PCR results and rescue of infectious virus upon RNA transfection. In contrast, formaldehyde fixation reduced drastically the detectability of viral RNA. This method represents a safe and inexpensive alternative to -70 degrees C (dry ice) storage or transport of samples, and abolishes the biosafety risks involved in shipping deep-frozen infectious materials.

Animals↗

[In vitro translation of RNA from lizard epididymis and identification of poly A RNA coding for a major androgen-dependent protein].

During the reproductive period (spring) the lizard epididymis secretes a soluble protein of an apparent molecular weight (MW) of 19,000, the protein L. This androgen dependent protein disappears during post-nuptial atrophy of the epididymis (summer). At two time intervals (spring and summer) total RNA were extracted and poly (A) RNA were prepared. The RNA were translated in a cell-free system (rabbit reticulocyte lysate) in the presence of 35S methionine. Labelled translation products were analyzed by polyacrylamide gel electrophoresis under denaturing conditions. Electrophoresis were preceded or not by immunoprecipitation with an antiserum raised against protein L. RNA extracted during spring coded for several unique bands including five immunoprecipitated proteins with close-related MW (21,000 to 25,000). When RNA were translated in the presence of dog microsomes, the five previously detected protein bands disappear although a 19,000 MW immunoprecipitated protein was clearly demonstrated. These proteins were not detected when RNA extracted in summer were used. The protein L appears to be synthesized as preprotein(s). Its (unique or several?) messenger is of poly A type; it is present in spring and absent or undetectable in these experimental conditions in summer.

Androgens↗

Simultaneous extraction of total RNA and peptides from tissues: application to tachykinins.

Methods for extraction and isolation of intact RNA are often laborious, time consuming, and preclude the direct analysis of peptides. Similarly, the conditions for extraction and isolation of peptides are unsuitable for the isolation of intact RNA. Thus, to study changes in the levels of neuropeptides and gene expression of the corresponding mRNAs, separate procedures are required. A simple and rapid method for the simultaneous extraction of RNA and peptides from tissues is described. RNA and peptides are extracted with guanidinium isothiocyanate, followed by delipidation, and peptides are isolated by a simple solid-phase extraction procedure. RNA is isolated by differentially partitioning DNA into an organic phase, followed by precipitation with ethanol. The RNA and peptides isolated by this method are of high yield and quality. Furthermore, this method for RNA isolation is successful and efficient, even with tissues that proved recalcitrant with other procedures, and allows the simultaneous processing of multiple samples. We describe the successful application of this procedure for measuring tachykinins and the corresponding preprotachykinin A mRNA from tissues. Extraction of neuropeptide K, a 36-mer tachykinin, was dramatically more efficient with the present method than other methods in common use.

Animals↗

Design of a real time quantitative PCR assay to assess global mRNA amplification of small size specimens for microarray hybridisation.

BACKGROUND: Low RNA yields from clinical samples are a limiting step for microarray technology. AIMS: To design an accurate real time quantitative polymerase chain reaction (PCR) assay to assess the crucial step of global mRNA amplification performed before microarray hybridisation, using less than 1 microg total RNA. METHODS: Three RNA extraction procedures were compared for small size samples. Total RNA was amplified from universal RNA or the BC-H1 breast cancer micrometastatic cell line using three different protocols. Real time quantitative PCR technology was used for accurate measurement of urokinase plasminogen activator receptor and cytokeratin 8 RNA amplification rates and ratios, using primer sets binding at various distances from the 3' end of transcripts. A 50 mer oligomeric array targeting 87 genes potentially involved in breast cancer metastatic progression was built and hybridised with amplified RNA. RESULTS: Eighteen nanograms of total RNA could be purified from 1000 BC-H1 micrometastatic cells. Amplification rates of 25,000 to 100,000 were achieved with as little as 10 ng of starting material. However, results were highly variable, depending on the amount of starting material, gene characteristics, sample quality, and protocols used. Oligomeric array hybridisation with 20 microg reference RNA resulted in specific and reproducible signals for 83% of the genes, whereas mRNA amplification from less than 400 ng of starting material resulted in selective detection of signals from highly expressed genes. CONCLUSIONS: Improvements in the design of global mRNA amplification procedures and oligomeric arrays are needed to extract informative gene expression data from clinical samples containing limited cell numbers.

Base Sequence↗

Sequence analysis of murine leukemia virus envelope gene from inoculated mice.

Introduction of amino acids substitutions in murine leukemia virus genome is a powerful method to determine the relative importance of various viral factors in pathogenesis. However, introduction of such amino acids substitution could result in viruses at a selective disadvantage, and eventual selection of revertants. It is thus essential to verify if the mutation is maintained stably in replicating virus and in infected tumor cells. In the present study, viral nucleic acid sequences from diseased animals were determined using different approaches. Small blood samples were found adequate for direct RNA extraction and reverse transcriptase-PCR amplification followed by automated DNA sequencing. Alternatively, replication-competent viruses were recovered specifically by applying blood samples onto permissive cells; viral RNA is then extracted from tissue culture medium and similarly sequenced. Tissue samples were also used to amplify viral sequences from tumors DNA while small pieces of tumors tissues were applied onto permissive cells to isolate replicating viruses. The combined experimental approach was used to show sequence conservation using a mutant altered in the intracytoplasmic region of viral envelope glycoprotein. No difference was observed between viruses recovered directly from the animal and those amplified onto cultured cells.

Amino Acid Sequence↗

Presence of angiotensinogen messenger RNA in various cultured cell lines.

The presence of angiotensinogen messenger RNA (mRNA) was assessed in total RNA extracted from hepatoma, glioma, neuroblastoma, and glioma-neuroblastoma hybrid cell lines. Total RNA from 1 X 10(7) cells was extracted, transferred to a membrane, and hybridized with a 32P-labeled, full-length (1650-base pair) rat angiotensinogen complementary DNA (cDNA). Angiotensinogen RNA sequences could be definitively detected only in hepatoma cells. Steroids were used in an attempt to increase the angiotensinogen mRNA level. Dexamethasone (2 X 10(-6) M) or 17 beta-estradiol (1 X 10(-7) M) was added to the cultures 18 to 24 hours prior to harvest. Dexamethasone treatment of the hepatoma cells resulted in a large increase in angiotensinogen mRNA, whereas estradiol had no effect. Steroids failed to induce detectable levels of angiotensinogen mRNA in total RNA from the other cell lines. That the RNA was intact was ensured by hybridizing duplicate Northern blots to a 32P-labeled actin cDNA. Actin mRNA sequences were detected in all cell lines. Blot hybridization of poly(A)+RNA resulted in the visualization of a weak angiotensinogen mRNA signal for a glioma cell line and a glioma-neuroblastoma hybrid line. However, the ability to detect angiotensinogen mRNA in a cell may depend on the phenotype expressed, which can be governed by culture conditions.

Angiotensinogen↗

Expression of P450 isoenzymes during rat liver organogenesis.

1. The expression of P450 isoenzymes in foetal and neonatal hepatic microsomes was determined by measuring the metabolism of marker substrates and by studying the expression of P450 isoenzymes at the protein and mRNA level. 2. Monooxygenase activities were not measurable at day 10 of gestation, but shortly before birth (day 20 of gestation) and thereafter a surge in monooxygenase activities was observed using ethoxyresorufin, aniline, nitroanisole, aminopyrine, dimethylnitrosamine and aldrin as substrates. 3. In contrast, as early as day 10 of gestation, post oxidative drug metabolism was measurable, when assessed for reactions catalysed by UDP-glucuronyltransferase, glutathione S-transferase and epoxide hydrolase. 4. Microsomal proteins isolated from foetal/perinatal rats did not crossreact with antibodies raised to CYP1A1, CYP1A2, CYP2A1, CYP2B1, CYP2E1, CYP3A1 and CYP4A1 at a protein loading of 3 micrograms total protein/well. 5. With the exception of CYP2E1 mRNA and CYP4A1 mRNA there was little evidence to suggest the expression of CYP1A1, CYP1A2 and CYP2A1 mRNA. 6. The mRNA of CYP2B1, CYP2C7 and CYP3A1 was not detectable in foetal/perinatal rat liver extracts at a loading rate of 10 micrograms total RNA. 7. Microsomal proteins isolated from neonatal rats crossreacted with antibodies raised to CYP2C6, CYP2E1, CYP3A1 and CYP4A1, albeit at varying intensities. 8. Concomitantly, CYP2A1, CYP2E1 and CYP4A1 mRNA transcripts were detectable in Northern blot hybridization experiments using neonatal rat liver RNA extracts.

Animals↗

Calcitonin gene-related peptide-containing neurons supplying the rat digestive system: differential distribution and expression pattern.

In the enteric nervous system, calcitonin gene-related peptide (CGRP) immunoreactivity is localized to a substantial number of capsaicin-sensitive afferent fibers and to intrinsic neurons and processes. CGRP immunoreactivity detected by immunohistochemistry represents the expression of two distinct genes, the calcitonin/alpha-CGRP and the beta-CGRP genes, which have different tissue distributions. In the present study, we used (1) in situ hybridization histochemistry and ribonucleic acid (RNA) blot hybridization with RNA probes complementary to the divergent sequences of alpha- and beta-CGRP messenger RNAs (mRNAs) to differentiate which CGRP gene was expressed in enteric and afferent neurons; and (2) axonal transport approaches in combination with CGRP immunohistochemistry to define the location of CGRP-containing afferent neurons supplying the digestive system. In situ hybridization histochemistry with [35S]-labeled RNA probes indicated that in the gastrointestinal tract beta-CGRP mRNA, but not alpha-CGRP mRNA, was expressed in enteric neurons confined to the myenteric and submucous plexuses of the small and large intestine. In dorsal root and vagal sensory ganglia, mRNAs for alpha-CGRP and beta-CGRP were both present in a vast population of neurons, with an overlapping pattern, even though the alpha-CGRP signal appeared more intense. RNA blot hybridization analysis showed a single band of hybridization at 1.2 Kb with the beta-CGRP RNA probe in RNA extracts from muscle layer-myenteric plexus and submucosal layer preparations of the ileum, and from dorsal root ganglia; it also showed a single band at 1.3 Kb with the alpha-CGRP RNA probe in extracts from dorsal root ganglia, but not from the intestine. These findings further support the differential expression of alpha- and beta-CGRP mRNAs. Retrograde transport of fast blue or fluorogold coupled with CGRP immunohistochemistry demonstrated that the vast majority of CGRP-containing afferent neurons supplying the stomach, proximal duodenum, and pancreas were located in dorsal root ganglia at the middle and lower thoracic and at the upper lumbar levels, and represented a major component of the afferent innervation of these viscera (up to 89%). Approximately 50% of CGRP-immunoreactive afferent neurons also expressed tachykinin (TK) immunoreactivity, as shown by triple labeling. Only a minor component of the afferent innervation of the stomach, duodenum, and pancreas derived from vagal CGRP-containing neurons (less than 8%). A large portion of these neurons (an average of 62%) also contained TK immunoreactivity.(ABSTRACT TRUNCATED AT 400 WORDS)

Afferent Pathways↗

The molecules that initiate cardiac hypertrophy are not species-specific.

Extracts from hypertrophying dog hearts perfused through isolated rat hearts increase the synthesis of messenger RNA and initiate hypertrophy in the treated hearts. Total RNA extracted from experimental and control hearts was translated in vitro and hybridized with polyuridylate. Synthesis of protein and polyadenylate-containing RNA was greater in rat hearts perfused with extracts of hypertrophying dog hearts than in control hearts. The results demonstrate that molecules from hypertrophying dog hearts are not species-specific since they are effective in stimulating transcription of messenger RNA in rat hearts as well as in dog hearts.

Animals↗

RT-PCR quantitation of cytokine responses in vivo from specimens containing small numbers of cells during bioimmunotherapy.

A Standard Template method has been developed to carry out semiquantitative RT-PCR analysis on mRNA extracted from small specimens that contain low yields of RNA. Using easily prepared templates (made from previously tested reference specimens), standard calibration curves were generated for each of two cytokine products of interest, specifically IL-10 and IFN-gamma. Also, internal standardization was accomplished by quantitating a well-characterized housekeeping gene (GAPDH). Simple densitometry of the RT-PCR product did not demonstrate sufficient reliability for quantitation since a logarithmic relationship was shown between product and template input. Peritoneal exudate cell specimens that were obtained from ovarian cancer patients during intraperitoneal immunotherapy were utilized for the demonstration of IL-10 and IFN-gamma transcript in vivo. Briefly, this method consists of: (1) template preparation: a PCR product for the cytokine of interest is generated from a previously identified positive specimen, purified and stored at -20 degrees C. (2) RT-PCR: cDNAs are produced from RNA extracted from patient specimens. Replicates of each cDNA and serial dilutions of the corresponding template are amplified with primers specific for each cytokine of interest. (3) Quantitation: photographs are made of the PCR products displayed on an agarose gel and are analyzed by densitometry. Determinations of fold-differences in cytokine transcript expression are normalized to the mRNA content of each specimen (based on the expression of GAPDH).

Ascitic Fluid↗