Simultaneous isolation of high molecular weight RNA and DNA from limited amounts of tissues and cells

Experimental study of tropism in cultivated canine coronavirus in the small intestine of puppies

The varying extents of natural disease induced by coronavirus in dogs are not completely clear because the pathogenesis of coronavirus enteritis is not studied sufficiently. In this study, based on the results of clinical, virological, morphological and histochemical studies, we determined the pathogenic role of coronavirus in infected dogs using experimental infection, per os, of isolated canine coronavirus (Nick) with titer of infectious activity equaling 4.8 ± 0.04 lg TCID50/cm, cultivated on heterologous cell cultures. This allowed us to determine, supplement, and generalize the data on pathogenesis of the disease and determine the histological changes in the small intestine, where the initial replication of the pathogen takes place. It was found that lesions and the pattern of the pathomorphological changes (destruction, necrosis and edema of the stroma of the villi, lysis of the cytoplasm, deformation of the enterocyte nuclei) in the small intestine of experimentally infected dogs depend on the development of the pathological process related not only to the changes in histoarchitectonics of the wall of the intestine, but also to tension of the histochemical statics, and obviously the dynamic of the cells (accumulation of the main and acidic proteins in enterocytes’ cytoplasm, hypersecretion of the mucus by goblet cells, decrease of Schiff iodine acid-positive substances in the enterocytes’ cytoplasm, formation of basophilous inclusion bodies), which leads to disorders in metabolic processes in the organism of infected dogs as a response to the virus infection. The examined dogs were found to have morphological changes in the small intestine similar to those in spontaneously infected animals. During the action of coronavirus, the contacts between the enterocytes become damaged, which leads to inhibition of the protective functions of the intestine. At the same time, the pathological process in the experimentally infected animals developed rapidly and had an acute course. Thus, coronavirus enteritis as a separate disease is practically unobserved in field conditions, which makes microscopic survey of the pathogenic impact of the latter on the organism of dogs impossible. Therefore, experimental mono-infection allows a detailed study to be conducted of pathomorphological changes of the initial place of the reproduction of the virus – the small intestine affected by coronavirus enteritis.

An mRNA and DNA co-isolation method for forensic casework samples

RNA analysis is expected to play an increasingly important role in the area of biomolecular forensic analysis. For example, mRNA expression analysis performed on a total RNA sample isolated from a biological stain may be used to identify the nature of the tissue(s) comprising the stain. Many of the physiological stains encountered at crime scenes involve heterogeneous mixtures of different body fluids (e.g., semen and saliva, semen and vaginal secretions). Separate sampling of these mixed stains from different "geographical" locations of the stains to isolate DNA and RNA could result in a misleading estimate of the ratio of the body fluids present and, in extreme cases, even fail to detect one of the contributors. Thus, a prerequisite for the use of mRNA expression profiling in routine forensic analysis is the ability to co-extract DNA and RNA from the same stain. This article describes an optimized method that was specifically developed to co-extract mRNA and DNA from the same physiological stain and that appears to be sufficiently sensitive and robust for routine forensic use.

Uptake and intracellular stability of glycosylphosphatidylinositol-specific phospholipase D in neuroblastoma cells

Glycosylphosphatidylinositol-specific phospholipase D from mammalian serum has been described to be relatively stable towards the action of proteases in vitro, and it has been speculated that the enzyme may only be active on glycosylphosphatidylinositol-anchored substrates after its proteolytic processing in an intracellular compartment following uptake from body fluids. To test this hypothesis, we studied the possible uptake and intracellular processing of purified glycosylphosphatidylinositol-specific phospholipase D into the mouse neuroblastoma cell line N2A. We found that after incubation of neuroblastoma cells with glycosylphosphatidylinositol-specific phospholipase D at 37 degrees C the amount of cell-associated glycosylphosphatidylinositol-specific phospholipase D activity increased in a concentration- and time-dependent way. A similar uptake was also observed with 125I-labeled intact and trypsin-treated form of glycosylphosphatidylinositol-specific phospholipase D. We found that the incorporated radiolabeled proteins were processed intracellularly to distinct low molecular mass products, and that this process was in part inhibited by the presence of chloroquine during incubation.

The mouse lymphoma L5178Y Tk+/- cell line is heterozygous for a codon 170 mutation in the p53 tumor suppressor gene

The p53 tumor suppressor protein plays an important role in regulating the cellular response to DNA damage, including cell cycle arrest and apoptosis induction. Normal p53 function is critical for the maintenance of genomic stability. The mouse lymphoma L5178Y/TK(+/-)-3.7.2C cell line is widely used in genetic toxicology for mutagenesis and clastogenesis testing. A related line L5178Y-R, has previously been shown to react with antibodies specific for mutant as well as wild-type p53 protein and to exhibit delayed cell death after radiation. For this reason, as well as the mouse lymphoma assay's reputation for high sensitivity of detection for genotoxic agents but low specificity, we examined several clones of L5178Y cells for mutations in the conserved core domain (exons 5-8) of the p53 gene. Using single-strand conformational polymorphism analysis, we found evidence for the same mutation in exon 5 of p53 in L5178Y-R, L5178Y-S and L5178Y/TK(+/+)-3.7.2C cells. The mutation was identified by sequencing of exon 5 as a TGC (Cys) to CGC (Arg) transition in codon 170 (= codon 176 in humans). Sequencing showed approximately equivalent signals for the mutant and normal alleles for all 3 lines. The mutation in codon 170 is adjacent to a mutation hotspot of the human p53 gene (codon 175) and eliminates a critical zinc-coordinating cysteine residue such that the mutant protein is likely to be denatured and have a dominant negative effect on normal p53 function. Western blots showed approximately 100-fold higher levels of p53 protein in unirradiated L5178Y cells as compared to induced levels of p53 in normal mouse splenocytes 4 h after 5 Gy of gamma radiation. The high levels of p53 protein in L5178Y cells were not further inducible by radiation, whereas an 11-fold induction was seen in the irradiated splenocytes. These results indicate that p53 protein in L5178Y cells is dysfunctional and suggest that this line may therefore be abnormally susceptible to the induction of genetic alterations.

Distribution of glycosylphosphatidylinositol-specific phospholipase D mRNA in bovine tissue sections

It has been reported that mammalian serum, and to a lower extent mammalian liver, brain, pancreas, udder, and milk, contain glycosylphosphatidylinositol-specific phospholipase D activity. However, the sites of synthesis have not been determined. In order to study in which cell(s) of the organism synthesis of glycosylphosphatidylinositol-specific phospholipase D takes place, we undertook a systematic screening of 12 different bovine tissues. In situ hybridization experiments with a specific anti-sense RNA probe, derived from a bovine liver cDNA, revealed that glycosylphosphatidylinositol-specific phospholipase D mRNA is present in mast cells of the adrenal gland, lung, and liver. On the other hand, our specific probe detected no mRNA in bovine pancreas, brain, and udder, although enzyme activity has been reported in these tissues. Northern blot analysis of total bovine liver RNA demonstrated two distinct glycosylphosphatidylinositol-specific phospholipase D mRNAs of approximately 3.3 kb and 4 kb length suggesting that two forms of the enzyme may exist.

Biliary glycoprotein, a potential human cell adhesion molecule, is down-regulated in colorectal carcinomas

Biliary glycoprotein (BGP) is the human homologue of a cell adhesion molecule (CAM) of the rat designated Cell-CAM. The BGP gene is a member of the carcinoembryonic antigen gene family, which belongs to the immunoglobulin superfamily. BGP is expressed in cells of epithelial and myeloid origin. In granulocytes, BGP is a main antigen of the CD66 cluster of differentiation antigens that mediate the binding to endothelial E-selectin. Since BGP is a major human CAM, the expression of BGP was studied in 21 colorectal carcinoma tissue specimens and in the respective adjacent normal mucosae. As an internal control for epithelial mRNA, the expression of cytokeratin 18 was evaluated in parallel. In addition, the expression of carcinoembryonic antigen and nonspecific crossreacting antigen, which are highly homologous to BGP, was investigated. Two BGP mRNAs of 3.9 and 1.5 kilobases were detected in the normal colonic mucosa samples. The median of the tumor-to-normal ratios of mRNA expression was 0.2 for both BGP mRNAs. In contrast, the median was 1.2 for cytokeratin, 1.0 for carcinoembryonic antigen, and 1.4 for nonspecific crossreacting antigen. Relative to cytokeratin 18 expression, the expression of BGP was reduced to < or = 0.1 in half of the tumors and to < or = 0.4 in > 80% of the tumors. These findings indicate that the loss or reduced expression of the adhesion molecule BGP is a major event in colorectal carcinogenesis.

The structure and function of the H-ras proto-oncogene are not altered in rat liver tumors initiated by 2-acetylaminofluorene, 2-acetylaminophenanthrene and trans-4-acetylaminostilbene

Liver tumors were generated in Wistar rats in an initiation-promotion experiment. 2-Acetylaminofluorene (AAF), 2-acetylaminophenanthrene (AAP), and trans-4-acetylaminostilbene (AAS) were administered to newborn animals as initiators, and phenobarbital as a promoter was added to the drinking water after weaning. Livers were examined after 26, 52, 78, and 104 weeks. Tumors were present in all groups except for at the first time point. The potency of the initiators decreased in the order AAS > AAP > AAF. DNA from tumors of all groups and of control livers was analyzed for mutations in the H-ras gene, but no mutations could be found. The sequence of almost the entire H-ras gene was determined and was compared to other H-ras genes. There are some differences with the sequence in other rat strains, particularly in intron D containing the alternative splicing site. The expression of the H-ras gene has also been studied by various methods in enzyme altered foci and tumors, but no alterations could be found. It is, therefore, concluded that structural of functional alterations of this proto-oncogene are not involved in the generation of liver tumors in Wistar rats by the three genotoxic arylamines.

Differential expression of HPV types 6 and 11 in condylomas and cervical preneoplastic lesions

Tumor biopsies from exophytic and flat condylomas at different locations on the genital epithelium (10 cases) and in cervical intraepithelial neoplasia (CIN) grades 1-2 (6 cases) were analysed for HPV types 6 and 11 DNA and RNA. The presence of mRNA species which could encode the E6, E7, E1M, E2, E2C, E4, E5 and L1 proteins was determined using the RNA polymerase chain reaction (PCR) technique with primers that flank previously mapped or predicted splice sites. The state of the viral DNA in the tumor biopsies was established by Southern blot analysis. We could detect the various mRNA species in biopsies from condylomas associated with both HPV types. The size of the RNA PCR products were in agreement with the previously mapped splice sites of mRNAs recovered from an experimental condyloma induced by HPV11. The major viral transcript encoding the E1i--E4 protein was detected in all the tumor biopsies. From the rare transcripts the rate of detection of mRNA species encoding the E1M, E2C proteins was the highest. In 2 of 6 CIN biopsies analysed only the major viral transcript was detected. The overall results of this study suggest that early gene products of HPV types 6 and 11 may be important in the induction of cellular proliferation and condylamatous differentiation but these possibly may not be required for the development of the HPV-associated cervical neoplasia.

Expression and splicing patterns of human papillomavirus type-16 mRNAs in pre-cancerous lesions and carcinomas of the cervix, in human keratinocytes immortalized by HPV 16, and in cell lines established from cervical cancers

We have analysed the splicing patterns of human papillomavirus (HPV) type-16 mRNAs in a human epithelial cell line immortalized by HPV 16 (HPKII), in cell lines established from cervical carcinomas (SiHa and CaSki) and in pre-invasive and invasive carcinomas of the cervix. The presence of mRNA species previously described, which could encode the E6, E6I, E6II, E6III, E7, E2, E2C, E4, E5 and L1 proteins, was determined, using the RNA polymerase chain reaction (PCR) technique with primers that flank unique splice sites. The state of the viral DNA in the tumor biopsies was established by Southern blot analysis. The various HPV 16 transcripts could be detected in cell lines and in tumor biopsies. The size of the RNA PCR products were in agreement with the previously mapped splice sites. The full range of transcripts was revealed in the HPKII cell line and in a number of pre-invasive carcinomas. Messenger RNAs which could encode the E6III, E4 and E5 proteins were most prevalent in all types of tumor. The overall results of DNA and RNA analyses in cell lines and tumor specimens indicate that (1) expression of either of the early or late transcripts studied is not specifically related to (a) tumor stage or (b) the physical state of the viral genome; and (2) alterations in the splicing patterns of HPV 16 transcripts may not be involved in tumor progression.

Activation of the Ki-ras gene in spontaneous and chemically induced lung tumors in CD-1 mice

As part of an evaluation of the effectiveness of using ras mutation analysis for distinguishing carcinogen-induced from spontaneous tumors, we examined the profile of ras gene point mutations in spontaneous, 7,12-dimethylbenz[a]anthracene (DMBA)-induced, and N-nitrosodiethylamine (DEN)-induced lung tumors from Crl:CD-1(ICR)BR (CD-1) mice. Although all of the lung tumors were assayed for mutations in the Ha-ras, Ki-ras, and N-ras genes (codons 12, 13, and 61), only Ki-ras mutations were found, which is consistent with other studies that have noted a strong preference for Ki-ras gene activation in mouse, rat, and human lung tumors. We found that spontaneous CD-1 mouse lung tumors had a very high frequency of Ki-ras gene activation (17 of 20 tumors; 85%), distributed among codons 12 (5 of 20), 13 (1 of 20), and 61 (11 of 20). DMBA-induced lung tumors had a slightly higher frequency of Ki-ras gene mutations (16 of 16; 100%), again distributed among codons 12 (5 of 16), 13 (2 of 16), and 61 (9 of 16). However, seven of the DMBA tumors had mutations qualitatively different from those found in spontaneous tumors. In contrast to DMBA-induced tumors, DEN-induced tumors had a lower frequency of Ki-ras mutations (36%) when compared with spontaneous lung tumors, suggesting that DEN primarily induces lung carcinogenesis by a mechanism other than ras gene activation. Thus, although spontaneous and induced CD-1 mouse lung tumors have a strong tissue-specific preference for carrying an activated Ki-ras gene, the nature of the initiating carcinogen can influence the frequency or profile of Ki-ras mutations.

Expression of the breast cancer associated gene pS2 and the pancreatic spasmolytic polypeptide gene (hSP) in diffuse type of stomach carcinoma

Expression of the pancreatic spasmolytic peptide (hSP) gene and pS2 (a gene isolated from oestrogen-induced breast carcinoma cells) were analysed in 36 samples of human stomach carcinoma. 17 tumours were investigated at the RNA level (by northern blots) as well as at the gene product level (by immunochemistry). Since pS2 had been shown to be expressed in normal stomach mucosa its activity in carcinoma samples was expected. Surprisingly, strong pS2 immunoreactivity was noted in the diffuse carcinoma type, whereas the intestinal type displayed weak reactivity. The tumour samples showing strong immunostaining expressed the regular 0.6 kb pS2 RNA band and weak staining was paralleled by aberrant transcripts. Additionally, only in tumour samples with regular pS2 transcription was the typical 0.7 kb hSP RNA band seen; samples with aberrant pS2 bands did not express hSP at all. This is the first demonstration of hSP gene activity in a human tumour.

Simultaneous isolation of total cellular RNA and DNA from tissue culture cells using phenol and lithium chloride

A rapid procedure for the isolation of intact total cellular RNA from cultured cells is described. This method combines the simultaneous disruption of cells and extraction of nucleic acids in a single step with the use of phenol and a buffer containing 100 mM LiCl. Total cellular RNA can be isolated in approximately 2 hours. The yield and quality of the RNA is comparable to the more widely employed methods requiring extensive preparatory steps such as extraction using guanidinium thiocyanate and subsequent CsCl gradient centrifugation. The RNA isolated using our procedure contains transcripts up to 10 kb in length and is suitable for Northern analysis. This procedure also yields high-molecular-weight DNA, which is a suitable substrate for restriction endonucleases.

The cellular myb oncogene is amplified, rearranged and activated in human glioblastoma cell lines

The human c-myb gene which encodes a DNA binding protein and which is rarely amplified in neoplastic cells was found to be altered in four human glioblastoma cell lines. It exists in multiple copies in 2 out of 4 cases studied. The degree of amplification as determined by densitometry was about 10-fold, a rearrangement within the coding region and an enhanced gene activity of c-myb were noted. The observation of c-myb oncogene amplification and activity in glioblastoma cell lines presents the first report of this effect in human brain tumor cells.

Repression of nuclear lamin A and C gene expression in human acute lymphoblastic leukemia and non-Hodgkin's lymphoma cells

The lamins A, B and C which are differentially expressed during ontogenesis and differentiation are karyoskeletal proteins forming a polymeric meshwork at the inner nuclear membrane. Using Northern blot analyses we investigated the steady state levels of the three lamin specific RNA transcripts in neoplastic cells derived from 16 untreated patients with acute lymphoblastic leukemia (ALL) or non-Hodgkin's lymphoma (NHL) and in ALL and NHL established cell lines. Whereas lamin B mRNA was present in all, lamin A and C transcripts were observed in none of the malignant cell samples except one of a common-ALL patient (precursor B-ALL, cytoplasmic mu chain negative). All three lamin mRNAs were detected in normal peripheral blood lymphocytes, however, only after mitogenic stimulation with concanavalin A. Our results provide evidence that expression of lamin A and C is repressed in neoplastic blast cells derived from patients with ALL or NHL and suggest that lamin A and C gene repression is not related to cell proliferation but might be relevant to the differentiated stages of the lymphoid cells in vivo.

In vivo footprinting of a muscle specific enhancer by ligation mediated PCR

In vivo protein-DNA interactions at the developmentally regulated enhancer of the mouse muscle creatine kinase (MCK) gene were examined by a newly developed polymerase chain reaction (PCR) footprinting procedure. This ligation mediated, single-sided PCR technique permits the exponential amplification of an entire sequence ladder. Several footprints were detected in terminally differentiated muscle cells where the MCK gene is actively transcribed. None were observed in myogenic cells prior to differentiation or in nonmuscle cells. Two footprints appear to correspond to sites that can bind the myogenic regulator MyoD1 in vitro, whereas two others represent muscle specific use of apparently general factors. Because MyoD1 is synthesized by undifferentiated myoblasts, these data imply that additional regulatory mechanisms must restrict the interaction between this protein and its target site prior to differentiation.

Regional localization and molecular characterization of a DNA sequence on the long arm of chromosome 22

A human genomic DNA fragment, p22hom13 (D22S16), was isolated from a chromosome 22-specific library. After elimination of repetitive sequences, a single copy BamHI-EcoRI fragment was subcloned into pTZ18. By using mouse/human somatic cell hybrids and in situ hybridization, the new DNA probe was mapped to chromosome 22q13-qter. Its application in the analysis of the distal part of chromosome 22 and its diagnostic use in translocations are discussed.

Human KRAS oncogene expression in meningioma

Expression of 16 oncogenes was investigated in a series of human meningiomas showing a normal chromosome complement or the characteristic monosomy 22 but no structural aberrations detectable by banding analysis. By dot hybridization, the only expressed sequence detected was KRAS. The expression was elevated approximately 6--8-fold in comparison to matrix tissue (meninges) and to fibroblasts of the corresponding patient. Northern blot analysis displayed the typical banding pattern and an 8--10-fold overexpression. DNA analysis did not reveal gene amplification or major rearrangements in the KRAS gene structure.

Molecular cloning of a cDNA coding biliary glycoprotein I: primary structure of a glycoprotein immunologically crossreactive with carcinoembryonic antigen

We have isolated and sequenced four overlapping cDNA clones from a normal adult human colon library, which together gave the entire nucleotide sequence for biliary glycoprotein I (BGP I). BGP I is a member of the carcinoembryonic antigen (CEA) gene family, which is a subfamily in the immunoglobulin gene superfamily. The deduced amino acid sequence of the combined clones for BGP I revealed a 34-residue leader sequence followed by a 108-residue N-terminal domain, a 178-residue immunoglobulin-like domain, a 108-residue region specific to BGP I, a 24-residue transmembrane domain, and a 35-residue cytoplasmic domain. The nucleotide sequence of BGP I exhibited greater than 80% identity with CEA and nonspecific crossreacting antigen (NCA) in the leader peptide, N-terminal domain, and immunoglobulin-like domain. The BGP I-specific domain, designated A', was 56.7% and 55.8% identical at the nucleotide level and 42.6% and 39.6% identical at the amino acid level to the immunoglobulin-like domain of NCA and the first immunoglobulin-like domain of CEA, respectively. Beyond nucleotide position 1375 the 3' region of the BGP I cDNA was found to be specific for BGP I. Hybridization of a probe from this region to electrophoretic blots of RNAs from different human tissues showed a predominant 2.8-kilobase (kb) message accompanied by weaker bands 4.1 and 2.1 kb in size. The same probe gave a single band in Southern blot analysis of restricted total human DNA. Using a coding region probe from the BGP I domain A', we observed 4.1- and 2.1-kb messages. Lack of the 2.8-kb band suggested that different forms of BGP I may be generated by posttranscriptional modification of the same gene. We propose that BGP I diverged from NCA by acquiring an immunoglobulin-like domain substantially different from the domains found in NCA or CEA and also a new cytoplasmic domain. The latter feature should result in a substantially different membrane anchorage mechanism of BGP I compared to CEA, which lacks the cytoplasmic domain and is anchored via a phosphatidylinositol-glycan structure. Protein structural analysis of BGP I isolated from human bile revealed a blocked N terminus, 129 amino acids of internal sequence that are in agreement with the translated cDNA sequence, and five glycosylation sites in the peptides sequenced.