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Evaluation of two viral extraction methods for the detection of human noroviruses in shellfish with conventional and real-time reverse transcriptase PCR.

AIMS: Comparison of two viral extraction methods in order to establish a sensitive and simple detection method for human noroviruses (NV) in bivalve shellfish. METHODS AND RESULTS: A direct RNA extraction method and an alkaline virus elution-concentration method were tested on artificially contaminated mussels. The latter used an alkaline buffer and polyethylene glycol (PEG) to isolate and concentrate the virus particles from shellfish. In both methods Trizol was used to release RNA. The final RNA extracts were amplified and detected with conventional and real-time reverse transcriptase PCR. The direct RNA extraction method was not able to detect low inoculation levels. However, the virus elution-concentration method was more sensitive. CONCLUSIONS: The alkaline elution-PEG concentration method followed by Trizol effectively removed inhibitory components and fulfilled the demands to be a useful tool for routine testing of shellfish for NV detection. SIGNIFICANCE AND IMPACT OF THE STUDY: Because of the lack of standardized methods to detect NV in shellfish, many 'in-house' extraction methods are used in practice. A comparison of these methods aims to determine a simple, rapid and sensitive method that could be a candidate method for screening suspected shellfish.

Animals↗

RT-PCR without RNA isolation.

Reverse transcription-PCR (RT-PCR) has traditionally required time-consuming RNA extraction and purification. This report demonstrates that one can completely avoid the RNA extraction step in RT-PCR by basing the comparison of samples on cell number rather than micrograms of total RNA. A new method for lysing cells while preserving RNA is described. RT-PCR is carried out (i) by rapidly freezing cells in the presence of ribonuclease inhibitor (RNase inhibitor) plus dithiothreitol and (ii) by using extracts of 250 or fewer cells directly in the RT-PCR assay. Aldolase mRNA, extracted by freeze-thawing cells in the presence of RNase inhibitor, was found to be stable at 42 degrees C for over three hours. Since the RT step can be completed within 1 h, there is minimal degradation of mRNA. This simple procedure avoids the use of harsh reagents, which may inhibit enzymes involved in RT-PCR, and produces results virtually identical to methods that employ guanidinium thiocyanate and phenol for RNA extraction. Optimized conditions for each parameter of the procedure are described that permit amplification of mRNA from as few as four cells.

Freezing↗

Improved RT-PCR amplification for molecular analyses with long-term preserved formalin-fixed, paraffin-embedded tissue specimens.

Recently, in addition to DNA, RNA extracted from archival tissue specimens has become an invaluable source of material for molecular biological analysis. Successful amplification with PCR/RT-PCR is problematic when using amplicons of short size due to degradation of DNA or RNA. We established an improved method for efficient RT-PCR amplification of RNA extracted from archival formalin-fixed, paraffin-embedded tissue by the elimination of RNA modification and the restoration of RNA template activity. Namely, the preheating in citrate buffer (pH 4.0) of RNA extracted from long-term preserved tissue specimens resulted in significantly increased efficiency of RT-PCR.

Buffers↗

Isolation of DNA after extraction of RNA To detect the presence of Borrelia burgdorferi and expression of host cellular genes from the same tissue sample.

We are investigating the neuropathogenesis of Lyme disease caused by Borrelia burgdorferi in a nonhuman primate model. In the past, two separate pieces of tissue had to be used when both analyzing for the presence of the spirochete and examining the host response to infection. We have modified a procedure to purify DNA from the same sample after the extraction of RNA. The remaining material containing the DNA was precipitated, and residual organic reagent was removed prior to deproteinization and extraction of the DNA. This procedure now allows us to both assay for the presence of the Lyme microorganism and analyze the host response in the same tissue preparation.

Animals↗

Genome expression and mRNA maturation at late stages of productive adenovirus type 2 infection.

RNA from adenovirus 2-infected KB cells was annealed in liquid with RNA in vast excess to viral heavy (l) and light (r) 32P-labeled DNA strands. Hybridization kinetics were analyzed by computer to estimate the number of viral RNA abundance classes, their relative concentrations, and the fraction of each DNA strand from which they originated. Early whole cell RNA extracted 5 h postinfection annealed rapidly to 10 to 15% of l and r strands and then slowly to final values of 60 and 40% of l and r strands. By 9 h postinfection the expression of late genes was apparent and whole cell RNA annealed to 20 and 75% of l and r strands. Whole cell RNA extracted between 12 and 36 h postinfection annealed to 7 to 15% and 75 to 90% of l and r strands. Late nuclear RNA hybridized to 10 and 90% of l and r strands, and late polyribosomal RNA hybridized to 20 and 75% of l and r strands. Based upon kinetic analyses, we estimate that mRNA synthesized exclusively during late stages arises from about 6 to 8% and 45 to 49% of l and r strands. This assumes that the early class I mRNA (in low concentration late) originates from 8 to 10% and 6 to 10% of l and r strands and that early class II mRNA (in high concentration late) is derived from 2% and 8 to 13% of l and r strands. Mixing experiments indicated that early mRNA is a subset of RNA extracted from polyribosomes late after infection and that late nuclear RNA contains sequences complementary to early l strand class I nRNA. RNA-RNA hybrids were isolated from late mRNA containing sequences from 60% of l and r strands, but it is not known when these were synthesized, and therefore whether complementary RNA transcripts are synthesized late after infection, as they are known to be synthesized early. These results demonstrate that portions of the genome are transcribed into RNA sequences that remain confined to the nucleus and are not exported to polyribosomes as mRNA.

Adenoviruses, Human↗

Expression of mRNA for plasminogen activators and protease nexin-1 in innervated and denervated mouse skeletal muscle.

Plasminogen activators (urokinase-type, u-PA and tissue-type, t-PA) are serine proteases that have been suggested to play important roles in synaptic remodeling. The enzymatic activity of u-PA in particular has previously been shown to increase dramatically after denervation of skeletal muscle. Using (32)P-labeled riboprobes and Northern blots the expression of mRNA for u-PA, t-PA and the inhibitor protease nexin-1 (PN-1) has been studied in innervated and 1-10-days denervated hind-limb muscle from mouse. Using RNA extracted from innervated and 6-days-denervated mouse hemidiaphragm muscles the expression of these mRNAs has also been investigated in synaptic and extrasynaptic muscle regions. For both u-PA and t-PA the observed autoradiographic signals were similar for RNA extracted from innervated and denervated leg muscles. The signals were also similar for RNA extracted from perisynaptic and extrasynaptic regions of hemidiaphragm muscle but u-PA signals were lower in denervated than in innervated hemidiaphragm. No such difference was observed for t-PA. PN-1 mRNA levels were also found to decrease after denervation in the hemidiaphragm but no substantial decrease was observed in denervated hind-limb muscles. No difference was observed between PN-1 expression in perisynaptic and extrasynaptic regions. The effect of denervation on PA enzymatic activity in skeletal muscle is therefore likely to be mediated at some post-transcriptional level.

Amyloid beta-Protein Precursor↗

A method for examining differential mRNA expression along the crypt-villus axis of the human small intestine.

1. The aim of this study was to devise a method of segregating crypt and villus cell subpopulations from endoscopic human small intestinal biopsies which might be used to examine changes associated with functional differentiation at the molecular level. 2. Routine endoscopic biopsies from the human small intestine were subjected to a modified protocol of mechanical disruption and chelation to yield subpopulations of different cell types. The purity and character of the cell populations isolated was assessed by measuring enzyme activity and thymidine incorporation and by histology. A guanidinium isothiocyanate method was adapted for small samples to extract RNA from the isolated subpopulations, and probes for RNA with a known predilection for crypt and villus cells were used to further investigate the application and usefulness of the technique. 3. Sequential histological examination during the segregation protocol demonstrated that different cell types were removed serially from the biopsy samples. Cell-type enrichment of the segregated subpopulations was demonstrated by differential alkaline phosphatase activity and by differences in thymidine incorporation in the samples isolated. Sufficient quantities of RNA could be extracted from the segregated subpopulations for Northern blot analysis and the differential expression of mRNA for sucrase-isomaltase and transferrin receptor was demonstrated in the villus and crypt subpopulations respectively. 4. Messenger RNA can be successfully extracted from different cell types segregated from routine human endoscopic small intestinal biopsies. This technique should prove useful for investigating the mechanisms regulating the functional differentiation of epithelial cells in the small intestine and the regulatory mechanisms governing absorption of macromolecules.

Biopsy↗

Epidermal growth factor and its receptor, basic fibroblast growth factor, transforming growth factor beta-1, and interleukin-1 alpha messenger RNA production in human corneal endothelial cells.

The authors tried to determine whether human corneal endothelial cells in primary culture synthesize messenger RNA (mRNA) coding for epidermal growth factor (EGF), EGF receptor, basic fibroblast growth factor (FGFb), transforming growth factor beta-1 (TGFb1), and interleukin-1 alpha (IL-1 alpha). Oligodeoxythymidine-primed complementary DNA (cDNA) was generated from total cellular RNA extracted from eight independent primary corneal endothelial cell cultures. Four of these cultures, maintained 18-51 days, had obvious increases in cell numbers and mass over the 2 weeks before RNA extraction and were populated primarily with cells that were small, uniform, and mononuclear (proliferative cultures). The morphology of the cells in other four cultures, maintained 47-78 days, was predominantly large, irregular, vacuolated, and occasionally multinucleated. These cells were identical to senescent cells found in previous studies, and the cell number did not increase in these cultures over the 2 weeks preceding RNA extraction (senescent cultures). The polymerase chain reaction (PCR) was used to amplify the growth factors (EGF, FGFb, TGFb1, and IL-1 alpha), EGF receptor, and beta actin sequences from each of the cDNA samples. The EGF receptor, FGFb, and beta actin mRNAs were present in all eight cDNA samples. The EGF mRNAs were detected by PCR alone in four of the samples from proliferative cultures, TGFb1 mRNAs in three, and IL-1 alpha mRNAs in three. In the samples from senescent cultures, 0, 1, and 0 mRNAs were detected, respectively. Southern blots of the PCR products were probed with oligonucleotides complementary to sequences in each of the amplified products. This technique showed that the appropriately sized amplification products were specific.(ABSTRACT TRUNCATED AT 250 WORDS)

Actins↗

Nucleic acid amplification technology screening for hepatitis C virus and human immunodeficiency virus for blood donations.

OBJECTIVE: To investigate the performance of the commercial Roche COBAS AmpliScreen assay, and demonstrate whether the COBAS AmpliScreen human immunodeficiency virus-1 (HIV-1) test, v1.5, and COBAS AmpliScreen hepatitis C virus (HCV) v 2.0 for screening for HIV-1 and HCV RNA in the donated blood units from which plasma mini pools were collected, by nucleic acid amplification technology (NAT), could detect the positive pools and reduce the risk of transmission of infections for those routinely tested by serological assays. METHODS: The study was performed on 3288 plasma samples collected from blood donors in a period of 13 months, from August 2004 to August 2005, at Al-Hada Armed Forces Hospital, Molecular Pathology Laboratory, Taif, Kingdom of Saudi Arabia. The samples were tested by the reverse transcriptase polymerase chain reaction (RT-PCR) after RNA extraction (this represents the major method in NAT assays), in parallel with the routine serological testing to detect qualitatively for HIV-1 and HCV. RESULTS: The NAT assays that include an automated COBAS AmpliPrep system for RNA extraction and COBAS Amplicor Analyzer using AmpliScreen kits for RT-PCR assays, and the routine serological screening assays for the detection of the HIV-1 and HCV RNA in the plasma samples from the blood donors have shown to be a reliable combination that would meet our requirements. The collected data further confirms the results from the serological assays and enables us to decrease the residual risk of transmission to a minimum with the finding of no seronegative window period donation. The results demonstrate that out of 3288 samples, the percentages of RT-PCR (NAT) negative blood donations that were also confirmed as seronegative were 99% for HCV, and 99.1% for HIV-1. CONCLUSION: The modified combined systems (automated COBAS AmpliPrep system for RNA extraction and COBAS Amplicor Analyzer using AmpliScreen kits for RT-PCR assays) for NAT screening assays has allowed the release of all blood donations supplied in the specified period of the study with no seronegative window period donations. This facilitates keeping the residual risk of transmission of HIV-1 and HCV to its minimum through blood transfusion.

Blood Donors↗

Expression and sequences of genes encoding glutamate receptors and transporters in primate retina determined using 3'-end amplification polymerase chain reaction.

PURPOSE: Our long-term goal is to compare how expression of glutamate receptor and non-vesicular transporter subunits differs between single neurons in the primate retina. Here we set out to ascertain general expression in the retina of Macaca fascicularis using a robust technique suitable for both levels of analysis. We constructed full-complement cDNAs from whole retina RNA using a protocol optimized for detection of even low-abundance transcripts and for transcripts of various lengths. We probed these libraries for expression of genes encoding the AMPA- (GluR1-4) and kainate-sensitive (GluR5-7, KA1-2) ionotropic glutamate receptors, the metabotropic glutamate receptors (mGluR1-8), and five non-vesicular glutamate transporters (EAAT1-5) in the macaque retina and brain and determined large portions of coding sequences for each. We also asked whether each gene can be detected in cDNA generated from a limited amount of RNA extracted from an aldehyde-fixed retinal slice, a technique useful for probing gene expression in tissue used for histological studies. METHODS: We constructed full-length cDNA from RNA harvested from the macaque retina using a modified version of the 3'-end amplification (TPEA) technique of Dixon et al. With this technique, the 3' region is amplified arbitrarily using multiple primers to produce amplified cDNA containing as diverse and complete sample of genes as possible. We probed the cDNA for expression of glutamate receptors and non-vesicular transporters using gene-specific RT-PCR and assembled sequences from the reaction products using a series of overlapping primer pairs. We also used TPEA to compare expression in a small amount of RNA extracted from a fixed retinal slice. RESULTS: Macaque retinal cDNA created using TPEA contains a high abundance of transcripts of various lengths. Gene-specific PCR using primers designed against human sequences indicates expression for all GluR, mGluR, and non-vesicular transporter subunits for which we probed. Expression patterns were similar between two different macaque retinas, but different in brain. Several differences also exist between macaque and human brain. For some subunits, this is the first demonstration of expression in the macaque retina. The expression pattern obtained probing cDNA libraries generated from fixed tissue RNA with a different primer set was similar to that for fresh tissue. We sequenced between 1865 (mGluR8a) and 3697 (mGluR1) total nucleotides for each macaque gene and obtained complete coding sequences for GluR1-7, mGluR3 and mGluR4. A comparison with the corresponding human sequences reveal that the coding region of macaque GluR6 demonstrates the highest homology with only 26 nucleotide substitutions (99% homology), while mGluR4 demonstrates the lowest with 68 substitutions (97.5%). CONCLUSIONS: Neural tissue cDNA created using TPEA contains diverse transcripts of varying size, abundance, and homology. We established using TPEA the expression of all nine AMPA- and kainate-sensitive GluRs, all eight mGluRs and all five non-vesicular glutamate transporters and found that expression differs between macaque retina, macaque brain and human brain. The nucleotide sequences for the coding regions differed moderately between the human and macaque genes. We also found a similar expression pattern in a smaller amount of RNA extracted from a fixed retinal slice. Thus, this technique could be useful for comparing gene expression in cells extracted from fixed tissue pre-labeled using specific markers.

3' Flanking Region↗

Pre-proparathyroid hormone: fidelity of the translation of parathyroid messenger RNA by extracts of wheat germ.

Pre-proparathyroid hormone is the major protein synthesized in wheat-germ extracts in response to addition of an 8-15S fraction of parathyroid RNA. The accuracy of the translation of the mRNA from parathyroid tissue was examined by analysis of the carboxyl-terminal tryptic peptide and the amino-terminal amino acid of the protein, by analysis of the size distribution of the mRNA, and by translation of the mRNA in a second cell-free extract. When 8-15S RNA was fractionated on a sucrose gradient containing formamide, RNA that supported the synthesis of pre-proparathyroid hormone was present in a single symmetrical peak, suggesting that it was homogeneous. Analyses by paper chromatography and electrophoresis of the proline-containing tryptic peptides of pre-proparathyroid hormone indicate that they are identical with the corresponding proline-containing peptides of parathyroid hormone. Because the COOH-terminal tryptic peptide of parathyroid hormone contains proline, the data indicate that the COOH termini of pre-proparathyroid hormone and parathyroid hormone are identical. Methionine from initiator [35S]Met-tRNAfMet was rapidly incorporated into pre-proparathyroid hormone by the wheat-germ extract, and a single-step Edman degradation selectively removed almost all of the initiator [35S]methionine present in pre-proparathyroid hormone. Translation of the 8-15S RNA in a cell-free extract from Krebs-II ascites cells resulted in a protein that comigrated with pre-proparathyroid hormone on sodium dodecyl sulfate-acrylamide gel electrophoresis. These data support the conclusion that the wheat-germ system accurately translates the mRNA for parathyroid hormone, and they strengthen the contention that pre-proparathyroid hormone is the initial biosynthetic product.

Animals↗

Development of an RNA isolation procedure for the characterisation of human endothelial cell interactions with polyurethane cardiovascular bypass grafts.

To date no reliable method has been developed for the isolation of RNA from cells seeded onto cylindrical vascular grafts. This study was performed in order to develop a reliable methodology for isolating RNA from cylindrical conduits made from poly(carbonate-urea)urethane (PU). Human umbilical vein EC were seeded onto PU vascular grafts and an Alamar blue assay performed to assess cell viability. Cells were prepared for RNA extraction by trypsinisation, cell scraping and direct application of cell lysis buffer. In all cases RNA was extracted using a "Qiagen RNeasy" kit. Alamar blue showed viable cells were present on all of the seeded PU vascular grafts. Levels of RNA extracted from the cells removed from the graft by the trypsinisation yielded 0.130 microg/microl, by scraping 0.078 microg/microl and by direct lysing 0.093 microg/microl of RNA, respectively. RTPCR was conducted successfully for GAPDH and TGF-beta1. Trypsinisation prior to RNA extraction provided the highest RNA yield and attained near complete cell removal ensuring that gene expression obtained was representative.

Biocompatible Materials↗

Optimized methodology for sequential extraction of RNA and protein from small human skin biopsies.

Current translational human studies are moving in the direction of concurrent genomic and proteomic analysis using small clinical samples. Skin tissue, although easily accessible, is difficult to process owing to its natural resistance to mechanical shearing and high levels of RNases and proteases. Currently, these complications result in degraded RNA samples with variable yield. We have developed a method of sequential extraction of high quality RNA and protein from a single 3 mm full thickness skin punch biopsy. This method yields 1-2 microg of RNA and 150 microg of protein, which is usable in many sensitive downstream applications including microarray, quantitative real-time PCR, two-dimensional gel electrophoresis and Western blot analysis.

Biochemistry↗

Changes in vascular extracellular matrix accumulation reflect phenotypic differences between the arterial wall of pigeons resistant and susceptible to the development of spontaneous atherosclerosis.

White Carneau pigeons have previously been shown to be genetically susceptible to the development of spontaneous atherogenesis. The severity of development of atheromatous lesions is considerably greater than a more resistant breed of Show Racer pigeons. Analysis of levels of total hydroxyproline and isodesmosine in the thoracic aorta and celiac bifurcation of prelesion, six-week-old White Carneau and Show Racer pigeons, revealed an increased accumulation of total collagen and cross-linked elastin in the White Carneau arterial tissue. Using dot blot hybridization, measurements of steady state levels of several mRNAs in total RNA extracted from pigeon aortic tissue were also determined. While the increased deposition of extracellular matrix proteins was paralleled by a significantly greater recovery of mRNAs coding for pro alpha 1(1) collagen and elastin, in RNA extracted from White Carneau aortal tissue, increased recovery of mRNAs coding for an intracellular protein, gamma-actin were also observed in White Carneau aortal tissue. No differences in steady state levels of mRNAs coding for pro alpha 1(1) collagen and elastin were observed in RNA extracted from pigeon liver, suggesting a tissue specific increase in the mRNAs coding for these connective tissue proteins in aorta. A markedly reduced cell population however, was responsible for this overall increase in biosynthetic activity in White Carneau pigeon aortic tissue. This was demonstrated by a reduced cell count and by the recovery of reduced levels of total DNA in the thoracic aorta and celiac bifurcation of the White Carneau pigeon. The cell population in White Carneau aortic tissue exhibits therefore a markedly different phenotype with respect to a capacity for the biosynthesis of extracellular and intracellular proteins.

Actins↗

Detection of bovine viral diarrhea (BVD) virus using the polymerase chain reaction.

The approach of reverse transcription (RT) followed by the polymerase chain reaction (PCR) was used to amplify three different fragments of the bovine viral diarrhea virus (BVDV) genome. Two sets of primers framed two different regions within the gene coding for protein p80, the third set of primers was selected to amplify cDNA within the envelope glycoprotein (gp53) region. All three sequences could be detected in the homologous strain (NADL), whereas only some of the fragments could be amplified in heterologous strains of BVDV. RNA extracted from infected cells as well as RNA extracted from viral particles could be detected using RT-PCR. The detection limit was 10(-1)-10(-2) TCID50 in ethidium bromide stained gels and could be further enhanced to 10(-2)-10(-4) TCID50 by hybridization after Southern transfer. The speed and the sensitivity of this method might be of relevance for diagnostic purposes as well as for studies on epidemiology and pathogenesis of infection with BVD virus.

Animals↗

Real-time quantitative PCR measurement of circulatory rhodopsin mRNA in healthy subjects and patients with diabetic retinopathy.

Diabetic retinopathy is the commonest complication of diabetes and is the biggest single cause of registered blindness in the UK. No biochemical tests exist to determine the precise state and rate of change of the eyes in the diabetic patient. In the present study, using real-time quantitative reverse transcriptase polymerase chain reaction (RT-PCR), we measured mRNA encoding the retina-specific pigment protein rhodopsin (RHO) in the peripheral blood of healthy individuals (n = 20) and diabetic patients (n = 46) with and without retinopathy. Beta-actin mRNA was also assayed and results are expressed as a ratio of RHO to beta-actin mRNA. Peripheral blood was taken by venipucture directly into PAXgene Blood RNA collection tubes and RNA extracted by use of the PAXgene Blood RNA extraction kit, as per the manufacturer's (Qiagen) instructions. Diabetic patients were divided into three groups defined by the severity of retinopathy as assessed by fundoscopy: A, diabetic without retinopathy; B, background retinopathy; and C, preproliferative retinopathy. Medians of the ratios between groups were compared. RHO mRNA was successfully detected and quantified in peripheral blood in all healthy and diabetic groups, with levels shown to be significantly higher in diabetic patients than in healthy controls (2.54 x 10(-5) vs. 1.29 x 10(-5); P = 0.002). Significant differences in RHO mRNA levels were also seen between healthy control subjects and diabetic groups A (2.52 x 10(-5); P = 0.022), B (1.98 x 10(-5); P = 0.028), and C (5.08 x 10(-5); P = 0.002). The results suggest that there is an increase in circulatory RHO mRNA with the severity of diabetic retinopathy.

Biomarkers, Tumor↗

Exon skipping in the ATM gene in normal individuals: the effect of blood sample storage on RT-PCR analysis.

Mutations in ATM, the gene defective in the human genetic disorder ataxia-telangiectasia (A-T), have been described in A-T patients and in a variety of tumor samples. Most of these arise due to exon skipping. We developed an RT-PCR based protein truncation test (PTT) to screen for ATM mutations in breast cancer patients showing adverse response to radiotherapy. An additional PTT product was evident in the ATM gene in peripheral blood mononuclear cells (PBMCs) from blood samples that were collected 2 days or more prior to RNA extraction. Lymphoblastoid cell lines established from the same blood samples showed no evidence of the additional band. Cloning and sequencing of the additional RT-PCR product revealed an exact deletion of exon 20 (2639 del 200), pointing to exon skipping. RT-PCR analysis of RNA extracted from freshly prepared PBMCs from 3 normal individuals showed no evidence of the additional RT-PCR product but when the blood was stored for 2-3 days prior to RNA extraction the lower molecular weight band was evident in every sample. DNA sequencing confirmed this to be due to loss of exon 20. These data suggest that mRNA-based mutation analysis on ATM should be carried out on unstored blood samples to avoid artificial loss of exons that give rise to apparent mutations.

Alternative Splicing↗

RNA sequences of opposite polarities transcribed from a large part of vaccinia virus genome are accumulated in the cytoplasm.

Labelled vaccinia virus DNA was used in saturation-hybridization experiments with RNA extracted from virus-infected cells. An excess of "late" cytoplasmic RNA converted 45% of DNA into DNA-RNA hybrids, whereas 17% of DNA could be converted into hybrids by RNA extracted from purified nuclei. RNA-RNA hybrids obtained from cytoplasmic RNA by self-annealing and ribonuclease treatment, were melted and used in hybridization with DNA: 36% of DNA was hybridized at the maximal concentration used.

Animals↗