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Interleukin-1 receptor antagonist ribonucleic acid and protein expression by cultured Graves' and normal orbital fibroblasts is differentially modulated by dexamethasone and irradiation.

Recent data have indicated that orbital fibroblasts (OF) can be stimulated to produce marked quantities of interleukin-1 receptor antagonist (IL-1RA), a powerful inhibitor of the proinflammatory activities of interleukin-1 in the orbital tissues in Graves' ophthalmopathy (GO). We examined whether the beneficial effects of dexamethasone or irradiation, the two main therapeutic modalities applied in patients with active GO, may be related to their capacity to alter IL-1RA ribonucleic acid (RNA) and protein expression in OF. Early passages of cultured OF were obtained from orbital connective tissue and extraocular muscle of patients with severe active GO and five control subjects. Modulation of the two variants of IL-1RA, intracellular IL-1RA (icIL-1RA) and soluble IL-1RA (sIL-1RA), was studied after exposure of OF to increasing concentrations of dexamethasone (10(-10)-(10(-6) mol/L)), the glucocorticoid receptor antagonist RU 38486 (10(-3) mol/L), or combinations thereof. Alternatively, cell monolayers were exposed to increasing doses of UV irradiation (0.1-1 J/cm2) or ionizing irradiation (0.2-2 Gy). The IL-1RA gene and protein variants were analyzed by RT-PCR, immunocytochemistry, immunoblotting, and enzyme-linked immunosorbent assay. Dexamethasone inhibited IL-1RA RNA steady state levels in GO OF and control OF in a dose-dependent manner. Combined exposure of OF to dexamethasone and RU 38486 completely restored baseline levels of IL-1RA RNA. By contrast, low doses of UV and ionizing irradiation dose dependently up-regulated IL-1RA-specific transcripts in GO OF and control OF, whereas higher doses were less effective. Immunoblotting and enzyme-linked immunosorbent assay revealed suppression of IL-1RA immunoreactivity after treatment with dexamethasone and enhanced expression of IL-1RA by GO OF and normal OF after low doses of UV and ionizing irradiation. Our results indicate that, in contrast to dexamethasone, low doses of irradiation stimulate expression of the IL-1RA gene and protein variants in OF. Induction by irradiation of IL-1RA expression in target cells of the orbital immune process represents an as yet unrecognized mechanism by which orbital radiotherapy may exert some of its beneficial therapeutic effects in patients with active GO.

Cells, Cultured↗

Analysis of the effect of a strain-specific alteration in the upstream octamer region on transcription of a mouse V kappa Ser light chain gene.

Previous studies had shown that several phenotypic markers expressed by several strains of mice (C58, AKR, PL, RF) involve a light chain group, called V kappa Ser, encoded by a single germ-line gene (Igk-VSera). Most other inbred strains (e.g., BALB/c) contain an allele (Igk-VSerb) which differs from Igk-VSera both in coding regions and in an upstream octamer region known to be important for transcription. Since no evidence for expression of the Igk-VSerb gene product has been observed, experiments were undertaken to determine whether the alteration in the regulatory octamer region of BALB/c might have rendered it defective for transcription. The upstream octamer-containing region of a cloned functional V kappa Ser gene expressed by the C.C58 myeloma M75 was replaced by the corresponding region from BALB/c or deleted entirely. Constructs were transfected into J558L cells and quantity of transcription and site of transcription initiation were compared. Results suggest that the BALB/c octamer (CTTTGCGT), which differs at two of eight nucleotides from the consensus octamer sequence (ATTTGCAT), is fully functional in transcription initiation. This is consistent with results of S1 nuclease protection experiments which indicate the presence of small amounts of correctly initiated V kappa Ser-related RNA in BALB/c spleen.

Animals↗

Evidence for incorporation of intact dietary pyrimidine (but not purine) nucleosides into hepatic RNA.

The absorption and metabolism of dietary nucleic acids have received less attention than those of other organic nutrients, largely because of methodological difficulties. We supplemented the rations of poultry and mice with the edible alga Spirulina platensis, which had been uniformly labeled with 13C by hydroponic culture in 13CO2. The rations were ingested by a hen for 4 wk and by four mice for 6 days; two mice were fed a normal diet and two were fed a nucleic acid-deficient diet. The animals were killed and nucleosides were isolated from hepatic RNA. The isotopic enrichment of all mass isotopomers of the nucleosides was analyzed by selected ion monitoring of the negative chemical ionization mass spectrum and the labeling pattern was deconvoluted by reference to the enrichment pattern of the tracer material. We found a distinct difference in the 13C enrichment pattern between pyrimidine and purine nucleosides; the isotopic enrichment of uniformly labeled [M + 9] isotopomers of pyrimidines exceeded that of purines [M + 10] by > 2 orders of magnitude in the avian nucleic acids and by 7- and 14-fold in the murine nucleic acids. The purines were more enriched in lower mass isotopomers, those less than [M + 3], than the pyrimidines. Our results suggest that large quantities of dietary pyrimidine nucleosides and almost no dietary purine nucleosides are incorporated into hepatic nucleic acids without hydrolytic removal of the ribose moiety. In addition, our results support a potential nutritional role for nucleosides and suggest that pyrimidines are conditionally essential organic nutrients.

Adenosine↗

Mutant transcripts of the LDL receptor gene: mRNA structure and quantity.

mRNA of the low-density lipoprotein receptor (LDLR) gene from 22 heterozygous familial hypercholesterolemic subjects possessing different mutations in this gene was analyzed by Northern blot analysis and reverse transcription-polymerase chain reaction (RT-PCR) in order to detect abnormally spliced transcripts. These analyses revealed abnormally spliced transcripts for the two splice-site mutations 1359-1G-->A and 1705 + 1G-->T. The abnormally spliced transcript for mutation 1359-1G-->A was caused by activation of a cryptic acceptor splice site in exon 10. As a result, seven nucleotides of exon 10 were deleted. For mutation 1705 + 1G-->T, two mutant transcripts were observed. In the first transcript, exon 10 was spliced to exon 13, and in the second transcript intron 11 was retained. The relative amount of mutant transcripts from 14 of the 22 subjects was determined by use of an RT-PCR-based method. Quantitation of the relative amounts of mutant transcripts for five missense mutations resulted in a mean value (+/-SD) of 52.8% (+/-4.55). In comparison, quantitation of the relative amounts of mutant transcripts for five nonsense mutations resulted in a mean value of 31.8% (+/-6.91). This value was significantly lower than the value of 54.2% (+/-2.38) obtained for nine healthy subjects (P < 0.0001). The relative amount of mutant transcripts for the 1705 + 1G-->T mutation was 36%. Thus, transcripts from alleles containing premature stop codons are present in reduced amounts, whereas transcripts from alleles containing missense mutations are present in normal amounts. These findings underscore the importance of determining how mutations affect mRNA structure and quantity in order to understand how mutations cause disease.

Alleles↗

Quantitative polymerase chain reaction by monitoring enzymatic activity of DNA polymerase.

Nucleic acid amplification by polymerase chain reaction (PCR) is a very powerful technique in terms of sensitivity but is limited in terms of ability to perform accurate quantitation. While there is a theoretical correlation between copies of input target sequence and those of PCR product, the quantitative nature of this relationship is obscured by unpredictable variations in reaction conditions and by inhibitory and/or stimulatory substances which might be present in sample preparations, especially those derived from biological fluids. To reliably estimate copies of input DNA target from PCR product, we designed a combination of internal and external control systems coupled to DNA/RNA hybridization and enzymatic immunodetection techniques. The internal control system served to monitor amplification efficiency and to correct for the effects of inhibitors or stimuli on the efficiency of the DNA amplification. The assay is quantitative, nonisotopic, and can be widely applied to assessment of the quantity of DNA present in a wide range of preparations.

Base Sequence↗

A robust technique for assembly of nucleic acid hybridization chips based on electrochemically templated chitosan.

A nucleic acid hybridization assay was assembled onto a robust and readily addressable silicon-based chip using polysaccharide chitosan as a scaffold for the covalent coupling of probe DNA to the chip's surface. Chitosan is a unique polymer, ideally suited for this application because its net charge and solubility are pH dependent. Specifically in this work, gold-patterned electrodes were created using standard photolithographic techniques, chitosan was electrodeposited in a spatially resolved manner onto the polarized electrodes, probe DNA was covalently assembled onto the chitosan, and both DNA:DNA and DNA:mRNA hybridization detection schemes were evaluated. Hybridization of target nucleic acid was quantifiable, reproducible, and robust; the surface was regenerated and rehybridized up to eight times without loss of signal. Finally, transcriptional upregulation of the Escherichia coli chaperone, DnaK, which is an indicator of cellular stress, was observed using the hybridization chip sandwich assay. Thus, this method enables rapid and facile monitoring of gene expression in a format that is reusable and requires minimal reagent quantities.

Chitin↗

Alternative processing of the maize Ac transcript in Arabidopsis.

The successful application of the maize transposable element system Ac/Ds as a genome mutagen in heterologous plant species has recently proved the versatility and power of this technique in plant molecular biology. However, the frequency of Ac/Ds transposition is considerably lower in Arabidopsis thaliana than in most other dicot plant species that have been studied. Since previous research has established that transcripts derived from monocot genes can be alternatively processed in dicot plants, we have investigated both the efficiency of intron splicing and polyadenylation of the maize Ac transposase pre-mRNA in Arabidopsis thaliana, Nicotiana tabacum, Nicotiana plumbaginifolia and Zea mays. In this paper, we demonstrate that intron 4 is alternatively spliced within Arabidopsis, using cryptic 5' and 3'splice sites within the intron sequence, leading to a heterogeneous population of full length of transposase transcript. Furthermore, analysis of transposase transcript polyadenylation revealed that at least four alternative poly(A) sites were utilized between introns 2 and 3, resulting in truncated transposase transcripts. Finally, by Northern blotting, we established that the truncated transposase transcript was the most abundant form of transposase message in Arabidopsis. In contrast to these findings, the alternative splicing and premature polyadenylation of Ac message in Arabidopsis was unparalleled in the other species examined. We suggest that the poor frequency of transposition of Ac in Arabidopsis may be in part due to the low quantity of correctly processed transposase transcript available in this species.

Alternative Splicing↗

Divergence of U2 snRNA sequences in the genome of D. melanogaster.

Four different U2-snRNA genes/related sequences of D. melanogaster were cloned and characterized. The sequences of all four genes suggest that they were generated by a DNA-mediated mechanism. These genes/related sequences were found to be located in two loci, each locus containing two U2 snRNA sequences. Using coding sequences as well as flanking sequences as hybridization probes against polytene chromosomes of D. melanogaster Oregon R we were able to map these loci separately at positions 34BC and 84C. By Northern analysis we observed that the quantities of U2- and U1-snRNA are coordinated and change during the embryonic development of the fly.

Animals↗

Effect of foscarnet on quantities of cytomegalovirus and human immunodeficiency virus in blood of persons with AIDS.

Four intravenous dosages of foscarnet given for 10 days were compared with no therapy in persons with AIDS who had asymptomatic cytomegalovirus (CMV) viremia. CMV viremia was quantitated by endpoint cell dilution microcultures, pp65 antigenemia assay, and measurement of CMV DNA in peripheral blood leukocytes by a quantitative-competitive PCR. Human immunodeficiency virus type 1 (HIV-1) viremia was quantitated by endpoint cell dilution microculture, serum p24 antigen assay, and PCR for HIV-1 RNA in plasma. Twenty-seven subjects who had received a median of 22 months of nucleoside antiretroviral therapy were enrolled. Twenty-two subjects received foscarnet, which was well tolerated and decreased the CMV burden, as reflected by all three indicator assays. During the 10 days of dosing, the level of CMV viremia, as measured by 50 percent tissue culture infective doses, decreased from 117.5 to 12.7 (P = 0.001), the amount of CMV DNA decreased from 20,328 copies to 622 copies per 150,000 leukocytes (P = 0.02), and the level of CMV pp65 antigenemia decreased from 14.9 to 1.6 positive peripheral blood mononuclear cells per 50,000 leukocytes (P = 0.008). A significant pharmacodynamic relationship was found between the peak foscarnet concentration and a decrease in the level of CMV antigenemia (P < 0.05). Foscarnet had no effect on quantitative HIV-1 microcultures during the 10 days of treatment, but the HIV-1 p24 antigen level in serum decreased significantly, from 454 to 305 pg/ml (P = 0.01). Also, a significant pharmacodynamic relationship was seen between plasma HIV-1 RNA concentrations and both peak foscarnet concentration (P < 0.01) and the area under the foscarnet time-concentration curve (P < 0.05). Reductions in the levels of CMV and HIV-1 viremia correlated quantitatively with systemic exposure to foscarnet, whereas control subjects actually experienced an increase in CMV and HIV-1 burdens. The dual antiviral activity of foscarnet shown in this trial encourages investigation of its use in combination with other antiretroviral therapies for persons with AIDS.

AIDS-Related Opportunistic Infections↗

Intracellular mammalian DNA stimulates myeloid dendritic cells to produce type I interferons predominantly through a toll-like receptor 9-independent pathway.

OBJECTIVE: Exogenous nucleic acids, including bacterial unmethylated DNA and viral single-stranded RNA, are potent activators of innate immunity through interaction with the Toll-like receptors (TLRs). In contrast, mammalian DNA has been generally thought to have a limited activation effect, or even a suppressive effect, on innate immunity. Since DNA is a major component of dying cells and recent studies indicate that mammalian nucleic acids may be stimulatory under certain conditions, we undertook this study to examine the effect of intracellular mammalian DNA on myeloid dendritic cell (DC) activation. METHODS: Mammalian DNA was introduced into murine bone marrow-derived DCs (BMDCs) by transfection. BMDC activation was determined by flow cytometry (CD40, CD86). Production of tumor necrosis factor alpha and interleukin-6 was measured by enzyme-linked immunosorbent assay, and production of type I interferons (IFNs) by bioassay. Parallel studies were conducted using BMDCs from mice deficient in myeloid differentiation 88 (MyD88), TLR-9, and IFNalpha/beta receptor. RESULTS: Intracellular mammalian DNA activated immature BMDCs, as determined by the up-regulation of CD40 and CD86 as well as by the production of significant quantities of type I IFN. The interferogenic response was shown to be relatively independent of TLR-9, and the TLR adaptor MyD88. The IFN response to intracellular DNA was reduced in BMDCs lacking IFNalpha/beta receptor but was intact in embryonic fibroblasts lacking protein kinase R. CONCLUSION: These results indicate that intracellular DNA stimulates BMDC maturation and IFN production predominantly through a TLR-independent pathway, and support a model whereby inefficient clearance and/or degradation of endogenous DNA may stimulate innate immune responses similar to the TLR-independent response to exogenous (i.e., viral) double-stranded RNA.

Adaptor Proteins, Signal Transducing↗

Distribution of dopamine D1, D2, and D5 receptor mRNAs in the monkey brain: ribonuclease protection assay analysis.

The distribution of the mRNAs encoding the dopamine D1, D2 and D5 receptors was determined in brain tissues obtained from intact female rhesus monkeys, using a ribonuclease protection assay. Tissue blocks from the frontal cortex, striatum, thalamus, hippocampus and substantia nigra were dissected and total RNA was extracted. Dopamine D2 and D5 receptor DNA fragments were generated from rhesus monkey genomic DNA using polymerase chain reaction. To generate dopamine receptor subtype-specific cRNA probes, DNA fragments corresponding to the carboxy terminus of the rhesus monkey D1 and D2 receptor genes and to the putative transmembrane domain regions (IV-VI) of the D5 receptor gene, were subcloned into the pGEM3Z/4Z vectors. Expression of D1 receptor mRNA exhibited significant regional differences: striatum > > > cerebral cortex > or = hippocampus > or = lateral thalamus. D1 receptor mRNA was found in low quantities in the medial thalamus, but was not consistently expressed in the substantia nigra area. In contrast, D2 receptor mRNA was detected in all regions that were studied: striatum > > > substantia nigra > > hippocampus > or = cerebral cortex > or = medial thalamus > or = lateral thalamus. D5 receptor mRNA was also expressed in all regions, with highest levels in the cerebral cortex, striatum and lateral thalamus, and moderate levels in the substantia nigra, medial thalamus and the hippocampus. The D5 receptor mRNA appears to be widely distributed in the monkey brain. Most interesting is the expression of D5 receptor mRNA in tissues of the substantia nigra area.

Animals↗

Fine structure of IMR-90 cells in culture as examined by scanning and transmission electron microscopy.

Cells from the new strain IMR-90 were examined by scanning (SEM) and transmission (TEM) electron microscopy at early, middle, and late population doubling levels. The cells are characteristically flattened and elongated and arranged in clusters from 1 to several cells thick. Long thin processes extend from the poles and sides of the cells. The number of blebs and microvilli on the cell surface varies. In later population doubling level (PDL) cultures, a larger number of cells have greater quantities of microvilli on their surface. It is suggested that the increased number of microvilli might represent an increased level of differentiation. By TEM the cells typically have elongated to oval shaped nuclei which are sometimes deeply invaginated. The cytoplasm contains a well developed Golgi region, elongated mitochondria, microtubules, filaments, a variety of vesicles, vacuoles and dense bodies and large amounts of RNA in the form of granular endoplasmic reticulum and ribosomes. Cytoplasmic appearance, particularly the number of dense bodies, varies widely at all PDL. With increasing PDL, cells tend to have nuclei with more condensed chromatin, and a cytoplasm containing less mitochondria and granular endoplasmic reticulum and more dense bodies. Also at later PDL there is a higher frequency of cells containing long, thin dense mitochondria as well as bizarre shaped mitochondria. In older populations there are many cells in a state of filamentous degeneration. Cells with large numbbers of surface projections (microvilli) tend to be correlated with an osmiophilic cytoplasm containing many filaments and numerous dense bodies.

Cell Line↗

Bacterial expression and enzymatic activity analysis of ME1, a ribosome-inactivating protein from Mirabilis expansa.

Ribosome-inactivating proteins (RIPs) are toxic proteins synthesized by many plants and some bacteria, that specifically depurinate the 28S RNA and thus interrupt protein translation. RIPs hold broad interest because of their potential use as plant defense factors against pathogens. However, study of the activity of type I RIPs has been hampered since their expression in Escherichia coli has typically been toxic to the model system. Mirabilis expansa, an Andean root crop, produces a type I RIP called ME1 in large quantities in its storage roots. In this study, the cDNA sequence of ME1 was used to successfully express the recombinant ME1 protein in E. coli. The production of recombinant ME1 in E. coli was confirmed by Western blot analysis using anti-ME1 antibodies. The studies with fluorescence-labeled ME1 showed that ME1 can enter bacteria and be distributed in the cytoplasm uniformly, indicating its ability to access the protein synthesis machinery of the bacteria. The recombinant enzyme was active and depurinated yeast ribosomes. However, both native and recombinant ME1 proteins failed to depurinate the E. coli ribosomes, explaining the non-toxicity of recombinant ME1 to E. coli. Structural modeling of ME1 showed that it has folding patterns similar to other RIPs, indicating that ME1 and PAP, which share a similar folding pattern, can show different substrate specificity towards E. coli ribosomes. The results presented here are very significant, as few reports are available in the area of bacterial interaction with type I RIPs.

Base Sequence↗

An efficient prebiotic synthesis of cytosine and uracil.

In contrast to the purines, the routes that have been proposed for the prebiotic synthesis of pyrimidines from simple precursors give only low yields. Cytosine can be synthesized from cyanoacetylene and cyanate; the former precursor is produced from a spark discharge in a CH4/N2 mixture and is an abundant interstellar molecule. But this reaction requires relatively high concentrations of cyanate (> 0.1 M), which are unlikely to occur in aqueous media as cyanate is hydrolysed rapidly to CO2 and NH3. An alternative route that has been explored is the reaction of cyanoacetaldehyde (formed by hydrolysis of cyanoacetylene) with urea. But at low concentrations of urea, this reaction produces no detectable quantities of cytosine. Here we show that in concentrated urea solution--such as might have been found in an evaporating lagoon or in pools on drying beaches on the early Earth--cyanoacetaldehyde reacts to form cytosine in yields of 30-50%, from which uracil can be formed by hydrolysis. These reactions provide a plausible route to the pyrimidine bases required in the RNA world.

Acetaldehyde↗

Defective human interleukin 2 receptor gamma chain in an atypical X chromosome-linked severe combined immunodeficiency with peripheral T cells.

X chromosome-linked severe combined immunodeficiency disease (SCIDX1) is characterized by the absence of T-cell and natural killer cell development and results from molecular mutations of the interleukin 2 receptor (IL-2R) gamma chain. The IL-2R gamma chain is a common component of the IL-2, IL-4, and IL-7 receptor systems, which may explain the severe immunophenotype in SCIDX1. We have previously described an atypical SCIDX1 syndrome demonstrating poorly functioning peripheral T cells, which we hypothesized to represent a variant allele at the SCIDX1 locus. We now demonstrate that a splice site mutation in the IL-2R gamma gene is responsible for this atypical SCIDX1. Aberrant RNA splicing resulted in the generation of two IL-2R gamma transcripts: an abundant, nonfunctional isoform containing a small intronic insertion and a second functional isoform with a single amino acid substitution present in limited amounts. Radiolabeled IL-2 binding studies revealed a 5-fold decreased level of expression of functional high-affinity IL-2Rs, which correlated with the quantity of full-length IL-2R gamma transcripts. Further analysis of the T-cell antigen receptor beta-chain repertoire of the patient's T cells demonstrated oligoclonality in multiple V beta families, thus strongly suggesting that the defect in the IL-2R gamma chain generated a limited number of peripheral T-cell clones. This atypical SCIDX1 patient demonstrates that certain IL-2R gamma chain abnormalities can also result in partial immunodeficiency phenotypes, potentially through differential effects on the IL-2, IL-4, or IL-7 receptor systems.

Amino Acid Sequence↗

Determining protein identity from sieve element sap in Ricinus communis L. by quadrupole time of flight (Q-TOF) mass spectrometry.

The phloem transport system is a complex tissue that primarily carries photoassimilate from source to sink. Its function depends on anucleate sieve elements (SE) supported by companion cells (CC). In this study, SE sap was sampled and the protein identity of soluble proteins was determined with the aim of understanding the function of proteins within the conduit. Unlike many plants, SE sap exudes from incisions in the bark of Ricinus communis and, although there is a greater possibility of contamination from tissues other than SE, sap can be obtained in sufficient quantities to separate proteins using 2D electrophoresis. Spots were excised for trypsin digest, then analysed by quadrupole time of flight (Q-TOF) mass spectrometry (MS) and database searched to determine sequence identity. Overall, 18 proteins were identified in the SE-enriched sap. Proteins identified that have not previously been identified directly from SE sap included a glycine-rich RNA-binding protein, metallothionein, phosphoglycerate mutase, and phosphopyruvate hydratase. The potential role of the identified protein in SE function is discussed. The protein identification in this study provides a first step towards the goal of a greater understanding of the function of proteins within the SE.

Amino Acid Sequence↗

Amplification of protein expression in a cell free system.

Large quantities of a catalytically active protein have been produced in a cell free system. More than 10(9) copies of protein were produced from each DNA plasmid containing DNAfol, the bacterial gene encoding dihydrofolate reductase (DHFR). The strategy employed, denoted gene amplification with transcription/translation (GATT), involves sequential coupling of (i) DNA amplification by the polymerase chain reaction (PCR) and (ii) in vitro RNA transcription by T7 RNA polymerase, followed by (iii) translation of the run-off transcripts in a rabbit reticulocyte system. The protein product had the expected size (18 kDa) and catalyzed the NADPH-dependent reduction of 7,8-dihydrofolic acid to 5,6,7,8-tetrahydrofolic acid as efficiently as authentic DHFR. Potential applications of the strategy include large scale production of enzymes containing synthetic amino acids and facilitation of the characterization of the function of genes encountered in genomic mapping studies.

Cell-Free System↗

Conditions required for induction of interferon by rotaviruses and for their sensitivity to its action.

Our investigations of interferon induction by rotaviruses showed that only when cells were pretreated with interferon, i.e., primed, could infectious rotaviruses induce significant quantities of interferon. As little as 0.5 U of interferon provided sufficient priming for this induction. UV-irradiated rotaviruses induced significant levels of interferon, and priming only marginally enhanced the yields. Neither heat-inactivated virus nor serum-neutralized virus was able to induce interferon, even when cells were primed. When cells were treated with purified virus double-stranded RNA in the presence of DEAE-dextran to facilitate uptake, interferon was induced, although priming did not enhance yields. These results strongly implicate the viral double-stranded RNA as the effector for interferon induction. The insensitivity of rotaviruses to interferon in vitro was also studied. Results suggested that this lack of sensitivity was not due to any inherent resistance of the virus to the antiviral proteins, but rather to lack of activation of cellular enzymes exhibiting antiviral activity.

Animals↗