Surveillance of transcriptomes in basic military trainees with normal, febrile respiratory illness, and convalescent phenotypes

Gene expression profiles permit analysis of host immune response at the transcriptome level. We used the Pax gene Blood RNA (PAX) System and Affymetrix microarrays (HG-U133A&B) to survey profiles in basic military trainees and to classify them as healthy, febrile respiratory illness (FRI) without adenovirus, FRI with adenovirus, and convalescent from FRI with adenovirus. We assessed quality metrics of RNA processing for microarrays. Class prediction analysis discovered nested sets of transcripts that could categorize the phenotypes with optimized accuracy of 99% (nonfebrile vs febrile, P<0.0005), 87% (healthy vs convalescent, P=0.001), and 91% (febrile without vs with adenovirus, P<0.0005). The discovered set for classification of nonfebrile vs febrile patients consisted of 40 transcripts with functions related to interferon induced genes, complement cascades, and TNF and IL1 signaling. The set of seven transcripts for distinguishing healthy vs convalescent individuals included those associated with ribosomal structure, humoral immunity, and cell adhesion. The set of 10 transcripts for distinguishing FRI without vs with adenovirus had functions related to interferon induced genes, IL1 receptor accessory protein, and cell interactions. These results are the first in vivo demonstration of classification of infectious diseases via host signature transcripts and move us towards using the transcriptome in bio-surveillance.

Phenotypic determinants of adenovirus E1A gene autoregulation: variable region between conserved coding domains 2 and 3

Different serotypes and evolutionary variants of human adenoviruses exhibit distinctive patterns of positive and negative autoregulation of the viral E1A gene. An autoregulatory E1A promoter mutation of the adenovirus type 3 (Ad3) E1A gene renders Ad3hr15 incapable of growth in normally permissive cells. The promoter mutation is complemented in trans by E1A products of the heterologous helper adenovirus type 5 (Ad5). Second-site revertants of Ad3hr15 restore viability with high levels of E1A gene expression. The revertant E1A genotypes retain the mutant E1A promoter and have small in-frame deletions in the nonconserved region between the repression- and activation-associated conserved domains CR2 and CR3. Plasmid expression vectors were constructed as 12S and 13S cDNA forms of revertant E1A genes. These were used in cotransfection experiments with a reporter gene plasmid under transcriptional control of the mutant Ad3hr15 E1A promoter. The repression of the Ad3hr15 E1A promoter by helper Ad5 or revertant 12S E1A cDNA was consistently greater than that effected wild-type Ad3 12S cDNAs expression. Significantly greater levels of positive transactivation were observed in cotransfections with 13S cDNAs of Ad5 or with the 13S E1A cDNA of Ad3hr15 revertants, compared to the transactivation observed with the mutant-encoded wild-type Ad3 13S E1A cDNA. The Ad5 helper and dI-revertant phenotype of Ad3hr15 appear to be related to transactivation activities of coexpressed E1A genes. The nonconserved region which separates the conserved coding regions CR2 and CR3 of the type 3 E1A gene acts to attenuate E1A-mediated repression and transactivation of transcription.

Induction of mutations by replication of malondialdehyde-modified M13 DNA in Escherichia coli: determination of the extent of DNA modification, genetic requirements for mutagenesis, and types of mutations induced

The mutagenicity of the lipid peroxidation product, malondialdehyde (MDA), was measured in the lacZ alpha forward mutation assay using a recombinant M13 phage, M13MB102. Single-stranded M13MB102 DNA was reacted with MDA at neutral pH and the modified DNA was transformed into strains of Escherichia coli induced for the SOS response. Increasing concentrations of MDA led to an increase in lacZ alpha-mutations coincident with an increase in the level of the major MDA-deoxyguanosine adduct. Spontaneous and MDA-induced M13MB102 mutants were collected and the lacZ alpha target region was subjected to automated DNA sequence analysis. The most common sequence changes induced by MDA were base-pair substitutions (76%). Of these, 43% (29/68) were transversions, most of which were G-->T (24/29). Transitions account for 57% of the base-pair substitutions (39/68) and were comprised exclusively of C-->T (22/39) and A-->G (17/39). Frameshift mutations were identified in 16% of the induced mutants and were comprised of mainly single base additions occurring in runs of reiterated bases (11/14). The diversity of base-pair substitution and frameshift mutations induced by MDA at low levels of adduction suggests it may be an important contributor to endogenous mutagenesis and carcinogenesis in aerobic organisms.

Fiber gene and genomic origin of human adenovirus type 4

The origin of human adenovirus type 4 (Ad4), an important pathogen and candidate vaccine vector, has been the subject of speculation. Ad4 is unusual among adenoviruses, because it is the single known serotype of subgroup E. Some biological and biochemical properties of Ad4 resemble those of serotypes from subgroups B and C. The length of Ad4 fiber is intermediate between that of subgroup B and C fibers. We sequenced the Ad4 fiber gene, locus of the determinant(s) of adenovirus serotype. The number of repeating DNA sequence motifs in the shaft domain of the Ad4 fiber gene is consistent with its reported length. Regional phylogenetic analysis of Ad4 was undertaken, comparing DNA sequences of early genes and fiber genes from representative adenoviruses. The Ad4 fiber gene has close phylogenetic relationship to subgroup C fiber genes. This is in distinct contrast to the closer relationship of Ad4 to subgroup B adenoviruses in early gene sequences, distributed across the left 70% of the viral genome. We propose that Ad4 originated by recombination of genomes resembling contemporary subgroup B and subgroup C adenoviruses. This event may have occurred so recently that divergence of subgroup E serological determinants has yet to be observed.

Functional diversity of E1A gene autoregulation among human adenoviruses

Autoregulation of the adenovirus E1A gene involves its constitutive expression and positively and negatively regulated transcription. Dissection of this process will identify basal-level cis elements and autoregulatory targets of the E1A promoter and functional domains within the trans-acting E1A gene products. In this report, the DNA sequence of the human subgroup B adenovirus type 3 (Ad3) E1A gene is presented and compared with that of the E1A genes of similar and distantly related human adenoviruses. The cDNA forms of the Ad3 E1A gene, corresponding to two major early mRNA species, are cloned, sequenced, and subcloned into plasmid expression vectors. Cotransfections of cell cultures are performed with Ad5 or Ad3 E1A gene expression plasmids and a reporter gene under control of the Ad5 or Ad3 E1A promoter. The Ad5 and Ad3 E1A promoters are similarly repressed by either serotype's 12S cDNA gene products. The Ad3 E1A promoter responds much more strongly than the Ad5 E1A promoter to transactivation by 13S cDNA gene products. In contrast, the 13S cDNA gene of Ad5 has greater transactivation activity than that of Ad3. Experiments with missense mutations of the Ad5 E1A gene indicate that transactivation of the Ad5 E1A promoter is weak, just reversing or balancing negative autorepression. Single amino acid substitutions in the conserved, repressive functional domain 2 of the E1A gene modulate transactivating activity that is usually associated with the separate and distal conserved functional domain 3. These results suggest a strong structure-function relationship influenced by the variable sequences separating these conserved domains.

Mutation spectrum and sequence alkylation selectivity resulting from modification of bacteriophage M13mp18 DNA with S-(2-chloroethyl)glutathione. Evidence for a role of S-(2-N7-guanyl)ethyl)glutathione as a mutagenic lesion formed from ethylene dibromide

The major DNA adduct (greater than 95% total) resulting from the bioactivation of ethylene dibromide by conjugation with GSH is S-(2-(N7-guanyl)ethyl)GSH. The mutagenic potential of this adduct has been uncertain, however, because the observed mutagenicity might be caused by other adducts present at much lower levels, e.g. S-(2-N1-adenyl)ethyl)GSH. To assess the formation of other potential adducts, S-(2-(N3-deoxycytidyl)ethyl)GSH, S-(2-(O6-deoxyguanosyl)ethyl)GSH, and S-(2-(N2-deoxyguanosyl)ethyl)GSH were prepared and used as standards in the analysis of calf thymus DNA modified by treatment with [1,2-14C]ethylene dibromide and GSH in the presence of rat liver cytosol; only minor amounts (less than 0.2%) were found. A forward mutation assay in (repair-deficient) Salmonella typhimurium TA100 and sequence analysis were utilized to determine the type, site, and frequency of mutations in a portion of the lacZ gene resulting from in vitro modification of bacteriophage M13mp18 DNA with S-(2-chloroethyl)GSH, an analog of the ethylene dibromide-GSH conjugate. An adduct level of approximately 8 nmol (mg DNA)-1 resulted in a 10-fold increase in mutation frequency relative to the spontaneous level. The spectrum of spontaneous mutations was quite varied, but the spectrum of S-(2-chloroethyl)GSH-induced mutations consisted primarily of base substitutions of which G:C to A:T transitions accounted for 75% (70% of the total mutations). All available evidence implicates S-(2-(N7-guanyl)ethyl)GSH as the cause of these mutations inasmuch as the levels of the minor adducts are not consistent with the mutation frequency observed in this system. The sequence selectivity of alkylation was determined by treatment of end-labeled lac DNA fragments with S-(2-chloroethyl)GSH, cleavage of the DNA at adduct sites, and electrophoretic analysis. Comparison of the sequence selectivity with the mutation spectrum revealed no obligate relationship between the extent of adduct formation and the number of mutations which resulted at different sites. We suggest that the mechanism of mutagenesis involves DNA sequence-dependent alterations in the interaction of the polymerase with the (modified) template and incoming nucleotide.

Neighboring nucleotide interactions during DNA sequencing gel electrophoresis

Electrophoretic separation of oligonucleotides in denaturing polyacrylamide gels is primarily a function of length-dependent mobility. The 3' terminal nucleotide sequence of the oligonucleotide is a significant, secondary determinant of mobility and separation. Oligomers with 3'-ddT migrate more slowly than expected on the basis of length alone, and thus are better separated from the preceding, shorter oligomers in the sequencing ladder. Oligomers with 3'-ddC are relatively faster than expected, and are therefore less separated. At the 3' penultimate position, -dC- increases and -dT- reduces separation. Purines at the 3' terminal or penultimate positions of oligonucleotides affect separation less than the pyrimidines. These results suggest specific interactions among neighboring nucleotides with important effects on the conformation of oligonucleotides during electrophoresis. These interactions are compared to compression artifacts, which represent more extreme anomalies of length-dependent separation of oligonucleotides. Knowledge of base-specific effects on electrophoretic behavior of DNA oligomers supplements the usual information available for determination of sequences; additionally it provides an avenue to thermodynamic and hydrodynamic investigations of DNA structure.

Rat angiotensin II receptor: cDNA sequence and regulation of the gene expression

The nucleotide and amino acid sequences for rat type I angiotensin II receptor were deduced through molecular cloning and sequence analysis of its complementary DNAs. The rat angiotensin II receptor consists of 359 amino acid residues and has a sequence similar to G protein-coupled receptors. The expression of this receptor gene was detected in the adrenal, liver and kidney by Northern blotting. Sodium deprivation positively modulated the expression of the receptor gene in the adrenal. No detectable change was observed in the expression levels of this receptor gene between spontaneously hypertensive rats and Wistar-Kyoto rats in the tissues examined including the adrenal, brain, kidney and liver. Interestingly the expression of this receptor gene was developmentally regulated.

Upstream DNA sequences determine different autoregulatory responses of the adenovirus types 5 and 3 E1A promoters

Adenovirus types 5 and 3 (Ad5 and Ad3), two human adenovirus serotypes of evolutionarily divergent subgroups, show very different levels of E1A gene expression early after infection of permissive cells. Since adenovirus E1A gene expression is known to be transcriptionally autoregulated, we have investigated the difference between Ad3 and Ad5 by monitoring transient expression of a reporter gene under transcriptional control of the E1A promoter of Ad5 or Ad3. There was only a modest difference between the basal levels of transcription driven by these two E1A promoters. This difference was amplified from 10 to 100 times by the different net responses of the E1A promoters to concomitantly expressed E1A genes. Each promoter had a characteristic net response to positive and negative regulation by E1A gene products. The Ad5 E1A promoter was more strongly repressed, whereas the Ad3 E1A promoter was more strongly activated by E1A gene products. Experiments with a chimeric Ad5/3 E1A promoter indicated that these different autoregulatory responses are determined by DNA sequences which are more than 50 base pairs upstream from the E1A transcriptional start site. A plausible target DNA sequence for positive and negative autoregulation by E1A gene products is discussed.

Adenovirus E1A gene autorepression: revertants of an E1A promoter mutation encode altered E1A proteins

Revertants have been isolated from Ad3hr15, a mutant of human adenovirus type 3 that carries a defective E1A promoter. Transcription of these revertant E1A genes is restored--from nil for Ad3hr15 mutant to levels exceeding that of the wild-type virus. The mutant Ad3hr15 virus and the revertants all have an aberrant E1A promoter that contains two short tandem duplications of viral DNA sequence. The E1A gene-coding region of the mutant is the same as that for wild-type adenovirus type 3, whereas the revertants are characterized by short in-frame deletions within the 5' exon region of their E1A genes. Location of these reverting, second-site deletions is discussed in relation to E1A gene autoregulation and the evolved diversity of E1A-related oncogenic potential among different human adenoviruses.

An E1A mutant of adenovirus type 3: Ad3hr15 has reiterated DNA sequences 5' to its E1A gene

Defective variants of adenovirus type 3 (Ad3) have been isolated from a heterogeneous, high multiplicity passage stock of the virus. A strikingly defective variant, Ad3hr15, fails to propagate on normally permissive A549 cells, yet has greater infectivity than wild type Ad3 in the adenovirus type 5 (Ad5) DNA-transformed 293 cell line. Investigation of its genomic alterations revealed that Ad3hr15 bears two short tandem duplications of viral DNA sequences near its left end, 5' to the E1A gene. The variant also bears a large tandem triplication at its right end. Marker rescue experiments with plasmid-cloned left end DNA sequences of Ad3 implicate that the duplications 5' to E1A are responsible for the Ad3hr15 defect and the E1A structural gene of the variant is functional. Northern analysis revealed no detectable E1A transcripts early after Ad3hr15 infection of A549 cells. The 293 cell line, however, supports high levels of transcription of the Ad3 E1A gene by the mutant Ad3hr15 E1A promoter.

Autoregulation of adenovirus E1A gene expression

We examined E1A gene expression by two evolutionarily divergent human adenoviruses, type 5 (subgroup C) and type 3 (subgroup B). Adenovirus type 3 (Ad3)-infected A549 cells contained much larger amounts of E1A-specific RNA than adenovirus type 5 (Ad5)-infected cells, from very early (3 h) through the late stages (20 h) after infection. The appearance of such abundant Ad3 E1A transcripts was delayed after infection of Ad5 E1A-expressing 293 cells, suggesting a down regulation of the Ad3 E1A gene by Ad5 E1A gene products. In a reciprocal manner, coinfection of A549 cells led to typically early and intense Ad3 E1A transcription and strongly inhibited transcription of the Ad5 E1A gene. Transient expression assays were developed so that the autoregulation of the E1A gene could be studied apart from the more complex background of infected cells. The DNA sequence surrounding the transcription start site of the Ad3 E1A gene was placed 5' to the sequence which encodes the bacterial chloramphenicol acetyltransferase gene. Cotransfection of HeLa cells with Ad3 or Ad5 E1A-expression plasmids increased the expression of the Ad3 E1A promoter-driven chloramphenicol acetyltransferase gene. Taken together, these results suggest dual autoregulatory features of adenovirus E1A gene expression. The positive and negative effects appear to be temporally distinguished under different conditions, both in viral infection and in transient assays with plasmid-cloned genes.

Spontaneous reiterations of DNA sequences near the ends of adenovirus type 3 genomes

Repeated passage of adenovirus type 3 in HeLa cells has led to a novel stock of variant genomes. Most of the DNA molecules in this stock are characterized by deletions and substitutions of DNA sequences near the left end of the adenovirus type 3 genome map, as reported earlier (C.C. Robinson and C. Tibbetts (1984) Virology 137, 276-286). In this report the characterization of the variant genomes is extended and reveals elongated DNA molecules bearing tandem repetitions of viral DNA sequences near the left and right ends of the viral DNA. Evidence is also presented supporting the cellular DNA origin of short insert sequences found in substitution variants. The elongated variants are of interest because of their novel repeated DNA structures. The locations of these aberrant sequences raise questions about their potential impact on viral gene expression.

Atrial natriuretic factor: purification of active peptides, cloning of cDNA and determination of structures of active peptides and precursors

Four peptides possessing both natriuretic and smooth muscle relaxant activities were purified from rat heart atrium and their amino acid sequences were determined. All contained a common sequence which contains a macro-ring structure formed by 17 amino acid residues and a disulphide bridge. The major atrial peptide in the atrium was identified as that containing 31 amino acid residues. The cDNA of the atrial peptide precursor was cloned and its nucleotide sequence determined. The amino acid sequence of the precursor deduced from the nucleotide sequence contained 152 residues and a potential signal peptide sequence characteristic of secretory polypeptides.

Polar encapsidation of adenovirus DNA: evolutionary variants reveal dispensable sequences near the left ends of Ad3 genomes

Repeated passage of adenovirus type 3 in HeLa cells has led to a novel stock of variant genomes, characterized by deletions and substitutions of DNA sequences within the left-end 750 base pairs. This heterogeneous stock retains few if any parental genomes--the majority of variants appear viable. Analysis of viable variants with deleted sequences reveals the 182 nucleotides proximal to the left-end inverted terminal repeat (136-318 bp) are not required for Ad3 infectivity in cultured human cell lines nor for maintenance of viral DNA encapsidation polarity.

Structure of rat atrial natriuretic factor precursor deduced from cDNA sequence

The atrium of the heart contains peptides, termed atrial natriuretic factors ( ANFs ), diuretic and smooth-muscle-relaxing activities. In view of its potent effects on salt metabolism in the kidney and on vascular smooth muscle, ANF is considered to play an important part in the control of fluid volume and vascular function. Several different ANF peptides varying in size have been isolated and their amino acid sequences determined. Analysis of the sequences of the peptides suggests that they are derived by proteolysis from the same precursor. To examine this hypothesis, we have cloned cDNAs of the ANF precursor using rat atrial mRNA, determined its nucleotide sequence and deduced its amino acid sequence. The ANF precursor consists of 152 amino acid residues including a putative signal peptide sequence. This sequence contains the amino acid sequences of all the ANF peptides reported to date.

A standard optometric headache history

Many optometric patients present with headache as their chief complaint, or as an ancillary symptom. Since most cases of head pain are associated with few or inconstant physical signs, the key to an accurate diagnosis lies largely in a careful, systematic history. This article provides a scheme by which the busy optometric clinician can expeditiously obtain an incisive and relevant profile of every headache patient, and thereby determine the appropriate mode of management, and referral.

Antibodies to native DNA and serum complement (C3) levels. Application to diagnosis and classification of systemic lupus erythematosus

The sensitivity and specificity of the presence of antibodies to native DNA and low serum C3 levels were investigated in a prospective study in 98 patients with systemic lupus erythematosus who were followed for a mean of 38.4 months. Hospitalized patients, patients with other connective tissue diseases, and subjects without any disease served as the control group. Seventy-two percent of the patients with systemic lupus erythematosus had a high DNA-binding value (more than 33 percent) initially, and an additional 20 percent had a high DNA-binding value later in the course of the illness. Similarly, C3 levels were low (less than 81 mg/100 ml) in 38 percent of the patients with systemic lupus erythematosus initially and in 66 percent of the patients at any time during the study. High DNA-binding and low C3 levels each showed extremely high predictive value (94 percent) for the diagnosis of systemic lupus erythematosus when applied in a patient population in which that diagnosis was considered. The presence of both abnormalities was 100 percent correct in predicting the diagnosis os systemic lupus erythematosus. Both tests should be included in future criteria for the diagnosis and classification of systemic lupus erythematosus.

Polar encapsidation of adenovirus DNA: cloning and DNA sequence of the left end of adenovirus type 3

The left-end adenovirus type 3 DNA sequence is very similar to those of other subgroup B adenoviruses, especially in the area between the HinfI site (320 base pairs) and the early-region Ia gene. This segment of the genome has been implicated as necessary for the left-end polarity of adenovirus DNA encapsidation. This segment and the sequences flanking it are compared with the corresponding sequences of adenovirus type 5 and adenovirus type 12, and the extent and pattern of intersubgroup homologies are discussed.

Reassociation rate limited displacement of DNA strands by branch migration

Large branched DNA structures are constructed by two-step reassociation of separated complementary strands from restriction fragments of different lengths. The displacement of DNA strands initially annealed to longer complementary DNA sequences, a process mediated by branch migration, is very rapid and has thus far been followed only under conditions which are second order, DNA reassociation rate limiting. The average lifetime of branched DNA leading to displacement of 1.6 Kb strands is estimated to be less than 10 seconds under conditions of DNA reassociation, Tm-25 degrees C. Several DNA-binding drugs, including intercalating dyes, have been tested to determine their influence, if any, on the kinetics of DNA strand displacements by branch migration. Only actinomycin D was found to have significant effect under the conditions we have described. The kinetics of the strand displacement in the presence of low concentrations of actinomycin D remain second order and slower rate of strand displacement must be attributed to decreased rate of reassociation of DNA strands to form the branched intermediates. Consideration is given to the potential manipulation of DNA structures at site-directed branches and the limitations due to rapid strand displacements. The feasibility of constructing sufficiently large branched DNA regions to approach first order, branch migration rate limiting kinetics is also discussed.

Targeted deletions of sequences from closed circular DNA

Closed circular DNA interacts with complementary sequences of single-stranded DNA to form displacement loop (D loop) structures in vitro. The site of D-loop formation can be directed by using single-stranded DNA derived from a selected restriction fragment. Circular DNA containing a D loop can then be linearized by cleavage with endonuclease S1. This cleavage appears to remove a limited number of nucleotides from each strand of the circular DNA substrate. Incubation with polynucleotide ligase followed by propagation in vivo leads to circular DNA molecules that bear small, single deletions in the region of the single-stranded DNA sequence chosen for the formation of the D loops. We have utilized these manipulations of DNA to construct tetracycline-sensitive deletion mutants of plasmid pBR322. The level of mutagenesis obtained by the procedure is sufficiently high that selective growth and screening procedures are not necessary for the isolation or identification of mutants. The frequency, variety, and small size of the deletions obtained within the selected target regions present considerable advantage for genetic and biochemical analysis. The method is quite general in rationale and should be immediately applicable to phage and viruses having infectious circular DNA genomes or recombinant DNA species propagated in circular plasmid vectors.

In vitro association of empty adenovirus capsids with double-stranded DNA

Several lines of evidence suggest that empty adenovirus capsids are preassembled intermediates in the pathway of virion assembly. We have observed that purified empty capsids of subgroup B adenoviruses have a remarkable affinity for DNA in vitro. The products of capsid-DNA association are sufficiently stable, once formed in low-salt solution, to permit purification and characterization in CsCl density gradients. Neither virions nor the DNA-containing incomplete particles of subgroup B adenoviruses can give rise to such in vitro reaction products. The average molecular weight of the empty adenovirus capsids is about 123 X 10(6), consistent with the absence of viral core peptides and a small deficiency of exterior shell polypeptides. Electron microscopy of negatively stained capsids and the capsids bound to DNA reveals a typical adenovirus size and architecture. The particles appear with a surface discontinuity that is presumed to expose the DNA binding site(s). The DNA molecules associated with the empty capsids are susceptible to the actions of DNase and restriction endonucleases. The dependence of rate of capsid-DNA association on DNA length suggests randomly distributed binding sites on the DNA molecules. Although the DNA molecules can successively acquire additional empty capsids, the empty particles themselves are restricted to interactionwith only one DNA molecule. Electron microscopy of the capsid-DNA complexes spread in cytochrome c films shows that the particles are bo-nd along the contour of extended duplex DNA. The amount of DNA within each bound particle appears to be less than 300 base pairs, as estimated by the length of the DNA molecules visible outside of the bound particle. The empty capsid-DNA association product described in this report provides an interesting substrate for further investigation of the DNA packaging process in a defined in vitro system, with extracts or purified components from infected cells.

Viral DNA sequences and gene products in hamster cells transformed by adenovirus type 2

Complementary strand-specific adenovirus DNA of full length or from endonuclease BamHI fragments was used as a probe to estimate the fractional representation and abundance of viral sequences in five hamster cell lines (Ad2HE1-5) transformed with UV-inactivated adenovirus type 2. The fraction of the viral genome present in the five transformed cell lines varied from 44% in the Ad2HE5 cell line to 84% in the Ad2HE3 cell line. The number of viral DNA copies per diploid cell equivalent ranged from 1.8 in the Ad2HE1 line to 7.1 in the Ad2HE4 line. In vivo labeling with [35S]methionine followed by immunoprecipitation with an antiserum against adenovirus type 2 early proteins revealed virus-specific polypeptides with molecular weights of 42,000 to 58,000 in extracts from all five hamster cell lines. Several other early viral polypeptides were detected in some of the adenovirus type 2-transformed hamster cell lines.

Physical organization of subgroup B human adenovirus genomes

Cleavage sites of nine bacterial restriction endonucleases were mapped in the DNA of adenovirus type 3 (Ad3) and Ad7, representative serotypes of the "weakly oncogenic" subgroup B human adenoviruses. Of 94 sites mapped, 82 were common to both serotypes, in accord with the high overall sequence homology of DNA among members of the same subgroups. Of the sites in Ad3 and Ad7 DNA, fewer than 20% corresponded to mapped restriction sites in the DNA of Ad2 or Ad5. The latter serotypes represent the "nononcogenic" subgroup C, having only 10 to 20% overall sequence homology with the DNA of subgroup B adenoviruses. Hybridization mapping of viral mRNA from Ad7-infected cells resulted in a complex physical map that was nearly identical to the map of early and late gene clusters in Ad2 DNA. Thus the DNA sequences of human adenoviruses of subgroups B and C have significantly diverged in the course of viral evolution, but the complex organization of the adenovirus genome has been rigidly conserved.

Viral DNA sequences from incomplete particles of human adenovirus type 7

Large pools of empty viral capsids accumulate in cells infected by subgroup B human adenoviruses. Such infected cells also yield DNA-containing incomplete particles in larger quantities than cells infected with serotypes representing other adenovirus subgroups. DNA isolated from carefully purified classes of Ad7 incomplete particles was analyzed by restriction endonuclease cleavage, gel electrophoresis and electron microscopy. At least 90% of the DNA molecules in each sample consisted of sequences that extended from the left end of the viral genome map by variable lengths toward the right end. The average length of DNA is linearly related to the average buoyant density of the incomplete particles from which the DNA is isolated. The results indicate that each capsid contains one DNA molecule. There is also a specific association of the left end of the viral genome with assembled or assembling capsids. The characteristic distributions of Ad7 incomplete particles may result from intracellular pools of assembly intermediates in which the incompletely packaged DNA has been fragmented in vivo or by shear during preparative procedures.

Reassociation of complementary strand-specific adenovirus type 2 DNA with viral DNA sequences of transformed cells

Complementary strand-specific adenovirus DNA, either full length or from restriction enzyme cleavage fragments, was used to estimate the fractional representation and abundance of viral sequences in two adenovirus type 2 (Ad2)-transformed rat cell lines, A2F19 and A2T2C4. The reassociation method introduced is based on the linear relationship, after exhaustive hybridization, between the inverted fraction of hybrid DNA and the molar ratio of probe to cellular DNA in the reaction mixture. The amount of viral DNA in A2F19 cells represents 12 to 14% of the viral genome at a level of around seven copies per diploid cell equivalent. For the cell line A2T2C4, the pattern of integrated viral DNA sequences is more complex. With full-length Ad2 DNA strands as a probe, about 56% of the probe was represented in cellular DNA. When each of the four BamHI fragment strands of Ad2 DNA was used as a probe, the fraction of the viral DNA present also amounted to around 56% with one to five copies from different regions of the viral genome. The results demonstrate the advantage of using strand-specific viral DNA as a probe in reassociation analysis with denatured cell DNA. The method should be useful in any system in which complementary strand separation of viral DNA sequences can be achieved.

Relationship of mRNA from productively infected cells to the complementary strands of adenovirus type 2 DNA

The complementary strands of adenovirus type 2 (Ad2) DNA were separated by buoyant density gradient centrifugation with poly (U, G). The complementary strand DNA was shown to remain intact through the course of strand separation. The l-strand of Ad2 DNA, appearing in the less dense complex with poly (U, G) in neutral CsCl density gradients, was shown to have a buoyant density in alkaline (pH 12.5) CsCl density gradients which is 2 to 3 mg per ml greater than that of its complement (h-strand). Renaturation of purified complementary strand DNA was observed only in mixtures of h- and l-strand DNA, and then with the second-order reaction rate expected for Ad2 DNA. Hybridization of the complementary strands of Ad2 DNA with cytoplasmic mRNA isolated from infected HeLa cells was performed in liquid phase and analyzed by hydroxylapatite chromatography. Before viral DNA synthesis (6 h after infection), 13 to 18% of the h-strand and 30 to 35% of the l-strand were represented in viral mRNA. Late (18 h) after infection the mRNA represented 20 to 25% and 63 to 68% of the h- and l-strands, respectively. Most, if not all sequences present in viral mRNA before viral DNA synthesis were also present in the cytoplasm late in infection.

Hydroxyapatite chromatography and formamide denaturation of adenovirus DNA

Denatured adenovirus DNA was retained by hydroxyapatite columns under conditions generally used for selective retention of double-stranded DNA, probably due to several partially complementary sequences within single-stranded DNA. It was found that addition of formamide reduced the fraction of sonically treated, denatured adenovirus DNA bound to hydroxyapatite from about 30% to less than 1%. This led to a study of the effect of formamide on the melting temperature (T(m)) of double-stranded DNA in solution or bound to hydroxyapatite. The T(m) of DNA decreases 0.56 C/1% formamide, a value determined in buffered solutions with purified formamide.