Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans.

The genome sequences of Caenorhabditis elegans, Drosophila melanogaster and Arabidopsis thaliana have been predicted to contain 19,000, 13,600 and 25,500 genes, respectively. Before this information can be fully used for evolutionary and functional studies, several issues need to be addressed. First, the gene number estimates obtained in silico and not yet supported by any experimental data need to be verified. For example, it seems biologically paradoxical that C. elegans would have 50% more genes than Drosophilia. Second, intron/exon predictions need to be tested experimentally. Third, complete sets of open reading frames (ORFs), or "ORFeomes," need to be cloned into various expression vectors. To address these issues simultaneously, we have designed and applied to C. elegans the following strategy. Predicted ORFs are amplified by PCR from a highly representative cDNA library using ORF-specific primers, cloned by Gateway recombination cloning and then sequenced to generate ORF sequence tags (OSTs) as a way to verify identity and splicing. In a sample (n=1,222) of the nearly 10,000 genes predicted ab initio (that is, for which no expressed sequence tag (EST) is available so far), at least 70% were verified by OSTs. We also observed that 27% of these experimentally confirmed genes have a structure different from that predicted by GeneFinder. We now have experimental evidence that supports the existence of at least 17,300 genes in C. elegans. Hence we suggest that gene counts based primarily on ESTs may underestimate the number of genes in human and in other organisms.

Protein interaction mapping in C. elegans using proteins involved in vulval development.

Protein interaction mapping using large-scale two-hybrid analysis has been proposed as a way to functionally annotate large numbers of uncharacterized proteins predicted by complete genome sequences. This approach was examined in Caenorhabditis elegans, starting with 27 proteins involved in vulval development. The resulting map reveals both known and new potential interactions and provides a functional annotation for approximately 100 uncharacterized gene products. A protein interaction mapping project is now feasible for C. elegans on a genome-wide scale and should contribute to the understanding of molecular mechanisms in this organism and in human diseases.

Oncogenic association of specific human papillomavirus types with cervical neoplasia.

Molecular hybridization analysis of human papillomavirus (HPV) DNA from 190 cervical biopsy specimens from women in the United States, Brazil, and Peru revealed viral sequences in 2 (9%) of 23 biopsy specimens of normal mature squamous epithelium, 7 (44%) of 16 biopsy specimens of metaplastic squamous epithelia, 60 (77%) of 78 cervical intraepithelial neoplasia (CIN), 57 (89%) of 64 invasive squamous carcinomas, and 8 (89%) of 9 endocervical adenocarcinomas. HPV typing by DNA hybridization revealed HPV 6 and HPV 11 sequences in metaplastic squamous epithelia, CIN I, and CIN II, but not in CIN III lesions or invasive carcinomas. HPV 16 was detected in metaplastic epithelium and in nearly half of the invasive squamous carcinomas and adenocarcinomas. It was present in 31% of CIN lesions, increasing in frequency with the severity of CIN from 20% of CIN I to 50% of CIN III. HPV 16 showed a striking difference in geographic distribution, being detected in 36% of the carcinomas from the United States compared to 64% of the carcinomas from Brazil and Peru. HPV 18 was found in metaplastic epithelia and in 17% of carcinomas but in only 1% of CIN lesions. HPV 31 was not found in metaplastic epithelium but was present in 6% of carcinomas and in 18% of CIN lesions. In addition, a group of uncharacterized HPVs, not corresponding to any of the probes used, was found in 5% of normal and metaplastic epithelia and in 18% of CIN and 19% of invasive cancers. These results suggest that individual HPV types that infect the cervix have varying degrees of oncogenic association. HPV 6 and HPV 11 appear to have very little oncogenic association, HPV 31 has low oncogenic association, and HPV 16 and HPV 18 have high oncogenic association.

Bioassay for specific DNA sequences using a non-radioactive probe.

A novel method for detecting specific DNA sequences is described. The method uses a non-radioactive DNA probe, called a probe-vector, that can transform competent Escherichia coli cells at high efficiency only when it has hybridized to a specific DNA target, thus forming a circular, double-stranded, plasmid-like molecule. The probe-vector carries a plasmid origin of replication and a gene that confers antibiotic resistance on transformed E. coli. The output of the assay--colored bacterial colonies on an agar plate--is quantitative and proportional over a wide range of target concentrations. The utility of the probe-vector method for detecting hepatitis B virus (HBV) DNA in human serum is demonstrated. The assay can detect as little as 0.1 pg HBV DNA. The presence of an internal standard monitors DNA recovery and E. coli transformation efficiency for each sample. The assay has the potential to simultaneously measure the DNA of two or more pathogens within the same clinical sample.

Correlation of cellular atypia and human papillomavirus deoxyribonucleic acid sequences in exfoliated cells of the uterine cervix.

Restriction enzyme digestion and Southern blot hybridization were used to analyze deoxyribonucleic acid (DNA) extracted from exfoliated cervical cells for the presence of human papillomavirus sequences and these results were correlated with cytologic findings on Papanicolaou smears. Specimens (N = 204) were obtained from a nonselected population of women undergoing routine cytologic screening and human papillomavirus DNA sequences were detected in 33 (16%) women. Thirteen smears contained atypical squamous cells, ranging from very mild dysplasia to moderate dysplasia; all showed associated morphologic evidence of human papillomavirus infection characterized by koilocytosis, nuclear enlargement, wrinkling, and hyperchromasia, and human papillomavirus DNA was demonstrable in 12 (92%) smears. Of the remaining 191 samples with normal cytology, 21 (11%) also contained human papillomavirus DNA sequences. Reevaluation of the smears from these women resulted in a revision of the cytologic diagnosis to very mild dysplasia in four cases. These data suggest that human papillomavirus infection occurs more frequently than predicted by cytologic screening.

Separation and translation of the mRNAs coding for and chains of rabbit globin.

A method is presented to separate the mRNAs coding for alpha and beta globins of rabbit reticulocytes. 10S RNA was extracted from the light and heavy polysomes created by incubation of reticulocytes with L-O-methylthreonine, and assayed for mRNA activity in an ascites cell-free extract. Tryptic digests of the in vitro products demonstrated that the heavy polysomes yielded beta globin mRNA at least 90% free of alpha mRNA activity, and that the light polysomes yielded alpha mRNA at least 70% free of beta mRNA activity.

Cloning and characterization of the DNA of a new human papillomavirus from a woman with dysplasia of the uterine cervix.

A previous analysis of 121 female genital tract lesions from the United States and South America had revealed that a large number contained DNA sequences that were weakly homologous to a panel of human papillomavirus (HPV) probes. The DNA sequences of one of these viruses have been molecularly cloned and shown to be a new type of HPV which is called HPV 31. Among the cloned HPV genomes, HPV 31 is most closely related to HPV 16. Although absent from all genital condylomas studied, HPV 31 was present in approximately 20% of the mild and moderate dysplasias and in 6% of the invasive cervical cancers

Authentic beta-globin mRNA sequences in homozygous betaO-thalassemia.

In a patient with homozygous betaO-thalassemia in whom studies of reticulocyte hemoglobin synthesis showed no beta-globin chain synthesis in vivo and in vitro, molecular hybridization studies revealed RNA sequences complementary to beta-globin cDNA. The fact that these sequences were authentic beta-globin mRNA was shown by fingerprint analysis of T1 ribonuclease-digested mRNA and by sequencing of oligonucleotides unique to beta-globin mRNA. The beta-mRNA that failed to direct beta-globin chain synthesis was not detectably shortened or degraded and contained poly(A) sequences.

DNA cloning using in vitro site-specific recombination.

As a result of numerous genome sequencing projects, large numbers of candidate open reading frames are being identified, many of which have no known function. Analysis of these genes typically involves the transfer of DNA segments into a variety of vector backgrounds for protein expression and functional analysis. We describe a method called recombinational cloning that uses in vitro site-specific recombination to accomplish the directional cloning of PCR products and the subsequent automatic subcloning of the DNA segment into new vector backbones at high efficiency. Numerous DNA segments can be transferred in parallel into many different vector backgrounds, providing an approach to high-throughput, in-depth functional analysis of genes and rapid optimization of protein expression. The resulting subclones maintain orientation and reading frame register, allowing amino- and carboxy-terminal translation fusions to be generated. In this paper, we outline the concepts of this approach and provide several examples that highlight some of its potential.

Suppression of the nonsense mutation in homozygous beta 0 thalassaemia.

The common form of beta thalassaemia associated with elevated haemoglobin A2 levels can be broadly classified as beta + or beta 0 type according to the presence or absence of beta-globin chain synthesis in the homozygous state. The molecular pathology of each type is heterogeneous. Apart from a subgroup of Indo-Pakistani patients, the beta-globin structural gene is intact in the majority of patients with beta 0 thalassaemia. The amount of beta-globin mRNA present in the reticulocytes of these patients varies: in some it is absent or barely detectable; in others, a substantial amount is present, but it is nonfunctional. We recently demonstrated that the molecular lesion in a Chinese patient with nonfunctional beta-globin mRNA was due to the mutation of the normal lysine codon AAG at amino acid 17 to the amber terminator codon UAG, which prematurely terminates the beta-globin chain. In the present study we demonstrate the first example of a nonsense mutation in humans which can be suppressed in vitro by the suppressor tRNA, as has been found in other eukaryotic cells and viruses.

The nucleotide sequences of the untranslated 5' regions of human alpha- and beta-globin mRNAs.

The complete sequences of the untranslated 5' regions of human alpha- and beta-globin mRNAs were determined by sequence analysis of full-length cDNAs. The single-stranded cDNAs were digested with the restriction endonuclease Hae III, and the two 3'-terminal fragments of 75 and 132 nucleotides, complementary to the 5' termini of the alpha- and beta-globin mRNAs, respectively, were isolated and sequenced. Including the initiation codon AUG, the untranslated 5' regions of human alpha- and beta-globin mRNAs contain 41 and 54 nucleotides, respectively, and exhibit striking homologies with the corresponding sequences in the rabbit. Human alpha- and beta-globin mRNAs have five bases in the region of the initiation codon that may form base pairs with the 3' terminus of 18S rRNA. Stable secondary structures with hairpin loops can be constructed in the untranslated 5' regions.

Construction of a functional human suppressor tRNA gene: an approach to gene therapy for beta-thalassaemia.

A human tRNALys gene was converted to an amber suppressor by site-specific mutagenesis of the anticodon. The mutated tRNALys gene directed synthesis of a tRNA that suppressed the UAG amber nonsense mutation in beta O thalassemia mRNA. Such genes may be used to detect other nonsense mutations in mammalian cells and may provide an approach to gene therapy for beta O thalassaemia due to nonsense mutations.

A new type of papillomavirus associated with cancer of the uterine cervix.

A new human papillomavirus (HPV) type was detected by low-stringency Southern blot hybridization analysis of DNA from an endocervical adenocarcinoma. The genomic DNA of the virus, which was obtained as two BamHI fragments of 3.75 and 4.1 kb, was molecularly cloned into lambda L47 and subsequently subcloned into pBR322 for further characterization. Hybridization studies demonstrated that these viral DNA isolates were only distantly related to other HPV and thus represented a new type of HPV, called HPV 35. A restriction enzyme map was prepared which allowed a comparison of the genetic organization of this HPV with that of HPV 6b; the results demonstrated collinearity of the HPV 35 genome with that of HPV 6b. Prevalence studies revealed that HPV 35 was present in 2 of 158 (1%) anogenital intraepithelial neoplasia and in 3 of 69 (4%) anogenital cancers. Thus HPV 35 is a low-prevalence human papillomavirus associated with anogenital intraepithelial neoplasia and cancer.

Human papillomavirus type 52: a new virus associated with cervical neoplasia.

Analysis of biopsies of cervical intraepithelial neoplasia (CIN) revealed a high percentage of human papillomavirus (HPV) sequences that would hybridize to a mixture of HPV probes only under conditions of relaxed stringency. The DNA sequences of one of these viruses was molecularly cloned and shown to be a new HPV, type 52 (HPV-52). This virus is most closely related to HPV-33. Hybridization analysis with restriction fragments of HPV-52 showed collinearity with the HPV-33 genome. DNA sequencing revealed a high level of conservation between the two viruses within the L1 open reading frame but significant divergence in the non-coding region of the viral genomes. Prevalence studies indicated that HPV-52 sequences were present in three of 137 (2%) CIN and in one of 48 (2%) cervical squamous cell cancers studied in the U.S.A.

Nucleotide sequence of human papillomavirus type 31: a cervical neoplasia-associated virus.

The nucleotide sequence of human papillomavirus (HPV) 31 DNA (7912 bp) was determined and used to deduce the genomic organization of this cervical cancer-associated virus. Based on comparisons of the HPV 31 DNA sequence to other sequenced HPVs, HPV 31 is a typical papillomavirus most related to HPV 16 (70% identical nucleotides). The E6 and E7 open reading frames (ORF) of HPV 31 contain several potential DNA binding motifs (Cys-X-X-Cys), the locations of which are conserved in all HPVs. The E6 ORF also has the potential to code for an E6* protein. The E7 ORF of HPV31 encodes a polypeptide motif which appears to distinguish HPVs associated with cervical cancer, such as types 16, 18, 31, and 33, from HPVs found primarily in benign lesions, such as types 6 and 11.

Human papillomavirus type 56: a new virus detected in cervical cancers.

A new human papillomavirus type (HPV-56) was identified by low stringency Southern blot analysis with an HPV-31 DNA probe, in a cervical intraepithelial neoplasm (CIN). The DNA of this virus was molecularly cloned and shown to be a new HPV type based on the absence of cross-reactivity to HPV types 1 to 55 under high-stringency hybridization conditions. At low stringency, HPV-56 was most related to HPV types 30 and 45. The deduced organization of the open reading frames of HPV-56, from hybridization and partial nucleotide sequence analyses, reveals a typical HPV genome. HPV-56 was detected in two of 464 normal cervical tissues, in five of 227 cervical condylomas and CIN, and in two of 84 invasive cancers of the cervix.

Temporal associations of human papillomavirus infection with cervical cytologic abnormalities.

The relationship between infection with different human papillomavirus types and cervical intraepithelial neoplasia was studied in a group of 398 women seen in a private gynecology practice in Washington, D.C. Each woman was assessed for human papillomavirus infection by Southern blot hybridization analysis of cervical cells obtained by swab. The human papillomavirus results were correlated with the results of Papanicolaou smears taken the same day and with data abstracted from medical records regarding past cervical disease. Subjects with normal cytologic findings at the time of human papillomavirus testing were followed up for an average of 2 to 3 years with additional Papanicolaou smears. At the time of human papillomavirus testing, 58% (19/33) of women with cervical intraepithelial neoplasia had detectable human papillomavirus deoxyribonucleic acid in contrast to 10% (28/289) of women with normal cytologic findings (p less than 0.001). This association persisted after statistical adjustment for age and current use of oral contraceptives, a factor that appeared to increase the detection of human papillomavirus. Among women with no current cytologic evidence of neoplasia, human papillomavirus detection was more likely in those with a history of past genital neoplasia (p = 0.05). In the follow-up study, 15% (3 of 20) of cytologically normal women who were human papillomavirus-positive at baseline subsequently exhibited cervical cells suggestive of cervical intraepithelial neoplasia compared with only 5% (9 of 195) of human papillomavirus-negative women. However, this difference reflected recurrent and not incident neoplasia.

Cloning and partial DNA sequencing of two new human papillomavirus types associated with condylomas and low-grade cervical neoplasia.

Using low-stringency Southern blot analysis and cloning in lambda bacteriophage, two new human papillomavirus types (HPV-43 and HPV-44) were identified and their DNAs were cloned from vulvar tissues. The isolates were characterized by restriction endonuclease mapping and shown to be new HPV types on the basis of their minimal hybridization with all other known HPV types at high stringency. Both HPVs are most closely related to types 6, 11, and 13. HPV-43 did not exhibit any cross-reactivity with these HPV types at high stringency. HPV-44 showed minimal cross-reactivity to HPV-13, which was in the range of 20 to 25% according to liquid hybridization analysis. The deduced genomic organization of each of the two new HPVs was colinear with HPV-6b. Prevalence studies revealed that HPV-43 and HPV-44 together were found in 6 of 439 normal cervical tissues, in 8 of 195 cervical intraepithelial neoplasms, but in none of 56 cervical cancers tested thus far.