High risk human papillomavirus genotyping in clinical samples: evaluation of different commercial tests

The aim of the present study is to compare the performance of several commercial human papillomavirus (HPV) tests in a cohort of 281 women. The hybrid capture II, the PreTect-HPV-Proofer, the linear array, and DR.HPVTMIVD were utilized to detect and type HPV in parallel with in-house PCR tests followed by direct automated sequencing or by sub-cloning and sequencing. The concordance levels along with other tests were evaluated with a Cohen's K value varying between 0.60 to 0.88, indicating good correlation with nearly perfect agreement between hybrid capture II, (HCII) and the linear array test. High sensitivity was recorded by the linear array and HCII with 100% (95% CI, 0.8021 to 1.0000) detection of cervical intraepithelial neoplasia (CIN) III by both methods. Conversely, the PreTect-HPV-Proofer showed high specificity with 12% (95% CI, 0.7966 to 0.9163) positivity on normal samples. The genotyping analysis showed that agreement among tests was only low to moderate with great differences between different HPV types. Multiple infections were detected with poor concordance and sub-cloning assays revealed the presence of a lower number of HPV in comparison to the other methods. In summary, the use of different HPV tests applied to the same group of cervical smears may possibly lead to incongruent results, suggesting the need to standardize type-specific sensitivity of genotyping methods and the need to evaluate their accuracy in detecting multiple HPV infections. This would be a prerequisite for the use of genotyping assays in cervical cancer screening programs.

Predictors of human papilloma virus (HPV) infection in Italian women

HPV infection is a "necessary cause" of cervical cancer and it is sexually transmitted. Due to upcoming mass vaccination investigation on risk factors for infection is the basis to implement prophylactic strategy even in older women. The aim of the study was to evaluate predictors of high-risk (HR) HPV infection in adult women. Between 2006 and 2008, 100 women aged >18 years, with no previous treatment for cervical lesions, were screened for HR HPV infection in Rome, Italy. Risk factors for HPV infection were investigated through a questionnaire including: ethnicity, religion, education, marital status, sexual behavior, gynecological and obstetrical history, smoking and alcohol intake. Multivariate analysis identified the "never married-separated/divorced" status (OR: 3.38; 95% CI: 1.14-10.12) as predictor of HPV infection, while having a higher age at the first sexual intercourse (FSI) shows a protective effect (OR: 0.84; 95% CI: 0.71-1.00). A trend for the association between the infection and having more than three lifetime partners was also observed (OR: 2.57; 95% CI: 0.86-7.71). No significant association was found for other demographic characteristics investigated. These findings provide a contribution in the knowledge of an adult population defining a "high-risk" sexual behavioral profile and could be helpful to target prophylactic strategies in older woman.

HPV genotypes concordance between sex partners

The HPV genotype concordance in the sexual couples could support the sexual viral transmission of HPV infection. The present study contains a case-report of a stable Italian sex couple harbouring the same five HPV genotypes in their genital samples. The female partner, affected by vulvar condilomatosis, evidenced positivity in her cervicovaginal scraping with high risk HPV DNA Hybrid Capture 2 test and was negative at liquid-based performed Pap Test and at colposcopic examination. The male partner was clinically healthy regarding his external genitalia. In both male and female genital scrapings, the following HPV genotypes were detected by means of a PCR-based assay: 6, 16, 53, 73 and 84. This considerably high genotype concordance does not appear to be casual and supports, in our opinion, the hypothesis that genital HPV types are sexually transmitted agents

Molecular paleontology

Molecular paleontology, i.e., the recovery of DNA from ancient human, animal, and plant remains is an innovative research field that has received progressively more attention from the scientific community since the 1980s. In the last decade, the field was punctuated by claims which aroused great interest but eventually turned out to be fakes--the most famous being the sequence of dinosaur DNA later shown to be of human origin. At present, the discipline is characterized by some certainties and many doubts. We know, for example, that we have reasonable chances to recover authentic DNA from a mammoth carcass, while our chances are negligible (or nonexistent) in the case of a dynastic mummy from Egypt. On the other hand, though we are developing convincing models of DNA decay in bone, we are not yet able to predict whether a certain paleontological or archeological site will yield material amenable to DNA analysis. This article reviews some of the most important and promising investigations using molecular paleontology approaches, such as studies on the conservation of DNA in human bone, the quest for ancient DNA in permafrost-frozen fauna, the Tyrolean iceman, and the Neandertals.

Sequence analysis of bacterial DNA in the colon and stomach of the Tyrolean Iceman

The male human body found in an Alpine glacier on September 19, 1991 ("Tyrolean Iceman") has, for the first time in history, given scientists a chance to perform detailed anatomical, histological, and molecular investigations on the organs of a person from the Neolithic Age (5350-5100 B.P.). In the present study, tissue samples aseptically taken from the stomach and the colon of the mummy were utilized for DNA extraction, and the DNA was PCR-amplified, using primer pairs designed to bind to fragments of the 16s ribosomal RNA gene (16s rDNA) of a broad range of bacteria. The PCR products were cloned in plasmid vectors, and the recombinant clones (amplicons) were sequenced. The sequence data were finally used for scanning data libraries containing the corresponding sequences of present-day bacteria, to infer the putative ecophysiology of the ancient ones. The same procedure was repeated on some fragments of grass from the clothing found near the corpse. These fragments were taken as a control of the microbiological situation of the glacier. The results show that the flora of the Iceman's stomach is entirely composed of Burkholderia pickettii, an organism commonly found in aquatic habitats. The colon, on the other hand, contains several members of the fecal flora of humans, such as Clostridium perfringens, C. ghonii, C. sordellii, Eubacterium tenue, and Bacteroides sp. The Iceman's colon, however, was found to contain, rather unexpectedly, also some members of the genus Vibrio. The results are discussed in light of what is known about the preservation of microbial DNA at the Iceman's site and of previous parasitological studies performed on the Iceman himself and on human coprolites.

Analysis of bacterial DNA in skin and muscle of the Tyrolean iceman offers new insight into the mummification process

About 80 sequences (16s ribosomal RNA gene) of bacterial DNA in samples of skin and muscle taken directly from the Tyrolean iceman (3350-3100 years B.C.) or recovered during the 1992 archaeological expedition at the Alpine site were analyzed to obtain clues to the natural mummification process that allowed the corpse of the Neolithic shepherd/hunter to be preserved for more than 5,000 years. The investigation was made more complex by the fact that the surface of the mummy had been swabbed with phenol soon after the discovery (September 19, 1991). Our results show that no trace of microbial DNA is left on the actual surface of the body, while the untreated skin still bears the remains of large numbers of bacteria belonging to the genera Sphingomonas, Afipia, Curtobacterium, Microbacterium, Agromyces, and others. Compared to the untreated skin, the iceman's muscle is also very rich in bacterial DNA. However, this DNA comes, with few exceptions, from the species Clostridium algidicarnis. The sharp difference in the bacterial DNA composition of skin and muscle suggests that the remains of the original cadaveric microflora of the latter have not disappeared during the iceman's taphonomic history. On the other hand, the massive presence of C. algidicarnis, a cold-adapted sporigenous, the DNA of which was previously (Ubaldi et al. [1998] Am. J. Phys. Anthropol. 107:285-295) found in the soft tissue of a naturally desiccated Andean mummy, indicates that the hypothesis that the iceman's corpse underwent rapid dehydration by the effect of a warm wind (föhn) is no longer plausible. The results best fit with the hypothesis (Bereuter et al. [1997] Chem. Eur. J. 7:1032-1038) that the body was first covered by snow and ice, and then underwent thawing and, finally, desiccation.

The small-subunit rRNA gene sequences of venerids and the phylogeny of bivalvia

The complete nucleotide sequence of the 18S subunit of ribosomal DNA (rDNA) was determined for the venerid clams Callista chione (Pitarinae) and Venus verrucosa (Venerinae). Comparison of the new sequences with the published sequences of 1 annelid, 2 gastropods, 2 polyplacophorans, and 19 bivalves showed that when the annelids are used as outgroup the gastropods diverge from the bivalves, which form a cluster including the polyplacophorans. When the gastropods alone were compared with the bivalves, the latter split in two groups corresponding to the two subclasses of Heterodonta and Pteriomorpha. The former include two taxa that diverged early, Galeomma and Tridacna, while the Veneridae and Mactridae form two sister groups. In contrast to previous reports and in line with morphological data, the Ostreidae are included in the Pteriomorphia and form a monophyletic group.

How microbial ancient DNA, found in association with human remains, can be interpreted

The analysis of the DNA of ancient micro-organisms in archaeological and palaeontological human remains can contribute to the understanding of issues as different as the spreading of a new disease, a mummification process or the effect of diets on historical human populations. The quest for this type of DNA, however, can represent a particularly demanding task. This is mainly due to the abundance and diffusion of bacteria, fungi, yeasts, algae and protozoans in the most diverse environments of the present-day biosphere and the resulting difficulty in distinguishing between ancient and modern DNA. Nevertheless, at least under some special circumstances, by using rigorous protocols, which include an archaeometric survey of the specimens and evaluation of the palaeoecological consistency of the results of DNA sequence analysis, glimpses of the composition of the original microbial flora (e.g. colonic flora) can be caught in ancient human remains. Potentials and pitfalls of this research field are illustrated by the results of research works performed on prehistoric, pre-Columbian and Renaissance human mummies.

Sequence analysis of bacterial DNA in the colon of an Andean mummy

We have isolated DNA from 14 tissue samples from the internal organs of an Andean human mummy (10th-11th century A.D.) and have checked the persistence of the original human and bacterial templates using the following main approaches: 1) amino acid racemization test; 2) quantification of mitochondrial DNA copy number; 3) survey of bacterial DNA in the different organs; 4) sequence analysis of bacterial amplicons of different lengths. The results demonstrate that both the original human DNA and the DNA of the bacteria of the mummy gut are preserved. In particular, sequence analysis of two (respectively 100 and 196 bp in length) libraries of bacterial 16s ribosomal RNA gene amplicons from the mummy colon shows that while the shortest amplicons give only modest and biased indications about the bacterial taxa, the longer amplicons allow the identification several species of the genus Clostridium which are typical of the human colon. This work represents a first example of a methodological approach which is applicable, in principle, to many other natural and artificial mummies and might open the way to the study of the structure of the human microbial ecosystem from prehistory to present.

Phylogenetic analysis of Veneridae (Bivalvia): comparison of molecular and palaeontological data

An approximately 400-bp-long portion of the 16s rRNA gene sequence has been determined for the venerid clams Chamelea gallina (Chioninae), Dosinia lupinus (Dosiniinae), Pitar rudis, Callista chione (Pitarinae), Tapes decussatus, T. philippinarum, Venerupis (= Paphia) aurea (Tapetinae), and Venus verrucosa (Venerinae). Neighbor-joining and maximum parsimony trees support the results of traditional classification methods at the subfamily level but do not support the concept of a genus Tapes. The transversion divergence rate estimated on the basis of the palaeontological record for the C. gallina/V. verrucosa separation and for the Pitarinae is very close (0.14-0.16% per Myr, respectively) to that of ungulates and cetaceans, while the Tapetinae exhibit a much higher (0.36% per Myr) rate.

Molecular phylogeny of the fungi of the Iceman's grass clothing

To investigate the origin of the fungal hyphae that cover the grass clothing (cloak, boots) found near the neolithic mummy known as the Tyrolean Iceman, two radiocarbon-dated samples of grass were submitted to DNA extraction. The DNA was then PCR amplified using, respectively, primers specific for the region containing the internal transcribed spacers and the 5.8s rDNA (ITS), and primers specific for an approximately 600-bp long fragment of the nuclear small-subunit ribosomal DNA (SSU rDNA) repeat units of eukaryotes. The amplification products were cloned and sequenced. Sequence analysis of 20 individual ITS clones and of ten SSU rDNA clones indicated that three types of fungal DNA can be extracted from the grass. Phylogenetic analyses, using 5.8s and SSU rDNA fungal reference sequences from EMBL and GenBank databases, suggest that the DNAs come, respectively, from a psychrophilic basidiomycetous yeast, phylogenetically close to Leucosporidium scottii, and from two ascomycetes, one of which is possibly related to the Eurotiales.

Nucleic acids in mummified plant seeds: biochemistry and molecular genetics of pre-Columbian maize

Nucleic acids fractions were isolated from pre-Columbian maize seeds and characterized using different approaches such as polyacrylamide gel electrophoresis, anti-DNA antibody binding, HPLC fractionation, molecular hybridization with cloned genes, and DNA amplification by the polymerase chain reaction. The nucleic acids were found to be very depolymerized (less than or equal to 140 base pairs in length) and composed mainly of ribosomal RNA. Despite the very low amount and degree of polymerization of seed DNA, specific maize nuclear Mu1, Mu4, Mu8 and, possibly, Mu5 element components could be detected, thanks to the use of amplification systems as short as 90 bp. The results suggest that evaluation of the relative proportions of Mu-type element components and, possibly, other maize genomic components in single mummified kernels, may offer a new key to the study of ancient maize populations.

Monitoring a genetically engineered bacterium in a freshwater environment by rapid enzymatic amplification of a synthetic DNA ?number-plate?

In order to set up a sensitive and reliable detection method to monitor environmentally released genetically engineered microorganisms (GEMs) a 72-bp, double-stranded DNA fragment has been built by annealing and ligating four synthetic oligonucleotides. Binding sites for two 20-mer oligonucleotides are situated inside the DNA fragment, flanking the centre. Into the central part of the construction a 30-nucleotide identification sequence has been fitted. Thanks to the presence of the two oligonucleotide binding sites, the synthetic construction ("number-plate") can be submitted to enzymatic amplification using the polymerase chain reaction (PCR), thus enabling the identification system to take advantage of the outstanding sensitivity of this technique. When released into a freshwater microcosm, cells of Pseudomonas putida carrying a "number-plated" chromosome could be easily and rapidly detected merely by submitting boiled cell sediments to PCR amplification.

Highly sensitive and fast detection of Phoma tracheiphila by polymerase chain reaction

A new method for the diagnosis of the plant pathogenic fungus Phoma tracheiphila has been developed. The method takes advantage of the enzymatic amplification of a specific 102 bp-long target sequence of fungal DNA by the polymerase chain reaction (PCR) using Thermus aquaticus DNA polymerase. The amplified DNA was characterized by agarose-gel electrophoresis, molecular hybridization using a synthetic oligonucleotide probe and direct sequencing. The application of the new method makes possible fast and direct detection of the pathogen in lignified plant tissues, a goal not previously achieved when a cloned probe and a dot-blot test were employed. In addition the PCR test can be used to advantage as a particularly simple and fast way of typing fungal isolates. This is achieved by submitting to DNA amplification crude homogenates of fungal mycelium and analysing the amplified DNA on an agarose mini-gel.

Comparative analysis of alternating purine-pyrimidine sites in yeast chromosomes

It is known that under some circumstances DNA sequences made up of purine and pyrimidines in repeated alternation can undergo a transition from the right-handed to a left handed helical configuration which has been called Z-DNA. We have analyzed yeast chromosomal DNAs for the presence of alternating purine-pyrimidine stretches using a new strategy. Our strategy takes advantage of pulsed field gel electrophoresis (PFGE) to separate yeast chromosomal DNAs. They are subsequently analyzed by molecular hybridization with radioactive (dC-dA)n.(dG-dT)n or (dG-dC)n.(dC-dG)n probes, autoradiography and densitometric scanning. Preliminary results obtained by the application of the new method to Saccharomyces cerevisiae are described.

Comparative analysis of alternating purine-pyrimidine tracts and potential Z-DNA sequences in DNA plant viruses

The DNAs of several plant viruses were analyzed for the presence of alternating purine-pyrimidine sequences that can potentially undergo B to Z transition. The DNA of the caulimoviruses (plant retroviruses) was compared with that of the geminiviruses, with the cDNA of an RNA plant virus, and with several computer-generated random sequences. Our analysis indicates that potential Z-DNA sites tend to be restricted in the DNA of the caulimoviruses, whereas the same does not occur significantly in the other viral DNAs examined. This result is discussed in relation to the mode of replication of the caulimoviral DNA and offers additional evidence of the existence of selection processes regulating the frequency and distribution of the Z-DNA sites in the different genomes.

A simple and low cost DNA amplifier

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Polymerase chain reaction fingerprints

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Nucleic acids in mummified plant seeds: screening of twelve specimens by gel-electrophoresis, molecular hybridization and DNA cloning

Twelve seed specimens of varying ages and from different archaeological sites were analyzed for the presence of polymerized DNA and RNA. Amongst the samples tested, one of Vitis vinifera from an archaeological site in Iran (2,000-3,000 B.C.) was found to be completely devoid of nucleic acids. Zea mais seeds of Precolumbial age from Peru (about 800 A.D.) contained depolymerized DNA and RNA. Samples of Vitis vinifera and Rubus sp. from a Lombard archaeological site (800 A.D.) as well as radiocarbon dated seeds from the site of the "Spring Sanctuary" near Metaponto (I-IV century B.C.) were found to contain polymerized DNA and rRNA bands. However the electrophoretic properties of the rRNAs in one case and hybridization experiments performed with cloned seed DNA in the other, clearly demonstrated that the polymerized nucleic acids were not of plant origin.

Characterisation by molecular hybridization of RNA fragments isolated from ancient (1400 B.C.) seeds

The analysis of cress seeds from Thebes dated approximately 1400 years B.C. showed that fragments of RNA up to 10 bases in length were still present in the ancient seeds. After having been made radioactive at the 5'OH terminus, the RNA fragments were used as probes in a spot hybridization experiment. They were shown to hybridize to cress DNA and, to a lesser extent, to that of phylogenetically distant species. When fixed onto nitrocellulose and probed with different cloned genes, the RNA fragments were shown to originate from breakage of the 25 and 18s cytoplasmic rRNA.

Effect of fusicoccin on plant cell cultures and protoplasts

We have assayed the capacity of the fungal toxin fusicoccin to induce some of its characteristic effects (acidification of the medium, stimulation of K(+), and of 3-O-methyl-D-glucose uptake) in cell suspensions of Parthenocissus tricuspidata (Siebold et Zucc.) Planchon, Acer pseudoplatanus L. and Oryza sativa L., and in protoplast suspensions prepared from leaves of Nicotiana tabacum L. and Spinacia oleracea L. or from cultures of P. tricuspidata. Evidence is presented showing that all tested biological materials respond to the addition of fusicoccin. The observation that the toxin is also active on protoplasts indicates that the cell wall is not involved in the mechanism of action of fusicoccin.