Molecular characterization of human adenoviruses isolated in Italy

There is little information on the epidemiology of Human Adenoviruses (HAdVs) in Italy. In this study, 103 HAdV isolates, collected by the A. Gemelli Hospital (Catholic University Medical School of Rome, Italy) between 1987 and 2005, were genotyped by sequencing and phylogenetic analysis on a partial hexon gene region. Nine different serotypes belonging to all six HAdV species were identified. Serotype 2 was the most frequent (53.4%), followed by serotype 1 (15.53%) and serotype 41 (9.7%). Partial-hexon-based identification was confirmed as an effective tool for studying the molecular epidemiology of HAdVs.     

Acute porphyrias in the Argentinean population: a review.

The porphyrias are a group of inherited metabolic disorders of heme biosynthesis which result from a partial deficiency in one of its seven specific enzymes, after its first and rate limiting enzyme, delta-aminolevulinic acid synthetase. They can be classified on the basis of their clinical manifestations into cutaneous, acute and mixed disorders. Acute intermittent porphyria (AIP) is the most common type of hepatic acute porphyrias, inherited as an autosomal dominant trait, caused by a defect in the gene which codifies for the heme enzyme porphobilinogen deaminase. Its prevalence in the Argentinean population is about 1:125,000. A partial deficiency in another enzyme, protoporphyrinogen oxidase, produces variegate porphyria (VP), the second acute porphyria most frequent in the Argentinean population (1:600,000). Here, we review all the mutations we have found in 46 AIP and 9 VP unrelated Argentinean patients. To screen for mutations in symptomatic patients, we have proposed a geneticresearch strategy.     

Molecular characterization of noroviruses and rotaviruses involved in a large outbreak of gastroenteritis in Northern Italy

Noroviruses and rotaviruses from a gastroenteritis outbreak affecting >300 people near Garda Lake (Northern Italy) in 2009 were investigated. Characterization of viruses from 40 patient stool samples and 5 environmental samples identified three distinct rotavirus and five norovirus genotypes; two of the latter were detected in both patient and environmental samples.     

Molecular genetics in clinical practice: evolution of a DNA diagnostic service.

The development of a molecular genetics diagnostic service over a three year period was studied in a National Health Service region with a population of three million. Starting from a time when few diagnostic applications were possible, the number of disorders and the overall demand had grown rapidly. Conditions for which molecular genetic diagnosis had been provided included Duchenne and Becker muscular dystrophy, myotonic dystrophy, Huntington''s disease, and cystic fibrosis. Of 405 requests for diagnosis, 151 (37%) related to determination of carrier state, 187 (46%) to determining the feasibility of future prenatal diagnosis, and 67 (17%) were prenatal diagnostic biopsy samples, almost exclusively of first trimester chorion. DNA samples for future diagnostic use with a wide range of genetic disorders had also been banked. The study showed a need for close integration with clinical genetics services to allow satisfactory genetic counselling and interpretation of risks.     

Hepatitis viruses: characterization and diagnostic techniques.

Two human hypatitis viruses have been identified and characterized, but one or more additional agents exist. Hepatitis B virus (HBV) is a complex 42-nm predominantly double-stranded DNA virus with distinct surface and core antigens and an endogenous DNA polymerase. Hepatitis A virus (HAV) is a 27-nm RNA virus with enterovirus-like properties. Progressively more sensitive and specific immunologic assays have been applied to the study of viral hepatitis and are available for routine diagnostic purposes. As a result we recognize distinct serologic response patterns to infection, new antigenic markers, biochemical-biophysical characteristics of the viruses, and their epidemiologic features. Recombinant DNA technology has permitted the cloning of HBV genetic material and gene products in E. coli, but the virus has not been cultivated in vitro. In contrast, successful in vitro cultivation of HAV has finally been accomplished. Application of sensitive serologic tests for HAV and HBV has revealed that "non-A, non-B" agents account for a substantial proportion of transfusion-associated hepatitis as well as hepatitis occurring in the absence of percutaneous exposure. These agents have been transmitted to chimpanzees, and several putative virus antigen-antibody systems have been described; however, a specific association between these virus antigens and non-A, non-B hepatitis has not been established.     

Molecular characterization of a phosphatidylcholine-hydrolyzing phospholipase C.

While searching for a phospholipase C (PLC) specific for phosphatidylcholine in mammalian tissues, we came across such an activity originating from a contamination of Pseudomonas fluorescens. This psychrophilic bacterium was found to contaminate placental extracts upon processing in the cold. The secreted phosphatidylcholine-hydrolyzing PLC was purified by a combination of chromatographic procedures. As substrates, the enzyme preferred dipalmitoyl-phosphatidylcholine and 1-palmitoyl-2-arachidonoyl-phosphatidylcholine over phosphatidylinositol. The active enzyme is a monomer of approximately 40 kDa. As for other bacterial PLCs, the enzyme requires Ca2+ and Zn2+ for activity; dithiothreitol affected the activity due to its chelation of Zn2+, but this inhibition could be compensated for by addition of ZnCl2. The compound D609, described to selectively inhibit phosphatidylcholine-specific PLCs, caused half-inhibition of the P. fluorescens enzyme at approximately 420 microM, while 50-fold lower concentrations similarly affected PLCs from Bacillus cereus and Clostridium perfringens. Partial peptide sequences obtained from the pure P. fluorescens enzyme after tryptic cleavage were used to clone a DNA fragment of 3.5 kb from a P. fluorescens gene library prepared from our laboratory isolate. It contains an ORF of 1155 nucleotides encoding the PLC. There is no significant sequence homology to other PLCs, suggesting that the P. fluorescens enzyme represents a distinct subclass of bacterial PLCs. The protein lacks cysteine residues and consequently contains no disulfide bonds. Interestingly, P. fluorescens reference strain DSMZ 50090 is devoid of the PLC activity described here as well as of the relevant coding sequence.     

Molecular characterization of a newly recognized mouse parvovirus.

Mouse parvovirus (MPV), formerly known as orphan parvovirus, is a newly recognized rodent parvovirus distinct from both serotypes of minute virus of mice (MVM). Restriction analysis of the MPV genome indicated that many restriction sites in the capsid region were different from those of MVM, but most sites in the nonstructural (NS) region of the genome were conserved. MPV resembled MVM in genome size, replication intermediates, and NS proteins. Replication intermediates in infected cells were the same for MPV and MVM, including packaging of the 5-kb minus (V) strand. Furthermore, the MPV NS proteins were the same size as and present at the same ratio as the MVM(i) proteins in infected cells. Cloning and sequencing of the MPV genome revealed a genome organization closely resembling that of MVM, with conservation of open reading frames, promoter sequences, and splice sites. The left terminal hairpin was identical to that of MVM(i), but the right terminus was not conserved. Also, the MPV genome was unique in that it contained 1.8 copies of the terminal repeat sequence rather than the 1 or 2 copies found in other parvoviruses. The predicted amino acid sequence of the NS proteins of MPV and MVM(i) were nearly identical. In contrast, the predicted amino acid sequence of the capsid proteins of MPV was different from sequences of other parvoviruses. These results confirm that MPV is a distinct murine parvovirus and account for the antigenic differences between MPV and MVM.     

Molecular characterization and phylogenetic inferences of Dermanyssus gallinae isolates in Italy within an European framework

In order to investigate the genetic relationships between Dermanyssus gallinae (Metastigmata: Dermanyssidae) (de Geer) isolates from poultry farms in Italy and other European countries, phylogenetic analysis was performed using a portion of the cytochrome c oxidase subunit 1 (cox1) gene of the mitochondrial DNA and the internal transcribed spacers (ITS1+5.8S+ITS2) of the ribosomal DNA. A total of 360 cox1 sequences and 360 ITS+ sequences were obtained from mites collected on 24 different poultry farms in 10 different regions of Northern and Southern Italy. Phylogenetic analysis of the cox1 sequences resulted in the clustering of two groups (A and B), whereas phylogenetic analysis of the ITS+ resulted in largely unresolved clusters. Knowledge of the genetic make‐up of mite populations within countries, together with comparative analyses of D. gallinae isolates from different countries, will provide better understanding of the population dynamics of D. gallinae. This will also allow the identification of genetic markers of emerging acaricide resistance and the development of alternative strategies for the prevention and treatment of infestations.     

Molecular characterization of p53 mutations in primary and secondary liver tumors: diagnostic and therapeutic perspectives

p53 is one of the most mutated genes in human cancer. We have performed the molecular characterization of p53 and have searched for correlations with etiological factors and clinical parameters in primary and secondary liver tumors. A systematic study was carried out, innovative in many respects, to determine the mutational pattern of all 11 exons of p53 and analysis was extended also to exons 1–4 and 9–11 and the exon/intron junctions. Our analyses were performed on case histories of 114 patients from the European area and highlighted p53 mutation patterns different from those reported in the literature for the same tumors. In our case history, different tumors of the same organ showed a different frequency and distribution of mutations. In analyzed tumor types, gene status was a prognostic indicator of survival because patients undergoing liver resection without mutated p53 had a more favorable prognosis than mutated patients. This suggests p53 molecular diagnosis could become a further criterion in the decision for surgery and possible therapies. We describe the ideal conditions for polymerase chain reaction (PCR), single-strand conformation polymorphism (SSCP), and direct sequencing, which we have set in order to optimize yields, sensitivity, and time of what might become a massive molecular screening.     

Molecular characterization of {beta}-trace protein in human serum and urine: a potential diagnostic marker for renal diseases

We have isolated ß-trace protein from cerebrospinalfluid, serum, plasma, and urine samples of normal volunteersand sera and hemofiltrate of patients with chronic renal failure.Blood-derived and urinary ß-trace have significantlyhigher molecular weights than their cerebrospinal fluid counterpart,the amino acid sequences being identical. Oligosaccharide structuralanalysis revealed these molecular weight differences to be dueto different N-glycosylation. ß-Trace from hemofiltrateand urine has larger sugar chains and concurrently significantlyhigher sialylation than cerebrospinal fluid-ß-tracewhich bears truncated "brain-type" oligosaccharide chains (publishedpreviously). ß-Trace concentrations were about 40ng/ml for normal sera and plasma. 2000–6000 ng/ml weremeasured in sera of dialysis patients whereas in normal humancerebrospinal fluid, ß-trace concentration was about8000 ng/ml. A reduced amount of 900 ng/ml was found in a singlecase of hydrocephalus cerebri. The sialylated glycoforms ofß-trace detected in the blood are presumably derivedfrom resorbed cerebrospinal fluid protein whereas ß-TP-mole-culesbearing asialo-oligosaccharides are absent due to their hepaticclearance. The residual, sialylated ß-TP-species areprobably eliminated from the blood via the kidney. This physiologicalclearance mechanism for the sialylated glycoforms is disturbedin hemodialysis patients resulting in about 100-fold elevatedserum concentrations. These results let us suggest ß-tracemay become a useful novel diagnostic protein in renal diseases. "brain-type" N-glycosylation hepatic clearance human ß-trace kidney failure serum glycoproteins     

Molecular characterization of a zygote wall protein: an extensin-like molecule in Chlamydomonas reinhardtii.

The green alga Chlamydomonas reinhardtii elaborates two biochemically and morphologically distinct cell walls during its life cycle: one surrounds the vegetative and gametic cell and the other encompasses the zygote. Hydroxyproline-rich glycoproteins (HRGPs) constitute a major component of both walls. We describe the isolation and characterization of a zygote-specific gene encoding a wall HRGP. The derived amino acid sequence of this algal HRGP is similar to those of higher plant extensins, rich in proline and serine residues and possessing repeating amino acid motifs, notably X(Pro)3 and (Ser-Pro)n. Antiserum against this zygote wall protein detected common epitopes in several other zygote polypeptides, at least one of which is also encoded by a zygote-specific gene. We conclude that there is one set of HRGP wall genes expressed only in zygotes and another set that is specific to vegetative and gametic cells.     

Molecular characterization of a host-range-determining locus from Agrobacterium tumefaciens.

The virulence loci play an essential role in tumor formation by Agrobacterium tumefaciens. This study focused on the virC locus, which affects the host range Agrobacterium species. virC mutants display an attenuated or avirulent phenotype on certain host plants, but remain fully virulent on other plant hosts. The nucleotide sequence revealed that the virC locus of pTiA6NC is an operon consisting of two open reading frames. These two open reading frames, designated virC1 and virC2, encode protein products of 25,713 and 22,710 daltons, respectively, which were visualized by polyacrylamide gel electrophoresis. Only two nucleotides separated the stop codon for virC1 from the start codon for virC2, indicating that these genes may be translationally coupled.     

Phytoclimatic characterization ofQuercus frainetto Ten. stands in peninsular Italy

The floristic differentiation of the deciduousQuercus frainetto forests along the climatic gradients of Apennine Italy has been studied. The ecological amplitude of this oak, and the bioclimatological relationships here assessed, suggest potentiality for the growth ofQ. frainetto-rich communities as broad zonal vegetation belt, ranging from NW to SE along the W side of peninsular Italy. Strong floristical and ecological similarities to the balcanic stands are described.The status of real vegetation belt for the ItalianQuercion frainetto s.l. is here emphasized.     

Molecular characterization of a protease secreted by Erwinia amylovora.

A protease with a molecular mass of 48 kDa is secreted by the fire blight pathogen Erwinia amylovora in minimal medium. We characterized this activity as a metalloprotease, since the enzyme was inhibited by EDTA and o -phenanthroline. A gene cluster was determined to encode four genes connected to protease expression, including a structural gene (prtA) and three genes (prtD, prtE, prtF) for secretion of the protease, which are transcribed in the same direction. The organization of the protease gene cluster in E. amylovora is different from that in other Gram-negative bacteria, such as Erwinia chrysanthemi, Pseudomonas aeruginosa and Serratia marcescens. On the basis of the conservative motif of metalloproteases, PrtA was identified to be a member of the metzincin subfamily of zinc-binding metalloproteases, and was confirmed to be the 48 kDa protease on gels by sequencing of tryptic peptide fragments derived from the protein. The protease is apparently secreted into the external medium through the type I secretion pathway via PrtD, PrtE and PrtF which share more than 90% identity with the secretion apparatus for lipase of S. marcescens. A protease mutant was created by Tn 5 -insertions, and the mutation localized in the prtD gene. The lack of protease reduced colonization of an E. amylovora secretion mutant labelled with the gene for the green fluorescent protein (gfp) in the parenchyma of apple leaves.     

Molecular characterization of interleukin 12.

Interleukin 12 (IL-12), formerly known as cytotoxic lymphocyte maturation factor and natural killer cell stimulatory factor, is a cytokine secreted by a human B lymphoblastoid (NC-37) cell line when induced in culture with phorbol ester and calcium ionophore. This factor has been purified to homogeneity and shown to synergize with low concentrations of interleukin 2 in causing the induction of lymphokine-activated killer cells. In addition, purified IL-12 stimulated the proliferation of human phytohemagglutinin-activated lymphoblasts by itself and exerted additive effects when used in combination with suboptimal amounts of interleukin 2. The protein is a heterodimer composed of a 40- and a 35-kDa subunit. Amino acid sequence analysis confirmed predicted sequences from the cloned cDNAs of each subunit. Chemical and enzymatic deglycosylation of the heterodimer demonstrated that the 40- and 35-kDa subunits contain 10 and 20% carbohydrate, respectively. Structural analysis of IL-12 using site-specific chemical modification revealed that intact disulfide bonds are essential for bioactivity. The 40-kDa subunit of IL-12 was identified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and confirmed by immunoblotting as being present in NC-37 cell supernatant solutions in relatively large amounts uncomplexed to the 35-kDa subunit. Previously it had been shown that the 40-kDa subunit alone does not cause the proliferation of activated human T lymphocytes or enhance the cytolytic activity of human natural killer cells. However, results obtained by site-specific chemical modification suggesting that a tryptophan residue is at or near the active site of IL-12 may imply a direct role of the subunit in interacting with the IL-12 receptor. These data may support the recent proposal (D.P. Gearing and D. Cosman (1991) Cell 66, 9-10) that IL-12 consists of a complex of cytokine and soluble receptor.