Reentrant melting of RNA with quenched sequence randomness.

The effect of quenched sequence disorder on the thermodynamics of RNA secondary structure formation is investigated for two- and four-letter alphabet models using the constrained annealing approach, from which the temperature behavior of the free energy, specific heat, and helicity is analytically obtained. For competing base pairing energies, the calculations reveal reentrant melting at low temperatures, in excellent agreement with numerical results. Our results suggest an additional mechanism for the experimental phenomenon of RNA cold denaturation.

The influence of age on the recovery of the ERG photostress test.

INTRODUCTION: Focal ERG associated with photostress test could be a useful diagnostic method for evaluating macular visual function. The main aim of this study was to evaluate the effect of age on the recovery time constant of the ERG photostress test. The second aim was to assess the sources of variability which affect the measurements. METHODS: Fifty-four healthy subjects (108 eyes), aged between 21 and 77, with corrected VA of 20/20 or more and absence of any ocular or systemic disease, were recruited. For each eye ERG response to focal (20° in diameter) 42-Hz stimulation was recorded: three series of 200 summations in base conditions and a six series of 42-Hz ERGs (100 summations each) at 10, 40, 80, 180, 300 and 420 s after bleaching by a white spot of light (20° in diameter) from a direct ophthalmoscope (800 cd/m²) pointed at macular region for 30 s. Fourier analysis was performed and amplitude of the first harmonica calculated. The relationship of basal amplitudes with subject age and gender, and the kinetics of macular function recovery were assessed through mixed-effects models. RESULTS: Mean basal amplitude decreases by 0.046 µV for year of life. The recovery after bleaching is proportional to age with an increase of 4.31 s for decade. Restoration of amplitude is slower in older subjects. DISCUSSION: There is a significant decrease in macular ERG amplitude with age. The macular recovery after photostress shows exponential kinetics that are less efficient in older subjects: this could be related to lower effectiveness of photopigment restoration in advanced age.

Mitochondrial DNA sequence variations in some Italian wild boar populations.

In order to investigate the relationships between Italian wild boar and major pig breeds, we studied the genetic variability of four wild boar populations in Italy (Arezzo, Pisa, Parma, Bergamo) using a 533-bp fragment of the mitochondrial control region. Sixty-nine wild boar samples were analysed, allowing the identification of 10 distinct haplotypes, which involve a total of 15 single nucleotide polymorphisms. Phylogenetic and network analyses were performed also considering several sequences of wild and domesticated forms available in the databases. The Bayesian phylogenetic tree and the Median-Joining network analyses show three main groups: the Italian (IT), European (EU) and Asian (AS) clades. The IT clade corresponds to the Maremma endemic wild boar population and also includes Sardinian individuals, while the EU and AS groups include wild boars as well as domestic pig breeds. Only two individuals from Pisa cluster in the IT group, whereas two haplotypes from Bergamo cluster in the AS group and all other samples cluster in the EU clade. These findings suggest that in Italy wild boar populations have a mixed origin, both EU and AS, and that an interbreeding between wild and domesticated strains has probably occurred. Eight of the 10 wild boars coming from the Migliarino-San Rossore-Massaciuccoli Regional Park (Pisa) belong to H2 and H3 haplotypes, and cluster into the EU clade, suggesting that this regional park is not anymore exclusive of the endemic Maremma wild boar.

Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species.

The mitochondrial genome (mtDNA) of Metazoa is a good model system for evolutionary genomic studies and the availability of more than 1000 sequences provides an almost unique opportunity to decode the mechanisms of genome evolution over a large phylogenetic range. In this paper, we review several structural features of the metazoan mtDNA, such as gene content, genome size, genome architecture and the new parameter of gene strand asymmetry in a phylogenetic framework. The data reviewed here show that: (1) the plasticity of Metazoa mtDNA is higher than previously thought and mainly due to variation in number and location of tRNA genes; (2) an exceptional trend towards stabilization of genomic features occurred in deuterostomes and was exacerbated in vertebrates, where gene content, genome architecture and gene strand asymmetry are almost invariant. Only tunicates exhibit a very high degree of genome variability comparable to that found outside deuterostomes. In order to analyse the genomic evolutionary process at short evolutionary distances, we have also compared mtDNAs of species belonging to the same genus: the variability observed in congeneric species significantly recapitulates the evolutionary dynamics observed at higher taxonomic ranks, especially for taxa showing high levels of genome plasticity and/or fast nucleotide substitution rates. Thus, the analysis of congeneric species promises to be a valuable approach for the assessment of the mtDNA evolutionary trend in poorly or not yet sampled metazoan groups.

Direct sequencing of long polymerase chain reaction fragments.

Direct sequencing of polymerase chain reaction (PCR)-generated templates is a commonly used technique in molecular biology laboratories. We describe an improved method for direct sequencing of PCR fragments longer than 20 kb obtained with a commercial mixture of Taq and Pwo DNA polymerases. The sequencing protocol was optimized for an automated infrared DNA sequencer, consistently yielding long reads (500-600 bases).

Increased reliability of selective PCR by using additionally mutated primers and a commercial Taq DNA polymerase enhancer.

A reliable selective PCR procedure that combines the use of additionally mutated primers with the specificity-enhancing properties of a commercial preparation (Perfect Match, Stratagene) is described. The human immunodeficiency virus type 1 pol gene point mutations known to confer in vitro resistance to azidothymidine were examined as a model for optimization of the assay. The usual strategy of deliberately introducing an additional mismatch 1 residue from the 3' end in the wild-type and mutant primers did not allow reproducible discrimination between wild-type and mutant target sequences. Addition of minimal amounts of Perfect Match to the same PCR mixtures resulted in a significantly enlarged range of selective annealing temperatures, providing a valuable and cost-effective means for reliable detection of known mutations by selective PCR.

[Comparison of flow-cytometry and immunohistochemistry with proliferating monoclonal antibody. Cell nuclear antigen (PCNA) in the study of proliferative kinetics of renal carcinoma]. / Confronto tra citometria a flusso e immunoistochimica con AcP monoclonale anti-proliferating. Cell nuclear antigen (PCNA) nello studio della cinetica proliferativa del carcinoma renale.

Tumor Proliferative Fraction (TPF) has been shown to correlate with prognosis in some malignancies. A reliable, accurate method for application in a clinical practice is still being sought. The aim of this study is to compare TPF as determined by Proliferating Cell Nuclear Antigen (PCNA) and Flow Cytometry (FC) in 36 consecutive patients affected by Renal Cell Carcinoma (RCC). Proliferating cells were identified in paraffined sections using a anti-PCNA monoclonal antibody (PC 10 Dako). Cell suspension for FC were prepared from fresh/frozen samples DNA index and S phase were evaluated using a computerized program (Multicycle, Phoenix). 16 samples (47.1%) were found to be aneuploid by FC (DI range 0.72-2.40). Aneuploid vs diploid tumors had significantly higher mean FC-S phase (p = 0.049) and PCNA LI (p = 0.034). Weak correlation (r-Spearman 0.416 p = 0.01) was found between PCNA LI and grading and near to significativity between PCNA LI and tumor size (r = 0.335 p = 0.0061). When patients are classified according to nuclear grading, is evident that all PCNA G4 are aneuploid and that 62.5% of PCNA G1 are diploid. A week correlation near to significativity is found between PCNA LI and S phase only in the aneuploid tumors. A more reliable measurement of TPF in RCC could be provided by combining the two methods. Further research on larger series is needed.

The type 2 capsule locus of Streptococcus pneumoniae.

The type 2 capsule locus of Streptococcus pneumoniae was characterized in Avery's strain D39, which is the parent strain of the standard transformation recipients currently used in pneumococcal research and is largely used as a virulent strain in studies on the pathogenesis of pneumococcal infections. The capsule locus was sequenced by using a 21.7-kb PCR fragment from the D39 genome as a template. Sequence data analysis showed the presence of 18 open reading frames, 17 of which have the same direction of transcription and all of which are potentially involved in capsule biosynthesis. It was also shown that R36A and R6, which are unencapsulated (rough) derivatives of D39, carry a 7,504-bp deletion involving nine capsule genes.

Characterization of cryptic plasmids pDP1 and pSMB1 of Streptococcus pneumoniae.

Cryptic plasmids pDP1 and pSMB1 from clinical strains of Streptococcus pneumoniae isolated 74 years apart were found to be essentially identical in their nucleotide sequence. pDP1, 3161 bp, contains five codirectional ORFs and presents all the general features of plasmids replicating by the rolling circle mechanism. The rep gene, 963 bp, is highly homologous to the rep gene of other streptococcal plasmids of the pC194 family.

Hic, a novel surface protein of Streptococcus pneumoniae that interferes with complement function.

The important human pathogen Streptococcus pneumoniae was found to absorb factor H, an inhibitor of complement, from human plasma. We identified the gene encoding a novel surface protein, factor H-binding inhibitor of complement (Hic), in the pspC locus of type 3 pneumococci. Unlike PspC proteins in other serotypes, Hic is anchored to the cell wall by means of an LPXTG motif, and the overall sequence homology to various PspC proteins is low. However, the NH(2)-terminal region showed significant homology to the NH(2)-terminal region of several PspC proteins. A fragment of Hic, covering this homologous region, was expressed as a glutathione S-transferase (GST) fusion protein. GST:Hic(39-261) bound radiolabeled factor H and inhibited binding of factor H to pneumococci of different serotypes. Interaction kinetics between GST:Hic(39-261) and factor H were studied with surface plasmon resonance and showed a high affinity binding (K(A) = 5 x 10(7), K(D) = 2.3 x 10(-)(8)). Mutant pneumococci lacking Hic showed no absorption of factor H in human plasma and no binding of radiolabeled factor H, suggesting that Hic is responsible for factor H-binding in type 3 pneumococci. Factor H-dependent inhibition of the alternative pathway was not diminished by the presence of GST:Hic(39-261). In addition, an intrinsic inhibitory effect of Hic is suggested.

Characterization of a genetic element carrying the macrolide efflux gene mef(A) in Streptococcus pneumoniae.

The mef(A) gene from a clinical isolate of Streptococcus pneumoniae exhibiting the M-type resistance to macrolides was found to be part of the 7,244-bp chromosomal element Tn1207.1, which contained 8 open reading frames. orf2 encodes a resolvase/invertase, and orf5 is a homolog of the macrolide-streptogramin B resistance gene msr(SA).

GeneSyn: a tool for detecting conserved gene order across genomes.

UNLABELLED: GeneSyn is a software tool that allows automatic detection of conserved gene order from annotated genomes. AVAILABILITY: Available free of charge for Unix/Linux/Cygwin platforms at ftp://159.149.110.11/pub/GeneSyn_1.0/ SUPPLEMENTARY INFORMATION: ftp://159.149.110.11/pub/GeneSyn_1.0/

The role of IgM anti-HBc in the etiologic diagnosis of HBsAg-positive acute and chronic hepatitis.

HBsAg, HBeAg, anti-HBc, anti-HBs, IgM anti-HAV, total and IgM anti-delta (RIA) and IgM anti-HBc (ELISA) have been determined on sera of 72 male patients with acute hepatitis (68 HBsAg positive and 4 anti-HBc-positive) at the onset of the disease and at 2, 4 and 6 months thereafter, and of 77 patients with HBsAg-positive chronic active hepatitis. The results indicate that testing for IgM anti-HBc in acute hepatitis is necessary to identify cases of hepatitis B even in the absence of positivity for HBsAg and/or HBeAg. HBsAg-positive cases, negative for IgM anti-HBc, were due to delta superinfection of chronic carriers of HBsAg. Recovery was always associated with negativity of IgM anti-HBc; IgM anti-HBc persistence was not found in all cases evolved to chronicity. In chronic hepatitis cases positivity for IgM anti-HBc was found only in 39% of the anti-delta-negative and only in 5.5% of the anti-delta-positive cases.

Macrolide efflux genes mef(A) and mef(E) are carried by different genetic elements in Streptococcus pneumoniae.

Susceptibilities to macrolides were evaluated in 267 Streptococcus pneumoniae isolates, of which 182 were from patients with invasive diseases and 85 were from healthy carriers. Of the 98 resistant isolates, 20 strains showed an M phenotype and carried mef. Strains that carried both mef(A) and mef(E) were found: 17 strains carried mef(A) and 3 carried mef(E). The characteristics of the strains carrying the mef genes and the properties of the mef-containing elements were studied. Strains carrying mef(A) belonged to serotype 14, were susceptible to all the antibiotics tested except erythromycin, and appeared to be clonally related by pulsed-field gel electrophoresis (PFGE). The three mef(E) strains belonged to different serotypes, showed different susceptibility profiles, and did not appear to be related by PFGE. The sequences of a fragment of the mef-containing element, which encompassed mef and the msr(A) homolog, were identical among the three mef(E)-positive strains and among the three mef(A)-positive strains, although there were differences between the sequences for the two variants at 168 positions. In all mef(A)-positive strains, the mef element was inserted in celB, which led to impairment of the competence of the strains. In line with insertion of the mef(E) element at a different site, the competence of the mef(E)-positive strains was maintained. Transfer of erythromycin resistance by conjugation was obtained from two of three mef(A) strains but from none of three mef(E) strains. Due to the important different characteristics of the strains carrying mef(A) or mef(E), we suggest that the distinction between the two genes be maintained.

Competence for genetic transformation in encapsulated strains of Streptococcus pneumoniae: two allelic variants of the peptide pheromone.

The nucleotide sequence of comC, the gene encoding the 17-residue competence-stimulating peptide (CSP) of Streptococcus pneumoniae (L. S. Havarstein, G. Coomaraswamy, and D. A. Morrison, Proc. Natl. Acad. Sci. USA 92:11140-11144, 1995) was determined with 42 encapsulated strains of different serotypes. A new allele, comC2, was found in 13 strains, including the type 3 Avery strain, A66, while all others carried a gene (now termed comC1) identical to that originally described for strain Rx1. The predicted mature product of comC2 is also a heptadecapeptide but differs from that of comC1 at eight residues. Both CSP-1 and CSP-2 synthetic peptides were used to induce competence in the 42 strains; 48% of the strains became competent after the addition of the synthetic peptide, whereas none were transformable without the added peptides.

The puzzle of zmpB and extensive chain formation, autolysis defect and non-translocation of choline-binding proteins in Streptococcus pneumoniae.

Choline-binding proteins (CBPs) from Streptococcus pneumoniae are involved in several important processes. Inactivation of zmpB, a gene that encodes a surface-located putative zinc metalloprotease, in a S. pneumoniae serotype 4 strain was recently reported to reveal a composite phenotype, including extensive chain formation, lysis defect and transformation deficiency. This phenotype was associated with the lack of surface expression of several CBPs, including the major autolysin LytA. LytA, normally 36 kDa in size, was reported to form an SDS-resistant 80 kDa complex with CinA. ZmpB was therefore proposed to control translocation of CBPs to the surface, possibly through the proteolytic release of CBPs (and RecA) from CinA. Based on the use of 12 independent mariner insertions in the zmpB gene of the well-characterized R6 laboratory strain, we could not confirm several of these observations. Our zmpB mutants: (i) did not form chains; (ii) lysed normally in the presence of deoxycholate, which indicates the presence of a functional autolysin; (iii) transformed at normal frequency; and (iv) contained bona fide CinA and LytA species. Polymorphism of ZmpB between R6 and the serotype 4 isolate could not account for the discrepancy, as inactivation of zmpB (through replacement by transposon-inactivated zmpB R6 alleles) in the latter strain did not affect separation of daughter cells and autolysis. The conflicting observations could be explained by our finding that the reportedly serotype 4 zmpB 'mutant' differed from its S. pneumoniae parent in lacking capsule and in exhibiting characteristic traits of the Streptococcus viridans group, including resistance to optochin.