The "one-out, all-out" principle entails the risk of imposing unnecessary restoration costs: a study case in two Mediterranean coastal lakes

The Water Framework Directive uses the "one-out, all-out" principle in assessing water bodies (i.e., the worst status of the elements used in the assessment determines the final status of the water body). In this study, we assessed the ecological status of two coastal lakes in Italy. Indices for all biological quality elements used in transitional waters from the Italian legislation and other European countries were employed and compared. Based on our analyses, the two lakes require restoration, despite the lush harbor seagrass beds, articulated macrobenthic communities and rich fish fauna. The "one-out, all-out" principle tends to inflate Type I errors, i.e., concludes that a water body is below the "good" status even if the water body actually has a "good" status. This may cause additional restoration costs where they are not necessarily needed. The results from this study strongly support the need for alternative approaches to the "one-out, all-out" principle.

Evaluation of a web-based network for reproducible T2* MRI assessment of iron overload in thalassemia

PURPOSE

To build and evaluate a national network able to improve the care of thalassemia, a genetic disorder in haemoglobin synthesis often associated with iron accumulation in a variety of organs, due to the continuous blood transfusions.

METHODS

The MIOT (Myocardial Iron Overload in Thalassemia) network is constituted by thalassemia and magnetic resonance imaging (MRI) centers. Thalassemia centers are responsible for patient recruitment and collection of anamnestic and clinical data. MRI centers have been equipped with a standardized acquisition technique and an affordable workstation for image analysis. They are able to perform feasible and reproducible heart and liver iron overload assessments for a consistent number of thalassemia patients in a robust manner. All centers are linked by a web-based network, configured to collect and share patient data.

RESULTS

On 30th March 2008, 695 thalassemia patients were involved in the network. The completion percentage of the patient records in the database was 85+/-6.5%. Six hundred and thirteen patients (88%) successfully underwent MRI examination. Each MRI center had a specific absorption capacity that remained constant over time, but the network was capable of sustaining an increasing number of patients due to continuous enrollment of new centers. The patient's comfort, assessed as the mean distance from the patient home locations to the MRI centers, significantly increased during the network's evolution.

CONCLUSION

The MIOT network seems to be a robust and scalable system in which T2* MRI-based cardiac and liver iron overload assessment is available, accessible and reachable for a significant and increasing number of thalassemia patients in Italy (about 420 per year), reducing the mean distance from the patient locations to the MRI sites from 951km to 387km. A solid, wide and homogeneous database will constitute an important scientific resource, shortening the time scale for diagnostic, prognostic and therapeutical evidence-based research on the management of thalassemia disease.

Molecular modeling and functional characterization of the monomeric primase-polymerase domain from the Sulfolobus solfataricus plasmid pIT3

A tri-functional monomeric primase-polymerase domain encoded by the plasmid pIT3 from Sulfolobus solfataricus strain IT3 was identified using a structural-functional approach. The N-terminal domain of the pIT3 replication protein encompassing residues 31-245 (i.e. Rep245) was modeled onto the crystallographic structure of the bifunctional primase-polymerase domain of the archaeal plasmid pRN1 and refined by molecular dynamics in solution. The Rep245 protein was purified following overexpression in Escherichia coli and its nucleic acid synthesis activity was characterized. The biochemical properties of the polymerase activity such as pH, temperature optima and divalent cation metal dependence were described. Rep245 was capable of utilizing both ribonucleotides and deoxyribonucleotides for de novo primer synthesis and it synthesized DNA products up to several kb in length in a template-dependent manner. Interestingly, the Rep245 primase-polymerase domain harbors also a terminal nucleotidyl transferase activity, being able to elongate the 3'-end of synthetic oligonucleotides in a non-templated manner. Comparative sequence-structural analysis of the modeled Rep245 domain with other archaeal primase-polymerases revealed some distinctive features that could account for the multifaceted activities exhibited by this domain. To the best of our knowledge, Rep245 typifies the shortest functional domain from a crenarchaeal plasmid endowed with DNA and RNA synthesis and terminal transferase activity.

Transcriptional analysis of the genetic element pSSVx: differential and temporal regulation of gene expression reveals correlation between transcription and replication

pSSVx from Sulfolobus islandicus strain REY15/4 is a hybrid between a plasmid and a fusellovirus. A systematic study performed by a combination of Northern blot analysis, primer extension, and reverse transcriptase PCR revealed the presence of nine major transcripts whose expression was differentially and temporally regulated over the growth cycle of S. islandicus. The map positions of the RNAs as well as the clockwise and the anticlockwise directions of their transcription were determined. Some genes were clustered and appeared to be transcribed as polycistronic messengers, among which one long transcriptional unit comprised the genes for the plasmid copy number control protein ORF60 (CopG), ORF91, and the replication protein ORF892 (RepA). We propose that a termination readthrough mechanism might be responsible for the formation of more than one RNA species from a single 5' end and therefore that the nine different RNAs corresponded to only seven different transcriptional starts. Three transcripts, ORF76 and two antisense RNAs, countertranscribed RNA1 (ctRNA1) and ctRNA2, were found to be specifically expressed during (and hence correlated to) the phase in which the pSSVx copy number is kept under stringent control, as they were completely switched off upon the onset of the induction of replication.

pIT3, a cryptic plasmid isolated from the hyperthermophilic crenarchaeon Sulfolobus solfataricus IT3

The plasmid pIT3 (4,967 bp) was isolated from the hyperthermophilic archaeon Sulfolobus solfataricus, strain IT3. The completely sequenced plasmid contains six open reading frames (ORFs), the largest (ORF915) spanning more than half of the plasmid and encoding a putative protein with significant similarity to the helicase domain of viral and plasmid primase proteins, as well as to the newly described archaeal primase-polymerase domain. A small ORF, (ORF80), located upstream of this putative polymerase, encodes a putative copy number control protein. Specific transcripts corresponding to the ORF80 and ORF915, were detected by Northern blot analyses, and their transcriptional start sites were determined by primer extension. Moreover, the transfer and the maintenance of the plasmid in other Sulfolobus strains were demonstrated to be effective and stable.

Cross-presentation of a human malaria CTL epitope is conformation dependent

Little is known about the role of conformation on the antigen processing by antigen presenting cells. Using a well-defined antigen containing two disulfide bridges, the synthetic C-terminal fragment 282-383 derived from Plasmodium falciparum circumsporozoite protein (PfCS 282-383), we show that the reduced form is presented in vitro more efficiently than its oxidized counterpart, inducing stronger CTL recognition. In addition, only the reduced form can be presented by the TAP independent T2 cell line. Thus, the reduced form is processed by TAP dependent and independent pathways.

Development of a genetic system for hyperthermophilic Archaea: expression of a moderate thermophilic bacterial alcohol dehydrogenase gene in Sulfolobus solfataricus

The Escherichia coli/Sulfolobus solfataricus shuttle vector pEXSs was used as a cloning vehicle for the gene transfer and expression of two bacterial genes in Sulfolobus solfataricus. The alcohol dehydrogenase (adh) from the moderate thermophilic Bacillus stearothermophilus (strain LLDR) and a mutagenised version encoding a less thermostable ADH enzyme were the selected genes. S. solfataricus adh promoter and aspartate aminotransferase terminator were used to drive the heterologous gene expression and to guarantee the correct termination of the transcripts, respectively. The constructed vectors were found to be able to carry these 'passenger' genes without undergoing any rearrangements. The active transcription of bacillar mRNAs was ascertained in vivo by RT-PCR. Transformed S. solfataricus expressed functional exogenous ADHs that showed unaffected kinetic and chemical-physical features.

Flow cytometric microsphere-based immunoassay: analysis of secreted cytokines in whole-blood samples from asthmatics

The ability of flow cytometry to resolve multiple parameters was used in a microsphere-based flow cytometric assay for the simultaneous determination of several cytokines in a sample. The flow cytometer microsphere-based assay (FMBA) for cytokines consists of reagents and dedicated software, specifically designed for the quantitative determination of cytokines. We have made several improvements in the multiplex assay: (i) dedicated software specific for the quantitative multiplex assay that processes data automatically, (ii) a stored master calibration curve with a two-point recalibration to adjust the stored curve periodically, and (iii) an internal standard to normalize the detection step in each sample. Overall analytical performance, including sensitivity, reproducibility, and dynamic range, was investigated for interleukin-4 (IL-4), IL-6, IL-10, IL-12, gamma interferon (IFN-gamma), and tumor necrosis factor alpha. These assays were found to be reproducible and accurate, with a sensitivity in the picograms-per-milliliter range. Results obtained with FMBA correlate well with commercial enzyme-linked immunosorbent assay data (r > 0.98) for all cytokines assayed. This multiplex assay was applied to the determination of cytokine profiles in whole blood from atopic and nonatopic patients. Our results show that atopic subjects' blood produces more IL-4 (P = 0.003) and less IFN-gamma (P = 0.04) than the blood of nonatopic subjects. However, atopic asthmatic subjects' blood produces significantly more IFN-gamma than that of atopic nonasthmatic subjects (P = 0.03). The results obtained indicate that the FMBA technology constitutes a powerful system for the quantitative, simultaneous determination of secreted cytokines in immune diseases.

Simultaneous detection of multiplex-amplified human immunodeficiency virus type 1 RNA, hepatitis C virus RNA, and hepatitis B virus DNA using a flow cytometer microsphere-based hybridization assay

The feasibility of performing a multiplex assay for the detection of human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) RNAs and hepatitis B virus (HBV) DNA is demonstrated. This assay is based (i) on the coamplification of a 142-bp fragment from the gag region of the HIV-1 genome and a 142-bp HIV-1 quantitation standard fragment, a 244-bp fragment from the 5' noncoding region of the HCV genome, and a 104-bp fragment from the pre-C and C gene regions of the HBV genome, using three sets of specific primers; (ii) on the capacity of these four biotinylated PCR products to hybridize to their specific oligonucleotide probe-coated microspheres; and (iii) on the ability of the flow cytometer to discriminate between distinct fluorescent-microsphere categories. Absence of cross-hybridization between the unrelated oligonucleotide probes and PCR products generated by the multiplex reverse transcription-PCR (RT-PCR) and the highly sensitive detection method allowed us to assess unambiguously the HIV-1 viral load and the infectious status of 35 serologically well-established clinical samples and 20 seronegative blood donor plasma samples tested. The results indicate that multiplex RT-PCR and flow cytometer microsphere-based hybridization assays, when combined, provide a rapid, sensitive, and specific method for the quantitation and detection of the major viral agents of infectious diseases in a single plasma sample.

Relationships between natural T cells, atopy, IgE levels, and IL-4 production

BACKGROUND

Th2 cells govern allergic disorders. Mechanisms leading to the Th2 commitment are dominated by the requirement of IL-4. A potential source of this triggering IL-4 could be the CD4 + subset of a small population of T cells, natural T (NT) cells. Indeed, this subset is involved in IgE responses in mice and produces promptly high amounts of IL-4 in both mice and man.

METHODS

NT cells were identified in peripheral blood by flow cytometry with antibodies against Valpha24 and Vbeta11, recognizing the T-cell receptor specific for NT cells. Simultaneous staining with anti-CD3, anti-CD4, or anti-CD8 antibodies was performed. The frequency of NT cells in man was studied according to the presence of atopy defined by the positivity of skin tests, according to total IgE levels in serum, and according to IL-4 concentration of whole-blood culture supernatants determined by a flow cytometer microsphere-based assay.

RESULTS

Seventy subjects were included, of whom 30 were atopic. The number of CD4+ NT cells was higher in atopics than in nonatopics (P=0.009). This number was correlated to the total IgE levels (r = 0.34, P = 0.03). In addition, the number of CD4 + NT cells, but also of CD8 + NT cells, was correlated to the levels of IL-4 (r=0.71, P=0.01, and r=0.6, P=0.03, respectively).

CONCLUSIONS

These results show that the number of NT cells, particularly the CD4+ subset, is related to atopy, IL-4 production, and IgE levels. Therefore, this population of T cells is likely to play a role in the Th2 commitment initiating atopic diseases.

Effects of subclinical bovine paratuberculosis on in-vitro polymorphonuclear neutrophil migration

Migration of polymorphonuclear neutrophils (PMNs) [unstimulated or stimulated with zymosan-activated serum (ZAS)] from 18 cows was measured in a microwell filter assay. Of these animals, 10 were subclinically infected with Mycobacterium paratuberculosis and shown by culture to be excreting the organism in the faeces; the remaining eight were clinically normal and negative for M. paratuberculosis on faecal culture. PMN "net migration" (stimulated minus unstimulated cells) of the infected cows was significantly lower than that of the uninfected cows. Migration of unstimulated cells in the infected cows did not differ from that in the uninfected cows. It would therefore appear that the infection influenced only the migratory response of the ZAS-stimulated cells. 1999 Harcourt Publishers Ltd.

Antigenic mapping of human thyroglobulin--topographic relationship between antigenic regions and functional domains

We characterized 26 mAb to human thyroglobulin to obtain a topographic map of the thyroglobulin antigenic surface. Among these mAb, three bind thyroglobulin peptides that are located in the primary sequence of thyroglobulin at either the N terminus or in the middle part of the molecule, three bind thyroglobulin via epitopes comprising the thyroid-hormone moiety, and three bind thyroglobulin through epitopes involved in the recognition of the molecule by its receptor. The 18 remaining mAb bind thyroglobulin through undetermined epitopes; most of these epitopes are resistant to trypsinization. We used two methods to map the antigenic regions of thyroglobulin: all 26 mAb were grouped, by means of cross-inhibition experiments, in 11 clusters corresponding to 11 antigenic regions of the thyroglobulin surface; by means of thyroglobulin peptides of decreasing size, obtained by time-controlled tryptic digestion, we analyzed the relative distance between pairs of epitopes in sandwich immunoassays. By combining these two methods, we organized most of the 11 antigenic regions on a topographic representation of the thyroglobulin surface. This new topographic map of thyroglobulin led us to some unexpected features of the thyroglobulin structure. First, antigenic region 8 located far from the N-terminal region is in close contact with two remote N-terminal antigenic regions (1 and 4), both involved in hormone formation. This antigenic region is likely to play a role in the correct positioning of hormonogenic tyrosines so as to optimize iodination-coupling reactions. Secondly, the domain involved in the binding of thyroglobulin to its receptor, probed by three mAb, is shared by two distinct mid-molecule antigenic regions, one being the main autoantigenic region of thyroglobulin.

Autoantibodies to thyroid hormones: the role of thyroglobulin

Autoantibodies against thyroid hormones (THAA) are frequently detected in the sera of patients with thyroid disorders together with autoantibodies against thyroglobulin (TGAA). THAA are considered to be a subset of TGAA, but alternative possibilities have not been excluded. We hypothesize that if THAA arise through an immune response to iodothyronines carried by circulating thyroglobulin (hTg), THAA should be found together with autoantibodies against the peptide backbone of hTg (TPAA) close to the hormone-forming sites. We measured TPAA in 178 serum samples, obtained from healthy subjects and patients with thyroid disorders, using two hormone-forming peptides isolated from hTg. The occurrence of TPAA was much lower than that of TGAA. Autoantibodies to the hormone-rich peptide, P3, were significantly more common than autoantibodies to the hormone-poor peptide, P1 (111/178 = 62.3% for TGAA versus 21/178 = 11.8% for anti-P3 TPAA and 7/178 = 3.9% for anti-P1 TPAA). The presence of autoantibodies to thyroid hormones was investigated in 25 TPAA+ and 26 TPAA- sera. THAA were found more frequently in TPAA+ sera (10/25 = 40% for TPAA+ and 4/26 = 15.3% for TPAA-). Correlation analysis shows that the anti-P3, but not the anti-P1 binding activity, correlates positively with the THAA-binding activity (P < 0.001 for anti-T4 THAA; P < 0.01 for anti-T3 THAA). Specificity of anti-P3 TPAA indicates that a subset of the anti-P3 antibodies is directed against the thyroid hormone moiety and another subset is directed against the peptide backbone near the hormone-forming peptide, according to our hypothesis. These results indicate that the THAA response is an anti-hTg response directed, in a significant number of cases, against the hormone-forming site included in the P3 peptide. This response seems to be elicited by either native hormone-rich hTg or by hTg fragments.