Bacterial isolates from Argentine Pampas and their ability to degrade glyphosate

Glyphosate is a synthetic phosphonate compound characterized by a carbon‑phosphorus bond. Glyphosate based herbicides (GBH) are widely distributed in most of the economically productive lands in which crop production is mainly based on glyphosate-resistant genetically modified plants. Naturally, glyphosate is remediated by soil microorganisms, which accelerate its degradation. Technology based on microorganisms is considered highly efficient, low-cost and eco-friendly to remediate contaminated environments, denoting the importance of characterizing new bacterial strains able to degrade glyphosate to perform its bioremediation. In this work, 13 different bacterial strains able to grow in GBH as only phosphorous source were isolated from different environmental samples from the Argentine vastly productive glyphosate-resistant soybean crop area. These strains were identified and they belong to the genera Acinetobacter, Achromobacter, Agrobacterium, Ochrobactrum, Pantoea and Pseudomonas. Their ability to grow and consume GBH, glyphosate or the aminomethylphosphonic acid (AMPA), another phosphonate derived from glyphosate degradation, was evaluated. The best degradation performance was observed for bacteria from the genera Achromobacter, Agrobacterium and Ochrobactrum. The genome of the highly efficient GBH degrader Agrobacterium tumefaciens CHLDO was sequenced revealing the presence of a phn cluster, responsible for phosphonate metabolization. Expression analysis of A. tumefaciens CHLDO phn genes in the presence of 1.5 mM GBH compared to inorganic phosphorous showed that most of them are highly expressed during growth in the presence of the herbicide, suggesting a strong participation of phn cluster in GBH degradation. The importance of discovering new bacterial strains and the value of deciphering molecular determinants of GBH degradation give promising tools for bioremediation techniques to be used in glyphosate-contaminated environments is discussed.

Fatal respiratory infection due to ST308 VIM-1-producing Pseudomonas aeruginosa in a lung transplant recipient: case report and review of the literature

Background

Data regarding the prevalence of metallo-β-lactamases (MBLs) among Pseudomonas aeruginosa isolates in cystic fibrosis patients are scarce. Furthermore, there is limited knowledge on the effect of MBL production on patient outcomes. Here we describe a fatal respiratory infection due to P. aeruginosa producing VIM-type MBLs in a lung transplant recipient and the results of the subsequent epidemiological investigation.

Case presentation

P. aeruginosa isolates collected in the index patient and among patients temporally or spatially linked with the index patient were analyzed in terms of antibiotic susceptibility profile and MBL production. Whole-genome sequencing and phylogenetic reconstruction were also performed for all P. aeruginosa isolates producing VIM-type MBLs. A VIM-producing P. aeruginosa strain was identified in a lung biopsy of a lung transplant recipient with cystic fibrosis. The strain was VIM-1-producer and belonged to the ST308. Despite aggressive treatment, the transplant patient succumbed to the pulmonary infection due to the ST308 strain. A VIM-producing P. aeruginosa strain was also collected from the respiratory samples of a different cystic fibrosis patient attending the same cystic fibrosis center. This isolate harbored the blaVIM-2 gene and belonged to the clone ST175. This patient did not experience an adverse outcome.

Conclusions

This is the first description of a fatal infection due to P. aeruginosa producing VIM-type MBLs in a lung transplant recipient. The circulation of P. aeruginosa isolates harboring MBLs pose a substantial risk to the cystic fibrosis population due to the limited therapeutic options available and their spreading potential.

Targeted genotyping by sequencing: a new way to genome profile the cat

Targeted GBS is a recent approach for obtaining an effective characterization for hundreds to thousands of markers. The high throughput of next-generation sequencing technologies, moreover, allows sample multiplexing. The aims of this study were to (i) define a panel of single nucleotide polymorphisms (SNPs) in the cat, (ii) use GBS for profiling 16 cats, and (iii) evaluate the performance with respect to the inference using standard approaches at different coverage thresholds, thereby providing useful information for designing similar experiments. Probes for sequencing 230 variants were designed based on the Felis_catus_8.0. 8.0 genome. The regions comprised anonymous and non-anonymous SNPs. Sixteen cat samples were analysed, some of which had already been genotyped in a large group of loci and one having been whole-genome sequenced in the 99_Lives Cat Genome Sequencing Project. The accuracy of the method was assessed by comparing the GBS results with the genotypes already available. Overall, GBS achieved good performance, with 92-96% correct assignments, depending on the coverage threshold used to define the set of trustable genotypes. Analyses confirmed that (i) the reliability of the inference of each genotype depends on the coverage at that locus and (ii) the fraction of target loci whose genotype can be inferred correctly is a function of the total coverage. GBS proves to be a valid alternative to other methods. Data suggested a depth of less than 11× is required for greater than 95% accuracy. However, sequencing depth must be adapted to the total size of the targets to ensure proper genotype inference.

Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe

European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non-steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.

Environmental Bacteria Involved in Manganese(II) Oxidation and Removal From Groundwater

The presence of iron (Fe) and manganese (Mn) in groundwater is an important concern in populations that use it as source of drinking water. The ingestion of high concentrations of these metals may affect human health. In addition, these metals cause aesthetic and organoleptic problems that affect water quality and also induce corrosion in distribution networks, generating operational and system maintenance problems. Biological sand filter systems are widely used to remove Fe and Mn from groundwater since they are a cost-effective technology and minimize the use of chemical oxidants. In this work, the bacterial communities of two biological water treatment plants from Argentina, exposed to long term presence of Mn(II) and with a high Mn(II) removal efficiency, were characterized using 16S rRNA gene Illumina sequencing. Several selective media were used to culture Mn-oxidizing bacteria (MOB) and a large number of known MOB and several isolates that have never been reported before as MOB were cultivated. These bacteria were characterized to select those with the highest Mn(II) oxidation and biofilm formation capacities and also those that can oxidize Mn(II) at different environmental growth conditions. In addition, studies were performed to determine if the selected MOB were able to oxidize Mn(II) present in groundwater while immobilized on sand. This work allowed the isolation of several bacterial strains adequate to develop an inoculum applicable to improve Mn(II) removal efficiency of sand filter water treatment plants.

Analysis of Some Factors Effecting Survival in Malignant Gliomas

Many factors, including the histological aspect, are known to effect the survival of patients with malignant gliomas. The relation between survival and diagnoses such as primary and secondary glioblastoma, anaplastic astrocytoma, etc., is not definitely clear. In 324 malignant gliomas the relationship between survival and age, sex, tumor pathology, occurrence of lymphoplasmacytic infiltrations, and size of the examined specimen was studied. Preoperative intervals of primary and secondary glioblastomas do not differ; anaplastic astrocytomas show definitely longer preoperative intervals and slightly but not significantly longer postoperative patient survival. The correlations are discussed, focusing on importance of knowing the survival times of untreated cases in order to evaluate the efficacy of chemotherapeutic drugs in malignant gliomas.

Virtual crossmatch in kidney transplantation

BACKGROUND

The Luminex Single-Antigen Beads (LSA) assay allows an accurate detection and characterization of preexisting donor-specific antibodies (DSA) in kidney transplant candidates. But the ability of LSA to detect quite low levels of antibodies makes it hard to correctly predict crossmatch results in donor selection. In this study we retrospectively analyzed the accuracy of our virtual crossmatch (v-XM) protocol, which was used for selection of potential kidney transplant recipients, in predicting the results of actual crossmatch (a-XM) in cadaver-donor renal transplantation. We also investigated correlation between negative a-XM results and strength/specificity of preformed DSA.

METHODS

The correlation between negative v-XMs and a-XMs performed in 2007-2012 at the Regional Transplant Center of the Lazio Region, Italy, was analyzed. In carrying out v-XM, the donor HLA molecules against which patients showed LSA-detected DSA with normalized mean fluorescence intensity (MFI)≥5,000 were considered to be "unacceptable DSA," and LSA-DSA showing MFI<5,000 were defined as "acceptable DSA." All cadaver donors had been typed for HLA-A, -B, -DR, and -DQB molecules by sequence-specific primer methods. On the basis of a negative v-XM, we performed 507 a-XMs between serum samples from 256 renal transplant candidates and T/B lymphocytes from 302 cadaver donors with the use of both complement-dependent cytotoxicity (CDC) and flow cytometry (FC) methods.

RESULTS

The v-XM negative results showed good correlation with both CDC and FC a-XMs (97% and 90%, respectively). The sensitivity of v-XM was 100%; this high value was related to the lack of false-negative DSA results. The limited specificity with both techniques (CDC-XM, 74%; FC-XM, 79%) was due to the presence of "acceptable" and/or anti-DQA/DPB DSA in some patient sera used to perform the a-XMs. During the study period, 171 (67%) of the 256 sensitized patients received a kidney transplant: 30% of these had "acceptable DSA" and/or anti-DQA/DPB DSA. No antibody-mediated rejection due to preformed HLA-DSA was observed.

CONCLUSIONS

Our v-XM protocol showed high sensitivity in predicting donor-recipient immunologic compatibility. The results of this study also demonstrated the importance of evaluating DSA strength for implementing v-XM results in the selection of kidney transplant recipients. Moreover, the finding of anti-DQA/DPB DSA, especially in serum samples that gave positive results with the use of both CDC and FC a-XMs, highlights the importance of defining all of the donor HLA molecules to perform an accurate v-XM.

An Overview of Proteomics Tools for Understanding Plant Defense Against Pathogens

Plant diseases are responsible for important losses in crops and cause serious impacts in agricultural production. In the last years, proteomics has been used to examine plant defense responses against pathogens. Such studies may be pioneer in the generation of crops with enhanced resistance. In this review, we focus on proteomics advances in the understanding of host and non-host resistance against pathogens.

The dual nature of trehalose in citrus canker disease: a virulence factor for Xanthomonas citri subsp. citri and a trigger for plant defence responses

Xanthomonas citri subsp. citri (Xcc) is a bacterial pathogen that causes citrus canker in susceptible Citrus spp. The Xcc genome contains genes encoding enzymes from three separate pathways of trehalose biosynthesis. Expression of genes encoding trehalose-6-phosphate synthase (otsA) and trehalose phosphatase (otsB) was highly induced during canker development, suggesting that the two-step pathway of trehalose biosynthesis via trehalose-6-phosphate has a function in pathogenesis. This pathway was eliminated from the bacterium by deletion of the otsA gene. The resulting XccΔotsA mutant produced less trehalose than the wild-type strain, was less resistant to salt and oxidative stresses, and was less able to colonize plant tissues. Gene expression and proteomic analyses of infected leaves showed that infection with XccΔotsA triggered only weak defence responses in the plant compared with infection with Xcc, and had less impact on the host plant's metabolism than the wild-type strain. These results suggested that trehalose of bacterial origin, synthesized via the otsA-otsB pathway, in Xcc, plays a role in modifying the host plant's metabolism to its own advantage but is also perceived by the plant as a sign of pathogen attack. Thus, trehalose biosynthesis has both positive and negative consequences for Xcc. On the one hand, it enables this bacterial pathogen to survive in the inhospitable environment of the leaf surface before infection and exploit the host plant's resources after infection, but on the other hand, it is a tell-tale sign of the pathogen's presence that triggers the plant to defend itself against infection.

A Molecular survey of Anaplasma spp., Rickettsia spp., Ehrlichia canis and Babesia microti in foxes and fleas from Sicily

Fleas (Insecta: Siphonaptera) are obligate bloodsucking insects, which parasitize birds and mammals, and are distributed throughout the world. Several species have been implicated in pathogen transmission. This study aimed to monitor red foxes and the fleas isolated from them in the Palermo and Ragusa provinces of Sicily, Italy, as these organisms are potential reservoirs and vectors of pathogens. Thirteen foxes (Vulpes vulpes) and 110 fleas were analysed by polymerase chain reaction (PCR) to detect DNA of the pathogens Ehrlichia canis, Babesia microti, Rickettsia spp., Anaplasma phagocytophilum, Anaplasma platys, Anaplasma marginale and Anaplasma ovis. In the foxes, A. ovis was detected in only one animal, whereas the prevalence of the E. canis pathogen was 31%. B. microti and Rickettsia spp. were not detected. Of all of the collected fleas, 75 belonged to the species Xenopsylla cheopis, 32 belonged to Ctenocephalides canis, two belonged to Ctenocephalides felis and one belonged to Cediopsylla inaequalis. In the fleas, the following pathogens were found: A. ovis (prevalence 25%), A. marginale (1%), A. phagocytophilum (1%), Rickettsia felis (2%) and E. canis (3%). X. cheopis was the flea species most frequently infected with Anaplasma, in particular A. ovis (33%), A. marginale (1%) and A. phagocytophilum (1%). Both C. felis exemplars were positive for R. felis. E. canis was found in the lone C. inaequalis and also in 3% of the X. cheopis specimens. No fleas were positive for B. microti or A. platys. As foxes often live in proximity to domestic areas, they may constitute potential reservoirs for human and animal parasites. Further studies should be performed on fleas to determine their vectorial capacity.

Prevalence of IgM and IgG antibodies to West Nile virus among blood donors in an affected area of north-eastern Italy, summer 2009

Following reports of West Nile neuroinvasive disease in the north-eastern area of Italy in 2009, all blood donations dating from the period between 1 August and 31 October 2009 in the Rovigo province of the Veneto region were routinely checked to exclude those with a positive nucleic acid test for West Nile virus (WNV). Only one of 5,726 blood donations was positive (17.5 per 100,000 donations; 95% confidence interval (CI): 0.4–97.3). In addition, a selection of 2,507 blood donations collected during the period from 20 July to 15 November 2009 were screened by ELISA for IgG and IgM antibodies against WNV. A positive result was received for 94 of them. The positive sera were further evaluated using immunofluorescence and plaque reduction neutralisation test (PRNT), in which only 17 sera were confirmed positive. This corresponds to a prevalence of 6.8 per 1,000 sera (95% CI: 4.0–10.9). In a case-control study that matched each of the 17 PRNT-positive sera with four negative sera with the same date of donation and same donation centre, we did not find a significant association with age and sex of the donor; donors who worked mainly outdoors were significantly more at risk to have a positive PRNT for WNV.

Genome sequence analysis of the first human West Nile virus isolated in Italy in 2009

In 2009, six new human cases of West Nile neuroinvasive disease (WNND) were identified in Veneto region, following the six cases already reported in 2008. A human West Nile virus (WNV) isolate was obtained for the first time from an asymptomatic blood donor. Whole genome sequence of the human WNV isolate showed close phylogenetic relatedness to the Italy-1998-WNV strain and to other WNV strains recently isolated in Europe, with the new acquisition of the NS3-Thr249Pro mutation, a trait associated with avian virulence, increased virus transmission, and the occurrence of outbreaks in humans.

Genome sequence analysis of the first human West Nile virus isolated in Italy in 2009

In 2009, six new human cases of West Nile neuroinvasive disease (WNND) were identified in Veneto region, following the six cases already reported in 2008. A human West Nile virus (WNV) isolate was obtained for the first time from an asymptomatic blood donor. Whole genome sequence of the human WNV isolate showed close phylogenetic relatedness to the Italy-1998-WNV strain and to other WNV strains recently isolated in Europe, with the new acquisition of the NS3-Thr249Pro mutation, a trait associated with avian virulence, increased virus transmission, and the occurrence of outbreaks in humans.

Where is West Nile fever? Lessons learnt from recent human cases in northern Italy

West Nile disease in humans has been detected for the first time in Italy in two regions, Emilia-Romagna and Veneto. We conclude that also West Nile fever cases should be specifically targeted by surveillance.

Where is West Nile fever? Lessons learnt from recent human cases in northern Italy

West Nile disease in humans has been detected for the first time in Italy in two regions, Emilia-Romagna and Veneto. Surveillance subsequently set up in Veneto detected a case of West Nile neuroinvasive disease and a few asymptomatic infections, but no case of West Nile fever. We conclude that also West Nile fever cases should be specifically targeted by surveillance.

Identification of the very uncommon allele HLA-Cw*0716 in a Caucasian renal transplant recipient: extension of the exon 4 sequence

This report describes the unknown exon 4 sequence of the rare human leukocyte antigen-Cw*0716 allele, identified in a Caucasian renal transplant recipient from Italy. This sequence is identical to the Cw*070101 allele, and this result allowed us to confirm the hypothesis of the generation of Cw*0716 allele by an interallelic recombination event between Cw*0701/0706/0718 and Cw*020202 allele.

Analysis of Y-chromosomal SNP haplogroups and STR haplotypes in an Algerian population sample

The distribution of Y-chromosomal single nucleotide polymorphism (SNP) haplogroups and short tandem repeat (STR) haplotypes was determined in a sample of 102 unrelated men of Arab origin from northwestern Algeria (Oran area). A total of nine different haplogroups were identified by a panel of 22 binary markers. The most common haplogroups observed in the Algerian population were E3b2 (45.1%) and J1 (22.5%). Y-STR typing by a 17-loci multiplex system allowed 93 haplotypes to be defined (88 were unique). Striking differences in the allele distribution and gene diversity of Y-STR markers between haplogroups could be found. In particular, intermediate alleles at locus DYS458 specifically characterized the haplotypes of individuals carrying haplogroup J1. All the intermediate alleles shared a common repeat sequence structure, supporting the hypothesis that the variant originated from a single mutational event.

Renal Allograft Immune Response Is Influenced by Patient and Donor Cytokine Genotypes

This study investigated the impact of specific cytokine genotypes on the incidence of acute rejection episodes (ARE), chronic graft dysfunction (CGD), and anti-HLA donor-specific antibody (DS-Ab) production in 86 renal transplant recipients and 70 cadaveric donors. A PCR-SSP method was performed for the analysis of polymorphisms in TNF-alpha, IL-6, TGF-beta, IL-10, and IFN-gamma cytokines. DS-Ab monitoring of sera was performed using a FCXM analysis. Observed cytokine frequencies for patients and donors were not significantly different from the expected frequencies under Hardy-Weinberg equilibrium conditions. The evaluation in recipients revealed a higher frequency of DS-Ab-positive patients among the TNF-alpha high (50.0% vs 25.7%), and for the IL-10 cytokine a greater incidence of ARE-positive patients (35.8% vs 18.2%) with the high + intermediate, compared with the low genotype. The combined effect of these 2 genotypes predisposed to DS-Abs (71.4% vs 25.3%; P = 0.02; odds ratio [OR] = 7.37). As for the TGF-beta1 cytokine, we observed a higher number of CGD-positive patients among high compared with intermediate producers (14.3% vs 0%; P = .050). The analysis of donors revealed a significantly lower incidence of ARE-positive patients among recipients whose donors were carriers of the high IL-6 G/G-genotype compared with the G/C+C/C-genotypes (16.7% vs 41.2%; P = .03), suggesting a protective effect of the G/G genotype on ARE and a predisposing role of donor (-174)allele C. In addition, we noted an association between the IFN-gamma low A/A-genotype and a higher incidence of ARE (42.1% vs 0%; P = .002) and DS-Ab production (47.4% vs 12.5%; P = .02) compared with high producers.

Identification of the uncommon allele HLA-A*7403 in a Caucasian renal transplant cadaveric donor: extension of the exon 4 sequence

This report describes the unknown exon 4 sequence of the rare A*7403 allele, identified in a Caucasian renal transplant cadaveric donor from Italy. This sequence is identical to that of the only known A*7401 exon 4, and this result allowed us to confirm the hypothesis of the generation of A*7403 allele from the ancestor A*7402 by point mutation in exon 2.

14th International HLA and Immunogenetics Workshop: Report on the Prospective Chronic Rejection Project

An international collaborative study of 45 transplant centers was undertaken at the 14th International HLA (human leukocyte antigen) and Immunogenetics Workshop to see if HLA antibodies detected posttransplant are predictive of chronic graft failure. With the newly developed assay, MICA (major histocompatibility complex class I-related chain A) antibodies were also measured and their effect analyzed. Total of 5219 sera from patients who were more than 6 months posttransplant with functioning graft were tested for HLA antibodies by enzyme-linked immunosorbent assay, flow cytometry, or Luminex. HLA antibodies were found in 27.2% of kidney patients, 23.6% in the liver, 52.7% in the heart, and 21.7% in the lung. The method of antibody testing did not have a marked influence on the frequency of antibodies detected. MICA antibodies were detected in 15% of kidney patients, 30% of heart patients, and 31% of liver patients. Among 948 kidney patients who had HLA antibodies, 7.3% had rejected their graft within 1 year of testing, compared with 1.7% in 2615 patients without HLA antibodies (P= 0.8 x 10(-17)). Death occurred in 1.4% of total kidney patients and did not correlate to the presence of antibodies. We conclude that patients with posttransplant HLA antibodies indeed have a higher rate of chronic graft failure and that posttransplant antibodies are predictive of chronic rejection.

14th International HLA and Immunogenetics Workshop Prospective Chronic Rejection Project: a three-year follow-up analysis

The three-year follow-up of 4,144 patients of the 14th International Workshop Prospective Chronic Rejection study has reinforced the evidence that post-transplant HLA antibodies are predictive of long-term graft loss. Three years after a single testing for HLA antibodies, 10% of kidney recipients who were antibody-positive had lost their grafts, in contrast to only 5% of antibody-negative patients (p<0.0001). The adverse effect of post-transplant antibodies on graft survival was also observed in lung, heart, and liver transplants. Donor-specific antibodies and 'strong' non-DSA had stronger association with graft loss than 'moderate' non-DSA. Periodic antibody monitoring, combined with specificity and strength analysis, would help in the early identification of allograft recipients who are at high risk of graft failure.

Graft failure due to hemolytic uremic syndrome recurrence

The hemolytic uremic syndrome (HUS) is a severe disease characterized by microangiopathic hemolytic anemia, thrombocytopenia, and acute renal failure. We herein report our experience with a 43-year-old female patient who underwent a second cadaveric kidney transplantation in February 2005, for adult-onset HUS. The first renal transplantation, which was performed in 1996, required removal after 3 weeks for probable recurrence of HUS. The immunosuppressive regimen for the second transplant included basiliximab, tacrolimus, mycophenolate mofetil, and steroids. On postoperative day (POD) 7, she received steroid treatment for an acute rejection episode with improved renal function. On POD 19 due to worsening renal function, a graft biopsy showed HUS recurrence, thus we instituted hemodialysis and then plasmapheresis treatments. At two months after transplantation, the patient continued under plasmapheresis treatment due to clinical evidence of HUS. On POD 80, cytomegalovirus infection was diagnosed and intravenous gancyclovir treatment started for 3 weeks. After 110 days from transplant, a deterioration in renal function was evident: the graft was swollen and painful with Doppler ultrasound showing patency of both the renal artery and vein but, low blood flow. After 2 weeks of hemodialysis, the patient underwent transplantectomy. In adult-onset HUS the recurrence rate reduces graft survival, particularly among patients undergoing second transplantation.

Y-chromosomal STR haplotypes in Sicily

Eight Y-chromosomal short tandem repeats (STRs)-DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393 and DYS385-were typed in a population sample (n=255) of unrelated Sicilian males from nine different towns on the main island and from the island of Pantelleria.

Population data for Y-chromosome STR haplotypes from Piedmont (Italy)

Eight Y-chromosome STR loci (DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393 and DYS385) were analysed in a sample of 236 unrelated males from four towns of Piedmont (Trino, Biella, Cavaglià, Postua). One hundred and fifty six different haplotypes were observed and 55 of them were not previously observed in the Y-STR Haplotype Reference Database (http://www.ystr.org/).

Evidence that vitamin D3 reverses age-related inflammatory changes in the rat hippocampus

One of the major challenges in neuroscience is to identify the changes which accompany aging and which contribute to the well-documented age-related deterioration in cognitive function. This is a particular challenge in the light of the vast array of reported changes, which include morphological changes like synaptic and perhaps cell loss, alteration in membrane composition and the resultant changes in function of membrane proteins, modulation of the hypothalamo–pituitary axis, impaired calcium homoeostatic mechanisms, alteration in enzyme function and decreased neurotransmitter release. In the past few years, evidence suggesting that an aged brain exhibits signs of oxidative stress and inflammatory stress has been accumulating, and recent evidence using microarray analysis has added support to this view. In this paper, we provide evidence to suggest that vitamin D3 acts as an anti-inflammatory agent and reverses the age-related increase in microglial activation and the accompanying increase in IL-1β (interleukin-1β) concentration.

Characterization of a novel HLA-Cw*02 variant, Cw*0208, in a Caucasian individual

We describe an additional HLA-Cw*02 variant, HLA-Cw*0208, which has been identified in a renal transplant recipient of Caucasian origin (Italy). After performing preliminary serological typing, we analyzed exons 2 and 3 of the HLA-C locus polymorphism by cloning the amplified DNA and using a sequence-based typing method. The new allele differs from Cw*020202 by one nucleotide substitution at nucleotide 61 (G-->A) of exon 2, which translates to a difference of one amino acid at residue 21 (His-->Arg) of the HLA-C heavy chain. We propose that Cw*0208 was generated by a random point mutation in codon 21 from the Cw*020202 allele, or through gene conversion of Cw*020202 with another allele, probably the Cw*1205 and Cw*1602 alleles.

The TDI-FP assay in human Y chromosome SNP haplotyping

One of the many commercial technologies for genotyping single nucleotide polymorphisms (SNPs) is template direct dye-terminator incorporation with fluorescence-polarization (TDI-FP assay). It is a single-base extension assay followed by reading the fluorescence polarization values in an appropriate instrument. We have evaluated the suitability of the TDI-FP technique to detect haploid uniparentally inherited DNA polymorphisms on the nonrecombining portion of the Y chromosome. A sample of 47 individuals has been genotyped for 8 Y chromosome biallelic markers. The SNP typing was blindly duplicated by the denaturing high-performance liquid chromatography (DHPLC) technique for comparison. In the cases under examination the TDI-FP assay was able to resolve an allelic state fully. Such a result showed 100% concordance indicating how efficiently the TDI assay can be used to genotype Y chromosome DNA SNPs. However, a percentage of indeterminate genotypes remained unresolved by simple visual inspection: it varied from 0% to 11% depending on the SNP locus and on the success of amplification. This is consistent with previous findings. A maximum likelihood classificatory analysis allowed some of the indeterminate genotypes to be assigned and some potentially misclassified samples to be identified. Their percentage remains relatively high despite retyping and therefore alternative techniques for these noncompliant situations are required.

Y-chromosomal STR haplotypes in a population sample from continental Greece, and the islands of Crete and Chios

Eight Y-chromosomal short tandem repeats (STRs)--DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393, and DYS385--were typed in a population sample (n = 113) of unrelated males from seven different regions of Greece (Macedonia, Thessaly, Epirus, Central Greece, Peloponnese, Crete Island, and Chios Island).

Accuracy of semiquantitative immunoenzymatic methods in quantitation of anti-topoisomerase I (Scl-70) antibodies

Reports of a possible correlation between anti-Scl-70 antibody concentration and clinical manifestations in systemic sclerosis patients have recently appeared in the scientific literature. The goal of our study was to evaluate, by means of a multicenter study, the analytical reliability of immunoassay systems in the quantitative measurement of Scl-70 antibodies. Three blind samples (H, M, L) at different anti-Scl-70 antibody concentrations, and a low concentration antibody serum (LPC) used as a common calibrator, were sent three times in a 6-month time span to 39 Italian clinical laboratories. Each laboratory was asked to calculate dosages following the enzyme-linked immunosorbent assay (ELISA) method they used and report the optical density values of each sample (ODs), of the cutoff serum provided by the manufacturer of the kit used (ODco) and of LPC (ODLPC). The overall analytical imprecision (between methods and between laboratories) of the three different determinations of the values respectively expressed in ODs, ODs/ODco and ODs/ODLPCratio was 47.1, 52.8 and 34.0% for sample H, 56.2, 47.4% and 34% for sample M and 84.6, 86.0 and 86.6% for sample L. The average intra-method analytical imprecision was, respectively, 20.7, 29.8 and 18.6% for sample H, 24.6, 26.5 and 19.3% for sample M, and 30.6, 28.1 and 20.2% for sample L. The commercial ELISA methods currently used to determine the presence of anti-Scl-70 autoantibodies show considerable differences in the quantitative determination. The best results for reproducibility analyses have been obtained when the values were expressed as a ratio between the ODs of the sample and of the common calibrator (ODs/ODLPC). Forward-looking clinical studies that can clarify the usefulness of quantitative determination of anti-Scl-70 antibodies in the monitoring of diffuse scleroderma patients can be performed only when standard serum with a known antibody concentration and calibration curves for quantitative ELISA measurements are made available.

1 Hz rTMS enhances extrastriate cortex activity in migraine: Evidence of a reduced inhibition?

We recently reported a paradoxical facilitatory effect of 1 Hz repetitive TMS (rTMS) on the primary visual cortex in migraine possibly due to the failure of inhibitory circuits, unable to be upregulated by low frequency rTMS. To investigate if inhibitory circuit dysfunction extends beyond striate cortex in migraine with aura, we studied the effects of 1 Hz rTMS over the right extrastriate cortex on perception of illusory contours in these patients. Low-frequency rTMS enhanced activity of extrastriate cortex in migraineurs, speeding up reaction times on illusory contour perception. This finding supports the view of a failure of inhibitory circuits also involving the extrastriate cortex in migraine with aura.

Illusory contours and specific regions of human extrastriate cortex: evidence from rTMS

Functional magnetic resonance imaging studies showed that perception of illusory contours is associated with extrastriate cortex activation prevailing on the right side. 1 Hz repetitive transcranial magnetic stimulation (rTMS) is able to induce lasting inhibition of cortical activity. The objective of the study was to investigate the role of extrastriate cortex in illusory contour perception inducing 1 Hz rTMS interference in healthy subjects. Eight healthy subjects underwent 1 Hz rTMS (600 pulses) through a figure-of-eight coil over right and left occipital cortex (O1 and O2 of 10/20 EEG system); sham magnetic stimulation on the same sites and right motor cortex rTMS (in three subjects) were given as control. Subjects performed a computerized task requiring perception of illusory and real contours of Kanizsa squares in baseline and after rTMS. After stimulus presentation the subject made a forced-choice decision about the regularity or irregularity of stimulus contour, by hitting as fast as possible one of two keys on the computer keyboard. Reaction times (RT) were measured. Right occipital stimulation significantly increased RT for illusory contour perception (vs. baseline, P < 0.05). No significant RT changes were observed in the other experimental conditions with respect to the baseline condition. It is concluded that 1Hz rTMS of right extrastriate cortex can disrupt perception of illusory contours and the effect appears to be side-specific, being evident only after right occipital stimulation. This study supports the critical role of right extrastriate cortex in illusory contour perception.

1 Hz repetitive transcranial magnetic stimulation of the unaffected hemisphere ameliorates contralesional visuospatial neglect in humans

The aim of the study was to investigate whether low-frequency repetitive transcranial magnetic stimulation (rTMS) over the unaffected hemisphere can ameliorate visuospatial neglect. We treated three right brain damaged patients with left neglect. 900 pulses (1 Hz frequency) were given over left posterior parietal cortex every other day for 2 weeks. Patients performed a computerized task requiring length judgement of prebisected lines, tachistoscopically presented for 150 ms. With respect to rTMS the task was given 15 days before, at the beginning, at the end and 15 days after. At these times patients performed also line bisection and clock drawing tasks. rTMS induced a significant improvement of visuo-spatial performance that remained quite unchanged 15 days after. Patients performance at Time 3 and 4 improved also as concerns line bisection and clock drawing tasks.

Autosomal microsatellite and mtDNA genetic analysis in Sicily (Italy)

DNA samples from 465 blood donors living in 7 towns of Sicily, the largest island of Italy, have been collected according to well defined criteria, and their genetic heterogeneity tested on the basis of 9 autosomal microsatellite and mitochondrial DNA polymorphisms for a total of 85 microsatellite allele and 10 mtDNA haplogroup frequencies. A preliminary account of the results shows that: a) the samples are genetically heterogeneous; b) the first principal coordinates of the samples are correlated more with their longitude than with their latitude, and this result is even more remarkable when one outlier sample (Butera) is not considered; c) distances among samples calculated from allele and haplogroup frequencies and from the isonymy matrix are weakly correlated (r = 0.43, P = 0.06) but such correlation disappears (r = 0.16) if the mtDNA haplogroups alone are taken into account; d) mtDNA haplogroups and microsatellite distances suggest settlements of people occurred at different times: divergence times inferred from microsatellite data seem to describe a genetic composition of the town of Sciacca mainly derived from settlements after the Roman conquest of Sicily (First Punic war, 246 BC), while all other divergence times take root from the second to the first millennium BC, and therefore seem to backdate to the pre-Hellenistic period. A more reliable association of these diachronic genetic strata to different historical populations (e.g. Sicani, Elymi, Siculi), if possible, must be postponed to the analysis of more samples and hopefully more informative uniparental DNA markers such as the recently available DHPLC-SNP polymorphisms of the Y chromosome.

A transcranial magnetic stimulation study evaluating methylprednisolone treatment in multiple sclerosis

OBJECTIVE

To investigate the efficacy of two different high doses of intravenous methylprednisolone (IVMP) during Multiple Sclerosis (MS) relapses.

BACKGROUND

Transcranial Magnetic Stimulation (TMS) is the most sensitive neurophysiological ascertainment to quantify motor disability, to follow the recovery from an MS relapse, and to detect the response to treatment.

DESIGN AND METHOD

Twenty-four clinically definite relapsing - remitting MS patients presenting a relapse were randomly assigned to a treatment for 5 days with IVMP 1 or 2 g/day. The response to treatment of each patient was evaluated through Expanded Disability Status Scale (EDSS), Medical Research Council (MRC) score, and TMS by means of motor evoked potential (MEP) parameters.

RESULTS

Motor threshold (MT), central motor conduction time (CMCT) and MRC showed a higher improvement with the highest dose of IVMP. Silent period and EDSS improved with both treatments.

CONCLUSION

The dose of 2 g/day of IVMP is more effective in MS relapse.

Genetic heterogeneity in five Italian regions: analysis of PAH mutations and minihaplotypes

Molecular analysis of 289 chromosomes has been performed in a cohort of phenylketonuria (PKU) patients whose ancestors lived in five Italian regions, Calabria, Campania, Piemonte, Puglia/Basilicata and Sicilia. Phenylalaninehydroxylase (PAH) gene mutations and minihaplotypes (combinations of PAH gene STR and VNTR systems) have been determined for 78.5 and 64%, respectively, of the chromosomes studied. 21 different minihaplotypes and 24 PKU mutations were found. Heterogeneity tests carried out for the frequencies of mutations and minihaplotypes show that the distribution of eight mutations and four minihaplotypes is statistically heterogeneous in the five Italian regions. Although the evolutionary rate of microsatellites or the age of these mutations is difficult to estimate with accuracy, our findings taken together show a genetic stratification of the Italian population. These results rule out allelic homogeneity of PKU at the molecular level between regions of Italy, yet minihaplotype data may be of practical use for a multistep approach to PAH gene genotyping.