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Asthma and rhino-conjunctivitis are common chronic diseases in childhood. In this cross-sectional study, we performed a gene association analysis with current asthma and rhino-conjunctivitis in a cohort of Sicilian children aged 10–15 years. Overall, our findings reveal the importance of different genetic variants at 4p14, 16p12.1, 17q12, 6p12.2 and 17q21.1, identifying possible candidate genes responsible for susceptibility to asthma and rhino-conjunctivitis.

An inconsistency in the nomenclature used for the rapidly mutating (RM) Y-chromosomal short tandem repeat (Y-STR) marker DYS449 was noted in the above paper. In this paper, the DYS449 allele nomenclature introduced by Ballantyne et al. was used, instead of that described by Redd et al. and subsequently adopted by the International RM Y-STR User Group and in the AMPFlSTR® YFiler Plus kit.

The gastrin-releasing peptide receptor (GRPR) was implicated for the first time in the pathogenesis of Autism spectrum disorders (ASD) by Ishikawa-Brush et al. [Ishikawa-Brush et al. (1997): Hum Mol Genet 6: 1241-1250]. Since this original observation, only one association study [Marui et al. (2004): Brain Dev 26: 5-7] has further investigated, though unsuccessfully, the involvement of the GRPR gene in ASD. With the aim of contributing further information to this topic we have sequenced the entire coding region and the intron/exon junctions of the GRPR gene in 149 Italian autistic patients. The results of this study led to the identification of four novel point mutations, two of which, that is, C6S and L181F, involve amino acid changes identified in two patients with ASD and Rett syndrome, respectively. Both the leucine at position 181 and the cysteine at position 6 are strongly conserved in vertebrates. C6S and L181F mutant proteins were expressed in COS-7 and BALB/3T3 cells, but they did not affect either GRP's binding affinity or its potency for stimulating phospholipase C-mediated production of inositol 1,4,5-trisphosphate. In summary, our results do not provide support for a major role of the GRPR gene in ASD in the population of patients we have studied. However, there is a potential role of C6S and L181F mutations on GRPR function, and possibly in the pathogenesis of the autistic disorders in the two patients.

Recently introduced rapidly mutating Y-chromosomal short tandem repeat (RM Y-STR) loci, displaying a multiple-fold higher mutation rate relative to any other Y-STRs, including those conventionally used in forensic casework, have been demonstrated to improve the resolution of male lineage differentiation and to allow male relative separation usually impossible with standard Y-STRs. However, large and geographically-detailed frequency haplotype databases are required to estimate the statistical weight of RM Y-STR haplotype matches if observed in forensic casework. With this in mind, the Italian Working Group (GEFI) of the International Society for Forensic Genetics launched a collaborative exercise aimed at generating an Italian quality controlled forensic RM Y-STR haplotype database. Overall 1509 male individuals from 13 regional populations covering northern, central and southern areas of the Italian peninsula plus Sicily were collected, including both "rural'' and "urban'' samples classified according to population density in the sampling area. A subset of individuals was additionally genotyped for Y-STR loci included in the Yfiler and PowerPlex Y23 (PPY23) systems (75% and 62%, respectively), allowing the comparison of RM and conventional Y-STRs. Considering the whole set of 13 RM Y-STRs, 1501 unique haplotypes were observed among the 1509 sampled Italian men with a haplotype diversity of 0.999996, largely superior to Yfiler and PPY23 with 0.999914 and 0.999950, respectively. AMOVA indicated that 99.996% of the haplotype variation was within populations, confirming that genetic-geographic structure is almost undetected by RM Y-STRs. Haplotype sharing among regional Italian populations was not observed at all with the complete set of 13 RM Y-STRs. Haplotype sharing within Italian populations was very rare (0.27% non-unique haplotypes), and lower in urban (0.22%) than rural (0.29%) areas. Additionally, 422 father-son pairs were investigated, and 20.1% of them could be discriminated by the whole set of 13 RM Y-STRs, which was very close to the theoretically expected estimate of 19.5% given the mutation rates of the markers used. Results obtained from a high-coverage Italian haplotype dataset confirm on the regional scale the exceptional ability of RM Y-STRs to resolve male lineages previously observed globally, and attest the unsurpassed value of RM Y-STRs for male-relative differentiation purposes. (C) 2014 Elsevier Ireland Ltd. All rights reserved.

The role of DNA damage in PCR processivity/fidelity is a relevant topic in molecular investigation of aged/forensic samples. In order to reproduce one of the most common lesions occurring in postmortem tissues, a new protocol based on aqueous hydrolysis of the DNA was developed in vitro. Twenty-five forensic laboratories were then provided with 3.0 μg of a trial sample (TS) exhibiting, in mean, the loss of 1 base of 20, and a molecular weight below 300 bp. Each participating laboratory could freely choose any combination of methods, leading to the quantification and to the definition of the STR profile of the TS, through the documentation of each step of the analytical approaches selected. The results of the TS quantification by qPCR showed significant differences in the amount of DNA recorded by the participating laboratories using different commercial kits. These data show that only DNA quantification "relative" to the used kit (probe) is possible, being the "absolute" amount of DNA inversely related to the length of the target region (r(2) = 0.891). In addition, our results indicate that the absence of a shared stable and certified reference quantitative standard is also likely involved. STR profiling was carried out selecting five different commercial kits and amplifying the TS for a total number of 212 multiplex PCRs, thus representing an interesting overview of the different analytical protocols used by the participating laboratories. Nine laboratories decided to characterize the TS using a single kit, with a number of amplifications varying from 2 to 12, obtaining only partial STR profiles. Most of the participants determined partial or full profiles using a combination of two or more kits, and a number of amplifications varying from 2 to 27. The performance of each laboratory was described in terms of number of correctly characterized loci, dropped-out markers, unreliable genotypes, and incorrect results. The incidence of unreliable and incorrect genotypes was found to be higher for participants carrying out a limited number of amplifications, insufficient to define the correct genotypes from damaged DNA samples such as the TS. Finally, from a dataset containing about 4500 amplicons, the frequency of PCR artifacts (allele dropout, allele drop-in, and allelic imbalance) was calculated for each kit showing that the new chemistry of the kits is not able to overcome the concern of template-related factors. The results of this collaborative exercise emphasize the advantages of using a standardized degraded DNA sample in the definition of which analytical parameters are critical for the outcome of the STR profiles.

We have explored the role of the distal switch II region of the yeast RAS2 protein in determining the response to the nucleotide exchange factor CDC25. We first constructed yeast tester strains in which the deletion of the chromosomal CDC25, RAS1, and RAS2 genes, in combination with the chromosomal suppressor CRI4, resulted in detectable phenotypes in vivo and in vitro. Phenotypes included impaired growth at 37 degrees C, defective glucose-induced cyclic AMP signaling, and low adenylyl cyclase activity of membrane preparations. Tester strains were subsequently used for the reintroduction of various combinations of wild-type and mutated RAS2 and CDC25 genes by genetic techniques, as well as for in vitro reconstitution assays with the corresponding proteins. CDC25 restored both growth and glucose-induced cyclic AMP signaling in the presence, but not in the absence of wild-type RAS2. A gene encoding a RAS2 protein with a mutationally altered switch II region was expressed but was ineffective in reintegrating exchange factor-dependent responses in vivo. Wild-type, but not mutagenically altered, RAS2 proteins were stimulated by exchange factors in vitro. We conclude that the conserved distal switch II region is required for CDC25-dependent activation of RAS.

Review on SELE (selectin E, endothelial adhesion molecule 1), with data on DNA, on the protein encoded, and where the gene is implicated.

The dnaK homologue of Streptomyces coelicolor A3(2) strain M145 has been cloned and sequenced. Nucleotide sequence analysis of a 2.5-kb region revealed an open reading frame (ORF) encoding a predicted DnaK protein of 618 amino acids (Mr = 66 274). The dnaK coding sequence displays extreme codon bias and shows a strong preference for CGY and GGY, for Arg and Gly codons, respectively. The predicted DnaK sequence has a high Lys:Arg ratio which is not typical of streptomycete proteins. The region immediately downstream from dnaK contains an ORF for a GrpE-like protein; the predicted start codon of grpE overlaps the last two codons of dnaK, indicating that the two genes are translationally coupled. This organisation diners from that reported for other prokaryotes.

The SCH9 yeast gene, that was previously identified as a suppressor of cdc25 and ras1- ras2-ts temperature-sensitive mutants, encodes a putative protein kinase that positively regulates the progression of yeast cells through the G1 phase of the cell cycle. We have determined the structure of the SCH9 transcription unit, using primer extension and S1 mapping techniques. The corresponding mRNA included an unusually long 5' region of more than 600 nucleotides preceding the major open reading frame (ORF). While the latter corresponded to a protein of 824 amino acids, an upstream open reading frame (uORF) within the 5' leader could potentially encode a 54 amino acid peptide. To investigate the role of the AUGs within the uORF, we engineered chimaeric plasmid vectors in which SCH9 sequences including the promoter, the mRNA leader and the first 514 nucleotides of the major ORF were fused in-frame with beta-galactosidase-coding sequences. Upon introduction into yeast cells, the fusion protein was efficiently expressed. However, mutational disruption of the uORF using oligonucleotide-directed mutagenesis did not affect the level of expression of the fusion protein. This indicates that regulatory mechanisms in Saccharomyces cerevisiae prevent upstream AUGs within the SCH9 mRNA leader sequence from influencing translation from downstream initiation codons.

Islet transplantation, since the 90’s, has been resulting to be one of the best successful example of human cell therapy. Nevertheless, islet isolation procedure is not completely standardized; in fact, more than fifty percent of islets procedures don’t arrive to their transplantation. This is due both to the variability of donor’s pancreas and to an unpredictable enzymatic blend efficiency. Enzymes used in pancreas digestion are extracted from Clostridium histolyticum bacteria and digest several substrates. In particular they have strong collagenolytic activity compared to vertebrate collagenases. However, several impediments persist in human islet isolation success probably due to the variability in composition and concentration of collagenases used during the digestion phase‏. In islets isolation’s process neutral protease is also used and plays an important role. However, it should be considered as double-edged sword: it contributes to accelerate the tissue dissociation but, sometimes, its action could result decreased in islet yield, through their fragmentation, breakdown, inactivation‏. Proteases’ activities cannot be preciously adjusted in a narrow range since it doesn’t exist any approach showing the best possible dosage and composition of enzymes that can be used in a successful process of human islets pancreas extraction. At the moment, the available data on commercial enzymatic activity are not sufficient to predict their efficiency in the process of pancreas digestion and consequently it is very difficult to select which enzyme batches can be successfully used. For these reasons we apply to generate an innovative evaluation assay to select enzymes useful in islet pancreas isolation procedure.

We have previously shown that a conserved glycine at position 82 of the yeast RAS2 protein is involved in the conversion of RAS proteins from the GDP- to the GTP-bound form. We have now investigated the role of glycine 82 and neighbouring amino acids of the distal switch II region in the physiological mechanism of activation of RAS. We have introduced single and double amino acid substitutions at positions 80-83 of the RAS2 gene, and we have investigated the interaction of the corresponding proteins with a yeast GDP dissociation stimulator (SDC25 C-domain). Using purified RAS proteins, we have found that the SDC25-stimulated conversion of RAS from the GDP-bound inactive state to the GTP-bound active state was severely impaired by amino acid substitutions at positions 80-81. However, the rate and the extent of conversion from the GDP- to the GTP-bound form in the absence of dissociation factor was unaffected. The insensitivity of the mutated proteins to the dissociation factor in vitro was paralleled by an inhibitory effect on growth in vivo. The mutations did not significantly affect the interaction of RAS with adenylyl cyclase. These findings point to residues 80-82 as important determinants of the response of RAS to GDP dissociation factors. This suggests a molecular model for the enhancement of nucleotide release from RAS by such factors.

The extravasation of cancer cells is a key step of the metastatic cascade. Polymorphisms in genes encoding adhesion molecules can facilitate metastasis by increasing the strength of interaction between tumor and endothelial cells as well as impacting other properties of cancer cells. We investigated the Ser128Arg (a561c at the nucleotide level) polymorphism in the E-selectin gene in patients with metastatic colon cancer and its functional significance. Genotyping for a561c polymorphism was performed on 172 cancer patients and on an age-matched control population. The colon cancer group was divided into groups with (M+) and without observable metastasis (M−). For in vitro functional assays, Huvec transfected cells expressing wild-type (WT) or the S128R variant of E-selectin were established to study in vitro binding ability and signal transduction processes of T84 colon cancer cell line. Our results demonstrated that the Arginine128 allele was more prevalent in the M+ group than in the M− group or normal controls (p < 0.005; odds ratio, 1.56; 95% confidence interval (CI) 1.16–1.92; p < 0.001, odds ratio = 1.65; CI = 1.24–1.99, respectively). In vitro, S128R E-selectin transfected Huvec cells, supported increased adhesion as well as increased cellular signaling of T84 cancer cells compared to WT E-selectin and mock-transfected Huvec cells. These findings suggest that the E-selectin S128R polymorphism can functionally affect tumor-endothelial interactions as well as motility and signaling properties of neoplastic cells that may modulate the metastatic phenotype. © 2007 Wiley-Liss, Inc.

Within the framework of a FISH screening protocol to detect cryptic subtelomeric rearrangements in autistic disorder (AD), a patient bearing three copies of the subtelomeric portion of the q arm of chromosome 13 has been identified. Beside AD, the patient also has severe mental retardation and displays several dysmorphic features. Further FISH analyses revealed that the trisomy was caused by the translocation of a 13q subtelomeric fragment to the acrocentric tip of one chromosome 21 [46,XY.ish der(21) t(13;21) (q34;p13)(D13S1825+)]. Gene dosage experiments carried out with three multiallelic polymorphisms of the subtelomeric region of chromosome 13q showed that the putative length of the triplicate region does not exceed 300 kb about, that is, the distance from telomere to the first normally inherited marker. In addition, gene dosage analysis performed on the derivative chromosome 21, did not reveal loss of the most telomeric protein-encoding genes on 21p. The potential relationship between a postulated increased expression of genes on 13q34 and the complex phenotype in this trisomic patient is discussed.

We have screened 143 Sicilian (Italian) families with one autistic child to verify, by a linkage disequilibrium approach, the involvement of the 2q31.1 region in the cause of the disease in these families. Our study design includes the use of intrafamilial association to prevent a population stratification bias and ethnic homogeneity of the sample. The results of our analysis provided suggestive evidence of the occurrence of transmission disequilibrium between autism and the D2S2188 polymorphism in Sicilian TRIO families, a finding which provides further and independent support to the hypothesis of the existence of a susceptibility gene (or genes) for autism on chromosome 2q.

Lack of association of HOXA1 and HOXB1 mutations and autism in Sicilian (Italian) patients

RAS proteins regulate growth and differentiation in evolutionarily distant systems such as vertebrates and yeast (for reviews, see Tamanoi, 1988; Gibbs and Marshall, 1989; Broach and Deschenes, 1990). At the moleular level, a key function of the yeast RAS1 and RAS2 proteins (collectively referred to as RAS) is to positively regulate the production of cyclic AMP at the onset of the G1 phase of the cell cycle (Toda et al., 1985; De Vendittis et al., 1986). At this stage, RAS proteins are transiently activated by the noncovalent binding of a GTP molecule. Reversal of the effect occurs by the hydrolytic splitting of the ’γ-phosphate of GTP, that leaves a functionally inactive RASGDP complex, thus terminating cyclic AMP synthesis. While the mechanism and functional role of the binding of either GTP or GDP to RAS has been investigated in detail, less is known about the physiological role of covalent modifications of RAS involving phosphorylation of serine residues. A major obstacle to the analysis of the functional relevance of this covalent modification is represented by the very low concentration of RAS proteins into the cell. To bypass this difficulty, we have taken advantage of a mutated form of the RAS2 gene encoding a protein that can be overexpressed at ligh levels. This gene, which is called ras2-ts1, was previously isolated as an attenuated form of the wild-type RAS2 gene (Fasano et al., 1988). The corresponding ras2-tsl protein, that is functional at 30 °C while becoming nonfunctional at 37 °C, was easily labelled metabolically with radioactive 32P under the form of orthophosphate, and was immunoprecipitated with anti-RAS specific antibodies. We have used this protein to explore RAS2 phosphorylation in cells at different stages of the cell cycle.

In pancreatic islets purification, for cell therapy applications, the major enzymes used are obtained from Clostridium hystoliticum; class I and class II collagenases (COLL G and COLL H). They are used in a defined tissue dissociation enzyme (TDE) mixtures together neutral protease (Dispase) or thermolysin (Thermostable Neutral Protease). The TDE mixtures were in part responsible for the success of the Edmonton protocol; however, just to now, people working in islets purification found discrepancy in an application to another one. This variability in application see in the enzymatic blend composition the higher accused, such as the contamination from endotoxines due to extractive production methods to obtain them. Using electrophoresis and gelatin zymography approaches; together densitometry evaluation assays we compared in composition, stability and auto-digestion processes C. hystoliticum collagenases, Neutral protease and Thermolysin from Roches and Serva. Moreover, we have investigated about the stability of analyzed enzymes when they are in solution in relation to their storage processes at different temperatures (-20°C; 0°C and r.t.); such as, concerning their digestive activity when applied at different temperatures (working temperatures: 25°C; 30°C; 37°C and 42 °C). Our results shown an heterogeneous composition of the different blend of collagenases from Roches and Serva, furthermore, heterogeneity is observed by lot to lot; on the other hand, we have found several more proteins and/or fragments respect the HPLC profiles publish by vendors. In gelatin zymographyes several digestive bands were catalytic active showing very high complex degradative patterns. Additionally, in neutral protease from Serva contaminants with gelatinolytic activities were detected; not in thermolysin. In stability experiments we investigated an inactivation/auto-digestive processes of analyzed enzymes; nevertheless, at different working temperatures, a more stable activity of analyzed molecules at 25°C were observed; activity that can be compared to that detectable at 37°C at the beginning of digestive process, at this temperature in the times inactivation enzymes were observed. These data take together strongly imply a not controlled digestive processes due to several contaminants present in the blends and to autocatalytic processes. Moreover, the presence of low molecular weight gelatine/degradative activities mean the impossibility to control the islets digestion process due to aspecific catalytic activities. Generation of recombinant collagenases probably could be of help to overcome the variability in the extractive processes. In pancreatic islets isolation for cell therapy the major enzymes used are obtained from Clostridium hystoliticum: class I and class II collagenases. They are used in a defined tissue dissociation enzyme mixture together with neutral protease (Dispase) or thermolysin (Thermostable Neutral Protease). However, just to now, people working in islets production found variable outcomes in isolation procedures mainly due to large variability in enzymatic blend composition and efficacy. Using electrophoresis and gelatin zymography approaches together with densitometry evaluation assays we compared the composition, stability and auto-digestion processes of C. hystoliticum collagenases, Neutral protease and Thermolysin from Roches and Serva. Moreover, we have assessed: –the stability of enzymes when they are in solution at different temperatures (-20 C; 0 C and room temperature); –their digestive activity when applied at different working temperatures (25 C; 30 C; 37 C and 42 C). Our results shown a heterogeneous composition of the different enzymatic blend enzymes analyzed. Furthermore, heterogeneity is observed among different batch enzymes; we found several more proteins and/or fragments compare to HPLC profiles published by vendors. In gelatin zymographyes several digestive bands were catalytic, showing very high complex degradative patterns, in part active even in condition of calcium deprivation. Additionally, in neutral protease from Serva (and not in Thermolysin) contaminants with gelatinolytic activities were detected. An auto-digestive/inactivation processes of enzymes occurred at different working temperatures, reduced by lowering temperature up to 25 C. These data taken together strongly imply a not controlled digestive processes due to several contaminants in enzyme blends and to autocatalytic processes. Moreover, the presence of low molecular weight gelatine/degradative activities obstacles the possibility to control islet digestion due to aspecific catalytic activities. Generation of recombinant collagenases probably could be of help to overcome the variability in the extractive processes.

In pancreatic islets purification, for cell therapy applications, the major enzymes used are obtained from Clostridium hystoliticum; class I and class II collagenases (Coll-G and Coll-H). In a well defined composition Coll-G/Coll-H together enzymes working on hydrophobic amminoacid, the neutral protease (Dispase) or the thermolysin (Thermostable Neutral Protease), are used in Langerhans islets purification. By electrophoresis and gelatin zymography approaches, in combination to densitometry quantitative valuation we have compared in composition, stability and autodigestion processes C. hystoliticum collagenases, Neutral protease and Thermolysin from two different producers, Roche and Serva. On analyzed enzymes we have, also, explored about their stability when in solution in relation to storage processes at different temperatures (-20°C; 0°C and r.t.) and on their type-I collagen degradation activity when used at different temperatures (working temperatures: 25°C; 30°C; 37°C and 42 °C). Our results revealed an heterogeneous composition of the different blend of collagenases respect the HPLC profiles publish by vendors and an heterogeneity by lot to lot; moreover, we observed contamination from other enzymes in analysed samples. In fact, in gelatin zymographyes several digestive bands were catalytic active showing very high complex degradative patterns. Additionally, neutral protease from Serva contains gelatinolytic activities; not detected in thermolysin Roche. These data strongly suggest that a not controlled digestive processes can be associate to contaminants present in the blends and also due to auto-catalytic processes. In particular, the presence of low molecular weight gelatine/degradative activities denote the islets digestion process can not be control. Generation of recombinant collagenases probably could be the solution to overcome the variability in the extractive processes.

One of the best successful example of cell therapy is represented by islet transplantation since the '90. However islet isolation methods are not completely standardized yet. More than half of isolation procedures failed to isolate adequate islets for transplantation, due to variable pancreas condition, and to unpredictable enzymatic blend efficiency. Enzymes used for pancreas digestion are purified from Clostridium histolyticum; these enzymes has a broad substrate specificity and potent collagenolytic activity compared to vertebrate collagenases. However, a major obstacle in human islet isolation successful is due to the variability in composition and concentration of the collagenases used during digestion phase‏. Another protease involved in islet isolation is the neutral protease, it plays an important role, however, should be considered as a double-edged sword: it accelerates tissue dissociation but, on the other hand, it could result in a decrease in islet yield, through islet fragmentation and breakdown‏. Therefore, protease activity should be carefully adjusted in a narrow range, in fact, there are not sufficient studies showing optimal dosage and composition of proteases that must be use in human pancreas islets extraction procedure. The current parameters available to characterize enzymatic blend are not predictive their efficiency in pancreas digestion and therefore are not useful to select which enzyme bathes can be successfully used for islet isolation purpose. Our goal is in direction to maximize the yield of functional islets; therefore we set up a new in vitro method to better in vitro characterize enzymatic blend before its use in human pancreas. In our experimental approach we have growth human immortalized cells (ECV-304) or human islets, obtained using a canonical extractive approach, within a 3-D type-I collagen gel in 96 wells plate. After one culture day, cells and/or islets were treated with different commercial enzymes (Liberase, Serva NB1 premium grade, Collagenase type P, Thermolysin, Neutral proteases) from different batches at different concentrations and for different times. Digestion of 3-D type-I collagen fibril gels were monitored by optical dense absorption to a fix l; while, morphology of released cells and/or islets were valued by confocal microscopy analyses. Cells were immunostained about expression of some adhesion molecules, like: integrins, cadherins and associated molecules, catenins, to appreciate cells morphology and islets aggregation modifications. Moreover, using SYTO 13/Et/Br in viability assayes we have quantify the toxiticy or not of tested enzymes in the different experimental conditions. We found that Neutral proteases is less pure and more toxic than Thermolysin: it has collagenase activity and it significantly decrease cell viability. Isolated cells by Neutral proteases appeared to be 77,5 % died. Even viable cells showed an alterated morphology with an impairment of cell to cell communications. We, also, observed an higher efficiency in extraction by Serva NB1 compared to Liberase and Collagenasi type P, used in the same experimental conditions. By this in vitro method we were also able to compare the minimal active enzyme concentration of different enzyme blends: we found that Liberase has its best value as nuber of extracted cell/alive cells in 130 mg/ml; while, in actual protocols is used to 1,3 mg/ml. Preliminary results showed a correlation between data achieved in cell lines with those of human islets, thus confirming the predictive role of this method for the selection of enzymes for human pancreas digestion purpose.