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Background. The expression of BCR-ABL gene in Chronic Myeloid Leukemia (CML) is necessary for malignant transformation but the biologic basis of the progression from Chronic Phase (CP) to Blast Crisis (BC) is poorly understood. Aim. Identifying the genomic imbalances involved in the transition into BC, before clinical features, may provide diagnostic markers of progression; so we used SNP arrays to perform a high-resolution mapping of BC CML patients genomes. Methods. We analyzed 11 patients affected by BC CML disease. Genomic DNA were extracted from bone marrow or peripheral blood mononuclear cells archived both at the time of diagnosis and progression. SNP array-based karyotyping was carried out using Affymetrix GeneChip Human Mapping arrays. Copy number (CN) analysis was performed using Hapmap normal individuals as reference set and two different softwares. Results. After exclusion of genomic copy number variations (CNVs), the following results were achieved: five patients showed huge amplifications and deletions, ranging from 30Mb to 160Mb, on chromosomes 9, 7, 3 and 6. We also found several heterozygous micro-deletions and micro-amplifications spreading all over the genome. This analysis has identified abnormalities in genes involved in apoptosis (e.g., GADD45A, FOXO3A, GAS6), DNA damage response (e.g., MYST as known as Hmof, XRCC2), tumor suppression (e.g., C/EBPdelta, LATS1), chromatin regulation (e.g., HDAC9), and genes belonged to ABC transporters (e.g., ABCB1), ras family and transcriptional/translational factors (e.g., ETV1). Moreover were found copy number changes (gain/loss) in genes associated with malignancy, in particular TNFRSF17, MET, IGFBPL1, EVI1, PTENP1. Other alterations affected key pathways including cell cycle regulation and WNT signaling. Conclusions. The use of the genomic tool Genome-Wide Human SNP array allowed us to identify, at submicroscopic level, genetic lesions in patients affected by CML in BC. Our results will be further validated by real-time PCR for the altered genes involved key pathways, while sequencing and mutation analysis will be performed on the remaining allele of putative tumor suppressor genes to identify their residual activity. All these validations and the increased number of analyzed patients will provide new insights into the genetic profiling that lead disease progression from CP to BC and consequently new opportunities to develop specific target therapies.

By contrast with the extensive palaeolimnological studies carried out in North America and Europe, relatively few studies have described the anthropogenic and/or climate impacts in Patagonian lakes. We addressed these issues by analysing geochemistry, lithology, pigments and chironomid remains from sediment cores collected from Lake Hess (41° 22´ 20” S, 71° 44´ 0” W) located in the Nahuel Huapi National Park, in northern Patagonia. The aim of this study is to provide a palaeoenvironmental and climate reconstruction of the past ca. three centuries for this cold oligotrophic, quasi-pristine lake which receives melt waters from the Tronador ice cap. Chronology was based on 137Cs and 210Pb measurements of the upper sediments and the inferred sedimentation rate of 23.2 mg cm-2 y-1 (0.15 cm y-1) was consistent with both sets of measurements. The sediment from Lake Hess was rich in tephra deposits particularly evident in the lower part of the cores. Tephras are valuable to use for core correlation and can be traced through peaks in the magnetic susceptibility profiles. Results from the multiproxy analyses in the longest core (83 cm) identify three main phases of change. From the bottom up to 42 cm (ca. A.D.1800), the sediment is composed of light-grey organically rich clays. Both pigments and chironomids suggest variable trends in productivity and precipitation regime. At the end of the Little Ice Age chronozone (A.D. 1770-1850), pigment concentrations were very low. From 42 cm to ca. 25 cm (A.D. 1800-1940), the sedimentary record is composed of alternating black and dark organic-matter rich mud with variable amounts of macrophyte remains. Pigment concentrations and chironomid head capsule counts were also very low. These facies are composed of very fine plastic sediments with some faintly laminated intervals and an organic matter composition gradually decreasing towards the top of the zone. A sharp change occurs at 25 cm (ca. A.D. 1940) showing a strong increase in organic matter content, algal nutrients, and plant pigments together with a change in the chironomid assemblages. This might document a change in the trophic condition of the lake associated with changes in erosion/deposition rates. Although there are records of human impact in the area studied, involving the use of fires, most of the observed chemical and biological changes in Lake Hess sediment sequence were interpreted in terms of climate changes, especially to changes in moisture balance brought about by variations in the strength of the westerlies.

La evaluación por competencias es entendida como la capacidad de realización situada y afectada por el contexto en el que se desenvuelve el sujeto. Este enfoque requiere modificar concepciones y prácticas muy arraigadas. Al cursar Química, una competencia que los alumnos deben alcanzar se refiere al aprendizaje y la comprensión del lenguaje de la Química. En este dominio, una fórmula química emplea para su escritura dos sistemas de símbolos, el alfabeto y los números arábigos, pero siguiendo reglas diferentes al del uso en la vida cotidiana (comunicación verbal y matemática). En este trabajo nos proponemos reconocer algunos de los significados que las fórmulas tienen para los alumnos que inician el cursado de la asignatura, esto nos permitirá identificar estándares que ayudarán a definir en que nivel de competencia respecto del lenguaje químico se encuentran los alumnos.

The murine resistance gene Lsh/Ity/Bcg regulates activation of macrophages for tumour necrosis factor-alpha (TNF-alpha)-dependent production of nitric oxide mediating antimicrobial activity against Leishmania, Salmonella and Mycobacterium. As Lsh is differentially expressed in macrophages from different tissue sites, experiments were performed to determine whether interaction with extracellular matrix (ECM) proteins would influence the macrophage TNF-alpha response. Plating of bone marrow-derived macrophages onto purified fibrinogen or fibronectin-rich L929 cell-derived matrices, but not onto mannan, was itself sufficient to stimulate TNF-alpha release, with significantly higher levels released from congenic B10.L-Lshr compared to C57BL/10ScSn (Lshs) macrophages. Only macrophages plated onto fibrinogen also released measurable levels of nitrites, again higher in Lshr compared to Lshs macrophages. Addition of interferon-gamma (IFN-gamma), but not bacterial lipopolysaccharide or mycobacterial lipoarabinomannan, as a second signal enhanced the TNF-alpha and nitrite responses of macrophages plated onto fibrinogen, particularly in the Lshr macrophages. Interaction with fibrinogen and fibronectin also primed macrophages for an enhanced TNF-alpha response to leishmanial parasites, but this was only translated into enhanced nitrite responses in the presence of IFN-gamma. In these experiments, Lshr macrophages remained superior in their TNF-alpha responses throughout, but to a degree which reflected the magnitude of the difference observed on ECM alone. Hence, the specificity for the enhanced TNF-alpha responses of Lshr macrophages lay in their interaction with fibrinogen and fibronectin ECM, while a differential nitrite response was only observed with fibrinogen and/or IFN-gamma. The results are discussed in relation to the possible function of the recently cloned candidate gene Nramp, which has structural identity to eukaryote transporters and an N-terminal cytoplasmic proline/serine-rich putative SH3 binding domain.

A pilot study using Affymetrix Gene Chip(R) Porcine Genome Arrays was set up to evaluate the impact of time lags from death on gene expression profiling of porcine skeletal muscle at four post mortem times (up to 24 h) during the routine processing of fresh thighs. All post chip parameters and data analyses (Average background, Scale Factors, Percent Presence, 3'/5' ratios of beta-actin and glyceraldehyde-3-phosphase dehydrogenase control genes, RNA degradation diagnostics, principal component analysis, hierarchical clustering, mixed regression models with time effects) did not show any effect of post mortem time. Therefore, microarray data obtained from muscle specimens collected in a processing plan over a quite long period have the potential to identify treatments or pre mortem conditions without any potential bias derived from subtle RNA degradation. These results open new perspectives to develop and analyse gene expression biomarkers for pig production and product authentication.

Approximately 10%-15% of gastrointestinal stromal tumors (GISTs) in adults do not harbor any mutation in the KIT or PDGFRA genes (ie, KIT/PDGFRA wild-type GISTs). Recently, mutations in SDHB and SDHC (which encode succinate dehydrogenase subunits B and C, respectively) but not in SDHA and SDHD (which encode subunits A and D, respectively) were identified in KIT/PDGFRA wild-type GISTs. To search for novel pathogenic mutations, we sequenced the tumor transcriptome of two young adult patients who developed sporadic KIT/PDGFRA wild-type GISTs by using a massively parallel sequencing approach. The only variants identified as disease related by computational analysis were in SDHA. One patient carried the homozygous nonsense mutation p.Ser384X, the other patient was a compound heterozygote harboring a p.Arg31X nonsense mutation and a p.Arg589Trp missense mutation. The heterozygous nonsense mutations in both patients were present in germline DNA isolated from peripheral blood. Protein structure analysis indicates that all three mutations lead to functional inactivation of the protein. This is the first report, to our knowle dge, that identifies SDHA inactivation as a common oncogenic event in GISTs that lack a mutation in KIT and PDGFRA.

In addition to KIT and PDGFRA mutations, sequential accumulation of other genetic events is involved in the development and progression of gastrointestinal stromal tumors (GISTs). Until recently, the significance of these other alterations has not been thoroughly investigated. We report the first study that integrates gene expression profiling and high-resolution genomic copy number analyses in GIST. Fresh tissue specimens from 25 patients with GIST were collected, and gene expression profiling and high-resolution genomic copy number analyses were performed, using Affymetrix U133Plus and SNP array 6.0. We found that all 21 mutant GIST patients showed both macroscopic cytogenetic alterations and cryptic microdeletions or amplifications, whereas 75% (three of four) of wild-type patients with GIST did not show genomic imbalances. The most frequently observed chromosomal alterations in patients with mutant GIST included 14q complete or partial deletion (17 of 25), 1p deletion (14 of 25) and 22q deletion (10 of 25). Genetic targets of the chromosomal aberrations were selected by integrated analysis of copy number and gene expression data. We detected the involvement of known oncogenes and tumor suppressors including KRAS in chr 12p amplification and KIF1B, PPM1A, NF2 in chr 1p, 14q and 22p deletions, respectively. The genomic segment most frequently altered in mutated samples was the 14q23.1 region, which contains potentially novel tumor suppressors, including DAAM1, RTN1 and DACT1. siRNA-mediated RTN1 downregulation showed evidence for the potential role in GIST pathogenesis. The combination of gene expression profiling and high-resolution genomic copy number analysis offers a detailed molecular portrait of GISTs, providing an essential comprehensive knowledge necessary to guide the discovery of novel target genes involved in tumor development and progression.

Comment on: "Pediatric-type" gastrointestinal stromal tumors in adults: distinctive histology predicts genotype and clinical behavior. Rege TA, Wagner AJ, Corless CL, Heinrich MC, Hornick JL. Am J Surg Pathol. 2011 Apr; 35(4):495-504.

Genetic heterogeneity in drug-metabolizing enzyme/transporter (DMET) genes affects specific drug-related cancer phenotypes. To investigate the relationships between genetic variation and response to treatment in acute myeloid leukemia (AML), we genotyped 1931 variants on DMET genes in 94 CD33-positive AML patients enrolled in a phase III multicenter clinical trial combining Gemtuzumab-Ozogamicin (GO) with Fludarabine-Cytarabine-Idarubicin (FLAI) regimen, with the DMET Plus platform. Two ADH1A variants showed statistically significant differences (odds ratio (OR)=5.68, P=0.0006; OR=5.35, P=0.0009) in allele frequencies between patients in complete/partial remission and patients without response, two substitutions on CYP2E1 (OR=0.13, P=0.001; OR=0.09, P=0.003) and one on SLCO1B1 (OR=4.68, P=0.002) were found to differently influence liver toxicity, and two nucleotide changes on SULTB1 and SLC22A12 genes correlated with response to GO (OR=0.24, P=0.0009; OR=2.75, P=0.0029). Genetic variants were thus found for the first time to be potentially associated with differential response and toxicity in AML patients treated with a combination of GO-FLAI regimen.

BackgroundGenome-wide association studies of pooled DNA samples were shown to be a valuable tool to identify candidate SNPs associated to a phenotype. No such study was up to now applied to childhood allergic asthma, even if the very high complexity of asthma genetics is an appropriate field to explore the potential of pooled GWAS approach.Methodology/principal findingsWe performed a pooled GWAS and individual genotyping in 269 children with allergic respiratory diseases comparing allergic children with and without asthma. We used a modular approach to identify the most significant loci associated with asthma by combining silhouette statistics and physical distance method with cluster-adapted thresholding. We found 97% concordance between pooled GWAS and individual genotyping, with 36 out of 37 top-scoring SNPs significant at individual genotyping level. The most significant SNP is located inside the coding sequence of C5, an already identified asthma susceptibility gene, while the other loci regulate functions that are relevant to bronchial physiopathology, as immune- or inflammation-mediated mechanisms and airway smooth muscle contraction. Integration with gene expression data showed that almost half of the putative susceptibility genes are differentially expressed in experimental asthma mouse models.Conclusion/significanceCombined silhouette statistics and cluster-adapted physical distance threshold analysis of pooled GWAS data is an efficient method to identify candidate SNP associated to asthma development in an allergic pediatric population.

In Italia l’idea di nazione si è costituita intorno a una dimensione letteraria, oltre che linguistica. Va da sé che si trattò ancora di un’identità ideale, di un’utopia che, nutrita di valori letterari e di una salda tradizione umanistica, si tradusse in un “mito”. La ricorrenza di siffatte rivendicazioni è tanto più frequente quanto più debole è il tessuto connettivo di tipo politico o economico. In una prolusione del 1803 tenuta all’Università di Pavia e dedicata all’"Obbligo di onorare i primi scopritori del vero in fatto di scienze" Vincenzo Monti ammoniva che il ricordo delle glorie nazionali è tanto più cogente per quei popoli «cui né forze marittime né commerciali stabilimenti né formidabili eserciti né unità nazionale ponno rendere rispettato». Benché oppressa militarmente dagli invasori stranieri e politicamente divisa, l’Italia si riscatta con la supremazia delle sue opere d’ingegno e con i suoi meriti letterari, estesi alle opere di filosofi come Campanella e di scienziati come Galileo. Già nel Settecento si diffonde la tesi di quel primato della nazione italiana che troverà la sua continuazione e il suo apice, alla metà del secolo successivo, nell’opera di Vincenzo Gioberti. A rafforzare il senso di appartenenza nazionale della letteratura italiana furono gli attacchi che le vennero mossi dai francesi, eccitatori dapprima della querelle letteraria intercorsa tra Dominique Bouhours e gli italiani rappresentati da Giovanni Giuseppe Orsi e poi del veemente auspicio del misogallico Alfieri, quello che, con il tipico lessico del linguaggio profetico, gli fece predire che «Giorno verrà, tornerà ’l giorno, in cui / redivivi omai gl’Itali, staranno / in campo audaci». Certo, anche qui si nota un tono enfatico di maniera. Nondimeno, per quanto al momento irrealizzabile, il sogno visionario alfieriano, di natura tutta letteraria, è servito a indicare una meta alle generazioni del Risorgimento. La sua visione aristocratica e astratta è diventata nell’Ottocento strumento tangibile di propaganda. Ecco perché Alfieri è stato opportunamente definito «poeta della vigilia», dopo che Foscolo per primo ne ha propagato questa iconografia raffigurandolo nei "Sepolcri" con «il pallor della morte e la speranza» (v. 195). Al tempo della Rivoluzione francese sorse una nuova forma di culto laico i cui protagonisti furono i poeti, fatti oggetto di una venerazione patriottica. Del resto proprio Alfieri compì nel 1783 un pellegrinaggio ad Arquà, a Ferrara e a Ravenna sulle tombe di Petrarca, Ariosto e Dante. In ciò non c’è niente di archeologico o di museografico, perché la storia passata doveva diventare l’impulso per il presente. Lo intese benissimo Leopardi nella canzone "Sopra il monumento di Dante". Poco dopo Manzoni compendiava in due versi dell’ode "Marzo 1821" la sua idea di nazione nella quale non poteva mancare la condivisione della lingua: «una d’arme, di lingua, d’altare, / di memorie, di sangue e di cor». A istituire una più diffusa disamina in questo senso fu Gioberti, mettendo però in chiaro il livello tradizionalmente elitario della letteratura italiana, che ricorre unitariamente alla «lingua scritta ed illustre», ma è ancora divisa nella «favella popolare». Altri autori presi in esame sono Nievo e De Sanctis.

AIMS: To compare the genomic signatures of wild-type (WT) and mutated GISTs and the murine interstitial cells of Cajal (ICCs) to find markers of cell differentiation and other functions that may identify cells that give rise to WT tumours. METHODS AND RESULTS: We analysed the gene expression profiles of a total of 30 tumour samples (four WT GISTs and 26 mutated GISTs), selected the genes most differentially expressed (P < 0.001:448 probe sets) and validated these results by quantitative polymerase chain reaction (PCR) and immunohistochemistry. In addition, we conducted a meta-analysis merging data from human GISTs with a genomic data set from murine ICCs. The gene expression profiles of WT and mutated GISTs differed profoundly, especially in the expression of those genes restricted primarily to neural tissues. We found that mature ICCs are more similar to mutated GISTs than WT GISTs. CONCLUSIONS: WT GISTs have different genomic profiles from both mutated GISTs and murine mature ICCs. Considering that IGF1R expression is common to both WT GISTs and putative precursor ICCs, this study suggests that WT GISTs may derive either from ICCs at a different step of differentiation or from a different cell of origin.

Background: Genetic heterogeneity in drug-metabolizing enzyme and transporter genes affects specific drug-related phenotypes in cancer. In order to investigate a relationship between genetic variation and response in AML, we comprehensively assessed the allele frequencies of 1936 genetic variations of 225 absorption, distribution, metabolism and excretion genes in 94 CD33-positive AML patients younger than 65 years, using the new Affymetrix drug-metabolizing enzyme and transport (DMET Plus) genotyping platform. Patients and methods: All patients were enrolled in a phase III multicenter clinical trial combining low dose of Gemtuzumab-ozogamicin (GO) with FLAI regimen (Fludarabine, Cytarabine, Idarubicin) as Induction chemotherapy (ClinicalTrials.gov NCT00909168). Cytogenetics, multidrug-resistance phenotype, FLT3 and NPM mutation status, as well as WT1 quantitative expression analyses were performed at diagnosis. Furthermore, high-resolution single nucleotide polymorphism (SNP) array and DMET genotyping analyses (Affymetrix) were also performed. Results: Of the 94 patients, genotype results were evaluable for 91 cases. The median call rate was 99.48 (range, 96.32-100). Firstly, we tested the association among SNPs and response to the induction cycle (FLAI + GO) comparing the genotyping profile of 80 patients in complete (85%) and partial (3%) remission with that of patients (12%) with no response. A highly significant difference (p < 0.001) in the allele frequency of 2 variants, in complete linkage disequilibrium, in the alcohol dehydrogenase enzyme (ADH1A) was found. ADH1A metabolizes the conversion of ethanol to acetaldehyde which is thereafter converted to acetate by ALDH1, which is well known as stem cell marker. These variants were not associated with high risk AML, FLT3 and NPM1 mutations, but strongly influenced response to the induction phase also in a multivariate analysis. Secondly, SNPs were stratified according to liver toxicity and a significant difference in the allele frequency in CYP2E1, involved in the alcohol metabolism was found to be associated with a grade I/II liver toxicity. Conclusions: Genetic variations in ADH1A and CYP2E1 genes were for the first time identified and associated with response and toxicity in AML patients treated with a combination of GO and FLAI regimen. Supported by European LeukemiaNet, AIL, AIRC, FIRB 2006, Ateneo RFO grants, Project of integrated program, Programma di Ricerca Regione – Università 2007–2009.