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Background The majority of patients with stage III–IV epithelial ovarian cancer (EOC) relapse after initially responding to platinum-based chemotherapy, and develop resistance. The genomic features involved in drug resistance are unknown. To unravel some of these features, we investigated the mutational profile of genes involved in pathways related to drug sensitivity in a cohort of matched tumors obtained at first surgery (Ft-S) and second surgery (Sd-S). Patients and methods Matched biopsies (33) taken at Ft-S and Sd-S were selected from the ‘Pandora’ tumor tissue collection. DNA libraries for 65 genes were generated using the TruSeq Custom Amplicon kit and sequenced on MiSeq (Illumina). Data were analyzed using a high-performance cluster computing platform (Cloud4CARE project) and independently validated. Results A total of 2270 somatic mutations were identified (89.85% base substitutions 8.19% indels, and 1.92% unknown). Homologous recombination (HR) genes and TP53 were mutated in the majority of Ft-S, while ATM, ATR, TOP2A and TOP2B were mutated in the entire dataset. Only 2% of mutations were conserved between matched Ft-S and Sd-S. Mutations detected at second surgery clustered patients in two groups characterized by different mutational profiles in genes associated with HR, PI3K, miRNA biogenesis and signal transduction. Conclusions There was a low level of concordance between Ft-S and Sd-S in terms of mutations in genes involved in key processes of tumor growth and drug resistance. This result suggests the importance of future longitudinal analyses to improve the clinical management of relapsed EOC.

Sanger sequencing primers. Schematic representation of the primers used for PCR and Sanger sequencing. (PPTX 302 kb)

Trabectedin clustering analysis. Unsupervised clustering analysis of trabectedin treated samples and control samples. The colors of the tree branches indicate distinct groups calculated by the clustering algorithm. Green boxes around the sample names indicate control samples, while red boxes show trabectedin-treated samples. (PPTX 68 kb)

A case characterized by a rare synchronous occurrence of transitional cell carcinoma of the renal pelvis and renal cell carcinoma in the contralateral kidney is presented. The simultaneous occurrence of renal adenocarcinoma and transitional cell carcinoma of the renal pelvis in the opposite kidney is unusual.

In the genus Eulemur (Malagasy lemurs) karyotype diversification has occurred mainly through Robertsonian mechanisms of chromosome fusion (Rumpler et al., 1976). Eulemur coronatus is the sole species to have the largest genome size, due to a very large amount of C-heterochromatin, mostly located at the pericentromeric regions of the largest chromosomes (Warter and Rumpler, 1985). This increase in C-heterochromatin was thought to be due to DNA amplification (Ronchetti et al., 1993). The aim of this work was to investigate whether the large C-heterochromatin of Eulemur coronatus might have derived by amplification of the smaller C-heterochromatin of Eulemur macaco, a closely related species with smaller genome size. To obtain information on the overall base composition of the total genomes, on the relative interspersion of AT and GC base paris along the DNA molecule and on the structural differences in C-heterochromatin, we used a quantitative cyto-chemical approach, based on fluorescence resonance energy transfer (FRET) between DNA-specific fluorochromes (i.e. the AT-specific Hoechst 33258, and the non base-specific dye, propidium iodide). Micro-spectrofluorometry and image analysis were used to investigate both the overall FRET efficiency and its spatial distribution along the chromosome arms. FRET efficiency values of the DNA in C-heterochromatin were significantly different in the two Eulemur species, indicating a different qualitative composition of repetitive DNA. This suggests that the repetitive DNA of Eulemur coronatus cannot have originated by amplification in toto of the repetitive DNA sequences of Eulemur macaco.

DNA analysis by quantitative cytochemistry has been a widely exploited approach to investigate chromatin superstructural changes in relation to cell function and cell cycle progress. To this aim, a number of dyes (especially fluorochromes) for nucleic acids have been used, exhibiting different peculiarities, in terms of both binding mechanism and base specificity. Less attention has been paid to the application of different DNA staining techniques for studying possible differences in genome organization among different taxa. The purpose of this paper is to review and discuss the present reports in the literature, concerning the cytochemical analysis of genome organization, in a comparative perspective. Special attention is given to the integration of quantitative studies based on cytofluorometric and imaging techniques.

The genome sizes (GS) and AT contents of five species of Anguilliformes (Anguilla anguilla, Anguilla rostrata, Conger conger, Gymnothorax unicolor and Muraena helena) belonging to three families (Anguillidae, Congridae and Muraenidae) were determined by flow cytometry and densitometry. Differences in Gs between Anguillidae-Congridae (about 3 pg) and Muraenidae (about 5 pg) were found, which correlate with the relative amounts of AT base pairs (around 42-43% for Anguillidae-Congridae and 51-52% for Muraenidae). Correlation of these results to karyotype parameters testified to a close phylogenetic relationship between Anguillidae and Congridae.

A method is proposed to evaluate the amount of DNA resistant to the C-banding pretreatments (C-heterochromatic-DNA) in metaphase chromosomes. Measurements were performed by microfluorometry on propidium iodide stained metaphases of man, gorilla and mouse; in these species, C-heterochromatin exhibits significant differences of both base composition and distribution along the chromosomes. The amount of C-heterochromatic-DNA was found to be about 16%, 28% and 58% of the total DNA content (genome size) in man, gorilla and mouse, respectively. The areas of C-bands after Giemsa staining were also assessed by microdensitometry, and corresponded to about 8%, 15% and 14% of the total karyotype area of man, gorilla and mouse respectively. No direct relation thus exists between C-band areas and the amount of DNA resistant to the C-banding pretreatments. In man and gorilla, the amount of C-heterochromatic-DNA accounts for the differences observed in genome size.

Statistical data analysis has been enriched by the development of several new tools. This book discusses the advances which they are making possible - often into unexplored territory - and the trends they are foreshadowing. The topics range from theoretical considerations to practical concerns.

Preoperative cardiovascular hemodynamics and percutaneous liver biopsies were used to evaluate the pathophysiologic factors determining the operative prognosis of patients with cirrhotic liver disease and bleeding esophageal varices. These studies confirm the observations of Siegel that the greater the magnitude of the peripheral abnormalities in vascular tone and oxygen consumption the better must be the capability of the ventricular function, if the cirrhotic is to survive emergency or urgent portal decompressive surgery. These studies also show that the cardiovascular hemodynamics are directly correllated with the nature and degree of the abnormalities in the liver biopsy, and that pathologic and physiologic features of this disease which impact on surgical prognosis can be expressed through the easily obtained Survival Index. Bleeding cirrhotic patients with poor quality hemodynamics and poor histologic characteristics should be treated non operatively, since the operative mortality appears greater than that produced by a strategy of medical supportive therapy and delayed surgery if stabilization occurs.

In this paper, we present the results of an ongoing research involving the design and implementation of systems supporting personalized access to multi-version resources in an eGovernment scenario. Personalization is supported by means of Semantic Web techniques and is based on an ontology-based profiling of users (citizens). Resources we consider are collections of norm documents in XML format but can also be generic Web pages and portals or eGovernment services. We introduce a reference infrastructure, describe the organization and present performance figures of a prototype system we have developed.

The amounts of nuclear DNA and the AT and GC content of four Eulemur (Prosimii, Lemuridae) species and of an E. coronatus x E. macaco hybrid were measured by flow cytometry in peripheral blood leukocytes, following propidium iodide, Hoechst 33258, and mithramycin staining. Hoechst 33258 and mithramycin were also used to evaluate the base composition of genomic DNA in the chromosomes. The amount of DNA resisting C-banding pretreatment (C-heterochromatic DNA) was measured in metaphase chromosomes by static fluorometry. The genome of E. coronatus was significantly larger than the genomes of all other species examined, due to a higher content of pericentromeric, mainly GC-rich, heterochromatic DNA. The restriction banding patterns produced by BamHI digestion and ethidium bromide staining on extracted DNA were studied in the hybrid and its parental species (E. coronatus and E. macaco). The restriction banding pattern of the sole E. coronatus individual showed two bands which were repeated in the restriction banding pattern of the hybrid. The qualitative and quantitative differences of C-heterochromatic DNA in E. coronatus confirm the "splitting" processes and the phylogenetic relationships in the genus Eulemur suggested by Jung et al. (1992) on the basis of the restriction banding patterns produced by endonuclease digestion.

In this paper, we present some results of an ongoing research involving the design and implementation, in an eGovernment scenario, of a multi-version repository of norm texts supporting efficient and personalized access. In particular we defined a multi-version XML data model supporting both temporal versioning –essential in normative systems– and semantic versioning. Semantic versioning is based on the applicability of different norm parts to different classes of citizens and allows users to retrieve personalized norm versions only containing provisions which are applicable to their personal case. We describe the organization and present preliminary performance figures of a prototype system we developed.

In this paper, we present the results of an ongoing research involving the design and implementation, in an eGovernment scenario, of a semantic-aware system supporting efficient and personalized access to a multi-version repository of normative texts. The research activity is entitled “Semantic web techniques for the management of digital identity and the access to norms”. In the context of a complete and modular infrastructure, we defined a multi-version XML data model and developed a temporal and semantical XML query processor supporting both temporal versioning –essential in normative systems– and semantic versioning. Semantic versioning is based on the applicability of different norm parts to different classes of citizens and allows users to retrieve personalized norm versions only containing provisions which are applicable to their personal case. The whole infrastructure, which we plan to complete in the near future, will integrate the querying component with several auxiliary services, including automatic citizen identification and classification and assisted update of the repository data.

Colonic anastomoses made both by a new Compression Anastomotic Device (CAD) and by a traditional stapler (Autosuture CDEEA) were evaluated in impaired anastomotic healing induced by systemic cortisone in the dog. Twenty dogs were given daily i.m. hydrocortisone (25 mg/kg) starting one month before surgery and then until sacrifice. Eight untreated dogs served as controls. Surgery consisted of colonic transection and anastomosis done with CAD-25 in half the cases and with CDEEA-25 in the remaining half. The dogs were sacrificed six and 13 days after surgery. Macroscopic assessment, bursting pressure test, and histology were performed on the anastomosis. One dog died from peritonitis due to anastomotic dehiscence. No other clinical complications were observed. Although the number of observations was too small to attain statistical significance, CAD anastomoses appeared better than stapled ones as regards peri-anastomotic adhesions, anastomotic index, and histology. This preliminary study suggests that compression is as reliable as the stapler in the construction of colon anastomosis even in such situations of delayed anastomotic healing. Further experience is required to substantiate this conclusion.