An Outlook on Ovarian Cancer and Borderline Ovarian Tumors: Focus on Genomic and Proteomic Findings

Among the gynaecological malignancies, ovarian cancer is one of the neoplastic forms with the poorest prognosis and with the bad overall and disease-free survival rates than other gynaecological cancers. Ovarian tumors can be classified on the basis of the cells of origin in epithelial, stromal and germ cell tumors. Epithelial ovarian tumors display great histological heterogeneity and can be further subdivided into benign, intermediate or borderline, and invasive tumors. Several studies on ovarian tumors, have focused on the identification of both diagnostic and prognostic markers for applications in clinical practice. High-throughput technologies have accelerated the process of biomolecular study and genomic discovery; unfortunately, validity of these should be still demonstrated by extensive researches on sensibility and sensitivity of ovarian cancer novel biomarkers, determining whether gene profiling and proteomics could help differentiate between patients with metastatic ovarian cancer and primary ovarian carcinomas, and their potential impact on management. Therefore, considerable interest lies in identifying molecular and protein biomarkers and indicators to guide treatment decisions and clinical follow up. In this review, the current state of knowledge about the genoproteomic and potential clinical value of gene expression profiling in ovarian cancer and ovarian borderline tumors is discussed, focusing on three main areas: distinguishing normal ovarian tissue from ovarian cancers and borderline tumors, identifying different genotypes of ovarian tissue and identifying proteins linked to cancer or tumor development. By these targets, authors focus on the use of novel molecules, developed on the proteomics and genomics researches, as potential protein biomarkers in the management of ovarian cancer or borderline tumor, overlooking on current state of the art and on future perspectives of researches.Key Words: Ovarian cancer, borderline ovarian tumors, markers, genomics, proteomics, oncogenes.     

Use and value of serologic tests for the diagnosis of systemic candidiasis in cancer patients: A prospective study of 146 patients

Sera from 146 cancer patients at risk for disseminated candidiasis were studied prospectively with immunodiffusion (ID), counterelectrophoresis (CEP), and latex agglutination (LA) tests to determine their diagnostic value in the detection of antibodies to theCandida species. Serial serum samples, cultures, and clinical data were obtained after a malignancy was diagnosed. Patients were classified into three groups (I, II, and III) on the basis of cultural, histological, and clinical evidence for superficial (Group I) versus disseminated (Group III)Candida infection. Thirty-two of 78 patients (41%) in Group I had positive ID, CEP, and LA titers. In Group II, those patients lacking histological confirmation of disseminated infection, 16 of 18 (89%) had positive titers. Thirty-six of 50 (72%) in Group III were positive by all three tests. Heavy colonization of the gastrointestinal tract, without evidence of tissue invasion, produced positive test results. Negative serologic tests were encountered in immunosuppressed patients with rapidly progressive candidiasis.C. krusei infections produced specific antibody titers detected by the homologous antigen but not byC. albicans antigen. Stable or decreasing LA titers were correlated with clinical improvement in patients receiving effective antifungal therapy.     

Sexuality and Genetic Identity in the Agaricus Section Arvenses

Twelve wild collections and one commercial strain were used to characterize breeding systems and to develop molecular identities in the Arvenses section of the genus Agaricus, which includes the “horse mushroom” A. arvensis. Two morphotypes were identified based on macro- and micromorphological features. However, not all collections could be delimited by conventional taxonomic characters. Sequencing of the small subunit intergenic spacer (ITS) region (368 to 370 bp) of the rRNA genes clearly resolved the 13 collections into two clusters consistent with the identified morphotypes. Single-spore progenies and mating type testers were established and used to test intra- and interstock compatibility. The two compatibility groups identified were consistent with ITS clusters. Compatibility group I stocks readily interbred within the constraints of a unifactorial heterothallic system with a multiallelic mating type factor. Compatibility group II had a more restricted breeding pattern, and interactions were difficult to predict on the basis of mating type. Morphological data, ITS sequences, and the ability to interbreed suggest that these collections are part of a complex of interrelated species. Single-spore, homokaryotic isolates from both compatibility groups were able to fruit in compost culture, and two of the collections may represent natural homokaryotic fruiting. We conclude that species from the section Arvenses have versatile unifactorial heterothallic life cycles that permit both interbreeding and homokaryotic fruiting.     

Use of macroporous polypropylene filter to allow identification of bacteria by PCR in human fecal samples

The detection of pathogenic bacteria directly in human fecal specimens by PCR, requires removal of PCR-inhibitory substances. To investigate whether five different macroporous filters (polypropylene, nylon, polyester, polyethylene, fluorocarbon) could retain polysaccharides, major PCR inhibitors, an in vitro model and human fecal samples were used. The in vitro model consisted of Xanthum gum solutions (3 mg/ml PBS), a bacterial polysaccharide, to which Helicobacter pylori cells were added. Fecal samples from healthy volunteers were spiked with H. pylori and Mycobacterium paratuberculosis cells. Polysaccharide concentrations were significantly reduced only by the polypropylene but not by the other filters. Accordingly, both Xanthum gum solutions and spiked fecal specimens became PCR positive only after filtration with the polypropylene filter. We conclude that this filter can be used to prepare a bacterial DNA template suitable for PCR analysis from human feces.     

Eosinophils contribute to killing of adult Onchocerca ochengi within onchocercomata following elimination of Wolbachia

Many filarial nematodes, including Onchocerca volvulus (the cause of human 'River Blindness'), have a mutually dependent relationship with Wolbachia bacteria. There has been much interest in Wolbachia as a chemotherapeutic target, since there are no macrofilaricidal drugs (i.e., lethal to adult worms) of low toxicity. Using the bovine parasite O. ochengi, we previously demonstrated that combined intensive and intermittent (COM) oxytetracycline treatment induces a sustained depletion of Wolbachia and is macrofilaricidal, whereas a short intensive regimen (SIR) is non-macrofilaricidal. To understand how targeting Wolbachia with oxytetracycline can lead to worm death, O. ochengi nodules (onchocercomata) were sequentially excised from cattle administered COM or SIR therapy, and cell infiltrates were microscopically quantified. Pre-treatment, worms were surrounded by neutrophils, with eosinophils rare or absent. At 8-12weeks after either regimen, eosinophils increased around worms and were observed degranulating on the cuticle. However, with the SIR treatment, neutrophils returned to predominance by 48weeks, while in the COM group, eosinophilia persisted. These observations suggest that accumulation of degranulating eosinophils over a prolonged period is a cause rather than an effect of parasite death, and the macrofilaricidal mechanism of antibiotics may relate to facilitation of eosinophil infiltration around worms by ablation of Wolbachia-mediated neutrophilia.     

Systematics and Leaf Architecture of the Gunneraceae

Cladistic and phenetic analyses of leaf and other morphological characters ofGunnera strongly support monophyly of the genus, with the Saxifragaceae s.str. as the closest sister group. This morphologically based phylogeny provides a more coherent understanding of the evolutionary history ofGunnera than do recent phylogenetic hypotheses based on genetic data sets with Myrothamnaceae as the sister group. Simple, crenate, palinactinodromously veined leaves lacking freely ending veinlets and tricolpate, tectate-perforate pollen with a reticulate exine indicate a shared ancestry. Within the genusGunnera all six traditionally recognized subgenera are monophyletic, as supported by leaf architectural apomorphies. The monotypic subgenusOstenigunnera is the sister group to the other five subgenera, which can be divided into two principal lineages. One lineage includes the subgeneraMilligania andMisandra, characterized by a prostate stoloniferous habit with small, low-rank leaves and exclusively unisexual flowers, whereas the other lineage includes the subgeneraPerpensum, Pseudo Gunnera, andPanke, all of which possess at least some hermaphroditic flowers and larger, high-rank leaves. When the phylogeny of the subgenera is considered in light of biogeography and the fossil record, a number of cladogenetic events can be explained by continental vicariance in the Late Cretaceous. The AfricanPerpensum became distinct from the other large-leafed lineage with the separation of the African continent ca. 90 Ma. The two small-leafed lineages, the subgeneraMilligania andMisandra, split with the separation of New Zealand from Western Gondwana, about 80 Ma.Pseudo-Gunnera became isolated fromPanke prior to this time, whenPanke fossils occur in North America.Gunnera probably arose out of an early herbaceous radiation of tricolpate eudicots having close affinity to the basal Saxifragaceae, espethe genusChrysosplenium.     

Multicenter evaluation of reverse line blot assay for detection of drug resistance in Mycobacterium tuberculosis clinical isolates

A multicenter study was conducted with the objective to evaluate a reverse line blot (RLB) assay to detect resistance to rifampin (RIF), isoniazid (INH), streptomycin (STR), and ethambutol (EMB) in clinical isolates of Mycobacterium tuberculosis. Oligonucleotides specific for wild type and mutant (drug resistance linked) alleles of the selected codons in the genes rpoB, inhA, ahpC, rpsL, rrs, embB, were immobilized on a nylon membrane. The RLB assay conditions were optimized following analysis of DNA samples with known sequences of the targeted genes. For validation of the method at different geographical locations, the membranes were sent to seven laboratories in six countries representing the regions with high burdens of multudrug-resistant tuberculosis. The reproducibility of the assay for detection of rpoB genotypes was initially evaluated on a blinded set of twenty reference DNA samples with known allele types and overall concordant results were obtained. Further mutation analysis was performed by each laboratory on the local strains. Upon RLB analysis of 315 clinical isolates from different countries, 132 (85.2%) of 155 RIF-resistant and 28 (51.0%) of 55 EMB-resistant isolates were correctly identified, showing applicability of the assay when targeting the rpoB hot-spot region and embB306. Mutations in the inhA and ahpC promoter regions, conferring resistance to INH, were successfully identified in respectively 16.9% and 13.2% of INH-resistant strains. Likewise, mutations in rrs513 and rpsL88 that confer resistance to STR were identified in respectively 15.1% and 10.7% of STR-resistant strains. It should be mentioned that mutation analysis of the above targets usually requires rather costly DNA sequencing to which the proposed RLB assay presents rapid and inexpensive alternative. Furthermore, the proposed method requires the same simple equipment as that used for spoligotyping and permits simultaneous analysis of up to 40 samples. This technique is a first attempt to combine different targets in a single assay for prediction of antituberculosis drugs resistance. It is open to further development as it allows easy incorporation of new probes for detection of mutations in other genes associated with resistance to second-line (e.g., fluoroquinolones) and new antituberculosis compounds.     

Phylogeny and biogeography of the Malagasy and Australasian rainbowfishes (Teleostei: Melanotaenioidei): Gondwanan vicariance and evolution in freshwater

Phylogenetic relationships of the Malagasy and Australasian rainbowfishes are investigated using 4394 characters derived from five mitochondrial genes (12S, 16S, tRNA-Valine, ND5, and COI), three nuclear genes (28S, histone H3, and TMO-4c4), and 102 morphological transformations. This study represents the first phylogenetic analysis of the endemic Malagasy family Bedotiidae and includes a nearly complete taxonomic review of all nominal species, as well as numerous undescribed species. Simultaneous analysis of the molecular and morphological datasets results in two equally most parsimonious trees. Results indicate that Bedotiidae (Bedotia+Rheocles) and Bedotia are monophyletic, whereas Rheocles is paraphyletic with the inclusion of two recently described species from northeastern Madagascar, R. vatosoa, and R. derhami. Rheocles vatosoa and R. derhami are sister taxa, and this clade is recovered as the sister group to Bedotia. The remaining species of Rheocles are not sexually dimorphic and comprise a clade that is recovered as the sister group to Bedotia+(R. derhami+R. vatosoa), all of which are sexually dichromatic, and sexually dimorphic for pigmentation and fin development. Three geographically distinct clades are recovered within Bedotia, one comprising species with distributions ranging from mid- to southeastern Madagascar, another including species restricted to eastern drainages north of the Masoala Peninsula, and a third comprising taxa with distributions extending from the Masoala Peninsula south to the Ivoloina River. The Australian/New Guinean melanotaeniids are monophyletic and are recovered as the sister group to Bedotiidae. The Australasian Telmatherinidae and Pseudomugilidae comprise a clade that is recovered as the sister group to the Melanotaeniidae-Bedotiidae clade. This sister-group relationship between Malagasy bedotiids and a clade restricted to Australia-New Guinea, and the absence of a close relationship between bedotiids and African or Mascarene atheriniforms, is congruent with the break-up of Gondwana, not a scenario reliant on Cenozoic trans-oceanic dispersal. Finally, results of the phylogenetic analysis indicate that Atheriniformes is polyphyletic and further corroborate recent morphological hypotheses, which have recovered Bedotiidae in a derived position within Atherinoidei.     

Organization of Methanobacterium thermoautotrophicum bacteriophage psi M1 DNA

Summary M1 is a virulent bacteriophage of Methanobacterium thermoautotrophicum strain Marburg. Restriction enzyme analysis of the linear, 30.4 kb phage DNA led to a circular map of the 27.1 kb M1 genome. M1 is thus circularly permuted and exhibits terminal redundancy of approximately 3 kb. Packaging of M1 DNA from a concatemeric precursor initiates at the pac site which was identified at coordinate 4.6 kb on the circular genome map. It proceeds clockwise for at least five packaging rounds. Headful packaging was also shown for M2, a phage variant with a 0.7 kb deletion at coordinate 23.25 on the map.