High-level detection of gene amplification and chromosome aneuploidy in extracted nuclei from paraffin-embedded tissue of human cancer using FISH: a new approach for retrospective studies

A novel application of fluorescence in situ hybridization (FISH) to isolated nuclei is described. The method detects gene amplification and chromosome aneuploidy in extracted nuclei from paraffin-embedded tissue of human cancer with greater sensitivity and specificity than existing FISH methods. In this study, the method is applied to signal detection of the HER-2/neu (c-erbB-2) gene, whose amplification is one of the most common genetic alterations associated with human breast cancer. Nuclei were extracted and isolated from formalin fixed, paraffin embedded tissue of 43 different carcinomas (breast, ovary, endometrium, gastrointestinal stromal tumor and malignant mesothelioma). FISH was performed both on sections and extracted nuclei of each tissue using chromosome enumeration probes (CEP) for the centromeric regions of chromosomes 8 and 17, and a locus specific identifier (LSI) for the HER-2/neu oncogene. Differences between ploidy calculated in sections and extracted nuclei were seen in 3 breast carcinomas and 1 gastrointestinal stromal tumor (GIST). Furthermore, 1 breast cancer, previously considered to be borderline for HER-2/neu gene amplification turned out to be clearly amplified. Nuclei extraction and isolation bypass all the problems related to signal interpretation in tissue sections, and the adoption of this new technique, which improves the signal quality in several neoplastic samples, is suggested

Does predation risk affect spatial use in an introduced ungulate species? The case of a Mediterranean mouflon alpine colony

Predation risk is known to affect the spatial use of prey species, imposing a trade-off between feeding requirements and predation avoidance. As a result, prey species can leave high-quality forage areas to use sub-optimal, but safer, habitat patches, defined as “refuge areas.” In this study, we describe changes in the spatial use of an introduced ungulate species, the Mediterranean mouflon Ovis aries musimon, following the recolonization (in 1996) of wolves Canis lupus into the Albergian Hunting Estate (Italian Western Alps). Since 1988, we monitored the mouflon population by spring counts from vantage points. We georeferenced all observations and recorded the size and structure of the spotted groups. Finally, we identified available refuges by selecting patches characterized by (i) the presence of rocks and (ii) high values of steepness and ruggedness. We found that mouflons significantly reduced the average distance from refuge areas over the years, with the yearly average distance from refuges being 56% lower after wolves recolonized the area (i.e., 93.8 ± 32.1 vs. 213.1 ± 40.9 m). The analysis of orographic parameters showed that mouflons used patches with higher values in elevation, slope, ruggedness, and a significant difference in all three parameters when comparing years pre and post wolf return. Both sexes were significantly affected, but ewes were particularly sensitive and selected patches closer to refuge areas (75.8 ± 30.3 m) than males (131.0 ± 53.6 m). Our results suggest that the presence of new predators can alter the distribution of an introduced species such as the Mediterranean mouflon, triggering the resurgence of anti-predation behavior

Cadmium accumulation and interactions with zinc, copper, and manganese, analysed by ICP-MS in a long-term Caco-2 TC7 cell model

The influence of long-term exposure to cadmium (Cd) on essential minerals was investigated using a Caco-2 TC7 cells and a multi-analytical tool: microwave digestion and inductively coupled plasma mass spectrometry. Intracellular levels, effects on cadmium accumulation, distribution, and reference concentration ranges of the following elements were determined: Na, Mg, Ca, Cr, Fe, Mn, Co, Ni, Cu, Zn, Mo, and Cd. Results showed that Caco-2 TC7 cells incubated long-term with cadmium concentrations ranging from 0 to 10 lmol Cd/l for 5 weeks exhibited a significant increase in cadmium accumulation. Furthermore, this accumulation was more marked in cells exposed long-term to cadmium compared with controls, and that this exposure resulted in a significant accumulation of copper and zinc but not of the other elements measured. Interactions of Cd with three elements: zinc, copper, and manganese were particularly studied. Exposed to 30 lmol/l of the element, manganese showed the highest inhibition and copper the lowest on cadmium intracellular accumulation but Zn, Cu, and Mn behave differently in terms of their mutual competition with Cd. Indeed, increasing cadmium in the culture medium resulted in a gradual and significant increase in the accumulation of zinc. There was a significant decrease in manganese from 5 lmol Cd/l exposure, and no variation was observed with copper. Abbreviation: AAS – Atomic absorption spectrometry; CRM– Certified reference material; PBS – Phosphate buffered saline without calcium and magnesium; DMEM – Dubelcco’s modified Eagle’s medium

Oral chondroitin sulfate and prebiotics for the treatment of canine Inflammatory Bowel Disease: a randomized, controlled clinical trial

BACKGROUND Canine inflammatory bowel disease (IBD) is a chronic enteropathy of unknown etiology, although microbiome dysbiosis, genetic susceptibility, and dietary and/or environmental factors are hypothesized to be involved in its pathogenesis. Since some of the current therapies are associated with severe side effects, novel therapeutic modalities are needed. A new oral supplement for long-term management of canine IBD containing chondroitin sulfate (CS) and prebiotics (resistant starch, β-glucans and mannaoligosaccharides) was developed to target intestinal inflammation and oxidative stress, and restore normobiosis, without exhibiting any side effects. This double-blinded, randomized, placebo-controlled trial in dogs with IBD aims to evaluate the effects of 180 days administration of this supplement together with a hydrolyzed diet on clinical signs, intestinal histology, gut microbiota, and serum biomarkers of inflammation and oxidative stress. RESULTS Twenty-seven client-owned biopsy-confirmed IBD dogs were included in the study, switched to the same hydrolyzed diet and classified into one of two groups: supplement and placebo. Initially, there were no significant differences between groups (p > 0.05) for any of the studied parameters. Final data analysis (supplement: n = 9; placebo: n = 10) showed a significant decrease in canine IBD activity index (CIBDAI) score in both groups after treatment (p < 0.001). After treatment, a significant decrease (1.53-fold; p < 0.01) in histologic score was seen only in the supplement group. When groups were compared, the supplement group showed significantly higher serum cholesterol (p < 0.05) and paraoxonase-1 (PON1) levels after 60 days of treatment (p < 0.01), and the placebo group showed significantly reduced serum total antioxidant capacity (TAC) levels after 120 days (p < 0.05). No significant differences were found between groups at any time point for CIBDAI, WSAVA histologic score and fecal microbiota evaluated by PCR-restriction fragment length polymorphism (PCR-RFLP). No side effects were reported in any group. CONCLUSIONS The combined administration of the supplement with hydrolyzed diet over 180 days was safe and induced improvements in selected serum biomarkers, possibly suggesting a reduction in disease activity. This study was likely underpowered, therefore larger studies are warranted in order to demonstrate a supplemental effect to dietary treatment of this supplement on intestinal histology and CIBDAI

Integrated photonic quantum gates for polarization qubits

Integrated photonic circuits have a strong potential to perform quantum information processing. Indeed, the ability to manipulate quantum states of light by integrated devices may open new perspectives both for fundamental tests of quantum mechanics and for novel technological applications. However, the technology for handling polarization encoded qubits, the most commonly adopted approach, is still missing in quantum optical circuits. Here we demonstrate the first integrated photonic Controlled-NOT (CNOT) gate for polarization encoded qubits. This result has been enabled by the integration, based on femtosecond laser waveguide writing, of partially polarizing beam splitters on a glass chip. We characterize the logical truth table of the quantum gate demonstrating its high fidelity to the expected one. In addition, we show the ability of this gate to transform separable states into entangled ones and vice versa. Finally, the full accessibility of our device is exploited to carry out a complete characterization of the CNOT gate through a quantum process tomography.Comment: 6 pages, 4 figure

Dynamic SU(2) Structure from Seven-branes

We obtain a family of supersymmetric solutions of type IIB supergravity with dynamic SU(2) structure, which describe the local geometry near a stack of four D7-branes and one O7-plane wrapping a rigid four-cycle. The deformation to a generalized complex geometry is interpreted as a consequence of nonperturbative effects in the seven-brane gauge theory. We formulate the problem for seven-branes wrapping the base of an appropriate del Pezzo cone, and in the near-stack limit in which the four-cycle is flat, we obtain an exact solution in closed form. Our solutions serve to characterize the local geometry of nonperturbatively-stabilized flux compactifications.Comment: 49 pages, 2 figures; v2: minor corrections, references adde

Twelve recommendations for advancing marine conservation in European and contiguous seas

Like most ocean regions today, the European and contiguous seas experience cumulative impacts from local human activities and global pressures. They are largely in poor environmental condition with deteriorating trends. Despite several success stories, European policies for marine conservation fall short of being effective. Acknowledging the challenges for marine conservation, a 4-year multi-national network, MarCons, supported collaborative marine conservation efforts to bridge the gap between science, management and policy, aiming to contribute in reversing present negative trends. By consolidating a large network of more than 100 scientists from 26 countries, and conducting a series of workshops over 4 years (2016–2020), MarCons analyzed challenges, opportunities and obstacles for advancing marine conservation in the European and contiguous seas. Here, we synthesize the major issues that emerged from this analysis and make 12 key recommendations for policy makers, marine managers, and researchers. To increase the effectiveness of marine conservation planning, we recommend (1) designing coherent networks of marine protected areas (MPAs) in the framework of marine spatial planning (MSP) and applying systematic conservation planning principles, including re-evaluation of existing management zones, (2) designing MPA networks within a broader transboundary planning framework, and (3) implementing integrated land-freshwater-sea approaches. To address inadequate or poorly informed management, we recommend (4) developing and implementing adaptive management plans in all sites of the Natura 2000 European conservation network and revising the Natura 2000 framework, (5) embedding and implementing cumulative effects assessments into a risk management process and making them operational, and (6) promoting actions to reach ‘good environmental status’ in all European waters. To account for global change in conservation planning and management, we further recommend (7) developing conservation strategies to address the impacts of global change, for example identifying climate-change refugia as high priority conservation areas, and (8) incorporating biological invasions in conservation plans and prioritizing management actions to control invasive species. Finally, to improve current practices that may compromise the effectiveness of conservation actions, we recommend (9) reinforcing the collection of high-quality open-access data, (10) improving mechanisms for public participation in MPA planning and management, (11) prioritizing conservation goals in full collaboration with stakeholders, and (12) addressing gender inequality in marine sciences and conservation

Inherited biotic protection in a Neotropical pioneer plant

Chelonanthus alatus is a bat-pollinated, pioneer Gentianaceae that clusters in patches where still-standing, dried-out stems are interspersed among live individuals. Flowers bear circum-floral nectaries (CFNs) that are attractive to ants, and seed dispersal is both barochorous and anemochorous. Although, in this study, live individuals never sheltered ant colonies, dried-out hollow stems - that can remain standing for 2 years - did. Workers from species nesting in dried-out stems as well as from ground-nesting species exploited the CFNs of live C. alatus individuals in the same patches during the daytime, but were absent at night (when bat pollination occurs) on 60.5% of the plants. By visiting the CFNs, the ants indirectly protect the flowers - but not the plant foliage - from herbivorous insects. We show that this protection is provided mostly by species nesting in dried-out stems, predominantly Pseudomyrmex gracilis. That dried-out stems remain standing for years and are regularly replaced results in an opportunistic, but stable association where colonies are sheltered by one generation of dead C. alatus while the live individuals nearby, belonging to the next generation, provide them with nectar; in turn, the ants protect their flowers from herbivores. We suggest that the investment in wood by C. alatus individuals permitting stillstanding, dried-out stems to shelter ant colonies constitutes an extended phenotype because foraging workers protect the flowers of live individuals in the same patch. Also, through this process these dried-out stems indirectly favor the reproduction (and so the fitness) of the next generation including both their own offspring and that of their siblings, alladding up to a potential case of inclusive fitness in plants

Estimation of Pap-test coverage in an area with an organised screening program: challenges for survey methods

BACKGROUND: The cytological screening programme of Viterbo has completed the second round of invitations to the entire target population (age 25–64). From a public health perspective, it is important to know the Pap-test coverage rate and the use of opportunistic screening. The most commonly used study design is the survey, but the validity of self-reports and the assumptions made about non respondents are often questioned. METHODS: From the target population, 940 women were sampled, and responded to a telephone interview about Pap-test utilisation. The answers were compared with the screening program registry; comparing the dates of Pap-tests reported by both sources. Sensitivity analyses were performed for coverage over a 36-month period, according to various assumptions regarding non respondents. RESULTS: The response rate was 68%. The coverage over 36 months was 86.4% if we assume that non respondents had the same coverage as respondents, 66% if we assume they were not covered at all, and 74.6% if we adjust for screening compliance in the non respondents. The sensitivity and specificity of the question, "have you ever had a Pap test with the screening programme" were 84.5% and 82.2% respectively. The test dates reported in the interview tended to be more recent than those reported in the registry, but 68% were within 12 months of each other. CONCLUSION: Surveys are useful tools to understand the effectiveness of a screening programme and women's self-report was sufficiently reliable in our setting, but the coverage estimates were strongly influenced by the assumptions we made regarding non respondents