Economic Evaluation and Biodiversity Conservation of Animal Genetic Resources

Rapidly declining biodiversity has made international and national policies focus on the question of how best to protect genetic resources. Loss of biodiversity does not only concern wildlife, but equally affects agriculturally used species. These species, of foremost importance for the subsistence of humankind, are subject to pressures sometimes similar and sometimes very distinct from those of their wild counterparts. And so are the losses implied by this decline in diversity. This handbook was conceived within the project Sustainable conservation of animal genetic resources in marginal rural areas: Integrating molecular genetics, socio-economics and geostatistical approaches (ECONOGENE – EC-QLK5-CT-2001-02461) to review and design methods that can serve as a basis to guide conservation policies for livestock breeds at risk of extinction. It is part of the broader effort of a multidisciplinary research team assessing the diversity of European sheep and goat breeds. The final goal of the project is to assess the impact of current and future policies on these breeds. --

Integrated Pest Management Portfolios in UK Arable Farming: Results of a Farmer Survey

BACKGROUND. Farmers are faced with a wide range of pest management (PM) options which can be adopted in isolation or alongside complement or substitute strategies. This paper presents the results of a survey of UK cereal producers focusing on the character and diversity of PM strategies currently used by, or available to, farmers. In addition, the survey asked various questions pertaining to agricultural policy participation, attitude toward environmental issues, sources of PM advice and information and the important characteristics of PM technologies. RESULTS. The results indicate that many farmers do make use of a suite of PM techniques and that their choice of integrated PM (IPM) portfolio appears to be jointly dictated by farm characteristics and Government policy. Results also indicate that portfolio choice does affect the number of subsequent insecticide applications per crop. CONCLUSIONS. These results help to identify the type of IPM portfolios considered adoptable by farmers and highlight the importance of substitution in IPM portfolios. As such, these results will help to direct R&D effort toward the realisation of more sustainable PM approaches and aid the identification of potential portfolio adopters. These findings highlight the opportunity a revised agri-environmental policy design could generate in terms of by enhancing coherent IPM portfolio adoption.Pest management; pesticide alternatives; technology and portfolio approaches;

Livestock biodiversity conservation : the case of sheep and goat breeds in European marginal areas

To address the conservation of sheep and goat breeds and their contribution to rural development in marginal areas, this Thesis adopts an interdisciplinary approach, structured around four aspects: society and policy choices, noticeably the Common Agricultural Policy (CAP); geographic location and marginality; farmers' choices; and the functioning of human actors and networks. The limited impact of CAP funds for livestock biodiversity conservation is assessed and alternatives to paying direct subsidies are treated. The importance of farmers' participation in education programmes focused on this type of animal breeding and of the adoption of ad-hoc marketing strategies is found to be paramount for successful on-farm conservation in the framework of an econometric ordered choice model. This model is complemented by an index measuring the relative marginality of a region. The index is built in a Geographic Information System in order to assess the impact of the farm location on breeding choices. It combines regional socio-demographic and economic variables with a concept of marginality based on land-use. Findings reveal that the farm location in a marginal area adversely affects the development of local breeds. A sociological qualitative case study provides further insights into motives and practices driving local breed conservation dynamics. Combining results from the various parts points to the need for an integrated approach to rural development that takes into account the functioning of networks and the importance of social capital. It is suggested that a multiple-stakeholder participative approach to problem-solving be adopted. This shall address issues such as the conflict over access to resources and the creation of new and niche marketing approaches that may enhance the contact between breeders and consumers

GAEC workshop 2012 technical report

The report describes the main technical findings and results of the Good Agricultural and Environmental Condition (GAEC) workshop 2012 organised by the Joint Research Centre (JRC). The workshop was held at the JRC in Ispra from 8th-10th October 2012. 110 delegates attended the workshop representing 24 European Union Member States, two candidate countries (Croatia and Iceland) and Commission services. The workshop focussed on implementation and control issues related to the identification and measure of landscape features and buffer strips, as well as on scientific references for definition and mapping of soil related issues (e. g. soil erosion or soil organic matter). Participants also showed much interest on technical aspects related to the implementation of the future CAP with particular reference to landscape features in the framework of the so-called Ecological Focus Area. The workshop allows setting up and fine-tuning future main JRC activities taking into account DG AGRI and Member States inputs.JRC.H.4-Monitoring Agricultural Resource

Cropland and grassland management data needs from existing IACS sources

This report analyses the use of IACS and other datasets for reporting and accounting Greenhouse Gas (GHG) emissions and removals in the land use sector. The land use sector comprises land use, land use change and forestry (LULUCF) as well as agriculture, jointly referred to as agriculture, forestry and other land use (AFOLU). Decision 529/2013/EU of the European Council and the Parliament of 21 May 2013 brings the LULUCF sector in the EU emission accounting obligations. These new accounting obligations for EU member states are phased in over a period extending to 2022. This Report, as part of work performed by the JRC for DG Climate Action under an Administrative Arrangement (AA), aims at exploring the usefulness for cropland management (CM) and grazing land management (GM) accounting of the vast amount of data already regularly collected on the EU level in the context of environmental and agricultural policies. One of the most promising datasets to meet LULUCF reporting obligations is the “Integrated Administration and Control System” (IACS) that has been set up by all member states to manage the implementation of the Common Agricultural Policy, and its GIS, “the Land Parcel Identification System” (LPIS). The data the LPIS holds are geo-referenced polygons of land parcels (units of management or production), and information on the type of land cover, as a minimum in terms of broad categories such as arable land, grassland, permanent crops, and broad families of crops, with their area (eligible hectares). The LPIS is a pan-EU database that provides very detailed and accurate information on the status of agricultural land cover at any given time since 2005. The potential of the LPIS to efficiently track land use changes is derived from its pan-European semantic definition of agricultural land cover types, and the mandatory adequate update cycle of the dataset. This study assessed other potential datasets, including Eurostat “Land Use/Cover Area Frame Survey” (LUCAS); the Farm Structure Surveys (FSS); the Farm Accountancy Data Network; CORINE Land Cover.JRC.D.5-Food Securit

Retrospective study testing next generation sequencing of selected cancer-associated genes in resected prostate cancer

PURPOSE: Prostate cancer (PCa) has a highly heterogeneous outcome. Beyond Gleason Score, Prostate Serum Antigen and tumor stage, nowadays there are no biological prognostic factors to discriminate between indolent and aggressive tumors. The most common known genomic alterations are the TMPRSS-ETS translocation and mutations in the PI3K, MAPK pathways and in p53, RB and c-MYC genes. The aim of this retrospective study was to identify by next generation sequencing the most frequent genetic variations (GVs) in localized and locally advanced PCa underwent prostatectomy and to investigate their correlation with clinical-pathological variables and disease progression. RESULTS: Identified non-synonymous GVs included TP53 p.P72R (78% of tumors), two CSFR1 SNPs, rs2066934 and rs2066933 (70%), KDR p.Q472H (67%), KIT p.M541L (28%), PIK3CA p.I391M (19%), MET p.V378I (10%) and FGFR3 p.F384L/p.F386L (8%). TP53 p.P72R, MET p.V378I and CSFR1 SNPs were significantly associated with the HI risk group, TP53 and MET variations with T≥T2c. FGFR3 p.F384L/p.F386L was correlated with T≤T2b. MET p.V378I mutation, detected in 20% of HI risk patients, was associated with early biochemical recurrence. EXPERIMENTAL DESIGN: Nucleic acids were obtained from tissue samples of 30 high (HI) and 30 low-intermediate (LM) risk patients, according to D'Amico criteria. Genomic DNA was explored with the Ion_AmpliSeq_Cancer_Hotspot_Panel_v.2 including 50 cancer-associated genes. GVs with allelic frequency (AF) ≥10%, affecting protein function or previously associated with cancer, were correlated with clinical-pathological variables. CONCLUSION: Our results confirm a complex mutational profile in PCa, supporting the involvement of TP53, MET, FGFR3, CSF1R GVs in tumor progression and aggressiveness

Biological and clinical effects of abiraterone on anti-resorptive and anabolic activity in bone microenvironment

Abiraterone acetate (ABI) is associated not only with a significant survival advantage in both chemotherapy-naive and -treated patients with metastatic castration-resistant prostate cancer (mCRPC), but also with a delay in time to development of Skeletal Related Events and in radiological skeletal progression. These bone benefits may be related to a direct effect on prostate cancer cells in bone or to a specific mechanism directed to bone microenvironment. To test this hypothesis we designed an in vitro study aimed to evaluate a potential direct effect of ABI on human primary osteoclasts/osteoblasts (OCLs/OBLs). We also assessed changes in bone turnover markers, serum carboxy-terminal collagen crosslinks (CTX) and alkaline phosphatase (ALP), in 49 mCRPC patients treated with ABI.Our results showed that non-cytotoxic doses of ABI have a statistically significant inhibitory effect on OCL differentiation and activity inducing a down-modulation of OCL marker genes TRAP, cathepsin K and metalloproteinase-9. Furthermore ABI promoted OBL differentiation and bone matrix deposition up-regulating OBL specific genes, ALP and osteocalcin. Finally, we observed a significant decrease of serum CTX values and an increase of ALP in ABI-treated patients.These findings suggest a novel biological mechanism of action of ABI consisting in a direct bone anabolic and anti-resorptive activity

Performing oncological procedures during COVID-19 outbreak: a picture from an Italian cancer center

Aim: Since SARS-CoV-2 infection rapidly spread around the world, Italy has quickly become one of the most affected countries. Healthcare systems introduced strict infection control measures to ensure optimal care, especially in frail groups such as cancer patients (pts). This study investigated the efficacy of SARS-CoV-2 pre-procedure screening and whether COVID-19 influenced timely diagnosis and therapy. Methods: Data of oncological procedures of pts with confirmed or suspected cancer diagnosis, treated at Oncology Department or coming from Emergency Department of San Luigi Gonzaga Hospital between June 2020 and March 2021 were retrospectively collected. A nasopharyngeal swab (NPS) was performed in outpatients 24/48 h before procedures. Inpatients were tested by NPS before and after hospitalization. Results: Two hundred and twenty-one pts were included in this analysis. Median age was 73 years, males were 58%. Eastern Cooperative Oncology Group (ECOG) Performance Status was 0 or 1 in 88% of pts. The most frequent cancer type was lung cancer (57%). Stages IV were 77%. Two hundred and forty-three scheduled procedures were performed with diagnostic (n: 142; 58%), therapeutic (n: 55; 23%), and palliative (n: 46; 19%) intent. One hundred and four and 139 procedures were performed in out- and in-pts, respectively. Of the 234 NPS performed, 10 (4%) were positive. Two pts were infected during hospitalization, 8 in community. Most of them were asymptomatic, while only 2 had mild symptoms. Eight procedures (3%) were postponed, 1 cancelled, while 2 were performed in positive pts. Median time to resolution of the infection was 17 days (11–36). Median delay in the procedures was 25 days (14–55). Five pts started systemic treatment, after a median time of 37.5 days (13–57). Conclusions: SARS-CoV-2 infection led to the postponement of a small, but not negligible percentage of oncological procedures. However, the low infection rate observed suggests that structured screening for COVID-19 is critical for the best management of scheduled procedures during pandemic

Comparing T Cell Subsets in Broncho-Alveolar Lavage (BAL) and Peripheral Blood in Patients with Advanced Lung Cancer

Background: Lung cancer (LC) tissue for immunological characterization is often scarce. We explored and compared T cell characteristics between broncho-alveolar lavage from tumor affected (t-BAL) and contralateral lung (cl-BAL), with matched peripheral blood (PB). Methods: BAL and PB were collected during bronchoscopy for diagnostic and/or therapeutic purposes in patients with monolateral primary lesion. Results: Of 33 patients undergoing BAL and PB sampling, 21 had histologically-confirmed LC. Most cases were locally-advanced or metastatic non-small cell LC. T cell characteristics were not significantly different in t-BAL vs. cl-BAL. Compared to PB, CD8 T cells in BAL presented features of immune activation and exhaustion (high PD-1, low IFN-g production). Accordingly, regulatory CD4 T cells were also higher in BAL vs. PB. When dichotomizing T cell density in t-BAL in high and low, we found that PD-L1 expression in LC was associated with T cell density in t-BAL. T-BAL with high T cell density had higher %IFN-g+CD8 T cells and lower %T-regs. Conclusion: In BAL from advanced LC patients, T cells present features of exhaustion. T cells in t-BAL could be the best surrogate of tumor-infiltrating T cell, and future studies should evaluate T cell phenotype and density as potential biomarkers for cancer immunotherapy outcome