MAES Service Case: Wetland ecosystem condition mapping (v.1.0)

SWOS Technical publicationThe MAES working group is preparing the workshop on “ecosystem condition mapping” to streamline the efforts done so far with regards to the mapping and assessment of the condition of Europe’s ecosystems. The MAES WG has requested directly to SWOS partners a specific document to support the mapping and assessing wetland ecosystem condition for this workshop. This document shall highlight the different elements to take into account for the mapping and assessment of wetland ecosystems with the aim of supporting Member States and the European Commission in their efforts to better describe the situation of wetland ecosystems in Europe. This document represents the major output of the MAES Service case that shall show how SWOS outputs are useful to support the MAES WG with regards to wetland ecosystem mapping and assessment

The use of Earth Observation for wetland inventory, assessment and monitoring

The use of Earth Observation (EO) provides Contracting Parties to the Ramsar Convention on Wetlands with new approaches to ensure the wise use and conservation of wetlands at the national and global levels. EO has many applications including the inventory, assessment and monitoring of wetlands. As technology advances, previous limitations of EO will be reduced, and it is anticipated that the use of EO in the management of wetlands will increase. This Ramsar Technical Report aims to provide practitioners with an overview and illustration, through case studies, on the use of EO for implementation of the Convention and the wise use of wetlands more broadly

The Mediterranean Island Wetlands (MedIsWet) inventory: strengths and shortfalls of the currently available floristic data

MedIsWet (Conservation of the island wetlands of the Mediterranean Basin) is a MAVA funded project which aims at investigating all seasonal or permanent island wetlands both natural and artificial, with a minimum extent of 0.1 hectares. More than 16,000 wetlands from almost all the Mediterranean, including islands from France, Italy, Malta, Croatia, Cyprus, Tunisia, Turkey, Greece and Spain were mapped. Over 2,500 of them were inventoried in the field and more than 500 scientific contributions catalogued. In total, more than 35,000 plant occurrences were uploaded, in a standardised and comparable way, on the national open-source web portals. These can be related to the recorded threats, uses and other spatially retrievable information. Here, we show strengths and shortfalls of the already available information about the floristic records. Although further improvements are needed, we discuss how these data can be used for research and policy actions and to develop conservation projects

Critical Early Roles for col27a1a and col27a1b in Zebrafish Notochord Morphogenesis, Vertebral Mineralization and Post-embryonic Axial Growth

Fibrillar collagens are well known for their links to human diseases, with which all have been associated except for the two most recently identified fibrillar collagens, type XXIV collagen and type XXVII collagen. To assess functions and potential disease phenotypes of type XXVII collagen, we examined its roles in zebrafish embryonic and post-embryonic development.We identified two type XXVII collagen genes in zebrafish, col27a1a and col27a1b. Both col27a1a and col27a1b were expressed in notochord and cartilage in the embryo and early larva. To determine sites of type XXVII collagen function, col27a1a and col27a1b were knocked down using morpholino antisense oligonucleotides. Knockdown of col27a1a singly or in conjunction with col27a1b resulted in curvature of the notochord at early stages and formation of scoliotic curves as well as dysmorphic vertebrae at later stages. These defects were accompanied by abnormal distributions of cells and protein localization in the notochord, as visualized by transmission electron microscopy, as well as delayed vertebral mineralization as detected histologically.Together, our findings indicate a key role for type XXVII collagen in notochord morphogenesis and axial skeletogenesis and suggest a possible human disease phenotype

Importance of pre-analytical steps for transcriptome and RT-qPCR analyses in the context of the phase II randomised multicentre trial REMAGUS02 of neoadjuvant chemotherapy in breast cancer patients

<p>Abstract</p> <p>Background</p> <p>Identification of predictive markers of response to treatment is a major objective in breast cancer. A major problem in clinical sampling is the variability of RNA templates, requiring accurate management of tumour material and subsequent analyses for future translation in clinical practice. Our aim was to establish the feasibility and reliability of high throughput RNA analysis in a prospective trial.</p> <p>Methods</p> <p>This study was conducted on RNA from initial biopsies, in a prospective trial of neoadjuvant chemotherapy in 327 patients with inoperable breast cancer. Four independent centres included patients and samples. Human U133 GeneChips plus 2.0 arrays for transcriptome analysis and quantitative RT-qPCR of 45 target genes and 6 reference genes were analysed on total RNA.</p> <p>Results</p> <p>Thirty seven samples were excluded because <it>i) </it>they contained less than 30% malignant cells, or <it>ii) </it>they provided RNA Integrity Number (RIN) of poor quality. Among the 290 remaining cases, taking into account strict quality control criteria initially defined to ensure good quality of sampling, 78% and 82% samples were eligible for transcriptome and RT-qPCR analyses, respectively. For RT-qPCR, efficiency was corrected by using standard curves for each gene and each plate. It was greater than 90% for all genes. Clustering analysis highlighted relevant breast cancer phenotypes for both techniques (ER+, PR+, HER2+, triple negative). Interestingly, clustering on trancriptome data also demonstrated a "centre effect", probably due to the sampling or extraction methods used in on of the centres. Conversely, the calibration of RT-qPCR analysis led to the centre effect withdrawing, allowing multicentre analysis of gene transcripts with high accuracy.</p> <p>Conclusions</p> <p>Our data showed that strict quality criteria for RNA integrity assessment and well calibrated and standardized RT-qPCR allows multicentre analysis of genes transcripts with high accuracy in the clinical context. More stringent criteria are needed for transcriptome analysis for clinical applications.</p