First report of "Cotoneaster pannosus" Franch. ("Rosaceae") in Tarragona Province, and updated distribution area in Spain

Cotoneaster pannosus (Rosaceae), an ornamental shrub native to China, is reported for the first time in Tarragona Province (Catalonia, Spain). Data on demography and accompanying species for the new locality are provided, in addition to a chrorological update at nation level.

Pollinators of an endemic and endangered species, Mammillaria gaumeri (Cactaceae), in its natural habitat (coastal dune) and in a botanical garden.

Mammillaria gaumeri (Britton & Ross) Orcutt (Cactaceae), an endemic plant of the Yucatan Peninsula, is included by the Mexican government in the list of species that require special protection. Its natural habitat is now restricted to fragmented areas and protection programs involve botanical gardens in growing individuals rescued from disturbed areas. Little information is available on the reproductive characteristics of this species and nothing is known of its pollinators. We investigated the visitors of M. gaumeri flowers, collecting and observing bee species in its natural habitat (i.e., coastal dune) and in a botanical garden, where coastal dune vegetation had been created. Observations were made on plants whose density was artificially increased by grouping flowering individuals. At each site, we: 1) collected insects visiting the flowers; 2) recorded number of visits; and 3) video-recorded bee movements on the flowers. As expected, the number of bee species and visitation frequency were higher at the botanical garden than at the coastal dune. After landing on a flower, bees either inspected the anthers or dived among them. These behaviors, carried out by all observed species, seemed related to the state of the anthers (full or empty of pollen) and stigma lobes (opened or closed). Specifically, visits lasted longer when anthers were full of pollen and stigma lobes were opened. The same bee species recorded on the dune were also recorded at the botanical garden, suggesting that the artificial dune at the botanical garden offered suitable conditions for the natural pollinators of this endangered cactus.

Collaborative artistic laboratories. Transfrontier spaces of cultural production

The appearance of the open code paradigm and the demands of social movements have permeated the ways in which today’s cultural institutions are organized. This article analyzes the birth of a new critical and cooperative spatiality and how it is transforming current modes of cultural research and production. It centers on the potential for establishing the new means of cooperation that are being tested in what are defined as collaborative artistic laboratories. These are hybrid spaces of research and creation based on networked and cooperative structures producing a new societal-technical body that forces us to reconsider the traditional organic conditions of the productive scenarios of knowledge and artistic practice.

The Interlaboratory Robustness Of Next-Generation Sequencing (IRON) Study Phase II: Deep-Sequencing Analyses Of Hematological Malignancies Performed In 8,867 Cases By An International Network Involving 27 Laboratories

Introduction: Amplicon deep-sequencing using second-generation sequencing technology is an innovative molecular diagnostic technique and enables a highly-sensitive detection of mutations. As an international consortium we had investigated previously the robustness, precision, and reproducibility of 454 amplicon next-generation sequencing (NGS) across 10 laboratories from 8 countries (Leukemia, 2011;25:1840-8).

Aims: In Phase II of the study, we established distinct working groups for various hematological malignancies, i.e. acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN), and multiple myeloma. Currently, 27 laboratories from 13 countries are part of this research consortium. In total, 74 gene targets were selected by the working groups and amplicons were developed for a NGS deep-sequencing assay (454 Life Sciences, Branford, CT). A data analysis pipeline was developed to standardize mutation interpretation both for accessing raw data (Roche Amplicon Variant Analyzer, 454 Life Sciences) and variant interpretation (Sequence Pilot, JSI Medical Systems, Kippenheim, Germany).

Results: We will report on the design, standardization, quality control aspects, landscape of mutations, as well as the prognostic and predictive utility of this assay in a cohort of 8,867 cases. Overall, 1,146 primer sequences were designed and tested. In detail, for example in AML, 924 cases had been screened for CEBPA mutations. RUNX1 mutations were analyzed in 1,888 cases applying the deep-sequencing read counts to study the stability of such mutations at relapse and their utility as a biomarker to detect residual disease. Analyses of DNMT3A (n=1,041) were focused to perform landscape investigations and to address the prognostic relevance. Additionally, this working group is focusing on TET2, ASXL1, and TP53 analyses. A novel prognostic model is being developed allowing stratification of AML into prognostic subgroups based on molecular markers only. In ALL, 1,124 pediatric and adult cases have been screened, including 763 assays for TP53 mutations both at diagnosis and relapse of ALL. Pediatric and adult leukemia expert labs developed additional content to study the mutation incidence of other B and T lineage markers such as IKZF1, JAK2, IL7R, PAX5, EP300, LEF1, CRLF2, PHF6, WT1, JAK1, PTEN, AKT1, IL7R, NOTCH1, CREBBP, or FBXW7. Further, the molecular landscape of CLL is changing rapidly. As such, a separate working group focused on analyses including NOTCH1, SF3B1, MYD88, XPO1, FBXW7 and BIRC3. Currently, 922 cases were screened to investigate the range of mutational burden of NOTCH1 mutations for their prognostic relevance. In MDS, RUNX1 mutation analyses were performed in 977 cases. The prognostic relevance of TP53 mutations in MDS was assessed in additional 327 cases, including isolated deletions of chromosome 5q. Next, content was developed targeting genes of the cellular splicing component, e.g. SF3B1, SRSF2, U2AF1, and ZRSR2. In BCR-ABL1-negative MPN, nine genes of interest (JAK2, MPL, TET2, CBL, KRAS, EZH2, IDH1, IDH2, ASXL1) have been analyzed in a cohort of 155 primary myelofibrosis cases searching for novel somatic mutations and addressing their relevance for disease progression and leukemia transformation. Moreover, an assay was developed and applied to CMML cases allowing the simultaneous analysis of 25 leukemia-associated target genes in a single sequencing run using just 20 ng of starting DNA. Finally, nine laboratories are studying CML, applying ultra-deep sequencing of the BCR-ABL1 tyrosine kinase domain. Analyses were performed on 615 cases investigating the dynamics of expansion of mutated clones under various tyrosine kinase inhibitor therapies.

Conclusion: Molecular characterization of hematological malignancies today requires high diagnostic sensitivity and specificity. As part of the IRON-II study, a network of laboratories analyzed a variety of disease entities applying amplicon-based NGS assays. Importantly, the consortium not only standardized assay design for disease-specific panels, but also achieved consensus on a common data analysis pipeline for mutation interpretation. Distinct working groups have been forged to address scientific tasks and in total 8,867 cases had been analyzed thus far.

Botanical travel, climate and David Moore’s moral geographies of Europe

During his forty-year curatorship of the Royal Dublin Society's botanical gardens in Glasnevin (1838–1879), David Moore undertook a number of excursions to continental Europe. These served to deepen the networks of plant exchange between Dublin and other botanical institutions and allowed him to examine the relationships between climate, plant survivability and societal development. This paper focuses on two trips taken in the 1860s to Scandinavia and Iberia and charts how Moore situated his experience of these places within a climatic hermeneutic. Moore's understanding of northern and southern Europe was organized around a set of judgments about their relative backwardness or advancement with respect to his experience of home and was seen through the lens of a moral climatology. Moreover, his Scots Presbyterian background and his commitment to natural theology informed his interpretation of the landscapes he encountered in his excursions across Europe.

Identification of vegetable oil botanical speciation in refined vegetable oil blends using an innovative combination of chromatographic and spectroscopic techniques

European Regulation 1169/2011 requires producers of foods that contain refined vegetable oils to label the oil types. A novel rapid and staged methodology has been developed for the first time to identify common oil species in oil blends. The qualitative method consists of a combination of a Fourier Transform Infrared (FTIR) spectroscopy to profile the oils and fatty acid chromatographic analysis to confirm the composition of the oils when required. Calibration models and specific classification criteria were developed and all data were fused into a simple decision-making system. The single lab validation of the method demonstrated the very good performance (96% correct classification, 100% specificity, 4% false positive rate). Only a small fraction of the samples needed to be confirmed with the majority of oils identified rapidly using only the spectroscopic procedure. The results demonstrate the huge potential of the methodology for a wide range of oil authenticity work.

Guidance for laboratories performing molecular pathology for cancer patients

Molecular testing is becoming an important part of the diagnosis of any patient with cancer. The challenge to laboratories is to meet this need, using reliable methods and processes to ensure that patients receive a timely and accurate report on which their treatment will be based. The aim of this paper is to provide minimum requirements for the management of molecular pathology laboratories. This general guidance should be augmented by the specific guidance available for different tumour types and tests. Preanalytical considerations are important, and careful consideration of the way in which specimens are obtained and reach the laboratory is necessary. Sample receipt and handling follow standard operating procedures, but some alterations may be necessary if molecular testing is to be performed, for instance to control tissue fixation. DNA and RNA extraction can be standardised and should be checked for quality and quantity of output on a regular basis. The choice of analytical method(s) depends on clinical requirements, desired turnaround time, and expertise available. Internal quality control, regular internal audit of the whole testing process, laboratory accreditation, and continual participation in external quality assessment schemes are prerequisites for delivery of a reliable service. A molecular pathology report should accurately convey the information the clinician needs to treat the patient with sufficient information to allow for correct interpretation of the result. Molecular pathology is developing rapidly, and further detailed evidence-based recommendations are required for many of the topics covered here.