A Case Report: Building communities with training and resources for Open Science trainers

To foster responsible research and innovation, research communities, institutions, and funders are shifting their practices and requirements towards Open Science. Open Science skills are becoming increasingly essential for researchers. Indeed general awareness of Open Science has grown among EU researchers, but the practical adoption can be further improved. Recognizing a gap between the needed and the provided training offer, the FOSTER project offers practical guidance and training to help researchers learn how to open up their research within a particular domain or research environment. Aiming for a sustainable approach, FOSTER focused on strengthening the Open Science training capacity by establishing and supporting a community of trainers. The creation of an Open Science training handbook was a first step towards bringing together trainers to share their experiences and to create an open and living knowledge resource. A subsequent series of train-the-trainer bootcamps helped trainers to find inspiration, improve their skills and to intensify exchange within a peer group. Four trainers, who attended one of the bootcamps, contributed a case study on their experiences and how they rolled out Open Science training within their own institutions. On its platform the project provides a range of online courses and resources to learn about key Open Science topics. FOSTER awards users gamification badges when completing courses in order to provide incentives and rewards, and to spur them on to even greater achievements in learning. The paper at hand describes FOSTER Plus’ training strategies, shares the lessons learnt and provides guidance on how to reuse the project’s materials and training approaches

ORGANISATIONAL CULTURE IN BAKING COMPANY

V diplomskem delu sem predstavila organizacijsko kulturo v pekarskem podjetju Pekarna Blatnik d.o.o. in jo analizirala s pomočjo Harrisonovega vprašalnika. Vprašalnik je pokazal, da zaposleni niso najbolj zadovoljni s sedanjo organizacijsko kulturo, željni so sprememb in nove kulture. Organizacije bi morale namenjati več pozornosti organizacijski kulturi, saj je le ta pomembna za njeno trenutno in nadaljnjo delovanje. Z rednimi meritvami bi lahko vodstvo spremljalo stanje kulture v sami organizaciji. Vodstvo bi s tem pridobilo najbolj celosten in natančen vpogled v organizacijo in ugotovilo, ali je trenutna kultura ustrezna, uspešna in če omogoča dolgoročni uspeh.This undergraduate thesis discusses the organisational culture in a bakery company Pekarna Blatnik d.o.o. and analyses it with Harrison\u27s questionnaire. The questionnaire revealed that the employees are not entirely satisfied with the current organisational culture and that they wish for changes and new culture. Organisations should pay more attention to the organisational culture because this is important for its current and further services. Using regular measurements the management could monitor the state of culture in the organisation. Thus the management would gain an overall and accurate insight into the organisation and find out if the current culture is suitable and successful and if it enables a long-term success

Identification of markers and development of protein biochips for characterization of proteome and typing of malignant tissues

Malgré une incidence en décroissance, le cancer gastrique reste un des plus fréquents chez l homme et constitue la seconde cause de mortalité liée au cancer. Un des principaux obstacles pour améliorer le taux de survie est le manque de marqueurs diagnostiques permettant de déterminer les stages de développement cancéreux. Afin d isoler des molécules affines utilisables comme nouveaux marqueurs, une approche originale a été développée pour la construction d une banque de chaînes lourdes d anticorps de lama. La bibliothèque a été sélectionnée de manière différentielle par exposition sur phage en utilisant des extraits protéiques de tissus gastriques cancéreux et normaux. Après sélection, un ensemble de phages, démontrant une affinité différentielle pour les tissus sains et cancéreux, a permis la production d anticorps solubles et la purification par chromatographie d affinité des antigènes correspondants. Les antigènes exprimés de manière différentielle ont été résolus par électrophorèse 2D et identifiés par spectrométrie de masse. De plus, des domaines variables de chaînes lourdes de haute affinité reconnaissant spécifiquement les marqueurs cancéreux p53, Bcl-2 et VEGF ont été isolés de la bibliothèque et caractérisés en terme d expression, de production, de solubilité, de spécificité et d affinité. Sur les bases des séquences obtenues, un algorithme a été développé pour révéler les mécanismes de co-évolution entre la boucle CDR3 et le squelette des anticorps.Despite a declining incidence, gastric cancer is one of the commonest human cancers and is the second most frequent cause of cancer-related death. The main barrier for improving the survival rate is the lack of diagnostic markers able to determine developmental stages of the cancer. In order to isolate binders for novel cancer markers, an original approach was developed for construction of a heavy chain antibody library from llamas. The library was differentially screened on healthy versus tumorous gastric protein extracts using phage display. After selection, a pool of phages showing differential binding on cancerous vs normal tissue was used for soluble antibody production and further used for affinity chromatography of human cancerous tissue protein extracts. Differentially expressed antigens were resolved by 2D-electrophoresis and identified using mass spectrometry. In addition, high affinity heavy chain antibodies, specifically recognizing recombinant cancer biomarkers p53, Bcl-2 and VEGF were isolated from recombinant library and characterized in terms of expression, production, solubility, specificity and affinity. Isolated and publically available sequences were used to develop an original algorithm for the detection of somatic co-evolution processes at the interface between CDR3 hyper-variable loop and the antibody scaffold.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

The Global Sequence Signature algorithm unveils a structural network surrounding heavy chain CDR3 loop in Camelidae variable domains

International audienceBackground: A large fraction of camelid (camels and llamas) antibodies is composed of heavy chain-only homodimers, able to recognise antigens with their variable domain. Events in somatic assembly and maturation of antibodies such as hypermutations and rearrangement of variable loops (CDRs - complementary determining regions) and selection among a wide range of framework variants are generally considered to be random processes. Methods: An original algorithmic approach (Global Sequence Signature-GSS) was developed, able to take into account multiple functional and/or local sequence properties to detect scattered evolutionary constraints into sequences. Results: Using the GSS approach, we show that the length of the main hypervariable loop (CDR3) is linked to the nature of 19 surrounding residues on the scaffold. Surprisingly, the relation between CDR3 size and scaffold residues strongly depends on the considered species, illustrating either significant differences in selection mechanisms or functional constraints during antibody maturation. Conclusions: Combined with the statistical coupling analysis (SCA) approach at the level of scaffold residues, this study has unravelled a robust interaction network on antibody structure surrounding the CDR3 loop. General significance: In addition to the general applicability of the GSS algorithm, which can bring together functional and sequence data to locate hot spots of constrained evolution, the relationship between CDR3 and scaffold discussed here should be taken into account in protein engineering when designing antibody libraries. (c) 2013 Elsevier B.V. All rights reserved

Protein profiling gastric cancer and neighboring control tissues using high-content antibody microarrays

In this study, protein profiling was performed on gastric cancer tissue samples in order to identify proteins that could be utilized for an effective diagnosis of this highly heterogeneous disease and as targets for therapeutic approaches. To this end, 16 pairs of postoperative gastric adenocarcinomas and adjacent non-cancerous control tissues were analyzed on microarrays that contain 813 antibodies targeting 724 proteins. Only 17 proteins were found to be differentially regulated, with much fewer molecules than the numbers usually identified in studies comparing tumor to healthy control tissues. Insulin-like growth factor-binding protein 7 (IGFBP7), S100 calcium binding protein A9 (S100A9), interleukin-10 (IL-10) and mucin 6 (MUC6) exhibited the most profound variations. For an evaluation of the proteins\u27 capacity for discriminating gastric cancer, a Receiver Operating Characteristic curve analysis was performed, yielding an accuracy (area under the curve) value of 89.2% for distinguishing tumor from non-tumorous tissue. For confirmation, immunohistological analyses were done on tissue slices prepared from another cohort of patients with gastric cancer. The utility of the 17 marker proteins, and particularly the four molecules with the highest specificity for gastric adenocarcinoma, is discussed for them to act as candidates for diagnosis, even in serum, and targets for therapeutic approaches

Protein Profiling Gastric Cancer and Neighboring Control Tissues Using High-Content Antibody Microarrays

In this study, protein profiling was performed on gastric cancer tissue samples in order to identify proteins that could be utilized for an effective diagnosis of this highly heterogeneous disease and as targets for therapeutic approaches. To this end, 16 pairs of postoperative gastric adenocarcinomas and adjacent non-cancerous control tissues were analyzed on microarrays that contain 813 antibodies targeting 724 proteins. Only 17 proteins were found to be differentially regulated, with much fewer molecules than the numbers usually identified in studies comparing tumor to healthy control tissues. Insulin-like growth factor-binding protein 7 (IGFBP7), S100 calcium binding protein A9 (S100A9), interleukin-10 (IL‐10) and mucin 6 (MUC6) exhibited the most profound variations. For an evaluation of the proteins’ capacity for discriminating gastric cancer, a Receiver Operating Characteristic curve analysis was performed, yielding an accuracy (area under the curve) value of 89.2% for distinguishing tumor from non-tumorous tissue. For confirmation, immunohistological analyses were done on tissue slices prepared from another cohort of patients with gastric cancer. The utility of the 17 marker proteins, and particularly the four molecules with the highest specificity for gastric adenocarcinoma, is discussed for them to act as candidates for diagnosis, even in serum, and targets for therapeutic approaches

Exploiting sequence and stability information for directing nanobody stability engineering

[Background] Variable domains of camelid heavy-chain antibodies, commonly named nanobodies, have highbiotechnological potential. In view of their broad range of applications in research, diagnostics and therapy,engineering their stability is of particular interest. One important aspect is the improvement of thermostability,because it can have immediate effects on conformational stability, protease resistance and aggregation pro-pensity of the protein[Methods] We analyzed the sequences and thermostabilities of 78 purified nanobody binders. From this data,potentially stabilizing amino acid variations were identified and studied experimentally.Results:Some mutations improved the stability of nanobodies by up to 6.1 °C, with an average of 2.3 °C acrosseight modified nanobodies. The stabilizing mechanism involves an improvement of both conformational stabilityand aggregation behavior, explaining the variable degree of stabilization in individual molecules. In some in-stances, variations predicted to be stabilizing actually led to thermal destabilization of the proteins. The reasonsfor this contradiction between prediction and experiment were investigated.[Conclusions] The results reveal a mutational strategy to improve the biophysical behavior of nanobody bindersand indicate a species-specificity of nanobody architecture[General significance] This study illustrates the potential and limitations of engineering nanobody thermostabilityby merging sequence information with stability data, an aspect that is becoming increasingly important with therecent development of high-throughput biophysical methodsWe thank NanoTemper Technologies in Munich for its generous support with free DSF measurements. Funding by the European Union(grantnumber: Health-F4-2010-241481) as part of the Affinomics consortium is gratefully acknowledged.Peer reviewe