From science to practice: Bringing innovations to agronomy and forestry

The challenge of the work presented here is to make innovative research output in the agronomy and forestry domain accessible to end-users, so that it can be practically applied. We have developed an approach that consists of three key-elements: an ontology with domain knowledge, a set of documents that have been annotated and meta-annotated, and a system (ask-Valerie) that is based on a dialogue to represent the interaction between end user and system.<br/> We show that the dialogue-metaphor is a good way of modelling the interaction between user and system. The system helps the user in formulating his question and in answering it in a useful way. Meta-annotations of key-paragraphs in the document-base turn out to be relevant in assessing in one glance what the content of a document is. <br/> End-users are very enthusiastic about the possibilities that ask-Valerie offers them in translating scientific results to their own situation

Engineering and Modeling the Electrophoretic Trapping of a Single Protein Inside a Nanopore

The ability to confine and to study single molecules has enabled important advances in natural and applied sciences. Recently, we have shown that unlabeled proteins can be confined inside the biological nanopore Cytolysin A (ClyA) and conformational changes monitored by ionic current recordings. However, trapping small proteins remains a challenge. Here we describe a system where steric, electrostatic, electrophoretic, and electroosmotic forces are exploited to immobilize a small protein, dihydrofolate reductase (DHFR), inside ClyA. Assisted by electrostatic simulations, we show that the dwell time of DHFR inside ClyA can be increased by orders of magnitude (from milliseconds to seconds) by manipulation of the DHFR charge distribution. Further, we describe a physical model that includes a double energy barrier and the main electrophoretic components for trapping DHFR inside the nanopore. Simultaneous fits to the voltage dependence of the dwell times allowed retrieving direct estimates of the cis and trans translocation probabilities, the mean dwell time, and the force exerted by the electroosmotic flow on the protein (≅9 pN at -50 mV). The observed binding of NADPH to the trapped DHFR molecules suggested that the engineered proteins remained folded and functional inside ClyA. Contact-free confinement of single proteins inside nanopores can be employed for the manipulation and localized delivery of individual proteins and will have further applications in single-molecule analyte sensing and enzymology studies

Обоснование критериев оценки биологической активности минеральных вод

Автори під час проведення порівняльного аналізу біологічної дії борвміщуючих мінеральних вод різної мінералізації виявила якісну та кількісну однаковість їх впливу. Інтегративні показники властивостей мінеральних вод, що використовуються на сьогоднішній день, не пояснюють виявлені особливості дії. Автори роблять висновок, що застосування відносних показників властивостей мінеральних вод, прив’язаних до 1 граму мінеральних речовин, які містяться у воді, дозволить більш точно оцінювати властивості мінеральних вод.Authors, carrying out the comparative analysis of biological action of the boron containing mineral waters of a different mineralization, have found out qualitative and quantitative similarity of their influence. Used for today integrate indicators of properties of mineral waters do not explain the taped features of action. Authors come to conclusion that transition to relative indicators of properties of the mineral waters, adhered to 1 gram of the mineral substances containing in water, allows to estimate properties of mineral waters more precisely

Local impact analysis of climate change on precipitation extremes : are high-resolution climate models needed for realistic simulations?

This study explores whether climate models with higher spatial resolutions provide higher accuracy for precipitation simulations and/or different climate change signals. The outputs from two convection-permitting climate models (ALARO and CCLM) with a spatial resolution of 3-4 km are compared with those from the coarse-scale driving models or reanalysis data for simulating/projecting daily and sub-daily precipitation quantiles. Validation of historical design precipitation statistics derived from intensityduration-frequency (IDF) curves shows a better match of the convection-permitting model results with the observations-based IDF statistics compared to the driving GCMs and reanalysis data. This is the case for simulation of local subdaily precipitation extremes during the summer season, while the convection-permitting models do not appear to bring added value to simulation of daily precipitation extremes. Results moreover indicate that one has to be careful in assuming spatial-scale independency of climate change signals for the delta change downscaling method, as high-resolution models may show larger changes in extreme precipitation. These larger changes appear to be dependent on the timescale, since such intensification is not observed for daily timescales for both the ALARO and CCLM models

Harmonising the Teaching of Scientific Communication Skills Through the Development of an E-Learning Tool

Effective communication is a fundamental graduate attribute. University graduates are expected to be critical thinkers who can apply their knowledge and research skills to solve complex problems in a range of contexts. Developing and applying these skills requires a consistent approach to teaching and assessment of scientific communication at the undergraduate level. Despite being taught by leading academics with an abundance of scientific communication experience, anecdotal student feedback suggests that instruction across disciplines varies; creating student confusion and a lack of confidence in scientific literacy more broadly. Given the importance of preparing research-ready graduates, our project adopted a multidisciplinary approach to harmonise teaching scientific communication skills across subjects in the School of Biomedical Sciences. This was achieved through the development of an e-learning module designed to teach the requisite skills that can be applied across all forms of scientific communication. The module is innovative in enhancing students’ scientific literacy skills. Students can develop, practise and demonstrate their critical thinking and communication skills, as well as improve their understanding of scientific writing by completing the activities embedded within the two-level module; with the added benefit of strengthening their understanding of scientific communication (and associated skills) and thereby improving student employability

The CORDEX.be initiative as a foundation for climate services in Belgium

The CORDEX.be project created the foundations for Belgian climate services by producing high-resolution Belgian climate information that (a) incorporates the expertise of the different Belgian climate modeling groups and that (b) is consistent with the outcomes of the international CORDEX ("COordinated Regional Climate Downscaling Experiment") project. The key practical tasks for the project were the coordination of activities among different Belgian climate groups, fostering the links to specific international initiatives and the creation of a stakeholder dialogue. Scientifically, the CORDEX.be project contributed to the EURO-CORDEX project, created a small ensemble of High-Resolution (H-Res) future projections over Belgium at convection-permitting resolutions and coupled these to seven Local Impact Models. Several impact studies have been carried out. The project also addressed some aspects of climate change uncertainties. The interactions and feedback from the stakeholder dialogue led to different practical applications at the Belgian national level

Impact of infection on proteome-wide glycosylation revealed by distinct signatures for bacterial and viral pathogens

Mechanisms of infection and pathogenesis have predominantly been studied based on differential gene or protein expression. Less is known about posttranslational modifications, which are essential for protein functional diversity. We applied an innovative glycoproteomics method to study the systemic proteome-wide glycosylation in response to infection. The protein site-specific glycosylation was characterized in plasma derived from well-defined controls and patients. We found 3862 unique features, of which we identified 463 distinct intact glycopeptides, that could be mapped to more than 30 different proteins. Statistical analyses were used to derive a glycopeptide signature that enabled significant differentiation between patients with a bacterial or viral infection. Furthermore, supported by a machine learning algorithm, we demonstrated the ability to identify the causative pathogens based on the distinctive host blood plasma glycopeptide signatures. These results illustrate that glycoproteomics holds enormous potential as an innovative approach to improve the interpretation of relevant biological changes in response to infection

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.

Levels of circulating glucose are tightly regulated. To identify new loci influencing glycemic traits, we performed meta-analyses of 21 genome-wide association studies informative for fasting glucose, fasting insulin and indices of beta-cell function (HOMA-B) and insulin resistance (HOMA-IR) in up to 46,186 nondiabetic participants. Follow-up of 25 loci in up to 76,558 additional subjects identified 16 loci associated with fasting glucose and HOMA-B and two loci associated with fasting insulin and HOMA-IR. These include nine loci newly associated with fasting glucose (in or near ADCY5, MADD, ADRA2A, CRY2, FADS1, GLIS3, SLC2A2, PROX1 and C2CD4B) and one influencing fasting insulin and HOMA-IR (near IGF1). We also demonstrated association of ADCY5, PROX1, GCK, GCKR and DGKB-TMEM195 with type 2 diabetes. Within these loci, likely biological candidate genes influence signal transduction, cell proliferation, development, glucose-sensing and circadian regulation. Our results demonstrate that genetic studies of glycemic traits can identify type 2 diabetes risk loci, as well as loci containing gene variants that are associated with a modest elevation in glucose levels but are not associated with overt diabetes

Plasma Metabolomics Identifies Markers of Impaired Renal Function: A Meta-analysis of 3089 Persons with Type 2 Diabetes

CONTEXT: There is a need for novel biomarkers and better understanding of the pathophysiology of diabetic kidney disease. OBJECTIVE: To investigate associations between plasma metabolites and kidney function in people with type 2 diabetes (T2D). DESIGN: 3089 samples from individuals with T2D, collected between 1999 and 2015, from 5 independent Dutch cohort studies were included. Up to 7 years follow-up was available in 1100 individuals from 2 of the cohorts. MAIN OUTCOME MEASURES: Plasma metabolites (n = 149) were measured by nuclear magnetic resonance spectroscopy. Associations between metabolites and estimated glomerular filtration rate (eGFR), urinary albumin-to-creatinine ratio (UACR), and eGFR slopes were investigated in each study followed by random effect meta-analysis. Adjustments included traditional cardiovascular risk factors and correction for multiple testing. RESULTS: In total, 125 metabolites were significantly associated (PFDR = 1.5×10-32 - 0.046; β = -11.98-2.17) with eGFR. Inverse associations with eGFR were demonstrated for branched-chain and aromatic amino acids (AAAs), glycoprotein acetyls, triglycerides (TGs), lipids in very low-density lipoproteins (VLDL) subclasses, and fatty acids (PFDR < 0.03). We observed positive associations with cholesterol and phospholipids in high-density lipoproteins (HDL) and apolipoprotein A1 (PFDR < 0.05). Albeit some metabolites were associated with UACR levels (P < 0.05), significance was lost after correction for multiple testing. Tyrosine and HDL-related metabolites were positively associated with eGFR slopes before adjustment for multiple testing (PTyr = 0.003; PHDLrelated < 0.05), but not after. CONCLUSIONS: This study identified metabolites associated with impaired kidney function in T2D, implying involvement of lipid and amino acid metabolism in the pathogenesis. Whether these processes precede or are consequences of renal impairment needs further investigation