Optical quality assurance of GEM foils

An analysis software was developed for the high aspect ratio optical scanning system in the Detec- tor Laboratory of the University of Helsinki and the Helsinki Institute of Physics. The system is used e.g. in the quality assurance of the GEM-TPC detectors being developed for the beam diagnostics system of the SuperFRS at future FAIR facility. The software was tested by analyzing five CERN standard GEM foils scanned with the optical scanning system. The measurement uncertainty of the diameter of the GEM holes and the pitch of the hole pattern was found to be 0.5 {\mu}m and 0.3 {\mu}m, respectively. The software design and the performance are discussed. The correlation between the GEM hole size distribution and the corresponding gain variation was studied by comparing them against a detailed gain mapping of a foil and a set of six lower precision control measurements. It can be seen that a qualitative estimation of the behavior of the local variation in gain across the GEM foil can be made based on the measured sizes of the outer and inner holes.Comment: 12 pages, 29 figure

Keinot edistää sää- ja ilmastoriskien hallintaa

ELASTINEN-tutkimushankkeessa selvitettiin sää- ja ilmastoriskien hallinnan tilaa Suomessa ja arvioitiin riskienhallintakeinoja sekä eri toimijoiden roolia. Lisäksi tarkasteltiin, miten riskienhallinnan kustannuksia ja hyötyjä arvioidaan sekä miten riskienhallinta voidaan kääntää liiketoiminnaksi. Yhteiskunnan toimivuuden ja turvallisuuden ylläpitäminen edellyttää aktiivista varautumista sään ääriilmiöihin. Hankkeen tulosten mukaan suomalaiset organisaatiot eivät usein arvioi sää- ja ilmastoriskejä systemaattisesti. Varautumisessa tulee ottaa huomioon, että ilmastonmuutos voi muuttaa sään ääri-ilmiöitä, niiden esiintymistiheyttä ja voimakkuutta. Näin varautuminen sään ääri ilmiöihin on myös osa sopeutumista ilmastonmuutokseen. ELASTINEN-hanke esittää kolme suositusta, joilla sää- ja ilmastoriskien hallintaa voitaisiin parantaa ja sopeutumistyötä tukea: 1) monipuolistetaan tiedon tuottoa ja käyttöä, 2) vahvistetaan yhteistyötä ja kehitetään toimintatapoja sekä 3) kehitetään palveluita ja liiketoimintamahdollisuuksia. Suositusten toteuttamiseksi esitetään toimenpide-ehdotuksia, minkä lisäksi on tunnistettu toimien toteuttajatahoja. Nykyistä monipuolisempi ja helpommin saatavilla oleva tieto parantaisi mahdollisuuksia arvioida ja hallita sää- ja ilmastoriskejä sekä kykyä sopeutua ilmastonmuutoksen vaikutuksiin. Suomessa tulisi myös arvioida säännöllisesti Suomen ulkopuolella tapahtuvia ilmastonmuutoksen vaikutuksia, jotka voivat heijastua Suomeen. Sää- ja ilmastoriskien hallintatoimia tulisi valita ja arvioida myös taloudellisen tehokkuuden näkökulmasta

Cinnamic Acid and Sorbic acid Conversion Are Mediated by the Same Transcriptional Regulator in Aspergillus niger

Cinnamic acid is an aromatic compound commonly found in plants and functions as a central intermediate in lignin synthesis. Filamentous fungi are able to degrade cinnamic acid through multiple metabolic pathways. One of the best studied pathways is the non-oxidative decarboxylation of cinnamic acid to styrene. In Aspergillus niger, the enzymes cinnamic acid decarboxylase (CdcA, formally ferulic acid decarboxylase) and the flavin prenyltransferase (PadA) catalyze together the non-oxidative decarboxylation of cinnamic acid and sorbic acid. The corresponding genes, cdcA and padA, are clustered in the genome together with a putative transcription factor previously named sorbic acid decarboxylase regulator (SdrA). While SdrA was predicted to be involved in the regulation of the non-oxidative decarboxylation of cinnamic acid and sorbic acid, this was never functionally analyzed. In this study, A. niger deletion mutants of sdrA, cdcA, and padA were made to further investigate the role of SdrA in cinnamic acid metabolism. Phenotypic analysis revealed that cdcA, sdrA and padA are exclusively involved in the degradation of cinnamic acid and sorbic acid and not required for other related aromatic compounds. Whole genome transcriptome analysis of ΔsdrA grown on different cinnamic acid related compounds, revealed additional target genes, which were also clustered with cdcA, sdrA, and padA in the A. niger genome. Synteny analysis using 30 Aspergillus genomes demonstrated a conserved cinnamic acid decarboxylation gene cluster in most Aspergilli of the Nigri clade. Aspergilli lacking certain genes in the cluster were unable to grow on cinnamic acid, but could still grow on related aromatic compounds, confirming the specific role of these three genes for cinnamic acid metabolism of A. niger.Peer reviewe

Large-scale production of cellulose-binding domains : adsorption studies using CBD-FITC conjugates

A method for the gram-scale production of cellulose-binding domains (CBD) through the proteolytic digestion of a commercial nzymatic preparation (Celluclast) was developed. The CBD obtained, isolated from Trichoderma reesei cellobiohydrolase I, is highly pure and heavily glycosylated. The purified peptide has a molecular weight of 8.43 kDa, comprising the binding module, a part of the linker, and about 30% glycosidic moiety. Its properties may thus be different from recombinant ones expressed in bacteria. CBDfluorescein isothiocyanate conjugates were used to study the CBD-cellulose interaction. The presence of fluorescent peptides adsorbed on crystalline and amorphous cellulose fibers suggests that amorphous regions have a higher concentration of binding sites. The adsorption is reversible, but desorption is a very slow process.Fundação para a Ciência e a Tecnologia (FCT

Policy monitoring in the EU: The impact of institutions, implementation, and quality

Policy monitoring is often seen as a crucial ingredient of policy evaluation, but theoretically informed empirical analyses of real-world policy monitoring practices are still rare. This paper addresses this gap by focusing on climate policy monitoring in the European Union, which has a relatively stringent system of greenhouse gas monitoring but a much less demanding approach to monitoring policies. It explores how institutional settings, policy implementation, and the quality of information may impact the practices and politics of policy monitoring. Drawing on quantitative regression models and qualitative interviews, it demonstrates that policy monitoring has evolved over time and is itself subject to implementation pressures, but also exhibits learning effects that improve its quality. In further developing both everyday policy monitoring practices and academic understanding of them, there is a need to pay attention to their design—specifically, the impact of any overarching rules, the institutional support for implementation, and the criteria governing the quality of the information they deliver. In short, policy monitoring should be treated as a governance activity in its own right, raising many different design challenges

Implications of climate change for agricultural productivity in the early twenty-first century

This paper reviews recent literature concerning a wide range of processes through which climate change could potentially impact global-scale agricultural productivity, and presents projections of changes in relevant meteorological, hydrological and plant physiological quantities from a climate model ensemble to illustrate key areas of uncertainty. Few global-scale assessments have been carried out, and these are limited in their ability to capture the uncertainty in climate projections, and omit potentially important aspects such as extreme events and changes in pests and diseases. There is a lack of clarity on how climate change impacts on drought are best quantified from an agricultural perspective, with different metrics giving very different impressions of future risk. The dependence of some regional agriculture on remote rainfall, snowmelt and glaciers adds to the complexity. Indirect impacts via sea-level rise, storms and diseases have not been quantified. Perhaps most seriously, there is high uncertainty in the extent to which the direct effects of CO2 rise on plant physiology will interact with climate change in affecting productivity. At present, the aggregate impacts of climate change on global-scale agricultural productivity cannot be reliably quantified

Closely related fungi employ diverse enzymatic strategies to degrade plant biomass

Background Plant biomass is the major substrate for the production of biofuels and biochemicals, as well as food, textiles and other products. It is also the major carbon source for many fungi and enzymes of these fungi are essential for the depolymerization of plant polysaccharides in industrial processes. This is a highly complex process that involves a large number of extracellular enzymes as well as non-hydrolytic proteins, whose production in fungi is controlled by a set of transcriptional regulators. Aspergillus species form one of the best studied fungal genera in this field, and several species are used for the production of commercial enzyme cocktails. Results It is often assumed that related fungi use similar enzymatic approaches to degrade plant polysaccharides. In this study we have compared the genomic content and the enzymes produced by eight Aspergilli for the degradation of plant biomass. All tested Aspergilli have a similar genomic potential to degrade plant biomass, with the exception of A. clavatus that has a strongly reduced pectinolytic ability. Despite this similar genomic potential their approaches to degrade plant biomass differ markedly in the overall activities as well as the specific enzymes they employ. While many of the genes have orthologs in (nearly) all tested species, only very few of the corresponding enzymes are produced by all species during growth on wheat bran or sugar beet pulp. In addition, significant differences were observed between the enzyme sets produced on these feedstocks, largely correlating with their polysaccharide composition. Conclusions These data demonstrate that Aspergillus species and possibly also other related fungi employ significantly different approaches to degrade plant biomass. This makes sense from an ecological perspective where mixed populations of fungi together degrade plant biomass. The results of this study indicate that combining the approaches from different species could result in improved enzyme mixtures for industrial applications, in particular saccharification of plant biomass for biofuel production. Such an approach may result in a much better improvement of saccharification efficiency than adding specific enzymes to the mixture of a single fungus, which is currently the most common approach used in biotechnology.Peer reviewe

Stability mechanisms of a thermophilic laccase probed by molecular dynamics.

Laccases are highly stable, industrially important enzymes capable of oxidizing a large range of substrates. Causes for their stability are, as for other proteins, poorly understood. In this work, multiple-seed molecular dynamics (MD) was applied to a Trametes versicolor laccase in response to variable ionic strengths, temperatures, and glycosylation status. Near-physiological conditions provided excellent agreement with the crystal structure (average RMSD ∼0.92 Å) and residual agreement with experimental B-factors. The persistence of backbone hydrogen bonds was identified as a key descriptor of structural response to environment, whereas solvent-accessibility, radius of gyration, and fluctuations were only locally relevant. Backbone hydrogen bonds decreased systematically with temperature in all simulations (∼9 per 50 K), probing structural changes associated with enthalpy-entropy compensation. Approaching T opt (∼350 K) from 300 K, this change correlated with a beginning "unzipping" of critical β-sheets. 0 M ionic strength triggered partial denucleation of the C-terminal (known experimentally to be sensitive) at 400 K, suggesting a general salt stabilization effect. In contrast, F(-) (but not Cl(-)) specifically impaired secondary structure by formation of strong hydrogen bonds with backbone NH, providing a mechanism for experimentally observed small anion destabilization, potentially remedied by site-directed mutagenesis at critical intrusion sites. N-glycosylation was found to support structural integrity by increasing persistent backbone hydrogen bonds by ∼4 across simulations, mainly via prevention of F(-) intrusion. Hydrogen-bond loss in distinct loop regions and ends of critical β-sheets suggest potential strategies for laboratory optimization of these industrially important enzymes