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  • Isakova, Elena P.; Matushkina, Irina N.; Popova, Tatyana N.; Dergacheva, Darya I.; Gessler, Natalya N.; Klein, Olga I.; Semenikhina, Anastasya V.; Deryabina, Yulia I.; La Porta, Nicola; Saris, Nils-Eric L. (Multidisciplinary Digital Publishing Institute, 2020)
    In this study, we evaluated the metabolic profile of the aerobic microorganism of <i>Endomyces magnusii</i> with a complete respiration chain and well-developed mitochondria system during long-lasting cultivation. The yeast was grown in batches using glycerol and glucose as the sole carbon source for a week. The profile included the cellular biological and chemical parameters, which determined the redox status of the yeast cells. We studied the activities of the antioxidant systems (catalases and superoxide dismutases), glutathione system enzymes (glutathione peroxidase and reductase), aconitase, as well as the main enzymes maintaining NADPH levels in the cells (glucose-6-phosphate dehydrogenase and NADP<sup>+</sup>-isocitrate dehydrogenase) during aging of <i>Endomyces magnusii</i> on two kinds of substrates. We also investigated the dynamics of change in oxidized and reduced glutathione, conjugated dienes, and reactive oxidative species in the cells at different growth stages, including the deep stationary stages. Our results revealed a similar trend in the changes in the activity of all the enzymes tested, which increased 2&ndash;4-fold upon aging. The yeast cytosol had a very high reduced glutathione content, 22 times than that of <i>Saccharomyces cerevisiae</i>, and remained unchanged during growth, whereas there was a 7.5-fold increase in the reduced glutathione-to-oxidized glutathione ratio. The much higher level of reactive oxidative species was observed in the cells in the late and deep stationary phases, especially in the cells using glycerol. Cell aging of the culture grown on glycerol, which promotes active oxidative phosphorylation in the mitochondria, facilitated the functioning of powerful antioxidant systems (catalases, superoxide dismutases, and glutathione system enzymes) induced by reactive oxidative species. Moreover, it stimulated NADPH synthesis, regulating the cytosolic reduced glutathione level, which in turn determines the redox potential of the yeast cell during the early aging process.
  • Hussein, Tareq; Atashi, Nahid; Sogacheva, Larisa; Hakala, Simo; Dada, Lubna; Petäjä, Tuukka; Kulmala, Markku (Multidisciplinary Digital Publishing Institute, 2020)
    We characterized new particle formation (NPF) events in the urban background of Amman during August 2016&ndash;July 2017. The monthly mean of submicron particle number concentration was 1.2 &times; 10<sup>4</sup>&ndash;3.7 &times; 10<sup>4</sup> cm<sup>&minus;3</sup> (exhibited seasonal, weekly, and diurnal variation). Nucleation mode<i> </i>(10&ndash;15 nm) concentration was 0.7 &times; 10<sup>3</sup>&ndash;1.1 &times; 10<sup>3</sup> cm<sup>&minus;3</sup> during daytime with a sharp peak (1.1 &times; 10<sup>3</sup>&ndash;1.8 &times; 10<sup>3</sup> cm<sup>&minus;3</sup>) around noon. We identified 110 NPF events (&asymp;34% of all days) of which 55 showed a decreasing mode diameter after growth. The NPF event occurrence was higher in summer than in winter, and events were accompanied with air mass back trajectories crossing over the Eastern Mediterranean. The mean nucleation rate (<i>J</i><sub>10</sub>) was 1.9 &plusmn; 1.1 cm<sup>&minus;3</sup> s<sup>&minus;1</sup> (monthly mean 1.6&ndash;2.7 cm<sup>&minus;3</sup> s<sup>&minus;1</sup>) and the mean growth rate was 6.8 &plusmn; 3.1 nm/h (4.1&ndash;8.8 nm/h). The formation rate did not have a seasonal pattern, but the growth rate had a seasonal variation (maximum around August and minimum in winter). The mean condensable vapor source rate was 4.1 &plusmn; 2.2 10<sup>5</sup> molecules/cm<sup>3</sup> s (2.6&ndash;6.9 &times; 10<sup>5</sup> molecules/cm<sup>3</sup> s) with a seasonal pattern (maximum around August). The mean condensation sink was 8.9 &plusmn; 3.3 &times; 10<sup>&minus;3</sup> s<sup>&minus;1</sup> (6.4&ndash;14.8 &times; 10<sup>&minus;3</sup> s<sup>&minus;1</sup>) with a seasonal pattern (minimum around June and maximum in winter).
  • Veloz Villavicencio, Eliana; Mali, Tuulia; Mattila, Hans K.; Lundell, Taina (Multidisciplinary Digital Publishing Institute, 2020)
    Four well-studied saprotrophic <i>Basidiomycota Agaricomycetes</i> species with different decay strategies were cultivated on solid lignocellulose substrates to compare their extracellular decomposing carbohydrate-active and lignin-attacking enzyme production profiles. Two <i>Polyporales</i> species, the white rot fungus <i>Phlebia radiata</i> and brown rot fungus <i>Fomitopsis pinicola</i>, as well as one <i>Agaricales</i> species, the intermediate &ldquo;grey&rdquo; rot fungus <i>Schizophyllum commune</i>, were cultivated on birch wood pieces for 12 weeks, whereas the second <i>Agaricales</i> species, the litter-decomposing fungus <i>Coprinopsis cinerea</i> was cultivated on barley straw for 6 weeks under laboratory conditions. During 3 months of growth on birch wood, only the white rot fungus <i>P. </i><i>radiata</i> produced high laccase and MnP activities. The brown rot fungus <i>F. pinicola</i> demonstrated notable production of xylanase activity up to 43 nkat/mL on birch wood, together with moderate &beta;-glucosidase and endoglucanase cellulolytic activities. The intermediate rot fungus <i>S. commune</i> was the strongest producer of &beta;-glucosidase with activities up to 54 nkat/mL, and a notable producer of xylanase activity, even up to 620 nkat/mL, on birch wood. Low lignin-attacking but moderate activities against cellulose and hemicellulose were observed with the litter-decomposer <i>C. cinerea</i> on barley straw. Overall, our results imply that plant cell wall decomposition ability of taxonomically and ecologically divergent fungi is in line with their enzymatic decay strategy, which is fundamental in understanding their physiology and potential for biotechnological applications.
  • Starr, Mike; Deng, Biar; Helenius, Juha (Multidisciplinary Digital Publishing Institute, 2020)
    The dependency on rainfed agriculture and weak adaptability of the agricultural sector to climate change threaten food security in Sub-Saharan Africa (SSA). Biochar has widely been touted as a relatively easy means of increasing the soil water storage capacity of soils and thereby improving or maintaining crop yields. In this study we simulated the effect of biochar amendment on sorghum aboveground biomass and grain yield at a site in South Sudan. We used the model <i>AquaCrop</i> parameterized using site, soil, and cropping management data from a field experiment carried out at the site in 2011 and 2012, which were both wet years. Changes in soil hydraulic properties due to biochar were based on a published meta-analysis study. In order to investigate whether the response to biochar differed in dry years, simulations were also carried out for 1990, which was the driest year during the period 1979&ndash;2014. Measured and modelled biomass and yields with and without biochar for 2011 and 2012 were compared. Simulated and measured yields depended on growing season rainfall and distribution. The simulations showed that biochar amendment had an effect on rooting zone soil water content and sorghum biomass and grain yield in 1990, but not in 2011 and 2012. In view of expected climate change, the results have important implications for sorghum production and the potential use of biochar in SSA. Given the limited response of grain yield to biochar shown in our simulations, careful selection of sorghum variety and cultivar and consideration of planting date may be a more effective means of improving yields than applying biochar.
  • Nowakowska, Maria B.; Douillard, François P.; Lindström, Miia (Multidisciplinary Digital Publishing Institute, 2019)
    The botulinum neurotoxin (BoNT) has been extensively researched over the years in regard to its structure, mode of action, and applications. Nevertheless, the biological roles of four proteins encoded from a number of BoNT gene clusters, i.e., OrfX1-3 and P47, are unknown. Here, we investigated the diversity of <em>orfX-p47</em> gene clusters using in silico analytical tools. We show that the orfX-p47 cluster was not only present in the genomes of BoNT-producing bacteria but also in a substantially wider range of bacterial species across the bacterial phylogenetic tree. Remarkably, the <em>orfX-p47</em> cluster was consistently located in proximity to genes coding for various toxins, suggesting that OrfX1-3 and P47 may have a conserved function related to toxinogenesis and/or pathogenesis, regardless of the toxin produced by the bacterium. Our work also led to the identification of a putative novel BoNT-like toxin gene cluster in a Bacillus isolate. This gene cluster shares striking similarities to the BoNT cluster, encoding a <em>bont/ntnh</em>-like gene and <em>orfX-p47</em>, but also differs from it markedly, displaying additional genes putatively encoding the components of a polymorphic ABC toxin complex. These findings provide novel insights into the biological roles of OrfX1, OrfX2, OrfX3, and P47 in toxinogenesis and pathogenesis of BoNT-producing and non-producing bacteria.
  • Repo, Petteri; Matschoss, Kaisa (Multidisciplinary Digital Publishing Institute, 2019)
    Social innovation is concerned with social mobilization and impact, and is increasingly seen as an option to address sustainability challenges. Nevertheless, the concept of social innovation is quite open in character and requires empirical accommodation to establish how it differs from other types of innovation in this setting. This article contributes empirically to the concept of social innovation as it reviews categories of success factors of social innovation against those of five other innovation types (product, service, governmental, organizational, system) in 202 innovation cases that focus on climate action, environment, resource efficiency and raw materials. Statistical analysis with contingency tables is applied to examine the distribution of five kinds of success factors across the innovation types: economic, environmental, political, social, and technological. The results confirm empirically that social innovation is indeed a distinct type of innovation. There are statistically significant differences in the distribution of categories of success factors between social innovation on the one hand and product, service and governance innovation on the other. In addition to the prevalence of social success factors, social innovation is characterized by a lesser emphasis on political and technological success factors.
  • Nieminen, Juuso Henrik; Valtteri Pesonen, Henri (Multidisciplinary Digital Publishing Institute, 2019)
    Universal Design has been promoted to address the diversity of learners in higher education. However, rarely have Universal Design implementations been evaluated by listening to the voices of disabled students. For this study, we investigated the perceptions of three disabled students who took part in an undergraduate mathematics course designed with the principles of Universal Design for Learning and Assessment. The study consists of two parts. First, we observed the experiences students had in relation to the accessibility of the course design. The second part consisted of a further analysis of the students identifying processes to understand how they talked about their learning disabilities during the course. Our results highlight many opportunities and challenges that the course offered to the students, whilst also raising concerns about how the students excluded themselves from their student cohort in their identifying narratives. Based on our results, we argue that Universal Design should be returned to its roots by connecting it with the social model of disability. We call for future research to learn from our mistakes and consider the identifying processes of the students while designing, and hopefully co-designing, inclusive learning environments in mathematics.
  • Tuomainen, Katja; Al-Samadi, Ahmed; Potdar, Swapnil; Turunen, Laura; Turunen, Minna; Karhemo, Piia-Riitta; Bergman, Paula; Risteli, Maija; Åström, Pirjo; Tiikkaja, Riia; Grenman, Reidar; Wennerberg, Krister; Monni, Outi; Salo, Tuula (Multidisciplinary Digital Publishing Institute, 2019)
    In vitro cancer drug testing carries a low predictive value. We developed the human leiomyoma&ndash;derived matrix &ldquo;Myogel&rdquo; to better mimic the human tumor microenvironment (TME). We hypothesized that Myogel could provide an appropriate microenvironment for cancer cells, thereby allowing more in vivo&ndash;relevant drug testing. We screened 19 anticancer compounds, targeting the epidermal growth factor receptor (EGFR), MEK, and PI3K/mTOR on 12 head and neck squamous cell carcinoma (HNSCC) cell lines cultured on plastic, mouse sarcoma&ndash;derived Matrigel (MSDM), and Myogel. We applied a high-throughput drug screening assay under five different culturing conditions: cells in two-dimensional (2D) plastic wells and on top or embedded in Matrigel or Myogel. We then compared the efficacy of the anticancer compounds to the response rates of 19 HNSCC monotherapy clinical trials. Cancer cells on top of Myogel responded less to EGFR and MEK inhibitors compared to cells cultured on plastic or Matrigel. However, we found a similar response to the PI3K/mTOR inhibitors under all culturing conditions. Cells grown on Myogel more closely resembled the response rates reported in EGFR-inhibitor monotherapy clinical trials. Our findings suggest that a human tumor matrix improves the predictability of in vitro anticancer drug testing compared to current 2D and MSDM methods.
  • Hussein, Tareq; Alameer, Ali; Jaghbeir, Omar; Albeitshaweesh, Kolthoum; Malkawi, Mazen; Boor, Brandon E.; Koivisto, Antti Joonas; Löndahl, Jakob; Alrifai, Osama; Al-Hunaiti, Afnan (Multidisciplinary Digital Publishing Institute, 2019)
    There is limited research on indoor air quality in the Middle East. In this study, concentrations and size distributions of indoor particles were measured in eight Jordanian dwellings during the winter and summer. Supplemental measurements of selected gaseous pollutants were also conducted. Indoor cooking, heating via the combustion of natural gas and kerosene, and tobacco/shisha smoking were associated with significant increases in the concentrations of ultrafine, fine, and coarse particles. Particle number (PN) and particle mass (PM) size distributions varied with the different indoor emission sources and among the eight dwellings. Natural gas cooking and natural gas or kerosene heaters were associated with PN concentrations on the order of 100,000 to 400,000 cm<sup>&minus;3</sup> and PM<sub>2.5</sub> concentrations often in the range of 10 to 150 &micro;g/m<sup>3</sup>. Tobacco and shisha (waterpipe or hookah) smoking, the latter of which is common in Jordan, were found to be strong emitters of indoor ultrafine and fine particles in the dwellings. Non-combustion cooking activities emitted comparably less PN and PM<sub>2.5</sub>. Indoor cooking and combustion processes were also found to increase concentrations of carbon monoxide, nitrogen dioxide, and volatile organic compounds. In general, concentrations of indoor particles were lower during the summer compared to the winter. In the absence of indoor activities, indoor PN and PM<sub>2.5</sub> concentrations were generally below 10,000 cm<sup>&minus;3</sup> and 30 &micro;g/m<sup>3</sup>, respectively. Collectively, the results suggest that Jordanian indoor environments can be heavily polluted when compared to the surrounding outdoor atmosphere primarily due to the ubiquity of indoor combustion associated with cooking, heating, and smoking.
  • Fung, Pak Lun; Zaidan, Martha A.; Sillanpää, Salla; Kousa, Anu; Niemi, Jarkko V.; Timonen, Hilkka; Kuula, Joel; Saukko, Erkka; Luoma, Krista; Petäjä, Tuukka; Tarkoma, Sasu; Kulmala, Markku; Hussein, Tareq (Multidisciplinary Digital Publishing Institute, 2019)
    Missing data has been a challenge in air quality measurement. In this study, we develop an input-adaptive proxy, which selects input variables of other air quality variables based on their correlation coefficients with the output variable. The proxy uses ordinary least squares regression model with robust optimization and limits the input variables to a maximum of three to avoid overfitting. The adaptive proxy learns from the data set and generates the best model evaluated by adjusted coefficient of determination (adjR<sup>2</sup>). In case of missing data in the input variables, the proposed adaptive proxy then uses the second-best model until all the missing data gaps are filled up. We estimated black carbon (BC) concentration by using the input-adaptive proxy in two sites in Helsinki, which respectively represent street canyon and urban background scenario, as a case study. Accumulation mode, traffic counts, nitrogen dioxide and lung deposited surface area are found as input variables in models with the top rank. In contrast to traditional proxy, which gives 20&ndash;80% of data, the input-adaptive proxy manages to give full continuous BC estimation. The newly developed adaptive proxy also gives generally accurate BC (street canyon: adjR<sup>2</sup> = 0.86&ndash;0.94; urban background: adjR<sup>2</sup> = 0.74&ndash;0.91) depending on different seasons and day of the week. Due to its flexibility and reliability, the adaptive proxy can be further extend to estimate other air quality parameters. It can also act as an air quality virtual sensor in support with on-site measurements in the future.
  • Lempiäinen, Juha; Ijäs, Petra; Niiranen, Teemu J.; Kaste, Markku; Karhunen, Pekka J.; Lindsberg, Perttu J.; Erkinjuntti, Timo; Melkas, Susanna (Multidisciplinary Digital Publishing Institute, 2019)
    Haptoglobin (Hp) is a plasma protein that binds free hemoglobin and protects tissues from oxidative damage. An Hp2 allele has been associated with an increased risk of cardiovascular complications. On the other hand, recent studies have suggested that Hp1 allele increases risk to develop severe cerebral small vessel disease. We aimed to replicate this finding in a first-ever stroke patient cohort. Hp was genotyped by PCR and gel electrophoresis in the Helsinki Stroke Aging Memory Study in patients with DNA and magnetic resonance imaging (MRI) available (SAM; <i>n</i> = 316). Lacunar infarcts and white matter lesions (WML) classified by Fazekas grading from brain MRI were associated with Hp genotypes. As population controls, we used participants of Cardiovascular diseases&mdash;a sub study of Health 2000 Survey (<i>n</i> = 1417). In the SAM cohort, 63.0% of Hp1-1 carriers (<i>n</i> = 46), 52.5% of Hp1-2 carriers (<i>n</i> = 141) and 51.2% of Hp2-2 carriers (<i>n</i> = 129) had severe WML (<i>p</i> = 0.372). There was no difference in severe WMLs between Hp1-1 vs. Hp1-2 and Hp2-2 carriers (<i>p</i> = 0.201). In addition, 68.9% of Hp1-1 carriers (<i>n</i> = 45), 58.5% of Hp1-2 carriers (<i>n</i> = 135), and 61.8% of Hp2-2 carriers (<i>n</i> = 126) had one or more lacunar lesions (<i>p</i> = 0.472). There was no difference in the number of patients with at least one lacunar infarct between Hp1-1 vs. Hp1-2 and Hp2-2 groups (<i>p</i> = 0.322). Neither was there any difference when diabetic patients (type I and II) were examined separately. Hp1 allele is not associated with an increased risk for cerebral small vessel disease in a well-characterized Finnish stroke patient cohort.
  • Myllys, Nanna; Ponkkonen, Tuomo; Chee, Sabrina; Smith, James (Multidisciplinary Digital Publishing Institute, 2019)
    The role of an oxidation product of trimethylamine, trimethylamine oxide, in atmospheric particle formation is studied using quantum chemical methods and cluster formation simulations. Molecular-level cluster formation mechanisms are resolved, and theoretical results on particle formation are confirmed with mass spectrometer measurements. Trimethylamine oxide is capable of forming only one hydrogen bond with sulfuric acid, but unlike amines, trimethylamine oxide can form stable clusters via ion&ndash;dipole interactions. That is because of its zwitterionic structure, which causes a high dipole moment. Cluster growth occurs close to the acid:base ratio of 1:1, which is the same as for other monoprotic bases. Enhancement potential of trimethylamine oxide in particle formation is much higher than that of dimethylamine, but lower compared to guanidine. Therefore, at relatively low concentrations and high temperatures, guanidine and trimethylamine oxide may dominate particle formation events over amines.
  • Shishido, Tania Keiko; Popin, Rafael Vicentini; Jokela, Jouni; Wahlsten, Matti; Fiore, Marli Fatima; Fewer, David P.; Herfindal, Lars; Sivonen, Kaarina (Multidisciplinary Digital Publishing Institute, 2019)
    Cyanobacteria are photosynthetic organisms that produce a large diversity of natural products with interesting bioactivities for biotechnological and pharmaceutical applications. Cyanobacterial extracts exhibit toxicity towards other microorganisms and cancer cells and, therefore, represent a source of potentially novel natural products for drug discovery. We tested 62 cyanobacterial strains isolated from various Brazilian biomes for antileukemic and antimicrobial activities. Extracts from 39 strains induced selective apoptosis in acute myeloid leukemia (AML) cancer cell lines. Five of these extracts also exhibited antifungal and antibacterial activities. Chemical and dereplication analyses revealed the production of nine known natural products. Natural products possibly responsible for the observed bioactivities and five unknown, chemically related chlorinated compounds present only in Brazilian cyanobacteria were illustrated in a molecular network. Our results provide new information on the vast biosynthetic potential of cyanobacteria isolated from Brazilian environments.
  • Dubashynskaya, Natallia; Poshina, Daria; Raik, Sergei; Urtti, Arto; Skorik, Yury A. (Multidisciplinary Digital Publishing Institute, 2019)
    Polysaccharides, such as cellulose, hyaluronic acid, alginic acid, and chitosan, as well as polysaccharide derivatives, have been successfully used to augment drug delivery in the treatment of ocular pathologies. The properties of polysaccharides can be extensively modified to optimize ocular drug formulations and to obtain biocompatible and biodegradable drugs with improved bioavailability and tailored pharmacological effects. This review discusses the available polysaccharide choices for overcoming the difficulties associated with ocular drug delivery, and it explores the reasons for the dependence between the physicochemical properties of polysaccharide-based drug carriers and their efficiency in different formulations and applications. Polysaccharides will continue to be of great interest to researchers endeavoring to develop ophthalmic drugs with improved effectiveness and safety.
  • Li, Shitian; Ramakrishnan, Muthusamy; Vinod, Kunnummal Kurungara; Kalendar, Ruslan; Yrjälä, Kim; Zhou, Mingbing (Multidisciplinary Digital Publishing Institute, 2019)
    Bamboo, a non-timber grass species, known for exceptionally fast growth is a commercially viable crop. Long terminal repeat (LTR) retrotransposons, the main class I mobile genetic elements in plant genomes, are highly abundant (46%) in bamboo, contributing to genome diversity. They play significant roles in the regulation of gene expression, chromosome size and structure as well as in genome integrity. Due to their random insertion behavior, interspaces of retrotransposons can vary significantly among bamboo genotypes. Capitalizing this feature, inter-retrotransposon amplified polymorphism (IRAP) is a high-throughput marker system to study the genetic diversity of plant species. To date, there are no transposon based markers reported from the bamboo genome and particularly using IRAP markers on genetic diversity. <i>Phyllostachys</i> genus of Asian bamboo is the largest of the Bambusoideae subfamily, with great economic importance. We report structure-based analysis of bamboo genome for the LTR-retrotransposon superfamilies, <i>Ty3-gypsy</i> and <i>Ty1-copia</i>, which revealed a total of 98,850 retrotransposons with intact LTR sequences at both the ends. Grouped into 64,281 clusters/scaffold using CD-HIT-EST software, only 13 clusters of retroelements were found with more than 30 LTR sequences and with at least one copy having all intact protein domains such as <i>gag</i> and polyprotein. A total of 16 IRAP primers were synthesized, based on the high copy numbers of conserved LTR sequences. A study using these IRAP markers on genetic diversity and population structure of 58 Asian bamboo accessions belonging to the genus <i>Phyllostachys</i> revealed 3340 amplicons with an average of 98% polymorphism. The bamboo accessions were collected from nine different provinces of China, as well as from Italy and America. A three phased approach using hierarchical clustering, principal components and a model based population structure divided the bamboo accessions into four sub-populations, PhSP1, PhSP2, PhSP3 and PhSP4. All the three analyses produced significant sub-population wise consensus. Further, all the sub-populations revealed admixture of alleles. The analysis of molecular variance (AMOVA) among the sub-populations revealed high intra-population genetic variation (75%) than inter-population. The results suggest that <i>Phyllostachys</i> bamboos are not well evolutionarily diversified, although geographic speciation could have occurred at a limited level. This study highlights the usability of IRAP markers in determining the inter-species variability of Asian bamboos.
  • Candy, Seona; Turner, Graham; Larsen, Kirsten; Wingrove, Kate; Steenkamp, Julia; Friel, Sharon; Lawrence, Mark (Multidisciplinary Digital Publishing Institute, 2019)
    Dietary change has been suggested as a key strategy to maintain food security, improve health and reduce environmental impacts in the face of rising populations, resource scarcity and climate change impacts, particularly in developed countries. This paper presents findings from a quantitative modelling analysis of food availability and environmental implications of shifting the current average Australian dietary pattern to one of two alternative, healthy dietary patterns, the &lsquo;healthy mixed diet&rsquo;, with a mixture of animal and plant foods, and the &lsquo;healthy plant-based diet&rsquo;, with only plant foods. Both were constructed in accordance with the Australian Dietary Guideline recommendations, and four sustainability principles: Avoiding over-consumption, reducing intake of discretionary foods, reducing animal products, and reducing food waste. It was assumed that all food was provided domestically where possible, and export of foods only occurred when there was a surplus to domestic requirements. The authors compared the impacts of each dietary pattern on direct food availability, water use, land use, greenhouse gas emissions, fuel and energy use and fertiliser use. The plant-based diet had the best overall environmental and direct food availability outcomes, however had key vulnerabilities in terms of fertiliser and cropping land availability. For the agricultural sector overall, changes in diet had little effect on environmental impact due to the amount and nature of Australian exports, indicating that changes to production methods are also necessary. Likewise, changing diets had little effect on the existing environmentally intensive Australian economy, indicating that changes to other sectors are also necessary.
  • Lampiselkä, Jarkko; Kaasinen, Arja; Kinnunen, Päivi; Malmi, Lauri (Multidisciplinary Digital Publishing Institute, 2019)
    This study provides an overview of the didactic focus areas in educational research in biology, chemistry and physics, seeking to identify the focus areas that are investigated frequently and those that have been studied rarely or not at all. We applied the didactic focus-based categorization analysis method (DFCM), which is based on an extension of the didactic triangle. As the data set, we used 250 papers published in the <i>Nordic Studies in Science Education</i> (NorDiNa) between 2005 and 2013, and the European Science Education Research Association (ESERA) 2013 conference proceedings covering education at upper secondary and tertiary levels. The results show that the teacher&rsquo;s pedagogical actions and the student&ndash;content relationship were the most frequently studied aspects. On the other hand, teachers&rsquo; reflections on the students&rsquo; perceptions and attitudes about goals and content, and teachers&rsquo; conceptions of the students&rsquo; actions towards achieving the goals were studied least. Irrespective of the publication forum, the distributions of foci to different categories were quite similar. Our historical analysis completes the recent studies in the field as it is based on the theory driven categorization system instead of the data driven approaches used by the previous researchers. Moreover, our further observations on more recent publications suggest that no significant changes have taken place, and therefore wider discussion about the scope and the coverage of the research in science education is needed.
  • Lumen, Dave; Näkki, Simo; Imlimthan, Surachet; Lambidis, Elisavet; Sarparanta, Mirkka; Xu, Wujun; Lehto, Vesa-Pekka; Airaksinen, Anu J. (Multidisciplinary Digital Publishing Institute, 2019)
    Polyethylene glycol (PEG) has been successfully used for improving circulation time of several nanomaterials but prolonging the circulation of porous silicon nanoparticles (PSi NPs) has remained challenging. Here, we report a site specific radiolabeling of dual-PEGylated thermally oxidized porous silicon (DPEG-TOPSi) NPs and investigation of influence of the PEGylation on blood circulation time of TOPSi NPs. <i>Trans</i>-cyclooctene conjugated DPEG-TOPSi NPs were radiolabeled through a click reaction with [<sup>111</sup>In]In-DOTA-PEG<sub>4</sub>-tetrazine (DOTA = 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) and the particle behavior was evaluated in vivo in Balb/c mice bearing 4T1 murine breast cancer allografts. The dual-PEGylation significantly prolonged circulation of [<sup>111</sup>In]In-DPEG-TOPSi particles when compared to non-PEGylated control particles, yielding 10.8 &plusmn; 1.7% of the injected activity/g in blood at 15 min for [<sup>111</sup>In]In-DPEG-TOPSi NPs. The improved circulation time will be beneficial for the accumulation of targeted DPEG-TOPSi to tumors.
  • Ala-Poikela, Marjo; Rajamäki, Minna-Liisa; Valkonen, Jari P.T. (Multidisciplinary Digital Publishing Institute, 2019)
    Host proteins that are central to infection of potyviruses (genus <i>Potyvirus</i>; family Potyviridae) include the eukaryotic translation initiation factors eIF4E and eIF(iso)4E. The potyviral genome-linked protein (VPg) and the helper component proteinase (HCpro) interact with each other and with eIF4E and eIF(iso)4E and proteins are involved in the same functions during viral infection. VPg interacts with eIF4E/eIF(iso)4E via the 7-methylguanosine cap-binding region, whereas HCpro interacts with eIF4E/eIF(iso)4E via the 4E-binding motif YXXXXL&Phi;, similar to the motif in eIF4G. In this study, HCpro and VPg were found to interact in the nucleus, nucleolus, and cytoplasm in cells infected with the potyvirus potato virus A (PVA). In the cytoplasm, interactions between HCpro and VPg occurred in punctate bodies not associated with viral replication vesicles. In addition to HCpro, the 4E-binding motif was recognized in VPg of PVA. Mutations in the 4E-binding motif of VPg from PVA weakened interactions with eIF4E and heavily reduced PVA virulence. Furthermore, mutations in the 4G-binding domain of eIF4E reduced interactions with VPg and abolished interactions with HCpro. Thus, HCpro and VPg can both interact with eIF4E using the 4E-binding motif. Our results suggest a novel interaction network used by potyviruses to interact with host plants via translation initiation factors.
  • Strona, Giovanni; Fattorini, Simone; Fiasca, Barbara; Di Lorenzo, Tiziana; Di Cicco, Mattia; Lorenzetti, Walter; Boccacci, Francesco; Galassi, Diana M.P. (Multidisciplinary Digital Publishing Institute, 2019)
    We introduce a suite of software tools aimed at investigating multiple bio-ecological facets of aquatic Groundwater Dependent Ecosystems (GDEs). The suite focuses on: (1) threats posed by pollutants to GDE invertebrates (Ecological Risk, ER); (2) threats posed by hydrological and hydromorphological alterations on the subsurface zone of lotic systems and groundwater-fed springs (Hydrological-Hydromorphological Risk, HHR); and (3) the conservation priority of GDE communities (Groundwater Biodiversity Concern index, GBC). The ER is assessed by comparing tolerance limits of invertebrate species to specific pollutants with the maximum observed concentration of the same pollutants at the target site(s). Comparison is based on an original, comprehensive dataset including the most updated information on tolerance to 116 pollutants for 474 freshwater invertebrate species. The HHR is assessed by accounting for the main direct and indirect effects on both the hyporheic zone of lotic systems and groundwater-fed springs, and by scoring each impact according to the potential effect on subsurface invertebrates. Finally, the GBC index is computed on the basis of the taxonomical composition of a target community, and allows the evaluation of its conservation priority in comparison to others. The software suite is freely available at: by registered users.

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