Browsing by Subject "CAPTURE"

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  • Järviö, Natasha; Maljanen, Netta-Leena; Kobayashi, Yumi; Ryynänen, Toni; Tuomisto, Hanna (2021)
    Novel food production technologies are being developed to address the challenges of securing sustainable and healthy nutrition for the growing global population. This study assessed the environmental impacts of microbial protein (MP) produced by autotrophic hydrogen-oxidizing bacteria (HOB). Data was collected from a company currently producing MP using HOB (hereafter simply referred to as MP) on a small-scale. Earlier studies have performed an environmental assessment of MP on a theoretical basis but no study yet has used empirical data. An attributional life cycle assessment (LCA) with a cradle-to-gate approach was used to quantify global warming potential (GWP), land use, freshwater and marine eutrophication potential, water scarcity, human (non-)carcinogenic toxicity, and the cumulative energy demand (CED) of MP production in Finland. A Monte Carlo analysis was performed to assess uncertainties. The impacts of alternative production options and locations were explored. The impacts were compared with animal- and plant-based protein sources for human consumption as well as protein sources for feed. The results showed that electricity consumption had the highest contribution to environmental impacts. Therefore, the source of energy had a substantial impact on the results. MP production using hydropower as an energy source yielded 87.5% lower GWP compared to using the average Finnish electricity mix. In comparison with animal-based protein sources for food production, MP had 53-100% lower environmental impacts depending on the reference product and the source of energy assumed for MP production. When compared with plant-based protein sources for food production, MP had lower land and water use requirements, and eutrophication potential but GWP was reduced only if low-emission energy sources were used. Compared to protein sources for feed production, MP production often resulted in lower environmental impact for GWP (FHE), land use, and eutrophication and acidification potential, but generally caused high water scarcity and required more energy.
  • Zhao, Quingjian; Wen, Zuomin; Toppinen, Anne (2018)
    From the perspective of supply chain, benchmarking the embodied carbon flows and emissions landscape is to study the carbon footprint in supply chain production and process management. On the basis of the theory of a green supply chain, this paper conducted its research through the following steps. First, a multi-level supply chain model was proposed and established, and various sectors, production and management processes, and inputs and outputs of different resources were integrated into the supply chain network, and then divided into multiple levels. Second, a multi-level embodied carbon flow and emissions model was established through the Leontief Inverse. Third, based on the operation data of forestry-pulp and paper companies, the embodied carbon flows and emissions at all levels and sectors were estimated and analyzed. Finally, the dismantling and processing methods of complex carbon network structures were explored, the hot-spot carbon sources and paths were obtained, and the low-carbon innovation and development strategies were proposed. The research results show that: (1) Supply chain is a new idea and carrier to study the spatial and state changes of carbon, and also provides a platform for spatial landscape analysis of carbon; (2) The modeling and calculation of carbon flows and emissions offer a new solution of evaluating the environmental performance of companies with high pollution and emission such as forestry-pulp and paper companies, and provide the government effective technical support to implement environmental regulations and formulate carbon emission reduction policies.
  • Hoekman, David; LeVan, Katherine E.; Ball, George E.; Browne, Robert A.; Davidson, Robert L.; Erwin, Terry L.; Knisley, C. Barry; LaBonte, James R.; Lundgren, Jonathan; Maddison, David R.; Moore, Wendy; Niemelä, Jari; Ober, Karen A.; Pearson, David L.; Spence, John R.; Will, Kipling; Work, Timothy (2017)
    The National Ecological Observatory Network (NEON) will monitor ground beetle populations across a network of broadly distributed sites because beetles are prevalent in food webs, are sensitive to abiotic factors, and have an established role as indicator species of habitat and climatic shifts. We describe the design of ground beetle population sampling in the context of NEON's long-term, continentalscale monitoring program, emphasizing the sampling design, priorities, and collection methods. Freely available NEON ground beetle data and associated field and laboratory samples will increase scientific understanding of how biological communities are responding to land-use and climate change.
  • Mielonen, Outi I.; Pratas, Diogo; Hedman, Klaus; Sajantila, Antti; Perdomo , Maria (2022)
    Formalin fixation, albeit an outstanding method for morphological and molecular preservation, induces DNA damage and cross-linking, which can hinder nucleic acid screening. This is of particular concern in the detection of low-abundance targets, such as persistent DNA viruses. In the present study, we evaluated the analytical sensitivity of viral detection in lung, liver, and kidney specimens from four deceased individuals. The samples were either frozen or incubated in formalin (+/- paraffin embedding) for up to 10 days. We tested two DNA extraction protocols for the control of efficient yields and viral detections. We used short-amplicon qPCRs (63-159 nucleotides) to detect 11 DNA viruses, as well as hybridization capture of these plus 27 additional ones, followed by deep sequencing. We observed marginally higher ratios of amplifiable DNA and scantly higher viral genoprevalences in the samples extracted with the FFPE dedicated protocol. Based on the findings in the frozen samples, most viruses were detected regardless of the extended fixation times. False-negative calls, particularly by qPCR, correlated with low levels of viral DNA (150 base pairs). Our data suggest that low-copy viral DNAs can be satisfactorily investigated from FFPE specimens, and encourages further examination of historical materials.
  • Kilpeläinen, Markku; Theeuwes, Jan (2016)
    People use eye movements extremely effectively to find objects of interest in a cluttered visual scene. Distracting, task-irrelevant attention capturing regions in the visual field should be avoided as they jeopardize the efficiency of search. In the current study, we used eye tracking to determine whether people are able to avoid making saccades to a predetermined visual area associated with a financial penalty, while making fast and accurate saccades towards stimuli placed near the penalty area. We found that in comparison to the same task without a penalty area, the introduction of a penalty area immediately affected eye movement behaviour: the proportion of saccades to the penalty area was immediately reduced. Also, saccadic latencies increased, but quite modestly, and mainly for saccades towards stimuli near the penalty area. We conclude that eye movement behaviour is under efficient cognitive control and thus quite flexible: it can immediately be adapted to changing environmental conditions to improve reward outcome.
  • Wang, Jingwen; Skoog, Tiina; Einarsdottir, Elisabet; Kaartokallio, Tea; Laivuori, Hannele; Grauers, Anna; Gerdhem, Paul; Hytonen, Marjo; Lohi, Hannes; Kere, Juha; Jiao, Hong (2016)
    High-throughput sequencing using pooled DNA samples can facilitate genome-wide studies on rare and low-frequency variants in a large population. Some major questions concerning the pooling sequencing strategy are whether rare and low-frequency variants can be detected reliably, and whether estimated minor allele frequencies (MAFs) can represent the actual values obtained from individually genotyped samples. In this study, we evaluated MAF estimates using three variant detection tools with two sets of pooled whole exome sequencing (WES) and one set of pooled whole genome sequencing (WGS) data. Both GATK and Freebayes displayed high sensitivity, specificity and accuracy when detecting rare or low-frequency variants. For the WGS study, 56% of the low-frequency variants in Illumina array have identical MAFs and 26% have one allele difference between sequencing and individual genotyping data. The MAF estimates from WGS correlated well (r = 0.94) with those from Illumina arrays. The MAFs from the pooled WES data also showed high concordance (r = 0.88) with those from the individual genotyping data. In conclusion, the MAFs estimated from pooled DNA sequencing data reflect the MAFs in individually genotyped samples well. The pooling strategy can thus be a rapid and cost-effective approach for the initial screening in large-scale association studies.
  • Mannisto, Jere K.; Pavlovic, Ljiljana; Tiainen, Tony; Nieger, Martin; Sahari, Aleksi; Hopmann, Kathrin H.; Repo, Timo (2021)
    Capture of CO2 by amines is an attractive synthetic strategy for the formation of carbamates. Such reactions can be mediated by superbases, such as 1,1,3,3-tetramethylguanidine (TMG), with previous implications that zwitterionic superbase-CO2 adducts are able to actively transfer the carboxylate group to various substrates. Here we report a detailed investigation of zwitterionic TMG-CO2, including isolation, NMR behavior, reactivity, and mechanistic consequences in carboxylation of aniline-derivatives. Our computational and experimental mechanistic analysis shows that the reversible TMG-CO2 zwitterion is not a direct carboxylation agent. Instead, CO2 dissociates from TMG-CO2 before a concerted carboxylation occurs, where the role of the TMG is to deprotonate the amine as it is attacking a free CO2. This insight is significant, as it opens a rational way to design new synthesis strategies. As shown here, nucleophiles otherwise inert towards CO2 can be carboxylated, even without a CO2 atmosphere, using TMG-CO2 as a stoichiometric source of CO2. We also show that natural abundance N-15 NMR is sensitive for zwitterion formation, complementing variable-temperature NMR studies.
  • Le Joncour, Vadim; Karaman, Sinem; Laakkonen, Pirjo Maarit (2019)
    Highly selective by nature, the blood-brain barrier (BBB) is essential for the brain homeostasis in physiological conditions. However, in the context of brain tumors, the molecular selectivity of BBB also shields the neoplastic cells by blocking the delivery of peripherally administered chemotherapies. The development of novel drugs (including nanoparticles) targeting malignant brain tumors ideally requires the use of preclinical animal models to study the drug’s transcytosis and antitumor efficacy. In order to comply with the 3R principle (refine, reduce, and replace) to reduce the number of laboratory animals in experimental setup and perform the high-throughput screening of a large library of antitumor agents, we developed a reproducible in vitro human and murine mimic of the blood-brain tumor-barrier (BBTB) using three-layered cultures of endothelial cells, astrocytes, and patient-derived glioblastoma spheres. For higher scalability and reproducibility, commercial cell lines or immortalized cells have been used in tailored conditions to allow the formation of a barrier resembling the actual BBB. Here we describe a protocol to obtain a BBTB mimic by culturing endothelial cells in contact with astrocytes at specific cell densities on inserts. This BBTB mimic can be used, for instance, for the quantification and confocal imaging of the nanoparticle passage through the endothelial and astrocytic barriers, in addition to the evaluation of the tumor cell targeting within the same assay. Moreover, we show that the obtained data can be used to predict the behavior of nanoparticles in preclinical animal models. In a broader perspective, this in vitro model could be adapted to other neurodegenerative diseases for the determination of the passage of new therapeutic molecules through the BBB and/or be supplemented with brain organoids to directly evaluate the efficacy of drugs.
  • Silva, Sofia Marques; Ribas, Camila C.; Aleixo, Alexandre (2021)
    We assessed population structure and the spatio-temporal pattern of diversification in the Glossy Antshrike Sakesphorus luctuosus (Aves, Thamnophilidae) to understand the processes shaping the evolutionary history of Amazonian floodplains and address unresolved taxonomic controversies surrounding its species limits. By targeting ultraconserved elements (UCEs) from 32 specimens of S. luctuosus, we identified independent lineages and estimated their differentiation, divergence times, and migration rates. We also estimated current and past demographic histories for each recovered lineage. We found evidence confirming that S. luctuosus consists of a single species, comprising at least four populations, with some highly admixed individuals and overall similar levels of migration between populations. We confirmed the differentiation of the Araguaia River basin population (S. l. araguayae) and gathered circumstantial evidence indicating that the taxon S. hagmanni may represent a highly introgressed population between three distinct phylogroups of S. luctuosus. Divergences between populations occurred during the last 1.2 mya. Signs of population expansions were detected for populations attributed to subspecies S. l. luctuosus, but not for the S. l. araguayae population. Our results support that S. luctuosus has had a complex population history, resulting from a high dependence on southeastern "clear water" seasonally flooded habitats and their availability through time. Spatial and demographic expansions toward the western "white water" flooded forests might be related to recent changes in connectivity and availability of these habitats. Our study reinforces the view that isolation due to absence of suitable habitat has been an important driver of population differentiation within Amazonian flooded forests, but also that differences between varzeas ("white water" floodplains, mostly in southwestern Amazonia) and igapos ("clear water" floodplains, especially located in the east) should be further explored as drivers of micro-evolution for terrestrial species.
  • Krachko, Tetiana; Nicolas, Emmanuel; Ehlers, Andreas W.; Nieger, Martin; Slootweg, J. Chris (2018)
    Treatment of the preorganized frustrated Lewis pairs (FLPs) tBu(2)PCH(2)BPh(2) (1) and o-Ph2P(C6H4)BCat (Cat=catechol) (4) with 2-methyloxirane, 2-phenyloxirane and 2-(trifluoromethyl)oxirane resulted in epoxide ring-opening to yield the six- and seven-membered heterocycles 2a-c and 5a-c, respectively. These zwitterionic products were characterized spectroscopically, and compounds 2a, 2b, 5a and 5c were structurally characterized by single-crystal X-ray structure analyses. Based on computational and kinetic studies, the mechanism of these reactions was found to proceed via activation of the epoxide by the Lewis acidic borane moiety followed by nucleophilic attack of the phosphine of a second FLP molecule. The resulting chain-like intermediates afford the final cyclic products by ring-closure and concurrent release of the second equivalent of FLP that behaves as catalyst in this reaction.
  • Granvik, Mikael; Vaubaillon, Jeremie; Jedicke, Robert (2012)
  • Hoshian, Sasha; Kankuri, Esko; Ras, Robin H. A.; Franssila, Sami; Jokinen, Ville (2017)
    A top-down scalable method to produce flexible water and blood repellent tubes is introduced. The method is based on replication of overhanging nanostructures from an aluminum tube template to polydimethylsiloxane (PDMS) via atomic layer deposition (ALD) assisted sacrificial etching. The nanostructured PDMS/titania tubes are superhydrophobic with water contact angles 163 +/- 1 degrees (advancing) and 157 +/- 1 degrees (receding) without any further coating. Droplets are able to slide through a 4 mm (inner diameter) tube with low sliding angles of less than 10 degrees for a 35 mu L droplet. The superhydrophobic tube shows up to 5,000 times increase in acceleration of a sliding droplet compared to a control tube depending on the inclination angle. Compared to a free falling droplet, the superhydrophobic tube reduced the acceleration by only 38.55%, as compared to a 99.99% reduction for a control tube. The superhydrophobic tubes are blood repellent. Blood droplets (35 mu L) roll through the tubes at 15 degrees sliding angles without leaving a bloodstain. The tube surface is resistant to adhesion of activated platelets unlike planar control titania and smooth PDMS surfaces.