Browsing by Subject "TOOLS"

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  • Engeström, Ritva; Käyhkö, Leena (2021)
    Background: Recent alternative concepts of school knowledge emphasize knowledge creation via networks of learning around real-world phenomena. We studied entrepreneurship education as an example of new epistemic activity which opens institutional boundaries for active engagement with society in learning. Methods: We used a case-study strategy and a methodology informed by the cultural-historical activity theory for investigating an entrepreneurship course of a middle school. We focused on meaning making in object formation of learning of the groups involved in boundary crossing. Meaning making was studied in a context-sensitive way with an analytic tool designed in the study. Findings: Lacking a knowledge system of a disciplinary school subject, the findings show that entrepreneurship becomes constructed in practice epistemologically as a value-free and politically neutral learning object. In light of these findings we discuss the theoretical link between conceptual learning and learning around real-world phenomena. Contribution: In addition to economic activity, globalization and climate change are also presently forming the social realities of school learners. Our study shows that more theoretical and empirical research on intermediate epistemological practices is needed to avoid a risk that teachers are left on their own to sort out the complex epistemic interrelationships.
  • Zheng, Shuyu; Poczai, Peter; Hyvönen, Jaakko; Tang, Jing; Amiryousefi, Ali (2020)
    Understanding the complexity of genomic structures and their unique architecture is linked with the power of visualization tools used to represent these features. Such tools should be able to provide a realistic and scalable version of genomic content. Here, we present an online organelle plotting tool focused on chloroplasts, which were developed to visualize the exclusive structure of these genomes. The distinguished unique features of this program include its ability to represent the Single Short Copy (SSC) regions in reverse complement, which allows the depiction of the codon usage bias index for each gene, along with the possibility of the minor mismatches between inverted repeat (IR) regions and user-specified plotting layers. The versatile color schemes and diverse functionalities of the program are specifically designed to reflect the accurate scalable representation of the plastid genomes. We introduce a Shiny app website for easy use of the program; a more advanced application of the tool is possible by further development and modification of the downloadable source codes provided online. The software and its libraries are completely coded in R, available at https://irscope.shinyapps.io/chloroplot/.
  • Abdullah,; Henriquez, Claudia L.; Mehmood, Furrukh; Carlsen, Monica M.; Islam, Madiha; Waheed, Mohammad Tahir; Poczai, Peter; Croat, Thomas B.; Ahmed, Ibrar (2020)
    The subfamily Pothoideae belongs to the ecologically important plant family Araceae. Here, we report the chloroplast genomes of two species of the subfamily Pothoideae:Anthurium huixtlense(size: 163,116 bp) andPothos scandens(size: 164,719 bp). The chloroplast genome ofP. scandensshowed unique contraction and expansion of inverted repeats (IRs), thereby increasing the size of the large single-copy region (LSC: 102,956 bp) and decreasing the size of the small single-copy region (SSC: 6779 bp). This led to duplication of many single-copy genes due to transfer to IR regions from the small single-copy (SSC) region, whereas some duplicate genes became single copy due to transfer to large single-copy regions. The rate of evolution of protein-coding genes was affected by the contraction and expansion of IRs; we found higher mutation rates for genes that exist in single-copy regions as compared to those in IRs. We found a 2.3-fold increase of oligonucleotide repeats inP. scandenswhen compared withA. huixtlense, whereas amino acid frequency and codon usage revealed similarities. The ratio of transition to transversion mutations was 2.26 inP. scandensand 2.12 inA. huixtlense. Transversion mutations mostly translated in non-synonymous substitutions. The phylogenetic inference of the limited species showed the monophyly of the Araceae subfamilies. Our study provides insight into the molecular evolution of chloroplast genomes in the subfamily Pothoideae and family Araceae.
  • Shcherbakova, Daria M.; Cammer, Natasha Cox; Huisman, Tsipora M.; Verkhusha, Vladislav V.; Hodgson, Louis (2018)
    Direct visualization and light control of several cellular processes is a challenge, owing to the spectral overlap of available genetically encoded probes. Here we report the most red-shifted monomeric near-infrared (NIR) fluorescent protein, miRFP720, and the fully NIR Forster resonance energy transfer (FRET) pair miRFP670-miRFP720, which together enabled design of biosensors compatible with CFP-YFP imaging and blue-green optogenetic tools. We developed a NIR biosensor for Rac1 GTPase and demonstrated its use in multiplexed imaging and light control of Rho GTPase signaling pathways. Specifically, we combined the Rac1 biosensor with CFP-YFP FRET biosensors for RhoA and for Rac1-GDI binding, and concurrently used the LOV-TRAP tool for upstream Rac1 activation. We directly observed and quantified antagonism between RhoA and Rac1 dependent on the RhoA-downstream effector ROCK; showed that Rac1 activity and GDI binding closely depend on the spatiotemporal coordination between these two molecules; and simultaneously observed Rac1 activity during optogenetic manipulation of Rac1.
  • Romskaug, Rita; Skovlund, Eva; Straand, Jorund; Molden, Espen; Kersten, Hege; Pitkälä, Kaisu H.; Lundqvist, Christofer; Wyller, Torgeir Bruun (2020)
    IMPORTANCE Polypharmacy and inappropriate drug regimens are major health concerns among older adults. Various interventions focused on medication optimization strategies have been carried out, but the effect on patient-relevant outcomes remains uncertain. Objective To investigate the effect of clinical geriatric assessments and collaborative medication reviews by geriatrician and family physician (FP) on health-related quality of life and other patient-relevant outcomes in home-dwelling older patients receiving polypharmacy. Design, Setting, and Participants Cluster randomized, single-blind, clinical trial. Norwegian FPs were recruited from March 17, 2015, to March 16, 2017, to participate in the trial with their eligible patients. Participants were home-dwelling patients 70 years or older, using at least 7 medications regularly, and having their medications administered by the home nursing service. Patients in the control group received usual care. Randomization occurred at the FP level. A modified intent-to-treat analysis was used. Intervention The intervention consisted of 3 main parts: (1) clinical geriatric assessment of the patients combined with a thorough review of their medications; (2) a meeting between the geriatrician and the FP; and (3) clinical follow-up. Main Outcomes and Measures The primary outcome was health-related quality of life as assessed by the 15D instrument (score range, 0-1; higher scores indicate better quality of life, with a minimum clinically important change of +/- 0.015) at week 16. Secondary outcomes included changes in medication appropriateness, physical and cognitive functioning, use of health services, and mortality. Results Among 174 patients (mean [SD] age, 83.3 [7.3] years; 67.8% women; 87 randomized to the intervention group and 87 randomized to the control [usual care] group) in 70 FP clusters (36 intervention and 34 control), 158 (90.8%) completed the trial. The mean (SD) 15D instrument score at baseline was 0.708 (0.121) in the intervention group and 0.714 (0.113) in the control group. At week 16, the mean (SD) 15D instrument score was 0.698 (0.164) in the intervention group and 0.655 (0.184) in the control group, with an estimated between-group difference of 0.045 (95% CI, 0.004-0.086; P = .03). Several secondary outcomes were also in favor of the intervention. There were more drug withdrawals, reduced dosages, and new drug regimens started in the intervention group. Conclusions and Relevance This study's findings indicate that, among older patients exposed to polypharmacy, clinical geriatric assessments and collaborative medication reviews carried out by a geriatrician in cooperation with the patient's FP can result in positive effects on health-related quality of life.
  • Milovanov, Alexander; Zvyagin, Andrey; Daniyarov, Asset; Kalendar, Ruslan; Troshin, Leonid (2019)
    Cultivated grapevine (Vitis vinifera L. ssp. sativa D.C.) is one of the oldest agricultural crops, each variety comprising an array of clones obtained by vegetative propagation from a selected vine grown from a single seedling. Most clones within a variety are identical, but some show a different form of accession, giving rise to new divergent phenotypes. Understanding the associations among the genotypes within a variety is crucial to efficient management and effective grapevine improvement. Inter-primer binding-site (iPBS) markers may aid in determining the new clones inside closely related genotypes. Following this idea, iPBS markers were used to assess the genetic variation of 33 grapevine genotypes collected from Russia. We used molecular markers to identify the differences among and within five grapevine clonal populations and analysed the variation, using clustering and statistical approaches. Four of a total of 30 PBS primers were selected, based on amplification efficiency. Polymerase chain reaction (PCR) with PBS primers resulted in a total of 1412 bands ranging from 300 to 6000 bp, with a polymorphism ratio of 44%, ranging from 58 to 75 bands per group. In total, were identified seven private bands in 33 genotypes. Results of molecular variance analysis showed that 40% of the total variation was observed within groups and only 60% between groups. Cluster analysis clearly showed that grapevine genotypes are highly divergent and possess abundant genetic diversities. The iPBS PCR-based genome fingerprinting technology used in this study effectively differentiated genotypes into five grapevine groups and indicated that iPBS markers are useful tools for clonal selection. The number of differences between clones was sufficient to identify them as separate clones of studied varieties containing unique mutations. Our previous phenotypic and phenological studies have confirmed that these genotypes differ from those of maternal plants. This work emphasized the need for a better understanding of the genotypic differences among closely related varieties of grapevine and has implications for the management of its selection processes.
  • Ritari, Jarmo; Salojärvi, Jarkko; Lahti, Leo; de Vos, Willem M. (2015)
    Background: Current sequencing technology enables taxonomic profiling of microbial ecosystems at high resolution and depth by using the 16S rRNA gene as a phylogenetic marker. Taxonomic assignation of newly acquired data is based on sequence comparisons with comprehensive reference databases to find consensus taxonomy for representative sequences. Nevertheless, even with well-characterised ecosystems like the human intestinal microbiota it is challenging to assign genus and species level taxonomy to 16S rRNA amplicon reads. A part of the explanation may lie in the sheer size of the search space where competition from a multitude of highly similar sequences may not allow reliable assignation at low taxonomic levels. However, when studying a particular environment such as the human intestine, it can be argued that a reference database comprising only sequences that are native to the environment would be sufficient, effectively reducing the search space. Results: We constructed a 16S rRNA gene database based on high-quality sequences specific for human intestinal microbiota, resulting in curated data set consisting of 2473 unique prokaryotic species-like groups and their taxonomic lineages, and compared its performance against the Greengenes and Silva databases. The results showed that regardless of used assignment algorithm, our database improved taxonomic assignation of 16S rRNA sequencing data by enabling significantly higher species and genus level assignation rate while preserving taxonomic diversity and demanding less computational resources. Conclusion: The curated human intestinal 16S rRNA gene taxonomic database of about 2500 species-like groups described here provides a practical solution for significantly improved taxonomic assignment for phylogenetic studies of the human intestinal microbiota.
  • Rastas, Pasi (2017)
    Motivation: Accurate and dense linkage maps are useful in family-based linkage and association studies, quantitative trait locus mapping, analysis of genome synteny and other genomic data analyses. Moreover, linkage mapping is one of the best ways to detect errors in de novo genome assemblies, as well as to orient and place assembly contigs within chromosomes. A small mapping cross of tens of individuals will detect many errors where distant parts of the genome are erroneously joined together. With more individuals and markers, even more local errors can be detected and more contigs can be oriented. However, the tools that are currently available for constructing linkage maps are not well suited for large, possible low-coverage, whole genome sequencing datasets. Results: Here we present a linkage mapping software Lep-MAP3, capable of mapping high-throughput whole genome sequencing datasets. Such data allows cost-efficient genotyping of millions of single nucleotide polymorphisms (SNPs) for thousands of individual samples, enabling, among other analyses, comprehensive validation and refinement of de novo genome assemblies. The algorithms of Lep-MAP3 can analyse low-coverage datasets and reduce data filtering and curation on any data. This yields more markers in the final maps with less manual work even on problematic datasets. We demonstrate that Lep-MAP3 obtains very good performance already on 5x sequencing coverage and outperforms the fastest available software on simulated data on accuracy and often on speed. We also construct de novo linkage maps on 7-12x whole-genome data on the Red postman butterfly (Heliconius erato) with almost 3 million markers.
  • Leopold, Anna V.; Chernov, Konstantin G.; Shemetov, Anton A.; Verkhusha, Vladislav V. (2019)
    Optical control over the activity of receptor tyrosine kinases (RTKs) provides an efficient way to reversibly and non-invasively map their functions. We combined catalytic domains of Trk (tropomyosin receptor kinase) family of RTKs, naturally activated by neurotrophins, with photosensory core module of DrBphP bacterial phytochrome to develop opto-kinases, termed Dr-TrkA and Dr-TrkB, reversibly switchable on and off with near-infrared and far-red light. We validated Dr-Trk ability to reversibly light-control several RTK pathways, calcium level, and demonstrated that their activation triggers canonical Trk signaling. Dr-TrkA induced apoptosis in neuroblastoma and glioblastoma, but not in other cell types. Absence of spectral crosstalk between Dr-Trks and blue-light-activatable LOV-domain-based translocation system enabled intracellular targeting of Dr-TrkA independently of its activation, additionally modulating Trk signaling. Dr-Trks have several superior characteristics that make them the opto-kinases of choice for regulation of RTK signaling: high activation range, fast and reversible photoswitching, and multiplexing with visible-light-controllable optogenetic tools.
  • Kalendar, Ruslan; Shustov, Alexandr; Seppänen, Mervi Mirjam; Schulman, Alan Howard; Stoddard, Frederick Lothrop (2019)
    Genome walking (GW) refers to the capture and sequencing of unknown regions in a long DNA molecule that are adjacent to a region with a known sequence. A novel PCR-based method, palindromic sequence-targeted PCR (PST-PCR), was developed. PST-PCR is based on a distinctive design of walking primers and special thermal cycling conditions. The walking primers (PST primers) match palindromic sequences (PST sites) that are randomly distributed in natural DNA. The PST primers have palindromic sequences at their 3’ ends. Upstream of the palindromes there is a degenerate sequence (8-12 nucleotides long); defined adapters are present at the 5’-termini. The thermal cycling profile has a linear amplification phase and an exponential amplification phase differing in annealing temperature. Changing the annealing temperature to switch the amplification phases at a defined cycle controls the balance between sensitivity and specificity. In contrast to traditional genome walking methods, PST-PCR is rapid (two to three hours to produce GW fragments) as it uses only one or two PCR rounds. Using PST-PCR, previously unknown regions (the promoter and intron 1) of the VRN1 gene of Timothy-grass (Phleum pratense L.) were captured for sequencing. In our experience, PST-PCR had higher throughput and greater convenience in comparison to other GW methods.
  • Splichal, Jin Michael; Oshima, Jun; Oshima, Ritsuko (2018)
    Many studies attempt to effectively support student regulation of collaboration using CSCL tools to enrich learning outcomes. However, few studies are aimed at facilitating development of students' internal scripts for regulation of collaboration. This study focuses on developing and evaluating a computer-mediated learning environment for project-based learning to facilitate student internal scripts for regulation by designing external scripts for effective reflection. Forty- eight first-year university students participated in this study as part of their curriculum. Our analyses of their internal scripts before and after PBL participation revealed that significantly more students who encountered an unfamiliar situation during collaboration constructed new regulation scripts. Moreover, in case studies, we found that students augmented their scripts for socially shared regulation when recognizing socio-cognitive challenges, whereas they augmented co-regulation and self-regulation scripts when recognizing socio-emotional challenges.
  • Ndika, Joseph; Seemab, Umair; Poon, Wing-Lam; Fortino, Vittorio; El-Nezami, Hani; Karisola, Piia; Alenius, Harri (2019)
    After over a decade of nanosafety research, it is indisputable that the vast majority of nano-sized particles induce a plethora of adverse cellular responses - the severity of which is linked to the material's physicochemical properties. Differentiated THP-1 cells were previously exposed for 6 h and 24 h to silver, titanium dioxide, and zinc oxide nanoparticles at the maximum molar concentration at which no more than 15% cellular cytotoxicity was observed. All three nanoparticles differed in extent of induction of biological pathways corresponding to immune response signaling and metal ion homeostasis. In this study, we integrated gene and miRNA expression profiles from the same cells to propose miRNA biomarkers of adverse exposure to metal-based nanoparticles. We employed RNA sequencing together with a quantitative strategy that also enables analysis of the overlooked repertoire of length and sequence miRNA variants called isomiRs. Whilst only modest changes in expression were observed within the first 6 h of exposure, the miRNA/isomiR (miR) profiles of each nanoparticle were unique. Via canonical correlation and pathway enrichment analyses, we identified a co-regulated miR-mRNA cluster, predicted to be highly relevant for cellular response to metal ion homeostasis. These miRs were annotated to be canonical or variant isoforms of hsa-miR-142-5p, -342-3p, -5100, -6087, -6894-3p, and -7704. Hsa-miR-5100 was differentially expressed in response to each nanoparticle in both the 6 h and 24 h exposures. Taken together, this co-regulated miR-mRNA cluster could represent potential biomarkers of sub-toxic metal-based nanoparticle exposure.
  • Amponsah, Abigail Kusi; Björn, Annika; Bam, Victoria; Axelin, Anna (2019)
    Background: Nurses play an important role in children's pain assessment and management because they spend the majority of the time with them and provide care on a 24-hour basis. However, research studies continue to report on nurses' inadequate assessment and management of children's pain, which may be partly attributed to their insufficient education in this area. Objectives: This integrative review sought to examine the effect of strategies used in educating nurses on pediatric pain assessment and management. Design: An integrative review. Data Sources: Cumulative Index to Nursing and Allied Health Literature, Cochrane, PubMed/Medline and Scopus. Review/Analysis Methods: Four databases were searched up to February 2018 based on a prescribed eligibility criteria. The review included 37 studies with varied methodologic quality. Results: Our findings revealed that various types of educational strategies improve nurses' knowledge, attitudes, and practice of pain assessment, management, and/or documentation. Conclusions: Developing a responsive program that includes expectations of beneficiaries, integrating it into existing facility training systems and delivering it through multidisciplinary collaboration, offers the benefit of securing sustainability of the educational gains. (C) 2019 American Society for Pain Management Nursing. Published by Elsevier Inc. All rights reserved.
  • Ptchelkine, Denis; Gillum, Ashley; Mochizuki, Tomohiro; Lucas-Staat, Soizick; Liu, Ying; Krupovic, Mart; Phillips, Simon E. V.; Prangishvili, David; Huiskonen, Juha T. (2017)
    Archaeal viruses have evolved to infect hosts often thriving in extreme conditions such as high temperatures. However, there is a paucity of information on archaeal virion structures, genome packaging, and determinants of temperature resistance. The rod-shaped virus APBV1 (Aeropyrum pernix bacilliform virus 1) is among the most thermostable viruses known; it infects a hyperthermophile Aeropyrum pernix, which grows optimally at 90 degrees C. Here we report the structure of APBV1, determined by cryo-electron microscopy at near-atomic resolution. Tight packing of the major virion glycoprotein (VP1) is ensured by extended hydrophobic interfaces, and likely contributes to the extreme thermostability of the helical capsid. The double-stranded DNA is tightly packed in the capsid as a left-handed superhelix and held in place by the interactions with positively charged residues of VP1. The assembly is closed by specific capping structures at either end, which we propose to play a role in DNA packing and delivery.