Browsing by Subject "structure"

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  • Domanska, Ausra; Guryanov, Sergey; Butcher, Sarah J. (2021)
    Parechoviruses belong to the genus Parechovirus within the family Picornaviridae and are non-enveloped icosahedral viruses with a single-stranded RNA genome. Parechoviruses include human and animal pathogens classified into six species. Those that infect humans belong to the Parechovirus A species and can cause infections ranging from mild gastrointestinal or respiratory illness to severe neonatal sepsis. There are no approved antivirals available to treat parechovirus (nor any other picornavirus) infections. In this parechovirus review, we focus on the cleaved protein products resulting from the polyprotein processing after translation comparing and contrasting their known or predicted structures and functions to those of other picornaviruses. The review also includes our original analysis from sequence and structure prediction. This review highlights significant structural differences between parechoviral and other picornaviral proteins, suggesting that parechovirus drug development should specifically be directed to parechoviral targets.
  • Makkonen, Olli (Suomen metsätieteellinen seura, 1967)
  • Patomäki, Heikki (University of Helsinki, Helsinki Centre for Global Political Economy, 2021)
    Helsinki Global Political Economy Working Papers
    For decades, the concept of “structural reform” has been dominant in the economic policy discourse of the EU and most of its member states, from Greece to Finland. The term gets its meaning mainly from neoclassical economic theory, though there are also Schumpeterian and other elements. An analysis of the theoretical underpinnings of the concept (which emerged in the 1980s and was spread through the Bretton Woods institutions and the OECD) reveals conceptual and theoretical ambiguities and factual weaknesses. While many of these weaknesses are related to unrealistic assumptions, I argue further that the realisticness of particular assumptions is different from the realism of the approach and relevance of the problematic. Second, to explore the limitations of the concept in its current meaning, I outline a brief genealogy of the concept of structure in social sciences and then juxtapose the economistic concept of structure with that of realist social theory. Third, I explore the implications of this deeper ontological conception of structure to the meaning and nature of possible structural reforms. Fourth, I give a few examples of alternative structural reforms to make my points more concrete. The envisioned programme of structural changes would amount to reversing the current EU strategy for growth. In the end, I summarise the overall argument.
  • Grazhdankin, Evgeni (Helsingfors universitet, 2018)
    We have developed a software for homology modelling by satisfaction of distance restraints using MODELLER back-end. The protocols used extend exploration of distance restraints and conformational space. We drive the models in optimization cycle towards better structures as assessed by the used metrics on DOPE score, retrospective distance restraint realization and others. Hydrogen bond networks are optimized for their size and connectivity density. The performance of the method is evaluated for its ability to reconstruct GPCR structures and an extracellular loop 2. The software is written in object-oriented Python (v.2.7) and supports easy extension with additional modules. We built a relational PostgreSQL database for the restraints to allow for data-driven machine and deep learning applications. An important part of the work was the visualization of the distance restraints with custom PyMOL scripts for three-dimensional viewing. Additionally, we automatically generate a plethora of diagnostic plots for assessing the performance of the modelling protocols. The software utilizes parallelism and is computationally practical with compute requirements on an order of magnitude lower than those typically seen in molecular dynamics simulations. The main challenges left to be solved is the evaluation of restraint goodness, assigning secondary structures, restraint interconditioning, and water and ligand placement.
  • Puhakka, Eini; Ritala, Mikko; Lehto, Jukka (2020)
    Potassium cobalt hexacyanoferrate(II) [K2CoFe(CN)(6)] is an extremely selective ion exchanger for cesium ions. To examine the atomic level background for the selectivity a computational structural study using DFT modelling was carried out for K2CoFe(CN)(6) and for products where Cs has replaced K in the elemental cube cages closest to the surface. In the K-form compound the potassium ions are not in the center of the Co-Fe-CN elementary cube cages closest to the surface but locate about 140 pm from the cube center towards the surface. When cesium ions are exchanged to these potassium ions they locate much deeper from the surface, being only about 70 pm upwards from the cube center. 'Ibis apparently leads to much stronger bonding of cesium compared to potassium. Once taken up into the outermost cube cages on the surface of the crystallites cesium ions are not able to penetrate further since they are much larger than the electron window between the cubes. Furthermore, they are not able to return to the solution phase either leading to a practically irreversible sorption.
  • Euclid Collaboration; Bretonnière, H.; Huertas-Company, M.; Gozaliasl, G.; Keihänen, E.; Kirkpatrick , C. C.; Kurki-Suonio, H.; Lindholm, Valtteri; Väliviita, J. (2022)
    We present a machine learning framework to simulate realistic galaxies for the Euclid Survey, producing more complex and realistic galaxies than the analytical simulations currently used in Euclid. The proposed method combines a control on galaxy shape parameters offered by analytic models with realistic surface brightness distributions learned from real Hubble Space Telescope observations by deep generative models. We simulate a galaxy field of 0.4x2006;deg(2) as it will be seen by the Euclid visible imager VIS, and we show that galaxy structural parameters are recovered to an accuracy similar to that for pure analytic Sersic profiles. Based on these simulations, we estimate that the Euclid Wide Survey (EWS) will be able to resolve the internal morphological structure of galaxies down to a surface brightness of 22.5x2006;magx2006;arcsec(-2), and the Euclid Deep Survey (EDS) down to 24.9x2006;magx2006;arcsec(-2). This corresponds to approximately 250 million galaxies at the end of the mission and a 50% complete sample for stellar masses above 10(10.6)M(circle dot) (resp. 10(9.6)M(circle dot)) at a redshift zx2004;similar to 0.5 for the EWS (resp. EDS). The approach presented in this work can contribute to improving the preparation of future high-precision cosmological imaging surveys by allowing simulations to incorporate more realistic galaxies.
  • Laiho, Olavi (Suomen metsätieteellinen seura, 1965)
  • Toivola, Johanna Maria (Helsingfors universitet, 2015)
    The purpose of this study was to investigate the structure of ice cream, especially the effects of temperature, sugar composition and stabilizer-emulsifier concentration on the melt down, hardness and moulding properties of ice cream. The aim was to produce a soft and easily mouldable ice cream that suits the intended purpose. A sensory evaluation was conducted to the ice creams with desired structural properties. The literature review deals with ice cream ingredients, manufacturing process and factors affecting ice cream structure. For the experimental study, 16 ice creams with different compositions were made. The ice creams contained 12 or 6 % fat, different types of sugar compositions (A, B, C, D, E, F) and different concentrations of two types of stabilizer and emulsifier blends (A, B). Ice creams were stored at different temperatures. The hardness of ice cream was measured with a Texture Analyser, the melting rate was determined and the moulding properties were analysed with a moulding test. The two ice creams with desired structure were compared to a commercial ice cream in a sensory evaluation. The results of the hardness measurements revealed, that temperature and sugar composition affected hardness the most. Stabilizer and emulsifier concentration and type did not have an effect. The softest ice creams were those stored at higher temperatures and those made with sugar composition C, D, E and F. The slowest melting ice creams were the ones containing greater amounts of stabilizers and emulsifiers. The ice cream made with sugar composition D melted the fastest. For the moulding test, the softer ice creams were the easiest to mould. The ice cream made with sugar composition D was found to be too soft, almost runny, and the ones made with sugar composition A and B were found to be too hard. The ice creams made with sugar composition C, E and F were found pleasing. The batches containing a greater amount of stabilizer and emulsifier were found to be a bit gummy. In the sensory evaluation there were only one difference in sweetness found between the study ice creams and the commercial one. There were no differences found in creaminess and over all liking. From this can be concluded that the study ice creams are accepted by the consumers as well.
  • Heikkilä, Sampsa (2005)
    Etnografiani tutkii kokemuksen "samankaltaisuutta" erilaisissa sosiaali-historiallisissa olosuhteissa. Editoidun audiovisuaalisen materiaalin käyttöön perustuva systemaattinen tutkimus kartoittaa variabiliteettia, eli "jotenkin" samankaltaisuutta geneerisessä ilmaisukulttuurissa. Performanssiteorian, musiikkikokemuksen ja puheen etnografian metodien ja teorioiden pohjalta tehty työ tulkitsee näistä lähtökohdista käsin musiikillista mediaatiota erilaisissa symbolisissa kommunikaatioprosesseissa. Työn kontribuutio on näiden tutkimusalojen piirissä niin, että sen pohjalta tehtyjä antropologisia väittämiä voidaan hyödyntää esteettisiin konfiguraatioihin perustuvien performanssikulttuurien tutkimuksessa. Havaintojen validiteettia ja relevanssia lisää monipuolinen audiovisuaalisen materiaalin käyttö. Työ pohjautuu n. 5 kuukauden pituiseen kenttätyöhön Sevillan provinssissa Espanjassa. Etnografinen materiaali on flamenco-puheyhteisöistä. Etnografinen metodi hyödyntää haastatteluaineistoja, etnografista video-elokuvaa, sosiaalihistoriallisia dokumentteja sekä antropologista kirjallisuutta. Tutkimusongelma on yleisluonteinen: kuinka tulkita kyseistä informaation paljoutta? Ongelman jäsentämiseksi asetettu hypoteesi olettaa draamallisten muotojen kehityksen mahdollisuuden kokemuksen samankaltaisuudessa. Tutkimuskysymykset ovat näistä kaikista lähtökohdista käsin: Mitkä ovat ilmaisukulttuurin symbolisten kommunikaatioprosessien varioidut muodot ja mitkä niiden funktiot? Mitkä ovat sosiaalihistorian dynamiikan ehdollistamat performanssistruktuuritilanneriippuvaiset "ehdot"? Ongelmat ja kysymykset on tutkittu etnografian metodologian alueella analysoimalla ja tulkitsemalla työn visuaali-antropologinen toteutus. Puheen merkityksellisten tyylien, tyylillisten struktuurien sekä tyylillisten muotojen funktio ja merkitys sosiaalisesti jaettuina prosesseina nousee päällimäiseksi tulkinnaksi kahdella osa alueella. Kulttuurinen subversio ja metaforinen identifikaatio. Kumpaankin osa-alueeseen liittyy symbolisesti tulkitseva yksilö sosiaali-historiallisena agenttina ja aktorina. Osa-alueiden laajempaa tutkimusta ja oman työni rajallisia mahdollisuuksia hahmottaen on työn päätteksi ehdotettu metodologista reduktiota, jolla työn narratiivisesta kokonaisuudesta erottuvia piirteitä voidaan ymmärtää kahdella tavalla 1) ehdollisina "partikulaareina muotoina"; 2) performanssin yleisinä ehtoina. Yleisesti työn merkitys on paikallisessa kulttuurin jatkuvuuden tutkimuksessa ja symbolisten arvojen "taidevälityksessä". Yksilöä painottavan sosiaalitieteen kentässä sen merkitys on genren ja muiden symbolisten muotojen tulkitsevan käytön hahmottamisessa ja ymmärtämisessa.
  • Rissanen, Ilona; Stass, Robert; Krumm, Stefanie A.; Seow, Jeffrey; Hulswit, Ruben J.G.; Paesen, Guido C.; Hepojoki, Jussi; Vapalahti, O.; Lundkvist, Åke; Reynard, Olivier; Volchkov, Viktor; Doores, Katie J.; Huiskonen, Juha T.; Bowden, Thomas A. (2020)
    The intricate lattice of Gn and Gc glycoprotein spike complexes on the hantavirus envelope facilitates host-cell entry and is the primary target of the neutralizing antibody-mediated immune response. Through study of a neutralizing monoclonal antibody termed mAb P-4G2, which neutralizes the zoonotic pathogen Puumala virus (PUUV), we provide a molecular-level basis for antibody-mediated targeting of the hantaviral glycoprotein lattice. Crystallographic analysis demonstrates that P-4G2 binds to a multi-domain site on PUUV Gc and may preclude fusogenic rearrangements of the glycoprotein that are required for host-cell entry. Furthermore, cryo-electron microscopy of PUUV-like particles in the presence of P-4G2 reveals a lattice-independent configuration of the Gc, demonstrating that P-4G2 perturbs the (Gn-Gc)4 lattice. This work provides a structure-based blueprint for rationalizing antibody-mediated targeting of hantaviruses.
  • Ylitalo, Anna (Helsingin yliopisto, 2019)
    People are eating a lot of ice cream all over the world and new products must be developed to create new options for consumers. Unilever, for whom this thesis has been made, is interested in developing new ice cream structures. The objective of the thesis was to explore different possibilities of ice cream structures and create two new interesting structures to the ice cream market; one with long, stretchy and chewy texture and one with high overrun (HOR) and light mouthfeel. The idea was to change the amounts, types and mixes of emulsifiers and stabilizers from the recipe. Additionally, process parameters, homogenisation and overrun, were changed from the current values. Hence, the purpose was to influence the size and amount of air bubbles and fat globules. The study was conducted at Unilever Sipoo, Ingman ice cream factory at their pilot plant. In the experimental part of the study, various versions of new ice cream structures were tested and compared to the reference product. After sensory analysis, it was decided to proceed with three versions of the HOR structure and two versions of the stretchy structure. At the end there were five versions of two new structures produced and analyzed with various tests. The analytical methods suitable and available for this study were viscosity measurement, shelf-life test, chemical test and melting test. Furthermore, there were small sensory analysis done during the study and comprehensive, final sensory analysis was done at the end of the study, for the final products. In conclusion, both of the new structures succeeded well. The “HOR E NAS 4” proved to be the best version of the structures. The melting profile of “HOR E NAS 4” ice cream corresponded the reference product. The results of the shelf-life test were positive: all the new structures survived better than the reference product. Sensory evaluation showed that the structures differed statistically significantly from each other and especially from the traditional ice cream, which was the aim of the study. The “HOR E NAS 4 “ was evaluated to be more firm and not so creamy as the reference product, which have to take in consideration in further investigations. “HOR E NAS 4” will be published on the ice cream market next year, as a new product.
  • Petrova, E. V.; Grokhovsky, V. I.; Kohout, T.; Muftakhetdinova, R. F.; Yakovlev, G. A. (2019)
    A spherical geometry shock experiment with the light-colored lithology material of the Chelyabinsk LL5 ordinary chondrite was carried out. The material was affected by shock and thermal metamorphism whose grade ranged from initial stage S3-4 to complete melting. The temperature and pressure were estimated at >2000 degrees C and >90 GPa. The textural shock effects were studied by optical and electron microscopy. A single experimental impact has produced the whole the range of shock pressures and temperatures and, correspondingly, four zones identified by petrographic analysis: (1) a melt zone, (2) a zone of melting silicates, (3) a black ring zone, and (4) a zone of weakly shocked initial material. The following textural features of the material were identified: displacement of the metal and troilite phases from the central melt zone; the development of a zone of mixed lithology (light-colored fragments in silicate melt); the origin of a dark-colored lithology ring; and the generation of radiating shock veinlets. The experimental sample shows four textural zones that correspond to the different lithology types of the Chelyabinsk LL5 meteorite found in fragments of the meteoritic shower in the collection at the Ural Federal University. Our results prove that shock wave loading experiment can be successfully applied in modeling of space shocks and can be used to experimentally model processes at the small bodies of the solar system.
  • Rissanen, Ilona; Krumm, Stefanie A.; Stass, Robert; Whitaker, Annalis; Voss, James E.; Bruce, Emily A.; Rothenberger, Sylvia; Kunz, Stefan; Burton, Dennis R.; Huiskonen, Juha T.; Botten, Jason W.; Bowden, Thomas A.; Doores, Katie J. (2021)
    Hantaviruses are a group of emerging pathogens capable of causing severe disease upon zoonotic transmission to humans. The mature hantavirus surface presents higher-order tetrameric assemblies of two glycoproteins, Gn and Gc, which are responsible for negotiating host cell entry and constitute key therapeutic targets. Here, we demonstrate that recombinantly derived Gn from Hantaan virus (HTNV) elicits a neutralizing antibody response (serum dilution that inhibits 50% infection [ID50], 1:200 to 1:850) in an animal model. Using antigen-specific B cell sorting, we isolated monoclonal antibodies (mAbs) exhibiting neutralizing and non-neutralizing activity, termed mAb HTN-Gn1 and mAb nn-ITN-Gn2, respectively. Crystallographic analysis reveals that these mAbs target spatially distinct epitopes at disparate sites of the N-terminal region of the HTNV Gn ectodomain. Epitope mapping onto a model of the higher order (Gn-Gc)(4) spike supports the immune accessibility of the mAb HTN-Gn1 epitope, a hypothesis confirmed by electron cryo-tomography of the antibody with virus-like particles. These data define natively exposed regions of the hantaviral Gn that can be targeted in immunogen design. IMPORTANCE The spillover of pathogenic hantaviruses from rodent reservoirs into the human population poses a continued threat to human health. Here, we show that a recombinant form of the Hantaan virus (HTNV) surface-displayed glycoprotein, Gn, elicits a neutralizing antibody response in rabbits. We isolated a neutralizing (HTN-Gn1) and a non-neutralizing (nn-ITN-Gn2) monoclonal antibody and provide the first molecular-level insights into how the Gn glycoprotein may be targeted by the antibody-mediated immune response. These findings may guide rational vaccine design approaches focused on targeting the hantavirus glycoprotein envelope.
  • Watanabe, Yasunori; Raghwani, Jayna; Allen, Joel D.; Seabright, Gemma E.; Li, Sai; Moser, Felipe; Huiskonen, Juha T.; Strecker, Thomas; Bowden, Thomas A.; Crispin, Max (2018)
    Lassa virus is an Old World arenavirus endemic to West Africa that causes severe hemorrhagic fever. Vaccine development has focused on the envelope glycoprotein complex (GPC) that extends from the virion envelope. The often inadequate antibody immune response elicited by both vaccine and natural infection has been, in part, attributed to the abundance of N-linked glycosylation on the GPC. Here, using a virus-like-particle system that presents Lassa virus GPC in a native-like context, we determine the composite population of each of the N-linked glycosylation sites presented on the trimeric GPC spike. Our analysis reveals the presence of underprocessed oligomannose-type glycans, which form punctuated clusters that obscure the proteinous surface of both the GP1 attachment and GP2 fusion glycoprotein subunits of the Lassa virus GPC. These oligomannose clusters are seemingly derived as a result of sterically reduced accessibility to glycan processing enzymes, and limited amino acid diversification around these sites supports their role protecting against the humoral immune response. Combined, our data provide a structure-based blueprint for understanding how glycans render the glycoprotein spikes of Lassa virus and other Old World arenaviruses immunologically resistant targets.
  • Mikola, Peitsa (Suomen metsätieteellinen seura, 1965)
  • Kumpulainen, Kristiina; Kajamaa, Anu; Rajala, Antti (2018)
    This study investigates agency-structure dynamics in students and teachers' social activity in a novel design and making environment in the context of the Finnish school system, which has recently undergone major curricular reform. Understanding that agency is an important mediator of educational change, we ask the following questions: How are agency-structure dynamics manifested in the social activity of students and their teachers in a novel design and making environment? How do agency-structure dynamics create possibilities and obstacles for educational change? The data comprise 65 hours of video recordings and field notes of the social activity of students aged 9-12 years old (N = 94) and their teachers collected over a period of one semester. Our study shows how the introduction of the novel learning environment created a boundary space in which traditional teacher-centered activity patterns interacted and came into tension with student-centered modes of teaching and learning. Our study reveals three distinctive agency-structure dynamics that illuminate how the agentive actions of both teachers and students stabilized existing teacher-centered practices and, at other, times ruptured and broke away from existing patterns, thus giving rise to possibilities for educational change.
  • Laanto, Elina; Mantynen, Sari; De Colibus, Luigi; Marjakangas, Jenni; Gillum, Ashley; Stuart, David I.; Ravantti, Janne J.; Huiskonen, Juha T.; Sundberg, Lotta-Riina (2017)
    Viruses have impacted the biosphere in numerous ways since the dawn of life. However, the evolution, genetic, structural, and taxonomic diversity of viruses remain poorly understood, in part because sparse sampling of the virosphere has concentrated mostly on exploring the abundance and diversity of dsDNA viruses. Furthermore, viral genomes are highly diverse, and using only the current sequence-based methods for classifying viruses and studying their phylogeny is complicated. Here we describe a virus, FLiP (Flavobacterium-infecting, lipid-containing phage), with a circular ssDNA genome and an internal lipid membrane enclosed in the icosahedral capsid. The 9,174-nt-long genome showed limited sequence similarity to other known viruses. The genetic data imply that this virus might use replication mechanisms similar to those found in other ssDNA replicons. However, the structure of the viral major capsid protein, elucidated at near-atomic resolution using cryo-electron microscopy, is strikingly similar to that observed in dsDNA viruses of the PRD1-adenovirus lineage, characterized by a major capsid protein bearing two beta-barrels. The strong similarity between FLiP and another member of the structural lineage, bacteriophage PM2, extends to the capsid organization (pseudo T = 21 dextro) despite the difference in the genetic material packaged and the lack of significant sequence similarity.