Browsing by Subject "DOMAINS"

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  • Bakharev, F. L.; Taskinen, J. (2017)
    We study the spectral linear elasticity problem in an unbounded periodic waveguide, which consists of a sequence of identical bounded cells connected by thin ligaments of diameter of order h > 0. The essential spectrum of the problem is known to have band-gap structure. We derive asymptotic formulas for the position of the spectral bands and gaps, as h -> 0.
  • Ligthart, Kate; Belzer, Clara; de Vos, Willem M.; Tytgat, Hanne L.P. (2020)
    Cell-surface-located proteinaceous appendages, such as flagella and fimbriae or pili, are ubiquitous in bacterial communities. Here, we focus on conserved type IV pili (T4P) produced by bacteria in the intestinal tract, one of the most densely populated human ecosystems. Computational analysis revealed that approximately 30% of known intestinal bacteria are predicted to produce T4P. To rationalize how T4P allow intestinal bacteria to interact with their environment, other microbiota members, and host cells, we review their established role in gut commensals and pathogens with respect to adherence, motility, and biofilm formation, as well as protein secretion and DNA uptake. This work indicates that T4P are widely spread among the known members of the intestinal microbiota and that their contribution to human health might be underestimated.
  • Pakarinen, Annukka; Haven, Mai Ostergaard; Djajadi, Demi Tristan; Varnai, Aniko; Puranen, Terhi; Viikari, Liisa (2014)
  • Ikonen, Elina; Zhou, Xin (2021)
    Cholesterol represents the most abundant single lipid in mammalian cells. How its asymmetric distribution between subcellular membranes is achieved and maintained attracts considerable interest. One of the challenges is that cholesterol rarely is transported alone, but rather is coupled with heterotypic transport and metabolism of other lipids, in particular phosphoinositides, phosphatidylserine, and sphingolipids. This perspective summarizes the major exo- and endocytic cholesterol transport routes and how lipid transfer proteins at membrane contacts and membrane transport intersect along these routes. It discusses the cotransport of cholesterol with other lipids in mammalian cells and reviews emerging evidence related to the physiological relevance of this process.
  • Ellilä, Simo; Bromann, Paul; Nyyssönen, Mari; Itävaara, Merja; Koivula, Anu; Paulin, Lars; Kruus, Kristiina (2019)
    Xylanases are in important class of industrial enzymes that are essential for the complete hydrolysis of lignocellulosic biomass into fermentable sugars. In the present study, we report the cloning of novel xylanases with interesting properties from compost metagenomics libraries. Controlled composting of lignocellulosic materials was used to enrich the microbial population in lignocellulolytic organisms. DNA extracted from the compost samples was used to construct metagenomics libraries, which were screened for xylanase activity. In total, 40 clones exhibiting xylanase activity were identified and the thermostability of the discovered xylanases was assayed directly from the library clones. Five genes, including one belonging to the more rare family GH8, were selected for subcloning and the enzymes were expressed in recombinant form in E. coli. Preliminary characterization of the metagenome-derived xylanases revealed interesting properties of the novel enzymes, such as high thermostability and specific activity, and differences in hydrolysis profiles. One enzyme was found to perform better than a standard Trichoderma reesei xylanase in the hydrolysis of lignocellulose at elevated temperatures.
  • Neuvonen, Maarit; Manna, Moutusi; Mokkila, Sini; Javanainen, Matti; Rog, Tomasz; Liu, Zheng; Bittman, Robert; Vattulainen, Ilpo; Ikonen, Elina (2014)
  • Laakasuo, Michael; Sundvall, Jukka; Drosinou, Maria-Anna (2017)
    The role of emotional disgust and disgust sensitivity in moral judgment and decision-making has been debated intensively for over 20 years. Until very recently, there were two main evolutionary narratives for this rather puzzling association. One of the models suggest that it was developed through some form of group selection mechanism, where the internal norms of the groups were acting as pathogen safety mechanisms. Another model suggested that these mechanisms were developed through hygiene norms, which were piggybacking on pathogen disgust mechanisms. In this study we present another alternative, namely that this mechanism might have evolved through sexual disgust sensitivity. We note that though the role of disgust in moral judgment has been questioned recently, few studies have taken disgust sensitivity to account. We present data from a large sample (N=1300) where we analyzed the associations between The Three Domain Disgust Scale and the most commonly used 12 moral dilemmas measuring utilitarian/deontological preferences with Structural Equation Modeling. Our results indicate that of the three domains of disgust, only sexual disgust is associated with more deontological moral preferences. We also found that pathogen disgust was associated with more utilitarian preferences. Implications of the findings are discussed.
  • Santinho, Alexandre; Salo, Veijo T.; Chorlay, Aymeric; Li, Shiqian; Zhou, Xin; Omrane, Mohyeddine; Ikonen, Elina; Thiam, Abdou Rachid (2020)
    Lipid droplet (LD) biogenesis begins in the endoplasmic reticulum (ER) bilayer, but how the ER topology impacts this process is unclear. An early step in LD formation is nucleation, wherein free neutral lipids, mainly triacylglycerols (TGs) and sterol esters (SEs), condense into a nascent LD. How this transition occurs is poorly known. Here, we found that LDs preferably assemble at ER tubules, with higher curvature than ER sheets, independently of the LD assembly protein seipin. Indeed, the critical TG concentration required for initiating LD assembly is lower at curved versus flat membrane regions. In agreement with this finding, flat ER regions bear higher amounts of free TGs than tubular ones and present less LDs. By using an in vitro approach, we discovered that the presence of free TGs in tubules is energetically unfavorable, leading to outflow of TGs to flat membrane regions or condensation into LDs. Accordingly, in vitro LD nucleation can be achieved by the sole increase of membrane curvature. In contrast to TGs, the presence of free SEs is favored at tubules and increasing SE levels is inhibitory to the curvature-induced nucleation of TG LDs. Finally, we found that seipin is enriched at ER tubules and controls the condensation process, preventing excessive tubule-induced nucleation. The absence of seipin provokes erratic LD nucleation events determined by the abundance of ER tubules. In summary, our data indicate that membrane curvature catalyzes LD assembly.
  • Mänty, Minna; Lallukka, Tea; Lahti, Jouni; Pietilainen, Olli; Laaksonen, Mikko; Lahelma, Eero; Rahkonen, Ossi (2017)
    Background: Sickness absence has been shown to be a risk marker for severe future health outcomes, such as disability retirement and premature death. However, it is poorly understood how all-cause and diagnosis-specific sickness absence is reflected in subsequent physical and mental health functioning over time. The aim of this study was to examine the association of all-cause and diagnosis-specific sickness absence with subsequent changes in physical and mental health functioning among ageing municipal employees. Methods: Prospective survey and register data from the Finnish Helsinki Health Study and the Social Insurance Institution of Finland were used. Register based records for medically certified all-cause and diagnostic-specific sickness absence spells (> 14 consecutive calendar days) in 2004-2007 were examined in relation to subsequent physical and mental health functioning measured by Short-Form 36 questionnaire in 2007 and 2012. In total, 3079 respondents who were continuously employed over the sickness absence follow-up were included in the analyses. Repeated-measures analysis was used to examine the associations. Results: During the 3-year follow-up, 30% of the participants had at least one spell of medically certified sickness absence. All-cause sickness absence was associated with lower subsequent physical and mental health functioning in a stepwise manner: the more absence days, the poorer the subsequent physical and mental health functioning. These differences remained but narrowed slightly during the follow-up. Furthermore, the adverse association for physical health functioning was strongest among those with sickness absence due to diseases of musculoskeletal or respiratory systems, and on mental functioning among those with sickness absence due to mental disorders. Conclusions: Sickness absence showed a persistent adverse stepwise association with subsequent physical and mental health functioning. Evidence on health-related outcomes after long-term sickness absence may provide useful information for targeted interventions to promote health and workability.
  • Pietilä, Maija K.; Roine, Elina; Sencilo, Ana; Bamford, Dennis H.; Oksanen, Hanna M. (2016)
    Viruses infecting archaea show a variety of virion morphotypes, and they are currently classified into more than ten viral families or corresponding groups. A pleomorphic virus morphotype is very common among haloarchaeal viruses, and to date, several such viruses have been isolated. Here, we propose the classification of eight such viruses and formation of a new family, Pleolipoviridae (from the Greek pleo for more or many and lipos for lipid), containing three genera, Alpha-, Beta-, and Gammapleolipovirus. The proposal is currently under review by the International Committee on Taxonomy of Viruses (ICTV). The members of the proposed family Pleolipoviridae infect halophilic archaea and are nonlytic. They share structural and genomic features and differ from any other classified virus. The virion of pleolipoviruses is composed of a pleomorphic membrane vesicle enclosing the genome. All pleolipoviruses have two major structural protein species, internal membrane and spike proteins. Although the genomes of the pleolipoviruses are single- or double-stranded, linear or circular DNA molecules, they share the same genome organization and gene synteny and show significant similarity at the amino acid level. The canonical features common to all members of the proposed family Pleolipoviridae show that they are closely related and thus form a new viral family.
  • Asikainen, Anastasia (2021)
    While existing literature on third-sector support for ageing migrants shows that social clubs can be a vital source of social support, what remains unclear is how these positive outcomes are attained on an interactional level. Drawing on fieldwork conducted over the course of one year in a meeting place for older Russian-speaking migrants in the capital region of Finland, this paper adopts a processual approach to examine how a sense of groupness is negotiated in the meeting place. The attendees of the meeting place comprise of different nationalities and backgrounds, who mainly share age and Russian language. This heterogeneity creates a situation where the attendees, together with the organisers, negotiate a sense of groupness with the category of ‘Russian-speaking’. I argue that such a sense of groupness is reached by drawing from shared traits of culturality, while excluding aspects that could cause conflicts. The paper further contributes to the literature on groupness by analysing what role atmosphere plays in attaining a sense of groupness, and argues that the notion of atmosphere is important to take into consideration when thinking how different places can support ageing and wellbeing.
  • Anttila, Heidi; Tallqvist, Susanna; Munoz, Minna; Leppäjoki-Tiistola, Sanna; Mäkitie, Outi; Hiekkala, Sinikka (2021)
    Background Little is known about the spectrum of everyday challenges that people with skeletal dysplasia face because of their health and functioning. We aimed to identify factors related to health, functioning and disability in people with skeletal dysplasia, and their challenges with accessibility in order to form a self-reported questionnaire for national data collection. The comprehensive musculoskeletal post-acute core set of the International Classification of Functioning, Disability and Health (ICF) was used as a framework. Methods An iterative, participatory and qualitative process was used to formulate a questionnaire. Items were searched from Patient-Reported Outcomes Measurement Information System and from other self-report instruments, additional items were formulated using ICF linking rules. Expert panels from the target population assessed the face and content validity in thematic interviews. Results The questionnaire demonstrated its relevance, comprehensiveness and feasibility for people with skeletal dysplasia. The ICF linkages showed the contents' correspondence to the construct. Expert panels added 15 categories and one on chapter level to the core set and confirmed content validity. The final survey covers 86 ICF categories and 173 ICF-linked items that were grouped to 33 questions. Conclusions The content of the questionnaire proved to be sufficiently valid for people with skeletal dysplasia. It can be used to explore their health, functioning, disability and accessibility to develop care and rehabilitation policies, to plan services and to provide information to various parties involved.
  • Koverola, Mika; Kunnari, Anton Johannes Olavi; Drosinou, Maria-Anna; Palomäki, Jussi Petteri; Hannikainen, Ivar; Košová, Michaela; Kopecký, Robin; Sundvall, Jukka; Laakasuo, Michael (2022)
    In six vignette-based experiments, we assessed people's moral reactions towards various cognition-enhancing brain implants, including their overall approval and perceived fairness, as well as the dehumanization of brain-implanted agents. Across the domains of memory (Studies 1-4, 6), general intelligence (Study 5A), and emotional stability (Study 5B), people in general approved of alleviating ailments, and even of attaining optimal human performance, but expressed greater opposition towards superhuman levels of enhancement. Further analyses of individual differences indicated that the tendency to condemn transhumanist technologies, such as brain implants, was linked to sexual disgust sensitivity and the binding moral foundations - two characteristic correlates of a conservative worldview. In turn, exposure to science fiction was tied to greater approval of brain implants. We also examined potential idiosyncrasies associated with our stimulus materials and did not find reliable effects of any secondary factors on moral attitudes. Taken together, our studies reveal certain moral boundaries to neurotechnological enhancement, strong among those with conservative affective and moral dispositions but relaxed among those familiar with science fiction themes.
  • Aavikko, Mervi; Kaasinen, Eevi; Andersson, Noora; Pentinmikko, Nalle; Sulo, Päivi; Donner, Iikki; Pihlajamaa, Päivi; Kuosmanen, Anna; Bramante, Simona; Katainen, Riku; Sipilä, Lauri J; Martin, Samantha; Arola, Johanna; Carpén, Olli; Heiskanen, Ilkka; Mecklin, Jukka-Pekka; Taipale, Jussi; Ristimäki, Ari; Lehti, Kaisa; Gucciardo, Erika; Katajisto, Pekka; Schalin-Jäntti, Camilla; Vahteristo, Pia; Aaltonen, Lauri A. (2021)
    Many hereditary cancer syndromes are associated with an increased risk of small and large intestinal adenocarcinomas. However, conditions bearing a high risk to both adenocarcinomas and neuroendocrine tumors are yet to be described.We studied a family with 16 individuals in four generations affected by a wide spectrum of intestinal tumors, including hyperplastic polyps, adenomas, small intestinal neuroendocrine tumors, and colorectal and small intestinal adenocarcinomas.To assess the genetic susceptibility and understand the novel phenotype, we utilized multiple molecular methods, including whole genome sequencing, RNA sequencing, single cell sequencing, RNA in situ hybridization and organoid culture.We detected a heterozygous deletion at the cystic fibrosis locus (7q31.2) perfectly segregating with the intestinal tumor predisposition in the family. The deletion removes a topologically associating domain border between CFTR and WNT2, aberrantly activating WNT2 in the intestinal epithelium. These consequences suggest that the deletion predisposes to small intestinal neuroendocrine tumors and small and large intestinal adenocarcinomas, and reveals the broad tumorigenic effects of aberrant WNT activation in the human intestine.