Browsing by Subject "biotieteet"

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  • Suntio, Taina (Helsingin yliopisto, 2008)
    The diversity of functions of eukaryotic cells is preserved by enclosing different enzymatic activities into membrane-bound organelles. Separation of exocytic proteins from those which remain in the endoplasmic reticulum (ER) casts the foundation for correct compartmentalization. The secretory pathway, starting from the ER membrane, operates by the aid of cytosolic coat proteins (COPs). In anterograde transport, polymerization of the COPII coat on the ER membrane is essential for the ER exit of proteins. Polymerization of the COPI coatomer on the cis-Golgi membrane functions for the retrieval of proteins from the Golgi for repeated use in the ER. The COPII coat is formed by essential proteins; Sec13/31p and Sec23/24p have been thought to be indispensable for the ER exit of all exocytic proteins. However, we found that functional Sec13p was not required for the ER exit of yeast endogenous glycoprotein Hsp150 in the yeast Saccharomyces cerevisiae. Hsp150 turned out to be an ATP phosphatase. ATP hydrolysis by a Walker motif located in the C-terminal domain of Hsp150 was an active mediator for the Sec13p and Sec24p independent ER exit. Our results suggest that in yeast cells a fast track transport route operates in parallel with the previously described cisternal maturation route of the Golgi. The fast track is used by Hsp150 with the aid of its C-terminal ATPase activity at the ER-exit. Hsp150 is matured with a half time of less than one minute. The cisternal maturation track is several-fold slower and used by other exocytic proteins studied so far. Operative COPI coat is needed for ER exit by a subset of proteins but not by Hsp150. We located a second active determinant to the Hsp150 polypeptide s N-terminal portion that guided also heterologous fusion proteins out of the ER in COPII coated vesicles under non-functional COPI conditions for several hours. Our data indicate that ER exit is a selective, receptor-mediated event, not a bulk flow. Furthermore, it suggests the existence of another retrieval pathway for essential reusable components, besides the COPI-operated retrotransport route. Additional experiments suggest that activation of the COPI primer, ADP ribosylation factor (ARF), is essential also for Hsp150 transport. Moreover, it seemed that a subset of proteins directly needed activated ARF in the anterograde transport to complete the ER exit. Our results indicate that coat structures and transport routes are more variable than it has been imagined.
  • Yu, Liying (Helsingin yliopisto, 2009)
    Programed cell death (PCD) is a fundamental biological process that is as essential for the development and tissue homeostasis as cell proliferation, differentiation and adaptation. The main mode of PCD - apoptosis - occurs via specifi c pathways, such as mitochondrial or death receptor pathway. In the developing nervous system, programed death broadly occurs, mainly triggered by the defi ciency of different survival-promoting neurotrophic factors, but the respective death pathways are poorly studied. In one of the best-characterized models, sympathetic neurons deprived of nerve growth factor (NGF) die via the classical mitochondrial apoptotic pathway. The main aim of this study was to describe the death programs activated in these and other neuronal populations by using neuronal cultures deprived of other neurotrophic factors. First, this study showed that the cultured sympathetic neurons deprived of glial cell line-derived neurotrophic factor (GDNF) die via a novel non-classical death pathway, in which mitochondria and death receptors are not involved. Indeed, cytochrome c was not released into the cytosol, Bax, caspase-9, and caspase-3 were not involved, and Bcl-xL overexpression did not prevent the death. This pathway involved activation of mixed lineage kinases and c-jun, and crucially requires caspase-2 and -7. Second, it was shown that deprivation of neurotrophin-3 (NT-3) from cultured sensory neurons of the dorsal root ganglia kills them via a dependence receptor pathway, including cleavage of the NT- 3 receptor TrkC and liberation of a pro-apoptotic dependence domain. Indeed, death of NT-3-deprived neurons was blocked by a dominant-negative construct interfering with TrkC cleavage. Also, the uncleavable mutant of TrkC, replacing the siRNA-silenced endogeneous TrkC, was not able to trigger death upon NT-3 removal. Such a pathway was not activated in another subpopulation of sensory neurons deprived of NGF. Third, it was shown that cultured midbrain dopaminergic neurons deprived of GDNF or brainderived neurotrophic factor (BDNF) kills them by still a different pathway, in which death receptors and caspases, but not mitochondria, are activated. Indeed, cytochrome c was not released into the cytosol, Bax was not activated, and Bcl-xL did not block the death, but caspases were necessary for the death of these neurons. Blocking the components of the death receptor pathway - caspase-8, FADD, or Fas - blocked the death, whereas activation of Fas accelerated it. The activity of Fas in the dopaminergic neurons could be controlled by the apoptosis inhibitory molecule FAIML. For these studies we developed a novel assay to study apoptosis in the transfected dopaminergic neurons. Thus, a novel death pathway, characteristic for the dopaminergic neurons was described. The study suggests death receptors as possible targets for the treatment of Parkinson s disease, which is caused by the degeneration of dopaminergic neurons.
  • Vainio, Eeva Johanna (Helsingin yliopisto, 2008)
    Wood decay fungi belonging to the species complex Heterobasidion annosum sensu lato are among the most common and economically important species causing root rot and stem decay in conifers of the northern temperate regions. New infections by these pathogens can be suppressed by tree stump treatments using chemical or biological control agents. In Finland, the corticiaceous fungus Phlebiopsis gigantea has been formulated into a commercial biocontrol agent called Rotstop (Verdera Ltd.). This thesis addresses the ecological impacts of Rotstop biocontrol treatment on the mycoflora of conifer stumps. Locally, fungal communities within Rotstop-treated and untreated stumps were analyzed using a novel method based on DGGE profiling of small subunit ribosomal DNA fragments amplified directly from wood samples. Population analyses for P. gigantea and H. annosum s.l. were conducted to evaluate possible risks associated with local and/or global distribution of the Rotstop strain. Based on molecular community profiling by DGGE, we detected a few individual wood-inhabiting fungal species (OTUs) that seemed to have suffered or benefited from the Rotstop biocontrol treatment. The DGGE analyses also revealed fungal diversity not retrieved by cultivation and some fungal sequence types untypical for decomposing conifer wood. However, statistical analysis of DGGE community profiles obtained from Rotstop-treated and untreated conifer stumps revealed that the Rotstop treatment had not caused a statistically significant reduction in the species diversity of wood-inhabiting fungi within our experimental forest plots. Locally, ISSR genotyping of cultured P. gigantea strains showed that the Rotstop biocontrol strain was capable of surviving up to six years within treated Norway spruce stumps, while in Scots pine stumps it was sooner replaced by successor fungal species. In addition, the spread of resident P. gigantea strains into Rotstop-treated forest stands seemed effective in preventing the formation of genetically monomorphic populations in the short run. On a global scale, we detected a considerable level of genetic differentiation between the interfertile European and North American populations of P. gigantea. These results strongly suggest that local biocontrol strains should be used in order to prevent global spread of P. gigantea and hybrid formation between geographically isolated populations. The population analysis for H. annosum s.l. revealed a collection of Chinese fungal strains that showed a high degree of laboratory fertility with three different allopatric H. annosum s.l. taxa. However, based on the molecular markers, the Chinese strains could be clearly affiliated with the H. parviporum taxonomical cluster, which thus appears to have a continuous distribution range from Europe through southern Siberia to northern China. Keywords: Rotstop, wood decay, DGGE, ISSR fingerprinting, ribosomal DNA
  • Oksaharju, Anna (Helsingin yliopisto, 2012)
    Mast cells are immunological cells having an important function in host defense. Mast cells also participate in the regulation of many other physiological functions of the body, such as the regulation of tissue homeostasis, intestinal functions, and neuro-immune interactions, by producing multiple mediators including cytokines, chemokines, leukotrienes, prostaglandins, proteases, and biogenic amines. However, these same mast cell-derived mediators are involved in the pathogenesis of many inflammatory diseases, such as atherosclerosis and other metabolic disorders, as well as allergy and intestinal diseases. Considering the inflammatory nature of atherosclerosis, exploring the role of infection in the pathogenesis of the disease has recently gained attention. Components of microbial origin have been detected in atherosclerotic lesions and are suggested to promote the inflammatory status in the arteries. On the other hand, microbes with beneficial effects on human health, called probiotics, have been under extensive study regarding their ability to modulate immunological functions and, thus, their possible benefits in the prevention and alleviation of inflammatory diseases. The purpose of the present study was to investigate the ability of atherosclerosis-related and probiotic bacteria to activate mast cells and their possible effects on inflammation caused by infection or diet. The proatherogenic bacteria Chlamydia pneumoniae (Cpn) and Aggregatibacter actinomycetemcomitans (Aa) induced pro-inflammatory effects in cultured human peripheral-derived mast cells characterized by the elevated expression and secretion of pro-inflammatory cytokines, including tumor necrosis factor α (TNF-α), and chemokines, such as interleukin (IL)-8 and chemokine (C-C motif) ligand 2 (CCL-2). Cpn and Aa also increased the number of activated mast cells in the aortas of atherosclerosis-prone ApoE-/- mice. Aa was also observed to induce increased concentrations of serum lipopolysaccharide (LPS) and TNF-α in the mice. The probiotic Lactobacillus rhamnosus GG (GG) and Lactobacillus rhamnosus Lc705 (Lc705) induced the downregulation of several mast cell activation-related genes in cultured human peripheral-derived mast cells. In addition, GG, Lc705, Bifidobacterium animalis ssp. lactis Bb12 (Bb12), and a combination of these three strains with Propionibacter freudenreichii ssp. shermanii JS (PJS) upregulated the expression of Th1 type pro-inflammatory cytokines, including TNF-α and IL-1β, and chemokines CCL-2 and IL-8, as well as the anti-inflammatory cytokine IL-10. The administration of GG and PJS to high fat-fed ApoE*3Leiden mice reduced the number of intestinal mast cells and the concentrations of plasma markers of inflammation, including vascular cell adhesion molecule (VCAM) 1 E-selectin, and serum amyloid A (SAA). In conclusion, Cpn and Aa induced pro-inflammatory actions in cultured mast cells as well as the activation of mast cells and the induction of systemic inflammation markers in vivo. These effects might induce the inflammation in atherosclerotic lesions and, thus, promote the development of atherosclerosis. The probiotic GG and Lc705 suppressed the expression of genes related to mast cell activation and induced the production of Th1 type and anti-inflammatory cytokines. These changes are suggested to alleviate allergic inflammation. In addition, GG and PJS elicited several anti-inflammatory effects in mice with high-fat diet-induced inflammation, including decreases in the numbers of intestinal mast cells and in the concentrations of markers of systemic inflammation. These actions could be beneficial in the prevention or treatment of inflammatory diseases, such as metabolic disorders.
  • Häyry, Matti; Häyry, Heta (Yliopistopaino, 1997)
    Kirjoituksissaan maamme johtavat filosofiset bioeetikot esittävät keskusteluun provosoivalla tavalla omat vastauksensa moniin terveydenhuollon ja lääketieteen moraalikysymyksiin.
  • Nikula, Suvi (Helsingin yliopisto, 2011)
    Understanding the responses of species and ecosystems to human-induced global environmental change has become a high research priority. The main aim of this thesis was to investigate how certain environmental factors that relate to global change affect European aspen (Populus tremula), a keystone species in boreal forests, and hybrid aspen (P. tremula × P. tremuloides), cultivated in commercial plantations. The main points under consideration were the acclimatization potential of aspen through changes in leaf morphology, as well as effects on growth, leaf litter chemistry and decomposition. The thesis is based on two experiments, in which young aspen (< 1 year) were exposed either to an atmospheric pollutant [elevated ozone (O3)] or variable resource availability [water, nitrogen (N)]; and two field studies, in which mature trees (> 8 years) were growing in environments exposed to multiple environmental stress factors (roadside and urban environments). The field studies included litter decomposition experiments. The results show that young aspen, especially the native European aspen, was sensitive to O3 in terms of visible leaf injuries. Elevated O3 resulted in reduced biomass allocation to roots and accelerated leaf senescence, suggesting negative effects on growth in the long term. Water and N availability modified the frost hardening of young aspen: High N supply, especially when combined with drought, postponed the development of frost hardiness, which in turn may predispose trees to early autumn frosts. This effect was more pronounced in European aspen. The field studies showed that mature aspen acclimatized to roadside and urban environments by producing more xeromorphic leaves. Leaf morphology was also observed to vary in response to interannual climatic variation, which further indicates the ability of aspen for phenotypic plasticity. Intraspecific variation was found in several of the traits measured, although intraspecific differences in response to the abiotic factors examined were generally small throughout the studies. However, some differences between clones were found in sensitivity to O3 and the roadside environment. Aspen leaf litter decomposition was retarded in the roadside environment, but only initially. By contrast, decomposition was found to be faster in the urban than the rural environment throughout the study. The higher quality of urban litter (higher in N, lower in lignin and phenolics), as well as higher temperature, N deposition and humus pH at the urban site were factors likely to promote decay. The phenotypic plasticity combined with intraspecific variation found in the studies imply that aspen has potential for withstanding environmental changes, although some global change factors, such as rising O3 levels, may adversely affect its performance. The results also suggest that the multiple environmental changes taking place in urban areas which correspond closely with the main drivers of global change can modify ecosystem functioning by promoting litter decomposition, mediated partly by alterations in leaf litter quality.
  • Piltti, Katja (Helsingin yliopisto, 2009)
    Stem cells are responsible for tissue turnover throughout lifespan. Only highly controlled specific environment, the stem cell niche , can sustain undifferentiated stem cell-pool. The balance between maintenance and differentiation is crucial for individual s health: uncontrolled stem cell self-renewal or proliferation can lead to hyperplasia and mutations that further provoke malignant transformation of the cells. On the other hand, uninhibited differentiation may result in diminished stem cell population, which is unable to maintain tissue turnover. The mechanisms that control the switch from maintenance to differentiation in stem cells are not well known. The same mechanisms that direct the self-renewal and proliferation in normal stem cells are likely to be also involved in maintenance of cancer stem cell . Cancer stem cells exhibit stem cell like properties such as self-renewal- and differentiation capacity and they can also regenerate the tumor tissue. In this thesis, I have investigated the effect of classical oncogenes E6/E7 and c-Myc, tumor suppressors p53 and retinoblastoma (pRb) family, and vascular endothelial growth factor (VEGF) subfamily and glial cell line-derived neurothropic factor (GDNF) family ligands on behavior of embryonic neural stem cells (NSCs) and progenitors. The study includes also the characterization of cytoskeletal tumor suppressor neurofibromatosis 2 (NF2) protein merlin and ezrin-radixin-moesin (ERM) protein ezrin expression in neural progenitors cells and their progeny. This study reveals some potential mechanisms regarding to NSCs maintenance. In summary, the studied molecules are able to shift the balance either towards stem cell maintenance or differentiation; tumor suppressor p53 represses whereas E6/E7 oncogenes and c-Myc increase the proportion of self-renewing and proliferating NSCs or progenitors. The data suggests that active MEK-ERK signaling is critical for self-renewal of normal and oncogene expressing NSCs. In addition, the results indicate that expression of cytoskeletal tumor suppressor merlin and ERM protein ezrin in central nervous system (CNS) tissue and progenitors indicates their role in cell differentiation. Furthermore, the data suggests that VEGF-C a factor involved in lymphatic system development, angiogenesis, neovascularization and metastasis but also in maintenance of some neural populations in brain is a novel thropic factor for progenitors in early sympathetic nervous system (SNS). It seems that VEGF-C dose dependently through ERK-pathway supports the proliferation and survival of early sympathetic progenitor cells, and the effect is comparable to that of GDNF family ligands.
  • Neuvonen, Maarit (Helsingin yliopisto, 2011)
    Alphaviruses are positive strand RNA viruses that replicate in association with cellular membranes. The viral RNA replication complex consists of four non-structural proteins nsP1-nsP4 which are essential for viral replication. The functions of nsP1, nsP2 and nsP4 are well established, but the roles of nsP3 are mainly unknown. In this work I have clarified some of the functions of nsP3 in order to better understand the importance of this protein in virus replication. Semliki Forest virus (SFV) has been mostly used as a model alphavirus during this work, but some experiments have also been conducted with Sindbis and Chikungunya viruses. NsP3 is composed of three different protein domains. The N-terminus of nsP3 contains an evolutionarily conserved macrodomain, the central part of nsP3 contains a domain that is only found in alphaviruses, and the C-terminus of the protein is hypervariable and predicted to be unstructured. In this work I have analyzed the functions of nsP3 macrodomain, and shown that viral macrodomains bind poly(ADP-ribose) and that they do not resemble cellular macrodomains in their properties. Furthermore, I have shown that some macrodomains, including viral macrodomains of SFV and hepatitis E virus, also bind poly(A). Mutations in the ligand binding pocket of SFV macrodomain hamper virus replication but do not confer lethality, indicating that macrodomain function is beneficial but not mandatory for virus replication. The hypervariable C-terminus of nsP3 is heavily phosphorylated and is enriched in proline residues. In this work it is shown that this region harbors an SH3 domain binding motif (Sh3BM) PxRxPR through which cellular amphiphysin is recruited to viral replication sites and to nsP3 containing cytoplasmic aggregate structures. The function of Sh3BM was destroyed by a single point mutation, which led to impaired viral RNA replication in HeLa cells, pointing out the functional importance of amphiphysin recruitment by the Sh3BM. In addition, evidence is provided tho show that the endosomal localization of alphavirus replication is mediated by nsP3 and that the phosphorylation of hypervariable region might be important for the endosomal targeting. Together these findings demonstrate that nsP3 contains multiple important host interaction motifs and domains, which facilitate successful viral propagation in host cells.
  • Kerttula, Anne-Marie (Helsingin yliopisto, 2007)
    Staphylococcus aureus is one of the most important bacteria that cause disease in humans, and methicillin-resistant S. aureus (MRSA) has become the most commonly identified antibiotic-resistant pathogen in many parts of the world. MRSA rates have been stable for many years in the Nordic countries and the Netherlands with a low MRSA prevalence in Europe, but in the recent decades, MRSA rates have increased in those low-prevalence countries as well. MRSA has been established as a major hospital pathogen, but has also been found increasingly in long-term facilities (LTF) and in communities of persons with no connections to the health-care setting. In Finland, the annual number of MRSA isolates reported to the National Infectious Disease Register (NIDR) has constantly increased, especially outside the Helsinki metropolitan area. Molecular typing has revealed numerous outbreak strains of MRSA, some of which have previously been associated with community acquisition. In this work, data on MRSA cases notified to the NIDR and on MRSA strain types identified with pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and staphylococcal cassette chromosome mec (SCCmec) typing at the National Reference Laboratory (NRL) in Finland from 1997 to 2004 were analyzed. An increasing trend in MRSA incidence in Finland from 1997 to 2004 was shown. In addition, non-multi-drug resistant (NMDR) MRSA isolates, especially those resistant only to methicillin/oxacillin, showed an emerging trend. The predominant MRSA strains changed over time and place, but two internationally spread epidemic strains of MRSA, FIN-16 and FIN-21, were related to the increase detected most recently. Those strains were also one cause of the strikingly increasing invasive MRSA findings. The rise of MRSA strains with SCCmec types IV or V, possible community-acquired MRSA was also detected. With questionnaires, the diagnostic methods used for MRSA identification in Finnish microbiology laboratories and the number of MRSA screening specimens studied were reviewed. Surveys, which focused on the MRSA situation in long-term facilities in 2001 and on the background information of MRSA-positive persons in 2001-2003, were also carried out. The rates of MRSA and screening practices varied widely across geographic regions. Part of the NMDR MRSA strains could remain undetected in some laboratories because of insufficient diagnostic techniques used. The increasing proportion of elderly population carrying MRSA suggests that MRSA is an emerging problem in Finnish long-term facilities. Among the patients, 50% of the specimens were taken on a clinical basis, 43% on a screening basis after exposure to MRSA, 3% on a screening basis because of hospital contact abroad, and 4% for other reasons. In response to an outbreak of MRSA possessing a new genotype that occurred in a health care ward and in an associated nursing home of a small municipality in Northern Finland in autumn 2003, a point-prevalence survey was performed six months later. In the same study, the molecular epidemiology of MRSA and methicillin-sensitive S. aureus (MSSA) strains were also assessed, the results to the national strain collection compared, and the difficulties of MRSA screening with low-level oxacillin-resistant isolates encountered. The original MRSA outbreak in LTF, which consisted of isolates possessing a nationally new PFGE profile (FIN-22) and internationally rare MLST type (ST-27), was confined. Another previously unrecognized MRSA strain was found with additional screening, possibly indicating that current routine MRSA screening methods may be insufficiently sensitive for strains possessing low-level oxacillin resistance. Most of the MSSA strains found were genotypically related to the epidemic MRSA strains, but only a few of them had received the SCCmec element, and all those strains possessed the new SCCmec type V. In the second largest nursing home in Finland, the colonization of S. aureus and MRSA, and the role of screening sites along with broth enrichment culture on the sensitivity to detect S. aureus were studied. Combining the use of enrichment broth and perineal swabbing, in addition to nostrils and skin lesions swabbing, may be an alternative for throat swabs in the nursing home setting, especially when residents are uncooperative. Finally, in order to evaluate adequate phenotypic and genotypic methods needed for reliable laboratory diagnostics of MRSA, oxacillin disk diffusion and MIC tests to the cefoxitin disk diffusion method at both +35°C and +30°C, both with or without an addition of sodium chloride (NaCl) to the Müller Hinton test medium, and in-house PCR to two commercial molecular methods (the GenoType® MRSA test and the EVIGENETM MRSA Detection test) with different bacterial species in addition to S. aureus were compared. The cefoxitin disk diffusion method was superior to that of oxacillin disk diffusion and to the MIC tests in predicting mecA-mediated resistance in S. aureus when incubating at +35°C with or without the addition of NaCl to the test medium. Both the Geno Type® MRSA and EVIGENETM MRSA Detection tests are usable, accurate, cost-effective, and sufficiently fast methods for rapid MRSA confirmation from a pure culture.
  • Fagerlund, Riku (Helsingin yliopisto, 2008)
    The eukaryotic cell nucleoplasm is separated from the cytoplasm by the nuclear envelope. This compartmentation of eukaryotic cells requires that all nuclear proteins must be transported from the cytoplasm into the nucleus. Transport of macromolecules between the nucleus and the cytoplasm occurs through nuclear pore complexes (NPCs). Proteins to be targeted into the nucleus by the classical nuclear import system contain nuclear localization signals (NLSs), which are recognized by importin alpha, the NLS receptor. Importin alpha binds to importin beta, which docks the importin-cargo complex on the cytoplasmic side of the NPC and mediates the movement of the complex into the nucleus. Presently six human importin alpha isoforms have been identified. Transcription factors are among the most important regulators of gene expression in eukaryotic organisms. Transcription factors bind to specific DNA sequences on target genes and modulate the activity of the target gene. Many transcription factors, including signal transducers and activators of transcription (STAT) and nuclear factor kB (NF-kB), reside in the cytoplasm in an inactive form, and upon activation they are rapidly transported into the nucleus. In the nucleus STATs and NF-kB regulate the activity of genes whose products are critical in controlling numerous cellular and organismal processes, such as inflammatory and immune responses, cell growth, differentiation and survival. The aim of this study was to investigate the nuclear import mechanisms of STAT and NF-kB transcription factors. This work shows that STAT1 homodimers and STAT1/STAT2 heterodimers bind specifically and directly to importin alpha5 molecule via unconventional dimer-specific NLSs. Importin alpha molecules have two regions, which have been shown to directly interact with the amino acids in the NLS of the cargo molecule. The Arm repeats 2-4 comprise the N-terminal NLS binding site and Arm repeats 7-8 the C-terminal NLS binding site. In this work it is shown that the binding site for STAT1 homodimers and STAT1/STAT2 heterodimers is composed of Arm repeats 8 and 9 of importin alpha5 molecule. This work demonstrates that all NF-kB proteins are transported into the nucleus by importin alpha molecules. In addition, NLS was identified in RelB protein. The interactions between NF-kB proteins and importin alpha molecules were found to be directly mediated by the NLSs of NF-kB proteins. Moreover, we found that p50 binds to the N-terminal and p65 to the C-terminal NLS binding site of importin alpha3. The results from this thesis work identify previously uncharacterized mechanisms in nuclear import of STAT and NF-kB. These findings provide new insights into the molecular mechanisms regulating the signalling cascades of these important transcription factors from the cytoplasm into the nucleus to the target genes.
  • Johansson, Marie (Helsingin yliopisto, 2006)
    Oxysterol binding protein (OSBP) homologues have been found in eukaryotic organisms ranging from yeast to humans. These evolutionary conserved proteins have in common the presence of an OSBP-related domain (ORD) which contains the fully conserved EQVSHHPP sequence motif. The ORD forms a barrel structure that binds sterols in its interior. Other domains and sequence elements found in OSBP-homologues include pleckstrin homology domains, ankyrin repeats and two phenylalanines in an acidic tract (FFAT) motifs, which target the proteins to distinct subcellular compartments. OSBP homologues have been implicated in a wide range of intracellular processes, including vesicle trafficking, lipid metabolism and cell signaling, but little is known about the functional mechanisms of these proteins. The human family of OSBP homologues consists of twelve OSBP-related proteins (ORP). This thesis work is focused on one of the family members, ORP1, of which two variants were found to be expressed tissue-specifically in humans. The shorter variant, ORP1S contains an ORD only. The N-terminally extended variant, ORP1L, comprises a pleckstrin homology domain and three ankyrin repeats in addition to the ORD. The two ORP1 variants differ in intracellular localization. ORP1S is cytosolic, while the ankyrin repeat region of ORP1L targets the protein to late endosomes/lysosomes. This part of ORP1L also has profound effects on late endosomal morphology, inducing perinuclear clustering of late endosomes. A central aim of this study was to identify molecular interactions of ORP1L on late endosomes. The morphological changes of late endosomes induced by overexpressed ORP1L implies involvement of small Rab GTPases, regulators of organelle motility, tethering, docking and/or fusion, in generation of the phenotype. A direct interaction was demonstrated between ORP1L and active Rab7. ORP1L prolongs the active state of Rab7 by stabilizing its GTP-bound form. The clustering of late endosomes/lysosomes was also shown to be linked to the minus end-directed microtubule-based dynein-dynactin motor complex through the ankyrin repeat region of ORP1L. ORP1L, Rab7 and the Rab7-interacting lysosomal protein (RILP) were found to be part of the same effector complex recruiting the dynein-dynactin complex to late endosomes, thereby promoting minus end-directed movement. The proteins were found to be physically close to each other on late endosomes and RILP was found to stabilize the ORP1L-Rab7 interaction. It is possible that ORP1L and RILP bind to each other through their C-terminal and N-terminal regions, respectively, when they are bridged by Rab7. With the results of this study we have been able to place a member of the uncharacterized OSBP-family, ORP1L, in the endocytic pathway, where it regulates motility and possibly fusion of late endosomes through interaction with the small GTPase Rab7.
  • Nurmi, Katariina (Helsingin yliopisto, 2015)
    The innate immune system responds to infection or injury by initiating nonspecific inflammation, which functions to limit the spread of harmful microbes or the damage caused by tissue injury. The cells of the innate immune system are the first to encounter danger signals, and they mediate the rapid local immune response. Inflammatory reactions are normally beneficial for the host, and inflammation is usually resolved when the threat has been removed. However, in chronic inflammatory diseases, the danger signals either are not cleared or continue to be formed. Pathogen-derived molecules and danger signals induce the activation of pattern recognition receptors (PRRs) in the innate immune cells. Several families of PRRs exist, and their interplay is needed for the induction of efficient immune defense reactions. Nucleotide-binding domain and leucine-rich repeat-containing receptors (NLRs) are intracellular receptors that respond to a plethora of danger- and pathogen-associated molecular patterns. Their activation induces the assembly and activation of cytosolic multiprotein complexes called inflammasomes. Inflammasomes act as a primary checkpoint for the activation and secretion of the strong proinflammatory cytokines interleukin (IL)-1β and IL-18. Similar to other cellular functions, innate immune responses are operated via a complicated interplay between signalosomes. To become activated inflammasomes require the coordinated activation of Toll-like receptors (TLRs) and NLRs, which induce the activation and assembly of inflammasome complexes. The consequent secretion of inflammasome-derived cytokines is, in turn, modulated by autophagy. Inflammasome activation and autophagy also interact with cellular death pathways. Cellular death acts to limit the spread of intracellular pathogens by denying a protective niche to these pathogens, thereby inhibiting their replication and predisposing them for detection by the immune system. The aim of this study was to investigate the roles of ethanol and hemin in the modulation of innate immune cell functions, as well as the mechanisms underlying the reported protective effects of ethanol and hemin against chronic inflammatory diseases. Alcohol is the most commonly and widely used drug in the world. The consequences of alcohol consumption depend on both the pattern of consumption and the amounts consumed. Alcohol abuse predisposes to more frequent and severe infections, whereas the light to moderate consumption of alcoholic beverages has been associated with a reduced incidence of chronic inflammatory conditions, such as cardiovascular diseases and rheumatoid arthritis. These seemingly different responses may both derive from attenuated reactions of innate immunity. In the present thesis study, ethanol was shown to reduce the viability and proliferation of mast cells. This reduced viability resulted from the immunologically silent apoptotic death of mast cells. In macrophages, ethanol reduced the pyroptotic cell death induced by inflammasome activation and instead directed cell death toward apoptosis. Excessive inflammasome activation is a prominent feature of several chronic inflammatory diseases. The mechanisms that restrain inflammasome activation were studied in greater detail in cultured macrophages. Ethanol dose-dependently inhibited inflammasome activation and the secretion of IL-1β in human macrophages. It was further shown that the inhibitory effect of ethanol was mediated by a reduction in lysosomal disruption and the release of active cathepsin B, which thus contributed to diminished inflammasome assembly. The majority of mammalian cells are constantly renewed. Enormous numbers of senescent red blood cells are phagocytosed daily by macrophages. In certain pathologies, such as malarial infection, massive hemolysis occurs that exceeds the capacity of the scavenging and degradation systems of hemoglobin. As a consequence, free heme and hemin are released into the circulation. Free heme and hemin are cytotoxic and proinflammatory compounds. However, heme and hemin are also potent inducers of the heme oxygenase-1 (HO-1) enzyme, which possesses anti-inflammatory and cytoprotective effects. In the present thesis study, hemin and its synthetic derivative cobalt protoporphyrin (CoPP) blocked inflammasome activation and assembly. Decreased secretion of IL-1β was also observed in vivo in a nucleotide-binding domain and leucine-rich repeat-containing family, pyrin domain-containing 3 (NLRP3)-dependent peritonitis model in mice. The inhibitory effects of hemin and CoPP were partially dependent on the induction of HO-1 transcription by NF-E2-related factor-2 (Nrf2) and the enzymatic activity of HO-1. The inhibitory effects of hemin and CoPP were mediated by increased degradation of inflammasome components, which was due to elevated autophagy. Overall, the results of this study demonstrate that ethanol and hemin markedly prevent inflammatory cellular responses in macrophages and mast cells. This inhibition may contribute to the cardioprotective effect of ethanol and the anti-inflammatory effects of hemin. An enhanced molecular understanding of the mechanisms by which ethanol and hemin inhibit inflammation may help reveal new therapeutic options in the treatment of chronic inflammatory diseases.
  • Zohdy, Sarah (Helsingin yliopisto, 2012)
    Mouse lemurs are the world s smallest primates and a model species for ancestral primates that lived 55 million years ago. In captive conditions, mouse lemurs live over six times longer than similarly sized mice and have been found to exhibit many symptoms of human senescence, including Alzheimer s-like neurodegeneration. These traits make captive mouse lemurs an exemplary model for aging. Despite this, to date no study has examined the aging process in wild mouse lemurs. This thesis addresses multidisciplinary questions relating to mouse lemur aging and life history. Through mark-recapture data and a combination of field and laboratory techniques I examine the aging process in wild brown mouse lemurs (Microcebus rufus). To estimate ages of individual wild mouse lemurs a technique was developed using dental wear. I found that in their natural habitat these tiny primates live up to 8 years of age, well past the captive age of senescence (5 yrs). Among old individuals, both males and females are represented, and unlike other polygamous vertebrates age-dependent survival rates do not differ between sexes. With the ages of wild mouse lemurs identified, other age-related factors such as hormone levels and parasite loads were subsequently examined. Contrary to findings in captivity no observable physical symptoms of senescence were found in old mouse lemurs, i.e. over the age of five. Further, new findings highlight mouse lemurs as an exception to many assumptions of mammalian physiology. In this study, testosterone levels were found to be comparable in both males and females, potentially providing an explanation for the lack of difference in survival rates between sexes. Testosterone and DHEA-S, two hormones typically found to decrease with age, did not differ between young and old lemurs. However, cortisol, the stress hormone, did decrease with age in male mouse lemurs, but not in females. Differences in immunity with age were examined indirectly via parasite dynamics. Specifically, I described the ectoparasites found on brown mouse lemurs, and created and implemented a novel method which allows the tracking of the natural flow of parasites between known individuals in a wild. This method revealed that parasite movement between lemurs suggests a much more complex social network than indicated by trapping, provided new insight about how parasites/pathogens move among wild populations, and revealed that only a few individual lemurs could be responsible for population-wide louse-borne epidemic. In addition to shedding light on the social behavior of mouse lemurs, I used the presence of ecto- and endoparasites as an indicator of immune health in young and old individuals, exposing a decline in endoparasites with age, but not in ectoparasites. Hormone measures and parasite loads were also employed to test the immunocompetence handicap hypothesis (ICHH) (which implicates testosterone as a cause for immunosuppression and hence higher parasite intensities) in both sexes. Contrary to the ICHH no correlation between testosterone and parasite intensities was found; however, when cortisol and testosterone positively co-varied higher parasite loads were observed in both sexes. In conclusion, in the search for a better understanding of the aging process in wild brown mouse lemurs I examined the multifaceted physiological transformations (parasitological, endocrinological, and dental wear). This research produced novel, replicable methodologies and findings with wide-reaching implications that extend beyond aging and challenge some of the previously-held assumptions of mammalian biology.
  • Mannonen, Laura (Helsingin yliopisto, 2011)
    Chlamydia pneumoniae can cause acute respiratory infections including pneumonia. Repeated and persistent Chlamydia infections occur and persistent C. pneumoniae infection may have a role in the pathogenesis of atherosclerosis and coronary heart disease and may also contribute to the development of chronic inflammatory lung diseases like chronic obstructive pulmonary disease (COPD) and asthma. In this thesis in vitro models for persistent C. pneumonia infection were established in epithelial and monocyte/macrophage cell lines. Expression of host cell genes in the persistent C. pneumoniae infection model of epithelial cells was studied by microarray and RT-PCR. In the monocyte/macrophage infection model expression of selected C. pneumoniae genes were studied by RT-PCR and immunofluorescence microscopy. Chlamydia is able to modulate host cell gene expression and apoptosis of host cells, which may assist Chlamydia to evade the host cells' immune responses. This, in turn, may lead to extended survival of the organism inside epithelial cells and promote the development of persistent infection. To simulate persistent C. pneumoniae infection in vivo, we set up a persistent infection model exposing the HL cell cultures to IFN-gamma. When HL cell cultures were treated with moderate concentration of IFN-gamma, the replication of C. pneumoniae DNA was unaffected while differentiation into infectious elementary bodies (EB) was strongly inhibited. By transmission electron microscopy small atypical inclusions were identified in IFN-gamma treated cultures. No second cycle of infection was observed in cells exposed to IFN-gamma , whereas C. pneumoniae was able to undergo a second cycle of infection in unexposed HL cells. Although monocytic cells can naturally restrict chlamydial growth, IFN-gamma further reduced production of infectious C. pneumoniae in Mono Mac 6 cells. Under both studied conditions no second cycle of infection could be detected in monocytic cell line suggesting persistent infection in these cells. As a step toward understanding the role of host genes in the development and pathogenesis of persistent C. pneumoniae infection, modulation of host cell gene expression during IFN-gamma induced persistent infection was examined and compared to that seen during active C. pneumoniae infection or IFN-gamma treatment. Total RNA was collected at 6 to 150 h after infection of an epithelial cell line (HL) and analyzed by a cDNA array (available at that time) representing approximately 4000 human transcripts. In initial analysis 250 of the 4000 genes were identified as differentially expressed upon active and persistent chlamydial infection and IFN-gamma treatment. In persistent infection more potent up-regulation of many genes was observed in IFN-gamma induced persistent infection than in active infection or in IFN-gamma treated cell cultures. Also sustained up-regulation was observed for some genes. In addition, we could identify nine host cell genes whose transcription was specifically altered during the IFN-gamma induced persistent C. pneumoniae infection. Strongest up-regulation in persistent infection in relation to controls was identified for insulin like growth factor binding protein 6, interferon-stimulated protein 15 kDa, cyclin D1 and interleukin 7 receptor. These results suggest that during persistent infection, C. pneumoniae reprograms the host transcriptional machinery regulating a variety of cellular processes including adhesion, cell cycle regulation, growth and inflammatory response, all of which may play important roles in the pathogenesis of persistent C. pneumoniae infection. C. pneumoniae DNA can be detected in peripheral blood mononuclear cells indicating that the bacterium can also infect monocytic cells in vivo and thereby monocytes can assist the spread of infection from the lungs to other anatomical sites. Persistent infection established at these sites could promote inflammation and enhance pathology. Thus, the mononuclear cells are in a strategic position in the development of persistent infection. To investigate the intracellular replication and fate of C. pneumoniae in mononuclear cells we analyzed the transcription of 11 C. pneumoniae genes in Mono Mac 6 cells during infection by real time RT-PCR. Our results suggest that the transcriptional profile of the studied genes in monocytes is different from that seen in epithelial cells and that IFN-gamma has a less significant effect on C. pneumoniae transcription in monocytes. Furthermore, our study shows that type III secretion system (T3SS) related genes are transcribed and that Chlamydia possesses a functional T3SS during infection in monocytes. Since C. pneumoniae infection in monocytes has been implicated to have reduced antibiotic susceptibility, this creates opportunities for novel therapeutics targeting T3SS in the management of chlamydial infection in monocytes.
  • Li, Chun-Mei (Helsingin yliopisto, 2007)
    The type III secretion system (T3SS) is an essential requirement for the virulence of many Gram-negative bacteria which infect plants, animals and men. Pathogens use the T3SS to deliver effector proteins from the bacterial cytoplasm to the eukaryotic host cells, where the effectors subvert host defenses. The best candidates for directing effector protein traffic are the bacterial type III-associated appendages, called needles or pili. In plant pathogenic bacteria, the best characterized example of a T3SS-associated appendage is the HrpA pilus of the plant pathogen Pseudomonas syringae pv. tomato DC3000. The components of the T3SS in plant pathogens are encoded by a cluster of hrp (hypersensitive reaction and pathogenicity) genes. Two major classes of T3SS-secreted proteins are: harpin proteins such as HrpZ which are exported into extracellular space, and avirulence (Avr) proteins such as AvrPto which are translocated directly to the plant cytoplasm. This study deals with the structural and functional characterization of the T3SS-associated HrpA pilus and the T3SS-secreted harpins. By insertional mutagenesis analysis of HrpA, we located the optimal epitope insertion site in the amino-terminus of HrpA, and revealed the potential application of the HrpA pilus as a carrier of antigenic determinants for vaccination. By pulse-expression of proteins combined with immuno-electron microscopy, we discovered the Hrp pilus assembly strategy as addition of HrpA subunits to the distal end of the growing pilus, and we showed for the first time that secretion of HrpZ occurs at the tip of the pilus. The pilus thus functions as a conduit delivering proteins to the extracellular milieu. By using phage-display and scanning-insertion mutagenesis methods we identified a conserved HrpZ-binding peptide and localized the peptide-binding site to the central domain of HrpZ. We also found that the HrpZ specifically interacts with a host bean protein. Taken together, the current results provide deeper insight into the molecular mechanism of T3SS-associated pilus assembly and effector protein translocation, which will be helpful for further studies on the pathogenic mechanisms of Gram-negative bacteria and for developing new strategies to prevent bacterial infection.
  • Onttonen, Tiina (2012)
  • Tynell, Janne (Helsingin yliopisto, 2016)
    Respiratory virus infections are a major cause of morbidity and mortality worldwide. Decades of research have yielded many breakthroughs in our understanding of virus-host interactions, but many aspects of viral pathogenesis still remain unresolved. Vaccines and antiviral treatments have been developed, but they are imperfect or completely lacking for many viral agents. Novel emerging viruses form an additional challenge, which can only be overcome by proper preparation and quick response against these unexpected infectious threats. Understanding virus-host interactions is critical for elucidating aspects of viral pathogenesis and devising better treatment strategies against viral pathogens. Our research has focused on the virus-host interactions of two major respiratory pathogens with a recent history of outbreaks by a novel viral agent, the influenza A virus and coronavirus. Influenza A virus has plagued humankind throughout human history and continues to cause annual epidemics and occasional pandemics associated with significant mortality. NS1 protein is one of the major virulence factors of influenza A virus. It has a multitude of different interactions with host cell components that either aid viral replication or hamper the antiviral response exhibited by the host cell. These interactions are located both in the host cell nucleus and the cytoplasm, and three signals regulating the intracellular localization of NS1 protein have been identified. While the critical impact of nuclear localization signal 1 is well known, the other two localization signals have remained poorly characterized. In this work we provide a detailed description of the NS1 nuclear export signal (NES), showing that the NES region is well conserved within different influenza A strains and that certain mutations within the region cause attenuation of virus replication. Through the use of different mutant viruses, we show that the attenuated phenotype is not due to impaired localization alone, but rather involves defects in the functions of NS1. We also show that NS1 is not exported through the classical CRM1-dependent pathway and we establish the nucleolar proteins that bind NS1 and thus guide its nucleolar localization. Human coronaviruses are a major cause of the common cold. For a long time coronaviruses were thought to cause only mild upper respiratory tract infections in humans. However, this view changed with the emergence of the highly lethal SARS coronavirus in 2002 and the identification of MERS coronavirus in 2012. While the SARS outbreak was efficiently contained, MERS coronavirus continues to circulate in camels and causes repeated introductions into the human population in the Middle East. Our MERS coronavirus research concentrated on characterizing MERS infection of human macrophages and dendritic cells, two important cell types of the innate immune system. We show that MERS coronavirus does not replicate productively in these leucocytes, but a significant innate immune response is generated. Altogether this work identifies important aspects of virus-host interaction of two important respiratory pathogens. We provide new information on the mechanisms and impact of influenza A virus NS1 intracellular localization and we characterize MERS coronavirus infection in primary human leucocytes as well as highlight important differences in the host cell responses between MERS and SARS coronaviruses.