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  • Putkonen, Noora (Helsingin yliopisto, 2012)
    Neuronal cell death caused by excitotoxicity accompanies neurodegenerative disorders, such as Alzheimer s disease (AD) and Huntington s disease (HD), epilepsy and ischaemia. Glutamate is the major excitotoxin in the CNS and causes activation of glutamate receptors. Ionotropic glutamate receptors can directly cause calcium influx that further enables activation of cell death pathways. Kainic acid (KA) is a specific agonist for ionotropic non-NMDA glutamate receptors, namely KA and AMPA receptors. KA induces epiletic activity in rodents and causes hippocampal sclerosis, similar to human temporal epilepsy. HD, a neurodegenerative disease characterized by accumulation of mutant huntingtin protein, and causing cell death in the striatum of affected individuals, has also been shown to involve excitotoxic cell death. Intracellular organelles have been implicated in stress sensing and contribute to cell death signaling. Mitochondria have been closely linked to apoptotic pathways and recent research has also implicated other organelles, such as the endoplasmic reticulum (ER), lysosomes and Golgi apparatus in cell death. In this thesis, the involvement of ER stress was shown to accompany hippocampal cell death caused by KA in vivo and in vitro as well as in a cell model of HD. KA induced activation of ER stress sensors that aim to restore homeostasis via activation of the unfolded protein response (UPR). In prolonged stressful conditions, the UPR activates apoptotic pathways. Treatment with an ER stress inhibitor, Salubrinal (Sal), significantly attenuated cell death in hippocampal neurons in vivo and in vitro. ER stress was also activated in a cell model of HD and treatment with Sal reduced cell death and mutant hungtingtin aggregation. These data indicated for the first time the involvement of the ER in cell death pathways caused by excitotoxicity, and that inhibition of ER stress could be a potential treatment against neuronal cell death in HD and other disorders involving excitotoxicity. In search of other cell death mediators we focused on Cdk5 that has been implicated deregulated in excitotoxicity. Involved in multiple signaling pathways, Cdk5, has been implicated, for instance, in regulation of synaptic proteins, ER stress and cell death. In this thesis, a KA receptor important for mediating cell death in the hippocampus, GluR6, was shown to be regulated by Cdk5. Inhibition of Cdk5 reduced GluR6 downregulation by KA as well as cell death caused by KA in vitro. These data indicated Cdk5 involvement in KA excitotoxicity and could also present a potential drug target in neurological disorders. Moreover, this was the first time that Cdk5 was shown to contribute to KA receptor regulation.
  • 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.
  • Hynynen, Riikka (Helsingin yliopisto, 2009)
    ORP2 is a member of mammalian oxysterol binding protein (OSBP)-related protein/gene family (ORPs), which is found in almost every eukaryotic organism. ORPs have been suggested to participate in the regulation of cellular lipid metabolism, vesicle trafficking and cellular signaling. ORP2 is a cytosolic protein that is ubiquitously expressed and most abundant in the brain. In previous studies employing stable cell lines with constitutive ORP2 overexpression ORP2 was shown to affect cellular cholesterol metabolism. The aim of this study was to characterize the properties and function of ORP2 further. ORP2 ligands were searched for among sterols and phosphoinositides using purified ORP2 and in vitro binding assays. As expected, ORP2 bound several oxysterols and cholesterol, the highest affinity ligand being 22(R)hydroxycholesterol. In addition, affinity for anionic membrane phospholipids, phosphoinositides was observed, which may assist in the membrane targeting of ORP2. Intracellular localization of ORP2 was also investigated. ORP2 was observed on the surface of cytoplasmic lipid droplets, which are storage organelles for neutral lipids. Lipid droplet targeting of ORP2 was inhibited when 22(R)hydroxycholesterol was added to the cells or when the N-terminal FFAT-motif of ORP2 was mutated, suggesting that oxysterols and the N-terminus of ORP2 regulate the localization and the function of ORP2. The role of ORP2 in cellular lipid metabolism was studied using HeLa cell lines that can be induced to overexpress ORP2. Overexpression of ORP2 was shown to enhance cholesterol efflux from the cells resulting in a decreased amount of cellular free cholesterol. ORP2 overexpressing cells responded to the loss of cholesterol by upregulating cholesterol synthesis and uptake. Intriguingly, also cholesterol esterification was increased in ORP2 overexpressing cells. These results may be explained by the ability of ORP2 to bind and thus transport cholesterol, which most likely leads to changes in cholesterol metabolism when ORP2 is overexpressed. ORP2 function was further investigated by silencing the endogenous ORP2 expression with short interfering RNAs (siRNA) in A431 cells. Silencing of ORP2 led to a delayed break-down of triglycerides under lipolytic conditions and an increased amount of cholesteryl esters in the presence of excess triglycerides. Together these results suggest that ORP2 is a sterol-regulated protein that functions on the surface of cytoplasmic lipid droplets to regulate the metabolism of triglycerides and cholesteryl esters. Although the exact mode of ORP2 action still remains unclear, this study serves as a good basis to investigate the molecular mechanisms and possible cell type specific functions of ORP2.
  • Ramu, Päivi (Helsingin yliopisto, 2007)
    Salmonella enterica serovar Typhimurium is a common cause of gastroenteritis in humans and, occasionally, also causes systemic infection. During systemic infection an important characteristic of Salmonella is its ability to survive and replicate within macrophages. The outer membrane protease PgtE of S. enterica is a member of the omptin family of outer membrane aspartate proteases, which are beta-barrel proteins with five surface-exposed loops. The main goals of this study were to characterize biological substrates and pathogenesis-associated functions of PgtE and to determine the conditions where PgtE is fully active. In this study we found that PgtE requires rough lipopolysaccharide (LPS) to be functional but is sterically inhibited by the long O-antigen side chain in smooth LPS. Salmonella isolates normally are smooth with a long oligosaccharide O-antigen, and PgtE remains functionally cryptic in wild-type Salmonella cultivated in vitro. Interestingly, our results showed that due to increased expression of PgtE and to reduced length of the LPS O-antigen chains, the wild-type Salmonella expresses highly functional PgtE when isolated from mouse macrophage-like J774A.1 cells. Salmonella is thought to be continuously released from macrophages to infect new ones, and our results suggest that PgtE is functional during these transient extracellular growth phases. Six novel host protein substrates were identified for PgtE in this work. PgtE was previously known to activate human plasminogen (Plg) to plasmin, a broad-spectrum serine protease, and in this study PgtE was shown to interfere with the Plg system by inactivating the main inhibitor of plasmin, alpha2-antiplasmin. PgtE also interferes with another important proteolytic system of mammals by activating pro-matrix metalloproteinase-9 to an active gelatinase. PgtE also directly degrades gelatin, a component of extracellular matrices. PgtE also increases bacterial resistance against complement-mediated killing in human serum and enhances survival of Salmonella within murine macrophages as well as in the liver and spleen of intraperitoneally infected mice. Taken together, the results in this study suggest that PgtE is a virulence factor of Salmonella that has adapted to interfere with host proteolytic systems and to modify extracellular matrix; these features likely assist the migration of Salmonella during systemic salmonellosis.
  • Lundell, Robin (Helsingin yliopisto, 2011)
    Winter is a significant period for the seasonality of northern plants, but is often overlooked when studying the interactions of plants and their environment. This study focuses on the effects of overwintering conditions, including warm winter periods, snow, and snowmelt on boreal and sub-Arctic field layer plants. Wintertime photosynthesis and related physiological factors of evergreen dwarf shrubs, particularly of Vaccinium vitis-idaea, are emphasised. The work combines experiments both in the field and in growth chambers with measurements in natural field conditions. Evergreen dwarf shrubs are predominantly covered by snow in the winter. The protective snow cover provides favourable conditions for photosynthesis, especially during the spring before snowmelt. The results of this study indicate that photosynthesis occurs under the snow in V. vitis-idaea. The light response of photosynthesis determined in field conditions during the period of snow cover shows that positive net CO2 exchange is possible under the snow in the prevailing light and temperature. Photosynthetic capacity increases readily during warm periods in winter and the plants are thus able to replenish carbohydrate reserves lost through respiration. Exposure to low temperatures in combination with high light following early snowmelt can set back photosynthesis as sustained photoprotective measures are activated and photodamage begins to build up. Freezing may further decrease the photosynthetic capacity. The small-scale distribution of many field layer plants, including V. vitis-idaea and other dwarf shrubs, correlates with the snow distribution in a forest. The results of this study indicate that there are species-specific differences in the snow depth affinity of the field and ground layer species. Events and processes taking place in winter can have a profound effect on the overall performance of plants and on the interactions between plants and their environment. Understanding the processes involved in the overwintering of plants is increasingly important as the wintertime climate in the north is predicted to change in the future.
  • Welling, Annikki (Helsingin yliopisto, 2003)
  • Gorbikova, Elena (Helsingin yliopisto, 2009)
    Energy conversion by living organisms is central dogma of bioenergetics. The effectiveness of the energy extraction by aerobic organisms is much greater than by anaerobic ones. In aerobic organisms the final stage of energy conversion occurs in respiratory chain that is located in the inner membrane of mitochondria or cell membrane of some aerobic bacteria. The terminal complex of the respiratory chain is cytochrome c oxidase (CcO) - the subject of this study. The primary function of CcO is to reduce oxygen to water. For this, CcO accepts electrons from a small soluble enzyme cytochrome c from one side of the membrane and protons from another side. Moreover, CcO translocates protons across the membrane. Both oxygen reduction and proton translocation contributes to generation of transmembrane electrochemical gradient that is used for ATP synthesis and different types of work in the cell. Although the structure of CcO is defined with a relatively high atomic resolution (1.8 Å), its function can hardly be elucidated from the structure. The electron transfer route within CcO and its steps are very well defined. Meanwhile, the proton transfer roots were predicted from the site-specific mutagenesis and later proved by X-ray crystallography, however, the more strong proof of the players of the proton translocation machine is still required. In this work we developed new methods to study CcO function based on FTIR (Fourier Transform Infrared) spectroscopy. Mainly with use of these methods we answered several questions that were controversial for many years: [i] the donor of H+ for dioxygen bond splitting was identified and [ii] the protolytic transitions of Glu-278 one of the key amino acid in proton translocation mechanism was shown for the first time.
  • Ahlfors, Reetta (University of Helsinki, 2008)
    Tropospheric ozone (O3) is one of the most common air pollutants in industrialized countries, and an increasing problem in rapidly industrialising and developing countries in Asia, Africa and South America. Elevated concentrations of tropospheric O3 can lead to decrease in photosynthesis rate and therefore affect the normal metabolism, growth and seed production. Acute and high O3 episodes can lead to extensive damage leading to dead tissue in plants. Thus, O3 derived growth defects can lead to reduction in crop yield thereby leading to economical losses. Despite the extensive research on this area, many questions remain open on how these processes are controlled. In this study, the stress-induced signaling routes and the components involved were elucidated in more detail starting from visual damage to changes in gene expression, signaling routes and plant hormone interactions that are involved in O3-induced cell death. In order to elucidate O3-induced responses in Arabidopsis, mitogen-activated protein kinase (MAPK) signaling was studied using different hormonal signaling mutants. MAPKs were activated at the beginning of the O3 exposure. The activity of MAPKs, which were identified as AtMPK3 and AtMPK6, reached the maximum at 1 and 2 hours after the start of the exposure, respectively. The activity decreased back to clean air levels at 8 hours after the start of the exposure. Both AtMPK3 and AtMPK6 were translocated to nucleus at the beginning of the O3 exposure where they most likely affect gene expression. Differences were seen between different hormonal signaling mutants. Functional SA signaling was shown to be needed for the full protein levels and activation of AtMPK3. In addition, AtMPK3 and AtMPK6 activation was not dependent on ethylene signaling. Finally, jasmonic acid was also shown to have an impact on AtMPK3 protein levels and AtMPK3 activity. To further study O3-induced cell death, an earlier isolated O3 sensitive Arabidopsis mutant rcd1 was mapped, cloned and further characterized. RCD1 was shown to encode a gene with WWE and ADP-ribosylation domains known to be involved in protein-protein interactions and cell signaling. rcd1 was shown to be involved in many processes including hormonal signaling and regulation of stress-responsive genes. rcd1 is sensitive against O3 and apoplastic superoxide, but tolerant against paraquat that produces superoxide in chloroplast. rcd1 is also partially insensitive to glucose and has alterations in hormone responses. These alterations are seen as ABA insensitivity, reduced jasmonic acid sensitivity and reduced ethylene sensitivity. All these features suggest that RCD1 acts as an integrative node in hormonal signaling and it is involved in the hormonal regulation of several specific stress-responsive genes. Further studies with the rcd1 mutant showed that it exhibits the classical features of programmed cell death, PCD, in response to O3. These include nuclear shrinkage, chromatin condensation, nuclear DNA degradation, cytosol vesiculation and accumulation of phenolic compounds and eventually patches of HR-like lesions. rcd1 was found to produce extensive amount of salicylic acid and jasmonic acid in response to O3. Double mutant studies showed that SA independent and dependent processes were involved in the O3-induced PCD in rcd1 and that increased sensitivity against JA led to increased sensitivity against O3. Furthermore, rcd1 had alterations in MAPK signature that resembled changes that were previously seen in mutants defective in SA and JA signaling. Nitric oxide accumulation and its impact on O3-induced cell death were also studied. Transient accumulation of NO was seen at the beginning of the O3 exposure, and during late time points, NO accumulation coincided with the HR-like lesions. NO was shown to modify defense gene expression, such as, SA and ethylene biosynthetic genes. Furthermore, rcd1 was shown to produce more NO in control conditions. In conclusion, NO was shown to be involved in O3-induced signaling leading to attenuation of SA biosynthesis and other defense related genes.
  • Kainov, Denis (Helsingin yliopisto, 2005)
  • Couchoux, Christelle (Helsingin yliopisto, 2013)
    In my thesis I investigated the foraging behaviour of the wasp Hyposoter horticola, an egg-larval parasitoid of the Glanville fritillary butterfly Melitaea cinxia, in the Åland islands in Finland. The particularity of this system is that the wasp is resource limited and faces strong intraspecific competition. ---------- I first focused on behaviour at an individual scale. In a series of experiments I tested how H. horticola s host searching behaviour was affected by developmental timing of both the parasitoid and the host, and direct intraspecific competition among foraging females. I found that the wasps visit host egg clusters before the hosts are susceptible to parasitism, presumably to cope with the limited time availability of the hosts. As the unparasitized hosts matured their value increased, competition became more frequent, and the wasps foraged more actively. Competition can also affect the parasitoid at earlier stages in its life. As larvae inside the hosts, the immature H. horticola suffered from competition due to superparasitism. Combining behavioural experiments in the laboratory and genetic analyses of sibship, I found that adult H. horticola deposit a chemical marking after oviposition that deters conspecifics from parasitizing a previously exploited host cluster. This protects parasitized host clusters from further exploitation. I found that the effectiveness of the deterrent persisted under natural conditions, where individual host egg clusters were each primarily parasitized by a single female H. horticola. Even when several females parasitized a cluster, the great majority of the offspring were full-siblings and the parasitism rate did not increase above the average 1/3 observed throughout the population. Considering that H. horticola is resource limited and faces intraspecific competition when foraging for hosts, it is surprising that only they parasitize a fraction of the hosts in each host egg cluster. After testing several physiological and evolutionary hypotheses for what might lead to this sub-maximal rate of host exploitation, I concluded that optimal foraging with avoidance of superparasitism was the most plausible explanation, as long as the search time between host clusters was low. ------ Then, I worked at a larger scale than individual behaviour. In the Åland islands, the butterfly host lives as a classic metapopulation with a high extinction rate of local populations. Due to strong competition, almost all the M. cinxia egg clusters in the population are found and parasitized by H. horticola. This suggests that the wasps must be good dispersers, which could influence the spatial genetic structure of the parasitoid population. I used DNA microsatellite markers and analysed H. horticola individuals sampled from over the entire population. My results indicate that, contrary to theory that higher trophic level species are more affected by habitat fragmentation than the species upon which they depend, the H. horticola population was less strongly genetically structured than the metapopulation of its butterfly host. It seems that H. horticola s dispersal ability allows it to compensate for the fragmented distribution of its host and not suffer from the metapopulation dynamics of the host local populations. Overall, the results of my thesis show that interactions between H. horticola and its host M. cinxia are strongly affected by competition among the adult female wasps. Intraspecific competition has an important role from an evolutionary perspective. Hyposoter horticola s deterrent marking behaviour has evolved in response to competition and the risk of superparasitism faced by immature offspring. Avoidance of superparasitism to limit competition is also the fundamental mechanism that controls H. horticola s optimal foraging strategy. And intraspecific competition modifies individual female host searching behaviour, increasing their foraging activity. -------- Interactions within a multitrophic system are complex and predictions concerning host-parasitoid interactions are difficult to generalise. However, as in this system, competition is factor that should receive more attention in empirical and theoretical studies of host-parasitoid interactions.
  • Marttila, Minttu (Helsingin yliopisto, 2014)
    We collected all mutations in TPM2 and TPM3 genes hitherto found to cause congenital myopathies, to perform genotype-phenotype correlations, and to increase our understanding of the pathogenetic mechanisms of congenital myopathies caused by mutations in the tropomyosin and nebulin genes. Nemaline myopathy (NM), a rare, genetic muscle disorder defined on the basis of muscle dysfunction and the presence of structural abnormalities in the muscle fibres (i.e. nemaline bodies), is caused by mutations in ten genes known to date: Nebulin (NEB), α-actin (ACTA1), α-tropomyosin (TPM3), β-tropomyosin (TPM2), troponin T (TNNT1), cofilin 2 (CFL2), KBTBD13, KLHL40, KLHL41 and leiomodin 3 (LMOD 3). Tropomyosin controls muscle contraction by inhibiting the actin myosin interaction in a calcium-sensitive manner. Mutations in tropomyosin genes may cause NM, cap myopathy, congenital fibre-type disproportion, distal arthrogryposes and Escobar syndrome. We correlated the clinical picture of these diseases to novel and previously published mutations to the TPM2 (30 mutations) and TPM3 (20 mutations) genes. Mutations in TPM2 and TPM3 caused an increased Ca2+ sensitivity, resulting in a hypercontractile molecular phenotype. We studied the pathogenetic mechanisms to which five disease-causing mutations in β-tropomyosin (p.Glu41Lys, p.Lys49del, p.Glu117Lys, p.Glu139del and p.Gln147Pro) lead. We showed that four of the mutations cause changes in the affinity for actin leading to muscle weakness in patients, while two mutations show defective Ca2+ activation of contractility. Nebulin (NEB) is a giant 600 900-kDa filamentous protein in thin filament. We produced four wild-type nebulin super-repeats and five corresponding mutation constructs (p.Glu2431Lys, p.Ser4665Ile, p.Thr5681Pro, p.Arg2478_Asp2512del and p.Val3681_Asn3686del) in the study. The mutations were identified in patients with NM or distal myopathy. We performed F-actin and tropomyosin-binding experiments for the nebulin fragments. Our results demonstrate actin nebulin interactions and, for the first time, tropomyosin nebulin interactions in vitro, and show that the interactions are altered by disease-causing mutations. This suggests that an abnormal interaction between aberrant thin filament proteins is a pathogenetic mechanism in NM and related disorders.
  • Al-Hello, Haider (Helsingin yliopisto, 2012)
    Enteroviruses (EVs) are small non-enveloped RNA viruses forming a large group of different serotypes. EVs belong to the family Picornaviridae. The primary replication site of an enterovirus is typically the epithelium of the respiratory tract and the gastrointestinal mucosa. Virus replication in the gastrointestinal mucosa may continue, often asymptomatically, for several weeks occasionally causing viremia. During the viremia the virus spreads through the lymphatic system and circulation. Organ-specific symptoms rise after viral replication in the secondary target tissues. Occasionally, cellular adaptation is required for a virus to initiate replication in the secondary target tissue(s). Adaptation is linked to mutation(s) which may lead to alteration in cellular tropism, e.g., recognition of new surface receptor molecules or other host cell constituents essential for virus entry and replication. However, the critical step may also occur later during in the interaction of the host cell and the replicating virus. In the present study, genetic changes responsible for altered phenotypic features were sought using two strains of Human enterovirus B (HEV-B) species. Firstly, a laboratory isolate of coxsackievirus B5 (CV-B5), strain DS, was passaged 15 times in mouse pancreas in vivo, which resulted in a diabetogenic mouse pancreas passaged virus strain (MPP). The concept of diabetogenic means the ability of the MPP strain to replicate, cause insulitis and dysregulation of the glucose metabolism in the mouse pancreas in vivo. The interaction between the MPP virus strain and insulin producing β-cells was further studied in cell culture using a mouse-derived insulinoma cell line, MIN-6 cells, as an experimental model. The replication of the MPP virus strain was clearly slower in the MIN-6 cells compared to the other tested cell lines. After three days of incubation, extensive replication of MPP was evident in MIN-6 cells and resulted in a MIN-6 cell-adapted virus strain (MCA). Secondly, the ability of the D207 virus strain, isolated from a type 1 diabetic patient, to replicate in a primary human β-cell culture was tested. D207 was initially serotyped as coxsackievirus A9 (CV-A9) in a virus-specific neutralization assay. The D207 virus strain was found to cause cytolysis in the primary human β-cells and, simultaneously, severe functional damage of the surviving β-cells. The genomes of the four virus strains DS, MPP, MCA and D207 were cloned and sequenced. The sequence comparison of three CV-B5 strains (DS, MPP, and MCA) revealed only limited changes, three capsid and two non-structural (NS) amino acid substitutions between MPP and DS, and two capsid and six NS amino acid substitutions between MCA and MPP. In order to determine which of the amino acid substitutions were responsible for the changed phenotype in vivo and in vitro, full-length infectious clones were constructed from the MPP virus and its parental DS virus. By using reverse mutagenesis and chimeric viruses (MPP/DS and DS/MPP), it was shown that a change from MPP to the MCA phenotype in MIN-6 cells was mediated by only a single amino acid at position 94 in VP1, while the in vivo adaptation of the DS virus strain to the inflammation-inducing MPP virus strain may require multiple genetic determinants in the virus capsid and probably also in the NS proteins. Sequence analyses of D207 revealed that the virus belonged to a genogroup D of E-11, but was also neutralized with monotypic antisera to CV-A9. The isolate D207 was found to be closely related to a specific E-11 strains known to cause uveitis. Uveitis-causing E-11 strains were also found to be well neutralized with both CV-A9- and E-11-specific antisera. In a further study, a wide range of E-11 isolates were included to test the observed dual neutralizibility among isolates belonging to the D genogroup. Five of the six studied strains belonging to genogroup D were also neutralized with antisera against coxsackievirus A9 Griggs. The peptide scanning technique was utilized to identify antigenic regions of the capsid proteins of the D207 strain responsible for the observed dual neutralization. Several regions in the capsid of D207 were found to cross-react with an antiserum raised against CV-A9. However, epitopes responsible for the cross-neutralization remained unidentified. In conclusion, these studies indicate that the specific location of mutation may affect the phenotype of an enterovirus more than the overall quantity of changes. In the experimental settings, radical changes in the viral phenotypic features occurred only after a few amino acid substitutions. The majority of the studied viruses in the genogroup D of E-11 maintained exceptional phenotypic property, the cross-neutralization with CV-A9 specific antiserum, despite their genetic divergence.
  • Ollila, Saara (Helsingfors universitet, 2008)
    Hereditary nonpolyposis colorectal cancer (HNPCC) is a hereditary cancer syndrome, which associates with high penetrance of early onset colorectal and endometrial tumours. Susceptibility for HNPCC is dominantly inherited with germline defects in the mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2. A truncating mutation in one of these genes leads to deficient MMR, predisposing the mutation carriers to HNPCC, but a nontruncating mutation can either be neutral or lead to increased cancer risk and HNPCC. The correct determination of the pathogenicity of a found mutation is very important, as the verification of the causative mutation enables genetic counselling and surveillance of mutation carriers. This has been shown to lead to significantly lowered mortality. MSH2 is the second most commonly mutated HNPCC susceptibility gene and defects in it account for 39% of all identified HNPCC mutations. The aim of this work was to gather functional evidence on the pathogenicity of patient-derived nontruncating MSH2 variants. The proteins corresponding to the original genetic variants were expressed and purified. The expression level, MMR efficiency, interaction with MSH6, mismatch binding, and mismatch release capabilities of the protein variants were studied. The results of the functional assays were compared to the clinical characteristics of the mutation carriers. 12 of the studied 18 mutations were found to exhibit severe defects in the functional assays, supporting the hypothesis that these mutations were the underlying cause of the cancer phenotype in mutation carriers. 2 mutations reduced but did not abolish the function of the protein, leaving their pathogenicity status inconclusive. 4 mutations showed no or only a minor defect in the assays, suggesting nonpathogenicity. The functional defects were mediated through different mechanisms. The majority of the MMR-deficient mutations which were located in the amino-terminal domains of MSH2 demonstrated defects in the protein expression level. Most of the carboxy-terminal mutations, situated in the ATPase domain, had an impact on the ability of the protein to bind or release mismatched DNA. When comparing the biochemical data to the tumour phenotype, a significant correlation between the functional deficiency in vitro and lack of expression of the corresponding protein in the tumour was observed. The analyses demonstrated that the location of the mutation affects the biochemistry of MMR, but may also have an effect on the phenotype of MSH2 mutation carriers. This study significantly contributed to the knowledge of MSH2-associated HNPCC tumorigenesis, especially facilitating the diagnostics and counselling of the associated families.
  • Kiialainen, Anna (Helsingin yliopisto, 2007)
    PATHOGENIC MECHANISMS OF PLOSL Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy (PLOSL), also known as Nasu-Hakola disease, is a recessively inherited disease of brain and bone. PLOSL manifests as early-onset progressive dementia and bone fractures. Mutations in the TYROBP (DAP12) and TREM2 genes have been identified as the primary cause of PLOSL. DAP12 and TREM2 encode important signalling molecules in cells of the innate immune system. The mechanism by which loss-of-function of the DAP12/TREM2 signalling complex leads to PLOSL is currently unknown. The aim of this thesis work was to gain insight into the pathogenic mechanisms behind PLOSL. To first identify the central nervous system (CNS) cell types that express both Dap12 and Trem2, the expression patterns of Dap12 and Trem2 in mouse CNS were analyzed. Dap12 and Trem2 expression was seen from embryonic stage to adulthood and microglial cells and oligodendrocytes were identified as the major Dap12/Trem2 producing cells of the CNS. To subsequently identify the pathways and biological processes associated with DAP12/TREM2 mediated signalling in human cells, genome wide transcript analysis of in vitro differentiated dendritic cells (DCs) of PLOSL patients representing functional knockouts of either DAP12 or TREM2 was performed. Both DAP12 and TREM2 deficient cells differentiated into DCs and responded to pathogenic stimuli. However, the DCs showed morphological differences compared to control cells due to defects in the actin filaments. Transcript profiles of the patient DCs showed differential expression of genes involved in immune response and for genes earlier associated with other disorders of the CNS as well as genes involved in the remodeling of bone, linking the findings with the tissue phenotype of PLOSL patients. To analyze the effect of Dap12 deficiency in the CNS, genome wide expression analysis of Dap12 deficient mouse brain and Dap12 deficient microglia as well as functional analysis of Dap12 deficient microglia was performed. Regulation of several pathways involved in synaptic function and transcripts coding for the myelin components was seen in Dap12 knockout mice. Decreased migration, morphological changes and shortened lifespan of the Dap12 knockout microglia was further observed. Taken together, this thesis work showed that both Dap12 and Trem2 are expressed by CNS microglia and that Dap12 deficiency results in functional defects of these cells. Lack of Dap12 in the CNS also leads to synaptic abnormalities even before pathological changes are seen in the tissue level.This work further showed that loss-of-function of DAP12 or TREM2 leads to changes in morphology and gene expression in human dendritic cells. These data underline the functional diversity of the molecules of the innate immune system and implies their significant contribution also in demyelinating CNS disorders, including those resulting in dementia.
  • Kariola, Tarja (Helsingin yliopisto, 2006)
    Erwinia carotovora subsp. carotovora is a bacterial phytopathogen that causes soft rot in various agronomically important crop plants. A genetically specified resistance to E. carotovora has not been defined, and plant resistance to this pathogen is established through nonspecific activation of basal defense responses. This, together with the broad host range, makes this pathogen a good model for studying the activation of plant defenses. Production and secretion of plant cell wall-degrading enzymes (PCWDE) are central to the virulence of E. carotovora. It also possesses the type III secretion system (TTSS) utilized by many Gram-negative bacteria to secrete virulence- promoting effector proteins to plant cells. This study elucidated the role of E. carotovora HrpN (HrpNEcc), an effector protein secreted through TTSS, and the contribution of this protein in the virulence of E. carotovora. Treatment of plants with HrpNEcc was demonstrated to induce a hypersensitive response (HR) as well as resistance to E. carotovora. Resistance induced by HrpNEcc required both salicylic acid (SA)- and jasmonate/ethylene (JA/ET)-dependent defense signaling in Arabidopsis. Simultaneous treatment of Arabidopsis with HrpNEcc and PCWDE polygalacturonase PehA elicited accelerated and enhanced induction of defense genes but also increased production of superoxide and lesion formation. This demonstrates mutual amplification of defense signaling by these two virulence factors of E. carotovora. Identification of genes that are rapidly induced in response to a pathogen can provide novel information about the early events occurring in the plant defense response. CHLOROPHYLLASE 1 (AtCLH1) and EARLY RESPONSIVE TO DEHYDRATION 15 (ERD15) are both rapidly triggered by E. carotovora in Arabidopsis. Characterization of AtCLH1 encoding chlorophyll-degrading enzyme chlorophyllase indicated that it might have a role in chlorophyll degradation during plant tissue damage. Silencing of this gene resulted in increased accumulation of reactive oxygen species (ROS) in response to pathogen infection in a light-dependent manner. This led to enhanced SA-dependent defenses and resistance to E. carotovora. Moreover, crosstalk between different defense signaling pathways was observed; JA-dependent defenses and resistance to fungal pathogen Alternaria brassicicola were impaired, indicating antagonism between SA- and JA-dependent signaling. Characterization of ERD15 suggested that it is a novel, negative regulator of abscisic acid (ABA) signaling in Arabidopsis. Overexpression of ERD15 resulted in insensitivity to ABA and reduced tolerance of the plants to dehydration stress. However, simultaneously, the resistance of the plants to E. carotovora was enhanced. Silencing of ERD15 improved freezing and drought tolerance of transgenic plants. This, together with the reducing effect of ABA on seed germination, indicated hypersensitivity to this phytohormone. ERD15 was hypothesized to act as a capacitor that controls the appropriate activation of ABA responses in Arabidopsis.
  • Kysenius, Kai (Helsingin yliopisto, 2015)
    Aging-related increase of neuronal stress may promote the development of sporadic late-onset Alzheimer s disease (LOAD) and other forms of dementia. LOAD risk is also increased by genetic factors such as ApoE4 and diseases such as type 2 diabetes (T2D). Early LOAD pathology is characterized by alterations in brain lipoprotein receptor expression and neuronal hypometabolism. Multifunctional lipoprotein receptors regulate neuronal plasticity, cholesterol and metabolic homeostasis. Lipoprotein receptors apolipoprotein receptor 2 (ApoER2) and very-low density lipoprotein receptor (VLDLR) bind ApoE, but also interact with proteins centrally involved in LOAD pathogenesis. Proprotein convertase subtilisin/kexin type 9 (PCSK9) and the nutraceutical berberine modulate lipoprotein receptor levels in vivo. PCSK9 inhibitors and berberine have recently surfaced as promising treatment options for hypercholesterolemia and T2D, respectively. Additionally, PCSK9 and berberine are implicated in pathways modulating neuronal viability, suggesting they may hold therapeutic potential against neurodegenerative diseases. However, the effects of PCSK9 and berberine on neuronal cell death and lipoprotein receptors are currently poorly understood. The objective of this study was to elucidate the role of PCSK9 and berberine as modulators of lipoprotein receptors and cell death in neurons. The effects of RNAi-mediated PCSK9 downregulation and berberine on neuronal viability were studied in mouse and rat primary neuron cultures. Mechanistic basis of effects were further studied in combination with lentiviral RNA interference, kinase inhibitors and various inducers of cellular stress and cell death. Cell viabilities were assessed by immunofluorescence, Western blotting, and cell toxicity and mitochondrial assays. The main conclusions of this study are: (1) reducing endogenous PCSK9 levels genetically by lentiviral-mediated RNAi protects neurons against apoptotic cell death in an ApoER2-dependent fashion; (2) a potential PCSK9 inhibitor and a widely used nutraceutical berberine causes mitochondria- and NMDA receptor-dependent neuronal cell death at micromolar concentrations; (3) at subtoxic nanomolar concentrations, berberine sensitizes neurons to rotenone and glutamate toxicity calling for caution in berberine dosing and chronic use; and (4) subtoxic stress, including berberine, increase neuronal VLDLR expression, associated with a biphasic effect on the stabilization of the transcription factors hypoxia-inducible factor 1α and β-catenin. To conclude, ApoER2, VLDLR and their modulators PCSK9 and berberine contribute to the regulation of neuronal cell death via multiple mechanisms, suggesting a potential role in neurodegenerative disease pathogenesis at the interface of metabolism and survival signaling.
  • Povelainen, Mira (Helsingin yliopisto, 2008)
    The ultimate goal of this study has been to construct metabolically engineered microbial strains capable of fermenting glucose into pentitols D-arabitol and, especially, xylitol. The path that was chosen to achieve this goal required discovery, isolation and sequencing of at least two pentitol phosphate dehydrogenases of different specificity, followed by cloning and expression of their genes and characterization of recombinant arabitol and xylitol phosphate dehydrogenases. An enzyme of a previously unknown specificity, D-arabitol phosphate dehydrogenase (APDH), was discovered in Enterococcus avium. The enzyme was purified to homogenity from E. avium strain ATCC 33665. SDS/PAGE revealed that the enzyme has a molecular mass of 41 ± 2 kDa, whereas a molecular mass of 160 ± 5 kDa was observed under non-denaturing conditions implying that the APDH may exist as a tetramer with identical subunits. Purified APDH was found to have narrow substrate specificity, converting only D-arabitol 1-phosphate and D-arabitol 5-phosphate into D-xylulose 5-phosphate and D-ribulose 5-phosphate, respectively, in the oxidative reaction. Both NAD+ and NADP+ were accepted as co-factors. Based on the partial protein sequences, the gene encoding APDH was cloned. Homology comparisons place APDH within the medium chain dehydrogenase family. Unlike most members of this family, APDH requires Mn2+ but no Zn2+ for enzymatic activity. The DNA sequence surrounding the gene suggests that it belongs to an operon that also contains several components of phosphotransferase system (PTS). The apparent role of the enzyme is to participate in arabitol catabolism via the arabitol phosphate route similar to the ribitol and xylitol catabolic routes described previously. Xylitol phosphate dehydrogenase (XPDH) was isolated from Lactobacillus rhamnosus strain ATCC 15820. The enzyme was partially sequenced. Amino acid sequences were used to isolate the gene encoding the enzyme. The homology comparisons of the deduced amino acid sequence of L. rhamnosus XPDH revealed several similar enzymes in genomes of various species of Gram-positive bacteria. Two enzymes of Clostridium difficile and an enzyme of Bacillus halodurans were cloned and their substrate specificities together with the substrate specificity of L. rhamnosus XPDH were compared. It was found that one of the XPDH enzymes of C. difficile and the XPDH of L. rhamnosus had the highest selectivity towards D-xylulose 5-phosphate. A known transketolase-deficient and D-ribose-producing mutant of Bacillus subtilis (ATCC 31094) was further modified by disrupting its rpi (D-ribose phosphate isomerase) gene to create D-ribulose- and D-xylulose-producing strain. Expression of APDH of E. avium and XPDH of L. rhamnosus and C. difficile in D-ribulose- and D-xylulose-producing strain of B. subtilis resulted in strains capable of converting D-glucose into D-arabitol and xylitol, respectively. The D-arabitol yield on D-glucose was 38 % (w/w). Xylitol production was accompanied by co-production of ribitol limiting xylitol yield to 23 %.
  • Marjamaa, Kaisa (Helsingin yliopisto, 2007)
    Lignin is a complex plant polymer synthesized through co-operation of multiple intracellular and extracellular enzymes. It is deposited to plant cell walls in cells where additional strength or stiffness are needed, such as in tracheary elements (TEs) in xylem, supporting sclerenchymal tissues and at the sites of wounding. Class III peroxidases (POXs) are secreted plant oxidoreductases with implications in many physiological processes such as the polymerization of lignin and suberin and auxin catabolism. POXs are able to oxidize various substrates in the presence of hydrogen peroxide, including lignin monomers, monolignols, thus enabling the monolignol polymerization to lignin by radical coupling. Trees produce large amounts of lignin in secondary xylem of stems, branches and roots. In this study, POXs of gymnosperm and angiosperm trees were studied in order to find POXs which are able to participate in lignin polymerization in developing secondary xylem i.e. are located at the site of lignin synthesis in tree stems and have the ability to oxidize monolignol substrates. Both in the gymnosperm species, Norway spruce and Scots pine, and in the angiosperm species silver birch the monolignol oxidizing POX activities originating from multiple POX isoforms were present in lignifying secondary xylem in stems during the period of annual growth. Most of the partially purified POXs from Norway spruce and silver birch xylem had highest oxidation rate with coniferyl alcohol, the main monomer in guaiacyl-lignin in conifers. The only exception was the most anionic POX fraction from silver birch, which clearly preferred sinapyl alcohol, the lignin monomer needed in the synthesis of syringyl-guaiacyl lignin in angiosperm trees. Three full-length pox cDNAs px1, px2 and px3 were cloned from the developing xylem of Norway spruce. It was shown that px1 and px2 are expressed in developing tracheids in spruce seedlings, whereas px3 transcripts were not detected suggesting low transcription level in young trees. The amino acid sequences of PX1, PX2 and PX3 were less than 60% identical to each other but showed up to 84% identity to other known POXs. They all begin with predicted N-terminal secretion signal (SS) peptides. PX2 and PX3 contained additional putative vacuolar localization determinants (VSDs) at C-terminus. Transient expression of EGFP-fusions of the SS- and VSD-peptides in tobacco protoplasts showed SS-peptides directed EGFP to secretion in tobacco cells, whereas only the PX2 C-terminal peptide seems to be a functional VSD. According to heterologous expression of px1 in Catharanthus roseus hairy roots, PX1 is a guaicol-oxidizing POX with isoelectric point (pI) approximately 10, similar to monolignol oxidizing POXs in protein extracts from Norway spruce lignifying xylem. Hence, PX1 has characteristics for participation to monolignol dehydrogenation in lignin synthesis, whereas the other two spruce POXs seem to have some other functions. Interesting topics in future include functional characterization of syringyl compound oxidizing POXs and components of POX activity regulation in trees.