Hepatiit C viiruse ja Chikungunya viiruse vastased lähenemised

Väitekirja elektrooniline versioon ei sisalda publikatsioone.Tänapäeval on võimalik ennast erinevate viiruste vastu vaktsineerida ning ka viirushaiguste ravi on muutunud oluliselt tõhusamaks. Samas leidub endiselt meditsiiniliselt olulisi viiruseid, mille vastu puudub vaktsiin ja/või mille poolt põhjustatud haigustele pole siiani adekvaatset ravi. Viirus-vastaste ühendite ja vaktsiinide väljatöötamist raskendavad nii viiruste suur mitmekesisus kui ka nende keeruline elutsükkel. Üheks selliseks viiruseks on C hepatiidi viirus (HCV), mis on kroonilise maksahaiguse levinuimaks tekkepõhjuseks. Hinnanguliselt on selle viirusega krooniliselt nakatunud ~3% inimkonnast. Kuigi HCV infektsiooni ravis on toimunud suur läbimurre, on viiruse geneetilise mitmekesisuse, ravimresistentsete vormide tekkimise ning patsientide ravile mitteallumise tõttu endiselt väga oluline uute HCV vastaste ravimite väljatöötamine. Antud uurimustöö üheks eesmärgiks oli analüüsida erinevaid tehnoloogilisi lahendusi HCV vastaste ühendite loomiseks. Ühe lähenemisena valiti FQSAR arvutiprogrammi põhiselt välja madal-molekulaarsed ühendid, mis seondudes HCV NS3/4A proteaasiga inhibeerivad HCV replikatsiooni, ja iseloomustati nende mõju viiruse infektsioonile. Kõik analüüsitud seitse ühendit omasid HCV-vastast efekti, kuid ainult üks ühend (23332) oli kasutatavas kontsentratsioonis mitte-toksiline. Teine lähenemisviis seisnes looduslikult esineva modifikatsiooni (8-oxo-dG) mõju analüüsimises oligonukleotiidsete (ON) inhibiitorite efektiivsusele. Kombineerides erinevaid modifikatsioone leiti ON ühend, mis inhibeeris HCV replikatsiooni nanomolaarsetel kontsentratsioonidel. Lisaks HCV uurimisele on võimalik käsitletud lähenemise kasutada ka teiste viiruste vastu suunatud ühendite väljatöötamisel. Chikungunya viirus (CHIKV, perekond Alfaviirus) on troopilistes piirkondades leviv arboviirus, mis on viimasel aastakümnel korduvalt väljunud oma tavalisest levialast ja põhjustanud epideemiaid erinevates maailmajagudes. Antud töö kolmandaks eesmärgiks oli analüüsida uudsete CHIKV-vastaste vaktsiinikandidaatide geneetilist stabiilsust ning uurida nendes sisalduvate viirust nõrgestavate mutatsioonide mõju CHIKV elutsüklile. Leiti, et viirustel CHIKVΔ5nsP3 ja CHIKVΔ6K on nõrgestatud fenotüüp ka pärast mitmekordset passeerimist koekultuuri rakkudes. Mitmetest analüüsitud CHIKV-vastastest vaktsiini kandidaatidest osutus kõige efektiivsemaks CHIKVΔ5nsP3. See nõrgestatud viirus sisaldab suurt deletsiooni nsP3 valgu C-terminaalses regioonis. Katsetest selgus, et nimetatud regioon interakteerub sama valgu keskmise domeeni ning nsP2 valgu C-terminaalse osaga ja need kontaktid on olulised viiruse replikatsioonil. Need avastused võimaldavad edaspidi välja selgitada CHIKVΔ5nsP3 mitte-patogeense fenotüübi põhjused. CHIKV Δ5nsP3 vaktsiini tüvi on kasutusele võetud edasiseks arendamiseks farmatseutilise firma poolt.Viruses have been and will be an important part of every ecosystem. In the past, viral outbreaks have left painful marks on mankind. Using vaccines and antivirals has greatly reduced the number of infections and virus-caused pathology. Despite extensive research, some viruses and viral diseases are still lacking any good vaccine or treatment. Viral features like high mutation rate, complexity of viral lifecycle and genome diversity are only some of the obstacles needed to overcome for antivirals and vaccines to be safe and efficient. Hepatitis C virus (HCV) is associated with different liver pathologies and it is estimated that approximately 3% of the world population is chronically infected with HCV. It is lacking efficient vaccine and the options for combating HCV infection, HCV-induced pathology, spread and persistence are limited to the use of antiviral drugs. One part of this dissertation is focused on the development of anti-HCV inhibitors using two different technological approaches. Firstly, a new FQSAR method based approach allowed rapid prediction of hit compounds targeting the NS3/4A protease of HCV. Seven compounds analysed in this project displayed some anti-HCV properties but only the effect caused by the non-cytotoxic compound 23332 can be considered to be direct. Secondly, a novel technology – incorporation of naturally occurring minimally modified nucleobases into ASOs – was evaluated using ASOs binding to the HCV non-structural region. This approach led to the development of ASO compounds with high anti-HCV activity. The technology based on the use of novel modified ONs is promising as well for the development antivirals for other viruses and diseases. Chikungunya virus (CHIKV) re-emerged in the past decade and is currently spreading around the world, affecting millions of people. The second part of this study is focused on the analysis of a laboratory-developed attenuated CHIKV vaccine strain. CHIKVΔ5nsP3 and CHIKVΔ6K viruses were found to have a stably attenuated phenotype and the introduced molecular changes were maintained during serial passages. From all studied vaccine candidates the CHIKVΔ5nsP3 was the most potent. Further studies revealed that the region removed from CHIKVΔ5nsP3 vaccine candidate, is apparently involved in interactions with another domain of nsP3 as well as with the C-terminal region of nsP2. These findings provide a platform for further analysis of biological reasons for the attenuation of CHIKVΔ5nsP3 vaccine candidate

Preferences for landscape openness and its influence on recreation

Selle uurimustöö eesmärgiks oli välja selgitada eestlaste ja välismaalaste maastikueelistused. Spetsiifilisemalt öeldes, uurida maastiku avatuse mõju inimeste eelistuste ja saadava rekreatsiooni suhtes. Täpsemalt uuriti ka erinevaid tegureid, mis võivad eelistust ja rekreatsiooni positiivselt või negatiivselt mõjutada. Eelnevate uurimustööde kirjandusele põhinedes tõstatati järgnevad küsimused: Kas inimesed eelistavad rekreatsiooniks avatud, suletud või poolavatud maastikke? Kas saadava rekreatsiooni ja maastikueelistuse vahel esineb korrelatsioon? Kas inimesed eelistavad maastikuvaate puhul teatud mõjusid, nagu vesi või inimtegevus? Andmete kogumiseks avaldati sotsiaal- ja informatsioonivõrgustikes küsitlus, millest võttis osa 101 vastajat, kokku 18-st eri riigist. Küsitlus koosnes 10-st eri maastikutüüpe kujutavast loodusfotost, millele järgnes kaheksa korduvat enesehindamise küsimust. Küsimustik põhines Ke-Tsung Hani (2003) SRRS-testil („Short-version revised restoration scale“), mis koosneb kaheksast bipolaarsest küsimusest, hõlmates nelja dimensiooni: kognitiivne, käitumuslik, emotsionaalne ja füsioloogiline reaktsioon. Küsitluses kasutatud maastikupildid esindasid kolme erinevat maastikutüüpi: visuaalselt avatud, suletud ja poolavatud maastikutüüp. Fotodel olid sarnased ilmastikuolud ja vaatepunktid, kuid nad sisaldasid erinevaid tegureid, selgitamaks inimeste suhtumist stseenis olevatesse faktoritesse. Tulemused näitasid eelistust visuaalselt avatud maastiku suhtes, millele järgnes meeldivuselt suletud maastikutüüp, poolavatud maastikustseenid said inimestelt madalaimad punktid. Kolm enimhinnatud pilti olid mererannikust, männimetsast ja aiast ning väikseima punktisummaga vaateks oli poolavatud loodusmaastik, kus olid mõned tehisobjektid. Rekreatiivsuse hinded olid vastavuses meeldivuse tulemustega, vaid madalamate punktidega piltide seas oli kergeid erinevusi. Statistiline andmeanalüüs näitas samuti tugevat korrelatsiooni rekreatiivsuse ja eelistuse hinnete vahel.The aim of given thesis was to ascertain the landscape preference of Estonian and foreign respondents. Specifically, the influence landscape openness has on preference and received recreation, and their possible dependence on each other. The thesis also explored the different factors that either positively or negatively influenced respondent’s preference and recreation ratings. Review of previous studies and different theories raised the following research questions: Do people prefer open, closed or semi-closed landscapes for recreational purposes? Is there a correlation between received recreation and landscape preference? Do people prefer certain content of the scene such as water and signs of human influence in the landscape? In order to collect data for the analysis, 101 respondents from 18 different countries filled out a photo-based questionnaire, which was published on social networking and information sites and further distributed through people. The survey consisted of 10 nature photographs from Estonia, depicting scenes from different landscape types, followed by eight repeating self-rating questions. The survey questionnaire is a slightly altered version of Ke-Tsung Han’s (2003) „Short-version revised restoration scale“. Landscape images in the survey represented three different landscape types: visually open, closed and semi-closed landscapes. The scenes had similar weather conditions and viewpoints, but all included different elements to determine respondent’s attitudes towards certain factors. Survey results showed greater preference for visually open landscapes, followed by closed landscape type, leaving semi-closed landscapes as the least preferred. Three highest rated scenes were views to the sea and coast, a pine forest and a garden. The scene with the lowest score showed a semi-closed natural landscape, with some visible artificial objects. Recreation scores corresponded with the preference ratings, with only minor differences in the lower rated images. Data analysis also showed strong correlation between recreative and preference values. Survey results answered all research questions and confirmed or opposed the raised hypothesis

Researching the Haxl Library

Selles lõputöös tutvustatakse ning demonstreeritakse päringute optimeerimise teeki Haxl. Teegi kasutamine, põhilised funktsionaalsused ning nende töötamise loogika tuuakse välja, luues kaks näidisprogrammi.Lisaks antakse Haxl’i kohta üldisem ülevaade, seejuures olulisemad Haskell’i osad, mida teegi loojad Haxl’i jaoks kasutasid. Lühidalt antakse ülevaade ka Haskell Database Connectivity teegi kohta.Töö tulemusena valmib kaks Haxl teeki tutvustavat näidisprogrammi ja nende seletused, mis demonstreerivad teegi kasutamist ning mille abil on võimalik lugejal otsustada teegi kasulikkuse ning keerukuse üle.This Bachelor’s thesis demonstrates and gives an overview of Haxl, a Haskell library for optimizing queries. The different features of the library will be explained by creating two sample programs.In addition, a more general overview will be given, such as why the library was created in the first place. Haskell Database Connectivity library will also be briefly covered.The result of this thesis is the two created sample programs, which with their explanations will allow the reader to decide on the usefulness and practicality of the library

Mutation of CD2AP and SH3KBP1 binding motif in alphavirus nsP3 hypervariable domain results in attenuated virus

Infection by Chikungunya virus (CHIKV) of the Old World alphaviruses (family Togaviridae) in humans can cause arthritis and arthralgia. The virus encodes four non-structural proteins (nsP) (nsP1, nsp2, nsP3 and nsP4) that act as subunits of the virus replicase. These proteins also interact with numerous host proteins and some crucial interactions are mediated by the unstructured C-terminal hypervariable domain (HVD) of nsP3. In this study, a human cell line expressing EGFP tagged with CHIKV nsP3 HVD was established. Using quantitative proteomics, it was found that CHIKV nsP3 HVD can bind cytoskeletal proteins, including CD2AP, SH3KBP1, CAPZA1, CAPZA2 and CAPZB. The interaction with CD2AP was found to be most evident; its binding site was mapped to the second SH3 ligand-like element in nsP3 HVD. Further assessment indicated that CD2AP can bind to nsP3 HVDs of many different New and Old World alphaviruses. Mutation of the short binding element hampered the ability of the virus to establish infection. The mutation also abolished ability of CD2AP to co-localise with nsP3 and replication complexes of CHIKV; the same was observed for Semliki Forest virus (SFV) harbouring a similar mutation. Similar to CD2AP, its homolog SH3KBP1 also bound the identified motif in CHIKV and SFV nsP3

Alphavirus-induced hyperactivation of PI3K/AKT directs pro-viral metabolic changes.

Virus reprogramming of cellular metabolism is recognised as a critical determinant for viral growth. While most viruses appear to activate central energy metabolism, different viruses have been shown to rely on alternative mechanisms of metabolic activation. Whether related viruses exploit conserved mechanisms and induce similar metabolic changes is currently unclear. In this work we investigate how two alphaviruses, Semliki Forest virus and Ross River virus, reprogram host metabolism and define the molecular mechanisms responsible. We demonstrate that in both cases the presence of a YXXM motif in the viral protein nsP3 is necessary for binding to the PI3K regulatory subunit p85 and for activating AKT. This leads to an increase in glucose metabolism towards the synthesis of fatty acids, although additional mechanisms of metabolic activation appear to be involved in Ross River virus infection. Importantly, a Ross River virus mutant that fails to activate AKT has an attenuated phenotype in vivo, suggesting that viral activation of PI3K/AKT contributes to virulence and disease

Associations of limbic-affective brain activity and severity of ongoing chronic arthritis pain are explained by trait anxiety

Functional magnetic resonance imaging studies (fMRI) have transformed our understanding of central processing of evoked pain but the typically used block and event-related designs are not best suited to the study of ongoing pain. Here we used arterial spin labelling (ASL) for cerebral blood flow mapping to characterise the neural correlates of perceived intensity of osteoarthritis (OA) pain and its interrelation with negative affect. Twenty-six patients with painful knee OA and twenty-seven healthy controls underwent pain phenotyping and ASL MRI at 3T. Intensity of OA pain correlated positively with blood flow in the anterior mid-cingulate cortex (aMCC), subgenual cingulate cortex (sgACC), bilateral hippocampi, bilateral amygdala, left central operculum, mid-insula, putamen and the brainstem. Additional control for trait anxiety scores reduced the pain-CBF association to the aMCC, whilst pain catastrophizing scores only explained some of the limbic correlations. In conclusion, we found that neural correlates of reported intensity of ongoing chronic pain intensity mapped to limbic-affective circuits, and that the association pattern apart from aMCC was explained by trait anxiety thus highlighting the importance of aversiveness in the experience of clinical pain

RNA Interference-Guided Targeting of Hepatitis C Virus Replication with Antisense Locked Nucleic Acid-Based Oligonucleotides Containing 8-oxo-dG Modifications

The inhibitory potency of an antisense oligonucleotide depends critically on its design and the accessibility of its target site. Here, we used an RNA interference-guided approach to select antisense oligonucleotide target sites in the coding region of the highly structured hepatitis C virus (HCV) RNA genome. We modified the conventional design of an antisense oligonucleotide containing locked nucleic acid (LNA) residues at its termini (LNA/DNA gapmer) by inserting 8-oxo-2'-deoxyguanosine (8-oxo-dG) residues into the central DNA region. Obtained compounds, designed with the aim to analyze the effects of 8-oxo-dG modifications on the antisense oligonucleotides, displayed a unique set of properties. Compared to conventional LNA/DNA gapmers, the melting temperatures of the duplexes formed by modified LNA/DNA gapmers and DNA or RNA targets were reduced by approximately 1.6-3.3 degrees C per modification. Comparative transfection studies showed that small interfering RNA was the most potent HCV RNA replication inhibitor (effective concentration 50 (EC50) : 0.13 nM), whereas isosequential standard and modified LNA/DNA gapmers were approximately 50-fold less efficient (EC50 : 5.5 and 7.1 nM, respectively). However, the presence of 8-oxo-dG residues led to a more complete suppression of HCV replication in transfected cells. These modifications did not affect the efficiency of RNase H cleavage of antisense oligonucleotide: RNA duplexes but did alter specificity, triggering the appearance of multiple cleavage products. Moreover, the incorporation of 8-oxo-dG residues increased the stability of antisense oligonucleotides of different configurations in human serum.Peer reviewe

Developmental alterations in noxious-evoked EEG activity recorded from rat primary somatosensory cortex

Primary somatosensory cortex (S1) contains a nociceptive map that localizes potential tissue damage on the body and encodes stimulus intensity. An objective and specific biomarker of pain however is currently lacking and is urgently required for use in non-verbal clinical populations as well as in the validation of pre-clinical pain models. Here we describe studies to see if the responses of the S1 in juvenile rats are different to those in the adult. We recorded electroencephalogram (EEG) responses from S1 of lightly-anesthetized Sprague–Dawley rats at either postnatal day 21 or postnatal day 40 during the presentation of noxious (55 °C) or innocuous (30 °C) thermal stimuli applied to the plantar surface of the left hindpaw. The total EEG power across the recording period was the same in both ages after stimulation but the frequency distribution was significantly affected by age. Noxious heat evoked a significant increase in theta band (4–8 Hz) activity in adults only (P < 0.0001 compared to baseline; P < 0.0001 compared to juveniles). There were no significant differences in EEG responses to innocuous thermal stimuli. These data show that there are significant alterations in the processing of nociceptive inputs within the maturing cortex and that cortical theta activity is involved only in the adult cortical response to noxious stimulation

The Aedes aegypti Domino Ortholog p400 Regulates Antiviral Exogenous Small Interfering RNA Pathway Activity and ago-2 Expression

Arboviruses are pathogens of humans and animals. A better understanding of the interactions between these pathogens and the arthropod vectors, such as mosquitoes, that transmit them is necessary to develop novel control measures. A major antiviral pathway in the mosquito vector is the exogenous small interfering RNA (exo-siRNA) pathway, which is induced by arbovirus-derived double-stranded RNA in infected cells. Although recent work has shown the key role played by Argonaute-2 (Ago-2) and Dicer-2 (Dcr-2) in this pathway, the regulatory mechanisms that govern these pathways have not been studied in mosquitoes. Here, we show that the Domino ortholog p400 has antiviral activity against the alphavirus Semliki Forest virus (Togaviridae) both in Aedes aegypti-derived cells and in vivo. Antiviral activity of p400 was also demonstrated against chikungunya virus (Togaviridae) and Bunyamwera virus (Peribunyaviridae) but not Zika virus (Flaviviridae). p400 was found to be expressed across mosquito tissues and regulated ago-2 but not dcr-2 transcript levels in A. aegypti mosquitoes. These findings provide novel insights into the regulation of an important aedine exo-siRNA pathway effector protein, Ago-2, by the Domino ortholog p400. They add functional insights to previous observations of this protein’s antiviral and RNA interference regulatory activities in Drosophila melanogaster