Resistance to potato virus A and potato virus Y in potato cultivars grown in Finland

Selostus: Suomessa viljeltävien perunalajikkeiden kestävyys A- ja Y-virusta vastaan

Pathogen derived resistance to Potato virus Y: mechanisms and risks

Selostus: Patogeenivälitteinen, siirtogeeninen kestävyys perunan Y-virusta vastaan: mekanismit ja riskit

Pressure to change and resistance against it: consumer perceptions and acceptance of nutritionally modified foods

Selostus: Muutospaineet ja muutosvastarinta: kuluttajien suhtautuminen ravitsemuksellisesti muunnettuihin elintarvikkeisiin

Consumer resistance to mobile commerce services

Oheinen opinnäytetyö on kvalitatiivinen tutkimus kuluttajavastarinnasta mobiilin kaupankäynnin palveluja kohtaan. Tutkimus kohdistuu läntisiin kulttuureihin, joissa kyseisen innovatiivisen palveluryhmän leviämistä tukevat monet aikaisemmat innovaatiot kuten matkapuhelin, Internet, digitaaliset pankkipalvelut. Tutkimus esittelee innovaatioiden vastarintatekijöitä ihmisen luonnollisena reaktiona tämän vakiintuneita elämäntapoja mullistavia keksintöjä kohtaan nimenomaan läntisissä kulttuureissa, joissa kuluttajat ovat perinteisesti hyvin teknologiamyönteisiä. Toisaalta tutkimusalueella on havaittavissa sosiaalisten ryhmien pirstoutuminen yhä pienemmiksi alaryhmiksi, mikä voi hidastaa sosiaalista oppimista. Tutkimus vastaa todelliseen tutkimusaukkoon. Aihe on samalla sekä ajankohtainen että relevantti vastatessaan nykyisin käytävään utopistiseen keskusteluun digitaalisen informaatioyhteiskunnan kehittymisestä ja merkityksestä modernille ihmiskunnalle. Tutkimuksen teoreettinen eksploratiivinen viitekehys rakentuu valikoiduista uusien tuotteiden ja palvelujen kehittämisen, palvelumarkkinoinnin ja sosiaalisen oppimisen teorioista sekä innovaatio- kommunikaatioteorioista. Empiirisen osan muodostavat kansainvälisten markkinatutkimuslaitosten ja haastateltujen asiantuntijoiden näkemykset alan kehityksestä. Tutkimus osoittaa, että kuluttajat eivät ole valmiita vastaanottamaan kehittyvien teknologioiden mahdollistamia mobiilin kaupankäynnin palveluita ennen kuin ne vastaavat kuluttajien perustarpeisiin ja rakenteelliset vastarintatekijät (alhainen käytettävyys, matala lisäarvo, koetut riskit, perinnevastarinta, palveluryhmän huono mielikuva) on poistettu. Tutkimus esittää, että mobiilin kaupankäynnin alalla toimivien yritysten tulisi työskennellä yhteistyössä keskenään ja kuluttajien kanssa luodakseen kuluttajien tarpeita ja toiveita vastaavia turvallisiksi koettuja mobiilin kaupankäynnin palveluita. Tutkimus ehdottaa, että kyselytutkimusten ohella käytettäisiin havaintomenetelmiä, jotta teknologiat voitaisiin valjastaa kuluttajien tarpeita ja kulutustottumuksia vastaaviksi.

Salmonella enterica– Mechanisms of fluoroquinolone and macrolide resistance

Salmonella enterica – Fluorokinoloni- ja makrolidiresistenssimekanisimit Vakavia salmonellainfektioita on pitkään hoidettu fluorokinoloniantibiooteilla, kuten siprofloksasiinilla. Fluorokinolonien runsas käyttö niin ihmisillä kuin eläimilläkin on kuitenkin johtanut fluorokinoloniresistenttien salmonellakantojen lisääntymiseen. Vuoteen 2002 asti kaikki matalan tason fluorokinoloniresistenssiä ilmentävät salmonellakannat olivat resistenttejä nalidiksiinihapolle, joka on vanha ensimmäisen polven kinoloniantibiootti jota ei enää käytetä infektioiden hoidossa. Vuonna 2003 havaitsimme aivan uudentyyppisen resistenssifenotyypin salmonelloissa. Kaikki uuden fenotyypin kannat osoittivat matalaa fluorokinoloniresistenssiä (MIC ≥0.125 mg/L), mutta useat kannat olivat yllättäen aikaisempaa herkempiä nalidiksiinihapolle (MIC ≤32 mg/L). Ilmiöllä on suuri merkitys salmonellan antibioottiherkkyyksien määrittämisessä, sillä jos kanta on ollut nalidiksiinihapolle herkkä, sitä on pidetty herkkänä myös fluorokinoloneille. Väitöskirjatyössä määritettiin vuosina 2003–2007 Suomessa kerättyjen kotimaisten ja ulkomaalaisten S. enterica -kantojen fluorokinoloniresistenssiä sekä tutkittiin uuden salmonellafenotyypin epidemiologiaa ja resistenssimekanismeja. Lisäksi tutkittiin salmonellan hoidossa mahdollisesti käyttökelpoisen makrolidiantibioottijohdannaisen, atsitromysiinin tehoa salmonelloihin ja erityisesti matalaa fluorokinoloniresistenssiä ilmentäviin kantoihin. Tutkimuksessa havaittiin, että matalaa fluorokinoloniresistenssiä osoittavien salmonellakantojen määrä vähenee. Lasku oli voimakkainta Kaakkois-Aasiasta tuoduissa kannoissa. Uusi resistenssifenotyyppi on plasmidivälitteinen ja qnr-geenit olivat ainoa plasmidivälitteinen kinoloniresistenssimekanismi, joka kannoista löydettiin. Myöskään kromosomaalisten gyrA, gyrB ja parE -geenien QRDR-alueelta ei löydetty fluorokinoloniresistenssiä aiheuttavia mutaatioita. Transformaatiolla osoitettiin qnr-plasmidien olevan siirtyviä ja uusi resistenssifenotyyppi saatiin ilmennettyä myös herkässä vastaanottajakannassa. Nämä tulokset osoittavat, että vaikka S. enterican qnr-fenotyyppi on toistaiseksi levinnyt pääasiassa Kaakkois-Aasiaan, se siirtyy helposti bakteerista toiseen ja tulee todennäköisesti aiheuttamaan hoito-ongelmia myös muualla maailmassa. Uudentyyppinen qnr-fenotyyppi voi olla vaikea havaita perinteisellä herkkyysmäärityksellä. Siksi laboratorioissa tulisi aina määrittää sekä siprofloksasiiniettä nalidiksiinihappoherkkyydet. Atsitromysiinin osoitettiin olevan herkkyysmääritysten mukaan tehokas salmonelloja kohtaan mukaanlukien matala-asteista fluorokinoloniresistenssiä ilmentävät bakteerikannat.

Use of pyrosequencing to identify streptococci and to detect mutations causing antimicrobial resistance

Rapid identification and resistance determination of pathogens in clinical specimens is vital for accurate treatment and monitoring of infectious diseases. Antimicrobial drug resistance is increasing globally and healthcare settings are facing this cost-intensive and even life-threatening problem. The incidence of resistant pathogens in Finland has remained relatively steady and manageable at least for the time being. DNA sequencing is the gold standard method for genotyping, mutation analysis, and identification of bacteria. Due to significant cost decrease in recent years, this technique is available to many research and clinical laboratories. Pyrosequencing technique, a rapid real-time DNA sequencing method especially suitable for analyzing fairly short stretches of DNA, was used in this study. Due to its robustness and versatility, pyrosequencing was applied in this study for identification of streptococci and detection of certain mutations causing antimicrobial resistance in different bacteria. Certain streptococcal species such as S. pneumoniae and S. pyogenes are significantly important clinical pathogens. S. pneumoniae causes e.g. pneumonia and otitis media and is one of the most important community-acquired pathogens. S. pyogenes, also known as group A streptococcus, causes e.g. angina and erysipelas. In contrast, the socalled alpha-haemolytic streptococci, such as S. mitis and S. oralis, belong to the normal microbiota, which are regarded to be non-pathogenic and are nearly impossible to identify by phenotypic methods. In this thesis, a pyrosequencing method was developed for identification of streptococcal species based on the 16S rRNA sequences. Almost all streptococcal species could be differentiated from one another by the developed method, including S. pneumoniae from its close relatives S. mitis and S. oralis . New resistance genes and their variants are constantly discovered and reported. In this study, new methods for detecting certain mutations causing macrolide resistance or extended spectrum beta-lactamase (ESBL) phenotype were developed. These resistance detection approaches are not only suitable for surveillance of mechanisms causing antimicrobial resistance but also for routine analysis of clinical samples particularly in epidemic settings. In conclusion, pyrosequencing was found to be an accurate, versatile, cost-effective, and rapid DNA sequencing method that is especially suitable for mutation analysis of short DNA fragments and identification of certain bacteria.

Antimicrobial Resistance in Campylobacter jejuni and Campylobacter coli

Antimicrobial Resistance in Campylobacter jejuni and Campylobacter coli Campylobacters are a common cause of bacterial gastroenteritis worldwide, with Campylobacter jejuni and C. coli being the most common species isolated in human infections. If antimicrobial treatment is required, the drugs of choice at the moment are the macrolides and fluoroquinolones. In this thesis, the in vitro resistance profiles of the C. jejuni and C. coli strains were evaluated with emphasis on multidrug resistance. The aim was also to evaluate the different resistance mechanisms against the macrolides. Further, the disk diffusion method was compared to agar dilution method and its repeatability was evaluated, since it has been widely used for the susceptibility testing of campylobacters. The results of the present study showed that resistance to the fluoroquinolones is common in strains isolated from Finnish patients, but resistance to the macrolides is still rare. Multidrug resistance was associated with resistance to both ciprofloxacin and erythromycin. Among the available per oral drugs, least resistance was observed to coamoxiclav There was no resistance to the carbapenems. Sitafloxacin and tigecycline were in vitro highly effective towards Campylobacter species. A point mutation A2059G of the 23S rRNA gene was the main mechanism behind the macrolide resistance, whereas the efflux pumps did not seem to play an important role when a strain had A2059G mutation. A five amino acids insertion, which has not been described previously, in the ribosomal protein L22 of one highly-resistant C. jejuni strain without mutation in the 23S rRNA gene was also detected. Concerning the disk diffusion method, there was variation in the repeatability In conclusion, macrolides still appear to be the first-choice alternative for suspected Campylobacter enteritis. The in vitro susceptibilities found suggest that co-amoxiclav might be a candidate for clinical trials on campylobacteriosis, but in life-threatening situations, a carbapenem may be the drug of choice. More studies are needed on whether the disk diffusion test method could be improved or whether all susceptibilities of campylobacters should be done using a MIC based method.

DPS-Like Peroxide Resistance Protein: Structural and Functional Studies on a Versatile Nanocontainer

Oxidative stress is a constant threat to almost all organisms. It damages a number of biomolecules and leads to the disruption of many crucial cellular functions. It is caused by reactive oxygen species (ROS), such as hydrogen peroxide (H2O₂), superoxide (•O₂ -), and hydroxyl radical (•OH). The most harmful of these compounds is •OH, which is only formed in cells in the presence of redox-cycling transition metals, such as iron and copper. Bacteria have developed a number of mechanisms to cope with ROS. One of the most widespread means employed by bacteria is the DNA-binding proteins from starved cells (Dps). Dps proteins protect the cells by binding and oxidizing Fe2+, thus greatly reducing the production of •OH. The oxidized iron is stored inside the protein as an iron core. In addition, Dps proteins bind directly to DNA forming a protective coating that shields DNA from harmful agents. Moreover, Dps proteins have been found to elicit other protective functions in cells and to participate in bacterial virulence. Dps proteins are of special importance to Streptococci owing to the lack of catalase in this genus of bacteria.This study was focused on structural and functional characterization of streptococcal Dpslike peroxide resistance (Dpr) proteins. Initially, crystal structures of Streptococcus pyogenes Dpr were determined. The data confirmed the presence of a di-metal ferroxidase center (FOC) in Dpr proteins and revealed the presence of a novel N-terminal helix as well as a surface metal-binding site. The crystal structures of Streptococcus suis Dpr complexed with transition metals demonstrated the metal specificity of the FOC. Solution binding studies also indicated the presence of a di-metal FOC. These results suggested a possible role for Dpr in the detoxification of various metals. Iron was found to mineralize inside the protein as ferrihydrite based on X-ray absorption spectroscopy data. The iron core was found to exhibit clear superparamagnetic behaviour using magnetic and Mössbauer measurements. The results from this study are expected to further increase our understanding on the binding, oxidation, and mineralization of iron and other metals in Dpr proteins. In particular, the structural and magnetic properties of the iron core can form a basis for potential new applications in nanotechnology. From the streptococcal viewpoint, the results would help in understanding better the complicated picture of bacterial pathogenesis. Dpr proteins may also provide a novel target for drug design due to their tight involvement in bacterial virulence.

Fate of fuel-bound nitrogen and sulfur in biomass-fired Industrial boilers

Användning av biomassa som energikälla för produktion av el och värme är ett sätt att minska beroendet av fossila bränslen och höja självförsörjningen av energi. Fossila bränslen är den främsta källan till koldioxid utsläpp förorsakad av människan. Biomassa, å andra sidan, betraktas som en koldioxidneutral energikälla. Svavlet och kvävet i biomassan bildar dock föroreningar såsom kväveoxider (NOX) och svaveldioxid (SO2), som bidrar till försurning av mark och sjöar. Svavlet i bränslet kan även både förorsaka och förhindra korrosion i en förbränningsanläggning, beroende på förbränningen och bränslet. Huvudsyftet med detta arbete var att få en bättre förståelse om hur utsläppen av NOX och SO2 bildas från bränslebundet kväve och svavel vid förbränning av olika biobränslen. Mätkampanjer i fullskaliga förbränningsanläggningar utfördes, där gassammansättningen mättes i eldstaden och rökgasen. Förståelsen om gaskemin i eldstaden är viktig, för att möjliggöra utvecklandet av renare och effektivare förbränningsanläggningar. Ett annat syfte med arbetet var att klargöra om sulfatering av askkomponenter vid förbränning av biobränslen med olika askegenskaper. Alkaliklorider som bildas vid biomassaförbränning kan orsaka korrosion av värmeöverföringsytor. Svavlet i bränslet visade sig ha en viktig roll i att sulfatera alkaliklorider till mindre korrosiva alkalisulfater. Närvaron av gasformig svavelsyra i rökgaskanalen av förbränningsanläggningar studerades även. Kondensering av svavelsyra leder till korrosion av rökgaskanalen och dess delar. Om svavelsyrakoncentrationen i rökgasen är känd, kan daggpunktstemperaturen beräknas och kondensering av svavelsyra förhindras. I arbetet utvecklades en mätmetod för att mäta låga koncentrationer av gasformig svavelsyra i rökgaser. Denna metod användes för att undersöka risken av lågtemperaturkorrosion orsakad av svavelsyra i förbränningsanläggningar. ------------------------------------------------------------------------------------------------------------ Käyttämällä biomassaa energianlähteenä voidaan vähentää sähkön- ja lämmöntuotannon riippuvuutta fossiilisiin polttoaineisiin. Biomassan käytöllä voidaan myös lisätä energiantuotannon omavaraisuutta. Fossiiliset polttoaineet ovat pääasiallinen syy ihmisen aiheuttamiin hiilidioksidipäästöihin. Biomassa sen sijaan luetaan hiilidioksidineutraaleihin energianlähteisiin. Biopolttoaineiden käytössä tosin vapautuu typpi- ja rikkioksideja, jotka edesauttavat maaperän ja merien happamoitumista. Lisäksi biopolttoaineen rikki voi sekä vähentää että aiheuttaa laitteiden korroosiota energiantuotannossa riippuen biopolttoaineesta ja palamisesta. Tämän työn päätavoitteena oli selvittää mitä biopolttoaineeseen sitoutuneelle typelle ja rikille tapahtuu teollisissa polttolaitoksissa. Kyseisten oksidien muodostumista tutkittiin polttamalla eri biomassoja polttolaitoksissa. Tutkimukset toteutettiin mittauskampanjoilla useissa polttolaitoksissa. Kaasujen koostumusta mitattiin sekä tulipesässä, että savukaasuista. Kaasujen koostumus varsinkin tulipesässä on tärkeää, jotta tulevaisuudessa voidaan rakentaa puhtaampia ja tehokkaampia polttolaitoksia. Työn toisena tavoitteena oli selvittää biomassan polton yhteydessä tapahtuvaa tuhkan sulfatoitumista. Alkalikloridit, joita muodostuu biomassan poltossa, voivat aiheuttaa lämmönsiirtopintojen korroosiota. Rikki osoittautui tärkeäksi osaksi prosessia, jossa korroosiota aiheuttavat alkalikloridit sulfatoituivat vähemmän korrosoiviksi alkalisulfaateiksi. Myös kaasumaisen rikkihapon läsnäoloa savukaasuissa tutkittiin. On todettu, että kaasumuotoinen rikkihappo johtaa korroosioon savukaasukanavan kylmässä päässä ja sen eri osissa rikkihapon tiivistyessä lämpötilan laskiessa. Mikäli rikkihapon pitoisuus savukaasussa tiedetään, sen kastepiste voidaan laskea ja tiivistyminen estää. Tässä työssä kehitettiin mittausmenetelmä rikkihapon alhaisten pitoisuuksien mittaamiseen. Menetelmää hyödynnettiin polttolaitoksissa, joissa tutkittiin rikkihapon tiivistymisestä johtuvaa korroosiota.

Reducing contact resistance in graphene devices

In this thesis, the contact resistance of graphene devices was investigated because high contact resistance is detrimental to the performance of graphene field-effect transistors (GFET). Method for increasing so-called edge-contact area was applied in device fabrication process, as few nanometers thick Ni layer was used as a catalytic etchant during the annealing process. Finally, Ni was also used as a metal for contact. GFETs were fabricated using electron beam lithography using graphene fabricated by chemical vapor deposition (CVD). Critical part of the fabrication process was to preserve the high quality of the graphene channel while etching the graphene at contact areas with Ni during the annealing. This was achieved by optimizing the combination of temperature and gas flows. The structural properties of graphene were studied using scanning electron microscopy, scanning confocal μ-Raman spectroscopy and optical microscopy. Evaluation of electric transport properties including contact resistance was carried out by transmission line method and four-probe method. The lowest contact resistance found was about at 350 Ωμm. In addition, different methods to transfer CVD graphene synthesized on copper were studied. Typical method using PMMA as a supporting layer leaves some residues after its removal, thus effecting on the performance of a graphene devices. In a metal assisted transfer method, metal is used as an interfacial layer between PMMA and graphene. This allows more effective removal of PMMA. However, Raman spectra of graphene transferred by metal assisted method showed somewhat lower quality than the PMMA assisted method

Chemical changes in biomass during torrefaction

Torrefaction is moderate thermal treatment (~200-300 °C) of biomass in an inert atmosphere. The torrefied fuel offers advantages to traditional biomass, such as higher heating value, reduced hydrophilic nature, increased its resistance to biological decay, and improved grindability. These factors could, for instance, lead to better handling and storage of biomass and increased use of biomass in pulverized combustors. In this work, we look at several aspects of changes in the biomass during torrefaction. We investigate the fate of carboxylic groups during torrefaction and its dependency to equilibrium moisture content. The changes in the wood components including carbohydrates, lignin, extractable materials and ashforming matters are also studied. And at last, the effect of K on torrefaction is investigated and then modeled. In biomass, carboxylic sites are partially responsible for its hydrophilic characteristic. These sites are degraded to varying extents during torrefaction. In this work, methylene blue sorption and potentiometric titration were applied to measure the concentration of carboxylic groups in torrefied spruce wood. The results from both methods were applicable and the values agreed well. A decrease in the equilibrium moisture content at different humidity was also measured for the torrefied wood samples, which is in good agreement with the decrease in carboxylic group contents. Thus, both methods offer a means of directly measuring the decomposition of carboxylic groups in biomass during torrefaction as a valuable parameter in evaluating the extent of torrefaction. This provides new information to the chemical changes occurring during torrefaction. The effect of torrefaction temperature on the chemistry of birch wood was investigated. The samples were from a pilot plant at Energy research Center of the Netherlands (ECN). And in that way they were representative of industrially produced samples. Sugar analysis was applied to analyze the hemicellulose and cellulose content during torrefaction. The results show a significant degradation of hemicellulose already at 240 °C, while cellulose degradation becomes significant above 270 °C torrefaction. Several methods including Klason lignin method, solid state NMR and Py-GC-MS analyses were applied to measure the changes in lignin during torrefaction. The changes in the ratio of phenyl, guaiacyl and syringyl units show that lignin degrades already at 240 °C to a small extent. To investigate the changes in the extractives from acetone extraction during torrefaction, gravimetric method, HP-SEC and GC-FID followed by GC-MS analysis were performed. The content of acetone-extractable material increases already at 240 °C torrefaction through the degradation of carbohydrate and lignin. The molecular weight of the acetone-extractable material decreases with increasing the torrefaction temperature. The formation of some valuable materials like syringaresinol or vanillin is also observed which is important from biorefinery perspective. To investigate the change in the chemical association of ash-forming elements in birch wood during torrefaction, chemical fractionation was performed on the original and torrefied birch samples. These results give a first understanding of the changes in the association of ashforming elements during torrefaction. The most significant changes can be seen in the distribution of calcium, magnesium and manganese, with some change in water solubility seen in potassium. These changes may in part be due to the destruction of carboxylic groups. In addition to some changes in water and acid solubility of phosphorous, a clear decrease in the concentration of both chlorine and sulfur was observed. This would be a significant additional benefit for the combustion of torrefied biomass. Another objective of this work is studying the impact of organically bound K, Na, Ca and Mn on mass loss of biomass during torrefaction. These elements were of interest because they have been shown to be catalytically active in solid fuels during pyrolysis and/or gasification. The biomasses were first acid washed to remove the ash-forming matters and then organic sites were doped with K, Na, Ca or Mn. The results show that K and Na bound to organic sites can significantly increase the mass loss during torrefaction. It is also seen that Mn bound to organic sites increases the mass loss and Ca addition does not influence the mass loss rate on torrefaction. This increase in mass loss during torrefaction with alkali addition is unlike what has been found in the case of pyrolysis where alkali addition resulted in a reduced mass loss. These results are important for the future operation of torrefaction plants, which will likely be designed to handle various biomasses with significantly different contents of K. The results imply that shorter retention times are possible for high K-containing biomasses. The mass loss of spruce wood with different content of K was modeled using a two-step reaction model based on four kinetic rate constants. The results show that it is possible to model the mass loss of spruce wood doped with different levels of K using the same activation energies but different pre-exponential factors for the rate constants. Three of the pre-exponential factors increased linearly with increasing K content, while one of the preexponential factors decreased with increasing K content. Therefore, a new torrefaction model was formulated using the hemicellulose and cellulose content and K content. The new torrefaction model was validated against the mass loss during the torrefaction of aspen, miscanthus, straw and bark. There is good agreement between the model and the experimental data for the other biomasses, except bark. For bark, the mass loss of acetone extractable material is also needed to be taken into account. The new model can describe the kinetics of mass loss during torrefaction of different types of biomass. This is important for considering fuel flexibility in torrefaction plants.