Diversitet och tillväxtfrämjande egenskaper hos Stenotrophomonas-endofyter isolerade från Calliandra calothyrsus Meisn. rotknölar

The bacterial genus Stenotrophomonas comprises 12 species. They are widely found throughout the environment and particularly S. maltophilia, S. rhizophila and S. pavanii are closely associated with plants. Strains of the most common Stenotrophomonas species, S. maltophilia, promote plant growth and health, degrade natural and man-made pollutants and produce biomolecules of biotechnological and economical value. Many S. maltophilia –strains are also multidrug resistant and can act as opportunistic human pathogens. During an INCO-project (1998-2002) rhizobia were collected from root nodules of the tropical leguminous tree Calliandra calothyrsus Meisn. from several countries in Central America, Africa and New Caledonia. The strains were identified by the N2-group (Helsinki university) and some strains turned out to be members of the genus Stenotrophomonas. Several Stenotrophomonas strains induced white tumor- or nodule-like structures on Calliandra?s roots in plant experiments. The strains could, besides from root nodules, also be isolated from surface sterilized roots and stems. The purpose of my work was to investigate if the Stenotrophomonas strains i) belong to a new Stenotrophomonas species, ii) have the same origin, iii) if there are other differences than colony morphology between phase variations of the same strain, iv) have plant growth-promoting (PGP) activity or other advantageous effects on plants, and v) like rhizobia have ability to induce root nodule formation. The genetic diversity and clustering of the Stenotrophomonas strains were analyzed with AFLP fingerprinting to get indications about their geographical origin. Differences in enzymatic properties and ability to use different carbon and energy sources were tested between the two phases of each strain with commercial API tests for bacterial identification. The ability to infect root hairs and induce root nodule formation was investigated both using plant tests with the host plant Calliandra and PCR amplification of nodA and nodC genes for nodulation. The PGP activity of the strains was tested in vitro mainly with plate methods. The impact on growth, nitrogen content and nodulation in vivo was investigated through greenhouse experiments with the legumes Phaseolus vulgaris and Galega orientalis. Both the genetic and phenotypic diversity among the Stenotrophomonas strains was small, which proposes that they have the same origin. The strains brought about changes on the root hairs of Calliandra and they also increased the amount of root hairs. However, no root nodules were detected. The strains produced IAA, protease and lipase in vitro. They also showed plant a growth-promoting effect on G. orientalis, both alone and together with R. galegae HAMBI 540, and also activated nodulation among efficient rhizobia on P. vulgaris in greenhouse. It requires further research to get a better picture about the mechanisms behind the positive effects. The results in this thesis, however, confirm earlier studies concerning Stenotrophomonas positive impact on plants.

Noncommutative Quantum Field Theory : Problem of Time and Some Applications

In this thesis the current status and some open problems of noncommutative quantum field theory are reviewed. The introduction aims to put these theories in their proper context as a part of the larger program to model the properties of quantized space-time. Throughout the thesis, special focus is put on the role of noncommutative time and how its nonlocal nature presents us with problems. Applications in scalar field theories as well as in gauge field theories are presented. The infinite nonlocality of space-time introduced by the noncommutative coordinate operators leads to interesting structure and new physics. High energy and low energy scales are mixed, causality and unitarity are threatened and in gauge theory the tools for model building are drastically reduced. As a case study in noncommutative gauge theory, the Dirac quantization condition of magnetic monopoles is examined with the conclusion that, at least in perturbation theory, it cannot be fulfilled in noncommutative space.

A microcomputer program to analyze the CD spectrum of proteins and nucleic acids—Use of LOTUS 1-2-3 spread sheet

A user friendly interactive computer program, CIRDIC, is developed which calculates the molar ellipticity and molar circular dichroic absorption coefficients from the CD spectrum. This, in combination with LOTUS 1-2-3 spread sheet, will give the spectra of above parameters vs wavelength. The code is implemented in MicroSoft FORTRAN 77 which runs on any IBM compatible PC under MSDOS environment.

Detection, epidemiology and host spectrum of cowpox and Borna disease virus infections

Several orthopoxviruses (OPV) and Borna disease virus (BDV) are enveloped, zoonotic viruses with a wide geographical distribution. OPV antibodies cross-react, and former smallpox vaccination has therefore protected human populations from another OPV infection, rodent-borne cowpox virus (CPXV). Cowpox in humans and cats usually manifests as a mild, self-limiting dermatitis and constitutional symptoms, but it can be severe and even life-threatening in the immunocompromised. Classical Borna disease is a progressive meningoencephalomyelitis in horses and sheep known in central Europe for centuries. Nowadays the virus or its close relative infects humans and also several other species in central Europe and elsewhere, but the existence of human Borna disease with its suspected neuropsychiatric symptoms is controversial. The epidemiology of BDV is largely unknown, and the present situation is even more intriguing following the recent detection of several-million-year-old, endogenized BDV genes in primate and various other vertebrate genomes. The aims of this study were to elucidate the importance of CPXV and BDV in Finland and in possible host species, and particularly to 1) establish relevant methods for the detection of CPXV and other OPVs as well as BDV in Finland, 2) determine whether CPXV and BDV exist in Finland, 3) discover how common OPV immunity is in different age groups in Finland, 4) characterize possible disease cases and clarify their epidemiological context, 5) establish the hosts and possible reservoir species of these viruses and their geographical distribution in wild rodents, and 6) elucidate the infection kinetics of BDV in the bank vole. An indirect immunofluorescence assay and avidity measurement were established for the detection, timing and verification of OPV or BDV antibodies in thousands of blood samples from humans, horses, ruminants, lynxes, gallinaceous birds, dogs, cats and rodents. The mostly vaccine-derived OPV seroprevalence was found to decrease gradually according to the year of birth of the sampled human subjects from 100% to 10% in those born after 1977. On the other hand, OPV antibodies indicating natural contact with CPXV or other OPVs were commonly found in domestic and wild animals: the horse, cow, lynx, dog, cat and, with a prevalence occasionally even as high as 92%, in wild rodents, including some previously undetected species and new regions. Antibodies to BDV were detected in humans, horses, a dog, cats, and for the first time in wild rodents, such as bank voles (Myodes glareolus). Because of the controversy within the human Borna disease field, extra verification methods were established for BDV antibody findings: recombinant nucleocapsid and phosphoproteins were produced in Escherichia coli and in a baculovirus system, and peptide arrays were additionally applied. With these verification assays, Finnish human, equine, feline and rodent BDV infections were confirmed. Taken together, wide host spectra were evident for both OPV and BDV infections based on the antibody findings, and OPV infections were found to be geographically broadly distributed. PCR amplification methods were utilised for hundreds of blood and tissue samples. The methods included conventional, nested and real-time PCRs with or without the reverse transcription step and detecting four or two genes of OPVs and BDV, respectively. OPV DNA could be amplified from two human patients and three bank voles, whereas no BDV RNA was detected in naturally infected individuals. Based on the phylogenetic analyses, the Finnish OPV sequences were closely related although not identical to a Russian CPXV isolate, and clearly different from other CPXV strains. Moreover, the Finnish sequences only equalled each other, but the short amplicons obtained from German rodents were identical to monkeypox virus, in addition to German CPXV variants. This reflects the close relationship of all OPVs. In summary, RNA of the Finnish BDV variant could not be detected with the available PCR methods, but OPV DNA infrequently could. The OPV species infecting the patients of this study was proven to be CPXV, which is most probably also responsible for the rodent infections. Multiple cell lines and some newborn rodents were utilised in the isolation of CPXV and BDV from patient and wildlife samples. CPXV could be isolated from a child with severe, generalised cowpox. BDV isolation attempts from rodents were unsuccessful in this study. However, in parallel studies, a transient BDV infection of cells inoculated with equine brain material was detected, and BDV antigens discovered in archival animal brains using established immunohistology. Thus, based on several independent methods, both CPXV and BDV (or a closely related agent) were shown to be present in Finland. Bank voles could be productively infected with BDV. This experimental infection did not result in notable pathological findings or symptoms, despite the intense spread of the virus in the central and peripheral nervous system. Infected voles commonly excreted the virus in urine and faeces, which emphasises their possible role as a BDV reservoir. Moreover, BDV RNA was regularly reverse transcribed into DNA in bank voles, which was detected by amplifying DNA by PCR without reverse transcription, and verified with nuclease treatments. This finding indicates that BDV genes could be endogenized during an acute infection. Although further transmission studies are needed, this experimental infection demonstrated that the bank vole can function as a potential BDV reservoir. In summary, multiple methods were established and applied in large panels to detect two zoonoses novel to Finland: cowpox virus and Borna disease virus. Moreover, new information was obtained on their geographical distribution, host spectrum, epidemiology and infection kinetics.

Hyperfine effects in the nuclear magnetic resonance of paramagnetic molecules

Paramagnetic, or open-shell, systems are often encountered in the context of metalloproteins, and they are also an essential part of molecular magnets. Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for chemical structure elucidation, but for paramagnetic molecules it is substantially more complicated than in the diamagnetic case. Before the present work, the theory of NMR of paramagnetic molecules was limited to spin-1/2 systems and it did not include relativistic corrections to the hyperfine effects. It also was not systematically expandable. --- The theory was first expanded by including hyperfine contributions up to the fourth power in the fine structure constant α. It was then reformulated and its scope widened to allow any spin state in any spatial symmetry. This involved including zero-field splitting effects. In both stages the theory was implemented into a separate analysis program. The different levels of theory were tested by demonstrative density functional calculations on molecules selected to showcase the relative strength of new NMR shielding terms. The theory was also tested in a joint experimental and computational effort to confirm assignment of 11 B signals. The new terms were found to be significant and comparable with the terms in the earlier levels of theory. The leading-order magnetic-field dependence of shielding in paramagnetic systems was formulated. The theory is now systematically expandable, allowing for higher-order field dependence and relativistic contributions. The prevailing experimental view of pseudocontact shift was found to be significantly incomplete, as it only includes specific geometric dependence, which is not present in most of the new terms introduced here. The computational uncertainty in density functional calculations of the Fermi contact hyperfine constant and zero-field splitting tensor sets a limit for quantitative prediction of paramagnetic shielding for now.

Detection and molecular epidemiology of tick-borne encephalitis virus infections

Pdf-file, link above

Gadamers hermeneutik och naturvetenskaplig experimentering

I detta arbete undersöks naturvetenskaplig kunskap ur ett filosofiskt perspektiv. Arbetets centrala ämne är det naturvetenskapliga experimenterandets praktiska aspekter och deras anknytningar till den teoretiska naturvetenskapliga kunskapen. Ämnet behandlas med hjälp av Hans-Georg Gadamers hermeneutiska filosofi i boken Wahrheit und Methode. Gadamers utgångspunkt i denna bok är att hermeneutiken beskriver vad som händer i texttolkning då en tolkare förstår en skriven text, men han antyder också att hermeneutiken har vidare tillämpningsområden, till och med att den universalt beskriver alla former av mänsklig förståelse. Syftet med detta arbete är att undersöka hur Gadamers hermeneutik kan tillämpas på naturvetenskaplig förståelse och vilka ändringar man då måste införliva i hermeneutiken samt att skissa grunddragen för en hermeneutisk modell av naturvetenskaplig kunskap. I arbetet presenteras först de centrala elementen i Gadamers hermeneutiska filosofi, speciellt föromdömens positiva inverkan på tolkandet och den verkningshistoriska effekten bakom varje tolkning. Sedan diskuteras bristerna i Gadamers argument för hermeneutikens universalitet, speciellt hans starka betoning av språket som grunden för all förståelse. Om Gadamers hermeneutik skall kunna tillämpas på naturvetenskapens område måste även observationer kunna vara föremål för tolkning. De dominanta trenderna i vetenskapsfilosofin då Gadamer skrev Wahrheit und Methode är en förklaring till att Gadamer starkt förbinder sig till textförståelsen och oftast diskuterar den naturvetenskapliga kunskapen endast som en negativ motpol till den humanvetenskapliga. Vetenskapsfilosofins utveckling efter Wahrheit und Methode, speciellt det faktum att fullständig objektivitet inte mera anses vara ett realistiskt ideal, höjer förväntningarna på hermeneutikens värde för naturvetenskapernas filosofi. Till följande diskuteras tre bidrag till naturvetenskapernas filosofi som är speciellt värdefulla för en hermeneutiken. Den första av dessa är Sylvain Brombergers analys av ovisshet i vetenskapliga undersökningar. Bromberger hävdar att vetenskaplig forskning riktas mot frågor vars svar forskaren inte kan föreställa sig på förhand. Brombergers analys tyder på att det finns en hermeneutisk dialektik av frågor och svar i naturvetenskapliga experiment där forskaren strävar till att göra observationer för att besvara sina frågor. Det andra bidraget är Michael Polanyis studie av den praktiska och personliga kunskapens betydelse för all vetenskaplig forskning. Här är speciellt det vetenskapliga språkets utveckling i samband med experimentering av intresse. Det tredje bidraget är Robert Creases studie av experimentella observationer som visar att observationstolkning innefattar många element som kan förknippas med hermeneutiken. Analysen av de tre ovannämnda studierna leder till följande slutsatser. Den naturvetenskapliga forskningens hermeneutiska element förväntas vara starkt framför allt i experimentell forskning där forskaren utreder nya frågor i en kontinuerlig dialog av tekniskt prövande, praktisk identifiering och språklig beskrivning av nya fenomen. Speciellt beaktansvärd är skillnaden mellan verifierande och upptäckande naturvetenskapliga undersökningar. Tidigare resultat kan verifieras med hjälp av mätningar som specificeras på förhand, men ingen kan på förhand specificera de tekniska och språkliga steg som krävs för ett framgångsrikt upptäckande experiment. Experimentella upptäckter kräver därför en praktisk kunskap som inte kan reduceras till ren teori eller metodologi. Denna praktiska kunskap kan beskrivas med hjälp av Gadamers hermeneutik. Till sist diskuteras vissa grundläggande drag som kan sägas vara karakteristiska för en hermeneutisk modell av naturvetenskaplig kunskap. Speciellt den naturvetenskapliga kunskapens historiska natur, fördomarnas betydelse i naturvetenskaplig forskning samt vikten av forskarens personliga perspektiv i den naturvetenskapliga observationen är viktiga stöttestenar som gör att den hermeneutiska naturvetenskapsmodellen skiljer sig betydligt från modeller som betonar naturvetenskapernas objektivitet. Men det hermeneutiska perspektivet utesluter inte nödvändigtvis andra perspektiv. Dess huvudsakliga nytta är att den tillåter oss att undersöka sidor av naturvetenskaplig kunskap som objektivitetsbetonande modeller lämnar alltför mycket i skymundan. Till dessa hör speciellt det praktiska arbetet i naturvetenskaplig experimentering.

Den medeltida svenska hustrun och lagen : En studie i förmyndarskap, begränsningar och möjligheter 1350-1442

Denna studie behandlar kvinnans juridiska handlingsutrymme under Magnus Erikssons lagar 1350-1442. Det har länge antagits att den gifta kvinnan under medeltiden var omyndig, eftersom hon enligt lagen skulle ha en målsman (på fornsvenska malsman). Senare tids forskning har dock börjat påpeka att kvinnan inte var omyndig i dagens bemärkelse, men inte desto djupare utvecklat frågan om hennes rättigheter. Genom att jämföra lagtexterna med praxis har jag undersökt hur lagutrymmet som stadgade att en make skulle vara sin hustrus malsman påverkade kvinnans rättigheter. Under den undersökta tidsperioden tycks malsmanskapet inte i någon större utsträckning ha juridiskt begränsat kvinnan, men praxis visar att tradition och praktikaliteter bjöd att maken i allmänhet representerade sin hustru i juridiska göromål. Studien visar att representation inte nödvändigtvis indikerade myndighet, och att det faktum att hustrun representerades av sin make inte medförde omyndighet. Männens konstanta kontakt med den juridiska världen och kvinnornas synnerligen begränsade dito kom ändå på sikt att minska hennes juridiska medvetenhet, och därmed hennes möjlighet att påverka. Den viktigaste slutsatsen är likväl denna begränsning inte var lagstadgad. I studien tar jag också ställning till olika genusteoretiska förklaringsmodeller, nämligen enkönsmodellen och teorin om skilda sfärer. Enligt enkönsmodellen, som utvecklades av Laqueur i början av 1990-talet, sågs inte kvinnan och mannen som två olika kön, utan som olika grader av en man. Kvinnan skulle enligt det vara en mindre utvecklad variant av mannen. Resultaten i studien tyder dock snarare på att kvinnor och män sågs som två olika kön, men att de verkade inom olika sfärer. Den avgörande faktorn var förmågan att föda barn, där de som födde barn tillhörde en privat sfär, med hemmet i centrum, och de som inte födde barn tillhörde en offentlig sfär, där juridik, politik och ekonomi ingick. Därför argumenterar jag för att män förväntades sköta de juridiska göromålen även för sin hustru, eftersom det tillhörde hans sfär. Hustrun hade dock möjligheten, både enligt lagen och enligt praxis, att själv sköta exempelvis försäljningar och upprätta testamenten, och begränsades snarare av sitt kön än av genusstrukturer. Studien lyfter också fram problematiken med det diversifierade svenska medeltida samhället, och ifrågasätter traditionen med en indelning i endast två genus, en manlighet och en kvinnlighet. Resultaten tyder på att det var stora lokala skillnader beträffande en hustrus begränsningar och möjligheter, och att lagarna mer fungerade som riktlinjer än som faktiska regler. På grund av källmaterialets beskaffenhet går det inte att avgöra på vilket sätt social status spelade in, även om det är rimligt att anta att det fanns betydande skillnader mellan rikets övre och lägre skikt. Däremot finns det inget som indikerar att hustruns malsman skulle ha varit liktydig med det nutida målsman någonstans i riket, eller i någon samhällsgrupp.