På grund av planerat tillverkningsstopp av instrumenten som används idag på Octapharma AB, så syftar detta projekt till nyutvecklingen av en kvantitativ PCR analysmetod för detektion av HIV-1 i human blodplasma, genom TaqMankemi. Projektet inkluderade design, testning och utvärdering av olika set av primer och probe sekvenser. För att säkerställa specificiteten hos metoden designades primrarna och proberna för att vara komplementära till olika konservativa regioner av HIV-1:s genom. Primer och probe set:en (P/P) testades både individuellt och kombinerat i spädningsserier och genotypspaneler. Analyserna visade att det inte fanns någon korrelation mellan felmatchning av P/P och referenssekvenser hos subtyper, och detektionsnivå. När P/P testades i kombination hittades falsk-positiva signaler i negativa kontroller (4 falsk-positiva signaler; n= 106). Detta åtgärdades genom att utesluta specifika prober(0 falsk-positiva signaler; n= 152)(p = 0,030, Fisher’s exact test). Kombinationen av primer och prober, med någraprober uteslutna, hade en högre detektionsnivå för HIV-1 subtyper än de individuella set:en (29 positiva prover vs 23.5; n= 64), och lyckadesäven detektera åtminstone ett positivt prov hos varje subtyp A, B, C, D, AE, F, G och H. Avsaknaden av korrelation mellan felmatchning av P/P och detektionsnivå, visar på att orsaken av den suboptimala detektionsnivån av subtyper var inte på grund av antalet felmatchningar mellan primer och probe set:en till målsekvenserna. Den högre specificiteten vid kombination av P/P indikerar även att primrar och prober som riktar in sig på olika regioner avHIV-1 genomet ytterligare ökar specificiteten och detektionsnivån hos metoden. / As a result of future instrument discontinuation by Octapharma AB’s manufacturers, this project sought to develop a new quantitative PCR analysis method for the detection of HIV-1 in human blood plasma using TaqMan chemistry. The project included the design, testing and statistical analysis of different sets of novel primer and probe sequences. To ensure specificity, the primer and probe sequences were designed to target conserved regions of the HIV-1 genome. The primer and probe sets were tested both individually and in combination in dilution series and genotype tests. Linear regression analyses showed no correlation between mismatches between the primer and probe sets and the subtype reference sequences tested, and detection rate. When the primer and probe setswere tested in combination, false positive signals were obtained in negative control samples (4 false positive signals; n= 106). However, this obstacle was overcome by the omission of certain probes, resulting in no false positive signals (0 false positive signals; n= 152)(p = 0.030, Fisher’s exact test).The combination of primer and probe sets, with certain probes omitted, had an increased HIV-1 subtype detection rate compared to the individual P/P (29 positive samples detected versus 23.5; n= 64), and were also able to detect at least one positive sample from each of the HIV-1 subtypes A, B, C, D, AE, F, G, and H. The absence of correlation between primer and probe set mismatch and detection rate, suggests that the cause of the suboptimal detection rate of the subtypes was not the result of primer and probe set mismatch to the target sequences. The increased subtype detection rate upon combining the P/P also indicates that targeting different region of the HIV-1 genome further improves the detection rate and specificity of the method.

Die genetischen Polymorphismen der humanen Biotransformationsenzyme Glutathion-S-Transferase Theta 1 (GSTT1-1) und Arylamin-N-Acetyltransferase 1 (NAT1) wurden zu Beginn der neunziger Jahre entdeckt. Es besteht derzeit ein großes Interesse an Untersuchungen zur Häufigkeit der Allele, zu deren phänotypischen Konsequenzen und pharmakologisch-toxikologischer Relevanz. Für die Untersuchungen in dieser Arbeit standen die Blutproben von 314 gesunden, deutschen Probanden mit bekanntem GSTT1- und/oder NAT1-Genotyp zur Verfügung. Es wurden Methoden etabliert und validiert, um im Hämolysat die Reaktionsgeschwindigkeiten bei der Umsetzung des GSTT1-1-spezifischen Substrats Dichlormethan sowie des NAT1-spezifischen Substrats p-Aminobenzoesäure mit vertretbarem Laboraufwand zu bestimmen. In der vorliegenden Arbeit wurde eine vollständige Übereinstimmung zwischen der homozygoten GSTT1-Gendeletion und dem defizienten Phänotyp bei 19,3% der Individuen gefunden. Bei 80,7% der Probanden war durch Genotypisierung mindestens ein GSTT1*A-Allel identifiziert worden. Mit Hilfe der Phänotypisierung konnten in dieser Gruppe zwei Phänotypen, der intermediäre und der hoch aktive Phänotyp, voneinander abgegrenzt werden. Damit bestand der Vorteil der Phänotypisierung darin, eine trimodale Verteilung der GSTT1-1-Aktivität nachweisen zu können. Dies wurde in der vorliegenden Arbeit erstmalig in einer größeren deutschen Population gezeigt. Weiterhin wurden in dieser Arbeit untersucht, ob zwei Phosphonsäurediester des Glutathions, die sich als kompetitive bzw. nicht-kompetitive Hemmstoffe anderer GST-Isoenzyme erwiesen hatten, sowie der Arzneistoff Tactin, ein Medikament zur Behandlung des Mobus Alzheimer eine Hemmwirkung auf die GSTT1-1-vermittelte Umsetzung von Dichlormethan besitzen. Gegenwärtig sind 24 verschiedene NAT1-Allele bekannt, wobei einige davon sehr selten auftreten. In der hier verwendeten deutschen Population waren sechs NAT1-Allele identifiziert worden. In den Blutproben der 105 Probanden wurde die funktionelle Konsequenz dieser Allele bestimmt. In vorliegender Arbeit wurde erstmalig für einen homozygoten Träger des NAT1*15-Allels das Fehlen jeglicher Enzymaktivität nachgewiesen. Bezüglich der Häufigkeit der GSTT1-Gendefizienz sowie des NAT1*11-Allels wurden in vorliegender Arbeit zwischen europäischen, d.h. einander ethnisch nahestehenden Bevölkerungsgruppen statistisch signifikante Unterschiede gefunden. / The genetic polymorphisms of the glutathione S-transferase theta 1-1 (GSTT1-1) and the arylamine N-acetyltransferase 1 (NAT1) were found in the beginning of the 90's. There is a great interest in genotype-phenotype relations in individuals and in pharmacological and toxicological consequences of the polymorphisms. In this work, hemolysate of 314 healthy German volunteers was used for several genotyping and phenotyping methods. A concordance between the homozygous GSTT1 gene deletion and the enzyme deficiency in 27 of 140 individuals (19,3%)was found. In 80,7% of the volunteers a discrimination between intermediate and rapid metabolizers was possible in a German population for the first time. In addition it was proved, if the ex-vivo metabolism of dichloromethane, catalyzed by GSTT1-1, is inhibited by phosphono-analoga of glutathione or tacrine, a drug for treatment of Alzheimers' disease. The NAT1 polymorphism is characterized by several point mutations and deletions or insertions of oligonucleotides. 24 NAT1 alleles are known so far. In this work, the functional consequences of various NAT1 allele combinations in the genotypes of 105 individuals were determinated. There were found interethnic differences in the frequency of the NAT1*11 allele and the frequency of the homozygous gene deletion between the German and other Caucasien populations.

Die Umwandlung in wasserlösliche Verbindungen, die renal ausgeschieden werden können, ist ein grundlegendes Prinzip im Abbau von Fremdstoffen. Hierbei unterscheidet man Phase-I- und Phase-II-Reaktionen. Die Aktivität vieler Phase-I- und Phase-II-Enzyme ist genetisch beeinflusst und kann starke interindividuelle Unterschiede im Metabolismus von Fremdstoffen verursachen und dadurch das Krebsrisiko und das Risiko für Arzneimittelnebenwirkungen beeinflussen. Die Häufigkeitsverteilungen der Allele der Gene, die Phase-I- und Phase-II-Enzyme kodieren, zeigen eine große interethnische Varianz. Die Polymorphismen dieser Enzyme wurden bisher jedoch noch nicht in der größten slawischen Volksgruppe, der russischen, untersucht. An der vorliegenden Studie nahm eine Gruppe von 325 Personen russischer Abstammung teil - gesunde Probanden bzw. Patienten, die nicht an einer malignen Erkrankung litten. Die Polymorphismen von zwei Enzymen der Phase I, CYP1A1 und CYP2D6, und von einem Enzym der Phase II, NAT2, wurden mittels PCR-RFLP-Genotypisierung und Real-time-PCR-Verfahren komplett untersucht. Die Häufigkeit der CYP1A1 Allele mit hoher Aktivität, CYP1A1*2A und CYP1A1*2B, betrug 4,6% (3,1%-6,5%) bzw. 5,1% (3,5%-7,1%). Die Häufigkeiten der genetischen Varianten von CYP1A1 waren: m1 (3801T>C) - 9,8% (95% Vertrauensbereich, 7,7%-12,4%), m2 (2455A>G) - 5,0% (95% VB, 3,5%-7,1%), m4 (2453C>A) - 2,5% (1,4%-4,0%), m5 (-4335G>A) - 25,8% (22,5%-29,4%), m6 (-3219C>T) - 6,0% (4,3%-8,1%), und m7 (-3229G>A) - 2,9% (1,8%-4,5%). Die Mutation m3, die bisher nur bei Afrikaner gefunden wurde, konnten wir nicht nachweisen. 5,9% (3,5%-9,2%) aller Probanden waren CYP2D6 Langsam-Metabolisierer und 3,4% (1,7%-6,3%) wurden als Ultraschnell-Metabolisierer identifiziert (CYP2D6*1x1/*1). Bei der Genotypisierung von acht verschiedenen Punktmutationen im NAT2-Gen ergab sich für 59,7% (54,1%-65,1%) der Studienteilnehmer ein Genotyp, der mit einer Langsam-Acetylierer-Status einhergeht. 34,7% (29,6%-40,2%) der Probanden hatten ein und 5,6% (3,3%-8,6%) zwei für die Schnellacetylierung kodierende Allele. Die Allelverteilung der für die wichtigsten Enzyme im Arzneimittelstoffwechsel kodierenden Gene ist bei Russen ähnlich wie bei anderen Kaukasiern. Es kann deshalb erwartet werden, dass die genetisch-bedingten Unterschiede in der Wirksamkeit und im Auftreten von Arzneimittelnebenwirkungen in der russischen Bevölkerung vergleichbar sind mit denen in anderen europäischen Populationen. / The basic principle of drug and xenobiotic metabolism in the body is to make them more water soluble and thus more readily excreted in the urine. Genetic polymorphisms of phases I and II xenobiotic transformation reactions are known to contribute considerably to interindividual variations in the metabolism of numerous drugs and xenobiotics and to associate with altered risk of adverse drug reactions and some cancers. The frequency of functionally important mutations and alleles of genes coding for xenobiotic metabolizing enzymes shows a wide ethnic variation. However, little is known of the frequency distribution of the major allelic variants in the Russian population. In this study we investigated 325 individuals of Russian origin, who were healthy volunteers or patients without malignant diseases. Our study included the complete investigation of two enzymes of phase I, CYP1A1 and CYP2D6, and one phase II enzyme, NAT2, using PCR-RFLP genotyping and LightCycler method. The frequencies of the CYP1A1 high-activity alleles, CYP1A1*2A and CYP1A1*2B, were 4.6% (3.1%-6.5%) and 5.1% (3.5%-7.1%), respectively. The mutations m1 (3801T>C), m2 (2455A>G), m4 (2453C>A), m5 (-4335G>A), m6 (-3219C>T), and m7 (-3229G>A) of CYP1A1 occurred in 9.8% (95% confidence interval, 7.7%-12.4%), 5.0% (95% C. I., 3.5%-7.1%), 2.5% (1.4%-4.0%), 25.8% (22.5%-29.4%), 6.0% (4.3%-8.1%), and 2.9% (1.8%-4.5%) of alleles, respectively. We did not find the m3 mutation, which has only been detected in Africans up to now. 5.9% (3.5%-9.2%) of all subjects were CYP2D6 poor metabolizers, whereas 3.4% (1.7%-6.3%) were identified as ultra-rapid metabolizers (CYP2D6*1x1/*1). Genotyping eight different single nucleotide polymorphisms in the NAT2 gene provided a genotype associated with slow acetylation in 59.7% (54.1%-65.1%) of individuals, 34.7% (29.6%-40.2%) of participants carried at least one allele encoding rapid acetylation, and 5.6% (3.3%-8.6%) were homozygous for the rapid-acetylation allele (wild-type allele *4 or mutant allele *12A). The overview of allele distribution of the important drug and xenobiotic metabolizing enzymes among Russians shows that the allele frequency is similar to that of other Caucasians. Therefore it may be expected that drug side effects and efficacy problems due to an individual's genetic background are similar compared to those in other European populations.

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The neural mechanisms underlying genetic risk for schizophrenia, a highly heritable psychiatric condition, are still under investigation. New schizophrenia risk genes discovered through genome-wide association studies (GWAS), such as neurogranin (NRGN), can be used to identify these mechanisms. In this study we examined the association of two common NRGN risk single nucleotide polymorphisms (SNPs) with functional and structural brain-based intermediate phenotypes for schizophrenia. We obtained structural, functional MRI and genotype data of 92 schizophrenia patients and 114 healthy volunteers from the multisite Mind Clinical Imaging Consortium study. Two schizophrenia-associated NRGN SNPs (rs12807809 and rs12541) were tested for association with working memory-elicited dorsolateral prefrontal cortex (DLPFC) activity and surface-wide cortical thickness. NRGN rs12541 risk allele homozygotes (TT) displayed increased working memory-related activity in several brain regions, including the left DLPFC, left insula, left somatosensory cortex and the cingulate cortex, when compared to non-risk allele carriers. NRGN rs12807809 non-risk allele (C) carriers showed reduced cortical gray matter thickness compared to risk allele homozygotes (TT) in an area comprising the right pericalcarine gyrus, the right cuneus, and the right lingual gyrus. Our study highlights the effects of schizophrenia risk variants in the NRGN gene on functional and structural brain-based intermediate phenotypes for schizophrenia. These results support recent GWAS findings and further implicate NRGN in the pathophysiology of schizophrenia by suggesting that genetic NRGN risk variants contribute to subtle changes in neural functioning and anatomy that can be quantified with neuroimaging methods.

The neural mechanisms underlying genetic risk for schizophrenia, a highly heritable psychiatric condition, are still under investigation. New schizophrenia risk genes discovered through genome-wide association studies (GWAS), such as neurogranin (NRGN), can be used to identify these mechanisms. In this study we examined the association of two common NRGN risk single nucleotide polymorphisms (SNPs) with functional and structural brain-based intermediate phenotypes for schizophrenia. We obtained structural, functional MRI and genotype data of 92 schizophrenia patients and 114 healthy volunteers from the multisite Mind Clinical Imaging Consortium study. Two schizophrenia-associated NRGN SNPs (rs12807809 and rs12541) were tested for association with working memory-elicited dorsolateral prefrontal cortex (DLPFC) activity and surface-wide cortical thickness. NRGN rs12541 risk allele homozygotes (TT) displayed increased working memory-related activity in several brain regions, including the left DLPFC, left insula, left somatosensory cortex and the cingulate cortex, when compared to non-risk allele carriers. NRGN rs12807809 non-risk allele (C) carriers showed reduced cortical gray matter thickness compared to risk allele homozygotes (TT) in an area comprising the right pericalcarine gyrus, the right cuneus, and the right lingual gyrus. Our study highlights the effects of schizophrenia risk variants in the NRGN gene on functional and structural brain-based intermediate phenotypes for schizophrenia. These results support recent GWAS findings and further implicate NRGN in the pathophysiology of schizophrenia by suggesting that genetic NRGN risk variants contribute to subtle changes in neural functioning and anatomy that can be quantified with neuroimaging methods.

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We chose to base our literature study on the meme phenomena. The meme is a portion of culture that is spread among us from mind to mind. Every time we learn something by copying others we use information that has been passed on from a previous person, that information can be seen as a meme. The theoretical frame for our methodology in our exam paper is founded on Forsberg och Wengström research on literature studies. Our aim is to describe to the reader in depth what a meme is and how they could be helpful in an academic and pedagogical setting.Our study will show how memes are seen predominantly as graphic designs and as artifacts for cultural representation parallel to their imagery. This means that the cultural reference is only clear to the beholder if they have corresponding prior knowledge to the reference.Our study will also show via concrete examples how this could be used in school settings and as pedagogical tools in the classroom.