This report is the result of a project in the course Independent Projekt in Molecular Biotechnology at Uppsala University during the spring of 2014. The foremost purpose of the course is to give students the opportunity to carry through exstensive work in a project environment. This project was formed based on a comission from the biotechnology company SweTree Technologies, and the goal has been to compose a summary of the different techniques and methods that exist in the field of mass propagation of trees through the method of somatic embryogenesis. The project group has obtained information about the area mainly throgh reading patents, trying to find key components and bottlenecks in other companies’ somatic embryogenesis technologies. This paper is divided into different sections, containing the patents of the automation of different steps in the process. This is to make it easier for readers to find information about the area they are interested in, as well as to illustrate the main parts of the process as percieved by the project group. Currently, there are several automated solutions for almost every step in the process, some of which are already in use. All the information obtained shows that the cost and labour has decreased with the development of this technology. While there is still room for significant devolopment in order to produce a complete automated process, there is no doubt that this method is becoming an ever more important asset in the area of forestry. Our hope is that this report may be a useful tool for companies or laymen to geta grasp of the field of automated mass production of trees.

Traditional immunological assays used to serotype Actinobacillus pleuropneumoniae have been problematic due to cross- reactivity between serotypes, particularly serotypes 6 and 8. To avoid these serological cross-reactions, a multiplex PCR assay was developed to detect A. pleuropneumoniae and identify serotypes 1, 2, and 8. Primers specific to the conserved capsular polysaccharide export region of A. pleuropneumoniae serotype 5 amplified a 880 bp fragment in all serotypes excluding serotype 4 or a 489 bp DNA fragment in all serotypes including serotype 4. Primers specific to the capsular polysaccharide biosynthesis regions of A. pleuropneumoniae serotypes 1, 2, and 8 amplified a 1.6 kb, a 1.7 kb, and 970 bp fragment in the respective serotype. This PCR assay detects A. pleuropneumoniae and identifies serotypes 1, 2, and 8. / Master of Science

Lygus Hahn (Hemiptera: Miridae) are serious pests of economically important field, fruit, vegetable, and greenhouse crops in Canada. The release of European Peristenus Förster (Hymenoptera: Braconidae) in the USA has resulted in significant suppression of this pest and has renewed interest in the release of European Peristenus spp. in Canada. Prior to the release of exotic Peristenus spp., ecological host range studies need to be conducted to define their habitat and host associations. <p>These associations can be difficult to study using conventional methods. Morphological similarity of related parasitoids prevents species-level identification by dissection. Host rearing is time-consuming and can result in high levels of host and parasitoid mortality. To facilitate identification of immature Peristenus spp. in their hosts, a multiplex PCR assay was developed. This assay provided a specific and sensitive tool to screen individual insects for three parasitoid species simultaneously. <p>To validate the utility of the multiplex PCR assay in ecological host range studies, parasitism and parasitoid species composition obtained using conventional and molecular techniques were compared. Molecular methods compared favorably with conventional methods; however, more complete species composition information was available with the multiplex assay. To improve the quality of risk assessment studies and extract the most accurate ecological host range data, molecular methods were used to evaluate host-parasitoid associations in mirid populations collected in two ecoregions. Several new host-parasitoid associations were recorded for <i>P. digoneutis</i> and <i>P. relictus</i>, but parasitism of non-target mirids was low. <p>Parasitism of the target host collected from different plant species was evaluated to help clarify Peristenus host-plant associations. Despite the investigation of three different host plant species, no difference was observed in the parasitism level or parasitoid species composition in <i>L. rugulipennis</i>. The post-release utility of the multiplex assay was investigated in Canada, where Lygus parasitoids may have dispersed following release in the USA. To confirm establishment, samples were analyzed using the multiplex PCR assay, and P. digoneutis was detected for the first time in southern Ontario.

Lygus Hahn (Hemiptera: Miridae) are serious pests of economically important field, fruit, vegetable, and greenhouse crops in Canada. The release of European Peristenus Förster (Hymenoptera: Braconidae) in the USA has resulted in significant suppression of this pest and has renewed interest in the release of European Peristenus spp. in Canada. Prior to the release of exotic Peristenus spp., ecological host range studies need to be conducted to define their habitat and host associations. <p>These associations can be difficult to study using conventional methods. Morphological similarity of related parasitoids prevents species-level identification by dissection. Host rearing is time-consuming and can result in high levels of host and parasitoid mortality. To facilitate identification of immature Peristenus spp. in their hosts, a multiplex PCR assay was developed. This assay provided a specific and sensitive tool to screen individual insects for three parasitoid species simultaneously. <p>To validate the utility of the multiplex PCR assay in ecological host range studies, parasitism and parasitoid species composition obtained using conventional and molecular techniques were compared. Molecular methods compared favorably with conventional methods; however, more complete species composition information was available with the multiplex assay. To improve the quality of risk assessment studies and extract the most accurate ecological host range data, molecular methods were used to evaluate host-parasitoid associations in mirid populations collected in two ecoregions. Several new host-parasitoid associations were recorded for <i>P. digoneutis</i> and <i>P. relictus</i>, but parasitism of non-target mirids was low. <p>Parasitism of the target host collected from different plant species was evaluated to help clarify Peristenus host-plant associations. Despite the investigation of three different host plant species, no difference was observed in the parasitism level or parasitoid species composition in <i>L. rugulipennis</i>. The post-release utility of the multiplex assay was investigated in Canada, where Lygus parasitoids may have dispersed following release in the USA. To confirm establishment, samples were analyzed using the multiplex PCR assay, and P. digoneutis was detected for the first time in southern Ontario.

The multiplex PCR experiment is to amplify multiple regions of a DNA sequence at the same time by using different primer pairs. Although, in recent years, there are lots of methods for PCR primer design, only a few of them focus on the multiplex PCR primer design. The multiplex PCR primer design is a tedious task since there are too many constraints to be satisfied. A new method for multiplex PCR primer design strategy using genetic algorithm is proposed. The proposed algorithm is able to find a set of suitable primer pairs more efficient and uses a MAP model to speed up the examination of the specificity constraint. The dry-dock experiment shows that the proposed algorithm finds several sets of primer pairs for multiplex PCR that not only obey the design properties, but also have specificity.

No presente trabalho, foi realizada uma MULTIPLEX-PCR para a detecção do DNA bacteriano de S. agalactiae, S.pneumoniae, N. meningitidis, H. influenzae e outros possíveis agentes etiológicos bacterianos das meningites. Este ensaio combina cinco diferentes iniciadores que detectam simultaneamente o gene crtA de N. meningitidis, o gene p6 de H. influenzae, o gene fbsA de S. agalactiae, o gene lytA de S. pneumoniae e o gene universal 16S rDNA para identificar a presença de agente bacteriano. Foram analisadas 447 amostras de LCR, o ensaio detectou 27 amostras positivas para cultura bacteriana e 13 amostras com resultado de cultura negativa. Estas amostras com cultura negativa apresentavam alterações bioquímicas, hematológicas, imunológicas ou microbiológicas (bacterioscopia) sugestivas de meningite, estes dados auxiliaram na análise dos resultados do MULTIPLEX-PCR. Este ensaio não apresentou reações inespecíficas com fungos, vírus e com outros agentes bacterianos testados (amplificando somente o gene 16S rDNA). A MULTIPLEX-PCR é um ensaio rápido, confiável, de fácil execução e facilmente implementável para a confirmação de meningite bacteriana. E este método pode auxiliar no diagnóstico de meningite com cultura de LCR negativa, particularmente para pacientes que previamente iniciaram antibioticoterapia e no diagnostico diferencial de meningite bacteriana ou viral. / In this work, a MULTIPLEX-PCR has conducted for the bacterial DNA detection of S. agalactiae, S.pneumoniae, N. meningitidis, H. influenza and other possible etiologic bacterial meningitis agents. This test combines five different primers that detect simultaneously the crtA gene of N. meningitides, the p6 gene of H. influenza, the fbsA gene of S. agalactiae, the lytA gene of S. pneumoniae and the 16S rDNA universal gene to identify the presence of bacterial agent. From the 447 samples of CSF that were analyzed, the test detected 27 positive samples for bacterial culture and 13 samples with the result of negative culture. These negative culture samples presented biochemical changes, hematological, immunological or microbiological (bacterioscopy) suggestive of meningitis, these data helped in the analysis of the MULTIPLEX-PCR results. This test showed no nonspecific reactions with fungi, viruses and other bacterial agents tested (only amplifying the gene 16S rDNA). The MULTIPLEX-PCR test is a fast, reliable, easy to implement and easily implementable for of bacterial meningitis confirmation. And this method can aid in the meningitis diagnosis with negative culture of CSF, particularly for patients who previously started antibiotic therapy and in the differential diagnosis of bacterial or viral meningitis.

S. pneumoniae coloniza a nasofaringe e é um dos principais agente de otite média, pneumonia, bacteremia e meningite com altas taxas de morbidade e mortalidade. Estima-se que 1,6 milhões de pessoas morram de doença pneumocócica por ano, a maioria crianças menores de cinco anos de idade, principalmente em países em desenvolvimento. A cápsula polissarídica antifagocitária é o principal fator de virulência deste microrganismo e determina os 93 sorotipos conhecidos, sendo o alvo de vacinas pneumocócicas. No presente trabalho foi padronizada a tipagem molecular por Multiplex PCR de S. pneumoniae, que compreende 30 pares de iniciadores agrupados em seis reações sequenciais. Foram tipadas 270 cepas de pneumococo isoladas entre janeiro de 2005 a setembro de 2011, proveniente de líquor (13%), sangue (76%) e líquido pleural (11%) de 232 pacientes atendidos no Hospital Universitário da USP. Além disso, a caraterização dessas amostras quanto ao perfil de sensibilidade aos antimicrobianos e à diversidade foi realizada, segundo o CLSI 2011 e a genotipagem molecular pelas técnicas de Multilocus Sequencie Typing Scheme (MLST) e Pulsed Field Eletrophoresis Gel (PFGE), respectivamente. A tipagem por Multiplex PCR detectou 24 sorotipos/sorogrupos diferentes, que foram: 14 (22%), 5 (12%), 12F/A (11%), 6A/B/C (10%), 7F/A (5%), 1 (4%), 3 (4%), 10A (4%), 19A (4%), 18 A/B/C/F (3%), 4 (3%), 8 (3%), 23F (3%), 19F (3%) e outros (9%) (9V/A, 9N/L, 15A, 22F, 11A/D, 31, 38, 34, 16F, 17F e não tipável). Este método apresentou 100% de especificidade e 98% de sensibilidade para determinação de sorogrupos e 66% para sorotipos. Os sorotipos 14, 6B, 5 e 19F foram significativamente mais comuns em criança até dois anos, já entre adultos, os sorotipos 5 e 12F foram os predominantes. O perfil de sensibilidade em infecções não meníngeas foi de 99% de sensibilidade e 1% de resistência intermediária para penicilina e ceftriaxona. Para infecções meníngeas os resultados mostraram 73% de sensibilidade e 27% de resistência para penicilina e 88% de sensibilidade e 12% de resistência intermediária para ceftriaxona. A resistência aos beta-lactâmicos está ligada principalmente ao sorotipo 14 que foi o sorotipo mais isolado com 52 cepas e dessas foram realizados MLST e PFGE. No MLST encontramos 51 cepas pertencentes ao clone Spain9V-3 (ST 156) que é predominante na região sul e sudeste do Brasil e uma cepa com um tipo de sequência ainda não depositada. Pela técnica de PFGE foram detectados três clusters e quatro amostras não relacionadas, o cluster A foi predominante com 41(79%) cepas com 81,7% de similaridade entre elas. A técnica de Multiplex PCR demonstrou ser excelente ferramenta para a detecção dos sorotipos/sorogrupos de S. pneumoniae. Não foi detectada resistência plena à penicilina e ceftriaxona em infecções não meníngeas consolidando a importância do uso da penicilina no tratamento da doença pneumocócica não meníngea. Houve grande similaridade genética entre cepas de S. pneumoniae sorotipo 14. / S.pneumoniae colonizes the nasopharynx and is a major agent of otitis media, pneumonia, bacteremia and meningitis with high morbidity and mortality. It is estimated that 1.6 million people die of pneumococcal disease every year, mostly children under five years old, mainly in developing countries. The antiphagocytic polissarídica capsule is the main virulence factor of this organism and determine the 93 serotypes known for being the target of pneumococcal vaccines. In the present study was standardized molecular typing by Multiplex PCR molecular typing, which comprises 30 primer pairs grouped into six sequential reactions. We performed antimicrobial susceptibility profile, according to the CLSI 2011 and the most frequent serotype was made by molecular genotyping techniques Multilocus Sequence Typing (MLST) and pulsed-field gel Eletrophoresis (PFGE). We studied 270 pneumococcal strains isolated from 2005 to September 2011, from CSF (13%), blood (76%) and pleural fluid (11%) of 232 patients attended at University Hospital of USP. Typing by Multiplex PCR detected 24 serotypes / serogroups different, which were: 14 (22%), 5 (12%), 12F / A (11%), 6A/B/C (10%), 7F / A (5 %), 1 (4%), 3 (4%), 10A (4%), 19A (4%), 18 A / B / C / F (3%), 4 (3%), 8 (3% ), 23F (3%), 19F (3%) and others (9%) (9V / A, 9N / L, 15A, 22F, 11A / D, 31, 38, 34, 16F, 17F and nontypable). This method showed 100% specificity and 98% sensitivity for the determination of 66% for serogroups and serotypes. Serotypes significantly more common in children under two years were: 14, 6B, 5 and 19F among adults serotypes 5 e12F were predominant. The sensitivity profile in non-meningeal infections was 99% sensitivity and 1% penicillin intermediate resistance to ceftriaxone. For meningeal infections the results showed 73% sensitivity and 27% resistance to penicillin and 88% sensitivity and 12% intermediate resistance to ceftriaxone. Resistance to beta-lactams is linked mainly to serotype 14 was the serotype most isolated, and of these 52 strains were performed MLST and PFGE. MLST found in 51 strains belonging to clone Spain9V-3 (ST 156) which is prevalent in south and southeastern Brazil and a strain with a type of sequence is not deposited. The technique of PFGE found three clusters and four non-related samples, cluster A predominated with 41 (79%) strains with 81.7% similarity between them. Multiplex PCR technique proved to be an excellent tool for the detection of serotypes/serogroups of S. pneumoniae. We did not detect full resistance to penicillin and ceftriaxone in non-meningeal infections showing the importance of use of penicillin in the treatment of pneumococcal non-meningeal disease. There was great genetic similarity among strains of S. pneumoniae serotype 14.

No presente trabalho, foi realizada uma MULTIPLEX-PCR para a detecção do DNA bacteriano de S. agalactiae, S.pneumoniae, N. meningitidis, H. influenzae e outros possíveis agentes etiológicos bacterianos das meningites. Este ensaio combina cinco diferentes iniciadores que detectam simultaneamente o gene crtA de N. meningitidis, o gene p6 de H. influenzae, o gene fbsA de S. agalactiae, o gene lytA de S. pneumoniae e o gene universal 16S rDNA para identificar a presença de agente bacteriano. Foram analisadas 447 amostras de LCR, o ensaio detectou 27 amostras positivas para cultura bacteriana e 13 amostras com resultado de cultura negativa. Estas amostras com cultura negativa apresentavam alterações bioquímicas, hematológicas, imunológicas ou microbiológicas (bacterioscopia) sugestivas de meningite, estes dados auxiliaram na análise dos resultados do MULTIPLEX-PCR. Este ensaio não apresentou reações inespecíficas com fungos, vírus e com outros agentes bacterianos testados (amplificando somente o gene 16S rDNA). A MULTIPLEX-PCR é um ensaio rápido, confiável, de fácil execução e facilmente implementável para a confirmação de meningite bacteriana. E este método pode auxiliar no diagnóstico de meningite com cultura de LCR negativa, particularmente para pacientes que previamente iniciaram antibioticoterapia e no diagnostico diferencial de meningite bacteriana ou viral. / In this work, a MULTIPLEX-PCR has conducted for the bacterial DNA detection of S. agalactiae, S.pneumoniae, N. meningitidis, H. influenza and other possible etiologic bacterial meningitis agents. This test combines five different primers that detect simultaneously the crtA gene of N. meningitides, the p6 gene of H. influenza, the fbsA gene of S. agalactiae, the lytA gene of S. pneumoniae and the 16S rDNA universal gene to identify the presence of bacterial agent. From the 447 samples of CSF that were analyzed, the test detected 27 positive samples for bacterial culture and 13 samples with the result of negative culture. These negative culture samples presented biochemical changes, hematological, immunological or microbiological (bacterioscopy) suggestive of meningitis, these data helped in the analysis of the MULTIPLEX-PCR results. This test showed no nonspecific reactions with fungi, viruses and other bacterial agents tested (only amplifying the gene 16S rDNA). The MULTIPLEX-PCR test is a fast, reliable, easy to implement and easily implementable for of bacterial meningitis confirmation. And this method can aid in the meningitis diagnosis with negative culture of CSF, particularly for patients who previously started antibiotic therapy and in the differential diagnosis of bacterial or viral meningitis.

In der molekularen Diagnostik besteht ein Bedarf an schnellen und spezifischen Testsystemen, die entweder für die Labordiagnostik oder in Point of Care-Umgebungen eingesetzt werden können. Um dieses Ziel zu erreichen, stehen die Miniaturisierung und Parallelisierung im Mittelpunkt des Forschungsinteresses. Die führende Methode im Bereich der DNA-Analytik ist derzeit die Realtime-PCR. Dieser Technologie sind hinsichtlich der Multiplexfähigkeit technologischen Hürden gesetzt, da derzeit nur eine Analyse von maximal vier Parametern parallel in einem Versuchsansatz erfolgen kann. Microarrays stellen hingegen die benötigten Voraussetzungen zur Verfügung, um als Werkzeuge für die Multiparameteranalyse in verschiedensten Anwendungsbereichen zu dienen. Ein Schwerpunkt dieser Arbeit war es, Multiplex-PCRs und diagnostische Microarrays zu entwickeln, die für analytische Fragestellungen eine schnelle und zuverlässige Multiparameteranalytik ermöglichen, um die bisherigen Einschränkungen aktueller Nachweisverfahren zu vermeiden. Als Anwendungen wurden zum einen ein Nachweissystem für acht relevante Geflügelpathogene zur Überwachung in der Geflügelzucht, zum anderen ein Nachweissystem zur Identifikation potentiell allergener Lebensmittelinhaltstoffe entwickelt. Neben der Entwicklung geeigneter PCR und Multiplex-PCR-Verfahren sowie spezifischer Microarrays für die Detektion der gesuchten Zielsequenzen stand auch die weiterführende Integration von DNA-Amplifikation und Microarray-Technologie im Fokus dieser Arbeit. Die OnChip-Amplifikation stellt eine Möglichkeit dar, um DNA-Analytik und Detektion in einem Reaktionsschritt zu integrieren. Entsprechend wurden die in der Arbeit entwickelten PCR- und Multiplex-PCR-Verfahren zum Nachweis potentieller allergener Lebensmittelinhaltsstoffe für die OnChip-Amplifikation adaptiert und Reaktionsbedingungen getestet, die eine Multiparameteranalyse auf dem Chip ermöglichen. Die entwickelten OnChip-PCR-Verfahren zeigten eine hohe Spezifität sowohl in Single- als auch in der Multiplex-OnChip-PCR. Eine Sensitivität von 10 Kopien bzw. <10ppm konnte in Single-OnChip-PCRs für den Nachweis allergener Lebensmittelinhaltsstoffe gezeigt werden. In Multiplex-OnChip-PCRs konnten 10-100ppm allergene Verunreinigungen spezifisch in unterschiedlichen Lebensmitteln nachgewiesen werden. Ein weiterer Schritt in Richtung einer möglichen Verwendung im Point of Care-Bereich stellt der Einsatz eines isothermalen Amplifikationsverfahrens dar. Vorteil eines solchen Verfahrens ist die Möglichkeit, auf das ansonsten benötigte Thermocycling zu verzichten. Dies vereinfacht eine Integration der OnChip-Amplifikation in mobile Analysegeräte oder Lab on Chip-Systeme und qualifiziert das Verfahren für den Einsatz in Point of Care-Umgebungen. In dieser Arbeit wurde eine noch junge isothermale Amplifikationsmethode, die helikase-abhängige Amplifikation (HDA), hinsichtlich ihrer Eignung für die Integration auf einem Microarray getestet. Hierfür konnte die bislang erste OnChip-HDA für Einzel- und Duplex-Nachweise von Pathogenen entwickelt werden. / In molecular diagnostics there is a need for fast and specific assay systems that could be used in the clinics and in point of care settings alike. Therefore miniaturisation and parallelisation are in the main focus of current assay development researches. The current gold standard for DNA analytics is the realtime PCR. However, this technology has its restraints in context to multiplex analysis. With the currently available technology an efficient multiplexing is only possible for four different targets per analysed sample. Microarrays in contrast offer the needed multiplex capabilities and have advanced to capable tools used in multiple fields of application. One focus of this work was the integration of Multiplex PCR and microarray technology, developing a microarray capable of analysing multiple parameters in one given sample, circumventing the problems and restraints of the exsisting technologies. As an example microarray assays for two different application fields were developed. One microarray assay for the detection of pathogens in poultry and another microarray assay for the detection of potentially allergenic food ingredients. Single- and Multiplex OnChip-PCR assays for both applications were developed and tested. OnChip-PCRs developed in this work showed high specificity in Single- and Multiplex-OnChip amplifications. The sensitivity was in the range of 10 DNA copies or 10ppm respectively for Single-OnChip-PCR in experiments for the detection of allergenic food contaminations. In Multiplex-OnChip-PCR experiments 100 DNA copies or 100ppm of food contaminents could be detected in different food matrices. A further focus of this work was the adaption of the OnChip amplification for the use in Point of Care settings. Isothermal amplification is a promising approach having the advantage of avoiding the thermocycling needed in the PCR. This opens up certain opportunities for the development of smaller, more flexible mobile diagnostic analysis devices. In this work we have evaluated the helicase dependent amplification (HDA) in terms of usability in OnChip amplification. In this work it was shown for the first time that HDA could be used for the detection of different pathogens in an Duplex-OnChip-PCR, showing the potential of this technology for integration in Point of Care settings.

Beta lactam resistance producing isolates of Enterobacteriacea and non-Enterobacteriacea have emerged since more than seventy years ago (Abraham and Chain, 1940). They are known to cause both community and hospital-acquired infections. Resistance against carbapenem is primarily mediated by the production of enzymes that destroy the beta lactam antimicrobials, which are produced by these isolates involving the expression of serine and metalobetalactamase genes KPC, IMP, VIM, NDM-1 and OXA-48. Quinolone resistance is predominanty mediated by mutations in the qnrA, qnrB, qnrS, and aac-6-Ib genes. Carbapenemase-producing organisms especially Klebsiella pneumoniae carbapenemases (KPCs) emerged as important pathogens especially among critically ill patients causing significant morbidity and mortality. This study aims to determine the prevalence and types of 15 quinolone resistance and carbapenemases genes among different isolates from patients admitted to the University Hospital of Leipzig over a period of ten months. During the period from January 2011 through October 2011, a total of 50 carbapenemases isolates were recovered from patients of the University Hospital of Leipzig/ Germany. The isolates were identified by biochemical tests and their susceptibility to antimicrobials was determined by the microbroth dilution method according to ISO standard. The KPC, IMP, VIM, OXA-48, NDM-1, and aac-6-Ib genes as well as qnrA, qnrB, and qnrS genes were detected by multiplex PCR, respectively. Results showed that KPC gene was detected in 82% of the isolates while 8% were KPC negative. The qnrA, qnrS, IMP, NDM-1, and OXA-48 genes were not detected in any of the isolates while qnrB and VIM genes were found in 2%. On the other hand, aac-6-Ib gene was the most prevalent gene among the study isolates and composed a percentage of 96%. Results also showed that KPC, and aac-6-Ib genes were detected in isolates collected from urine, blood, wounds, swabs, sputum, tracheal secretions, biopsies, and anal smears, while VIM gene was detected in one isolate collected from blood. The qnrB gene was found in one isolate collected from urine specimen. The wide spread of carbapenem and quinolone resistance-producing organisms is a critical problem that complicates the treatment of infections resulting from these organisms. Necessary measures must, therefore, be taken to limit their spread, which include appropriate antibiotic treatment, control of hospital infections, observe of personal hygiene, and the use of appropriate methods of sterilization and disinfection to prevent the dissemination of these organisms. Keywords: Resistance, carbapenemases, QRDR, multiplex PCR, antimicrobials