No description available.

Ongoing work in the laboratory of Professor Chris Backhouse is aimed at developing a portable and inexpensive lab on a chip instrument. A system capable of molecular biology protocols including sample preparation (SP), polymerase chain reaction (PCR), and melting curve analysis (MCA) would meet the requirements for point of care genetic analysis. The SP, PCR, and MCA modules were designed and tested on a standalone basis and then integrated for analysis of raw clinical samples. An automated XY stage was developed for magnetic bead-based DNA purification. In addition, a LED/CCD-based optical detection module was employed for real time PCR and MCA. Data analysis algorithms and protocols were implemented to remove noise and interpret data. This work culminated in proof of principle on-chip SP-PCR-MCA to detect ß2m DNA from human buccal cells in a modular and inexpensive system. / Biomedical Engineering

<p>A new European labeling directive (2003/89/EC) states that certain foods and products derived thereof must always be declared. Among the tree nuts specified is Macadamia nut (Macadamia spp.). During the last few years, cases of IgE-allergic reactions, even severe anaphylaxes, have been reported. Reliable methods for the detection of this nut are needed.</p><p>Protein from Macadamia nuts was isolated. Polyacrylamide gel electrophoresis in SDS revealed two main protein bands of about 20 and 50kDa. These protein bands were cut and extracted from the gel and rabbits were immunized with each protein.</p><p>Immunoblotting showed dominant reactivity with the respective antigens. The antisera were further tested for specificity in immunodiffusion and in rocket immunoelectrophoresis.</p><p>In addition, a specific DNA-method was developed, based on Real-Time PCR using Macadamia vicilin as target sequence. Two different primer pairs were tested. Specificity was tested against potentially related nuts. Optimisation of primer and probe concentrations was performed. The limit of detection was 2-4 pg DNA, corresponding to a macadamia nut concentration of 50 to 100 μg per g. In a background of soybean DNA, down to 0,01 % macadamia DNA could be detected.</p>

A new European labeling directive (2003/89/EC) states that certain foods and products derived thereof must always be declared. Among the tree nuts specified is Macadamia nut (Macadamia spp.). During the last few years, cases of IgE-allergic reactions, even severe anaphylaxes, have been reported. Reliable methods for the detection of this nut are needed. Protein from Macadamia nuts was isolated. Polyacrylamide gel electrophoresis in SDS revealed two main protein bands of about 20 and 50kDa. These protein bands were cut and extracted from the gel and rabbits were immunized with each protein. Immunoblotting showed dominant reactivity with the respective antigens. The antisera were further tested for specificity in immunodiffusion and in rocket immunoelectrophoresis. In addition, a specific DNA-method was developed, based on Real-Time PCR using Macadamia vicilin as target sequence. Two different primer pairs were tested. Specificity was tested against potentially related nuts. Optimisation of primer and probe concentrations was performed. The limit of detection was 2-4 pg DNA, corresponding to a macadamia nut concentration of 50 to 100 μg per g. In a background of soybean DNA, down to 0,01 % macadamia DNA could be detected.

Background: Critically ill patients are at particular risk of developing bloodstream infection. Such infections are associated with the development of sepsis, leading to a marked increase in mortality rate. Early detection of the causative organism and appropriate antibiotic treatment are therefore critical for optimum outcome of patients with nosocomial infection. Current infection diagnosis is based on standard blood culture techniques. However, microbiological culture has a number of limitations, not least that it takes several days to confirm infection and is therefore not useful in directing the early treatment with antibiotics. New techniques based on the detection of pathogen DNA using real-time polymerase chain reaction (PCR) technology have the potential to address these limitations but their clinical utility is still to be proved. Objectives: Develop and evaluate novel PCR-based approaches to bloodstream infection diagnosis in critical illness based on detection and identification of bacterial and fungal DNA in blood. Methods: A range of commercial and 'in-house' PCR-based assays for detection of bacterial and fungal DNA were developed and/or optimised for use in clinical blood samples. These included LightCycler SeptiFast, a CE-marked multi-pathogen assay for common bloodstream pathogens, BactScreen and GramScreen, broad spectrum bacterial assays based on 16S rRNA gene and real-time PCR assays developed to detect a range of clinically important fungal pathogens. Novel approaches to speciation of pathogen DNA using melting temperature (Tm) profiling and high resolution melting analysis (HRMA) were developed. Clinical evaluation of assays was either on blinded clinical isolates or blood samples from critically ill patients with clinical suspicion of bloodstream infection against conventional microbiological culture. Several techniques aimed at improving extraction of pathogen DNA from blood were also investigated. Results: The CE-marked commercial assay SeptiFast showed analytical sensitivity and specificity of 79% and 83% respectively. Concordance with positive culture results was good but high levels of 'false positives' were detected possibly attributed to detection of free pathogen DNA not associated with viable pathogens. The predictive value of a negative SeptiFast test was 98% suggesting that absence of pathogen DNA is a strong indicator of absence of infection. Further studies were aimed at detailed optimisation and validation of 16S rRNA gene real-time PCR assays for bacterial DNA. BactScreen and GramScreen were able to detect a broad range of clinically important bacteria down to <50 CFU/ml blood. A preliminary comparative evaluation against SeptiFast showed BactScreen gave excellent concordance with blood culture results with minimal false positive results compared to SeptiFast. Efficient extraction of pathogen DNA was shown to be a key factor in determining analytical sensitivity and several protocols were evaluated. Low cost approaches to speciation of bacterial DNA were developed by combining broad range real-time PCR with HRMA. A novel HRMA method based on Tm profiling was shown to identify 89% and 96% of blinded clinical isolates at species or genus level respectively. Real-time PCR/HRMA approaches were also successfully developed for detection and identification of fungal pathogens including a range of Candida and Aspergillus species associated with bloodstream fungal infection. Conclusions: These studies have highlighted some of the key factors that need to be considered when developing and validating PCR based assays for pathogen DNA detection in blood. A set of novel tools have been developed for rapid detection and identification of bacterial and fungal pathogens that could address the challenges of infection diagnosis based on pathogen DNA detection. Further work is required, not least in development of more efficient pathogen DNA extraction and detailed clinical validation but the tools described here have the potential to provide cost effective solutions to aid infection diagnosis that would be complementary to current culture-based methods. The provision of time critical information could have a positive impact on clinical decision-making leading to more effective management and treatment of patients with suspected bloodstream infection.

Bakgrund: Den pågående pandemin COVID-19 orsakas av viruset SARS-CoV-2. Sedan december 2020 har nya varianter av viruset med betydande genetiska förändringar upptäckts, gemensamt benämnt varianter av särskild betydelse eller variants of concern (VOC). Just nu är det tre VOC som bevakas särskilt; B.1.1.7 (först upptäckt i Storbritannien), B.1.351 (först upptäckt i Sydafrika) respektive P.1 (först upptäckt i Brasilien). Den tidigaste statistiken från Folkhälsomyndigheten om förekomsten av VOC i Region Dalarna är från februari 2021. Förekomsten av VOC innan dess är fortfarande okänd. I regionen delas analysering av prover vid misstanke om COVID-19 in i de olika kategorierna patienter, vårdpersonal, smittspårning och allmänhet. Befintlig statistik om förekomsten av VOC grundar sig nästan enbart på förekomsten bland allmänhetens prover. Syfte: Syftet med denna studie var att undersöka förekomsten av SARS-CoV-2 varianter av särskild betydelse i prover tagna från patienter, vårdpersonal och smittspårningar under december 2020-januari 2021 i Region Dalarna. Studien syftade också till att undersöka när spridningen av respektive VOC kan ha startat i regionen. Metod: Provmaterialet bestod av SARS-CoV-2 positiva prov tagna inom analyskategorierna under tidsperioden. Prover analyserades med RT-PCR och smältkurvsanalys för detektion av VOC-karaktäristiska mutationer. Resultat: Ett fåtal fall av B.1.1.7 detekterades redan i december och en stigande andel av B.1.1.7 påvisades inom analyskategorierna under januari, som tecken på att en regional spridning kan ha startat vid tidpunkten. Endast ett fåtal fall av B.1.351 och/eller P.1 detekterades inom analyskategorierna under tidsperioden, vilket tyder på att en regional spridning av dessa ännu inte hade startat i januari. / Background: The ongoing pandemic COVID-19 is caused by the virus SARS-CoV-2. Since December 2020 new variants of the virus with significant mutations have been discovered, referred to as variants of concern (VOC). At the point, the occurrence of three VOC is especially monitored; B.1.1.7 (discovered in UK), B.1.351 (discovered in South Africa) and P.1 (discovered in Brazil). The earliest statistics about the occurrence of VOC in Region Dalarna, Sweden, is from February 2021 and the occurrence before that is still unknown. In the region analysis of specimen in case of suspected COVID-19 is divided into the different categories patients, healthcare-staff, infection tracing and public. Existing statistics is based almost exclusively on the occurrence of VOC in specimen from the public. Aim: The aim of this study was to examine the occurrence of SARS-CoV-2 VOC among specimens collected from patients, healthcare staff and infection tracing in Region Dalarna during December 2020-January 2021. The study also aimed to examine when the spread of each VOC started in the region. Method: SARS-CoV-2 positive specimen collected within the categories during the time was analyzed with RT-PCR and melting curve analysis for detection of VOC-characteristic mutations. Results: A few cases of B.1.1.7 was detected already in December and an increased percentage of B.1.1.7 was detected within the categories during January, suggesting that a regional spread started at the time. Only a few cases of B.1.351 and/or P.1 was detected within the categories, suggesting that a regional spread of these had not yet started in January.

No description available.

Das Ziel der Untersuchungen war einen möglichen Einfluss von Genpolymorphismen auf den postoperativen Verlauf kardiochirurgischer Patienten aufzudecken. Es wurde präoperativ das zu untersuchende Blut entnommen und zentrifugiert. Das überstehende Blutplasma diente der Bestimmung des Catecholaminspiegels mittels HPLC. Aus den korpuskulären Bestandteilen wurde die DNA isoliert und zur Genanalyse verwendet. Die Polymerase-Ketten-Reaktion mit anschließender Schmelzkurvenanalyse ermöglichte eine Differenzierung der 145A>G, 1165G>C β1-Adrenorezeptor- und 472G>A COMT-Polymorphismen. Der postoperative Verlauf der Patienten wurde bis zu deren Entlassung aufgezeichnet. Unter Betrachtung der einzelnen Polymorphismen zeigten sich Unterschiede im postoperativen Noradrenalinverbrauch, im postoperativen Gesamtcatecholaminverbrauch, in der Aufenthaltsdauer im Krankenhaus und im präoperativen Noradrenalinplasmaspiegel. Patienten mit dem 145G/X und 1165CC waren signifikant länger im Krankenhaus als die Träger des 145AA und 1165G/X. Der postoperative Noradrenalinverbrauch und Gesamtcatecholaminverbrauch unterlag der Beeinflussung der drei Polymorphismen. Die Träger des 145G/X, 1165G/X und 472GG hatten einen signifikant höheren Noradrenalinverbrauch als die 145AA, 1165CC und 472A/X Träger. Im zweiten Schritt der Analyse wurden die SNP-Kombinationen berücksichtigt. Es stellte sich heraus, dass sich unter Betrachtung dieser die zuvor festgestellten signifikanten Zusammenhänge auflösten. Demzufolge ist eine Betrachtung der SNP-Kombinationen wichtig um genetische Risiken identifizieren zu können und keine Risiken in Datensätze hinein zu interpretieren.

Das Ziel der Untersuchungen war einen möglichen Einfluss von Genpolymorphismen auf den postoperativen Verlauf kardiochirurgischer Patienten aufzudecken. Es wurde präoperativ das zu untersuchende Blut entnommen und zentrifugiert. Das überstehende Blutplasma diente der Bestimmung des Catecholaminspiegels mittels HPLC. Aus den korpuskulären Bestandteilen wurde die DNA isoliert und zur Genanalyse verwendet. Die Polymerase-Ketten-Reaktion mit anschließender Schmelzkurvenanalyse ermöglichte eine Differenzierung der 145A>G, 1165G>C β1-Adrenorezeptor- und 472G>A COMT-Polymorphismen. Der postoperative Verlauf der Patienten wurde bis zu deren Entlassung aufgezeichnet. Unter Betrachtung der einzelnen Polymorphismen zeigten sich Unterschiede im postoperativen Noradrenalinverbrauch, im postoperativen Gesamtcatecholaminverbrauch, in der Aufenthaltsdauer im Krankenhaus und im präoperativen Noradrenalinplasmaspiegel. Patienten mit dem 145G/X und 1165CC waren signifikant länger im Krankenhaus als die Träger des 145AA und 1165G/X. Der postoperative Noradrenalinverbrauch und Gesamtcatecholaminverbrauch unterlag der Beeinflussung der drei Polymorphismen. Die Träger des 145G/X, 1165G/X und 472GG hatten einen signifikant höheren Noradrenalinverbrauch als die 145AA, 1165CC und 472A/X Träger. Im zweiten Schritt der Analyse wurden die SNP-Kombinationen berücksichtigt. Es stellte sich heraus, dass sich unter Betrachtung dieser die zuvor festgestellten signifikanten Zusammenhänge auflösten. Demzufolge ist eine Betrachtung der SNP-Kombinationen wichtig um genetische Risiken identifizieren zu können und keine Risiken in Datensätze hinein zu interpretieren.