Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniversitet, 2009. / Härtill 4 uppsatser.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniv., 2009. / Härtill 5 uppsatser.

Tuberculosis (TB) is the most common opportunistic infection in HIV-infected patients and the emergence of drug-resistant tuberculosis (DR-TB) is a growing problem in resource-limited settings (RLS). TB diagnosis in most RLS still depends on smear microscopy for acid-fast bacilli (AFB) while adequate infrastructure for testing drug sensitivity is unavailable. However, molecular diagnostics that detect Mycobacterium tuberculosis (Mtb) DNA and its genetic markers of drug resistance were recently developed. In this thesis I describe the use of a molecular diagnostic, Genotype MTBDRplus, for characterizing DR-TB and patterns of tuberculosis-like infection in two cities in south-west and north-central Nigeria. I found high rates of DR-TB in Nigerian HIV-infected individuals (9.3% for RIF or INH) with significantly different amounts by location (18.18% in south-west vs. 3.91% in north-central Nigeria, p=0.01). RIF resistance, indicative of MDR-TB, was found in 5.52% treatment-naïve patients, far exceeding the WHO predictions (0-4.3%). Furthermore, RIF resistance was genetically distinct, suggesting location-specific transmission of drug resistance (p=0.04). Genotype MTBDRplus correctly identified the drug-resistant samples compared to sequencing in 96.8% of cases. Mtb was confirmed in 56% of patients and was less likely to be found in patients on ART, while controlling for other relevant demographic characteristics (OR 0.29, P=0.02). Only abnormal respiratory findings on auscultation and the direct sputum smear grade greater than 3/100 were significant predictors of Mtb infection (OR 3.28, P=0.03; OR 6.40, p<0.01 respectively). Concentrated sputum smear was not significantly correlated with Mtb infection, except at the highest grades (>2+). Furthermore, in 49% of samples that were not confirmed for Mtb other actinomycetes were found: atypical Mycobacteria (ATM), Rhodococcus spp., Nocardia spp., Corynebacterium spp. I conclude that concentrated sputum AFB smears may misidentify bacteria as Mtb in a subset of HIV-infected patients. These individuals may have a different, even uncharacterized, actinomycete infection in the respiratory tract. Furthermore, total DR-TB in HIV-infection is high and transmission of DR-TB in HIV-infected patients in Nigeria is higher than estimated by the WHO. Molecular diagnostics are a rapid method for identifying Mtb and monitoring DR-TB, and can guide appropriate treatment decisions for respiratory infections in RLS with a high HIV burden.

Εισαγωγή: Η κλινική πορεία της οξείας παγκρεατίτιδας (ΟΠ) αντανακλά την ένταση της φλεγμονώδους αντίδρασης και ταξινομείται σε ήπια ΟΠ (ΗΟΠ) και βαριά ΟΠ (ΒΟΠ). Η έκφραση του γονιδίου της χημειοτακτικής πρωτεΐνης των μονοκυττάρων (MCP-1) επηρεάζεται από έναν A/G πολυμορφισμό (-2518) με το G αλληλόμορφο να αυξάνει την παραγωγή της MCP-1. Παχύσαρκοι ασθενείς εμφανίζουν αυξημένο κίνδυνο για επιπλοκές από ΟΠ. Το σύστημα APACHE-O έχει προταθεί ότι βελτιώνει την ακρίβεια του συστήματος APACHE-ΙΙ στην πρόγνωση της ανάπτυξης ΒΟΠ. Στόχοι: 1) Να διευκρινίσουμε αν ο πολυμορφισμός στο γονίδιο της MCP-1 στη θέση -2518 επηρεάζει την βαρύτητα της ΟΠ, 2) αν το σύστημα APACHE-O βελτιώνει την προγνωστική αξία του συστήματος APACHE-ΙΙ και 3) να διερευνήσουμε την υπόθεση ότι οι παχύσαρκοι ασθενείς βρίσκονται σε αυξημένο κίνδυνο για την ανάπτυξη ΒΟΠ λόγω της μεγαλύτερης φλεγμονώδους απόκρισης που παρουσιάζουν στην παγκρεατική προσβολή. Μέθοδοι: Μελετήθηκαν 102 ασθενείς με ΟΠ και 116 άτομα αποτέλεσαν την ομάδα των υγιών μαρτύρων. Ο A/G γονότυπος της MCP-1 ανιχνεύθηκε με την μέθοδο της αλυσιδωτής αντίδρασης της πολυμεράσης και με προσδιορισμό της αλληλουχίας του DNA. Τα επίπεδα της MCP-1 στον ορό μετρήθηκαν με φθορίζουσα ανοσολογική μέθοδο. Υπολογίσθηκαν οι καμπύλες ROC των συστημάτων APACHE-II και APACHE-O. Η παχυσαρκία και άλλες κλινικές παράμετροι εκτιμήθηκαν ως παράγοντες κινδύνου για την ανάπτυξη ΒΟΠ με τη χρήση ανάλυσης λογισμικής παλινδρόμησης. Συγκρίναμε τα επίπεδα των IL-6, MCP-1 και CRP στον ορό και των κριτηρίων του Ranson σε παχύσαρκους και μη-παχύσαρκους ασθενείς με ΟΠ. Αποτελέσματα: 19 ασθενείς ανέπτυξαν ανεπάρκεια οργάνων και ταξινομήθηκαν ως ΒΟΠ. Οι ασθενείς με ΒΟΠ βρέθηκαν να έχουν σημαντικά υψηλότερο ποσοστό του G αλληλομόρφου (86%) σε σχέση με τους ασθενείς με ΗΟΠ (46%) (p<0,007). Οι ασθενείς με ΒΟΠ είχαν επίσης υψηλότερα επίπεδα της MCP-1 στον ορό σε σχέση με τους ασθενείς με ΗΟΠ (p=0,002). Το 28% των ασθενών ήταν παχύσαρκοι (BMI >30). Τα συστήματα APACHE-O (AUC: 0,895) και APACHE-ΙΙ (AUC: 0,893) έδειξαν παρόμοια ακρίβεια στην πρόγνωση της ανάπτυξης ΒΟΠ. Η παχυσαρκία βρέθηκε να αποτελεί παράγοντα κινδύνου για την ανάπτυξη ΒΟΠ (OR: 2,8, p=0,048) και θνητότητας (OR: 11,2, p=0,022). Τα επίπεδα της CRP (p=0,0001) και τα κριτήρια Ranson (p=0,021) βρέθηκαν σημαντικά υψηλότερα στους παχύσαρκους ασθενείς. Τα επίπεδα των IL-6 και MCP-1 βρέθηκαν υψηλότερα στους παχύσαρκους ασθενείς, χωρίς όμως να είναι στατιστικώς σημαντικά. Συμπεράσματα: Το -2518 G αλληλόμορφο της MCP-1 αποτελεί παράγοντα κινδύνου για την ανάπτυξη ΒΟΠ. Τα επίπεδα της MCP-1 δείχνουν να αποτελούν ακριβή προγνωστικό δείκτη για την ανάπτυξη ΒΟΠ και θανάτου. Η παχυσαρκία αποτελεί επίσης ανεξάρτητο παράγοντα κινδύνου για την ανάπτυξη ΒΟΠ. Το σύστημα APACHE-O κατά την εισαγωγή των ασθενών δεν είναι πιο ακριβές από το σύστημα APACHE-ΙΙ. Τα αποτελέσματα της μελέτης μας προτείνουν ότι η παχυσαρκία αυξάνει την βαρύτητα της ΟΠ λόγω της μεγαλύτερης ανοσολογικής απόκρισης στην παγκρεατική προσβολή. / Background: Acute pancreatitis (AP) reflects the intensity of the inflammatory response and is divided into mild AP (MAP) or severe AP (SAP). Monocyte chemotactic protein-1 (MCP-1) gene expression is altered by an A/G polymorphism (-2518), with the G allele increasing MCP-1 production. Obese patients appear to be at risk for complications of AP. APACHE-O score has been suggested to improve APACHE-II accuracy in predicting severe outcome in AP. Aims: Τo determine whether: 1) the MCP-1 −2518 A/G polymorphism affects the severity of AP, 2) if APACHE-O score adds any predictive value to APACHE-II score and 3) to test the hypothesis that obese patients are at increased risk of SAP because of a more intense inflammatory response to pancreatic injury. Methods: 102 consecutive AP patients and 116 controls were evaluated. The A/G genotype was evaluated by polymerase chain reaction amplification and DNA sequencing. MCP-1 serum levels were quantified using a fluorescence bead-based immunoassay. Receiver operating curves (ROC) for prediction of SAP were calculated using admission APACHE-II and APACHE-O scores. Binary logistic regression was performed to assess if obesity is a risk for SAP and to determine the clinical factors associated with severe disease. Serum levels of IL-6, MCP-1 and CRP as well as Ranson’s scores were compared between obese and non-obese patients. Results: Nineteen patients developed organ dysfunction and were classified as SAP. Patients with SAP had a significantly greater proportion of the G allele (86%) than did MAP patients (46%) (p<0.007). As predicted by the genotype, the serum MCP-1 levels were significantly higher in the SAP patients when compared with the MAP patients (p=0.002). Using a body mass index (BMI) >30, 28% of the subjects were obese. Admission APACHE-O (Area under the curve AUC: 0.895) and APACHE-II (AUC: 0.893) showed similar accuracy in predicting severe outcome. BMI>30 was identified as a significant risk for SAP (OR: 2.8, p=0.048) and mortality (OR: 11.2, p=0.022). CRP levels were significantly higher in obese AP patients (p=0.0001) as well as Ranson’s score (p=0.021). IL-6 and MCP-1 levels were higher in obese patients but did not reach statistical significance. Conclusions: MCP-1 −2518 G allele is a risk factor for severe AP. MCP-1 serum levels, measured early in the course of AP, appear to be an accurate predictor of severity of acute pancreatitis and death. Obesity is an independent risk for severe acute pancreatitis. Admission APACHE-O score is not more accurate than APACHE-II score. Our study results suggest that obesity increases the severity of AP by amplifying the immune response to injury.

The ‘Blood-Type’ diet advises individuals to eat according to their ABO blood group to optimize health without the support of science evidence. The objective of this study was to determine whether consumption of a diet in accordance with an individual’s ABO genotype is associated with various biomarkers of cardiometabolic health. Study subjects (n=1,455) were participants of the Toronto Nutrigenomics and Health study. Dietary intake was assessed using a one-month, 196-item food frequency questionnaire and a diet score was calculated to determine relative adherence to each of the four blood type diets. ABO blood group was determined by genotyping rs8176719 and rs8176746 in the ABO gene. The results show that adherence to the Type-A, Type-AB, and Type-O diets were associated with favourable profile of certain cardiometabolic risk factors (P<0.05); however, these dietary effects were not dependent on someone’s ABO blood group. Therefore, the findings do not support the “Blood-Type” diet hypothesis

The ‘Blood-Type’ diet advises individuals to eat according to their ABO blood group to optimize health without the support of science evidence. The objective of this study was to determine whether consumption of a diet in accordance with an individual’s ABO genotype is associated with various biomarkers of cardiometabolic health. Study subjects (n=1,455) were participants of the Toronto Nutrigenomics and Health study. Dietary intake was assessed using a one-month, 196-item food frequency questionnaire and a diet score was calculated to determine relative adherence to each of the four blood type diets. ABO blood group was determined by genotyping rs8176719 and rs8176746 in the ABO gene. The results show that adherence to the Type-A, Type-AB, and Type-O diets were associated with favourable profile of certain cardiometabolic risk factors (P<0.05); however, these dietary effects were not dependent on someone’s ABO blood group. Therefore, the findings do not support the “Blood-Type” diet hypothesis

Hepatitis C virus (HCV) is a small single stranded RNA virus, that belongs to the Flaviviridae family. HCV can be classified into six major genotypes and more than 50 subtypes.

Darbo objektas – Alyvmedinių (Oleaceae) šeimos uosinių (Fraxinus) genties medis - paprastasis uosis (Fraxinus excelsior L.). Darbo tikslas – Išauginti in vitro paprastųjų uosių (Fraxinus excelsior L.), besiskiriančių džiūvimo laipsniu, palikuonis ir atlikti genetinės įvairovės įvertinimą. Darbo metodai – regeneravusių mikroūglių įvertinimas, palikuonių DNR nustatymas. Darbo rezultatai. Atlikus tyrimus įvertintos paprastojo uosio išauginimo in vitro sąlygos ir nustatyta genetinė įvairovė. Eksplantų sterilinimui tikslinga naudoti aseptinių tirpalų kombinaciją su „ACE“ ir AgNO3 0,2 proc., kad užtikrinti gyvybingų ir be užkrato eksplantų išlikimą. Aktyviausiai mikroūgliai regeneravo WPM (Woody Plant Medium) terpėje, kurios pH 5,0. Gyvybingiausi regenerantai atitinka mažiausiai pažeistą uosį pagal džiūvimo laipsnį. Sveikiausio genotipo uosių ex vitro sąlygomis adaptavosi 92 proc., labiausiai pažeisto - 53 proc. Tirtų dviejų paprastojo uosio individų turėjo skirtingus APPD fenotipus su naudotais dviem informatyviais pradmenimis. / The research object. – Oleaceae (Oleaceae) family of Ash (Fraxinus) tree of the genus - ash (Fraxinus excelsior L.). The aims of the study – Grown in vitro for common ash (Fraxinus excelsior L.), distinguished by the degree of drying, and a descendant of the genetic diversity assessment. Methods – regenerant microshoots evaluation of DNA detection. The results. After the tests evaluated in plain ash grown in vitro conditions and the genetic diversity. For explants sterile appropriate to use a combination of aseptic solutions with ACE and 0.2 percent AgNO3. to ensure the viability and survival of the explants without contamination. The most active shoots regenerate WPM (Woody Plant Medium) medium with pH 5.0. The most lively regenerants the least damaged ash according to the degree of drying. Healthiest genotype ashes of ex vitro specialized 92 percent. The most damaged - 53 percent. The results from two-ordinary ash individuals had different phenotypes APPD to use two informative primers.

In this thesis, the relationships between 17 traits including starch, fibre, culinary quality and agronomic parameters of potato were investigated. In two studies, 12 genotypes were grown at three locations in Ontario and 18 genotypes were grown at four locations in Manitoba, Ontario and New Brunswick. Genotype by environment interactions were significant for fibre and agronomic traits, except bake score and specific gravity. Correlations were found between some, but not all, starch, fibre and agronomic parameters. Several genotypes containing desirable starch, fibre and agronomic profiles with high stability were identified. Although no single genotype was superior in all analyzed traits, certain genotypes excelled in specific attributes. CV96044-3 had the best starch and fibre profile, but low yields compared to other cultivars. Three genotypes, CV96044-3, F04037 and Goldrush, may be useful parents in a breeding program to improve starch and fibre characteristics, producing cultivars containing all desirable traits. / AAFC, Agricultural Bioproducts Innovation Program, BioPotato Network

As genomic sequencing technologies continue to advance, researchers are furthering their understanding of the relationships between genetic variants and expressed traits (Hirschhorn and Daly, 2005). However, missing data can significantly limit the power of a genetic study. Here, the use of a regularized generalized linear model, denoted GLMNET is proposed to impute missing genotypes. The method aimed to address certain limitations of earlier regression approaches in regards to genotype imputation, particularly multicollinearity among predictors. The performance of GLMNET-based method is compared to the performance of the phase-based method fastPHASE. Two simulation settings were evaluated: a sparse-missing model, and a small-panel expan- sion model. The sparse-missing model simulated a scenario where SNPs were missing in a random fashion across the genome. In the small-panel expansion model, a set of test individuals that were only genotyped at a small subset of the SNPs of the large panel. Each imputation method was tested in the context of two data-sets: Canadian Holstein cattle data and human HapMap CEU data. Although the proposed method was able to perform with high accuracy (>90% in all simulations), fastPHASE per- formed with higher accuracy (>94%). However, the new method, which was coded in R, was able to impute genotypes with better time efficiency than fastPHASE and this could be further improved by optimizing in a compiled language.