Magistrantūros studijų baigiamajame darbe pateikiami veiksnių, lemiančių pluoštinių linų morfogenezę in vitro, tyrimų duomenys. Darbo objektas – keturios pluoštinių linų veislės 'Dangiai', 'Sartai', 'Snaigiai' ir 'Vaižgantas'. Darbo metodai. Pluoštinių linų morfogenezei somatinių audinių kultūroje tirti naudoti hipokotilio eksplantai. Eksplantai auginti MS terpėje su skirtingais augimo reguliatorių kiekiais auginimo kambaryje. Vertintas pridėtinių pumpurų formavimosi dažnis (%) ir pridėtinių ūglių kiekis iš eksplanto (vnt.). Darbo rezultatai. Egzogeninių augimo reguliatorių priedas indukcijos terpėje daugeliu atvejų skatino tirtų pluoštinių linų veislių ūglių regeneraciją, tačiau optimali šio junginio koncentracija priklausė nuo genotipo. Iš tirtų pluoštinių linų veislių didžiausia morfogenine galia pasižymėjo veislės 'Vaižgantas' izoliuoti hipokotiliai. Priklausomai nuo genotipo ir maitinamosios terpės sudėties pluoštinių linų pridėtinių pumpurų formavimosi procesas hipokotilių kultūroje vyko 2,87-94,50 % dažniu regeneruojant 1,67-6,00 ūglius iš eksplanto. Efektyviam veislės 'Dangiai' ūglių regeneravimui maitinamąją terpę tikslinga papildyti 2,0 mg l-1 BAP + 0,1 mg l-1 NAR bei eksplantus paveikti 4 °C temperatūra 24 valandas. Veislės 'Sartai' izoliuotų hipokotilių audinių antrinę diferenciaciją skatino 72 valandų 7 °C temperatūros poveikis bei citokinino 1,0 mg l-1 2iP priedas maitinamojoje terpėje. Intensyviausiai veislės 'Snaigiai' eksplantai pumpurus formavo maitinamojoje... [toliau žr. visą tekstą] / The master work presents the results of fibre flax morphogenesis in vitro affecting factors. Object of the research − four fibre flax cultivars 'Dangiai', 'Sartai', 'Snaigiai' and 'Vaižgantas'. Research methods. To study fiber flax morphogenesis of somatic tissues hypocotyls were used as explant. Explants were placed on MS medium supplemented with different combinations of growth regulators and cultivated in growth chamber. The percentage of bud regeneration and the number of shoots per explant were evaluated. Research results. Exogenous growth regulators concentration in induction media increased fiber flax shoots regeneration, and therefore specific combination of growth regulators must be designed for each genotype. Among investigated genotypes, the hypocotyls of cultivars 'Vaižgantas' manifested the best morphogenic capability. Depending on genotype and medium composition fiber flax adventitious buds regeneration frequency varied from 2.87-94.50% and the number of shoots per explant reached 1.67-6.0, respectively. Hypocotyls of cultivar 'Dangiai' showed the best response on medium supplemented by 2.0 mg l-1 BAP with 0.1 mg l-1 NAA and pretreated by 4 °C temperature 24 hours. In the presence of only cytokinins, the highest mean value of regenerated shoots was observed on medium supplemented with 1.0 mg l-1 2iP and 72 hours 7 °C temperature pretreatment for hypocotyls of 'Sartai'. Growth regulators combination 2.0 mg l-1 2iP with 0.1 mg l-1 NAA and treatment by 4 °C... [to full text]

Magistrantūros studijų baigiamajame darbe pateikiama šilokų pridėtinių ūglių regeneracija lapų segmentų kultūroje, priklausomai nuo genotipo ir augimo reguliatorių maitinamojoje terpėje. Darbo objektas – Sedum rupestre ‛Angeline’, Sedum reflexum ‛Cristatum’, Sedum fosterianum ‛Elegans’, Sedum maximum ‛Autumn Joy’ lapų audiniai. Darbo metodai: izoliuoti eksplantai auginti Murashige ir Skoog (MS) maitinamojoje terpėje su skirtingais augimo reguliatorių kiekiais. Susiformavę pridėtiniai ūgliai įšaknydinti MS maitinamojoje terpėje su skirtingais augimo reguliatorių kiekiais. Vertintas ūglių susiformavimo dažnis (%), ūglių kiekis iš eksplanto (vnt.) ir įsišaknijimo dažnis (%). Darbo rezultatai. Veislių ‛Elegans’ ir ‛Cristatum’ ūglių susiformavimo dažnį labiausiai skatino 0,75 mg l-1 BAP. Veislės ‛Angeline’ didžiausias ūglių susiformavimo dažnis nustatytas terpėje, papildytoje 3,0 mg l-1 BAP. Veislės ‛Autum joy’ izoliuoti lapo segmentai 100 % dažniu ūglius formavo terpėse su 3,0 mg l-1 BAP + 0,5 mg l-1 NAR ir 4,0 mg l-1 BAP + 0,5 mg l-1 NAR. Veislės ‛Elegans’ didžiausias ūglių kiekis eksplantui gautas terpėje papildytoje 0,75 mg l-1 BAP. Veislės ‛Angeline’ daugiausia ūglių iš eksplanto susiformavo terpėse su 0,75 mg l-1 BAP ir 3,0 mg l-1 BAP. Terpėje, papildytoje 3,0 mg l-1 BAP gautas didžiausias veislės ‛Cristatum’ ūglių kiekis vienam eksplantui. Veislės ‛Autum joy’ eksplantai daugiausia ūglių suformavo terpėse, papildytose 3,0 mg l-1 BAP + 0,5 mg l-1 NAR ir 4,0 mg l-1 BAP + 0,5... [toliau žr. visą tekstą] / The master work presents orpine adventitious shoots regeneration in leaves segments cultures, depending on genotype and growth regulators in the culture medium. Object of the work – Sedum rupestre ‛Angeline’, Sedum reflexum ‛Cristatum’, Sedum fosterianum ‛Elegans’, Sedum maximum ‛Autumn Joy’ leaves tissues. Method of the work – isolated explants were growing on Murashige ir Skoog (MS) nutrition medium with different content of growth regulators. Adventitious shoots were transferred to MS culture medium for rhizogenesis induction. Shoots formation frequency, number of shoots per explant and rooting frequency were evaluated. The results of work. The highest shoots formation frequency of orpine varieties ‛Elegans’ and ‛Cristatum’ has been obtained under influence of 0.75 mg l-1 BAP. The 3.0 mg l-1 BAP concentration in culture medium resulted in highest shoots regeneration frequency of variety ‛Angeline’. All isolated explants of ‛Autum joy’ formed adventitious shoots in the medium supplemented with 3.0 mg l-1 BAP + 0.5 mg l-1 NAA and 4.0 mg l-1 BAP + 0.5 mg l-1 NAA. While 0.75 mg l-1 BAP in culture medium stimulated shoots formation frequency of variety ‛Elegans’. The highest shoots number per explant of variety ‛Angeline’ has been establishing in medium with 0.75 mg l-1 BAP and 3.0 mg l-1 BAP. Medium supplemented with 3.0 mg l-1 BAP resulted in highest shoots number per explant of ‛Cristatum’. Explants of variety ‛Autum joy’ highest shoots number per explant formed in medium... [to full text]

In New Zealand, a formal tree improvement and breeding programme for Pinus radiata (D.Don) commenced in 1952. A countrywide series of progeny trials was progressively established on over seventy sites, and is managed by the Radiata Pine Breeding Company (RPBC). Diameter at breast height data from the series were used to investigate genotype x environment interaction with a view to establishing the need for partitioning breeding and deployment efforts for P. radiata. Nearly 300,000 measurements made this study one of the largest for genotype x environment interaction ever done. Bivariate analyses were conducted between all pairs of sites to determine genetic correlations between sites. Genetic correlations were used to construct a proximity matrix by subtracting each correlation from unity. The process of constructing the matrix highlighted issues of low connectivity between sites; whereby meaningful correlations between sites were established with just 5 % of the pairs. However, nearly two-thirds of these genetic correlations were between -1.0 and 0.6, indicating the presence of strong genotype x environment interactions. A technique known as multiple regression on resemblance matrices was carried out by regressing a number of environmental correlation matrices on the diameter at breast height correlation matrix. Genotype x environment interactions were found to be driven by extreme maximum temperatures (t-statistic of 2.03 against critical t-value of 1.96 at 95 % confidence level). When tested on its own, altitude was significant with genetic correlations between sites at the 90 % confidence level (t-statistic of 1.92 against critical t-value of 1.645). In addition, a method from Graph Theory using proximity thresholds was utilised as a form of clustering. However, this study highlighted the existence of high internal cohesion within trial series, and high external isolation between trial series. That is, grouping of sites (in terms of diameter) was observed to be a reflection of the series of trials for which each site was established. This characteristic is particularly unhelpful for partitioning sites into regions of similar propensity to genotype x environment interaction, as the genotype x environment effect is effectively over-ridden by the genotype effect. Better cohesion between past, present and future trial series, and more accurate bioclimatic data should allow more useful groupings of sites to be extracted from the data. Given this, however, it is clear that there are a large number of interactive families contained in the RPBC dataset. It is concluded that partitioning of New Zealand’s P. radiata breeding programme cannot be ruled out as an advantageous option.

In this thesis,we study how a meta-analysis of genetic association studies is influenced by the degree of genotype imputation uncertainty in the studies combined and the size of meta-analysis. We consider the fixed effect meta-analysis model to evaluate the accuracy and efficiency of imputation-based meta-analysis results under different levels of imputation accuracy. We also examine the impact of genotype imputation on the between-study heterogeneity and type 1 error in the random effects meta-analysis model. Simulation results reaffirm that meta-analysis boosts the power of detecting genetic associations compared to individual study results. However, the power deteriorates with increasing uncertainty in imputed genotypes. Genotype imputation affects a random effects meta-analysis in a non-obvious way as estimation of between-study heterogeneity and interpretation of association results depend heavily on the number of studies combined. We propose an adjusted fixed effect meta-analysis approach for adding imputation-based studies to a meta-analysis of existing typed studies in a controlled way to improve precision and reliability. The proposed method should help in designing an effective meta-analysis study.

Canada is the fourth largest producer of farmed salmon in the world, with Atlantic salmon being the major species cultivated. Paradoxically British Columbia (BC), which borders the Pacific Ocean, is the major producer province where Atlantic salmon was introduced in the mid-80’s. Escaped salmon may constitute a threat to natural populations of Pacific salmon as they compete for the same resources such as food and spawning territory. A potential solution to the aquaculture industry would be to further develop the aquaculture of native species in the region. The work presented here used semi-natural spawning channels to evaluate the effects of breeding strategies and early-rearing environments on the immune performance of Chinook salmon. Breeding strategy was tested analyzing artificial hatchery practices versus semi-natural propagation in spawning channels. Early-rearing environmental assessment contrasted indoor plastic hatchery tanks with outdoor gravelled-bottom spawning channels. A disease challenge involving over 1400 fish showed interaction effects between breeding strategy and rearing environment. Fish artificially mated presented a disease susceptibility influenced by the rearing environment. The contrary occurred in the offspring of self-breeding brood stock in the spawning channels, as no differences were observed in their susceptibility to the disease regardless of rearing environment. Monitoring of anti-Vibrio anguillarum antibodies during the disease challenge and a follow up of the survivors in sea net pens further confirmed the interaction between breeding strategy and rearing environment. Gene expression in pre- and post-infected artificially propagated fish showed differential gene expression when analyzed with a 695-gene cDNA microarray for Chinook salmon. Genotyping of major histocompatibility (MH) class II β1 alleles showed a tendency of a higher heterozygosity in survivors as expected, as well as a general tendency of a higher heterozygosity in semi-naturally propagated fish. The latter is likely a direct consequence of MH-linked mate choice, which was recently described in Chinook salmon (Neff et al., 2008). To further characterize the mating system of Chinook salmon in the spawning channels, brood stock were genotyped at 12 microsatellite loci. Females and males were found to mate randomly with regards to genetic pairwise relatedness, but they tended to mate with fish of similar condition as revealed by their pairwise differences in Fulton’s condition factor. This work demonstrated that genotype-by-environment interactions can modify the disease resistance of Chinook salmon. More importantly, these effects were seen after just one round of semi-natural spawning of domesticated hatchery fish, suggesting that further studies on spawning channels may highlight other hidden benefits. Therefore, breeding strategy and early-rearing environment should be considered when propagating cultured stocks. The use of more natural propagation methods such as spawning channels could improve the immune performance of Chinook salmon and help to expand the aquaculture of this native species in BC.

Group A streptococcus (GAS) is a strictly human pathogen that causes infections ranging from asymptomatic carriage to the highly lethal streptococcal toxic shock syndrome (STSS). GAS are classified according to the sequence of the variable 5’ end of the emm-gene that encodes the surface associated M-protein. In the late 1980s, outbreaks of GAS infections with high rates of STSS were reported in several parts of the world, including Sweden. Superantigens (SAgs), a group of exotoxins, have been described as key mediators of STSS due to their capacity to polyclonally activate T-cells and induce a massive release of inflammatory cytokines. Previous reports have revealed that sera from STSS patients have lower capacity to neutralize this SAg-mediated immune stimulation and a higher prevalence of GAS isolates with specific emm-genotypes during disease outbreaks. The aims of this thesis were to analyse the protective antibody response mounted by the host against SAgs produced by the infecting GAS isolate and to characterise the isolates emm-genotypes and SAg gene profiles. The clinical material examined was collected from patients with STSS, sepsis, erysipelas, or tonsillitis in Sweden between 1986 and 2001. Both acute- and convalescence-phase sera were analyzed, along with the infecting GAS isolates. The 92 clinical GAS isolates examined were found to exhibit a high degree of genetic diversity in terms of the number and identity of their SAg genes. Isolates with a given emm-genotype could be divided into subgroups on the basis of their SAg gene profiles. Ten different SAg gene profiles were identified in the 45 emm1 isolates examined; one of these ten was highly persistent, being observed in 22 isolates collected over 14 years. Two of the 11 known SAg genes in GAS, smeZ-1 and speA, were more prevalent in the emm1 associated profiles than in the SAg gene profiles of isolates with other emm-genotypes. Patients infected by GAS with the emm1-genotype were less likely to produce acute-phase sera that could effectively neutralize the T-cell mitogenicity induced by the infecting isolate’s extracellular products (EP). Sepsis patients whose sera exhibited this lack of neutralizing ability were more prone to developing STSS. Most patients whose acute-phase sera did not effectively neutralize the EP from the infecting isolate lacked protective antibodies in their convalescent-phase sera despite having elevated ELISA titers. The results reported herein show that combining SAg gene profiling with emm-genotyping may be useful for tracking the spread of GAS clones in the community. It was also shown that a lack of neutralizing activity in convalescence-phase sera might be due to an inability of those patients to mount a protective immune response against SAgs produced by the infecting GAS isolate.

No description available.

Variations in gene expression have long been hypothesised to be the major cause of individual differences. An initial focus of this research thesis is to elucidate the genetic regulatory architecture of gene expression. Expression quantitative trait locus (eQTL) mapping analyses have been performed on expression levels of over 22,000 mRNAs from three tissues of a panel of recombinant inbred mice. These analyses are "single-locus" where "linkage" (i.e. significant correlation) between an expression trait and a putative eQTL is considered independently of other loci. Major conclusions from these analyses are: 1. Gene expression is mainly influenced by genetic (sequence) variations that act in trans rather than in cis; 2. Subsets of genes are controlled by master regulators that influence multiple genes; 3. Gene expression is a polygenic trait with multiple regulators. Single-locus mapping analyses are not designed for detecting multiple regulators of gene expression, and so observation of multiple-linkages (i.e. one expression trait mapped to multiple eQTLs) formed the basis of the second objective of this research project: to investigate the relationship between multiple-linkages and genotype pattern-association. A locus-pair is said to have associated genotype patterns if they have similar inheritance pattern across a panel of individuals, and these are attributed to one of fours sources: 1. linkage disequilibrium between loci located on the same chromosome; 2. non-syntenic association; 3. random association; 4. un-associated. To understand the validity of multiple-linkages observed in single-locus mapping studies, a newly developed method, bqtl.twolocus, is applied to confirm two-locus effects for a total of 898 out of 1,233 multiple-linkages identified from the three studies mentioned above as well as from seven publicly available eQTL-mapping studies. Combining these results with information of genotype pattern-association, a subset of 478 multiple-linkages has been deduced for which there is high confidence to be real.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2007. / Härtill 5 uppsatser.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2007. / Härtill 4 uppsatser.