Mitochondrial genetics of alloplasmic male-sterile Brassica napus lines

Reliable and economical production of hybrid (F1) varieties requires efficient means to control pollination. The predominant system for pollination control of most field crops today is cytoplasmic male sterility (CMS). Since CMS is a consequence of disturbed nuclear-mitochondrial interactions, the CMS trait is maternally inherited. A common way to produce CMS plants is to combine the nuclear genome from one species with the mitochondria from another; plants of such origin are described as alloplasmic CMS. This thesis describes the production and molecular characterization of a novel alloplasmic CMS system produced from rapeseed (Brassica napus) (+) Arabidopsis thaliana somatic hybrids. A population of 170 B. napus (+) A. thaliana somatic hybrid lines was backcrossed to B. napus and 22 lines with male sterility and/or aberrant flower morphology were found. Nine of these were analysed for RFLP and found to contain nuclear and plastid DNA from B. napus, whilst the mitochondrial genomes were frequently recombined containing both B. napus and A. thaliana DNA. Besides the male-sterile trait, the majority of the lines displayed homeotic conversions of anthers to carpeloid organs. Vegetative growth was reduced to some extent in some of the lines. One CMS line segregated both fertile and sterile plants. Fertility co-segregated with molecular markers from A. thaliana chr III. By a dihaploidisation strategy we produced plants with a disomic addition of A. thaliana chr III, which had a stable inheritance of the fertile phenotype. Global mitochondrial mRNA expression was analysed in the fertility-restored line, the corresponding CMS line, B. napus and A. thaliana. Run-on experiments showed that transcriptional activities were highly variable between B. napus and A. thaliana and that in the CMS line transcriptional activity was reduced for several ribosomal protein genes and increased for orf139. Steady-state levels were more homogenous in comparison to transcriptional activities showing that RNA turnover is an important regulatory mechanism. Increased transcript abundance of several genes was observed in the CMS line, often correlated with presence of longer transcripts. Transcripts of three A. thaliana loci, orf139, orf240a and orf294 accumulated in the CMS line, but with reduced levels in the restored line. The orf139 and orf294 transcripts accumulated differentially in a tissue and genotype-specific manner, while orf240a was constitutively expressed throughout the plant. Both orf240a and orf294 transcripts can be polyadenylated, thus providing an explanation for their post-transcriptional regulation. Segregation analysis of sterile and fertile alloplasmic lines indicates that orf139 and orf240a are less likely candidates to be responsible for the male-sterile phenotype, whereas the orf294 can be CMS-associated. However, it is likely that more than one locus in the A. thaliana mt-DNA could encode CMS in the nuclear background of B. napus

X-ray microtomography measurements of bioactive glass scaffolds in rabbit femur samples at multiple stages of bone regeneration : reduction of image artefacts and a preliminary segmentation

A series of x-ray microtomography (micro-CT) measurements was performed on a set of rabbit femur bone samples containing artificial scaffolds of bioactive glass BAG-S53P4, implanted into an intentionally induced defect, i.e. a gap, in the femur. The scaffolds, some additionally enveloped in PLGA, were supportive structures composed of small granules of bioactive glass, intended to enhance, stimulate and guide the healing and regeneration of bone. The 34 samples were harvested from the rabbits at three different stages of healing and bone regeneration: 2 weeks, 4 weeks and 8 weeks. In addition to 27 samples that contained scaffolds of BAG-S53P4 or BAG-S53P4-PLGA, which had been implanted into the femur of a rabbit, 3 scaffolds of BAG-S53P4(-PLGA) that were not implanted and 7 control samples containing inert PMMA-implants were also included in the measurements for comparison. During the healing process the bioactive glass granules are gradually dissolved into the surrounding bodily fluids and a thin reaction layer composed of silica gel forms onto the surfaces of the granules. Subsequently an additional surface layer composed of HCA, a material that closely resembles natural hydroxyapatite, is formed onto the granules. As the healing process to regenerate the bone in the gap progresses, a complex three-dimensional network of newly formed trabecular bone grows in between the granules, attaching onto the surface layers and eventually enveloping the gradually dissolving granules entirely. Ultimately, the scaffold is intended to degrade completely, and a structure of regenerated, remodeled cortical bone is expected to be formed into the volume of the initial defect. As the thicknesses of both the surface layers of the granules and the individual trabeculae of the newly formed bone are in the micrometre range, x-ray microtomography was employed to evaluate and assess the complex three-dimensional structure, consisting of trabecular bone intertwined with granules at varying stages of dissolution. By evaluating the rate of formation of these structures at three different stages, i.e. time points, of regeneration, valuable information on the effectiveness of the bioactive glass BAG-S53P4(-PLGA) for the regeneration of defected bone can be obtained. The measurements were performed at University of Helsinki’s Laboratory of Microtomography using its Nanotom-apparatus with 80kV voltage, 150microA current and a voxel size of 15micrometres. 1000 projection images per sample were used in 37 reconstructions utilizing the FBP-algorithm. Subsequent image processing to analyze and compare the samples was conducted using ImageJ. A procedure to reduce image artefacts – due to metal parts in the samples – was developed, utilizing Gaussian filtering, as well as a preliminary image segmentation scheme, utilizing Morphological filtering, to automatically separate the bone from the granules and their surface layers

Archaeomagnetic intensity in Finland during the last 6400 years: problems in measurement techniques, dating errors or evidences for a non-dipole field

Archaeomagnetic intensity in Finland has been determined for the past 6400 years with the Thellier technique of bricks, potsherds and baked clays. The normalized intensity shows an increase from -4360 BC to the maximum at AD 500–AD 900, after which it decreases to the present value. The peak at AD 500–AD 900 is not a consequence of the applied Thellier technique since we are able to reproduce the known field values in the laboratory, and some of the bricks yield values which are in broad agreement with the observatory data. We have shown that variations in grain size of the magnetic carriers, cooling rate, fabrik or magnetic refraction are unlikely to cause systematic errors in intensity larger than ten percent. Previously we have demonstrated that the high intensity at AD 500 in Finland can be modelled by a non-dipole field producing enhanced latitude-normalized values at higher latitudes (Finland) and relatively weaker fields at lower latitudes (Bulgaria), and that extrapolation of the present field (IGRF 1990) back in time shows similar behaviour. However, the new Bulgarian smoothed archaeointensity curve by Daly and Le Goff (1996) shows a maximum in Bulgarian curve at ~AD 630 (i.e., 130 years later than in Finland) and another maximum at AD 950 (i.e., 50 years later than in Finland) , and the new relative intensity data of Finnish lake sediments (Saarinen, 1996) reveals a peak at ~AD 870 corresponding roughly with the second maximum. These new curves are somewhat controversial but they east doubt on the previous datings of the Finnish archaeomagnetic materials of the first millennia AD. Here we show that a better match of the Finnish and Bulgarian intensity data with the Finnish lake sediment data can be obtained if the Finnish ages of the first millennium are slightly younger than previously thought. However, the Finnish intensities are still significantly higher than the coeval Bulgarian intensities so that a non-dipole field enhancement may have also been operative

Protein content and HvNAM alleles in Nordic barley (Hordeum vulgare) during a century of breeding

Background Barley has been bred for more than a century in the Nordic countries, with dramatic improvements of yield traits. In this study we investigate if this has come at the cost of lower grain protein and micronutrient (iron, zinc) content, by analysing 80 accessions representing four different improvement stages. We further re-sequenced the two grain protein content associated genes HvNAM-1 and HvNAM-2 in full and performed expression analyses of the same genes to search for genetic associations with nutrient content. Results We found higher thousand grain weight in barley landraces and in accessions from the late improvement group compared to accessions from the mid of the twentieth century. Straw length was much reduced in late stage accessions. No significant temporal decrease in grain protein, iron or zinc content during twentieth century Nordic crop improvement could be detected. Out of the 80 accessions only two deviant HvNAM-1 sequences were found, represented by one accession each. These do not appear to be correlated to grain protein content. The sequence of HvNAM-2 was invariable in all accessions and no correlations between expression levels of HvNAM-1 and HvNAM-2 and with grain protein content was found. Conclusions In contrast to studies in wheat, where a strong negative correlation between straw length and grain protein and micronutrient content has been found, we do not see this relationship in Nordic barley. The last 60 years of breeding has reduced straw length but, contrary to expectations, not protein and micronutrient content. Variation in grain protein and micronutrient content was found among the Nordic barley accessions, but it is not explained by variation of HvNAM genes. This means that HvNAM is an unexploited source of genetic variation for nutrient content in Nordic barley

Intermediate ions as a strong indicator of new particle formation bursts in a boreal forest

Secondary aerosol formation from gas-phase precursors is a frequent phenomenon occurring in a boreal environment. Traditionally, this process is identified visually from observational data on total and ion number size distributions. Here, we introduce a new, objective classification method for the new particle formation events based on measured intermediate-ion concentrations. The intermediate-ion concentration is a suitable indicator of new particle formation, because it is linked to the atmospheric new particle formation. The concentration of intermediate ions is typically very low (below 5 cm(-3)) when there is no new particle formation or precipitation events occurring. In this study, we analysed concentrations of negative intermediate ions at the Station for Measuring Ecosystem Atmosphere Relations (SMEAR II) in Hyytiala, Finland, during the years 2003-2013. We found that the half-hour median concentration of negative intermediate ions in sizes 2-4 nm was > 20 cm(-3) during 77.5% of event days classified by traditional method. The corresponding value was 92.3% in the case of 2-7 nm negative ions. In addition, the intermediate-ion concentration varied seasonally in a similar manner as the number of event days, peaking in the spring. A typical diurnal variation of the intermediate-ion concentration resembled that of the particle concentration during the event days. We developed here a new method for classifying new particle formation events based on intermediate-ion concentrations. The new method is complementary to the traditional event analysis and it can also be used as an automatic way of determining new particle formation events from large data sets.Peer reviewe

Multicenter cohort study on duration of antiarrhythmic medication for supraventricular tachycardia in infants

Antiarrhythmic medication (AM) is commonly used to prevent supraventricular tachycardia (SVT) recurrence in infants. Our aim was to determine whether a shorter duration of AM is sufficient to prevent atrioventricular reentrant tachycardia (AVRT) recurrence and evaluate risk factors for recurrence of SVT after discontinued AM.This multicenter cohort study included all infants diagnosed with SVT in the five university hospitals in Finland between 2005 and 2017. Those diagnosed between 2005 and 2012 received AM for 12 months (group 1), and those diagnosed between 2013 and 2017 received AM for 6 months (group 2). A total of 278 infants presented with AVRT (group 1, n = 181; group 2, n = 97), and the median AM duration was 12.0 months (interquartile range [IQR] 11.4-13.4) and 7.0 months (IQR 6.0-10.2), respectively. Propranolol was the most frequently used first-line AM (92% and 95%). Recurrence-free survival rates were over 88% until 12 months after AM prophylaxis in both groups, without any statistically significant difference between them. Independent risk factors for recurrence of SVT after discontinuation of AM were need of combination AM (HR 2.2, 95% CI 1.14-4.20), Wolff-Parkinson White (WPW) syndrome (HR 2.4, 95% CI 1.25-4.59), and age over 1 month at admission (HR 2.2, 95% CI 1.12-4.48). Conclusion: Shortening AM duration in infants from 12 to 6 months does not seem to lead to more frequent SVT recurrence. The risk factors for recurrence of SVT were WPW syndrome, need of combination AM, and age over 1 month.Peer reviewe

Archaeological and historical materials as a means to explore Finnish crop history

In Northern Europe, barley (Hordeum vulgare L.) has been cultivated for almost 6000 years. Thus far, 150-year-old grains from historical collections have been used to investigate the distribution of barley diversity and how the species has spread across the region. Genetic studies of archaeobotanical material from agrarian sites could potentially clarify earlier migration patterns and cast further light on the origin of barley landraces. In this study, we aimed to evaluate different archaeological and historical materials with respect to DNA content, and to explore connections between Late Iron Age and medieval barley populations and historical samples of barley landraces in north-west Europe. The material analysed consisted of archaeological samples of charred barley grains from four sites in southern Finland, and historical material, with 33 samples obtained from two herbaria and the seed collections of the Swedish museum of cultural history.The DNA concentrations obtained from charred archaeological barley remains were too low for successful KASP genotyping confirming previously reported difficulties in obtaining aDNA from charred remains. Historical samples from herbaria and seed collection confirmed previously shown strong genetic differentiation between two-row and six-row barley. Six-row barley accessions from northern and southern Finland tended to cluster apart, while no geographical structuring was observed among two-row barley. Genotyping of functional markers revealed that the majority of barley cultivated in Finland in the late nineteenth and early twentieth century was late-flowering under increasing day-length, supporting previous findings from northern European barley.</p

Genetic diversity in gooseberry (Ribes uva-crispa), as estimated with SSR markers

European gooseberry (Ribes uva-crispa L.) is a popular berry crop in many European countries, including Sweden, Denmark and Ukraine. There is no active gooseberry breeding programme in either Sweden or Denmark, but a successful programme is operating in Ukraine. In Sweden and Denmark, research on gooseberries is primarily focused on collection and phenotypic evaluation of genetic resources. As part of these activities, a large number of inventory finds have been collected but have not yet been characterised morphologically or molecularly. The goal of this study was thus to characterise gooseberry germplasm with 15 simple sequence repeat (SSR) markers. From 242 accessions analysed, 153 unique genotypes were identified. Cultivars that have been in widespread cultivation in Sweden, such as the Finnish cultivars 'Hinnonma & BULL;en Keltainen' and 'Hinnonma & BULL;en Punainen', had relatively large numbers of synonymous samples. While many inventory finds were identifiable as synonyms of known cultivars, several were found to constitute unique genotypes within the germplasm studied. The studied genotypes clustered relatively well in three posterior groups, consisting of cultivars originating before and after the American gooseberry mildew (Sphaerotheca mors-uvae) outbreak around 1900 and cultivars originating from the territory of the former Soviet Union. A fourth genetic cluster consisting mainly of inventory finds from central and northern Sweden was also identified. In addition, it was possible to verify recorded and stipulated parentages for some of the cultivars studied and to identify three likely parent-parent-child trios. Thus, inventories of local gooseberry germplasm and a subsequent genotyping proved successful in finding unique local genotypes, with potential local adaptation. The data obtained provide a foundation for future studies of gooseberry genetic re-sources, while also illustrating the importance of a well-curated and phenotypically characterised set of reference cultivars for future studies

Patterns of Exchange of Multiplying Onion (Allium cepa L. Aggregatum-Group) in Fennoscandian Home Gardens

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