Browsing by Title

The Finnish dairy cattle population has been subjected to systematic quantitative studies over decades. The Western Finncattle (WFC) has evolved over the last century with a production level comparable to other remaining local breeds in Europe. The heritability is used in designing the data collection and in predicting the changes expected from the selection and the variation parameters are used in constructing the economic selection indices genetic improvement scheme and in computing the bulls’ and cows’ breeding values. WFC has no recent studies on the genetic variation in milk production traits. The thesis research was set to estimate the heritability of milk, fat and protein yield, fat%, protein%, protein-fat ratio and somatic cell count (SCC) and the genetic correlation amongst them. Records from Western Finncattle primiparous cows calving in the period 2002–2016 were used for the genetic analyses. The raw data consisted of 5455 cows distributed across 2512 herds. The variance components were estimated with single and multi-trait animal model using a Bayesian approach and R studio package MCMCglmm. With requiring at least 5 cows in each herd-year subclass in the estimation, the data size was reduced to 1763 cows in 233 herds. The heritability of milk, protein and fat yield, protein%, fat% and SCC was in single (and in brackets for multi) trait analysis 0.36 (0.37), 027(0.30), 0.32 (0.30), 0.61(0.43), 0.52 (0.49) and 0.06 (0.15), respectively. Amongst yield traits and also between the content traits the genetic correlation was high, 0.73–0.94 and 0.43–0.59, respectively. The content traits (with milk yield in the denominator) had a negative genetic correlation with milk yield while no correlation with the protein and fat yield. There was an environmental correlation between content and yield traits for protein and fat. No correlations exist between SCC and other traits except an environmental correlation with milk yield and protein content. Despite the small population size of the WFC population, the effective population size is satisfactory and therefore no reduction in genetic variation is expected. Overall, the analysis on production traits and pedigree data shows that the Western Finncattle have much potential for genetic improvement.

Antibiotic resistance is a worldwide problem and it threatens the prevention and treatment of infections caused by different pathogens. All living organisms produce natural products including ribosomal peptides with great variety. They are widely distributed in nature and they are playing more significant role in the search of new antimicrobial compounds used as therapeutical agents. Bacteria are a prolific source of peptides many of which are antimicrobial and microbial genomes are widely believed to encode new antimicrobial peptides. Genome mining has expanded the number of families of ribosomally synthesized natural products in recent years. These In silico approaches together with molecular biology and chemical analysis aim to identify novel compounds. In this study an unknown cyanobactin-like gene cluster was discovered by genome mining from genomes of cyanobacteria and also other bacteria. The aim of this work was to study the occurrence of the gene clusters in various bacterial genomes and the structures of novel peptides. The active biosynthesis of these peptides was tested by LCMS- and Q-TOF -analyses based on bioinformatic predictions. The production of the predicted peptides was also tested with stable sulphur isotope labelling. The aim was also to clone the genes needed for peptide biosynthesis into E. coli and to study antimicrobial activities of these peptides. Bioinformatic analyses suggested that the gene clusters encoded 1–8 precursor peptides together with protease. The precursor peptides had conserved leader sequence (LPxQxxPVxR) and a highly variable core sequences, often encoding an even number of cysteines. The mature peptide is eventually formed from core sequence through post-translational changes in the precursor peptide. The gene cluster was present in 38 bacterial genomes representing a diverse selection of bacterial phyla including cyanobacteria, proteobacteria, actinobacteria, bacteroidetes, firmicutes and planctomycetes. Analyses of the precursor peptide core regions suggested that the products are 8–131 amino acids in length. These peptides could be divided into two groups based on their structures: They form a selection of disulphide-bridge stabilized peptides with 2–5 disulphide-bridges as well as short cationic peptides with an ?-helical structure. Surprisingly, these types of peptides are common in eukaryotes and part of the innate immune system displaying potent antimicrobial properties but very rarely reported for bacteria. The peptides predicted from bioinformatic analysis were detected from Pseudanabaena sp. PCC 6802 using a combination of molecular biology and structural chemistry. Heterologous expression of the gene cluster from Pseudanabaena sp. PCC 6802 in E. coli confirmed that the gene cluster is active. A set of short cationic synthetic peptides with ?-helical structure predicted from Oscillatoria sp. PCC 10802, Dickeya zeae Ech1591, Vibrio nigripulchritudo SOn1, Agarivorans albus MKT 106, Roseibium sp. TrichSKD4 and Yersinia frederiksenii ATCC 33641 were shown to have potent antimicrobial activity between 0.8–100 ?g/ml. These findings prove that predicted cysteine containing peptides are produced by bacteria and some peptides from this novel family have antimicrobial activity, which might pave the way for new possible drugs derived from natural products.

Strawberry breeding in Finland began 60 years ago and has largely relied on traditional breeding methods. The geography of Finland, as well as local consumer preferences for darker-coloured strawberries, have been the main focus of selection in all implemented Finnish breeding programs. With several successful and popular cultivars have been released, the current focus is on increasing yield and disease resistance while maintaining the excellent fruit quality of breeders' selections. A panel of 175 garden strawberry accessions was created and trialled at the Natural Resources Institute Finland (Luke) as part of a Nordic-Baltic pre-breeding collaboration between the institute and the Norwegian breeding company Graminor AS. A medium-density, genome-wide scan for 50K SNPs has been performed on each individual of the panel. This panel represents the genetic diversity present and typical for cultivated strawberry in the Nordic-Baltic region, and it is expected to provide Nordic breeders with markers tailored to their plant material diversity, supporting their future selection decisions and accelerating their breeding cycles. In this study, symptom severities of two strawberry leaf diseases (leaf spot caused by Mycosphaerella fragariae and leaf scorch caused by Diplocarpon earlianum) and seven fruit quality traits (berry weight, skin colour, flesh colour, evenness of flesh colour, basket appearance, predominant berry shape and tip type) were scored in the panel. GAPIT and statgenGWAS statistical packages in R were used to run five different GWAS models: Significant SNP-trait associations were found using single-locus (GLM and MLM) and multi-locus (FarmCPU and BLINK) association mapping analyses. The study had shed a light on the importance of considering several statistical models and parameters for a maximum benefit of association mapping studies. Among significant SNP-trait associations for fruit weight, fruit skin colour and fruit flesh colour, four were partially characterized by inspecting their allelic effects. On chromosome Fvb6-1, appearance of consensus, significant signals from the flesh colour trait of secondary-position berries is discussed. Nine significant SNP-marker associations were detected for berry weight.

Fusarium Head Blight (FHB) is an important cereal disease worldwide and has become an essential breeding target in wheat. FHB generates considerable losses in terms of grain yield and quality of the seeds in cereal crops. The mycotoxins produced by some Fusarium species, such as deoxynivalenol (DON), directly impact the farmers. In fact, DON accumulation results in unmarketable harvest due to the associated health hazards (vomiting, diarrhea, fever etc). Facing DON risks, the European Commission had to establish a maximum concentration of the mycotoxin in unprocessed cereals. Avoidance mechanisms of the plants against disease infections were identified in diverse studies and are known as the passive resistance. These mechanisms related to phenotypic traits such as variations in plant height (PH), heading date (HD) or the presence of awns could possibly reduce the FHB infection of the wheat. On another hand, the active resistance is determined by genetic factors so called quantitative trait loci (QTL). QTL identification via population mapping was established to be a useful tool to find loci regions associated with FHB resistance. Therefore, in this study we aimed to find phenotypic and genotypic correlations with Fusarium Head Blight resistance among 108 winter bread wheat genotypes. By estimating the heritability of the agronomic traits, we wanted to determine if it would be efficient to breed for those traits. Furthermore, we had the objective to detect FHB resistance QTL from our winter bread wheat genotypes and finally, to observe the overlapping QTL’s regions between FHB resistance and the QTL of the HD or of the PH. It was found that the HD had strong negative phenotypic and genotypic coefficients of correlation with FHB severity and DON concentration. The HD had also an important heritability and direct effect on FHB severity. By performing a GWAS analysis, QTL associated to FHB resistance were found on the chromosomes 1B, 2B, 3A, 3B, 5A, 5B, 5D, 6A, 6B ,7B among the studied genotypes. Overlapping QTL were observed between FHB resistance and HD on the chromosomes 1B, 2B, 3B, 5A, 5B, 6B but also between FHB resistance and PH on the chromosomes 2B, 3A, 3B, 5A, 6A. In conclusion, the HD was considered as an escape mechanism against FHB. It seems to be feasible to select chromosomes fragments with favorable QTL for FHB genetic resistance. Those traits could be involved in marker assisted or genomic selection programmes after the approval of the observed QTL detected to develop FHB resistant cultivars.

Bilberry is a soft fruit, growing wild in the forests of Europe, and especially Nordic and East European countries. Its demand is growing on the market, thanks to its heath beneficial components like anthocyanins, present in both skin and flesh of the berry. It however has a very short shelf-life. The goal of this study was to identify pectinase genes, with a focus on two subfamilies, polygalacturonase (PG) and pectate lyase (PL). The main interest was to study those that are expressed during bilberry’s ripening, to get a better understanding of this process. Bioinformatics were used to identify the annotated genes from the bilberry genome, and point out candidates, from which transcripts are found during ripening, with BLAST searches within a transcriptome of ripening bilberry fruit. The expression of the PL candidates was then studied with qPCR analysis. The study identified 70 PG-coding genes and 25 PL-coding genes, of which 35 and 12, respectively, were found in the ripening berry. The expression of five PL genes was increased during ripening, suggesting a role in the softening of the fruit. Two of those had a notably higher relative increase, making them prime candidates for further study.

Kasvit tuottavat ensisijaisen aineenvaihdunnan eli primaarimetabolian avulla tarvitsemansa amino-, nukleiini- ja rasvahapot. Näitä molekyylejä kasvit käyttävät kasvuun ja kehitykseen sekä elintoimintojensa turvaamiseen. Suuri osa primaarimetabolian geeneistä on hyvin konservoituneita eli ne ovat säilyneet lähes muuttumattomana kasvilajista toiseen miljoonien vuosien ajan. Sekundaarimetaboliitteja kasvit tuottavat vuorovaikuttaakseen ympäristönsä kanssa. Sekundaarimetaboliittien biosynteesin voi laukaista esimerkiksi kasvin kokema stressi, joka aiheutuu kasvinsyöjistä, taudinaiheuttajista, toisista kasveista tai jos kasvi altistuu liikaa ultraviolettisäteilylle. Ympäristötekijöillä, kuten pH:lla, veden saatavuudella, lämpötilalla ja maaperän suolapitoisuudella on myös suuri vaikutus sekundaarimetaboliittien biosynteesiin sekä vaihteluun saman kasvilajin sisällä. Suurin osa kasvien sekundaarimetaboliiteista syntetisoidaan sikimaatti-, isoprenoidi- ja polyketidireittiä pitkin. Polyketidit toimivat muun muassa pigmentteinä ja osana kasvin puolustusjärjestelmää. Gerberassa esiintyy harvinaista polyketidijohdannaista, 4-hydroksi-5-metyylikumariinia (HMC), jonka biosynteesistä 2-pyronisyntaasi G2PS2:n on päätelty vastaavan. Tässä tutkielmassa selvitettiin g2ps2:n osallisuutta HMC:n biosynteesiin käyttämällä Virus induced gene silencing (VIGS)- menetelmää sekä proteiinin ylituottoa gerberan kallussolukossa. VIGS- menetelmä ei toiminut tässä kokeessa g2ps2- geenin aikaisen ekspression takia. Kokeet gerberan Regina- lajikkeen kallussolukossa sen sijaan vaikuttivat lupaavilta ja kallus osoittautui hyödylliseksi menetelmäksi gerberan polyketidisyntaasien tutkimiseen.

Recent trends in urbanization have contributed to re-defining urban demand and rural supply across the global agricultural landscape. These dynamic interactions occur within both formal agricultural economies, as well as within informal networks of non-commodity exchange. This research identifies on-the-ground systems of non-commodity exchange practiced in urban agroecology, and explores the implications of these systems of exchange upon the demand for changes in the ways humans relate to food, and the governing structures determining their distribution. Framed by the exploration of urban agroecology as a science, practice and social movement, this research probes exchange pathways across two city-sponsored urban agriculture networks: The P-Patch Community Gardening Program in Seattle, United States and the Allotment Gardens of Helsinki, Finland. As both garden networks are embedded within each city’s respective development plan, these sites offer the distinct benefit of probing civic responsibility and active engagement within civic agriculture outside of the discourse of food production for self as a political act. I employ an interdisciplinary approach to this research methodology which draws from the disciplines of planning, human geography, sociology, and agroecology. Data was collected and analyzed utilizing qualitative methods including semi-structured interview and ethnographic photography. I argue that the identification of these non-commodity exchange systems, and the fragmented urban place-based knowledge pockets from which they emerged, can be utilized to derive principals useful in the design and management of sustainable urban agroecosystems.

Gluteeniton kauraleivonta on teknologisesti haastavaa, sillä viskoelastisen gluteeniverkoston puuttuessa kaurataikinoita on hankalaa työstää ja kauraleivät jäävät usein tiiviiksi, kosteiksi ja tahmeiksi. Hyväksyttävän rakenteen aikaansaanti on vaikeaa ja gluteenittomille leiville on tyypillistä, että ne vanhenevat nopeasti. Leivän vanhenemiseen johtavina tekijöinä pidetään tärkkelyksen uudelleenkiteytymistä ja veden liikkumista leivässä säilytyksen aikana. Tutkimuksen tavoitteena oli parantaa gluteenittoman kauraleivän säilyvyyttä käyttämällä taikinassa esiliisteröityä tärkkelystä. Tutkimuksen hypoteesina oli, että velliksi esiliisteröidyn kaurajauhon käytöllä vesi saadaan sidottua tiukemmin tärkkelysgeeliin, jolloin säilytyksen aikana tapahtuva veden liikkuminen leivässä hidastuu. Kun rakennetta pehmentävä vesi puristuu hitaammin ulos tärkkelysgeelistä ja liisteröityneisiin, amorfisiin tärkkelysalueisiin on sitoutunut enemmän vettä, on leivän rakennetta kovettavien tärkkelyskiteiden muodostuminen hitaampaa. Lisäksi tutkimuksessa vertailtiin kauravellin hapatusta mikrobiologisella ja kemiallisella menetelmällä. Mikrobiologisen hapatuksen aikana jauhopartikkelit ehtivät vettyä ja liueta edelleen, ja tällä oletettiin olevan rakennetta pehmentävä vaikutus. Tutkimuksen kokeellisessa osassa kauraleipien rakenteen kovettumista tutkittiin kaksivaiheisella puristustestillä aineenkoestuslaitteella ja tärkkelyksen uudelleenkiteytymistä seurattiin DSC-kalorimetrillä. Taikinoiden ominaisuuksia havainnollistettiin erilaisin geelitestein. Tutkimuksessa havaittiin, että esiliisteröity kauravelli lisäsi kaurataikinan kaasunpidätyskykyä ja kasvatti kauraleivän ominaistilavuutta. Kemiallisesti hapatettua velliä sisältäneessä kauraleivässä rakenteen kovettuminen oli hitainta ja leipä oli tilastollisesti pehmein kuudenteen säilytyspäivään asti. Mikrobiologisesti hapatetun vellin käyttö taas nopeutti kauraleivän rakenteen vanhenemista. Esiliisteröidyn vellin käyttö pehmensi gluteenittoman kauraleivän rakennetta liisteröimällä enemmän tärkkelystä amorfiseen muotoon ja hidastamalla veden liikkumista leivässä säilytyksen aikana. Kauravellin kemiallinen hapatus pehmensi kauraleivän rakennetta edelleen, ja rakenne oli vellitöntä leipää pehmeämpi vielä kuudentena säilytyspäivänä. Tutkimuksessa onnistuttiin pidentämään gluteenittoman kauraleivän pehmeää aikaa käyttämällä taikinassa kemiallisesti hapatettua, esiliisteröityä velliä.

Gluten free baking differentiates from traditional wheat baking by the lack of structure stabilizing gluten network. The gluten in wheat flour mixed with water creates a visco-elastic dough that makes a good quality bread. In gluten free baking the structure of bread is improved with starches and hydrocolloids. Celiac decease, gluten yliherkkyys and wheat allergy are health related reasons to avoid gluten from wheat, barley and rye. There is no method for gluten free flours to predict the quality of the baked product like there is the farinograph water absorption method for wheat flour. These topics are discussed in the literature part of this work. The aim of this research was to look into the connection between gluten free dough consistency and the quality of baked bread. In the experimental part three different dough yields were selected: 190, 200 and 210. All dough yields were used with three different mixtures in consistency measurements: 100% buckwheat, 70 % buckwheat and 30 % tapioca and addition of 1 % psyllium to the latter mixture. Two different methods were tested (forward and backward extrusion) with Texture Analyser with all different dough variations. The principle in both methods are the same: the tests measure the compression force required for a piston to extrude the dough in a sample container. The doughs consistency and behavior were studied with farinograph to see if the results were consistent. Baking test was done with different dough yields with buckwheat, tapioca and psyllium mixture. Volume, baking loss and color were determined. Texture Profiler Analysis (TPA) was done 24h and 48h after baking. A sensory analysis conducted by professional panelists was done where porosity, softness, dryness, sponginess and intensity of buckwheat taste were assessed. Backward extrusion was found to be a better method for measuring consistency of the doughs. The results showed how the increasing water amount decreased consistency and same results were obtained with farinograph. Differences between breads were found with the sensory analysis as well. Intensity of flavor and porosity increased in bread with lower water amount whereas softness and moistness increased with increasing water amount when also the bread remained softer for longer. As a conclusion it can be stated that the backward extrusion is a suitable and reproducible method for buckwheat dough consistency measurements. Water absorption, bread structure and shelf life can be predicted and optimized based on consistency.

The glycolytic potential of muscles is a representation of the energy reserve of a muscle and takes into account all compounds that are present in the muscle, which can be converted into lactic acid. A total of 219 breast muscle samples from five hybrids of male broiler chickens were used in this study. All from fast growing lines, they hybrids used are Ross 508, Cobb, Hubbard H1, Ross 308 and Rowan. The birds were reared under the same conditions, and slaughtered randomly at different ages. The pH, initial and ultimate, glycogen and lactic acid were assessed in all the samples. The glycolytic potential was calculated using results from the lactate and glycogen analysis. Older birds were associated with low glycogen concentrations. Wooden Breast muscles showed a very high significant difference with pHu (P<0.0001) and high significant difference with glycolytic potential (P = 0.0004). Affected breast muscles were associated with high pHu values and low glycolytic potential, where there was strong positive correlation between pHu and Wooden Breast presentation (P<0.0001, r = 0.414), and a weak negative correlation between the glycolytic potential and the presentation of Wooden Breast (P<0.0001, r = -0.292). Among the hybrids, Hubbard H1 recorded the highest glycolytic potential mean value of 117.22 while Ross 308 had the least mean value of 105.9 ± 5.6.