Memories, museum artefacts and excavations in resolving the history of maternal lineages in the Finnhorse

We used historical DNA samples to examine the history of a native horse breed, the Finnhorse. Samples were collected from private collections, museums, schools and excavations, representing the times prior to, during, and after the foundation of the breed; from the end of the 19th century and throughout the 20th century. We sequenced a fragment of mitochondrial DNA from these historical samples to study the history and evolution of maternal lineages of horses back to the early days of the breed, compared the mitochondrial DNA sequence diversity of different historical periods and modern day Finnhorses, estimated the effective population sizes, and searched for both temporal and geographic population genetic structure. We observed high maternal haplotype and nucleotide diversity at the time during the foundation of the breed, and a decrease in both measures during 1931-1970. In addition, we observed losses of some haplotypes present in the early stages of the breed. There was only slight evidence of geographical or temporal population structure. This study is, to our knowledge, the first to use such temporal sampling to reveal the history of a specific animal breed.Peer reviewe

Memories, museum artefacts and excavations in resolving the history of maternal lineages in the Finnhorse

We used historical DNA samples to examine the history of a native horse breed, the Finnhorse. Samples were collected from private collections, museums, schools and excavations, representing the times prior to, during, and after the foundation of the breed; from the end of the 19th century and throughout the 20th century. We sequenced a fragment of mitochondrial DNA from these historical samples to study the history and evolution of maternal lineages of horses back to the early days of the breed, compared the mitochondrial DNA sequence diversity of different historical periods and modern day Finnhorses, estimated the effective population sizes, and searched for both temporal and geographic population genetic structure. We observed high maternal haplotype and nucleotide diversity at the time during the foundation of the breed, and a decrease in both measures during 1931-1970. In addition, we observed losses of some haplotypes present in the early stages of the breed. There was only slight evidence of geographical or temporal population structure. This study is, to our knowledge, the first to use such temporal sampling to reveal the history of a specific animal breed.Peer reviewe

A Partial Loss-of-Function Variant in AKT2 is Associated with Reduced Insulin-Mediated Glucose Uptake in Multiple Insulin Sensitive Tissues: a Genotype-Based Callback Positron Emission Tomography Study

Rare fully penetrant mutations in AKT2 are an established cause of monogenic disorders of glucose metabolism. Recently, a novel partial loss-of-function AKT2 coding variant (p.Pro50Thr) was identified that is nearly specific to Finns (frequency 1.1%), with the low-frequency allele associated with an increase in fasting plasma insulin level and risk of type 2 diabetes. The effects of p.Pro50Thr on insulin-stimulated glucose uptake (GU) in the whole body and in different tissues have not previously been investigated.  We identified carriers (N=20) and matched non-carriers (N=25) for this allele in the population-based METSIM study and invited these individuals back for positron emission tomography study with [18F]-fluorodeoxyglucose during euglycemic hyperinsulinemia. When we compared p.P50T/AKT2 carriers to non-carriers, we found a 39.4% reduction in whole body GU (P=0.006) and a 55.6% increase in the rate of endogenous glucose production (P=0.038). We found significant reductions in GU in multiple tissues: skeletal muscle (36.4%), liver (16.1%), brown adipose (29.7%), and bone marrow (32.9%), and increases of 16.8-19.1% in 7 tested brain regions. These data demonstrate that the P50T substitution of AKT2 influences insulin-mediated GU in multiple insulin sensitive tissues, and may explain, at least in part, the increased risk of type 2 diabetes in p.P50T/AKT2 carriers.</p

Sairaanhoitajaopiskelijoiden laskimoverinäytteenoton preanalyyttinen tietotaso

Preanalyyttinen vaihe on tärkeä osa laboratoriotutkimusprosessia ja iso osa (55 %) laboratoriotutkimusprosessin virheistä esiintyy sen aikana. Virheet preanalyyttisessa vaiheessa johtavat laadultaan huonoihin näytteisiin ja epäluotettaviin laboratoriotutkimustuloksiin vaarantaen potilasturvallisuuden. Sen vuoksi kaikkien laskimoverinäytteitä ottavien tulisi tuntea preanalytiikka, jotta he voisivat pyrkiä laadukkaaseen, potilaan senhetkistä tilaa parhaiten edustavaan laskimoverinäytteeseen. Tämä on tärkeää, sillä 60–80 % lääketieteellisistä päätöksistä pohjautuu laboratoriotutkimustuloksiin. Jokaisella asiakkaalla on oikeus luotettaviin laboratoriotutkimustuloksiin riippumatta siitä, kuka laskimoverinäytteen on ottanut. Opinnäytetyön tarkoituksena oli kartoittaa Oulun ammattikorkeakoulun sairaanhoitajaopiskelijoiden laskimoverinäytteenoton preanalyyttista tietotasoa. Tavoitteena oli tuottaa hyödynnettävää tietoa, jonka pohjalta hoitotyön koulutusohjelman sisältämää laskimoverinäytteenoton ja preanalytiikan opetusta voisi tarvittaessa kehittää. Tuotettu tieto auttaa bioanalytiikan opettajia sairaanhoitajille suunnatun opetuksen suunnittelussa, sekä kuvastaa opiskelijoiden saaman opetuksen vaikuttavuutta. Opinnäytetyön tilaajana toimi Oulun ammattikorkeakoulun bioanalytiikan koulutusohjelma. Opinnäytetyö toteutettiin kvantitatiivisena tutkimuksena ja aineisto tutkimukseen kerättiin sähköpostitse opiskelijoille lähetettävällä kyselylomakkeella. Kyselylomake lähetettiin yhteensä 284:lle opintonsa vuosina 2012−2015 aloittaneille, läsnä olevaksi ilmoittautuneille, Oulun ammattikorkeakoulun hoitotyön tutkinto-ohjelman sairaanhoitajaopiskelijoille. Vastausprosentiksi muodostui 31 (88/284). Saatu aineisto käsiteltiin ja analysoitiin ristiintaulukoimalla Webropol-ohjelman avulla. Tulokset ryhmiteltiin alaongelmien mukaan. Opinnäytetyön tuloksissa oli selvästi nähtävissä, että opiskelijoiden laskimoverinäytteenoton preanalyyttinen tietotaso on hyvä. Epävarmuutta opiskelijoissa aiheuttivat verinäyteputkien vakioitu näytteenottojärjestys ja sen merkitys, laboratoriokohtainen tutkimusohjekirja, asiakkaan ohjaaminen sekä hemolyysia aiheuttavat tekijät. Opinnäytetyön tulokset osoittivat, että opiskelijoiden saama laskimoverinäytteenotto-opetus kehittää opiskelijoiden laskimoverinäytteenoton preanalyyttista tietotasoa. Opinnäytetyöllä tuotettiin uutta tietoa sairaanhoitajaopiskelijoiden laskimoverinäytteenoton preanalyyttisesta tietotasosta ja tulokset ovat hyödynnettävissä suunniteltaessa laskimoverinäytteenottoa ja preanalytiikkaa käsittelevää opetusta.Preanalytical phase is an important part of the total testing process and most of the errors (55 %) in the total testing process appear during preanalytical phase. Errors in preanalytical phase lead to blood samples’ poor quality and unreliable test results which can risk the patient`s safety. That`s why everyone, who`s taking bloodsamples should have good preanalytical knowledge in venipuncture. It is important because 60–80 % of all medical decisions are based on laboratory test results. Every patient should have reliable laboratory test results and the quality of test results must not be depended on the person who performs the blood specimen collection. The purpose of the thesis was to survey Oulu University of Applied Sciences’ nursing students’ preanalytical knowledge in venipuncture. The aim was to produce useful information which could be used to develop the Degree Program’s teaching about venipuncture and preanalytical errors in venipuncture if necessary. The thesis was ordered by the degree Programme in Biomedical Laboratory Science of Oulu University of Applied Sciences. The study was quantitative. The material for study was collected with a questionnaire which was sent to students by e-mail. The questionnaire was sent to total of 284 (N=284) nursing students, who had started their studies during 2012−2015. The response rate was 31 % (88/284). The material produced with questionnaire was treated and analyzed with Webropol-program. The conclusions were made based on the thesis’ framework and research problem. The results showed that nursing students’ preanalytical knowledge is good. Students were not sure about the right sample collecting order and its purpose, laboratory test manual, quiding patients for venipuncture and things that can cause hemolysis. It is obvious that teaching about venipuncture has developed students’ preanalytical knowledge in venipuncture. The thesis produced new information about nursing students’ preanalytical knowledge in venipuncture and the results can be used to develop the degree Program’s teaching about venipuncture and preanalytical errors

Evolutionary and conservation genetics of European domestic and wild geese

Abstract Human actions are currently threatening the persistence of many species. Loss of genetic diversity and inbreeding can reduce evolutionary potential of species and may even lead to their extinction. Thus, genetic issues should be taken into account in conservation and management of wild and domestic species. In this thesis, I have studied evolutionary and conservation genetics of the taiga bean goose (Anser fabalis fabalis) and the European domestic goose, derived from the greylag goose (A. anser). The taiga bean goose, a subspecies of the bean goose, is of conservation concern as the population numbers have halved during the recent decades. Due to debated taxonomy of the bean goose, I studied the genomic differentiation between the taiga bean goose and another European subspecies, the tundra bean goose (A. f. rossicus). A subspecies status was verified for these taxa, due to low genome-wide differentiation and extensive gene flow between the subspecies. I also studied genetic structure within breeding taiga bean geese in Finland, but no structure was evident. Genetic diversity was at a moderate level, but signs of inbreeding and gene flow with pink-footed goose (A. brachyrhynchus) were discovered. I also studied subspecies composition of the bean goose hunting bag in Finland and found that about half of the hunting bag consisted of the taiga bean goose. Hunting of the tundra bean goose was concentrated in south-eastern Finland. Thus, by geographically limiting the hunting area, the declining taiga bean goose can be relieved from hunting pressure. I also studied over a thousand years of evolutionary history of the European domestic goose in Russia using ancient DNA extracted from archaeological bones. Three evolutionary lineages were discovered: domestic geese, eastern domestic/wild greylag geese and taiga bean geese. The taiga bean geese were present probably due to misidentification of bones in fragmented archaeological material. Undoubted domesticated geese were found from the High-Medieval period (11th century CE) onwards.Tiivistelmä Ihmistoiminta uhkaa monien lajien säilymistä. Geneettisen muuntelun vähäisyys ja sukusiitos voivat heikentää lajien evolutiivista potentiaalia ja johtaa jopa sukupuuttoon. Geneettiset näkökohdat tulisi siksi huomioida sekä villien että kesyjen lajien kannanhoidossa ja suojelussa. Tässä väitöskirjassa tutkin taigametsähanhen (Anser fabalis fabalis) ja merihanhesta (A. anser) polveutuneen eurooppalaisen kesyhanhen evoluutio- ja luonnonsuojelugenetiikkaa. Taigametsähanhi on yksi metsähanhen alalajeista. Sen populaatiokoko on puolittunut viime vuosikymmeninä, joten se on erityisesti suojelun tarpeessa. Metsähanhen taksonomiasta on ollut pitkään ristiriitaisia käsityksiä, joita selvittääkseni tutkin genomisen erilaistumisen määrää taigametsähanhen ja toisen eurooppalaisen alalajin, tundrametsähanhen (A. f. rossicus) välillä. Genomien erilaistumisen vähäisyys ja runsas geenivirta viittaa siihen, että nämä taksonit ovat saman lajin eri alalajeja. Tutkin myös Suomessa pesivien taigametsähanhien geneettistä rakennetta, mutta sitä ei löydetty. Geneettisen muuntelun määrä oli kohtuullisen suurta, mutta havaitsin viitteitä sukusiitoksesta. Lisäksi löysin merkkejä geenivirrasta lyhytnokkahanhen (A. brachyrhynchus) ja metsähanhen välillä. Tutkin myös Suomen metsähanhisaaliin alalajijakaumaa ja havaitsin, että noin puolet saaliista koostui taigametsähanhesta ja puolet tundrametsähanhesta. Tundrametsähanhen pyynti kohdistui Kaakkois-Suomeen, joten metsästysalueen rajaamisella sinne voidaan taantuva taigametsähanhi säästää metsästyspaineelta. Lisäksi tutkin eurooppalaisen kesyhanhen evolutiivista historiaa yli 1000 vuoden ajalta venäläisistä arkeologisista luista eristetyn muinais-DNA:n avulla. Löysin niistä kolme evolutiivista linjaa, jotka muodostuivat kesyhanhista, itäisistä kesy/merihanhista ja taigametsähanhista. Taigametsähanhilinjan löytyminen näytteistä johtuu luultavasti lajintunnistuksen hankaluudesta pirstaleisessa arkeologisessa luuaineistossa, mistä johtuen taigametsähanhien luut oli tulkittu kesyhanhien luiksi. Varmasti kesytettyjä hanhia aineistossa esiintyi sydänkeskiajalta eli 1000-luvulta lähtien

Determination of different predictors affecting DNA concentration isolated from historical hairs of the Finnhorse

Everyday objects manufactured from raw materials of animal origin, such as skin, hair and bone, are innumerable in cultural historical museums and private collections. Besides their value as memoirs of past techniques, livelihoods and communities, they are a unique source for studying past animal populations by means of molecular analysis.Here, we deal with horse mane and tail hair, a type of predecessor of modern synthetic material utilized, for example, for brushes, strings, tennis rackets, ropes, textiles, dolls' hair, rocking horses, and filling. By investigating the presence and quality of DNA in horsehair, we have studied the origins of the Finnhorse, the only native horse breed in Finland. Degradation of DNA in old samples is an issue that needs to be considered when selecting material for DNA analysis. For assessing the usability of historical artefacts for DNA-based studies, we study how DNA is preserved in horsehair and how well DNA can be isolated from 50 to 150-year-old artefacts, raw material bundles and archaeological finds. We investigate how the properties of hair and sample storage conditions affect the concentration of DNA extracts and success in Polymerase Chain Reaction (PCR).Our analysis showed that historical hair shafts, stored in various environments and used for multiple purposes, are of sufficient quantity and quality for amplification by PCR. Therefore, their value for the research of past animal populations should be noticed when curating cultural historical collections. We also provide advice for the storage conditions for hair samples.Peer reviewe

Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation

Several studies have uncovered a highly heterogeneous landscape of genetic differentiation across the genomes of closely related species. Specifically, genetic differentiation is often concentrated in particular genomic regions (“islands of differentiation”) that might contain barrier loci contributing to reproductive isolation, whereas the rest of the genome is homogenized by introgression. Alternatively, linked selection can produce differentiation islands in allopatry without introgression. We explored the influence of introgression on the landscape of genetic differentiation in two hybridizing goose taxa: the Taiga Bean Goose (Anser fabalis) and the Tundra Bean Goose (A. serrirostris). Using a combination of population genomic summary statistics and demographic modelling, we reconstructed the evolutionary history of these birds and quantified the impact of introgression on the build-up and maintenance of genetic differentiation. We found evidence for a scenario of allopatric divergence (about 2.5 million years ago) followed by recent secondary contact (about 60,000 years ago). Subsequent introgression events led to high levels of gene flow, mainly from the Tundra Bean Goose into the Taiga Bean Goose. This scenario resulted in a largely undifferentiated genomic landscape (genome-wide FST = 0.033) with a few notable differentiation peaks that were scattered across chromosomes. The summary statistics indicated that some peaks might contain barrier loci while others arose in allopatry through linked selection. Finally, based on the low genetic differentiation, considerable morphological variation and incomplete reproductive isolation, we argue that the Taiga and the Tundra Bean Goose should be treated as subspecies

Development and optimization of a novel environmental DNA‐based method for moor frog (Rana arvalis) monitoring and comparison with a commercial detection kit

Abstract Moor frogs (Rana arvalis) are protected by the European Union's Habitats Directive, often making them a target for environmental impact assessments. However, moor frog detection with the traditional method using their mating calls is difficult, time‐consuming, and limited to the short mating season. Environmental DNA (eDNA)‐based methods could be beneficial in moor frog detection since moor frogs are shy and co‐occurring common frogs (R. temporaria) are morphologically similar. Additionally, eDNA‐based methods could even extend the detection period of moor frogs. We tested two different DNA isolation methods and two different eDNA detection methods, Sanger sequencing and quantitative PCR (qPCR), and compared the results to the traditional mating call survey method. In addition, we tested whether linear polyacrylamide treatment would improve eDNA detection. We sampled 27 sites in Finland, of which moor frogs were detected in 17 sites by traditional acoustic survey method, in 20 sites with Sanger sequencing‐based eDNA method, and in 21 sites with qPCR‐based eDNA method. We sampled water bodies during and 3–4 weeks after the end of the mating season. Our results show that both tested eDNA methods (Sanger sequencing and qPCR) can be used to detect moor frogs and extend the moor frog detection period by at least 3–4 weeks, but qPCR slightly outperforms Sanger sequencing. Linear polyacrylamide treatment did not improve the results. Detection probabilities were similar or higher with the eDNA‐based methods than with the traditional survey method, as moor frogs were also detected in water bodies in which mating calls were not heard. Based on our results, eDNA‐based detection methods can be highly beneficial in monitoring the presence of moor frogs and can be used to complement traditional surveys

Genetic methods for determining subspecies composition of bean goose harvests

Session abstract A2.3201