Browsing by Subject "HYBRIDIZATION"

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  • Reinsalu, Olavi; Scheler, Ott; Mikelsaar, Ruth; Mikelsaar, Aavo-Valdur; Hallap, Triin; Jaakma, Ülle; Padrik, Peeter; Kavak, Ants; Salumets, Andres; Kurg, Ants (2019)
    Background: Usage of sexed semen that allows to choose the gender of the calves, is commonly practiced in livestock industry as a profitable breeding alternative, especially in dairy farming. The flow cytometric cell sorting is the only commercially available method for bovine sperm sexing. For validation of the sexing procedure several methods have been developed including sperm fluorescence in situ hybridisation techniques. Latter usually include the use of pre-labelled nucleotides for probe synthesis which is relatively expensive approach compared to combined application of aminoallyl-dUTP and chemical binding of fluorescent dyes. Here a sex determining dual colour bovine sperm fluorescence in situ hybridisation method is presented which is considered more cost-effective technique than the previously reported approaches. Results: The reliability of sex chromosome identifying probes, designed in silico, was proven on bovine metaphase plate chromosomes and through comparison with a commercially available standard method. In the dual colour FISH experiments of unsexed and sexed bovine sperm samples the hybridisation efficiency was at least 98%, whereas the determined sex ratios were not statistically different from the expected. Very few cells carried both of the sex chromosome-specific signals (less than 0.2%). Conclusions: A protocol for a dual colour bovine sperm FISH method is provided which is cost-effective, simple and fast for sex determination of spermatozoa in bull semen samples.
  • Ruotsalainen, Juho; Hujanen, Jaana; Villi, Mikko (2019)
    As pioneers of new ideas and practices, many entrepreneurial journalists spearhead the change of journalism towards hybridity. By applying appraisal theory, this article examines a hybrid of objectivity and dialogue in daily news articles by five entrepreneurial journalism outlets – Axios, MustRead, National Observer, The Skimm and the Voice of San Diego. For comparative purposes, a dataset from three legacy media outlets was also analysed. The results show that the entrepreneurial journalism outlets employ journalistic dialogue in otherwise stylistically objective news texts notably more often than do legacy media outlets. Dialogic registers provide subtle, non-partisan assessments of events and issues and make the news more informal. Such a hybrid form of journalism serves the functions of sense-making, establishing an interpersonal connection between ‘private’ audiences and ‘public’ news, and connecting journalism with fields outside of its core. By doing so, the hybrid journalism of entrepreneurial journalists offers a distinctive vision of the futures of news journalism.
  • Day-Williams, Aaron G.; McLay, Kirsten; Drury, Eleanor; Edkins, Sarah; Coffey, Alison J.; Palotie, Aarno; Zeggini, Eleftheria (2011)
  • Filppu, Pauliina; Ramanathan, Jayendrakishore Tanjore; Granberg, Kirsi J.; Gucciardo, Erika; Haapasalo, Hannu; Lehti, Kaisa; Nykter, Matti; Le Joncour, Vadim; Laakkonen, Pirjo (2021)
    Glioma stem cells (GSCs) drive propagation and therapeutic resistance of glioblastomas, the most aggressive diffuse brain tumors. However, the molecular mechanisms that maintain the stemness and promote therapy resistance remain poorly understood. Here we report CD109/STAT3 axis as crucial for the maintenance of stemness and tumorigenicity of GSCs and as a mediator of chemoresistance. Mechanistically, CD109 physically interacts with glycoprotein 130 to promote activation of the IL-6/STAT3 pathway in GSCs. Genetic depletion of CD109 abolished the stemness and self-renewal of GSCs and impaired tumorigenicity. Loss of stemness was accompanied with a phenotypic shift of GSCs to more differentiated astrocytic-like cells. Importantly, genetic or pharmacologic targeting of CD109/STAT3 axis sensitized the GSCs to chemotherapy, suggesting that targeting CD109/STAT3 axis has potential to overcome therapy resistance in glioblastoma.
  • Kallijärvi, Jukka; Stratoulias, Vassilis; Virtanen, Kristel; Hietakangas, Ville; Heino, Tapio I.; Saarma, Mart (2012)
  • Saura, Anssi; Von Schoultz, Barbara; Saura, Anja O.; Brown, JR., Keith S. (2013)
  • Benard-Slagter, Anne; Zondervan, Ilse; de Groot, Karel; Ghazavi, Farzaneh; Sarhadi, Virinder; Van Vlierberghe, Pieter; De Moerloose, Barbara; Schwab, Claire; Vettenranta, Kim; Harrison, Christine J.; Knuutila, Sakari; Schouten, Jan; Lammens, Tim; Savola, Suvi (2017)
    Recurrent and clonal genetic alterations are characteristic of different subtypes of T- and B-cell lymphoblastic leukemia (ALL), and several subtypes are strong independent predictors of clinical outcome. A next-generation sequencing based multiplex ligation-dependent probe amplification variant (digitalMLPA) has been developed enabling simultaneous detection of copy number alterations (CNAs) of up to 1000 target sequences. This novel digitalMLPA assay was designed and optimized to detect CNAs of 56 key target genes and regions in ALL. A set of digital karyotyping probes has been included for the detection of gross ploidy changes, to determine the extent of CNAs, while also serving as reference probes for data normalization. Sixty-seven ALL patient samples (including B- and T-cell ALL), previously characterized for genetic aberrations by standard MLPA, array comparative genomic hybridization, and/or single-nucleotide polymorphism array, were analyzed single blinded using digitalMLPA. The digitalMLPA assay reliably identified whole chromosome losses and gains (including high hyperdiploidy), whole gene deletions or gains, intrachromosomal amplification of chromosome 21, fusion genes, and intragenic deletions, which were confirmed by other methods. Furthermore, subclonal alterations were reliably detected if present in at least 20% to 30% of neoplastic cells. The diagnostic sensitivity of the digitaLMLPA assay was 98.9%, and the specificity was 97.8%. These results merit further consideration of digitalMLPA as a valuable alternative for genetic work-up of newly diagnosed ALL patients.
  • Metso, Leena; Maki, Minna; Tissari, Paivi; Remes, Ville; Piiparinen, Pasi; Kirveskari, Juha; Tarkka, Eveliina; Anttila, Veli-Jukka; Vaara, Martti; Huotari, Kaisa (2014)
  • Priklopil, Tadeas; Kisdi, Eva; Gyllenberg, Mats (2015)
    We consider mating strategies for females who search for males sequentially during a season of limited length. We show that the best strategy rejects a given male type if encountered before a time-threshold but accepts him after. For frequency-independent benefits, we obtain the optimal time-thresholds explicitly for both discrete and continuous distributions of males, and allow for mistakes being made in assessing the correct male type. When the benefits are indirect (genes for the offspring) and the population is under frequency-dependent ecological selection, the benefits depend on the mating strategy of other females as well. This case is particularly relevant to speciation models that seek to explore the stability of reproductive isolation by assortative mating under frequency-dependent ecological selection. We show that the indirect benefits are to be quantified by the reproductive values of couples, and describe how the evolutionarily stable time-thresholds can be found. We conclude with an example based on the Levene model, in which we analyze the evolutionarily stable assortative mating strategies and the strength of reproductive isolation provided by them.
  • Junnila, Siina; Kokkola, Arto; Karjalainen-Lindsberg, Marja; Puolakkainen, Pauli; Monni, Outi (2010)
  • Pulido-Santacruz, Paola; Aleixo, Alexandre; Weir, Jason T. (2020)
    The incidence of introgression during the diversification process and the timespan following divergence when introgression is possible are poorly understood in the neotropics where high species richness could provide extensive opportunities for genetic exchange. We used thousands of genome-wide SNPs to infer phylogenetic relationships, calculate ages of splitting, and to estimate the timing of introgression in a widespread avian neotropical genus of woodcreepers. Five distinct introgression events were reconstructed involving taxa classified both as subspecies and species including lineages descending from the basal-most split, dated to 7.3 million years ago. Introgression occurred between just a few hundred thousand to about 2.5 million years following divergence, suggesting substantial portions of the genome are capable of introgressing across taxa boundaries during a protracted time window of a few million years following divergence. Despite this protracted time window, we found that the proportion of the genome introgressing (6-11%) declines with the time of introgression following divergence, suggesting that the genome becomes progressively more immune to introgression as reproductive isolation increases.
  • Habermann, Jens K.; Buendgen, Nana K.; Gemoll, Timo; Hautaniemi, Sampsa; Lundgren, Caroline; Wangsa, Danny; Doering, Jana; Bruch, Hans-Peter; Nordstroem, Britta; Roblick, Uwe J.; Jornvall, Hans; Auer, Gert; Ried, Thomas (2011)
  • Crowgey, Erin L.; Soini, Tea; Shah, Nidhi; Pauniaho, Satu-Liisa; Lahdenne, Pekka; Wilson, David B.; Heikinheimo, Markku; Druley, Todd E. (2020)
    Purpose: Pediatric germ cell tumors are rare, representing about 3% of childhood malignancies in children less than 15 years of age, presenting in neonates or adolescents with a greater incidence noted in older adolescents. Aberrations in primordial germ cell proliferation/differentiation can lead to a variety of neoplasms, including teratomas, embryonal carcinoma, choriocarcinoma, and yolk sac tumors. Patients and Methods: Three Finnish families with varying familial germ cell tumors were identified, and whole-genome sequencing was performed using an Illumina sequencing platform. In total, 22 unique subjects across the three families were sequenced. Family 1 proband (female) was affected by malignant ovarian teratoma, Family 2 proband (female) was affected by sacrococcygeal teratoma with yolk sac tumor in the setting of Cornelia de Lange syndrome, and Family 3 proband (male) was affected by malignant testicular teratoma. Rare variants were identified using an autosomal recessive or de novo model of inheritance. Results: For family 1 proband (female), an autosomal recessive or de novo model of inheritance identified variants of interest in the following genes: CD109, IKBKB, and CTNNA3, SUPT6H, MUC5AC, and FRG1. Family 2 proband (female) analysis identified gene variants of interest in the following genes: LONRF2, ANO7, HS6ST1, PRB2, and DNM2. Family 3 proband (male) analysis identified the following potential genes: CRIPAK, KRTAP5-7, and CACNA1B. Conclusion: Leveraging deep pedigrees and next-generation sequencing, rare germline variants were identified that were enriched in three families from Finland with a history of familial germ cell tumors. The data presented support the importance of germline mutations when analyzing complex cancers with a low somatic mutation landscape.
  • Jamshidi, Maral; Fagerholm, Rainer; Muranen, Taru A.; Kaur, Sippy; Potdar, Swapnil; Khan, Sofia; Netti, Eliisa; Mpindi, John-Patrick; Yadav, Bhagwan; Kiiski, Johanna I.; Aittomäki, Kristiina; Heikkilä, Päivi; Saarela, Jani; Bützow, Ralf; Blomqvist, Carl; Nevanlinna, Heli (2021)
  • Mahlamaki, E H; Kauraniemi, P; Monni, O; Wolf, Maija; Hautaniemi, S; Kallioniemi, Anne (2004)
  • Zhou, Wenjing; Jirstrom, Karin; Johansson, Christine; Amini, Rose-Marie; Blomqvist, Carl; Agbaje, Olorunsola; Warnberg, Fredrik (2010)
    Background: Microarray gene-profiling of invasive breast cancer has identified different subtypes including luminal A, luminal B, HER2-overexpressing and basal-like groups. Basal-like invasive breast cancer is associated with a worse prognosis. However, the prognosis of basal-like ductal carcinoma in situ (DCIS) is still unknown. Our aim was to study the prognosis of basal-like DCIS in a large population-based cohort. Methods: All 458 women with a primary DCIS diagnosed between 1986 and 2004, in Uppland and Vastmanland, Sweden were included. TMA blocks were constructed. To classify the DCIS tumors, we used immunohistochemical (IHC) markers (estrogen-, progesterone-, HER2, cytokeratin 5/6 and epidermal growth factor receptor) as a surrogate for the gene expression profiling. The association with prognosis was examined for basal-like DCIS and other subtypes using Kaplan-Meier survival analyses and Cox proportional hazards regression models. Results: IHC data were complete for 392 women. Thirty-two were basal-like (8.2%), 351 were luminal or HER2-positive (89.5%) and 9 unclassified (2.3%). Seventy-six women had a local recurrence of which 34 were invasive. Another 3 women had general metastases as first event. Basal-like DCIS showed a higher risk of local recurrence and invasive recurrence 1.8 (Confidence interval (CI) 95%, 0.8-4.2) and 1.9 (0.7-5.1), respectively. However, the difference was not statistically significant. Also, no statistically significant increased risk was seen for triple-negative or high grade DCIS. Conclusions: Basal-like DCIS showed about a doubled, however not statistically significant risk for local recurrence and developing invasive cancer compared with the other molecular subtypes. Molecular subtyping was a better prognostic parameter than histopathological grade.
  • Asplund, Olof; Rung, Johan; Groop, Leif; Prasad, Rashmi B.; Hansson, Ola (2020)
    MuscleAtlasExplorer is a freely available web application that allows for the exploration of gene expression data from human skeletal muscle. It draws from an extensive publicly available dataset of 1654 skeletal muscle expression microarray samples. Detailed, manually curated, patient phenotype data, with information such as age, sex, BMI and disease status, are combined with skeletal muscle gene expression to provide insights into gene function in skeletal muscle. It aims to facilitate easy exploration of the data using powerful data visualization functions, while allowing for sample selection, in-depth inspection and further analysis using external tools. Availability: MuscleAtlasExplorer is available at (username 'muscle' and password 'explorer' pre-publication).
  • Harmoinen, Jenni; von Thaden, Alina; Aspi, Jouni; Kvist, Laura; Cocchiararo, Berardino; Jarausch, Anne; Gazzola, Andrea; Sin, Teodora; Lohi, Hannes; Hytönen, Marjo K.; Kojola, Ilpo; Stronen, Astrid Vik; Caniglia, Romolo; Mattucci, Federica; Galaverni, Marco; Godinho, Raquel; Ruiz-Gonzalez, Aritz; Randi, Ettore; Munoz-Fuentes, Violeta; Nowak, Carsten (2021)
    Background Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected a panel of 96 ancestry informative markers for wolves and dogs, derived from the Illumina CanineHD Whole-Genome BeadChip (174 K). We designed very short amplicons for genotyping on a microfluidic array, thus making the method suitable also for non-invasively collected samples. Results Genotypes based on 93 SNPs from wolves sampled throughout Europe, purebred and non-pedigree dogs, and suspected hybrids showed that the new panel accurately identifies parental individuals, first-generation hybrids and first-generation backcrosses to wolves, while second- and third-generation backcrosses to wolves were identified as advanced hybrids in almost all cases. Our results support the hybrid identity of suspect individuals and the non-hybrid status of individuals regarded as wolves. We also show the adequacy of these markers to assess hybridization at a European-wide scale and the importance of including samples from reference populations. Conclusions We showed that the proposed SNP panel is an efficient tool for detecting hybrids up to the third-generation backcrosses to wolves across Europe. Notably, the proposed genotyping method is suitable for a variety of samples, including non-invasive and museum samples, making this panel useful for wolf-dog hybrid assessments and wolf monitoring at both continental and different temporal scales.
  • Aubriot, Xavier; Knapp, Sandra; Syfert, Mindy; Poczai, Péter; Buerki, Sven (2018)
    • While brinjal eggplant (Solanum melongena L.) is the second most important solanaceaous vegetable crop, we lack firm knowledge of its evolutionary relationships. This in turn limits efficient use of crop wild relatives in eggplant improvement. Here, we examine the hypothesis of linear step-wise expansion of the eggplant group from Africa to Asia. • We use museum collections to generate nuclear and full-plastome data for all species of the eggplant clade. We combine a phylogenomic approach with distribution data to infer a biogeographic scenario for the clade. • The eggplant clade has Pleistocene origins in northern Africa. Dispersions to tropical Asia gave rise to Solanum insanum, the wild progenitor of the eggplant, and to Africa distinct lineages of widespread and southern-African species. Results suggest that spread of species to southern Africa is recent and was likely facilitated by large mammal herbivores feeding on Solanum fruits (African elephant, impala). • Rather than a linear ‘Out Of Africa’ sequence, our results are more consistent with an initial event into Asia, and subsequent wide dispersion and differentiation across Africa driven by large mammalian herbivores. Our evolutionary results will impact future work on eggplant domestication and use of wild relatives in breeding of this increasingly important solanaceous crop.
  • Khaitov, Vadim; Marchenko, Julia; Katolikova, Marina; Väinölä, Risto; Kingston, Sarah E.; Carlon, David B.; Gantsevich, Michael; Strelkov, Petr (2021)
    Cryptic and hybridizing species may lack diagnostic taxonomic characters leaving researchers with semi-diagnostic ones. Identification based on such characters is probabilistic, the probability of correct identification depending on the species composition in a mixed population. Here we test the possibilities of applying a semi-diagnostic conchological character for distinguishing two cryptic species of blue mussels, Mytilus edulis and M. trossulus. These ecologically, stratigraphically and economically important molluscs co-occur and hybridize in many areas of the North Atlantic and the neighboring Arctic. Any cues for distinguishing them in sympatry without genotyping would save much research effort. Recently these species have been shown to statistically differ in the White Sea, where a simple character of the shell was used to distinguish two mussel morphotypes. In this paper, we analyzed the associations between morphotypes and species-specific genotypes based on an abundant material from the waters of the Kola Peninsula (White Sea, Barents Sea) and a more limited material from Norway, the Baltic Sea, Scotland and the Gulf of Maine. The performance of the "morphotype test" for species identification was formally evaluated using approaches from evidence-based medicine. Interspecific differences in the morphotype frequencies were ubiquitous and unidirectional, but their scale varied geographically (from 75% in the White Sea to 15% in the Baltic Sea). In addition, salinity-related variation of this character within M. edulis was revealed in the Arctic Barents Sea. For every studied region, we established relationships between the proportions of the morphotypes in the populations as well as between the proportions of the morphotypes in samples and the probabilities of mussels of different morphotypes being M. trossulus and M. edulis. We provide recommendations for the application of the morphotype test to mussels from unstudied contact zones and note that they may apply equally well to other taxa identified by semi-diagnostic traits.