Browsing by Subject "AMPLIFICATION"

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  • Autio, Reija; Saarela, Matti; Jarvinen, Anna-Kaarina; Hautaniemi, Sampsa; Astola, Jaakko (2009)
  • Kuras, Anita; Antonius, Kristina; Kalendar, Ruslan; Kruczynska, Dorota; Korbin, Malgorzata (2013)
  • Utz, Begüm; Turpin, Rita; Lampe, Johanna; Pouwels, Jeroen; Klefström, Juha (2020)
    Breast cancer is the most common form of cancer in women. Despite significant therapeutic advances in recent years, breast cancer also still causes the greatest number of cancer-related deaths in women, the vast majority of which (>90%) are caused by metastases. However, very few mouse mammary cancer models exist that faithfully recapitulate the multistep metastatic process in human patients. Here we assessed the suitability of a syngrafting protocol for a Myc-driven mammary tumor model (WAP-Myc) to study autochthonous metastasis. A moderate but robust spontaneous lung metastasis rate of around 25% was attained. In addition, increased T cell infiltration was observed in metastatic tumors compared to donor and syngrafted primary tumors. Thus, the WAP-Myc syngrafting protocol is a suitable tool to study the mechanisms of metastasis in MYC-driven breast cancer.
  • Lei, Ruibo; Tian-Kunze, Xiangshan; Leppäranta, Matti; Wang, Jia; Kaleschke, Lars; Zhang, Zhanhai (2016)
    SSM/I sea ice concentration and CLARA black-sky composite albedo were used to estimate sea ice albedo in the region 70 degrees N-82 degrees N, 130 degrees W-180 degrees W. The long-term trends and seasonal evolutions of ice concentration, composite albedo, and ice albedo were then obtained. In July-August 1982-2009, the linear trend of the composite albedo and the ice albedo was -0.069 and -0.046 units per decade, respectively. During 1 June to 19 August, melting of sea ice resulted in an increase of solar heat input to the ice-ocean system by 282 MJ.m(-2) from 1982 to 2009. However, because of the counter-balancing effects of the loss of sea ice area and the enhanced ice surface melting, the trend of solar heat input to the ice was insignificant. The summer evolution of ice albedo matched the ice surface melting and ponding well at basin scale. The ice albedo showed a large difference between the multiyear and first-year ice because the latter melted completely by the end of a melt season. At the SHEBA geolocations, a distinct change in the ice albedo has occurred since 2007, because most of the multiyear ice has been replaced by first-year ice. A positive polarity in the Arctic Dipole Anomaly could be partly responsible for the rapid loss of summer ice within the study region in the recent years by bringing warmer air masses from the south and advecting more ice toward the north. Both these effects would enhance ice-albedo feedback.
  • Basavand, Esmaeil; Khodaygan, Pejman; Moradi, Mohammad; Mousavi, Seyed Abdollah; Lindstrom, Kristina; Sedaghati, Nasser (2022)
    Crown and stem gall caused by agrobacterial species is one of the most devastating diseases on different crops worldwide. In spring 2018, an alert concerning a disease forming galls on seedlings of pistachio in nurseries was received from Rafsanjan county, Kerman province, Iran. After isolation of bacteria from the galls by using conventional bacteriological methods, bacterial colonies were purified and selected for further analyses including biochemical, pathogenicity and molecular tests. Pathogenicity tests of all isolates on test plants and carrot discs were evaluated positive. Based on the results of biochemical and pathogenicity tests, supported by molecular phylogenies of housekeeping and pathogenicity genes, the isolates were identified as Agrobacterium radiobacter. Since agrobacteria could be easily spread through seedlings and agricultural materials between different areas, the identified Agrobacterium strains could be considered as a latent threat to the pistachio nurseries of Iran. The present study is the first report on the occurrence of crown and stem gall on pistachio caused by A. radiobacter worldwide.
  • Xiu, Yuanren; Li, Zhijun; Lei, Ruibo; Wang, Qingkai; Lu, Peng; Lepparanta, Matti (2020)
    In order to apply satellite data to guiding navigation in the Arctic more effectively, the sea ice concentrations (SIC) derived from passive microwave (PM) products were compared with ship-based visual observations (OBS) collected during the Chinese National Arctic Research Expeditions (CHINARE). A total of 3 667 observations were collected in the Arctic summers of 2010, 2012, 2014, 2016, and 2018. PM SIC were derived from the NASA-Team (NT), Bootstrap (BT) and Climate Data Record (CDR) algorithms based on the SSMIS sensor, as well as the BT, enhanced NASA-Team (NT2) and ARTIST Sea Ice (ASI) algorithms based on AMSR-E/AMSR-2 sensors. The daily arithmetic average of PM SIC values and the daily weighted average of OBS SIC values were used for the comparisons. The correlation coefficients (CC), biases and root mean square deviations (RMSD) between PM SIC and OBS SIC were compared in terms of the overall trend, and under mild/normal/severe ice conditions. Using the OBS data, the influences of floe size and ice thickness on the SIC retrieval of different PM products were evaluated by calculating the daily weighted average of floe size code and ice thickness. Our results show that CC values range from 0.89 (AMSR-E/AMSR-2 NT2) to 0.95 (SSMIS NT), biases range from -3.96% (SSMIS NT) to 12.05% (AMSR-E/AMSR-2 NT2), and RMSD values range from 10.81% (SSMIS NT) to 20.15% (AMSR-E/AMSR-2 NT2). Floe size has a significant influence on the SIC retrievals of the PM products, and most of the PM products tend to underestimate SIC under smaller floe size conditions and overestimate SIC under larger floe size conditions. Ice thickness thicker than 30 cm does not have a significant influence on the SIC retrieval of PM products. Overall, the best (worst) agreement occurs between OBS SIC and SSMIS NT (AMSR-E/AMSR-2 NT2) SIC in the Arctic summer.
  • Chen, Ping; Lepikhova, Tatiana; Hu, Yizhou; Monni, Outi; Hautaniemi, Sampsa (2011)
  • Rask, Gunilla; Nazemroaya, Anoosheh; Jansson, Malin; Wadsten, Charlotta; Nilsson, Greger; Blomqvist, Carl; Holmberg, Lars; Warnberg, Fredrik; Sund, Malin (2022)
    Purpose To investigate if molecular subtype is associated with outcome in stage 1 breast cancer (BC). Methods Tissue samples from 445 women with node-negative BC
  • Casar-Borota, Olivera; Boldt, Henning Bünsow; Engstrom, Britt Eden; Andersen, Marianne Skovsager; Baussart, Bertrand; Bengtsson, Daniel; Berinder, Katarina; Ekman, Bertil; Feldt-Rasmussen, Ulla; Hoybye, Charlotte; Jorgensen, Jens Otto L.; Kolnes, Anders Jensen; Korbonits, Marta; Rasmussen, Ase Krogh; Lindsay, John R.; Loughrey, Paul Benjamin; Maiter, Dominique; Manojlovic-Gacic, Emilija; Pahnke, Jens; Poliani, Pietro Luigi; Popovic, Vera; Ragnarsson, Oskar; Schalin-Jäntti, Camilla; Scheie, David; Toth, Miklos; Villa, Chiara; Wirenfeldt, Martin; Kunicki, Jacek; Burman, Pia (2021)
    Context: Aggressive pituitary tumors (APTs) are characterized by unusually rapid growth and lack of response to standard treatment. About 1% to 2% develop metastases being classified as pituitary carcinomas (PCs). For unknown reasons, the corticotroph tumors are overrepresented among APTs and PCs. Mutations in the alpha thalassemia/mental retardation syndrome X-linked (ATRX) gene, regulating chromatin remodeling and telomere maintenance, have been implicated in the development of several cancer types, including neuroendocrine tumors. Objective: To study ATRX protein expression and mutational status of the ATRX gene in APTs and PCs. Design: We investigated ATRX protein expression by using immunohistochemistry in 30 APTs and 18 PCs, mostly of Pit-1 and T-Pit cell lineage. In tumors lacking ATRX immunolabeling, mutational status of the ATRX gene was explored. Results: Nine of the 48 tumors (19%) demonstrated lack of ATRX immunolabelling with a higher proportion in patients with PCs (5/18; 28%) than in those with APTs (4/30;13%). Lack of ATRX was most common in the corticotroph tumors, 7/22 (32%), versus tumors of the Pit-1 lineage, 2/24 (8%). Loss-of-function ATRX mutations were found in all 9 ATRX immunonegative cases: nonsense mutations (n = 4), frameshift deletions (n = 4), and large deletions affecting 22-28 of the 36 exons (n = 3). More than 1 ATRX gene defect was identified in 2 PCs. Conclusion: ATRX mutations occur in a subset of APTs and are more common in corticotroph tumors. The findings provide a rationale for performing ATRX immunohistochemistry to identify patients at risk of developing aggressive and potentially metastatic pituitary tumors.
  • Kalendar, Ruslan; Shustov, Alexandr; Akhmetollaev, Ilyas; Kairov, Ulykbek (2022)
    Polymerase chain reaction (PCR) is a simple and rapid method that can detect nucleotide polymorphisms and sequence variation in basic research applications, agriculture, and medicine. Variants of PCR, collectively known as allele-specific PCR (AS-PCR), use a competitive reaction in the presence of allele-specific primers to preferentially amplify only certain alleles. This method, originally named by its developers as Kompetitive Allele Specific PCR (KASP), is an AS-PCR variant adapted for fluorescence-based detection of amplification results. We developed a bioinformatic tool for designing probe sequences for PCR-based genotyping assays. Probe sequences are designed in both directions, and both single nucleotide polymorphisms (SNPs) and insertion-deletions (InDels) may be targeted. In addition, the tool allows discrimination of up to four-allelic variants at a single SNP site. To increase both the reaction specificity and the discriminative power of SNP genotyping, each allele-specific primer is designed such that the penultimate base before the primer’s 3′ end base is positioned at the SNP site. The tool allows design of custom FRET cassette reporter systems for fluorescence-based assays. FastPCR is a user-friendly and powerful Java-based software that is freely available ( Using the FastPCR environment and the tool for designing AS-PCR provides unparalleled flexibility for developing genotyping assays and specific and sensitive diagnostic PCR-based tests, which translates into a greater likelihood of research success.
  • Ritari, Jarmo; Hultman, Jenni; Fingerroos, Rita; Tarkkanen, Jussi; Pullat, Janne; Paulin, Lars; Kivi, Niina; Auvinen, Petri; Auvinen, Eeva (2012)
  • Moon, Sangjun; Kim, Yun-Gon; Dong, Lingsheng; Lombardi, Michael; Haeggstrom, Edward; Jensen, Roderick V.; Hsiao, Li-Li; Demirci, Utkan (2011)
  • Vihma, Timo; Graversen, Rune G.; Chen, Linling; Handorf, Dörthe; Skific, Natasa; Francis, Jennifer A.; Tyrrell, Nicholas L; Hall, Richard; Hanna, Edward; Uotila, Petteri; Dethloff, Klaus; Karpechko, Alexey; Björnsson, Halldor; Overland, James E. (2020)
    We investigate factors influencing European winter (DJFM) air temperatures for the period 1979-2015 with the focus on changes during the recent period of rapid Arctic warming (1998-2015). We employ meteorological reanalyses analysed with a combination of correlation analysis, two pattern clustering techniques, and back-trajectory airmass identification. In all five selected European regions, severe cold winter events lasting at least 4 days are significantly correlated with warm Arctic episodes. Relationships during opposite conditions of warm Europe/cold Arctic are also significant. Correlations have become consistently stronger since 1998. Large-scale pattern analysis reveals that cold spells are associated with the negative phase of the North Atlantic Oscillation (NAO-) and the positive phase of the Scandinavian (SCA+) pattern, which in turn are correlated with the divergence of dry-static energy transport. Warm European extremes are associated with opposite phases of these patterns and the convergence of latent heat transport. Airmass trajectory analysis is consistent with these findings, as airmasses associated with extreme cold events typically originate over continents, while warm events tend to occur with prevailing maritime airmasses. Despite Arctic-wide warming, significant cooling has occurred in northeastern Europe owing to a decrease in adiabatic subsidence heating in airmasses arriving from the southeast, along with increased occurrence of circulation patterns favouring low temperature advection. These dynamic effects dominated over the increased mean temperature of most circulation patterns. Lagged correlation analysis reveals that SCA- and NAO+ are typically preceded by cold Arctic anomalies during the previous 2-3 months, which may aid seasonal forecasting.
  • Moschos, Vaios; Schmale, Julia; Aas, Wenche; Becagli, Silvia; Calzolai, Giulia; Eleftheriadis, Konstantinos; Moffett, Claire E.; Schnelle-Kreis, Jürgen; Severi, Mirko; Sharma, Sangeeta; Skov, Henrik; Vestenius, Mika; Zhang, Wendy; Hakola, Hannele; Hellen, Heidi; Huang, Lin; Jaffrezo, Jean-Luc; Massling, Andreas; Nøjgaard, Jakob K.; Petäjä, Tuukka; Popovicheva, Olga; Sheesley, Rebecca J.; Traversi, Rita; Yttri, Karl Espen; Prevot, Andre S. H.; Baltensperger, Urs; El Haddad, Imad (2022)
    The Arctic is warming two to three times faster than the global average, and the role of aerosols is not well constrained. Aerosol number concentrations can be very low in remote environments, rendering local cloud radiative properties highly sensitive to available aerosol. The composition and sources of the climate-relevant aerosols, affecting Arctic cloud formation and altering their microphysics, remain largely elusive due to a lack of harmonized concurrent multi-component, multi-site, and multi-season observations. Here, we present a dataset on the overall chemical composition and seasonal variability of the Arctic total particulate matter (with a size cut at 10 mu m, PM10, or without any size cut) at eight observatories representing all Arctic sectors. Our holistic observational approach includes the Russian Arctic, a significant emission source area with less dedicated aerosol monitoring, and extends beyond the more traditionally studied summer period and black carbon/sulfate or fine-mode pollutants. The major airborne Arctic PM components in terms of dry mass are sea salt, secondary (non-sea-salt, nss) sulfate, and organic aerosol (OA), with minor contributions from elemental carbon (EC) and ammonium. We observe substantial spatiotemporal variability in component ratios, such as EC/OA, ammonium/nss-sulfate and OA/nss-sulfate, and fractional contributions to PM. When combined with component-specific back-trajectory analysis to identify marine or terrestrial origins, as well as the companion study by Moschos et al 2022 Nat. Geosci. focusing on OA, the composition analysis provides policy-guiding observational insights into sector-based differences in natural and anthropogenic Arctic aerosol sources. In this regard, we first reveal major source regions of inner-Arctic sea salt, biogenic sulfate, and natural organics, and highlight an underappreciated wintertime source of primary carbonaceous aerosols (EC and OA) in West Siberia, potentially associated with the oil and gas sector. The presented dataset can assist in reducing uncertainties in modelling pan-Arctic aerosol-climate interactions, as the major contributors to yearly aerosol mass can be constrained. These models can then be used to predict the future evolution of individual inner-Arctic atmospheric PM components in light of current and emerging pollution mitigation measures and improved region-specific emission inventories.
  • Vuori-Holopainen, Elina; Salo, Eeva; Saxen, Harri; Hedman, Klaus; Hyypiä, Timo; Lahdenperä, Raija; Leinonen, Maija; Tarkka, Eveliina; Vaara, Martti; Peltola, Heikki (2002)
    Childhood pneumonia is usually treated without determining its etiology. The causative organism can be isolated from specimens of blood, empyema fluid, or lung aspirate, but this is rarely done. The potential of transthoracic needle aspiration for identification of causative agents was tested with use of modern microbiological methods. Aspiration was performed for 34 children who had radiological signs compatible with community-acquired pneumonia and had alveolar consolidation. In addition to bacterial and viral cultures and viral antigen detection, nucleic acid detection for common respiratory pathogens was performed on aspirate specimens. Aspiration disclosed the etiology in 20 (59%) of 34 cases overall and in 18 (69%) of 26 patients from whom a representative specimen was obtained. Aspiration's advantages are high microbiological yield and a relatively low risk of a clinically significant adverse event. Aspiration should be used if identification of the causative agent outweighs the modest risk of the procedure.
  • Tran, Tien Viet; Dang, Kien Xuan; Pham, Quynh Huong; Nguyen, Ung Dinh; Trinh, Nhung Thi Trang; Hoang, Luong Van; Ho, Son Anh; Nguyen, Ba Van; Nguyen, Duc Trong; Trinh, Dung Tuan; Tran, Dung Ngoc; Orpana, Arto; Stenman, Ulf-Håkan; Stenman, Jakob; Ho, Tho Huu (2020)
    Background The BRAF(V600E) gene encodes for the mutant BRAF(V600E) protein, which triggers downstream oncogenic signaling in thyroid cancer. Since most currently available methods have focused on detecting BRAF(V600E) mutations in tumor DNA, there is limited information about the level of BRAF(V600E) mRNA in primary tumors of thyroid cancer, and the diagnostic relevance of these RNA mutations is not known. Methods Sixty-two patients with thyroid cancer and non-malignant thyroid disease were included in the study. Armed with an ultrasensitive technique for mRNA-based mutation analysis based on a two step RT-qPCR method, we analysed the expression levels of the mutated BRAF(V600E) mRNA in formalin-fixed paraffin-embedded samples of thyroid tissues. Sanger sequencing for detection of BRAF(V600E) DNA was performed in parallel for comparison and normalization of BRAF(V600E) mRNA expression levels. Results The mRNA-based mutation detection assay enables detection of the BRAF(V600E) mRNA transcripts in a 10,000-fold excess of wildtype BRAF counterparts. While BRAF(V600E) mutations could be detected by Sanger sequencing in 13 out of 32 malignant thyroid cancer FFPE tissue samples, the mRNA-based assay detected mutations in additionally 5 cases, improving the detection rate from 40.6 to 56.3%. Furthermore, we observed a surprisingly large, 3-log variability, in the expression level of the BRAF(V600E) mRNA in FFPE samples of thyroid cancer tissue. Conclusions The expression levels of BRAF(V600E) mRNA was characterized in the primary tumors of thyroid cancer using an ultrasensitive mRNA-based mutation assay. Our data inspires further studies on the prognostic and diagnostic relevance of the BRAF(V600E) mRNA levels as a molecular biomarker for the diagnosis and monitoring of various genetic and malignant diseases.
  • Chen, Chi-Chuan; Hyvönen, Jaakko; Schneider, Harald (2020)
    The microsoroid ferns are one of the largest subfamilies of the Polypodiaceae with over 180 species mainly found in the humid forests of tropical Australasia. The phylogenetic relationships are still unclear, especially the delimitation of the genus Microsorum which has been recognized to be non-monophyletic. We analysed the microsoroid ferns using six chloroplast DNA regions (rbcL, rps4+rps4-trnS, trnL+trnL-trnF, atpA, atpB and matK) in order to present a robust hypothesis of their phylogeny. Our results suggest that they comprise up to 17 genera; of them, 12 agree with a previously accepted generic classification. Five tribes are proposed based on the phylogenetic relationships. Most of the species traditionally included in the genus Microsorum are found in six genera belonging to two tribes. In addition to the commonly used DNA markers, the additional atpA and matK are helpful to provide information about the phylogenetic relationships of the microsoroid ferns.
  • Algars, Annika; Avoranta, Tuulia; Osterlund, Pia; Lintunen, Minnamaija; Sundstrom, Jari; Jokilehto, Terhi; Ristimaki, Ari; Ristamaki, Raija; Carpen, Olli (2014)
  • Huhtaniemi, Riikka; Sipila, Petra; Junnila, Arttu; Oksala, Riikka; Knuuttila, Matias; Mehmood, Arfa; Aho, Eija; Laajala, Teemu D.; Aittokallio, Tero; Laiho, Asta; Elo, Laura; Ohlsson, Claes; Thulin, Malin Hagberg; Kallio, Pekka; Makela, Sari; Mustonen, Mika V. J.; Poutanen, Matti (2022)
    Antiandrogen treatment resistance is a major clinical concern in castration-resistant prostate cancer (CRPC) treatment. Using xenografts of VCaP cells we showed that growth of antiandrogen resistant CRPC tumors were characterized by a higher intratumor dihydrotestosterone (DHT) concentration than that of treatment responsive tumors. Furthermore, the slow tumor growth after adrenalectomy was associated with a low intratumor DHT concentration. Reactivation of androgen signaling in enzalutamide-resistant tumors was further shown by the expression of several androgen-dependent genes. The data indicate that intratumor DHT concentration and expression of several androgen-dependent genes in CRPC lesions is an indication of enzalutamide treatment resistance and an indication of the need for further androgen blockade. The presence of an androgen synthesis, independent of CYP17A1 activity, has been shown to exist in prostate cancer cells, and thus, novel androgen synthesis inhibitors are needed for the treatment of enzalutamide-resistant CRPC tumors that do not respond to abiraterone.