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SHEBA geolocations, a distinct change in the ice albedo has occurred since 2007, because most of the multiyear ice has been replaced by first-year ice.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.
  • 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)
  • 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.
  • 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.
  • 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)
  • Halavaara, Mika; Martelius, Timi; Järvinen, Asko; Antikainen, Jenni; Kuusela, Pentti; Salminen, Ulla-Stina; Anttila, Veli-Jukka (2019)
    Treatment of infective endocarditis (IE) should be initiated promptly. This might hamper the chances to identify the causative organism in blood cultures. Microbiological sampling of infected valve in patients undergoing surgery might identify the causative organism. The impact of pre-operative antimicrobial treatment on the yield of valve samples is not known. This study evaluated the impact of the duration of the pre-operative antibiotic treatment on valve culture and 16S rRNA PCR findings from resected endocardial samples. Patients meeting the modified Duke criteria of definite or possible IE and undergoing valve surgery due to IE during 2011–2016 were included from Southern Finland. Eighty-seven patients were included. In patients with shorter than 2 weeks of pre-operative antimicrobial treatment, PCR was positive in 91% (n = 42/46) and valve culture in 41% (n = 19/46) of cases. However, in patients who had 2 weeks or longer therapy before operation, PCR was positive in 53% (n = 18/34) and all valve cultures were negative. In 14% of patients, PCR had a diagnostic impact. In blood-culture negative cases (n = 13), PCR could detect the causative organism in ten patients (77%). These included five cases of Bartonella quintana, one Tropheryma whipplei, and one Coxiella burnetii. Long pre-operative antimicrobial treatment was shown to have a negative impact on microbiological tests done on resected endocardial material. After 2 weeks of therapy, all valve cultures were negative, but PCR was positive in half of the cases. PCR aided in diagnostic work-up, especially in blood culture negative cases.
  • 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.
  • Peltola, Katriina J.; Bono, Petri; Hugh Jones, Robert; Vjaters, Egils; Nykänen, Pirjo; Vuorela, Annamari; Oksala, Riikka; Pohjanjousi, Pasi; Mustonen, Mika V. J.; Fizazi, Karim; Massard, Christophe (2020)
    Background: Most prostate cancer patients develop castration-resistant prostate cancer (CRPC) after androgen deprivation therapy treatment. CRPC growth is mediated mostly by androgen receptor signalling driven by primary androgens synthesised largely by the CYP17A1 enzyme. Objective: To evaluate the safety profile and dose-limiting toxicities of ODM-204. Design, setting, and participants: In this open, uncontrolled, nonrandomised, multi-centre, tolerability and pharmacokinetic first-in-man phase I dose escalation study, patients with metastatic CRPC were randomised to receive ODM-204 in sequential cohorts of five dose levels (ie, 50, 100, 200, 300, and 500 mg twice daily) concomitantly with prednisone. Intervention: ODM-204, a novel, orally administered, investigational, nonsteroidal dual inhibitor of CYP17A1 and androgen receptor. Outcome measurements and statistical analysis: ODM-204 plasma concentrations, serum testosterone, and prostate-specific antigen (PSA) levels were evaluated and imaging of lesions was performed. Results and limitations: Of the 23 patients enrolled into the study, 60.9% experienced mild adverse effects considered to be related to the study treatment, which were fatigue, increased/decreased appetite, nausea, asthenia, diarrhoea, and weight decrease. ODM-204 area under the curve (AUC(0-12)) values increased dose dependently until the 300 mg dose. The AUC was lower on day 8 after repeated dosing compared with day 1 from the 200 mg dose upwards. Decreases in testosterone levels were seen with ODM-204 treatment confirming androgen deprivation. Of the patients, 13% also demonstrated a >50% decrease in PSA at week 12 and continued ODM-204 treatment for over a year. Conclusions: ODM-204 was well tolerated up to the highest evaluated dose. There were decreases in both testosterone and PSA levels, suggesting preliminary antitumour activity in the treatment of CRPC. The pharmacokinetic properties of the molecule, however, prevent further development. Patient summary: This study looked at the safety of ODM-204, a novel dual inhibitor of CYP17A1 and the androgen receptor, in castration-resistant prostate cancer patients. ODM-204 treatment was found to be well tolerated, and it also reduced both serum testosterone and prostate-specific antigen levels, but the properties of the molecule prevent further development. (C) 2018 European Association of Urology. Published by Elsevier B.V.
  • Backman, John; Schmeisser, Lauren; Virkkula, Aki; Ogren, John A.; Asmi, Eija; Starkweather, Sandra; Sharma, Sangeeta; Eleftheriadis, Konstantinos; Uttal, Taneil; Jefferson, Anne; Bergin, Michael; Makshtas, Alexander; Tunved, Peter; Fiebig, Markus (2017)
    Several types of filter-based instruments are used to estimate aerosol light absorption coefficients. Two significant results are presented based on Aethalometer measurements at six Arctic stations from 2012 to 2014. First, an alternative method of post-processing the Aethalometer data is presented, which reduces measurement noise and lowers the detection limit of the instrument more effectively than box-car averaging. The biggest benefit of this approach can be achieved if instrument drift is minimised. Moreover, by using an attenuation threshold criterion for data post-processing, the relative uncertainty from the electronic noise of the instrument is kept constant. This approach results in a time series with a variable collection time (Delta t) but with a constant relative uncertainty with regard to electronic noise in the instrument. An additional advantage of this method is that the detection limit of the instrument will be lowered at small aerosol concentrations at the expense of temporal resolution, whereas there is little to no loss in temporal resolution at high aerosol concentrations (>2.1-6.7Mm(-1) as measured by the Aethalometers). At high aerosol concentrations, minimising the detection limit of the instrument is less critical. Additionally, utilising co-located filter-based absorption photometers, a correction factor is presented for the Arctic that can be used in Aethalometer corrections available in literature. The correction factor of 3.45 was calculated for low-elevation Arctic stations. This correction factor harmonises Aethalometer attenuation coefficients with light absorption coefficients as measured by the co-located light absorption photometers. Using one correction factor for Arctic Aethalometers has the advantage that measurements between stations become more inter-comparable.
  • Kalendar, Ruslan; Shustov, Alexandr; Schulman, Alan (2021)
    Genome walking (GW), a strategy for capturing previously unsequenced DNA fragments that exist in proximity to a known sequence tag, is currently predominantly based on PCR. Recently developed PCR-based methods allow for combining of sequence-specific primers with designed capturing primers capable of annealing to unknown DNA targets, which offer the rapidity and effectiveness of PCR. This study presents a methodological improvement to the previously described GW technique known as Palindromic Sequence-Targeted PCR (PST-PCR). Like PST-PCR, this new method (called PST-PCR v.2) relies on targeting of capturing primers to palindromic sequences arbitrarily present in natural DNA templates. PST-PCR v.2 consists of two rounds of PCR. The first round uses a combination of one sequence-specific primer with one capturing (PST) primer. The second round uses a combination of a single (preferred) or two universal primers; one anneals to a 5’ tail attached to the sequence-specific primer and the other anneals to a different 5’ tail attached to the PST primer. The key advantage of PST-PCR v.2 is the convenience of using a single universal primer with invariable sequences in GW processes involving various templates. The entire procedure takes approximately 2–3 hours to produce the amplified PCR fragment, which contains a portion of a template flanked by the sequence-specific and capturing primers. PST-PCR v.2 is highly suitable for simultaneous work with multiple samples. For this reason, PST-PCR v.2 can be applied beyond the classical task of GW for studies in population genetics, in which PST-PCR v.2 is a preferred alternative to amplified fragment length polymorphism (AFLP) or next-generation sequencing. Furthermore, the conditions for PST-PCR v.2 are easier to optimize, as only one sequence-specific primer is used. This reduces non-specific Random Amplified Polymorphic DNA (RAPD)-like amplification and formation of non-templated amplification. Importantly, akin to the previous version, PST-PCR v.2 is not sensitive to template DNA sequence complexity or quality. This study illustrates the utility of PST-PCR v.2 for transposon display, which is a method to characterize inter- or intra-specific variability related to transposon integration sites. The Ac transposon sequence in the corn (Zea mays) genome was used as a sequence tag during the transposon display procedure to characterize the Ac integration sites.