Browsing by Subject "QUANTIFICATION"

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  • Puustinen, Lauri; Hakkarainen, Antti; Kivisaari, Reetta; Boyd, Sonja; Nieminen, Urpo; Färkkilä, Martti; Lundbom, Nina; Arkkila, Perttu (2017)
    Background: Liver biopsy is the gold standard in evaluating inflammation and fibrosis in autoimmune hepatitis.Aims: In search of non-invasive follow-up tools in autoimmune hepatitis, we evaluated (31)phosphorus magnetic resonance spectroscopy (P-31 MRS).Methods: Twelve consecutive AIH patients (mean age 42.8 years, 10 women) underwent liver biopsy, routine laboratory liver function tests, which were compared to findings in P-31 MRS and transient elastography (TE).Results: Phosphoenolpuryvate (PEP) correlated with the grade of inflammation (r=0.746, p=.005) and thromboplastin time (r=0.592, p=.043). It also differentiated patients with active inflammation from patients without (t=3.781, p=.009). There was no correlation between PEP and aminotransferase or immunoglobulin G levels.The phosphoethanolamine (PE)/phosphocholine (PC) ratio, PE/glyserophosphoethanolamine (GPE) ratio and PC/[total phosphomonoester (PME)+phosphodiester (PDE)] ratios correlated with immunoglobulin G (r=0.764, p=.006; r=0.618, p=.043; and r=-0.636, p=.035, respectively).PME/PDE and PE/GPE correlated with fibrosis (r=0.668, p=.018 and r=0.604, p=.037). PE/GPE also differentiated F3 from F0-2 patients (t=3.810, p=.003).Phosphorus metabolites did not correlate with TE results and TE did not correlate with liver histology or laboratory parameters.Conclusions: P-31 MRS seems to detect active inflammation and advanced fibrosis in AIH patients. TE was ineffective in fibrosis quantification.
  • Sanwald, Corinna; Robciuc, Alexandra; Ruokonen, Suvi-Katriina; Wiedmer, Susanne K.; Lammerhofer, Michael (2019)
    This work presents the development and validation of a quantitative HILIC UHPLC-ESI-QTOF-MS/MS method for amino acids combined with untargeted metabolic profiling of human corneal epithelial (HCE) cells after treatment with ionic liquids. The work included a preliminary metabotoxicity screening of 14 different ionic liquids, of which 9 carefully selected ionic liquids were chosen for a metabolomics study. This study is focused on the correlation between the toxicity of the ionic liquids and their metabolic profiles. The method development included the comparison of different MS/MS acquisition modes. A sequential window acquisition of all theoretical fragment ion mass spectra (SWATH) method with variable Q1 window widths and narrow Q1 target windows of 5 Da for most of the amino acids was selected as the optimal acquisition mode. Due to the absence of a true blank matrix, C-13,N-15-isotopically labelled amino acids were utilized as surrogate calibrants, instead of proteinogenic amino acids. Partial least squares (PLS) analysis of the median effective concentrations (EC50) of 9 selected ionic liquids showed a correlation with their metabolic profile measured by the untargeted screening.
  • Purhonen, Janne; Banerjee, Rishi; McDonald, Allison E.; Fellman, Vineta; Kallijarvi, Jukka (2020)
    Deoxyribonucleoside triphosphates (dNTPs) are vital for the biosynthesis and repair of DNA. Their cellular concentration peaks during the S phase of the cell cycle. In non-proliferating cells, dNTP concentrations are low, making their reliable quantification from tissue samples of heterogeneous cellular composition challenging. Partly because of this, the current knowledge related to the regulation of and disturbances in cellular dNTP concentrations derive mostly from cell culture experiments with little corroboration at the tissue or organismal level. Here, we fill the methodological gap by presenting a simple non-radioactive microplate assay for the quantification of dNTPs with a minimum requirement of 4-12 mg of biopsy material. In contrast to published assays, this assay is based on long synthetic single-stranded DNA templates (50-200 nucleotides), an inhibitor-resistant high-fidelity DNA polymerase, and the double-stranded-DNA-binding EvaGreen dye. The assay quantified reliably less than 50 fmol of each of the four dNTPs and discriminated well against ribonucleotides. Additionally, thermostable RNAse HII-mediated nicking of the reaction products and a subsequent shift in their melting temperature allowed near-complete elimination of the interfering ribonucleotide signal, if present. Importantly, the assay allowed measurement of minute dNTP concentrations in mouse liver, heart and skeletal muscle.
  • Richardson, Dominique; Itkonen, Jaakko; Nievas, Julia; Urtti, Arto; Casteleijn, Marco G. (2018)
    The use of living cells for the synthesis of pharmaceutical proteins, though state-of-the-art, is hindered by its lengthy process comprising of many steps that may affect the protein’s stability and activity. We aimed to integrate protein expression, purification, and bioconjugation in small volumes coupled with cell free protein synthesis for the target protein, ciliary neurotrophic factor. Split-intein mediated capture by use of capture peptides onto a solid surface was efficient at 89–93%. Proof-of-principle of light triggered release was compared to affinity chromatography (His6 fusion tag coupled with Ni-NTA). The latter was more efficient, but more time consuming. Light triggered release was clearly demonstrated. Moreover, we transferred biotin from the capture peptide to the target protein without further purification steps. Finally, the target protein was released in a buffer-volume and composition of our choice, omitting the need for protein concentration or changing the buffer. Split-intein mediated capture, protein trans splicing followed by light triggered release, and bioconjugation for proteins synthesized in cell free systems might be performed in an integrated workflow resulting in the fast production of the target protein.
  • Vitt, Anton; Babenka, Andrei; Bostrom, Elisabeth A.; Gustafsson, Anders; Lira, Ronaldo; Slizen, Veronica; Sorsa, Timo; Tervahartiala, Taina; Buhlin, Kåre (2020)
    To evaluate the effect of adjunctive antiseptic irrigation of periodontal pockets on microbial and cytokine profiles. Fifty-nine patients with severe periodontitis were allocated to one of three groups for scaling and root planing facilitated with different adjunctive antiseptics: 1% polyhexamethyleneguanidine phosphate (PHMG-P) (n = 19), 0.2% chlorhexidine (CHX) (n = 21) or distilled water (n = 19). Gingival crevicular fluid and subgingival bacterial samples were collected at baseline, and at 2 weeks, and 1 and 4 months. The levels of interleukin (IL)-1 beta, IL-8, IL-10, and IL-17A, matrix metalloproteinase (MMP)-8, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Fusobacterium nucleatum,Aggregatibacter actinomycetemcomitans, and Prevotella intermedia were determined. There were no intergroup differences in cytokine concentrations and bacterial counts at any follow-up, however, varying patterns were observed. In the PHMG-P and water groups IL-1 beta expression peaked at 2 weeks and then gradually declined. In all three groups, the dynamics of MMP-8 concentration were non-linear, increasing by 2 weeks and then declining to below baseline (p > 0.05). P. gingivalis and T. forsythia declined within the first month and increased thereafter, not regaining the baseline level. Adjunctive antiseptic treatment was associated with changes in biomarkers and bacterial counts in the course of the study. The effects of adjunctive antiseptic irrigation were limited in the applied protocol.
  • Avela, Henri F.; Siren, Heli (2020)
    The review concentrates on the properties of analytical and statistical ultrahigh-performance liquid chromatographic (UHPLC) - mass spectrometric (MS) methods suitable for glycero-, glycerophospho- and sphingolipids in lipidomics published between the years 2017 2019. Trends and fluctuations of conventional and nano-UHPLC methods with MS and tandem MS detection were observed in context of analysis conditions and tools used for data-analysis. Whereas general workflow characteristics are agreed upon, more details related to the chromatographic methodology (i.e. stationary and mobile phase conditions) need evidently agreements. Lipid quantitation relies upon isotope-labelled standards in targeted analyses and fully standardless algorithm-based untargeted analyses. Furthermore, a wide spectrum of setups have shown potential for the elucidation of complex and large datasets by minimizing the risks of systematic misinterpretation like false positives. This kind of evaluation was shown to have increased importance and usage for cross-validation and data-analysis. (C) 2020 Elsevier B.V. All rights reserved.
  • Harjumaki, Riina; Zhang, Xue; Nugroho, Robertus Wahyu N.; Farooq, Muhammad; Lou, Yan-Ru; Yliperttula, Marjo; Valle-Delgado, Juan Jose; Osterberg, Monika (2020)
    Transmembrane protein integrins play a key role in cell adhesion. Cell-biomaterial interactions are affected by integrin expression and conformation, which are actively controlled by cells. Although integrin structure and function have been studied in detail, quantitative analyses of integrin-mediated cell-biomaterial interactions are still scarce. Here, we have used atomic force spectroscopy to study how integrin distribution and activation (via intracellular mechanisms in living cells or by divalent cations) affect the interaction of human pluripotent stem cells (WA07) and human hepatocarcinoma cells (HepG2) with promising biomaterials.human recombinant laminin-521 (LN-521) and cellulose nanofibrils (CNF). Cell adhesion to LN-521-coated probes was remarkably influenced by cell viability, divalent cations, and integrin density in WA07 colonies, indicating that specific bonds between LN-521 and activated integrins play a significant role in the interactions between LN-521 and HepG2 and WA07 cells. In contrast, the interactions between CNF and cells were nonspecific and not influenced by cell viability or the presence of divalent cations. These results shed light on the underlying mechanisms of cell adhesion, with direct impact on cell culture and tissue engineering applications.
  • Patro, Rob; Salmela, Leena (2021)
    DNA and RNA sequencing is a core technology in biological andmedical research. The high throughput of these technologies and the consistent development of new experimental assays and biotechnologies demand the continuous development of methods to analyze the resulting data. The RECOMB SatelliteWorkshop on Massively Parallel Sequencing brings together leading researchers in computational genomics to discuss emerging frontiers in algorithm development for massively parallel sequencing data. The 10th meeting in this series, RECOMBSeq 2020, was scheduled to be held in Padua, Italy, but due to the ongoing COVID-19 pandemic, the meeting was carried out virtually instead. The online workshop featured keynote talks by Paola Bonizzoni and Zamin Iqbal, two highlight talks, ten regular talks, and three short talks. Seven of the works presented in the workshop are featured in this edition of iScience, and many of the talks are available online in the RECOMB-Seq 2020 YouTube channel.
  • Akhgari , Amir; Laakso, Into; Seppänen-Laakso, Tuulikki; Yrjönen, Teijo; Vuorela, Heikki; Oksman-Caldentey, Kirsi-Marja; Rischer, Heiko (2015)
    Rhazya stricta Decne. (Apocynaceae) contains a large number of terpenoid indole alkaloids (TIAs). This study focused on the composition of alkaloids obtained from transformed hairy root cultures of R. stricta employing ultra-performance liquid chromatography-mass spectrometry (UPLC-MS). In the UPLC-MS analyses, a total of 20 TIAs were identified from crude extracts. Eburenine and vincanine were the main alkaloids followed by polar glucoalkaloids, strictosidine lactam and strictosidine. Secodine-type alkaloids, tetrahydrosecodinol, tetrahydro- and dihydrosecodine were detected too. The occurrence of tetrahydrosecodinol was confirmed for the first time for R. stricta. Furthermore, two isomers of yohimbine, serpentine and vallesiachotamine were identified. The study shows that a characteristic pattern of biosynthetically related TIAs can be monitored in Rhazya hairy root crude extract by this chromatographic method.
  • Slighoua, Meryem; Mahdi, Ismail; Amrati, Fatima ez-Zahra; Di Cristo, Francesca; Amaghnouje, Amal; Grafov, Andrey; Boucetta, Nabil; Bari, Amina; Bousta, Dalila (2021)
    Ethnopharmacological relevance: Since the dawn of time, medicinal and aromatic plants (AMPs) represent a precious heritage for humanity, especially in developing countries, who exploit their virtues in traditional pharmacopoeia to cope with health problems such as diabetes, kidney stones, ulcer, and digestive disorders. Petroselinum sativum Hoffm. belongs to Apiaceae family. It is traditionally used to treat arterial hypertension, diabetes, cardiac disease, renal disease, and recently reported as a plant endowed with a female anti-infertility effect. Aim of the study: This study aims to evaluate the in vivo effect of hydro-ethanolic extract and polyphenols of Petroselinum sativum Hoffm. on cholesterol, protein and estrogen levels, and characterize the chemical composition of polyphenolic fraction. In addition, acute toxicity and anti-inflammatory activity of tested extract was also investigated. Materials and methods: Chemical composition of polyphenolic fraction was determined using High-Performance Liquid Chromatography with Diode-Array Detection (HPLC-DAD). First, toxicological investigations including sub-acute toxicity were performed by measuring animals' weights daily for four weeks. Afterwards, histopathological examination of livers and kidneys, and serum assay of ASAT and ALAT were also checked. Next, the acute in vivo anti-inflammatory study of the hydro-ethanolic extract and polyphenols of Petroselinum sativum Hoffm. versus Indomethacin was conducted. Furthermore, we evaluated the estrogenic effect of its hydroethanolic extract and the polyphenolic fraction following biochemical assays for the determination of proteins, cholesterol and estrogen levels. Results: The results revealed the presence of some phenolic compounds mainly ferulic acid, gallic acid and quercetin. Petroselinum sativum Hoffm. extracts also showed no evidence of hepatotoxicity nor nephrotoxicity, with remarkable anti-inflammatory activity, as well as a significant estrogenic effect compared to negative control. Conclusion: This study provides a scope of the potential use of Petroselinum sativum Hoffm. extracts in counteracting female infertility issues.
  • Malinen, Erja; Krogius-Kurikka, Lotta Kaisa; Lyra, Anna; Nikkila, Janne; Jaaskelainen, Anne; Rinttila, Teemu; Vilpponen-Salmela, Terttu; von Wright, Atte Johannes; Palva, Airi (2010)
  • Clark, David W.; Okada, Yukinori; Moore, Kristjan H. S.; Mason, Dan; Pirastu, Nicola; Gandin, Ilaria; Mattsson, Hannele; Barnes, Catriona L. K.; Lin, Kuang; Zhao, Jing Hua; Deelen, Patrick; Rohde, Rebecca; Schurmann, Claudia; Guo, Xiuqing; Giulianini, Franco; Zhang, Weihua; Medina-Gomez, Carolina; Karlsson, Robert; Bao, Yanchun; Bartz, Traci M.; Baumbach, Clemens; Biino, Ginevra; Bixley, Matthew J.; Brumat, Marco; Chai, Jin-Fang; Corre, Tanguy; Cousminer, Diana L.; Dekker, Annelot M.; Eccles, David A.; Van Eijk, Kristel R.; Fuchsberger, Christian; Gao, He; Germain, Marine; Gordon, Scott D.; de Haan, Hugoline G.; Harris, Sarah E.; Hofer, Edith; Huerta-Chagoya, Alicia; Igartua, Catherine; Jansen, Iris E.; Jia, Yucheng; Kacprowski, Tim; Karlsson, Torgny; Kleber, Marcus E.; Li, Shengchao Alfred; Li-Gao, Ruifang; Mahajan, Anubha; Matsuda, Koichi; Meidtner, Karina; Meng, Weihua; Montasser, May E.; van der Most, Peter J.; Munz, Matthias; Nutile, Teresa; Palviainen, Teemu; Prasad, Gauri; Prasad, Rashmi B.; Priyanka, Tallapragada Divya Sri; Rizzi, Federica; Salvi, Erika; Sapkota, Bishwa R.; Shriner, Daniel; Skotte, Line; Smart, Melissa C.; Smith, Albert Vernon; van der Spek, Ashley; Spracklen, Cassandra N.; Strawbridge, Rona J.; Tajuddin, Salman M.; Trompet, Stella; Turman, Constance; Verweij, Niek; Viberti, Clara; Wang, Lihua; Warren, Helen R.; Wootton, Robyn E.; Yanek, Lisa R.; Yao, Jie; Yousri, Noha A.; Zhao, Wei; Adeyemo, Adebowale A.; Afaq, Saima; Alberto Aguilar-Salinas, Carlos; Akiyama, Masato; Albert, Matthew L.; Allison, Matthew A.; Alver, Maris; Aung, Tin; Azizi, Fereidoun; Bentley, Amy R.; Boeing, Heiner; Boerwinkle, Eric; Borja, Judith B.; de Borst, Gert J.; Bottinger, Erwin P.; Broer, Linda; Campbell, Harry; Chanock, Stephen; Chee, Miao-Li; Chen, Guanjie; Chen, Yii-Der I.; Chen, Zhengming; Chiu, Yen-Feng; Cocca, Massimiliano; Collins, Francis S.; Concas, Maria Pina; Corley, Janie; Cugliari, Giovanni; Van Dam, Rob M.; Damulina, Anna; Daneshpour, Maryam S.; Day, Felix R.; Delgado, Graciela E.; Dhana, Klodian; Doney, Alexander S. F.; Doerr, Marcus; Doumatey, Ayo P.; Dzimiri, Nduna; Ebenesersdottir, S. Sunna; Elliott, Joshua; Elliott, Paul; Ewert, Ralf; Felix, Janine F.; Fischer, Krista; Freedman, Barry I.; Girotto, Giorgia; Goel, Anuj; Gogele, Martin; Goodarzi, Mark O.; Graff, Mariaelisa; Granot-Hershkovitz, Einat; Grodstein, Francine; Guarrera, Simonetta; Gudbjartsson, Daniel F.; Guity, Kamran; Gunnarsson, Bjarni; Guo, Yu; Hagenaars, Saskia P.; Haiman, Christopher A.; Halevy, Avner; Harris, Tamara B.; Hedayati, Mehdi; van Heel, David A.; Hirata, Makoto; Hofer, Imo; Hsiung, Chao Agnes; Huang, Jinyan; Hung, Yi-Jen; Ikram, M. Arfan; Jagadeesan, Anuradha; Jousilahti, Pekka; Kamatani, Yoichiro; Kanai, Masahiro; Kerrison, Nicola D.; Kessler, Thorsten; Khaw, Kay-Tee; Khor, Chiea Chuen; de Kleijn, Dominique P. V.; Koh, Woon-Puay; Kolcic, Ivana; Kraft, Peter; Kramer, Bernhard K.; Kutalik, Zoltan; Kuusisto, Johanna; Langenberg, Claudia; Launer, Lenore J.; Lawlor, Deborah A.; Lee, I-Te; Lee, Wen-Jane; Lerch, Markus M.; Li, Liming; Liu, Jianjun; Loh, Marie; London, Stephanie J.; Loomis, Stephanie; Lu, Yingchang; Luan, Jian'an; Magi, Reedik; Manichaikul, Ani W.; Manunta, Paolo; Masson, Gisli; Matoba, Nana; Mei, Xue W.; Meisinger, Christa; Meitinger, Thomas; Mezzavilla, Massimo; Milani, Lili; Millwood, Iona Y.; Momozawa, Yukihide; Moore, Amy; Morange, Pierre-Emmanuel; Moreno-Macias, Hortensia; Mori, Trevor A.; Morrison, Alanna C.; Muka, Taulant; Murakami, Yoshinori; Murray, Alison D.; de Mutsert, Renee; Mychaleckyj, Josyf C.; Nalls, Mike A.; Nauck, Matthias; Neville, Matt J.; Nolte, Ilja M.; Ong, Ken K.; Orozco, Lorena; Padmanabhan, Sandosh; Palsson, Gunnar; Pankow, James S.; Pattaro, Cristian; Pattie, Alison; Polasek, Ozren; Poulter, Neil; Pramstaller, Peter P.; Quintana-Murci, Lluis; Räikkönen, Katri; Ralhan, Sarju; Rao, Dabeeru C.; van Rheenen, Wouter; Rich, Stephen S.; Ridker, Paul M.; Rietveld, Cornelius A.; Robino, Antonietta; van Rooij, Frank J. A.; Ruggiero, Daniela; Saba, Yasaman; Sabanayagam, Charumathi; Sabater-Lleal, Maria; Felicita Sala, Cinzia; Salomaa, Veikko; Sandow, Kevin; Schmidt, Helena; Scott, Laura J.; Scott, William R.; Sedaghati-Khayat, Bahareh; Sennblad, Bengt; van Setten, Jessica; Sever, Peter J.; Sheu, Wayne H-H; Shi, Yuan; Shrestha, Smeeta; Shukla, Sharvari Rahul; Sigurdsson, Jon K.; Sikka, Timo Tonis; Singh, Jai Rup; Smith, Blair H.; Stancakova, Alena; Stanton, Alice; Starr, John M.; Stefansdottir, Lilja; Straker, Leon; Sulem, Patrick; Sveinbjornsson, Gardar; Swertz, Morris A.; Taylor, Adele M.; Taylor, Kent D.; Terzikhan, Natalie; Tham, Yih-Chung; Thorleifsson, Gudmar; Thorsteinsdottir, Unnur; Tillander, Annika; Tracy, Russell P.; Tusie-Luna, Teresa; Tzoulaki, Ioanna; Vaccargiu, Simona; Vangipurapu, Jagadish; Veldink, Jan H.; Vitart, Veronique; Volker, Uwe; Vuoksimaa, Eero; Wakil, Salma M.; Waldenberger, Melanie; Wander, Gurpreet S.; Wang, Ya Xing; Wareham, Nicholas J.; Wild, Sarah; Yajnik, Chittaranjan S.; Yuan, Jian-Min; Zeng, Lingyao; Zhang, Liang; Zhou, Jie; Amin, Najaf; Asselbergs, Folkert W.; Bakker, Stephan J. L.; Becker, Diane M.; Lehne, Benjamin; Bennett, David A.; van den Berg, Leonard H.; Berndt, Sonja I.; Bharadwaj, Dwaipayan; Bielak, Lawrence F.; Bochud, Murielle; Boehnke, Mike; Bouchard, Claude; Bradfield, Jonathan P.; Brody, Jennifer A.; Campbell, Archie; Carmi, Shai; Caulfield, Mark J.; Cesarini, David; Chambers, John C.; Chandak, Giriraj Ratan; Cheng, Ching-Yu; Ciullo, Marina; Cornelis, Marilyn; Cusi, Daniele; Smith, George Davey; Deary, Ian J.; Dorajoo, Rajkumar; van Duijn, Cornelia M.; Ellinghaus, David; Erdmann, Jeanette; Eriksson, Johan G.; Evangelou, Evangelos; Evans, Michele K.; Faul, Jessica D.; Feenstra, Bjarke; Feitosa, Mary; Foisy, Sylvain; Franke, Andre; Friedlander, Yechiel; Gasparini, Paolo; Gieger, Christian; Gonzalez, Clicerio; Goyette, Philippe; Grant, Struan F. A.; Griffiths, Lyn R.; Groop, Leif; Gudnason, Vilmundur; Gyllensten, Ulf; Hakonarson, Hakon; Hamsten, Anders; van der Harst, Pim; Heng, Chew-Kiat; Hicks, Andrew A.; Hochner, Hagit; Huikuri, Heikki; Hunt, Steven C.; Jaddoe, Vincent W. V.; De Jager, Philip L.; Johannesson, Magnus; Johansson, Asa; Jonas, Jost B.; Jukema, J. Wouter; Junttila, Juhani; Kaprio, Jaakko; Kardia, Sharon L. R.; Karpe, Fredrik; Kumari, Meena; Laakso, Markku; van der Laan, Sander W.; Lahti, Jari; Laudes, Matthias; Lea, Rodney A.; Lieb, Wolfgang; Lumley, Thomas; Martin, Nicholas G.; Marz, Winfried; Matullo, Giuseppe; McCarthy, Mark I.; Medland, Sarah E.; Merriman, Tony R.; Metspalu, Andres; Meyer, Brian F.; Mohlke, Karen L.; Montgomery, Grant W.; Mook-Kanamori, Dennis; Munroe, Patricia B.; North, Kari E.; Nyholt, Dale R.; O'connell, Jeffery R.; Ober, Carole; Oldehinkel, Albertine J.; Palmas, Walter; Palmer, Colin; Pasterkamp, Gerard G.; Patin, Etienne; Pennell, Craig E.; Perusse, Louis; Peyser, Patricia A.; Pirastu, Mario; Polderman, Tinca J. C.; Porteous, David J.; Posthuma, Danielle; Psaty, Bruce M.; Rioux, John D.; Rivadeneira, Fernando; Rotimi, Charles; Rotter, Jerome I.; Rudan, Igor; Den Ruijter, Hester M.; Sanghera, Dharambir K.; Sattar, Naveed; Schmidt, Reinhold; Schulze, Matthias B.; Schunkert, Heribert; Scott, Robert A.; Shuldiner, Alan R.; Sim, Xueling; Small, Neil; Smith, Jennifer A.; Sotoodehnia, Nona; Tai, E-Shyong; Teumer, Alexander; Timpson, Nicholas J.; Toniolo, Daniela; Tregouet, David-Alexandre; Tuomi, Tiinamaija; Vollenweider, Peter; Wang, Carol A.; Weir, David R.; Whitfield, John B.; Wijmenga, Cisca; Wong, Tien-Yin; Wright, John; Yang, Jingyun; Yu, Lei; Zemel, Babette S.; Zonderman, Alan B.; Perola, Markus; Magnusson, Patrik K. E.; Uitterlinden, Andre G.; Kooner, Jaspal S.; Chasman, Daniel I.; Loos, Ruth J. F.; Franceschini, Nora; Franke, Lude; Haley, Chris S.; Hayward, Caroline; Walters, Robin G.; Perry, John R. B.; Esko, Tonu; Helgason, Agnar; Stefansson, Kari; Joshi, Peter K.; Kubo, Michiaki; Wilson, James F. (2019)
    In many species, the offspring of related parents suffer reduced reproductive success, a phenomenon known as inbreeding depression. In humans, the importance of this effect has remained unclear, partly because reproduction between close relatives is both rare and frequently associated with confounding social factors. Here, using genomic inbreeding coefficients (F-ROH) for >1.4 million individuals, we show that F-ROH is significantly associated (p <0.0005) with apparently deleterious changes in 32 out of 100 traits analysed. These changes are associated with runs of homozygosity (ROH), but not with common variant homozygosity, suggesting that genetic variants associated with inbreeding depression are predominantly rare. The effect on fertility is striking: F-ROH equivalent to the offspring of first cousins is associated with a 55% decrease [95% CI 44-66%] in the odds of having children. Finally, the effects of F-ROH are confirmed within full-sibling pairs, where the variation in F-ROH is independent of all environmental confounding.
  • Karsten, Lennard; Janson, Nils; Le Joncour, Vadim; Alam, Sarfaraz; Müller, Benjamin; Tanjore Ramanathan, Jayendrakishore; Laakkonen, Pirjo; Sewald, Norbert; Mueller, Kristian M. (2022)
    Epidermal growth factor receptor (EGFR) is a validated tumor marker overexpressed in various cancers such as squamous cell carcinoma (SSC) of the head and neck and gliomas. We constructed protein-drug conjugates based on the anti-EGFR Designed Ankyrin Repeat Protein (DARPin) E01, and compared the bivalent DARPin dimer (DD1) and a DARPin-Fc (DFc) to the monomeric DARPin (DM) and the antibody derived scFv425-Fc (scFvFc) in cell culture and a mouse model. The modular conjugation system, which was successfully applied for the preparation of protein-drug and -dye conjugates, uses bio-orthogonal protein-aldehyde generation by the formylglycine-generating enzyme (FGE). The generated carbonyl moiety is addressed by a bifunctional linker with a pyrazolone for a tandem Knoevenagel reaction and an azide for strain-promoted azide-alkyne cycloaddition (SPAAC). The latter reaction with a PEGylated linker containing a dibenzocyclooctyne (DBCO) for SPAAC and monomethyl auristatin E (MMAE) as the toxin provided the stable conjugates DD1-MMAE (drug-antibody ratio, DAR = 2.0) and DFc-MMAE (DAR = 4.0) with sub-nanomolar cytotoxicity against the human squamous carcinoma derived A431 cells. In vivo imaging of Alexa Fluor 647-dye conjugates in A431-xenografted mice bearing subcutaneous tumors as the SCC model revealed unspecific binding of bivalent DARPins to the ubiquitously expressed EGFR. Tumor-targeting was verified 6 h post-injection solely for DD1 and scFvFc. The total of four administrations of 6.5 mg/kg DD1-MMAE or DFc-MMAE twice weekly did not cause any sequela in mice. MMAE conjugates showed no significant anti-tumor efficacy in vivo, but a trend towards increased necrotic areas (p = 0.2213) was observed for the DD1-MMAE (n = 5).
  • Saraswat, Mayank; Joenvaara, Sakari; Seppanen, Hanna; Mustonen, Harri; Haglund, Caj; Renkonen, Risto (2017)
    Finland ranks sixth among the countries having highest incidence rate of pancreatic cancer with mortality roughly equaling incidence. The average age of diagnosis for pancreatic cancer is 69years in Nordic males, whereas the average age of diagnosis of chronic pancreatitis is 40-50years, however, many cases overlap in age. By radiology, the evaluation of a pancreatic mass, that is, the differential diagnosis between chronic pancreatitis and pancreatic cancer is often difficult. Preoperative needle biopsies are difficult to obtain and are demanding to interpret. New blood based biomarkers are needed. The accuracy of the only established biomarker for pancreatic cancer, CA 19-9 is rather poor in differentiating between benign and malignant mass of the pancreas. In this study, we have performed mass spectrometry analysis (High Definition MSE) of serum samples from patients with chronic pancreatitis (13) and pancreatic cancer (22). We have quantified 291 proteins and performed detailed statistical analysis such as principal component analysis, orthogonal partial least square discriminant analysis and receiver operating curve analysis. The proteomic signature of chronic pancreatitis versus pancreatic cancer samples was able to separate the two groups by multiple statistical techniques. Some of the enriched pathways in the proteomic dataset were LXR/RXR activation, complement and coagulation systems and inflammatory response. We propose that multiple high-confidence biomarker candidates in our pilot study including Inter-alpha-trypsin inhibitor heavy chain H2 (Area under the curve, AUC: 0.947), protein AMBP (AUC: 0.951) and prothrombin (AUC: 0.917), which should be further evaluated in larger patient series as potential new biomarkers for differential diagnosis.
  • Wang, Kai; Zheng, Xunhua; Pihlatie, Mari; Vesala, Timo; Liu, Chunyan; Haapanala, Sami; Mammarella, Ivan; Rannik, Ullar; Liu, Huizhi (2013)
    Nitrous oxide (N2O) fluxes from a cotton field in northern China were measured for a year using the static chamber method based on a gas chromatograph (GC) and the eddy covariance (EC) technique based on a tunable diode laser (TDL). The aims were to compare the N2O fluxes obtained from both techniques, assess the uncertainties in the fluxes and evaluate the annual direct emission factors (EFds, i.e. the loss rate of fertilizer nitrogen via N2O emission) using the year-round datasets. During the experimental period, the hourly and daily mean chamber fluxes ranged from 0.6 to 781.8 and from 1.2 to 468.8 g N m−2 h−1, respectively. The simultaneously measured daily mean EC fluxes varied between −10.8 and 912.0 g N m−2 h−1. The EC measurements only provided trustworthy 30-min fluxes during high-emission period (a 20-day period immediately after the irrigation that followed the nitrogen fertilization event). A reliable comparison was confined to the high-emission period and showed that the chamber fluxes were 17–20% lower than the EC fluxes. This difference may implicate the magnitude of systematic underestimation in the fluxes from chamber measurements. The annual emission from the fertilized cotton field was estimated at 1.43 kg N ha−1 yr−1 by the chamber observations and 3.15 kg N ha−1 yr−1 by the EC measurements. The EFds calculated from the chamber and EC data were 1.04% and 1.65%, respectively. The chamber-based estimate was very close to the default value (1.0%) recommended by the Intergovernmental Panel on Climate Change. However, the difference in the EFds based on the two measurement techniques may vary greatly with changing environmental conditions and management practices. Further comparison studies are still needed to elucidate this issue.
  • Delayre, C.; Sammaljärvi, J.; Billon, S.; Muuri, E.; Sardini, P.; Siitari-Kauppi, M. (2020)
    This study aims to further develop the C-14-PMMA porosity calculation method with a novel autoradiography technique, the Micro-pattern gas detector autoradiography (MPGDA). In this study, the MPGDA is compared with phosphor screen autoradiography (SPA). A set of rock samples from Martinique Island exhibiting a large range of connected porosities was used to validate the MPGDA method. Calculated porosities were found to be in agreement with ones from the SPA and the triple-weight method (TW). The filmless nature of MPGDA as well as straightforward determination of C-14 radioactivity from the source rock makes the porosity calculation less uncertain. The real-time visualization of radioactivity from C-14 beta emissions by MPGDA is a noticeable improvement in comparison to SPA.
  • Yli-Jyrä, Anssi Mikael (The Association for Computational Linguistics, 2011)
    This paper describes a non-conventional method for compiling (phonological or morpho-syntactic) context restriction (CR) constraints into non-deterministic automata in finite-state tools and surface parsing systems. The method reduces any CR into a simple one that constraints the occurrences of the empty string and represents right contexts with co-determististic states. In cases where a fully deterministic representation would be exponentially larger, this kind of inward de- terminism in contexts can bring benefits over various De Morgan approaches where full determinization is necessary. In the method, an accepted word gets a unique path that is a projection of a ladder-shaped structure in the context recognizer. This projection is computed in time that is polynomial to the number of context states. However, it may be difficult to take advantage of the method in a finite-state library that coerces intermediate results into canonical automata and whose intersection operation assumes deterministic automata.
  • Marchet, Camille; Boucher, Christina; Puglisi, Simon J.; Medvedev, Paul; Salson, Mikael; Chikhi, Rayan (2021)
    High-throughput sequencing data sets are usually deposited in public repositories (e.g., the European Nucleotide Archive) to ensure reproducibility. As the amount of data has reached petabyte scale, repositories do not allow one to perform online sequence searches, yet, such a feature would be highly useful to investigators. Toward this goal, in the last few years several computational approaches have been introduced to index and query large collections of data sets. Here, we propose an accessible survey of these approaches, which are generally based on representing data sets as sets of k-mers. We review their properties, introduce a classification, and present their general intuition. We summarize their performance and highlight their current strengths and limitations.
  • Cruz, Cristina D.; Shah, Shreya; Tammela, Paivi (2018)
    BackgroundBiofilms are formed by a complex bacterial community encapsulated by a polymeric matrix, with strong adherent properties and persistent phenotype. Biofilms are considered one of the most challenging areas of modern medicine. Existing antibiotics have been developed against free-floating bacterial cells, and thus, many treatments of biofilm-related infection fail. In this study, we compared the effects of different media on biofilm growth of clinical reference strains of Staphylococci and Enterococci, including multi-drug resistant representatives. Further, we optimized the resazurin-based assay for determining the minimal biofilm inhibitory concentration (MBIC) of standard antibiotics, and evaluated its use for the determination of minimal biofilm eradication concentration (MBEC).ResultsWe showed that tryptic soy broth supplemented with 1% glucose was an optimal media for maximum biofilm growth of all strains tested, with an extended incubation time for Enterococci. A range of parameters were tested for the resazurin assay, including concentration, temperature and time of incubation. Using quality parameters to analyze the assay's performance, the conditions for the resazurin assay were set as follows: 4g/mL and 8g/mL, with incubation at 25 degrees C for 20min and 40min for Staphylococci and Enterococci, respectively.ConclusionsIn summary, we defined conditions for optimal biofilm growth and for standardized resazurin assay for MBIC determination against six Gram-positive clinical reference strains. We also observed that MBEC determination by the resazurin-based assay is limited due to the poor detection limit of the assay. Complementary cell counting data is needed for precise determination of MBEC.
  • Zhu, Yafeng; Orre, Lukas M.; Tran, Yan Zhou; Mermelekas, Georgios; Johansson, Henrik J.; Malyutina, Alina; Anders, Simon; Lehtiö, Janne (2020)
    Quantitative proteomics by mass spectrometry is widely used in biomarker research and basic biology research for investigation of phenotype level cellular events. Despite the wide application, the methodology for statistical analysis of differentially expressed proteins has not been unified. Various methods such as t test, linear model and mixed effect models are used to define changes in proteomics experiments. However, none of these methods consider the specific structure of MS-data. Choices between methods, often originally developed for other types of data, are based on compromises between features such as statistical power, general applicability and user friendliness. Furthermore, whether to include proteins identified with one peptide in statistical analysis of differential protein expression varies between studies. Here we present DEqMS, a robust statistical method developed specifically for differential protein expression analysis in mass spectrometry data. In all data sets investigated there is a clear dependence of variance on the number of PSMs or peptides used for protein quantification. DEqMS takes this feature into account when assessing differential protein expression. This allows for a more accurate data-dependent estimation of protein variance and inclusion of single peptide identifications without increasing false discoveries. The method was tested in several data sets including E. coli proteome spike-in data, using both label-free and TMT-labeled quantification. Compared with previous statistical methods used in quantitative proteomics, DEqMS showed consistently better accuracy in detecting altered protein levels compared with other statistical methods in both label-free and labeled quantitative proteomics data. DEqMS is available as an R package in Bioconductor.