Search results for "merkkiaineet"

Development of functionalized SYBR green II related cyanine dyes for viral RNA detection

2020

Fluorescent probes for sensing nucleic acids have found widespread use in the field of cell and molecular biology. However, probes combined with potential for post-synthetic conjugation, e.g. for intra-endosomal measurements of RNA, are unavailable. Herein we developed cyanine dyes that can be conjugated to viral capsid or other targets. First, we solved the crystal structure of SYBR Green II. The structural elucidation of this commonly used RNA probe provided the basis for synthesizing similar molecules with much desired function for post-synthetic conjugation. To address this need, cyanine dyes were prepared using an alternative synthesis protocol. All studied compounds showed considerabl…

isotracer: An R package for the analysis of tracer addition experiments

2022

Tracer addition experiments, particularly using isotopic tracers, are becoming increasingly important in a variety of studies aiming at characterizing the flows of molecules or nutrients at different levels of biological organization, from the cellular and tissue levels, to the organismal and ecosystem levels. However, performing rigorous statistical analyses to gain reliable quantitative insights from these experiments often remains challenging. We present an approach based on Hidden Markov Models (HMM) to estimate nutrient flow parameters across a network, and its implementation in the R package isotracer. The isotracer package is capable of handling a variety of tracer study designs, inc…

Development of DNA aptamers for visualization of glial brain tumors and detection of circulating tumor cells

2023

Here, we present DNA aptamers capable of specific binding to glial tumor cells in vitro, ex vivo, and in vivo for visualization diagnostics of central nervous system tumors. We selected the aptamers binding specifically to the postoperative human glial primary tumors and not to the healthy brain cells and meningioma, using a modified process of systematic evolution of ligands by exponential enrichment to cells; sequenced and analyzed ssDNA pools using bioinformatic tools and identified the best aptamers by their binding abilities; determined three-dimensional structures of lead aptamers (Gli-55 and Gli-233) with small-angle X-ray scattering and molecular modeling; isolated and identified mo…

Candida antarctica Lipase A-Based Enantiorecognition of a Highly Strained 4-Dibenzocyclooctynol (DIBO) Used for PET Imaging

2020

The enantiomers of aromatic 4-dibenzocyclooctynol (DIBO), used for radiolabeling and subsequent conjugation of biomolecules to form radioligands for positron emission tomography (PET), were separated by kinetic resolution using lipase A from Candida antarctica (CAL-A). In optimized conditions, (R)-DIBO [(R)-1, ee 95%] and its acetylated (S)-ester [(S)-2, ee 96%] were isolated. In silico docking results explained the ability of CAL-A to differentiate the enantiomers of DIBO and to accommodate various acyl donors. Anhydrous MgCl2 was used for binding water from the reaction medium and, thus, for obtaining higher conversion by preventing hydrolysis of the product (S)-2 into the starting materi…

Production of feeds for African catfish Clarias gariepinus using plant proteins

2012

Tracer migration in crystalline rock : application to geological barriers of nuclear waste storage

2016

This work deals with transport of radionuclides in the geosphere. The subject is investigated through characterisation of water conducting fractures, determining of rock transport properties and development of new methods for characterising geological samples. Here, as is often the case, radionuclide transport is investigated indirectly by characterising the structures, where the transport takes place, and directly by measuring transport properties in the gas phase. First water conducting fractures of three different types and the rock matrix surrounding them were analysed through rock samples from Olkiluoto. The analysis was done using X-ray tomography, the 14C-PMMA autoradiography techniq…

Exercise and inflammation with special reference to resistance training

2018

The aim of the present dissertation was to examine the acute and chronic effects of resistance exercise on inflammation markers in young men. In addition, the effect of combined resistance and endurance training on inflammation was assessed. The present dissertation consisted of four studies. Acute inflammation response was evaluated using cross-sectional design after hypertrophic and maximal (n=12) resistance exercise bouts (I). In addition, acute inflammation was examined before and after resistance training (RT) consisting either hypertrophic or maximal explosive (n=8) resistance exercise bouts (RE) (II). The effect of RT on basal levels of markers of systemic inflammation was evaluated …

Systematic study of SYBR green chromophore reveals major improvement with one heteroatom difference

2021

Five nucleic acid binding cyanine dyes were synthesized and their photophysical properties were evaluated. Changing a single heteroatom in the chromophore causes major differences both in brightness and photostability between the dyes. With such alteration, the brightness of the chromophore increased two-fold compared to the one found in SYBR Green I. peerReviewed