Search results for "kromi"
showing 10 items of 11 documents
Optogenetic Control of Bacterial Expression by Red Light
2022
In optogenetics, as in nature, sensory photoreceptors serve to control cellular processes by light. Bacteriophytochrome (BphP) photoreceptors sense red and far-red light via a biliverdin chromophore and, in response, cycle between the spectroscopically, structurally, and functionally distinct Pr and Pfr states. BphPs commonly belong to two-component systems that control the phosphorylation of cognate response regulators and downstream gene expression through histidine kinase modules. We recently demonstrated that the paradigm BphP from Deinococcus radiodurans exclusively acts as a phosphatase but that its photosensory module can control the histidine kinase activity of homologous receptors.…
How to preserve and handle fish liver samples to conserve RNA integrity
2019
As transcriptomic studies are becoming more and more common, it is important to ensure that the RNA used in the analyses is of good quality. The RNA integrity may be compromised by storage temperature or freeze-thaw cycles, but these have not been well studied in poikilothermic fishes. This work studied the effects of tissue storage time and temperature, and freeze-thaw cycles of tissue and extracted RNA on RNA integrity in brown trout (Salmo trutta L.) liver. The storage time and temperature had an effect on RNA integrity, but RNA suitable for quantitative reverse transcription PCR (RT-qPCR) (RIN > 7) was still obtained from samples preserved at − 20 °C for 6 months. Freeze-thaw cycles of …
Stereoselective synthesis of oligosaccharides by de novo saccharide welding
2012
Substrate Selectivity of Coumarin Derivatives by Human CYP1 Enzymes: In Vitro Enzyme Kinetics and In Silico Modeling
2021
Of the three enzymes in the human cytochrome P450 family 1, CYP1A2 is an important enzyme mediating metabolism of xenobiotics including drugs in the liver, while CYP1A1 and CYP1B1 are expressed in extrahepatic tissues. Currently used CYP substrates, such as 7-ethoxycoumarin and 7-ethoxyresorufin, are oxidized by all individual CYP1 forms. The main aim of this study was to find profluorescent coumarin substrates that are more selective for the individual CYP1 forms. Eleven 3-phenylcoumarin derivatives were synthetized, their enzyme kinetic parameters were determined, and their interactions in the active sites of CYP1 enzymes were analyzed by docking and molecular dynamic simulations. All cou…
Estradiol deficiency and skeletal muscle apoptosis: Possible contribution of microRNAs.
2020
Background Menopause leads to estradiol (E2) deficiency that is associated with decreases in muscle mass and strength. Here we studied the effect of E2 deficiency on miR-signaling that targets apoptotic pathways. Methods C57BL6 mice were divided into control (normal estrous cycle, n = 8), OVX (E2 deficiency, n = 7) and OVX + E2 groups (E2-pellet, n = 4). Six weeks following the OVX surgery, mice were sacrificed and RNA isolated from gastrocnemius muscles. miR-profiles were studied with Next-generation sequencing (NGS) and candidate miRs verified using qPCR. The target proteins of the miRs were found using in silico analysis and measured at mRNA (qPCR) and protein levels (Western blot). Resu…
Fluorescence labeling of the photosensory unit of Deinococcus radiodurans bacteriophytochrome for Förster resonance energy transfer studies
2016
Fytokromit ovat bakteerien, levien, kasvien ja sienten punaista valoa aistivia proteiineja. Keskeinen piirre fytokromien toiminnassa on valon vaikutuksesta tapahtuva siirtymä punaista valoa absorboivan (Pr) ja kaukopunaista valoa absorboivan (Pfr) tilan välillä. Deinococcus radiodurans -bakteerifytokromin valosensoriosa (CBD-PHY) on dimeerinen proteiini, joka koostuu C-terminaalisesta kromoforia sitovasta domeenista (CBD) ja fytokromiin liittyvästä domeenista (PHY). Viimeaikaiset CBD-PHY:n kristalli- ja liuosrakenteet ovat osoittaneet, että PHY-domeenien välinen etäisyys kasvaa, kun proteiini siirtyy Pr-tilasta Pfr-tilaan absorboituaan punaista valoa. Tässä työssä suunniteltiin Försterin re…
Monomerisaation vaikutus Deinococcus radioduransin fytokromiin
2014
Fytokromit ovat yksi kolmesta fotomorfogeneesiä säätelevistä proteiiniperheistä. Niitä löytyy kasveista, bakteereista ja sienistä. Fytokromit reagoivat ympäristön muuttuviin valaistusolosuhteisiin, ja niiden tehtäviin kuuluvat muun muassa kasveilla siementen kehittymisen ja bakteereilla solusyklin säätely. Luonnossa fytokromi esiintyy homodimeerinä. Fytokromin perusrakenne koostuu kromoforin sisältävästä fotoreseptorialueesta sekä signalointialueesta, joka välittää tiedon valaistusolosuhteiden muuttumisesta solussa eteenpäin. Tässä tutkielmassa käytetyn Deinococcus radiodurans -bakteerin bakteerifytokromin fotoreseptorialueen runko rakentuu Per/Arndt/Sim (PAS) ja cGMP fosfodiesteraasi/adeny…
Conserved histidine and tyrosine determine spectral responses through the water network in Deinococcus radiodurans phytochrome
2022
Funding Information: This work was supported by Academy of Finland grants 285461 (H.T.), 330678 (H.T., J.R.), 277194 (H.L.), and 290677 (S.M.). We acknowledge the European Synchrotron Radiation Facility (ESRF) for providing synchrotron access for crystal data collection. We thank Prof. Janne Ihalainen (University of Jyväskylä) for all the help in all aspects of the paper, Prof. Gerrit Groenhof (University of Jyväskylä) for support, and Prof. Nikolai V. Tkachenko (Tampere University) for help and facilities for time-resolved absorption spectroscopy. We also thank M.Sc. Alli Liukkonen (University of Jyväskylä) and Dr. Heikki Häkkänen (University of Jyväskylä) for the assistance in laboratory …
Protein purification of Agrobacterium tumefaciens phytochrome Agp1 and UV-vis spectroscopy analysis in comparison to DrBphP from Deinococcus Radiodur…
2015
Phytochromes are bimodal light switchable photosensors exist in plants, bacteria and fungi. Incorporating bilin as their chromophore, most bacteriophytochromes (BphPs) function as two-component histidine kinase affected by red/far-red light and regulate downstream physiological activities in the microorganism. The study aims on the purification of Agrobacterium phytochrome Agp1whose phosphorylation activity in its histidine kinase (HK) domain was recently found to be affected by the temperature. The purified proteins Agp1 were assembled with biliverdin IXα (BV) and monitored by UV-vis spectroscopy with BV incorporated DrBphP from Deinococcus radiodurans. Extinction coefficient spectra of “a…
Kromin liuottaminen ferrokromikuonasta ultraääniavusteisesti peroksidipohjaisten reagenssien avulla
2016
Tässä Pro gradu -tutkielmassa käytiin läpi erilaisissa metallurgisissa prosesseissa syntyneiden kuonien koostumusta sekä niiden mahdollista jatkokäyttöä. Prosesseissa syntyvien kuonien koostumuksen todettiin riippuvan käytetystä prosessista ja että joissain prosesseissa syntyvät kuonat voivat olla ympäristölle haitallisia, kun taas vastaavasti joitain kuonia voidaan käyttää esimerkiksi betonin täyteaineena. Metallurgisissa prosesseissa syntyneille kuonille olisi tärkeää keksiä jatkokäyttökohteita, sillä ne vievät runsaasti tilaa sekä aiheuttavat mahdollisia ympäristöhaittoja. Lisäksi kuonien jatkokäytöstä voitaisiin hyötyä taloudellisesti. Kokeellisessa osassa selvitettiin ferrokromin tuota…