Browsing by Subject "ENHANCEMENT"

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  • Kneis, David; Hiltunen, Teppo; Hess, Stefanie (2019)
    Horizontal gene transfer is an essential component of bacterial evolution. Quantitative information on transfer rates is particularly useful to better understand and possibly predict the spread of antimicrobial resistance. A variety of methods has been proposed to estimate the rates of plasmid-mediated gene transfer all of which require substantial labor input or financial resources. A cheap but reliable method with high-throughput capabilities is yet to be developed in order to better capture the variability of plasmid transfer rates, e.g. among strains or in response to environmental cues. We explored a new approach to the culture-based estimation of plasmid transfer rates in liquid media allowing for a large number of parallel experiments. It deviates from established approaches in the fact that it exploits data on the absence/presence of transconjugant cells in the wells of a well plate observed over time. Specifically, the binary observations are compared to the probability of transconjugant detection as predicted by a dynamic model. The bulk transfer rate is found as the best-fit value of a designated model parameter. The feasibility of the approach is demonstrated on mating experiments where the RP4 plasmid is transfered from Serratia marcescens to several Escherichia coil recipients. The methods uncertainty is explored via split sampling and virtual experiments.
  • Kouzi, Afamia; Puranen, Matti; Kontro, Merja H. (2020)
    Biogas production from sewage sludge volatile solids (VS) by anaerobic digestion slows down towards the end of the process, among inhibitory factors being pH increase upon ammonia accumulation, poorly digestible biomaterials, and high fixed solid (FS) content. The possibility of concentrating the digested sludge VS (41.7-56.6% on a dry weight basis) by surface and bottom layer separation with biogas post-production was studied. Furthermore, the potential to recycle concentrated VS and digested sludge back to the process after adjusting pH 7.0 to optimal for biogas-producing microbes and after acid, alkali, thermal, and sonolytic treatments was examined. In general, pH 7.0 control alone improved biogas production from the recycled digested sludge the most. An equally good improvement in biogas production was achieved by recycling the digested sludge, which had been heated until ammonia had evaporated and the pH dropped to 7.0 (1-2 h, 75 degrees C), and at the same time, VS was degraded. The biogas production from the sonicated and recycled sludge was almost as good as from the pH-adjusted, or heat-treated recycled sludge. After the acid and base treatments of the digested sludge, the recycled sludge yielded often the lowest biogas volume, as the added chemicals increased the FS concentration, which proved to be a more important inhibitory factor than poorly degradable VS. The high FS content significantly reduced the benefits of the treatments. By separating the surface and bottom layers with biogas post-production, the surface layer of VS was concentrated to 51.6-61.8%, while different compositions of the layers affected the biogas production.
  • Hablitz, Lauren M.; Vinitsky, Hanna S.; Sun, Qian; Staeger, Frederik Filip; Sigurdsson, Björn; Mortensen, Kristian N.; Lilius, Tuomas O.; Nedergaard, Maiken (2019)
    The glymphatic system is responsible for brain-wide delivery of nutrients and clearance of waste via influx of cerebrospinal fluid (CSF) alongside perivascular spaces and through the brain. Glymphatic system activity increases during sleep or ketamine/xylazine (K/X) anesthesia, yet the mechanism(s) facilitating CSF influx are poorly understood. Here, we correlated influx of a CSF tracer into the brain with electroencephalogram (EEG) power, heart rate, blood pressure, and respiratory rate in wild-type mice under six different anesthesia regimens. We found that glymphatic CSF tracer influx was highest under K/X followed by isoflurane (ISO) supplemented with dexmedetomidine and pentobarbital. Mice anesthetized with a-chloralose, Avertin, or ISO exhibited low CSF tracer influx. This is the first study to show that glymphatic influx correlates positively with cortical delta power in EEG recordings and negatively with beta power and heart rate.
  • Wlodarski, Maksymilian; Putkonen, Matti; Norek, Malgorzata (2020)
    Infrared (IR) spectroscopy is a powerful technique to characterize the chemical structure and dynamics of various types of samples. However, the signal-to-noise-ratio drops rapidly when the sample thickness gets much smaller than penetration depth, which is proportional to wavelength. This poses serious problems in analysis of thin films. In this work, an approach is demonstrated to overcome these problems. It is shown that a standard IR spectroscopy can be successfully employed to study the structure and composition of films as thin as 20 nm, when the layers were grown on porous substrates with a well-developed surface area. In contrast to IR spectra of the films deposited on flat Si substrates, the IR spectra of the same films but deposited on porous ceramic support show distinct bands that enabled reliable chemical analysis. The analysis of Zn-S ultrathin films synthesized by atomic layer deposition (ALD) from diethylzinc (DEZ) and 1,5-pentanedithiol (PDT) as precursors of Zn and S, respectively, served as proof of concept. However, the approach presented in this study can be applied to analysis of any ultrathin film deposited on target substrate and simultaneously on porous support, where the latter sample would be a reference sample dedicated for IR analysis of this film.
  • Wang, Shiqi; Wannasarit, Saowanee; Figueiredo, Patricia; Molinaro, Giuseppina; Ding, Yaping; Correia, Alexandra; Casettari, Luca; Wiwattanapatapee, Ruedeekorn; Hirvonen, Jouni; Liu, Dongfei; Li, Wei; Santos, Hélder A. (2021)
    In this study, a rationally designed nanocomposite (BUDPDA@MAP) composed of polydopamine (PDA) nanoparticle and anti‐inflammatory drug budesonide (BUD) encapsulated in a pH‐responsive endosomolytic polymer (poly(butyl methacrylate‐co‐methacrylic acid) grafted acetalated dextran, denoted by MAP), is proposed. The uniform nanocomposite is prepared using a microfluidic device. At low endosomal pH (5.5), MAP destabilizes the endosomal membranes for the cytoplasmic delivery of PDA, and releases BUD simultaneously, resulting in a greater reactive oxygen species scavenging capability than both the free drug and PDA alone. The combined therapeutic efficacy from PDA and BUD also leads to a successful macrophage phenotype switch from pro‐inflammatory M1 to anti‐inflammatory M2.
  • The ALICE collaboration; Acharya, S.; Brücken, E. J.; Chang, B.; Hilden, T. E.; Kim, D. J.; Litichevskyi, V.; Mieskolainen, M. M.; Orava, R.; Parkkila, J. E.; Rak, J.; Räsänen, S. S.; Saarinen, S.; Slupecki, M.; Snellman, T. W.; Trzaska, W. H.; Vargyas, M.; Viinikainen, J. (2019)
    The first measurement of dielectron (e(+)e(-)) production in central (0-10%) Pb-Pb collisions at root S-NN = 2.76 TeV at the LHC is presented. The dielectron invariant-mass spectrum is compared to the expected contributions from hadron decays in the invariant-mass range 0 < m(ee) < 3.5 GeV/c(2). The ratio of data and the cocktail of hadronic contributions without vacuum rho(0) is measured in the invariant-mass range 0.15 < m(ee) < 0.7 GeV/c(2), where an excess of dielectrons is observed in other experiments, and its value is 1.40 +/- 0.28 (stat.) +/- 0.08 (syst.) +/- 0.27 (cocktail). The dielectron spectrum measured in the invariant mass range 0 < m(ee) < 1 GeV/c(2) is consistent with the predictions from two theoretical model calculations that include thermal dielectron production from both partonic and hadronic phases with in-medium broadened rho(0) meson. The fraction of direct virtual photons over inclusive virtual photons is extracted for dielectron pairs with invariant mass 0.1 < m(ee) < 0.3 GeV/c(2) and in the transverse-momentum intervals 1 <( )p(T,ee) < 2 GeV/c and 2 < p(T,ee) < 4 GeV/c. The measured fraction of virtual direct photons is consistent with the measurement of real direct photons by ALICE and with the expectations from previous dielectron measurements at RHIC within the experimental uncertainties.
  • Virtala, P.; Huotilainen, M.; Partanen, E.; Tervaniemi, Mari (2014)
  • Adamova, D.; Brucken, E. J.; Chang, B.; Kim, D. J.; Litichevskyi, V.; Mieskolainen, M. M.; Orava, R.; Rak, J.; Räsänen, S. S.; Snellman, T. W.; Trzaska, W. H.; Viinikainen, J.; The ALICE collaboration (2017)
    The transverse momentum distributions of the strange and double-strange hyperon resonances ( Sigma ( 1385)(+/-), Xi ( 1530)(0)) produced in p-Pb collisions at root s(NN) = 5.02 TeV were measured in the rapidity range -0.5 <yCMS <0 for event classes corresponding to different charged-particle multiplicity densities, <dN(ch)/d eta(lab)> . The mean transverse momentumvalues are presented as a function of <dNch/d eta(lab)>, as well as a function of the particle masses and compared with previous results on hyperon production. The integrated yield ratios of excited to ground- state hyperons are constant as a function of <dN(ch)/d eta(lab)>. The equivalent ratios to pions exhibit an increase with <dN(ch)/ d eta(lab)>, depending on their strangeness content.
  • Heikkilä, Jenni; Fagerlund, Petra; Tiippana, Kaisa (2018)
    In the course of normal aging, memory functions show signs of impairment. Studies of memory in the elderly have previously focused on a single sensory modality, although multisensory encoding has been shown to improve memory performance in children and young adults. In this study, we investigated how audiovisual encoding affects auditory recognition memory in older (mean age 71 years) and younger (mean age 23 years) adults. Participants memorized auditory stimuli (sounds, spoken words) presented either alone or with semantically congruent visual stimuli (pictures, text) during encoding. Subsequent recognition memory performance of auditory stimuli was better for stimuli initially presented together with visual stimuli than for auditory stimuli presented alone during encoding. This facilitation was observed both in older and younger participants, while the overall memory performance was poorer in older participants. However, the pattern of facilitation was influenced by age. When encoding spoken words, the gain was greater for older adults. When encoding sounds, the gain was greater for younger adults. These findings show that semantically congruent audiovisual encoding improves memory performance in late adulthood, particularly for auditory verbal material.
  • Metsälä, Olli; Kreutzer, Joose; Högel, Heidi; Miikkulainen, Petra; Kallio, Pasi; Jaakkola, Panu M. (2018)
    BackgroundCells in solid tumours are variably hypoxic and hence resistant to radiotherapy - the essential role of oxygen in the efficiency of irradiation has been acknowledged for decades. However, the currently available methods for performing hypoxic experiments in vitro have several limitations, such as a limited amount of parallel experiments, incapability of keeping stable growth conditions and dependence on CO2 incubator or a hypoxia workstation. The purpose of this study was to evaluate the usability of a novel portable system (Minihypoxy) in performing in vitro irradiation studies under hypoxia, and present supporting biological data.Materials and methodsThis study was conducted on cancer cell cultures in vitro. The cells were cultured in normoxic (similar to 21% O-2) or in hypoxic (1% O-2) conditions either in conventional hypoxia workstation or in the Minihypoxy system and irradiated at dose rate 1.28Gy/min2.9%. The control samples were sham irradiated. To study the effects of hypoxia and irradiation on cell viability and DNA damage, western blotting, immunostainings and clonogenic assay were used. The oxygen level, pH, evaporation rate and osmolarity of the culturing media on cell cultures in different conditions were followed.ResultsThe oxygen concentration in interest (5, 1 or 0% O-2) was maintained inside the individual culturing chambers of the Minihypoxy system also during the irradiation. The radiosensitivity of the cells cultured in Minihypoxy chambers was declined measured as lower phosphorylation rate of H2A.X and increased clonogenic capacity compared to controls (OER similar to 3).Conclusions The Minihypoxy system allows continuous control of hypoxic environment in multiple wells and is transportable. Furthermore, the system maintains the low oxygen environment inside the individual culturing chambers during the transportation and irradiation in experiments which are typically conducted in separate facilities.