Browsing by Subject "RESOLUTION"

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  • Kassamakov, Ivan; Lecler, Sylvain; Nolvi, Anton; Leong-Hoi, Audrey; Montgomery, Paul; Haeggström, Edward (2017)
    We present quantitative three dimensional images of grooves on a writable Blu-ray Disc based on a single objective Mirau type interferometric microscope, enhanced with a microsphere which is considered as a photonic nanojet source. Along the optical axis the resolution of this microsphere assisted interferometry system is a few nanometers while the lateral resolution is around 112 nm. To understand the physical phenomena involved in this kind of imaging we have modelled the interaction between the photonic jet and the complex disc surface. Agreement between simulation and experimental results is demonstrated. We underline that although the ability of the microsphere to generate a photonic nanojet does not alone explain the resolution of the interferometer, the nanojet can be used to try to understand the imaging process. To partly explain the lateral super-resolution, the potential role of coherence is illustrated. The presented modality may have a large impact on many fields from bio-medicine to nanotechnology.
  • Salo, Raimo A.; Belevich, Ilya; Jokitalo, Eija; Gröhn, Olli; Sierra, Alejandra (2021)
    Validation and interpretation of diffusion magnetic resonance imaging (dMRI) requires detailed understanding of the actual microstructure restricting the diffusion of water molecules. In this study, we used serial block-face scanning electron microscopy (SBEM), a three-dimensional electron microscopy (3D-EM) technique, to image seven white and grey matter volumes in the rat brain. SBEM shows excellent contrast of cellular membranes, which are the major components restricting the diffusion of water in tissue. Additionally, we performed 3D structure tensor (3D-ST) analysis on the SBEM volumes and parameterised the resulting orientation distributions using Watson and angular central Gaussian (ACG) probability distributions as well as spherical harmonic (SH) decomposition. We analysed how these parameterisations described the underlying orientation distributions and compared their orientation and dispersion with corresponding parameters from two dMRI methods, neurite orientation dispersion and density imaging (NODDI) and constrained spherical deconvolution (CSD). Watson and ACG parameterisations and SH decomposition captured well the 3D-ST orientation distributions, but ACG and SH better represented the distributions due to its ability to model asymmetric dispersion. The dMRI parameters corresponded well with the 3D-ST parameters in the white matter volumes, but the correspondence was less evident in the more complex grey matter. SBEM imaging and 3D-ST analysis also revealed that the orientation distributions were often not axially symmetric, a property neatly captured by the ACG distribution. Overall, the ability of SBEM to image diffusion barriers in intricate detail, combined with 3D-ST analysis and parameterisation, provides a step forward toward interpreting and validating the dMRI signals in complex brain tissue microstructure.
  • Lu, Yiqun; Liu, Ling; Ning, An; Yang, Gan; Liu, Yiliang; Kurten, Theo; Vehkamäki, Hanna; Zhang, Xiuhui; Wang, Lin (2020)
    Sulfuric acid (SA)-dimethylamine (DMA)-H2O cluster formation has been proven to be responsible for a significant part of new particle formation (NPF) in a Chinese megacity. However, the possible involvement of common atmospheric acids in the subsequent growth of SA-DMA clusters remains elusive. We simulated formation and growth of clusters using atmospheric relevant concentrations of SA, DMA, and trifluoroacetic acid (TFA), a commonly observed atmospheric perfluorocarboxylic acid, using Density Functional Theory combined with Atmospheric Cluster Dynamics Code. The presence of TFA leads to complex cluster formation routes and an enhancement of NPF rates by up to 2.3 ([TFA] = 5.0 x 10(6) molecules cm(-3), [SA] = 1.0 x 10(6) molecules cm(-3), and [DMA] = 1.5 x 10(9) molecules cm(-3)). The agreement of (SA)(1)center dot(DMA)(1-2)center dot(TFA)(1) concentrations between simulations and ambient measurements during NPF events validates model predictions and implies that perfluorocarboxylic acids could potentially boost atmospheric SA-DMA NPF rates.
  • Reischl, Bernhard; Raiteri, Paolo; Gale, Julian D.; Rohl, Andrew L. (2019)
    Advances in atomic force microscopy (AFM) in water have enabled the study of hydration layer structures on crystal surfaces, and in a recent study on dolomite (CaMg(CO3)(2)), chemical sensitivity was demonstrated by observing significant differences in force-distance curves over the calcium and magnesium ions in the surface. Here, we present atomistic molecular dynamics simulations of a hydration layer structure and dynamics on the (10 (1) over bar4) surfaces of dolomite, calcite (CaCO3), and magnesite (MgCO3), as well as simulations of AFM imaging on these three surfaces with a model silica tip. Our results confirm that it should be possible to distinguish between water molecules coordinating the calcium and magnesium ions in dolomite, and the details gleaned from the atomistic simulations enable us to clarify the underlying imaging mechanism in the AFM experiments.
  • Ojala, Antti; Saarnisto, Matti; Jungner, Högne; Snowball, Ian; Muscheler, Raimund (2019)
    We present here radiocarbon dating results from two boreal lakes in Finland, which are permanently (meromictic) or seasonally stratified and contain continuous sequences of annually laminated sediments that started to form in the early Holocene. The radiocarbon dating results of different organic components were compared with the varve-based sediment chronologies. The deviation between the Lake Valkiajarvi varve chronology (8400 varve years 2-3% error estimate) and 33 C-14 dates taken from insoluble and soluble organic phases vary inconsistently throughout the Holocene. In extreme cases mean calibrated radiocarbon dates with 95.4% confidence levels (2 sigma) are -2350 and +2040 years offset when compared with the varve chronology. On average, the radiocarbon dates are offset by ca. +550 years. The deviation between the Lake Nautajarvi varve chronology (9898 varve years +/- 1% error estimate) and 26 C-14 dates analyzed with conventional and AMS methods indicates that radiocarbon dates are systematically older by 500-1300 years (about 900 years on average). This significant offset mean that radiocarbon dates obtained from organic bulk sediment of meromictic and seasonally hypoxic lakes must be cautiously interpreted because of the reservoir effect and carbon cycling at the sediment-water interface. Direct evidence was obtained from the dating of soluble fraction and insoluble organic matter from near bottom water in the monimolimnion of Lake Valkiajarvi, which yielded C-14 ages of 560 +/- 80 BP and 2070 +/- 140 BP, respectively. Our study reinforces previous results that age-depth models based on bulk sediment radiocarbon dates obtained on sediments of stratified lakes are of limited value for accurate dating of changes in land use and especially the commence of agriculture.
  • Yang, Xin; Leslie, Goska; Doroszuk, Alicja; Aittomäki, Kristiina; Blomqvist, Carl; Heikkinen, Tuomas; Nevanlinna, Heli; Tischkowitz, Marc (2020)
    PURPOSE To estimate age-specific relative and absolute cancer risks of breast cancer and to estimate risks of ovarian, pancreatic, male breast, prostate, and colorectal cancers associated with germline PALB2 pathogenic variants (PVs) because these risks have not been extensively characterized. METHODS We analyzed data from 524 families with PALB2 PVs from 21 countries. Complex segregation analysis was used to estimate relative risks (RRs; relative to country-specific population incidences) and absolute risks of cancers. The models allowed for residual familial aggregation of breast and ovarian cancer and were adjusted for the family-specific ascertainment schemes. RESULTS We found associations between PALB2 PVs and risk of female breast cancer (RR, 7.18; 95% CI, 5.82 to 8.85; P = 6.5 x 10(-76)), ovarian cancer (RR, 2.91; 95% CI, 1.40 to 6.04; P = 4.1 x 10(-3)), pancreatic cancer (RR, 2.37; 95% CI, 1.24 to 4.50; P = 8.7 x 10(-3)), and male breast cancer (RR, 7.34; 95% CI, 1.28 to 42.18; P = 2.6 x 10(-2)). There was no evidence for increased risks of prostate or colorectal cancer. The breast cancer RRs declined with age (P for trend = 2.0 x 10(-3)). After adjusting for family ascertainment, breast cancer risk estimates on the basis of multiple case families were similar to the estimates from families ascertained through population-based studies (P for difference = .41). On the basis of the combined data, the estimated risks to age 80 years were 53% (95% CI, 44% to 63%) for female breast cancer, 5% (95% CI, 2% to 10%) for ovarian cancer, 2%-3% (95% CI females, 1% to 4%; 95% CI males, 2% to 5%) for pancreatic cancer, and 1% (95% CI, 0.2% to 5%) for male breast cancer. CONCLUSION These results confirm PALB2 as a major breast cancer susceptibility gene and establish substantial associations between germline PALB2 PVs and ovarian, pancreatic, and male breast cancers. These findings will facilitate incorporation of PALB2 into risk prediction models and optimize the clinical cancer risk management of PALB2 PV carriers. (C) 2019 by American Society of Clinical Oncology
  • Voutilainen, Mikko; Miettinen, Arttu; Sardini, Paul; Parkkonen, Joni; Sammaljärvi, Juuso; Gylling, Björn; Selroos, Jan-Olof; Yli-Kaila, Maarit; Koskinen, Lasse; Siitari-Kauppi, Marja (2019)
    The spatial porosity and mineral distribution of geological materials strongly affects transport processes in them. X-ray micro computed tomography (X-mu CT) has proven to be a powerful tool for characterizing the spatial mineral distribution of geological samples in 3-D. However, limitations in resolution prevent an accurate characterization of pore space especially for tight crystalline rock samples and 2-D methods such as C-14-polymethylmethacrylate (C-14-PMMA) autoradiography and scanning electron microscopy (SEM) are needed. The spatial porosity and mineral distributions of tight crystalline rock samples from Aspo, Sweden, and Olkiluoto, Finland, were studied here. The X-mu CT were used to characterize the spatial distribution of the main minerals in 3-D. Total porosities, fracture porosities, fracture densities and porosity distributions of the samples were determined using the C-14-PMMA autoradiography and characterization of mineral-specific porosities were assisted using chemical staining of rock surfaces. SEM and energy dispersive X-ray spectroscopy (EDS) were used to determine pore apertures and identify the minerals. It was shown that combination of the different imaging techniques creates a powerful tool for the structural characterization of crystalline rock samples. The combination of the results from different methods allowed the construction of spatial porosity, mineral and mineral grain distributions of the samples in 3-D. These spatial distributions enable reactive transport modeling using a more realistic representation of the heterogeneous structure of samples. Furthermore, the realism of the spatial distributions were increased by determinig the densities and porosities of fractures and by the virtual construction heterogeneous mineral distributions of minerals that cannot be separated by X-mu CT.
  • Boyd, Christopher; Vehkalahti, Roope; Tirkkonen, Olav; Laaksonen, Antti (IEEE, 2019)
    IEEE International Symposium on Information Theory
    We study medium access control layer random access under the assumption that the receiver can perform successive interference cancellation, without feedback. During recent years, a number of protocols with impressive error performance have been suggested for this channel model. However, the random nature of these protocols causes an error floor which limits their usability when targeting ultra-reliable communications. In very recent works by Paolini et al. and Boyd et. al., it was shown that if each user employs predetermined combinatorial access patterns, this error floor disappears. In this paper, we develop code design criteria for deterministic random access protocols in the ultra-reliability region, and build codes based on these principles. The suggested design methods are supported by simulations.
  • Gorbikova, Elena; Kalendar, Ruslan (2020)
    Cytochrome c oxidase is terminal enzyme in the respiratory chain of mitochondria and many aerobic bacteria. It catalyzes reduction of oxygen to water. During its catalysis, CcO proceeds through several quite stable intermediates (R, A, PR/M, O/OH, E/EH). This work is concentrated on the elucidation of the differences between structures of oxidized intermediates O and OH in different CcO variants and at different pH values. Oxidized intermediates of wild type and mutated CcO from Paracoccus denitrificans were studied by means of static and time-resolved Fourier-transform infrared spectroscopy in acidic and alkaline conditions in the infrared region 1800–1000 cm−1. No reasonable differences were found between all variants in these conditions, and in this spectral region. This finding means that the binuclear center of oxygen reduction keeps a very similar structure and holds the same ligands in the studied conditions. The further investigation in search of differences should be performed in the 4000–2000 cm−1 IR region where water ligands absorb.
  • 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.
  • Kullberg, Peter; Toivonen, Tuuli; Pouzols, Federico Montesino; Lehtomäki, Joona; Di Minin, Enrico; Moilanen, Atte (2015)
    Complementarity and cost-efficiency are widely used principles for protected area network design. Despite the wide use and robust theoretical underpinnings, their effects on the performance and patterns of priority areas are rarely studied in detail. Here we compare two approaches for identifying the management priority areas inside the global protected area network: 1) a scoring-based approach, used in recently published analysis and 2) a spatial prioritization method, which accounts for complementarity and area-efficiency. Using the same IUCN species distribution data the complementarity method found an equal-area set of priority areas with double the mean species ranges covered compared to the scoringbased approach. The complementarity set also had 72% more species with full ranges covered, and lacked any coverage only for half of the species compared to the scoring approach. Protected areas in our complementarity-based solution were on average smaller and geographically more scattered. The large difference between the two solutions highlights the need for critical thinking about the selected prioritization method. According to our analysis, accounting for complementarity and area-efficiency can lead to considerable improvements when setting management priorities for the global protected area network.
  • Woiwode, Ulrich; Ferri, Martina; Maier, Norbert M.; Lindner, Wolfgang; Lämmerhofer, Michael (2018)
    Abstract A cardinal requirement for effective 2D-HPLC separations is sufficient complementarity in the retention profiles of first and second dimension separations. It is shown that retention and enantioselectivity of chiral selectors derived from cinchona alkaloids can be conveniently modulated by structural variation of the carbamate residue of the quinine/quinidine carbamate ligand of such chiral stationary phases (CSP). A variety of aliphatic and aromatic residues have been tested in comparison to non-carbamoylated quinine CSP. Various measures of orthogonality have been utilized to derive the CSP that is most complementary to the tert-butylcarbamoylated quinine CSP (tBuCQN CSP), which is commercially available as Chiralpak QN-AX column. It turned out that O-9-(2,6-diisopropylphenylcarbamoyl)-modified quinine is most promising in this respect. Its implementation as a complementary CSP for the separation of amino acids derivatized with Sanger’s reagent (2,4-dinitrophenylated amino acids) in the first dimension combined with a tBuCQN CSP in the second dimension revealed successful enantiomer separations in a comprehensive chiral×chiral 2D-HPLC setup. However, the degree of complementarity could be greatly enhanced when simultaneously the absolute configurations were exchanged from quinine to quinidine in the chiral selector of the first dimension separation resulting in opposite elution orders of the enantiomers in the two dimensions. The advantage of such a chiral×chiral over achiral×chiral 2D-HPLC setup, amongst others, is the perfect compatibility of the mobile phase because in both dimensions the identical eluent can be used.
  • Neumann, Mathias; Moreno, Adam; Thurnher, Christopher; Mues, Volker; Härkönen, Sanna; Mura, Matteo; Bouriaud, Olivier; Lang, Mait; Cardellini, Giuseppe; Thivolle-Cazat, Alain; Bronisz, Karol; Merganic, Jan; Alberdi, Iciar; Astrup, Rasmus; Mohren, Frits; Zhao, Maosheng; Hasenauer, Hubert (2016)
    Net primary production (NPP) is an important ecological metric for studying forest ecosystems and their carbon sequestration, for assessing the potential supply of food or timber and quantifying the impacts of climate change on ecosystems. The global MODIS NPP dataset using the MOD17 algorithm provides valuable information for monitoring NPP at 1-km resolution. Since coarse-resolution global climate data are used, the global dataset may contain uncertainties for Europe. We used a 1-km daily gridded European climate data set with the MOD17 algorithm to create the regional NPP dataset MODIS EURO. For evaluation of this new dataset, we compare MODIS EURO with terrestrial driven NPP from analyzing and harmonizing forest inventory data (NFI) from 196,434 plots in 12 European countries as well as the global MODIS NPP dataset for the years 2000 to 2012. Comparing these three NPP datasets, we found that the global MODIS NPP dataset differs from NFI NPP by 26%, while MODIS EURO only differs by 7%. MODIS EURO also agrees with NFI NPP across scales (from continental, regional to country) and gradients (elevation, location, tree age, dominant species, etc.). The agreement is particularly good for elevation, dominant species or tree height. This suggests that using improved climate data allows the MOD17 algorithm to provide realistic NPP estimates for Europe. Local discrepancies between MODIS EURO and NFI NPP can be related to differences in stand density due to forest management and the national carbon estimation methods. With this study, we provide a consistent, temporally continuous and spatially explicit productivity dataset for the years 2000 to 2012 on a 1-km resolution, which can be used to assess climate change impacts on ecosystems or the potential biomass supply of the European forests for an increasing bio-based economy. MODIS EURO data are made freely available at ftp://palantir.boku.ac.at/Public/MODIS_EURO.
  • Ruskamo, Salla; Krokengen, Oda C.; Kowal, Julia; Nieminen, Tuomo; Lehtimäki, Mari; Raasakka, Arne; Dandey, Venkata P.; Vattulainen, Ilpo; Stahlberg, Henning; Kursula, Petri (2020)
    Myelin protein P2 is a peripheral membrane protein of the fatty acid?binding protein family that functions in the formation and maintenance of the peripheral nerve myelin sheath. Several P2 gene mutations cause human Charcot-Marie-Tooth neuropathy, but the mature myelin sheath assembly mechanism is unclear. Here, cryo-EM of myelin-like proteolipid multilayers revealed an ordered three-dimensional (3D) lattice of P2 molecules between stacked lipid bilayers, visualizing supramolecular assembly at the myelin major dense line. The data disclosed that a single P2 layer is inserted between two bilayers in a tight intermembrane space of ?3 nm, implying direct interactions between P2 and two membrane surfaces. X-ray diffraction from P2-stacked bicelle multilayers revealed lateral protein organization, and surface mutagenesis of P2 coupled with structure-function experiments revealed a role for both the portal region of P2 and its opposite face in membrane interactions. Atomistic molecular dynamics simulations of P2 on model membrane surfaces suggested that Arg-88 is critical for P2-membrane interactions, in addition to the helical lid domain. Negatively charged lipid headgroups stably anchored P2 on the myelin-like bilayer surface. Membrane binding may be accompanied by opening of the P2 ?-barrel structure and ligand exchange with the apposing bilayer. Our results provide an unprecedented view into an ordered, multilayered biomolecular membrane system induced by the presence of a peripheral membrane protein from human myelin. This is an important step toward deciphering the 3D assembly of a mature myelin sheath at the molecular level.
  • Magney, Troy S.; Frankenberg, Christian; Kohler, Philipp; North, Gretchen; Davis, Thomas S.; Dold, Christian; Dutta, Debsunder; Fisher, Joshua B.; Grossmann, Katja; Harrington, Alexis; Hatfield, Jerry; Stutz, Jochen; Sun, Ying; Porcar-Castell, Albert (2019)
    Novel satellite measurements of solar-induced chlorophyll fluorescence (SIF) can improve our understanding of global photosynthesis; however, little is known about how to interpret the controls on its spectral variability. To address this, we disentangle simultaneous drivers of fluorescence spectra by coupling active and passive fluorescence measurements with photosynthesis. We show empirical and mechanistic evidence for where, why, and to what extent leaf fluorescence spectra change. Three distinct components explain more than 95% of the variance in leaf fluorescence spectra under both steady-state and changing illumination conditions. A single spectral shape of fluorescence explains 84% of the variance across a wide range of species. The magnitude of this shape responds to absorbed light and photosynthetic up/down regulation; meanwhile, chlorophyll concentration and nonphotochemical quenching control 9% and 3% of the remaining spectral variance, respectively. The spectral shape of fluorescence is remarkably stable where most current satellite retrievals occur (far-red, >740nm), and dynamic downregulation of photosynthesis reduces fluorescence magnitude similarly across the 670- to 850-nm range. We conduct an exploratory analysis of hourly red and far-red canopy SIF in soybean, which shows a subtle change in red:far-red fluorescence coincident with photosynthetic downregulation but is overshadowed by longer-term changes in canopy chlorophyll and structure. Based on our leaf and canopy analysis, caution should be taken when attributing large changes in the spectral shape of remotely sensed SIF to plant stress, particularly if data acquisition is temporally sparse. Ultimately, changes in SIF magnitude at wavelengths greater than 740 nm alone may prove sufficient for tracking photosynthetic dynamics. Plain Language Summary Satellite remote sensing provides a global picture of photosynthetic activity-allowing us to see when, where, and how much CO2 plants are assimilating. To do this, satellites measure a small emission of energy from the plants called chlorophyll fluorescence. However, this measurement is typically made across a narrow wavelength range, while the emission spectrum (650-850 nm) is quite dynamic. We show where, why, and to what extent leaf fluorescence spectra change across a diverse range of species and conditions, ultimately informing canopy remote sensing measurements. Results suggest that wavelengths currently used by satellites are stable enough to track the downregulation of photosynthesis resulting from stress, while spectral shape changes respond more strongly to dynamics in canopy structure and chlorophyll concentration.
  • Taylor, G.; Hillers, G. (2020)
    We present a new method for estimating time-series of relative seismic velocity changes (dv/v) within the Earth. Our approach is a Markov chain Monte Carlo (MCMC) technique that seeks to construct the full posterior probability distribution of the dv/v variations. Our method provides a robust, computationally efficient way to compute dv/v time-series that can incorporate information about measurement uncertainty, and any prior constraints that may be available. We demonstrate the method with a synthetic experiment, and then apply the MCMC algorithm to three data examples. In the first two examples we reproduce dv/v time-series associated with the response to the 2010 M 7.2 El Mayor-Cucapah earthquake at two sites in southern California, that have been studied in previous literature. In the San Jacinto fault zone environment we reproduce the dv/v signature of a deep creep slip sequence triggered by the El Mayor-Cucapah event, that is superimposed on a strong seasonal signal. At the Salton Sea Geothermal Field we corroborate the previously observed drop-and-recovery in seismic velocity caused by ground shaking related to the El Mayor-Cucapah event. In a third, new example we compute a month long velocity change time-series at hourly resolution at Pinion Flat, California. We observe a low amplitude variation in seismic velocity with a dominant frequency of 1 cycle per day, as well as a second transient signal with a frequency of 1.93 cycles per day. We attribute the 1-d periodicity in the dv/v variation to the combined effects of the diurnal tide and solar heating. The frequency of the signal at 1.93 cycles per day matches that of the lunar (semi-diurnal) tide. Analysis of the uncertainties in the Pinion Flat time-series shows that the error contains a signal with a frequency of 1 cycle per day. We attribute this variation to seismic noise produced by freight trains operating within the Coachella Valley. By demonstrating the applicability of the MCMC method in these examples, we show that it is well suited to tackle problems involving large data volumes that are typically associated with modern seismic experiments.
  • Euclid Collaboration; Ilbert, O.; Gozaliasl, G.; Keihänen, E.; Kurki-Suonio, H.; Väliviita, J.; Kirkpatrick, C. C. (2021)
    The analysis of weak gravitational lensing in wide-field imaging surveys is considered to be a major cosmological probe of dark energy. Our capacity to constrain the dark energy equation of state relies on an accurate knowledge of the galaxy mean redshift z. We investigate the possibility of measuring z with an accuracy better than 0.002 (1+z) in ten tomographic bins spanning the redshift interval 0.2 99.8%. The zPDF approach can also be successful if the zPDF is de-biased using a spectroscopic training sample. This approach requires deep imaging data but is weakly sensitive to spectroscopic redshift failures in the training sample. We improve the de-biasing method and confirm our finding by applying it to real-world weak-lensing datasets (COSMOS and KiDS+VIKING-450).
  • Laigle, C.; Davidzon, I.; Ilbert, O.; Devriendt, J.; Kashino, D.; Pichon, C.; Capak, P.; Arnouts, S.; de la Torre, S.; Dubois, Y.; Gozaliasl, G.; Le Borgne, D.; Lilly, S.; McCracken, H. J.; Salvato, M.; Slyz, A. (2019)
    Using the light-cone from the cosmological hydrodynamical simulation horizon-AGN, we produced a photometric catalogue over 0 <z <4 with apparent magnitudes in COSMOS, Dark Energy Survey, Large Synoptic Survey Telescope (LSST)-like, and Euclid-like filters at depths comparable to these surveys. The virtual photometry accounts for the complex star formation history (SFH) and metal enrichment of horizon-AGN galaxies, and consistently includes magnitude errors, dust attenuation, and absorption by intergalactic medium. The COSMOS-like photometry is fitted in the same configuration as the COSMOS2015 catalogue. We then quantify random and systematic errors of photometric redshifts, stellar masses, and star formation rates (SFR). Photometric redshifts and redshift errors capture the same dependencies on magnitude and redshift as found in COSMOS2015, excluding the impact of source extraction. COSMOS-like stellar masses are well recovered with a dispersion typically lower than 0.1 dex. The simple SFHs and metallicities of the templates induce a systematic underestimation of stellar masses at z <1.5 by at most 0.12 dex. SFR estimates exhibit a dust-induced bimodality combined with a larger scatter (typically between 0.2 and 0.6 dex). We also use our mock catalogue to predict photometric redshifts and stellar masses in future imaging surveys. We stress that adding Euclid near-infrared photometry to the LSST-like baseline improves redshift accuracy especially at the faint end and decreases the outlier fraction by a factor similar to 2. It also considerably improves stellar masses, reducing the scatter up to a factor 3. It would therefore be mutually beneficial for LSST and Euclid to work in synergy.
  • Raulinaitis, Vytas; Tossavainen, Helena; Aitio, Olli; Juuti, Jarmo T.; Hiramatsu, Keiichi; Kontinen, Vesa; Permi, Perttu (2017)
    We introduce LytU, a short member of the lysostaphin family of zinc-dependent pentaglycine endopeptidases. It is a potential antimicrobial agent for S. aureus infections and its gene transcription is highly upregulated upon antibiotic treatments along with other genes involved in cell wall synthesis. We found this enzyme to be responsible for the opening of the cell wall peptidoglycan layer during cell divisions in S. aureus. LytU is anchored in the plasma membrane with the active part residing in the periplasmic space. It has a unique Ile/Lys insertion at position 151 that resides in the catalytic site-neighbouring loop and is vital for the enzymatic activity but not affecting the overall structure common to the lysostaphin family. Purified LytU lyses S. aureus cells and cleaves pentaglycine, a reaction conveniently monitored by NMR spectroscopy. Substituting the cofactor zinc ion with a copper or cobalt ion remarkably increases the rate of pentaglycine cleavage. NMR and isothermal titration calorimetry further reveal that, uniquely for its family, LytU is able to bind a second zinc ion which is coordinated by catalytic histidines and is therefore inhibitory. The pH-dependence and high affinity of binding carry further physiological implications.
  • Lee, Kyung Min; Kivelä, Sami M.; Ivanov, Vladislav; Hausmann, Axel; Kaila, Lauri; Wahlberg, Niklas; Mutanen, Marko (2018)
    A rapid shift from traditional Sanger sequencing-based molecular methods to the phylogenomic approach with large numbers of loci is underway. Among phylogenomic methods, restriction site associated DNA (RAD) sequencing approaches have gained much attention as they enable rapid generation of up to thousands of loci randomly scattered across the genome and are suitable for nonmodel species. RAD data sets however suffer from large amounts of missing data and rapid locus dropout along with decreasing relatedness among taxa. The relationship between locus dropout and the amount of phylogenetic information retained in the data has remained largely uninvestigated. Similarly, phylogenetic hypotheses based on RAD have rarely been compared with phylogenetic hypotheses based on multilocus Sanger sequencing, even less so using exactly the same species and specimens. We compared the Sanger-based phylogenetic hypothesis (8 loci; 6172 bp) of 32 species of the diverse moth genus Eupithecia (Lepidoptera, Geometridae) to that based on double-digest RAD sequencing (3256 loci; 726,658 bp). We observed that topologies were largely congruent, with some notable exceptions that we discuss. The locus dropout effect was strong. We demonstrate that number of loci is not a precise measure of phylogenetic information since the number of single-nucleotide polymorphisms (SNPs) may remain low at very shallow phylogenetic levels despite large numbers of loci. As we hypothesize, the number of SNPs and parsimony informative SNPs (PIS) is low at shallow phylogenetic levels, peaks at intermediate levels and, thereafter, declines again at the deepest levels as a result of decay of available loci. Similarly, we demonstrate with empirical data that the locus dropout affects the type of loci retained, the loci found in many species tending to show lower interspecific distances than those shared among fewer species. We also examine the effects of the numbers of loci, SNPs, and PIS on nodal bootstrap support, but could not demonstrate with our data our expectation of a positive correlation between them. We conclude that RAD methods provide a powerful tool for phylogenomics at an intermediate phylogenetic level as indicated by its broad congruence with an eight-gene Sanger data set in a genus of moths. When assessing the quality of the data for phylogenetic inference, the focus should be on the distribution and number of SNPs and PIS rather than on loci.