Maankäytön vaikutus Etelä-Suomen pohjavesien bakteeriyhteisöihin

Tiivistelmä. Vesiekosysteemien ekologisen tilan heikkeneminen on lisännyt niiden suojelun ja lainsäädännöllisen säätelyn tarvetta. Pohjavesi ja siitä riippuvaiset ekosysteemit eivät ole saaneet kuitenkaan tarpeeksi huomiota, sillä pohjavesiä koskevat säädännöt liittyvät pääsääntöisesti veden kemiallisiin ominaisuuksiin vedenoton näkökulmasta. Mikrobit, ja erityisesti ravinneköyhille pohjavesiekosysteemeille tyypilliset bakteerit, ovat vielä nykypäivänäkin puutteellisesti tunnettu eliöryhmä, vaikka niiden merkitys pohjavesien tarjoamien ekosysteemipalveluiden kannalta on huomattava. Tutkielmassani selvitin, miten lähiympäristön maankäyttö vaikuttaa pohjavesiriippuvaisten ekosysteemien (lähteet) bakteeriyhteisöjen monimuotoisuuteen, lajikoostumukseen ja toimintaan (orgaanisen aineksen hajotus). Aineisto kerättiin 64 eteläisen Suomen lähteestä, joiden lähiympäristön maankäyttöä tarkasteltiin kahden kilometrin puskurivyöhykkeiden avulla. CORINE-maanpeiteaineiston perusteella tutkimuskohteet jaettiin 1) lähiympäristön maankäytöltään muuttumattomiin metsälähteisiin (vertailuryhmä), 2) viljelymaiden lähteisiin ja 3) rakennettujen alueiden ja viljelymaiden lähteisiin ja 4) rakennettujen alueiden lähteisiin. Tarkastelin eri maankäyttömuotojen vaikutusta pohjaveden kemialliseen laatuun (nitraatti- ja kloridipitoisuus), sekä miten nämä kemialliset muutokset heijastuivat bakteeriyhteisöissä (taksonomisesti ja toiminnallisesti). Tulokset osoittivat lähteen lähiympäristön rakentamisen ja maanviljelyn heikentävän pohjaveden kemiallista laatua. Maankäytön ympäröimät lähteet erosivat sekä nitraatti, että kloridipitoisuuden suhteen luonnontilaisista lähteistä. Maankäyttö vähensi bakteeriyhteisön monimuotoisuutta ja nitraattipitoisuuden osalta työssä havaittiin yksihuippuinen vaste, jossa bakteerien monimuotoisuus ensin kasvoi, mutta jo 100–300 µg L-1 pitoisuuksissa alkoi vähenemään. Maankäytön muuttamien lähteiden yhteisöt erosivat lajikoostumukseltaan vertailulähteistä ja pohjaveden kemialliset tekijät pääosin selittivät yhteisöjen rakennetta. Myös lajistovaihtelussa (β-diversiteetti) havaittiin eroja, mutta vastoin odotuksia, maankäytön muuttamien lähteiden yhteisöt olivat lajistoltaan vaihtelevampia vertailuryhmään verrattuna. Myös orgaanisen aineksen hajotuksen osalta työssä havaittiin yksihuippuinen vaste, jossa hajotustoiminta aluksi kasvoi, mutta heikentyi pohjaveden nitraattipitoisuuksien ylittäessä ~400 µg L-1. Tutkielman tulokset osoittavat, että lähialueen maankäyttö vaikuttaa pohjaveden kemiallisiin ominaisuuksiin, jotka vuorostaan aiheuttavat merkittäviä muutoksia pohjavedestä riippuvaisten ekosysteemien bakteeriyhteisöissä. Tulosten perusteella jo varsin pienet muutokset pohjaveden nitraattipitoisuudessa heikentävät bakteeriyhteisön monimuotoisuutta ja toimintaa, ja näin ollen pohjevesien nitraattipitoisuuden rajoja tulisikin uudelleen tarkastella pohjavesien ekologisen tilan näkökulmasta. Tutkielman tulokset korostavat bakteerien ekologista merkitystä pohjavesissä ja siitä riippuvaisissa ekosysteemeissä, sekä tuovat uutta tietoa tämän merkittävän eliöryhmän osalta

Polarization relaxation in thin-film relaxors compared to that in ferroelectrics

Epitaxial thin films of relaxor PbMg1/3Nb2/3O3 and PbSc0.5Nb0.5O3, and ferroelectric PbZr0.65Ti0.35O3, Pb0.955La0.045Zr0.65Ti0.35O3, and Ba0.4Sr0.6TiO3 were prepared, and their dielectric properties were studied in a broad range of the measurement conditions. In the ferroelectric state, the presence and the change of configuration of the domains determined both the dynamic dielectric nonlinearity and the polarization hysteresis. In thin-film relaxors, the orientation of the randomly interacting dipoles in a random field was responsible for the dynamic dielectric nonlinearity, while the observed hysteresis was suggested to arise due to connection between the applied field and the relaxation times of both the dipoles and the internal field. In thin-film (Ba,Sr)TiO3, the high-temperature dielectric hysteresis was found to be relaxorlike.Comment: 20 pages, 10 figures, submitted to Phys. Rev. B 17.03.200

Tissue distribution of the laminin β1 and β2 chain during embryonic and fetal human development

Laminins are the major glycoproteins present in all basement membranes. Previously, we showed that perlecan is present during human development. Although an overview of mRNA-expression of the laminin β1 and β2 chains in various developing fetal organs is already available, a systematic localization of the laminin β1 and β2 chains on the protein level during embryonic and fetal human development is missing. Therefore, we studied the immunohistochemical expression and tissue distribution of the laminin β1 and β2 chains in various developing embryonic and fetal human organs between gestational weeks 8 and 12. The laminin β1 chain was ubiquitously expressed in the basement membrane zones of the brain, ganglia, blood vessels, liver, kidney, skin, pancreas, intestine, heart and skeletal system. Furthermore, the laminin β2 chain was present in the basement membrane zones of the brain, ganglia, skin, heart and skeletal system. The findings of this study support and expand upon the theory that these two laminin chains are important during human development

Molecular Mechanism of the Constitutive Activation of the L250Q Human Melanocortin-4 Receptor Polymorphism †

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65471/1/j.1747-0285.2006.00362.x.pd

Palmitoylation and membrane cholesterol stabilize μ-opioid receptor homodimerization and G protein coupling

<p>Abstract</p> <p>Background</p> <p>A cholesterol-palmitoyl interaction has been reported to occur in the dimeric interface of the β₂-adrenergic receptor crystal structure. We sought to investigate whether a similar phenomenon could be observed with μ-opioid receptor (OPRM1), and if so, to assess the role of cholesterol in this class of G protein-coupled receptor (GPCR) signaling.</p> <p>Results</p> <p>C3.55(170) was determined to be the palmitoylation site of OPRM1. Mutation of this Cys to Ala did not affect the binding of agonists, but attenuated receptor signaling and decreased cholesterol associated with the receptor signaling complex. In addition, both attenuation of receptor palmitoylation (by mutation of C3.55[170] to Ala) and inhibition of cholesterol synthesis (by treating the cells with simvastatin, a HMG-CoA reductase inhibitor) impaired receptor signaling, possibly by decreasing receptor homodimerization and Gαi2 coupling; this was demonstrated by co-immunoprecipitation, immunofluorescence colocalization and fluorescence resonance energy transfer (FRET) analyses. A computational model of the OPRM1 homodimer structure indicated that a specific cholesterol-palmitoyl interaction can facilitate OPRM1 homodimerization at the TMH4-TMH4 interface.</p> <p>Conclusions</p> <p>We demonstrate that C3.55(170) is the palmitoylation site of OPRM1 and identify a cholesterol-palmitoyl interaction in the OPRM1 complex. Our findings suggest that this interaction contributes to OPRM1 signaling by facilitating receptor homodimerization and G protein coupling. This conclusion is supported by computational modeling of the OPRM1 homodimer.</p

Structure-Based Discovery of A2A Adenosine Receptor Ligands

The recent determination of X-ray structures of pharmacologically relevant GPCRs has made these targets accessible to structure-based ligand discovery. Here we explore whether novel chemotypes may be discovered for the A(2A) adenosine receptor, based on complementarity to its recently determined structure. The A(2A) adenosine receptor signals in the periphery and the CNS, with agonists explored as anti-inflammatory drugs and antagonists explored for neurodegenerative diseases. We used molecular docking to screen a 1.4 million compound database against the X-ray structure computationally and tested 20 high-ranking, previously unknown molecules experimentally. Of these 35% showed substantial activity with affinities between 200 nM and 9 microM. For the most potent of these new inhibitors, over 50-fold specificity was observed for the A(2A) versus the related A(1) and A(3) subtypes. These high hit rates and affinities at least partly reflect the bias of commercial libraries toward GPCR-like chemotypes, an issue that we attempt to investigate quantitatively. Despite this bias, many of the most potent new ligands were novel, dissimilar from known ligands, providing new lead structures for modulation of this medically important target

The c4h, tat, hppr and hppd Genes Prompted Engineering of Rosmarinic Acid Biosynthetic Pathway in Salvia miltiorrhiza Hairy Root Cultures

Rational engineering to produce biologically active plant compounds has been greatly impeded by our poor understanding of the regulatory and metabolic pathways underlying the biosynthesis of these compounds. Here we capitalized on our previously described gene-to-metabolite network in order to engineer rosmarinic acid (RA) biosynthesis pathway for the production of beneficial RA and lithospermic acid B (LAB) in Salvia miltiorrhiza hairy root cultures. Results showed their production was greatly elevated by (1) overexpression of single gene, including cinnamic acid 4-hydroxylase (c4h), tyrosine aminotransferase (tat), and 4-hydroxyphenylpyruvate reductase (hppr), (2) overexpression of both tat and hppr, and (3) suppression of 4-hydroxyphenylpyruvate dioxygenase (hppd). Co-expression of tat/hppr produced the most abundant RA (906 mg/liter) and LAB (992 mg/liter), which were 4.3 and 3.2-fold more than in their wild-type (wt) counterparts respectively. And the value of RA concentration was also higher than that reported before, that produced by means of nutrient medium optimization or elicitor treatment. It is the first report of boosting RA and LAB biosynthesis through genetic manipulation, providing an effective approach for their large-scale commercial production by using hairy root culture systems as bioreactors

Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies

The dramatic increase in heterogeneous types of biological data—in particular, the abundance of new protein sequences—requires fast and user-friendly methods for organizing this information in a way that enables functional inference. The most widely used strategy to link sequence or structure to function, homology-based function prediction, relies on the fundamental assumption that sequence or structural similarity implies functional similarity. New tools that extend this approach are still urgently needed to associate sequence data with biological information in ways that accommodate the real complexity of the problem, while being accessible to experimental as well as computational biologists. To address this, we have examined the application of sequence similarity networks for visualizing functional trends across protein superfamilies from the context of sequence similarity. Using three large groups of homologous proteins of varying types of structural and functional diversity—GPCRs and kinases from humans, and the crotonase superfamily of enzymes—we show that overlaying networks with orthogonal information is a powerful approach for observing functional themes and revealing outliers. In comparison to other primary methods, networks provide both a good representation of group-wise sequence similarity relationships and a strong visual and quantitative correlation with phylogenetic trees, while enabling analysis and visualization of much larger sets of sequences than trees or multiple sequence alignments can easily accommodate. We also define important limitations and caveats in the application of these networks. As a broadly accessible and effective tool for the exploration of protein superfamilies, sequence similarity networks show great potential for generating testable hypotheses about protein structure-function relationships

Environmentally induced changes in antioxidant phenolic compounds levels in wild plants

[EN] Different adverse environmental conditions cause oxidative stress in plants by generation of reactive oxygen species (ROS). Accordingly, a general response to abiotic stress is the activation of enzymatic and non-enzymatic antioxidant systems. Many phenolic compounds, especially flavonoids, are known antioxidants and efficient ROS scavengers in vitro, but their exact role in plant stress responses in nature is still under debate. The aim of our work is to investigate this role by correlating the degree of environmental stress with phenolic and flavonoid levels in stress-tolerant plants. Total phenolic and antioxidant flavonoid contents were determined in 19 wild species. Meteorological data and plant and soil samples were collected in three successive seasons from four Mediterranean ecosystems: salt marsh, dune, semiarid and gypsum habitats. Changes in phenolic and flavonoid levels were correlated with the environmental conditions of the plants and were found to depend on both the taxonomy and ecology of the investigated species. Despite species-specific differences, principal component analyses of the results established a positive correlation between plant phenolics and several environmental parameters, such as altitude, and those related to water stress: temperature, evapotranspiration, and soil water deficit. The correlation with salt stress was, however, very weak. The joint analysis of all the species showed the lowest phenolic and flavonoid levels in the halophytes from the salt marsh. This finding supports previous data indicating that the halophytes analysed here do not undergo oxidative stress in their natural habitat and therefore do not need to activate antioxidant systems as a defence against salinity.This work has been funded by the Spanish Ministry of Science and Innovation (Project CGL2008-00438/BOS), with contribution from the European Regional Development Fund. Thanks to Dr. Rafael Herrera for critical reading of the manuscript.Bautista, I.; Boscaiu, M.; Lidón, A.; Llinares Palacios, JV.; Lull, C.; Donat-Torres, MP.; Mayoral García-Berlanga, O.... (2016). Environmentally induced changes in antioxidant phenolic compounds levels in wild plants. Acta Physiologiae Plantarum. 38(1):1-15. https://doi.org/10.1007/s11738-015-2025-2S115381Agati G, Biricolti S, Guidi L, Ferrini F, Fini A, Tattini M (2011) The biosynthesis of flavonoids is enhanced similarly by UV radiation and root zone salinity in L. vulgare leaves. 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Modeling of Human Prokineticin Receptors: Interactions with Novel Small-Molecule Binders and Potential Off-Target Drugs

The Prokineticin receptor (PKR) 1 and 2 subtypes are novel members of family A GPCRs, which exhibit an unusually high degree of sequence similarity. Prokineticins (PKs), their cognate ligands, are small secreted proteins of ∼80 amino acids; however, non-peptidic low-molecular weight antagonists have also been identified. PKs and their receptors play important roles under various physiological conditions such as maintaining circadian rhythm and pain perception, as well as regulating angiogenesis and modulating immunity. Identifying binding sites for known antagonists and for additional potential binders will facilitate studying and regulating these novel receptors. Blocking PKRs may serve as a therapeutic tool for various diseases, including acute pain, inflammation and cancer.Ligand-based pharmacophore models were derived from known antagonists, and virtual screening performed on the DrugBank dataset identified potential human PKR (hPKR) ligands with novel scaffolds. Interestingly, these included several HIV protease inhibitors for which endothelial cell dysfunction is a documented side effect. Our results suggest that the side effects might be due to inhibition of the PKR signaling pathway. Docking of known binders to a 3D homology model of hPKR1 is in agreement with the well-established canonical TM-bundle binding site of family A GPCRs. Furthermore, the docking results highlight residues that may form specific contacts with the ligands. These contacts provide structural explanation for the importance of several chemical features that were obtained from the structure-activity analysis of known binders. With the exception of a single loop residue that might be perused in the future for obtaining subtype-specific regulation, the results suggest an identical TM-bundle binding site for hPKR1 and hPKR2. In addition, analysis of the intracellular regions highlights variable regions that may provide subtype specificity