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Mitochondrial dynamics and mitophagy play a key role in ensuring mitochondrial quality control. Impairment thereof was proposed to be causative to neurodegenerative diseases, diabetes, and cancer. Accumulation of mitochondrial dysfunction was further linked to aging. Here we applied a probabilistic modeling approach integrating our current knowledge on mitochondrial biology allowing us to simulate mitochondrial function and quality control during aging in silico. We demonstrate that cycles of fusion and fission and mitophagy indeed are essential for ensuring a high average quality of mitochondria, even under conditions in which random molecular damage is present. Prompted by earlier observations that mitochondrial fission itself can cause a partial drop in mitochondrial membrane potential, we tested the consequences of mitochondrial dynamics being harmful on its own. Next to directly impairing mitochondrial function, pre-existing molecular damage may be propagated and enhanced across the mitochondrial population by content mixing. In this situation, such an infection-like phenomenon impairs mitochondrial quality control progressively. However, when imposing an age-dependent deceleration of cycles of fusion and fission, we observe a delay in the loss of average quality of mitochondria. This provides a rational why fusion and fission rates are reduced during aging and why loss of a mitochondrial fission factor can extend life span in fungi. We propose the ‘mitochondrial infectious damage adaptation’ (MIDA) model according to which a deceleration of fusion–fission cycles reflects a systemic adaptation increasing life span.
Wittmann, Miriam ; Doble, Rosella ; Bachmann, Malte ; Pfeilschifter, Josef ; Werfel, Thomas ; Mühl, Heiko
IL-18 is an important mediator involved in chronic inflammatory conditions such as cutaneous lupus erythematosus, psoriasis and chronic eczema. An imbalance between IL-18 and its endogenous antagonist IL-18 binding protein (BP) may account for increased IL-18 activity. IL-27 is a cytokine with dual function displaying pro- and anti-inflammatory properties. Here we provide evidence for a yet not described anti-inflammatory mode of action on skin resident cells. Human keratinocytes and surprisingly also fibroblasts (which do not produce any IL-18) show a robust, dose-dependent and highly inducible mRNA expression and secretion of IL-18BP upon IL-27 stimulation. Other IL-12 family members failed to induce IL-18BP. The production of IL-18BP peaked between 48–72 h after stimulation and was sustained for up to 96 h. Investigation of the signalling pathway showed that IL-27 activates STAT1 in human keratinocytes and that a proximal GAS site at the IL-18BP promoter is of importance for the functional activity of IL-27. The data are in support of a significant anti-inflammatory effect of IL-27 on skin resident cells. An important novel property of IL-27 in skin pathobiology may be to counter-regulate IL-18 activities by acting on keratinocytes and importantly also on dermal fibroblasts.
Husson, Steven J. ; Liewald, Jana F. ; Schultheis, Christian ; Stirman, Jeffrey N. ; Lu, Hang ; Gottschalk, Alexander
Essentially any behavior in simple and complex animals depends on neuronal network function. Currently, the best-defined system to study neuronal circuits is the nematode Caenorhabditis elegans, as the connectivity of its 302 neurons is exactly known. Individual neurons can be activated by photostimulation of Channelrhodopsin-2 (ChR2) using blue light, allowing to directly probe the importance of a particular neuron for the respective behavioral output of the network under study. In analogy, other excitable cells can be inhibited by expressing Halorhodopsin from Natronomonas pharaonis (NpHR) and subsequent illumination with yellow light. However, inhibiting C. elegans neurons using NpHR is difficult. Recently, proton pumps from various sources were established as valuable alternative hyperpolarizers. Here we show that archaerhodopsin-3 (Arch) from Halorubrum sodomense and a proton pump from the fungus Leptosphaeria maculans (Mac) can be utilized to effectively inhibit excitable cells in C. elegans. Arch is the most powerful hyperpolarizer when illuminated with yellow or green light while the action spectrum of Mac is more blue-shifted, as analyzed by light-evoked behaviors and electrophysiology. This allows these tools to be combined in various ways with ChR2 to analyze different subsets of neurons within a circuit. We exemplify this by means of the polymodal aversive sensory ASH neurons, and the downstream command interneurons to which ASH neurons signal to trigger a reversal followed by a directional turn. Photostimulating ASH and subsequently inhibiting command interneurons using two-color illumination of different body segments, allows investigating temporal aspects of signaling downstream of ASH.
Using an electrophysiological assay the activity of NhaA was tested in a wide pH range from pH 5.0 to 9.5. Forward and reverse transport directions were investigated at zero membrane potential using preparations with inside-out and right side-out-oriented transporters with Na+ or H+ gradients as the driving force. Under symmetrical pH conditions with a Na+ gradient for activation, both the wt and the pH-shifted G338S variant exhibit highly symmetrical transport activity with bell-shaped pH dependences, but the optimal pH was shifted 1.8 pH units to the acidic range in the variant. In both strains the pH dependence was associated with a systematic increase of the Km for Na+ at acidic pH. Under symmetrical Na+ concentration with a pH gradient for NhaA activation, an unexpected novel characteristic of the antiporter was revealed; rather than being down-regulated, it remained active even at pH as low as 5. These data allowed a transport mechanism to advance based on competing Na+ and H+ binding to a common transport site and a kinetic model to develop quantitatively explaining the experimental results. In support of these results, both alkaline pH and Na+ induced the conformational change of NhaA associated with NhaA cation translocation as demonstrated here by trypsin digestion. Furthermore, Na+ translocation was found to be associated with the displacement of a negative charge. In conclusion, the electrophysiological assay allows the revelation of the mechanism of NhaA antiport and sheds new light on the concept of NhaA pH regulation.
Although essential for T cell function, the identity of the T cell receptor (TCR) “inside-out” pathway for the activation of lymphocyte function-associated antigen 1 (LFA-1) is unclear. SKAP1 (SKAP-55) is the upstream regulator needed for TCR-induced RapL-Rap1 complex formation and LFA-1 activation. In this paper, we show that SKAP1 is needed for RapL binding to membranes in a manner dependent on the PH domain of SKAP1 and the PI3K pathway. A SKAP1 PH domain-inactivating mutation (i.e. R131M) markedly impaired RapL translocation to membranes for Rap1 and LFA-1 binding and the up-regulation of LFA-1-intercellular adhesion molecule 1 (ICAM-1) binding. Further, N-terminal myr-tagged SKAP1 for membrane binding facilitated constitutive RapL membrane and Rap1 binding and effectively substituted for PI3K and TCR ligation in the activation of LFA-1 in T cells.
Objectives: Sepsis remains a disease with a high mortality in neonates. Microcirculatory impairment plays a pivotal role in the development of multiorgan failure in septic newborns. The hemodynamic effects of recombinant activated protein C (rhAPC) were tested in an animal model of neonatal septic shock focusing on intestinal microcirculation.
Materials and methods: Endotoxic shock was triggered by intravenous application of Escherichia coli lipopolysaccarides in newborn piglets. Thereafter, five animals received a continuous infusion of 24 µg/kg/h rhAPC, and five received vehicle for control. Over the course of three hours, intestinal microcirculation was assessed by intravital microscopy every 30 min. Macrocirculation and blood counts were monitored simultaneously.
Results: After a short hypotensive period in all animals, the arterial blood pressure returned to baseline in the rhAPC-treated piglets, whereas the hypotension became increasingly severe in the controls. By 90 min, mean blood pressure in the controls was significantly lower than in the treatment group. Similar observations were made regaring microcirculation. After an early impairment in all study animals, functional capillary density and intestinal microcirculatory red blood cell velocity and red blood cell flow recovered in the rhAPC group, but deteriorated further in the control piglets.
Conclusion: Recombinant activated protein C protects macro- and microcirculation from endotoxic shock.
Der verstärkte Umgang mit Wissen in den Wirtschaftswissenschaften ist in den letzten Jahren in den Fokus der Wissenschaftler geraten. Ausgeblendet wurde dabei größtenteils die Kehrseite von Wissen, die Frage nach dem "Nichtwissen". Das Nichtwissen ist aufgrund der vorherrschenden Auffassung des gesellschaftlichen Bildes mit einer negativen Notation behaftet. Die zunehmende Auseinandersetzung des Nichtwissens in den Geisteswissenschaften bringt die positiven Funktionen zur Geltung. Der vorliegende Artikel zeigt zunächst die erfolgsfördernden Funktionen des Nichtwissens auf und implementiert somit Chancen des Nichtwissens in einem wirtschaftwissenschaftlichen Rahmen. Im Anschluss werden empirische Befunde, resultierend aus einer Befragung, die an der Goethe Universität Frankfurt am Main durchgeführt wurde, präsentiert.
EFP1 is an ER stress-induced glycoprotein which interacts with the pro-apoptotic protein Par-4
(2009)
Appel, Sarah ; Vetterkind, Susanne ; Koplin, Ansgar ; Maertens, Barbara ; Boosen, Meike ; Preuss, Ute
We have isolated the rat ortholog of EFP1 (EF-hand binding protein 1) as a novel interaction partner of the pro-apoptotic protein Par-4 (prostate apoptosis response-4). Rat EFP1 contains two thioredoxin domains, the COOH-terminal one harboring a CGFC motif, and has a similar protein domain structure as members of the protein disulfide isomerase (PDI) family. In REF52.2 and CHO cells, EFP1 colocalized with the endoplasmic reticulum (ER) marker PDI. Furthermore, EFP1 possesses catalytic activity as demonstrated by an insulin disulfide reduction assay. Western blot analysis revealed two EFP1 protein bands of approximately 136 and 155 kDa, representing different glycosylation states of the protein. Complex formation between EFP1 and Par-4 was confirmed in vitro and in vivo by co-immunoprecipitation, dot blot overlay and pull-down experiments. In CHO cells, coexpression of EFP1 and Par-4 resulted in enhanced Par-4-mediated apoptosis, which required the catalytic activity of EFP1. Interestingly, EFP1 was specifically upregulated in NIH3T3 cells after induction of ER stress by thapsigargin, tunicamycin, and brefeldin A, but not by agents that induce oxidative stress or ER-independent apoptosis. Furthermore, we could show that the induction of apoptosis by Ca2+ stress-inducing agents was significantly decreased after siRNA oligonucleotide-mediated knockdown of Par-4. Our data suggest that EFP1 might represent a cell-protective enzyme that could play an important role in the decision between survival and initiation of Par-4-mediated apoptosis.
Michel, Sebastian ; Bigdeli, Amir Khosrow ; Beiras Fernández, Andrés ; Schmitz, Christoph ; Wolf, Manuel ; Sodian, Ralf ; Kaczmarek, Ingo
Background: Valvular aortic stenosis is a common disease in the elderly, often in multimorbid patients. It is often associated with coronary artery disease and peripheral artery disease. In this situation, the risk of conventional open-heart surgery is too high, and other treatment strategies have to be evaluated.
Case report: A 79-year-old female patient with severe aortic stenosis, coronary artery disease and end-stage chronic obstructive pulmonary disease suffering from dyspnea at rest and permanently dependent on oxygen was treated in three steps. Firstly, her pulmonary infection was treated with antibiotics for 7 days. Then, the left anterior descending artery was stented (bare-metal stent). In the same session, valvuloplasty of the aortic valve was performed. She was sent to rehabilitation to improve her pulmonary condition and took clopidogrel for 4 weeks. Finally, she underwent transapical aortic valve replacement. She was released to rehabilitation on postoperative day 12.
Conclusion: A combination of modern interventional and minimally invasive surgical techniques to treat aortic stenosis and coronary heart disease can be a viable option for multimorbid patients with extremely high risk in conventional open-heart surgery.
Meyer, Hartwig ; Stöver, Timo ; Fouchet, Florian ; Bastiat, Guillaume ; Saulnier, Patrick ; Bäumer, Wolfgang ; Lenarz, Thomas ; Scheper, Verena
Objective: Sensorineural hearing loss leads to the progressive degeneration of spiral ganglion cells (SGC). Next to postoperative fibrous tissue growth, which should be suppressed to assure a close nerve–electrode interaction, the density of healthy SGC is one factor that influences the efficiency of cochlear implants (CI), the choice of treatment for affected patients. Rolipram, a phosphodiesterase-4 inhibitor, has proven neuroprotective and anti-inflammatory effects and might also reduce SGC degeneration and fibrosis, but it has to pass the cellular membrane to be biologically active.
Methods: Lipidic nanocapsules (LNC) can be used as biodegradable drug carriers to increase the efficacy of conventional application methods. We examined the biological effects of rolipram and LNC's core encapsulated rolipram on SGC and dendritic cell (DC) tumor necrosis factor-α (TNF-α) production in vitro and on SGC survival in systemically-deafened guinea pigs in vivo.
Results: Our results prove that rolipram does not have a beneficial effect on cultured SGC. Incorporation of rolipram in LNC increased the survival of SGC significantly. In the DC study, rolipram significantly inhibited TNF-α in a dose-dependent manner. The rolipram-loaded LNC provided a significant cytokine inhibition as well. In vivo data do not confirm the in vitro results.
Conclusion: By transporting rolipram into the SGC cytoplasm, LNC enabled the neuroprotective effect of rolipram in vitro, but not in vivo. This might be due to dilution of test substances by perilymph or an inadequate release of rolipram based on differing in vivo and in vitro conditions. Nevertheless, based on in vitro results, proving a significantly increased neuronal survival when using LNC-rolipram compared to pure rolipram and pure LNC application, we believe that the combination of rolipram and LNC can potentially reduce neuronal degeneration and fibrosis after CI implantation. We conclude that rolipram is a promising drug that can be used in inner ear therapy and that LNC have potential as an inner ear drug-delivery system. Further experiments with modified conditions might reveal in vivo biological effects.
The most frequent neurodegenerative diseases (NDs) are Alzheimer’s disease (AD), Parkinson’s disease (PD), and frontotemporal lobar degeneration associated with protein TDP-43 (FTLD–TDP). Neuropathologically, NDs are characterized by abnormal intracellular and extra-cellular protein deposits and by disease-specific neuronal death. Practically all terminal stages of NDs are clinically associated with dementia. Therefore, major attention was directed to protein deposits and neuron loss in supratentorial (telencephalic) brain regions in the course of NDs. This was also true for PD, although the pathological hallmark of PD is degeneration of pigmented neurons of the brainstem’s substantia nigra (SN). However, PD pathophysiology was explained by dopamine depletion in the telencephalic basal ganglia due to insufficiency and degeneration of the projection neurons located in SN. In a similar line of argumentation AD- and FTLD-related clinical deficits were exclusively explained by supratentorial allo- and neo-cortical laminar neuronal necrosis. Recent comprehensive studies in AD and PD early stages found considerable and unexpected involvement of brainstem nuclei, which could have the potential to profoundly change our present concepts on origin, spread, and early clinical diagnosis of these diseases. In contrast with PD and AD, few studies addressed brainstem involvement in the course of the different types of FTLD–TDP. Some of the results, including ours, disclosed a higher and more widespread pathology than anticipated. The present review will focus mainly on the impact of brainstem changes during the course of the most frequent NDs including PD, AD, and FTLD–TDP, with special emphasis on the need for more comprehensive research on FTLDs.
The inability to faithfully segregate chromosomes in mitosis results in chromosome instability, a hallmark of solid tumors. Disruption of microtubule dynamics contributes highly to mitotic chromosome instability. The kinesin-13 family is critical in the regulation of microtubule dynamics and the best characterized member of the family, the mitotic centromere-associated kinesin (MCAK), has recently been attracting enormous attention. MCAK regulates microtubule dynamics as a potent depolymerizer of microtubules by removing tubulin subunits from the polymer end. This depolymerizing activity plays pivotal roles in spindle formation, in correcting erroneous attachments of microtubule-kinetochore and in chromosome movement. Thus, the accurate regulation of MCAK is important for ensuring the faithful segregation of chromosomes in mitosis and for safeguarding chromosome stability. In this review we summarize recent data concerning the regulation of MCAK by mitotic kinases, Aurora A/B, Polo-like kinase 1 and cyclin-dependent kinase 1. We propose a molecular model of the regulation of MCAK by these mitotic kinases and relevant phosphatases throughout mitosis. An ever-increasing quantity of data indicates that MCAK is aberrantly regulated in cancer cells. This deregulation is linked to increased malignance, invasiveness, metastasis and drug resistance, most probably due to increased chromosomal instability and remodeling of the microtubule cytoskeleton in cancer cells. Most interestingly, recent observations suggest that MCAK could be a novel molecular target for cancer therapy, as a new cancer antigen or as a mitotic regulator. This collection of new data indicates that MCAK could be a new star in the cancer research sky due to its critical roles in the control of genome stability and the cytoskeleton. Further investigations are required to dissect the fine details of the regulation of MCAK throughout mitosis and its involvements in oncogenesis.
Large crystals of the methyl ester of the N-a-benzyloxycarbonyl protected Ala-Phe dipeptide (Z-AF-OMe) were obtained after the very slow evaporation of a solution of the corresponding carboxylic acid (Z-AF-OH) in methanol containing an excess of HCl. The structure was confirmed by single crystal X-ray diffraction data. It crystallizes in the orthorhombic space group P212121 with unit cell dimensions a = 5.0655(6) Å, b = 8.4614(8) Å, c = 46.856(5) Å, V = 2008.3(4) Å3, Z = 4. In the crystal, the molecules form hydrogen bonded chains running along the a axis of the unit cell. Other secondary interactions are also discussed.
This study presents a global scale analysis of cropping intensity, crop duration and fallow land extent computed by using the global dataset on monthly irrigated and rainfed crop areas MIRCA2000. MIRCA2000 was mainly derived from census data and crop calendars from literature. Global cropland extent was 16 million km2 around the year 2000 of which 4.4 million km2 (28%) was fallow, resulting in an average cropping intensity of 0.82 for total cropland extent and of 1.13 when excluding fallow land. The lowest cropping intensities related to total cropland extent were found for Southern Africa (0.45), Central America (0.49) and Middle Africa (0.54), while highest cropping intensities were computed for Eastern Asia (1.04) and Southern Asia (1.0). In remote or arid regions where shifting cultivation is practiced, fallow periods last 3–10 years or even longer. In contrast, crops are harvested two or more times per year in highly populated, often irrigated tropical or subtropical lowlands where multi-cropping systems are common. This indicates that intensification of agricultural land use is a strategy that may be able to significantly improve global food security. There exist large uncertainties regarding extent of cropland, harvested crop area and therefore cropping intensity at larger scales. Satellite imagery and remote sensing techniques provide opportunities for decreasing these uncertainties and to improve the MIRCA2000 inventory.
Transition metal nitrides, carbides and borides have a high potential for industrial applications as they not only have a high melting point but are generally harder and less compressible than the pure metals. Here we summarize recent advances in the synthesis of binary transition metal nitrides, carbides and borides focusing on the reaction of the elements at extreme conditions generated within the laser-heated diamond anvil cell. The current knowledge of their structures and high-pressure properties like high-(p; T) stability, compressibility and hardness is described as obtained from experiments.
We report on screening tests of 66 extracts obtained from 35 marine sponge species from the Caribbean Sea (Curaçao) and from eight species from the Great Barrier Reef (Lizard Island). Extracts were prepared in aqueous and organic solvents and were tested for hemolytic, hemagglutinating, antibacterial and anti-acetylcholinesterase (AChE) activities, as well as their ability to inhibit or activate cell protein phosphatase 1 (PP1). The most interesting activities were obtained from extracts of Ircinia felix, Pandaros acanthifolium, Topsentia ophiraphidites, Verongula rigida and Neofibularia nolitangere. Aqueous and organic extracts of I. felix and V. rigida showed strong antibacterial activity. Topsentia aqueous and some organic extracts were strongly hemolytic, as were all organic extracts from I. felix. The strongest hemolytic activity was observed in aqueous extracts from P. acanthifolium. Organic extracts of N. nolitangere and I. felix inhibited PP1. The aqueous extract from Myrmekioderma styx possessed the strongest hemagglutinating activity, whilst AChE inhibiting activity was found only in a few sponges and was generally weak, except in the methanolic extract of T. ophiraphidites.
Spontaneous symmetry breaking is a general principle that constitutes the underlying concept of a vast number of physical phenomena ranging from ferromagnetism and superconductivity in condensed matter physics to the Higgs mechanism in the standard model of elementary particles. I focus on manifestations of spontaneously broken symmetries in systems that are not Lorentz invariant, which include both nonrelativistic systems as well as relativistic systems at nonzero density, providing a self-contained review of the properties of spontaneously broken symmetries specific to such theories. Topics covered include: (i) Introduction to the mathematics of spontaneous symmetry breaking and the Goldstone theorem. (ii) Minimization of Higgs-type potentials for higher-dimensional representations. (iii) Counting rules for Nambu–Goldstone bosons and their dispersion relations. (iv) Construction of effective Lagrangians. Specific examples in both relativistic and nonrelativistic physics are worked out in detail.
Self-organized complexity and Coherent Infomax from the viewpoint of Jaynes’s probability theory
(2012)
This paper discusses concepts of self-organized complexity and the theory of Coherent Infomax in the light of Jaynes’s probability theory. Coherent Infomax, shows, in principle, how adaptively self-organized complexity can be preserved and improved by using probabilistic inference that is context-sensitive. It argues that neural systems do this by combining local reliability with flexible, holistic, context-sensitivity. Jaynes argued that the logic of probabilistic inference shows it to be based upon Bayesian and Maximum Entropy methods or special cases of them. He presented his probability theory as the logic of science; here it is considered as the logic of life. It is concluded that the theory of Coherent Infomax specifies a general objective for probabilistic inference, and that contextual interactions in neural systems perform functions required of the scientist within Jaynes’s theory.
YS-121 [2-(4-chloro-6-(2,3-dimethylphenylamino)pyrimidin-2-ylthio)octanoic acid] is the result of target-oriented structural derivatization of pirinixic acid. It is a potent dual PPARα/γ-agonist, as well as a potent dual 5-LO/mPGES-1-inhibitor. Additionally, recent studies showed an anti-inflammatory efficacy in vivo. Because of its interference with many targets, YS-121 is a promising drug candidate for the treatment of inflammatory diseases. Ongoing preclinical studies will thus necessitate huge amounts of YS-121. To cope with those requirements, we have optimized the synthesis of YS-121. Surprisingly, we isolated and characterized byproducts during the resulting from nucleophilic aromatic substitution reactions by different tertiary alkylamines at a heteroaromatic halide. These amines should actually serve as assisting bases, because of their low nucleophilicity. This astonishing fact was not described in former publications concerning that type of reaction and, therefore, might be useful for further reaction improvement in general. Furthermore, we could develop a proposal for the mechanism of that byproduct formation.
El Antri, Ali ; Messouri, Ibtissam ; Bouktaib, Mohamed ; El Alami, Rachid ; Bolte, Michael ; El Bali, Brahim ; Lachkar, Mohammed
Two tetrahydroisoquinoline alkaloids were extracted from the alkaloid fraction of a methanol extract of the seeds of Calycotome Villosa Subsp. intermedia. Their structures were established as (R)-1-hydroxymethyl-7-8-dimethoxy-1,2,3,4-tetrahydro- isoquinoline (1) and (S)-7-hydroxymethyl-2-3-dimethoxy-7,8,9,10-tetrahydroisoquinoline chloride (2) by spectroscopic techniques and X-ray diffraction analysis.
The title thiourea was synthesized by reaction of 3,4,5-trimethoxybenzoyl isothiocyante with 3-fluoroaniline. The 3,4,5-trimethoxybenzoyl isothiocyante was produced in situ by reaction of 3,4,5-trimethoxybenzoyl chloride with ammonium thiocyanate in dry acetonitrile. The structure was confirmed by the spectroscopic, elemental analysis and single crystal X-ray diffraction data. It crystallizes in the monoclinic space group P21/c with unit cell dimensions a = 13.0966(9), b = 16.6460(13), c = 7.8448(5), β = 106.721(5)°, V 1637.9(2) ų, Z = 4.
Nollmann, Friederike I. ; Dowling, Andrea ; Kaiser, Marcel ; Deckmann, Klaus ; Grösch, Sabine ; French-Constant, Richard ; Bode, Helge Björn
The synthesis of the recently characterized depsipeptide szentiamide (1), which is produced by the entomopathogenic bacterium Xenorhabdus szentirmaii, is described. Whereas no biological activity was previously identified for 1, the material derived from the efficient synthesis enabled additional bioactivity tests leading to the identification of a notable activity against insect cells and Plasmodium falciparum, the causative agent of malaria.
Mol-ecules of the title compound, [Zn(8)(C(6)F(5))(8)O(4)(C(4)H(10)O)(4)], are located on a special position of site symmetry [Formula: see text]. As a result, there is just one quarter-mol-ecule in the asymmetric unit. The title compound features a Zn(4)O(4) cube. Each Zn atom in the cube carries a pentafluorophenyl substituent. Each O atom is bonded to a further Zn atom, which is connected to a pentafluorophenyl substituent and the O atom of a diethyl ether mol-ecule. All ether C atoms are disordered over two sets of sites with a site occupation factor of 0.51 (2) for the major occupied site.
Molecules of the title compound, C20H14O2, show approximate C s symmetry with the approximate mirror plane perpendicular to the central ring. The torsion angles about the acyclic bonds are 30.05 (15) and 30.77 (15)° in one half compared to −36.62 (14) and −18.60 (15)° in the other half of the molecule. The central aromatic ring makes dihedral angles of 47.78 (4) and 51.68 (3)° with the two terminal rings.
The title compound, C14H20O5S·0.5H2O, crystallizes with two organic molecules and a solvent water molecule in the asymmetric unit. In both molecules, the hexapyranosyl rings adopt a slightly distorted chair conformation (5 C 2) with four substituents in equatorial positions and one substituent in an axial position. The main difference between the organic molecules is the dihedral angle between the phenyl ring and the best plane defined by the O—C1—C2—C3 atoms (r.m.s deviations = 0.003 and 0.043 Å) of the hexapyranosyl rings [47.4 (4) and 86.5 (4)°]. In the asymmetric unit, molecules are linked by two strong O—H[cdots, three dots, centered]O hydrogen bonds. In the crystal, the components are linked by a total of 10 distinct O—H[cdots, three dots, centered]O hydrogen bonds, resulting in the formation of a two-dimensional network parallel to the ab plane.
The title compound, C15H15BrO2, was synthesized by a Brønsted acid-catalysed domino electrocyclization-halogenation reaction. The five-membered ring is essentially planar (r.m.s. deviation 0.006 Å) and forms a dihedral angle of 72.7 (3)° with the attached phenyl ring. The six-membered heterocycle adopts a half-chair conformation. The crystal packing is stabilized by a C—H[cdots, three dots, centered]O contact.
The title compound, C(21)H(18)ClN, was synthesized by an enanti-oselective Brønsted acid-catalysed transfer hydrogenation reaction. The six-membered heterocycle adopts a half-chair conformation. It has the biphenyl residue in an axial position. The two rings of the biphenyl residue are almost coplanar [dihedral angle = 2.65 (9)°]. The crystal packing is stabilized by N-H⋯Cl hydrogen bonds, which connect the mol-ecules into chains running along the a axis.
The title compound, C25H20N4O2, is a ditopic ortho-hydroquinone-based bis(pyrazol-1-yl)methane ligand. The dihedral angles between the planes of the pyrazole rings and their attached phenyl rings are 17.4 (3) and 5.9 (4)°. The pyrazole rings make a dihedral angle of 87.84 (16)°. One of the two hydroxy groups forms an intramolecular hydrogen bond to the other hydroxy group, whereas the second is involved in an intermolecular O—H[cdots, three dots, centered]N hydrogen bond. As a result of these intermolecular hydrogen bonds, helical chains running along the b axis are formed.
Ihler, Fritz ; Bertlich, Mattis ; Sharaf, Kariem ; Strieth, Sebastian ; Strupp, Michael ; Canis, Martin
Objective: Betahistine is a histamine H1-receptor agonist and H3-receptor antagonist that is administered to treat Menière’s disease. Despite widespread use, its pharmacological mode of action has not been entirely elucidated. This study investigated the effect of betahistine on guinea pigs at dosages corresponding to clinically used doses for cochlear microcirculation.
Methods: Thirty healthy Dunkin-Hartley guinea pigs were randomly assigned to five groups to receive betahistine dihydrochloride in a dose of 1,000 mg/kg b. w. (milligram per kilogram body weight), 0.100 mg/kg b. w., 0.010 mg/kg b. w., 0.001 mg/kg b. w. in NaCl 0.9% or NaCl 0.9% alone as placebo. Cochlear blood flow and mean arterial pressure were continuously monitored by intravital fluorescence microscopy and invasive blood pressure measurements 3 minutes before and 15 minutes after administration of betahistine.
Results: When betahistine was administered in a dose of 1.000 mg/kg b. w. cochlear blood flow was increased to a peak value of 1.340 arbitrary units (SD: 0.246; range: 0.933–1.546 arb. units) compared to baseline (p<0.05; Two Way Repeated Measures ANOVA/Bonferroni t-test). The lowest dosage of 0.001 mg/kg b. w. betahistine or NaCl 0.9% had the same effect as placebo. Nonlinear regression revealed that there was a sigmoid correlation between increase in blood flow and dosages.
Conclusions: Betahistine has a dose-dependent effect on the increase of blood flow in cochlear capillaries. The effects of the dosage range of betahistine on cochlear microcirculation corresponded well to clinically used single dosages to treat Menière’s disease. Our data suggest that the improved effects of higher doses of betahistine in the treatment of Menière’s disease might be due to a corresponding increase of cochlear blood flow.
Paulus, Patrick ; Ockelmann, Pia ; Tacke, Sabine ; Karnowski, Nora ; Ellinghaus, Peter ; Scheller, Bertram ; Holfeld, Johannes ; Urbschat, Anja ; Zacharowski, Kai
The main goal of adequate organ preservation is to avoid further cellular metabolism during the phase of ischemia. However, modern preservation solutions do rarely achieve this target. In donor organs hypoxia and ischemia induce a broad spectrum of pathologic molecular mechanisms favoring primary graft dysfunction (PGD) after transplantation. Increased hypoxia-induced transcriptional activity leads to increased vascular permeability which in turn is the soil of a reperfusion edema and the enhancement of a pro-inflammatory response in the graft after reperfusion. We hypothesize that inhibition of the respiration chain in mitochondria and thus inhibition of the hypoxia induced mechanisms might reduce reperfusion edema and consecutively improve survival in vivo. In this study we demonstrate that the rotenoid Deguelin reduces the expression of hypoxia induced target genes, and especially VEGF-A, dose-dependently in hypoxic human lung derived cells. Furthermore, Deguelin significantly suppresses the mRNA expression of the HIF target genes VEGF-A, the pro-inflammatory CXCR4 and ICAM-1 in ischemic lungs vs. control lungs. After lung transplantation, the VEGF-A induced reperfusion-edema is significantly lower in Deguelin-treated animals than in controls. Deguelin-treated rats exhibit a significantly increased survival-rate after transplantation. Additionally, a downregulation of the pro-inflammatory molecules ICAM-1 and CXCR4 and an increase in the recruitment of immunomodulatory monocytes (CD163+ and CD68+) to the transplanted organ involving the IL4 pathway was observed. Therefore, we conclude that ischemic periods preceding reperfusion are mainly responsible for the increased vascular permeability via upregulation of VEGF. Together with this, the resulting endothelial dysfunction also enhances inflammation and consequently lung dysfunction. Deguelin significantly decreases a VEGF-A induced reperfusion edema, induces the recruitment of immunomodulatory monocytes and thus improves organ function and survival after lung transplantation by interfering with hypoxia induced signaling.
Sphingosine kinases (SK) catalyze the phosphorylation of proapoptotic sphingosine to the prosurvival factor sphingosine 1-phosphate (S1P), thereby promoting oncogenic processes. Breast (MDA-MB-231), lung (NCI-H358), and colon (HCT 116) carcinoma cells were transduced with shRNA to downregulate SK-1 expression or treated with a pharmacologic SK-1 inhibitor. The effects of SK-1 targeting were investigated by measuring the level of intracellular sphingosine, the activity of protein kinase C (PKC) and cell cycle regulators, and the mitotic index. Functional assays included measurement of cell proliferation, colony formation, apoptosis, and cell cycle analysis. Downregulation of SK-1 or its pharmacologic inhibition increased intracellular sphingosine and decreased PKC activity as shown by reduced phosphorylation of PKC substrates. In MDA-MB-231 cells this effect was most pronounced and reduced cell proliferation and colony formation, which could be mimicked using exogenous sphingosine or the PKC inhibitor RO 31-8220. SK-1 downregulation in MDA-MB-231 cells increased the number of cells with 4N and 8N DNA content, and similar effects were observed upon treatment with sphingosine or inhibitors of SK-1 or PKC. Examination of cell cycle regulators unveiled decreased cdc2 activity and expression of Chk1, which may compromise spindle checkpoint function and cytokinesis. Indeed, SK-1 kd cells entered mitosis but failed to divide, and in the presence of taxol also failed to sustain mitotic arrest, resulting in further increased endoreduplication and apoptosis. Our findings delineate an intriguing link between SK-1, PKC and components of the cell cycle machinery, which underlines the significance of SK-1 as a target for cancer therapy.
The fused five- and six-membered rings in the title compound, C14H12N2O, are essentially planar, the largest deviation from the mean plane being 0.023 (2) Å. The dihedral angle between the benzimidazole mean plane and the phenyl ring is 68.50 (6)°. In the crystal, each molecule is linked to its symmetry equivalent created by a crystallographic inversion center by pairs of N—H[cdots, three dots, centered]O hydrogen bonds, forming inversion dimers.
In the mol-ecule of the title compound, C(12)H(12)BrN(3)O, the fused-ring system is essentially planar, the largest deviation from the mean plane being 0.0148 (3) Å. The two allyl groups are nearly perpendicular to the imidazo[4,5-b]pyridine plane [C-C-N-C torsion angles of 81.6 (4) and -77.2 (4)°] and point in the same direction. The planes through the atoms forming each allyl group are nearly perpendicular to the imidazo[4,5-b]pyridin-2-one system, as indicated by the dihedral angles between them of 80.8 (5) and 73.6 (5)°.
The two fused five- and six-membered rings building the molecule of the title compound, C13H10BrN3, are approximately planar, the largest deviation from the mean plane being 0.004 (2) Å. The dihedral angle between the imidazo[4,5-b]pyridine mean plane and that of the phenyl ring is 41.84 (11)°. The structure is held together by slipped π–π stacking between symmetry-related molecules, with an interplanar distance of 3.583 (1) Å and a centroid–centroid vector of 3.670 (2) Å.
The structure of the title compound, (C15H15N2O4)[AgI2], consists of an organic 4-[3-(isonicotinoyloxy)propoxycarbonyl]pyridinium cation which has a gauche–gauche (O/C/C/C—O/C/C/C or GG’) conformation and lies on a twofold rotation axis, which passes through the central C atom of the aliphatic chain, and an inorganic [AgI2]− anion. In the complex anion, the Ag+ cation is bound to two I− anions in a linear geometry. The anion was modelled assuming disorder around a crystallographic inversion centre near the location of the Ag+ cation. The crystal packing is stabilized by a strong intermolecular N—H[cdots, three dots, centered]N hydrogen bond, which links the cations into zigzag chains with graph-set notation C(16) running along the face diagonal of the ac plane. The N-bound H atom is disordered over two equally occupied symmetry-equivalent sites, so that the molecule has a pyridinium ring at one end and a pyridine ring at the other.
Rodi, Youssef Kandri ; Chahdi, Fouad Ouazzani ; Essassi, El Mokhtar ; Luis, Santiago V. ; Bolte, Michael ; El Ammari, Lahcen
In the molecular structure of the title compound, C21H18N2O, the fused-ring system is essentially planar, the largest deviation from the mean plane being 0.0121 (9) Å. The O atom and adjacent C atom are located in Wyckoff position 4e on a twofold axis (0, y, 1/4). The two benzyl groups are almost perpendicular to the benzimidazole plane, but point in opposite directions. The dihedral angle between the benzimidazole mean plane and the phenyl ring is 81.95 (5)°, whereas that between the two benzyl groups is 60.96 (7)°.
Rodi, Youssef Kandri ; Chahdi, Fouad Ouazzani ; Essassi, El Mokhtar ; Luis, Santiago V. ; Bolte, Michael ; El Ammari, Lahcen
The asymmetric unit of the title compound, C16H23ClN2O, comtains two independent molecules in which the fused-ring systems are essentially planar, the largest deviation from the mean plane of each molecule being 0.011 (2) Å and 0.016 (2) Å. The benzimidazole rings of the two molecules make a dihedral angle of 66.65 (7)°. The nonyl substituents are almost perpendicular to the benzimidazole planes [C—N—C—C tosrsion angles = 96.0 (3) and 81.0 (2)°]. In the crystal, each independent molecule forms an inversion dimer via a pair of N—H[cdots, three dots, centered]O hydrogen bonds. In one of the independent molecules, the terminal –CH2–CH3 group of the alkyl chain is disordered over two sets of sites with a refined occupancy ratio of 0.746 (7):0.254 (7).
The title compound, [Li4O4(C12H8BO)4(C4H10O)4], features a Li4O4 cube. Each Li atom in the cube is additionally coordinated by a diethyl ether molecule and each O atom in the cube carries a 9-oxa-10-boraanthracene residue. The crystal studied was a non-merohedral twin [twin law (-1 0 0 / 0 0 1 / 0 1 0); the contribution of the major twin component refined to 0.553 (3)] emulating apparent tetragonal symmetry, whereas the actual crystal system is just orthorhombic.
The crystal structure of the title compound, hexa-μ2-bromido-μ4-oxido-tetrakis[(diethyl ether)magnesium], [Mg4Br6O(C4H10O)4], determined from data measured at 173 K, differs from the previously known structure of diethyl ether magnesium oxybromide, which was determined from room-temperature data [Stucky & Rundle (1964 [triangle]). J. Am. Chem. Soc. 86, 4821–4825]. The title compound crystallizes in the tetragonal space group I An external file that holds a picture, illustration, etc. Object name is e-67-m1614-efi7.jpg, whereas the previously known structure crystallizes in a different tetragonal space group, namely P An external file that holds a picture, illustration, etc. Object name is e-67-m1614-efi7.jpg21 c. Both molecules have crystallographic An external file that holds a picture, illustration, etc. Object name is e-67-m1614-efi7.jpg symmetry and show almost identical geometric parameters for the Mg, Br and O atoms. The crystal of the title compound turned out to be a merohedral twin emulating a structure with apparent Laue symmetry 4/mmm, whereas the correct Laue group is just 4/m. The fractional contribution of the minor twin component converged to 0.462 (1).
The title compound, C26H18BrNO4, features a functionalized chromene. The cyclohexene ring adopts a sofa conformation and has the nitro group and the bromophenyl ring in an axial position. The ten atoms of the chromene moiety lie close to a common plane (r.m.s. deviation = 0.066 Å). The attached phenyl ring is twisted by 32.89 (10)° from the chromene plane. The crystal packing is stabilized by C—H[cdots, three dots, centered]O interactions.
Ouzidan, Younes ; Rodi, Youssef Kandri ; Essassi, El Mokhtar ; Luis, Santiago V. ; Bolte, Michael ; El Ammari, Lahcen
The title molecule, C17H25N3O3, is built up from fused six- and five-membered rings linked to a –C10H21 chain. The fused-ring system is essentially planar, the largest deviation from the mean plane being 0.009 (2) Å. The chain is roughly perpendicular to this plane, making a dihedral angle of 79.5 (2)°. In the crystal, N—H[cdots, three dots, centered]O hydrogen bonds build infinite chains along [010]. There are channels in the structure containing disordered hexane. The contribution of this solvent to the scattering power was suppressed using the SQUEEZE option in PLATON [Spek (2009 [triangle]). Acta Cryst. D65, 148–155].
The title compound, C(19)H(14)ClNO(3)·0.2H(2)O, crystallizes with five mol-ecules and a disordered water mol-ecule in the asymmetric unit. Four of the five mol-ecules form hydrogen-bonded dimers via N-H⋯O hydrogen bonds towards another symmetry-independent mol-ecule, whereas the fifth mol-ecule forms a hydrogen-bonded dimer with its symmetry equivalent, also via N-H⋯O hydrogen bonds. The dihedral angle between the planes of the fused benzene ring and the five-membered ring to which it is attached is 79.45 (13), 49.00 (15), 72.49 (16), 81.91 (18) and 76.38 (16)° for the five mol-ecules in the asymmetric unit.
The structure of the title compound, C14H12N2O2 {systematic name: 2,2′-[hydrazinediylidenebis(methanylylidene)]diphenol}, has already been determined in the triclinic space group P An external file that holds a picture, illustration, etc. Object name is e-68-0o255-efi1.jpg with Z = 4 [El-Medani, Aboaly, Abdalla & Ramadan (2004 [triangle]). Spectrosc. Lett. 37, 619–632]. However, the correct space group should be P21/c with Z = 4. This structure is a new polymorph of the already known monoclinic polymorph of salicyladehyde azine, which crystallizes in space group P21/n with Z = 2. The benzene rings form a dihedral angle of 46.12 (9)°. Two intramolucular O—H[cdots, three dots, centered]N hydrogen bonds occur.
In the title compound, C15H14N2O4, (I), the molecule lies on a twofold rotation axis which passes through the central C atom of the aliphatic chain, giving one half-molecule per asymmetric unit. The structure is a monoclinic polymorph of the triclinic structure previously reported [Brito, Vallejos, Bolte & López-Rodríguez (2010). Acta Cryst. E66, o792], (II). The most obvious difference between them is the O/C/C/C—O/C/C/C torsion angle [58.2 (7)° in (I) and 173.4 (3)/70.2 (3)° in (II) for GG and TG conformations, respectively]. Another important difference is observed in the dihedral angle between the planes of the aromatic rings [86.49 (7)° for (I) and 76.4 (3)° for (II)]. The crystal structure features a weak π–π interaction [centroid–centroid distance = 4.1397 (10)Å]; this latter kind of interaction is not evident in the triclinic polymorph.
In the title compound, [Ag(BF4)(C14H12N2O4)]n, the coordination of the Ag+ ion is trigonal–bipyramidal with the N atoms of two ethane-1,2-diyl bis(pyridine-3-carboxylate) ligands in the apical positions and three F atoms belonging to different tetrafluoridoborate anions in the equatorial plane. The material consists of infinite chains of [Ag(C14H12N2O4)] units running along [001], held together by BF4 − bridging anions.
Prostate cancer is one of the most common tumor diseases worldwide. Often being non-aggressive, prostate tumors in these cases do not need immediate treatment. However, about 20% of diagnosed prostate cancers tend to metastasize and require treatment. Existing diagnostic methods may fail to accurately recognize the transition of a dormant, non-aggressive tumor into highly malignant prostate cancer. Therefore, new diagnostic tools are needed to improve diagnosis and therapy of prostate carcinoma. This review evaluates existing methods to diagnose prostate carcinoma, such as the biochemical marker prostate-specific antigen (PSA), but also discusses the possibility to use the altered expression of integrins and laminin-332 in prostate carcinomas as diagnostic tools and therapeutic targets of prostate cancer.
Momic, Tatjana ; Arlinghaus, Franziska Therese ; Arien-Zakay, Hadar ; Katzhendler, Jeoshua ; Eble, Johannes A. ; Marcinkiewicz, Cezary ; Lazarovici, Philip
In Israel, Vipera xantina palestinae (V.x.p.) is the most common venomous snake, accounting for several hundred cases of envenomation in humans and domestic animals every year, with a mortality rate of 0.5 to 2%. In this review we will briefly address the research developments relevant to our present understanding of the structure and function of V.x.p. venom with emphasis on venom disintegrins. Venom proteomics indicated the presence of four families of pharmacologically active compounds: (i) neurotoxins; (ii) hemorrhagins; (iii) angioneurin growth factors; and (iv) different types of integrin inhibitors. Viperistatin, a α1β1selective KTS disintegrin and VP12, a α2β1 selective C-type lectin were discovered. These snake venom proteins represent promising tools for research and development of novel collagen receptor selective drugs. These discoveries are also relevant for future improvement of antivenom therapy towards V.x.p. envenomation.
Geiger, Florian ; Beverungen, Mirjam ; Lorenz, Helga ; Wieland, Julia ; Fehr, Michael ; Kasten, Philip
VEGF (vascular endothelial growth factor) promotes vascularization and remodeling of bone substitutes. The aim of this study was to examine the effect of distinct resorbable ceramic carriers on bone forming capacities of VEGF transfected bone marrow stromal cells (BMSC). A critical size defect of the radius in rabbits was filled either by a low surface scaffold called beta-TCP (tricalciumphsphate) or the high surface scaffold CDHA (calcium deficient hydroxy-apatite) loaded with autologous BMSC, which were either transfected with a control plasmid or a plasmid coding for phVEGF165. They were compared to unloaded scaffolds. Thus, six treatment groups (n = 6 in each group) were followed by X-ray over 16 weeks. After probe retrieval, the volume of new bone was measured by micro-CT scans and vascularization was assessed in histology. While only minor bone formation was found in both carriers when implanted alone, BMSC led to increased osteogenesis in both carriers. VEGF promoted vascularization of the scaffolds significantly in contrast to BMSC alone. Bone formation was increased in the beta-TCP group, whereas it was inhibited in the CDHA group that showed faster scaffold degradation. The results indicate that the interaction of VEGF transfected BMSC with resorbable ceramic carrier influences the ability to promote bone healing.
Urban areas develop on formal and informal levels. Informal development is often highly dynamic, leading to a lag of spatial information about urban structure types. In this work, an object-based remote sensing approach will be presented to map the migrant housing urban structure type in the Pearl River Delta, China. SPOT5 data were utilized for the classification (auxiliary data, particularly up-to-date cadastral data, were not available). A hierarchically structured classification process was used to create (spectral) independence from single satellite scenes and to arrive at a transferrable classification process. Using the presented classification approach, an overall classification accuracy of migrant housing of 68.0% is attained.
Quarcoo, David ; Scutaru, Cristian ; Henkel, Ulrich ; Spallek, Michael ; Uibel, Stefanie ; Vitzthum, Karin ; Mache, Stefanie ; Kusma, Bianca ; Groneberg, Jan David Alexander
Background: Professional working at computer notebooks is associated with high requirements on the body posture in the seated position. By the high continuous static muscle stress resulting from this position at notebooks, professionals frequently working at notebooks for long hours are exposed to an increased risk of musculoskeletal complaints. Especially in subjects with back pain, new notebooks should be evaluated with a focus on rehabilitative issues.
Methods: In a field study a new notebook design with adjustable screen was analyzed and compared to standard notebook position.
Results: There are highly significant differences in the visual axis of individuals who are seated in the novel notebook position in comparison to the standard position. Also, differences are present between further alternative notebook positions. Testing of gender and glasses did not reveal influences.
Conclusion: This study demonstrates that notebooks with adjustable screen may be used to improve the posture. Future studies may focus on patients with musculoskeletal diseases.
Speech production involves widely distributed brain regions. This MEG study focuses on the spectro-temporal dynamics that contribute to the setup of this network. In 21 participants performing a cue-target reading paradigm, we analyzed local oscillations during preparation for overt and covert reading in the time-frequency domain and localized sources using beamforming. Network dynamics were studied by comparing different dynamic causal models of beta phase coupling in and between hemispheres. While a broadband low frequency effect was found for any task preparation in bilateral prefrontal cortices, preparation for overt speech production was specifically associated with left-lateralized alpha and beta suppression in temporal cortices and beta suppression in motor-related brain regions. Beta phase coupling in the entire speech production network was modulated by anticipation of overt reading. We propose that the processes underlying the setup of the speech production network connect relevant brain regions by means of beta synchronization and prepare the network for left-lateralized information routing by suppression of inhibitory alpha and beta oscillations.
Bingold, Tobias Michael ; Pullmann, Barbara ; Sartorius, Sven ; Geiger, Emanuel Valentin ; Marzi, Ingo ; Zacharowski, Kai ; Wissing, Heimo ; Scheller, Bertram
Introduction: The triggering receptor expressed on myeloid cells-1 (TREM-1) is known to be expressed during bacterial infections. We investigated whether TREM-1 is also expressed in non-infectious inflammation following traumatic lung contusion.
Methods: In a study population of 45 adult patients with multiple trauma and lung contusion, we obtained bronchoalveolar lavage (BAL) (blind suctioning of 20 ml NaCl (0.9%) via jet catheter) and collected blood samples at two time points (16 hours and 40 hours) after trauma. Post hoc patients were assigned to one of four groups radiologically classified according to the severity of lung contusion based on the initial chest tomography. Concentration of soluble TREM-1 (sTREM-1) and bacterial growth were determined in the BAL. sTREM-1, IL-6, IL-10, lipopolysaccharide binding protein, procalcitonin, C-reactive protein and leukocyte count were assessed in blood samples. Pulmonary function was evaluated by the paO2/FiO2 ratio.
Results: Three patients were excluded due to positive bacterial growth in the initial BAL. In 42 patients the severity of lung contusion correlated with the levels of sTREM-1 16 hours and 40 hours after trauma. sTREM-1 levels were significantly (P < 0.01) elevated in patients with severe contusion (2,184 pg/ml (620 to 4,000 pg/ml)) in comparison with patients with mild (339 pg/ml (135 to 731 pg/ml)) or no (217 pg/ml (97 to 701 pg/ml)) contusion 40 hours following trauma. At both time points the paO2/FiO2 ratio correlated negatively with sTREM-1 levels (Spearman correlation coefficient = -0.446, P < 0.01).
Conclusions: sTREM-1 levels are elevated in the BAL of patients following pulmonary contusion. Furthermore, the levels of sTREM-1 in the BAL correlate well with both the severity of radiological pulmonary tissue damage and functional impairment of gas exchange (paO2/FiO2 ratio).
Cortical neurons are typically driven by several thousand synapses. The precise spatiotemporal pattern formed by these inputs can modulate the response of a post-synaptic cell. In this work, we explore how the temporal structure of pre-synaptic inhibitory and excitatory inputs impact the post-synaptic firing of a conductance-based integrate and fire neuron. Both the excitatory and inhibitory input was modeled by renewal gamma processes with varying shape factors for modeling regular and temporally random Poisson activity. We demonstrate that the temporal structure of mutually independent inputs affects the post-synaptic firing, while the strength of the effect depends on the firing rates of both the excitatory and inhibitory inputs. In a second step, we explore the effect of temporal structure of mutually independent inputs on a simple version of Hebbian learning, i.e., hard bound spike-timing-dependent plasticity. We explore both the equilibrium weight distribution and the speed of the transient weight dynamics for different mutually independent gamma processes. We find that both the equilibrium distribution of the synaptic weights and the speed of synaptic changes are modulated by the temporal structure of the input. Finally, we highlight that the sensitivity of both the post-synaptic firing as well as the spike-timing-dependent plasticity on the auto-structure of the input of a neuron could be used to modulate the learning rate of synaptic modification.
Background: Transfer entropy (TE) is a measure for the detection of directed interactions. Transfer entropy is an information theoretic implementation of Wiener's principle of observational causality. It offers an approach to the detection of neuronal interactions that is free of an explicit model of the interactions. Hence, it offers the power to analyze linear and nonlinear interactions alike. This allows for example the comprehensive analysis of directed interactions in neural networks at various levels of description. Here we present the open-source MATLAB toolbox TRENTOOL that allows the user to handle the considerable complexity of this measure and to validate the obtained results using non-parametrical statistical testing. We demonstrate the use of the toolbox and the performance of the algorithm on simulated data with nonlinear (quadratic) coupling and on local field potentials (LFP) recorded from the retina and the optic tectum of the turtle (Pseudemys scripta elegans) where a neuronal one-way connection is likely present.
Results: In simulated data TE detected information flow in the simulated direction reliably with false positives not exceeding the rates expected under the null hypothesis. In the LFP data we found directed interactions from the retina to the tectum, despite the complicated signal transformations between these stages. No false positive interactions in the reverse directions were detected.
Conclusions: TRENTOOL is an implementation of transfer entropy and mutual information analysis that aims to support the user in the application of this information theoretic measure. TRENTOOL is implemented as a MATLAB toolbox and available under an open source license (GPL v3). For the use with neural data TRENTOOL seamlessly integrates with the popular FieldTrip toolbox.
We conducted measurements of the five important short-lived organic bromine species in the marine boundary layer (MBL). Measurements were made in the Northern Hemisphere mid-latitudes (Sylt Island, North Sea) in June 2009 and in the tropical Western Pacific during the TransBrom ship campaign in October 2009. For the one-week time series on Sylt Island, mean mixing ratios of CHBr3, CH2Br2, CHBr2Cl and CH2BrCl were 2.0, 1.1, 0.2, 0.1 ppt, respectively. We found maxima of 5.8 and 1.6 ppt for the two main components CHBr3 and CH2Br2. Along the cruise track in the Western Pacific (between 41° N and 13° S) we measured mean mixing ratios of 0.9, 0.9, 0.2, 0.1 and 0.1 ppt for CHBr3, CH2Br2, CHBrCl2, CHBr2Cl and CH2BrCl. Air samples with coastal influence showed considerably higher mixing ratios than the samples with open ocean origin. Correlation analyses of the two data sets yielded strong linear relationships between the mixing ratios of four of the five species (except for CH2BrCl). Using a combined data set from the two campaigns and a comparison with the results from two former studies, rough estimates of the molar emission ratios between the correlated substances were: 9/1/0.35/0.35 for CHBr3/CH2Br2/CHBrCl2/CHBr2Cl. Additional measurements were made in the tropical tropopause layer (TTL) above Teresina (Brazil, 5° S) in June 2008, using balloon-borne cryogenic whole air sampling technique. Near the level of zero clear-sky net radiative heating (LZRH) at 14.8 km about 2.25 ppt organic bromine was bound to the five short-lived species, making up 13% of total organic bromine (17.82 ppt). CH2Br2 (1.45 ppt) and CHBr3 (0.56 ppt) accounted for 90% of the budget of short-lived compounds in that region. Near the tropopause (at 17.5 km) organic bromine from these substances was reduced to 1.35 ppt, with 1.07 and 0.12 ppt attributed to CH2Br2 and CHBr3, respectively.
We conducted measurements of up to the five important short-lived brominated species in the marine boundary layer (MBL) of the mid-latitudes (List/Sylt, North Sea) in June 2009 and of the tropical Western Pacific during the TransBrom ship campaign in October 2009. For the one-week time series in List mean mixing ratios of 2.0, 1.1, 0.2, 0.1 ppt were analysed for CHBr3, CH2Br2, CHBr2Cl and CH2BrCl, with maxima of 5.8 and 1.6 ppt for the two main components CHBr3 and CH2Br2. Along the cruise track in the Western Pacific (between 41° N and 13° S) mean mixing ratios of 1.0, 0.9, 0.2, 0.1 and 0.1 ppt for CHBr3, CH2Br2, CHBrCl2, CHBr2Cl and CH2BrCl were determined. Air samples with coastal influence showed considerably higher mixing ratios than the samples with open ocean origin. Correlation analyses of the two datasets yielded strong linear relationships between the mixing ratios of four of the five species (except for CH2BrCl). Using a combined dataset from the two campaigns, rough estimates of the molar emission ratios between the correlated substances were derived as follows: 9/1/0.3/0.3 for CHBr3/CH2Br2/CHBrCl2/CHBr2Cl. Additional measurements were made in the tropical tropopause layer (TTL) above Teresina (Brazil, 5.07° S, 42.87° W) in June 2008, using balloon-borne cryogenic whole air sampling technique. Near the level of zero clear-sky net radiative heating (LZRH) at 14.8 km about 2.25 ppt organic bromine was bound to the five short-lived species, making up 13 % of total organic bromine (17.82 ppt). CH2Br2 (1.45 ppt) and CHBr3 (0.56 ppt) accounted for 90 % of the budget of short-lived compounds in that region. Near the tropopause (at 17.5 km) organic bromine from short-lived substances was reduced to 1.35 ppt, with 1.07 ppt and 0.12 ppt attributed to CH2Br2 and CHBr3 respectively.
Balloon-borne stratospheric BrO measurements : comparison with Envisat/SCIAMACHY BrO limb profiles
(2005)
Dorf, Marcel ; Bösch, Hartmut ; Butz, Andre ; Camy-Peyret, Claude C. ; Chipperfield, Martyn P. ; Engel, Andreas ; Goutail, Florence ; Grunow, Katja ; Hendrick, François ; Hrechanyy, Serhiy ; Naujokat, Barbara ; Pommereau, Jean-Pierre ; Roozendael, Michel van ; Sioris, Christopher E. ; Stroh, Fred ; Weidner, Frank ; Pfeilsticker, Klaus
For the first time, results of all four existing stratospheric BrO profiling instruments, are presented and compared with reference to the SLIMCAT 3-dimensional chemical transport model (3-D CTM). Model calculations are used to infer a BrO profile validation set, measured by 3 different balloon sensors, for the new Envisat/SCIAMACHY (ENVIronment SATellite/SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY) satellite instrument. The balloon observations include (a) balloon-borne in situ resonance fluorescence detection of BrO, (b) balloon-borne solar occultation DOAS measurements (Differential Optical Absorption Spectroscopy) of BrO in the UV, and (c) BrO profiling from the solar occultation SAOZ (Systeme d'Analyse par Observation Zenithale) balloon instrument. Since stratospheric BrO is subject to considerable diurnal variation and none of the measurements are performed close enough in time and space for a direct comparison, all balloon observations are considered with reference to outputs from the 3-D CTM. The referencing is performed by forward and backward air mass trajectory calculations to match the balloon with the satellite observations. The diurnal variation of BrO is considered by 1-D photochemical model calculation along the trajectories. The 1-D photochemical model is initialised with output data of the 3-D model with additional constraints on the vertical transport, the total amount and photochemistry of stratospheric bromine as given by the various balloon observations. Total [Bry]=(20.1±2.8)pptv obtained from DOAS BrO observations at mid-latitudes in 2003, serves as an upper limit of the comparison. Most of the balloon observations agree with the photochemical model predictions within their given error estimates. First retrieval exercises of BrO limb profiling from the SCIAMACHY satellite instrument agree to <±50% with the photochemically-corrected balloon observations, and tend to show less agreement below 20 km.
Contribution of sulfuric acid and oxidized organic compounds to particle formation and growth
(2012)
Riccobono, Francesco ; Rondo, Linda ; Sipilä, Mikko ; Barmet, Peter ; Curtius, Joachim ; Dommen, Josef ; Ehn, Mikael ; Ehrhart, Sebastian ; Kulmala, Markku ; Kürten, Christoph Andreas ; Mikkilä, Jyri ; Petäjä, Tuukka ; Weingartner, Ernest ; Baltensperger, Urs
Lack of knowledge about the mechanisms underlying new particle formation and their subsequent growth is one of the main causes for the large uncertainty in estimating the radiative forcing of atmospheric aerosols in global models. We performed chamber experiments designed to study the contributions of sulfuric acid and organic vapors to formation and to the early growth of nucleated particles, respectively. Distinct experiments in the presence of two different organic precursors (1,3,5-trimethylbenzene and α-pinene) showed the ability of these compounds to reproduce the formation rates observed in the low troposphere. These results were obtained measuring the sulfuric acid concentrations with two Chemical Ionization Mass Spectrometers confirming the results of a previous study which modeled the sulfuric acid concentrations in presence of 1,3,5-trimethylbenzene.
New analysis methods were applied to the data collected with a Condensation Particle Counter battery and a Scanning Mobility Particle Sizer, allowing the assessment of the size resolved growth rates of freshly nucleated particles. The effect of organic vapors on particle growth was investigated by means of the growth rate enhancement factor (Γ), defined as the ratio between the measured growth rate in the presence of α-pinene and the kinetically limited growth rate of the sulfuric acid and water system. The observed Γ values indicate that the growth is dominated by organic compounds already at particle diameters of 2 nm. Both the absolute growth rates and Γ showed a strong dependence on particle size supporting the nano-Köhler theory. Moreover, the separation of the contributions from sulfuric acid and organic compounds to particles growth reveals that the organic contribution seems to be enhanced by the sulfuric acid concentration. The size resolved growth analysis finally indicates that both condensation of oxidized organic compounds and reactive uptake contribute to particle growth.
A comprehensive set of stratospheric balloon and aircraft samples was analyzed for the position-dependent isotopic composition of nitrous oxide (N2O). Results for a total of 220 samples from between 1987 and 2003 are presented, nearly tripling the number of mass-spectrometric N2O isotope measurements in the stratosphere published to date. Cryogenic balloon samples were obtained at polar (Kiruna/Sweden, 68° N), mid-latitude (southern France, 44° N) and tropical sites (Hyderabad/India, 18° N). Aircraft samples were collected with a newly-developed whole air sampler on board of the high-altitude aircraft M55 Geophysica during the EUPLEX 2003 campaign. All samples were analyzed by laboratory mass spectrometry for their 18O/16O and position-dependent 15N/14N isotope ratios with very high precision (standard deviation about 0.15 per mil for 18O/16O and average 15N/14N ratios, about 0.5 per mil for 15NNO/14NNO and N15NO/N14NO ratios). For mixing ratios above 200 nmol mol−1, relative isotope enrichments (δ values) and mixing ratios display a compact relationship, which is nearly independent of latitude and season and which can be explained equally well by Rayleigh fractionation or mixing. However, for mixing ratios below 200 nmol mol−1 this compact relationship gives way to meridional, seasonal and interannual variations. A comparison to a previously published mid-latitude balloon profile even shows large zonal variations, justifying the use of three-dimensional models for further data interpretation.
In general, the magnitude of the apparent fractionation constants (apparent isotope effects) increases continuously with altitude and decreases from the equator to the North pole, which can be qualitatively understood by the interplay between the time-scales of N2O photochemistry and transport. Deviations from this behavior occur where polar vortex air mixes with nearly N2O-free upper stratospheric/mesospheric air (e.g., during the boreal winter of 2003 and possibly 1992). Aircraft observations in the polar vortex at mixing ratios below 200 nmol mol−1 deviate from isotope variations expected for both Rayleigh fractionation and end-member mixing, but could be explained by continuous weak mixing between intravortex and extravortex air (Plumb et al., 2000). Finally, correlations between 18O/16O and average 15N/14N isotope ratios or between the position-dependent 15N/14N isotope ratios show that photo-oxidation makes a large contribution to the total N2O sink in the lower stratosphere (up to 100%). Towards higher altitudes, the temperature dependence of these isotope correlations becomes visible in the stratospheric observations.
Klein, Holger ; Nickovic, Slobodan ; Haunold, Werner ; Bundke, Ulrich ; Nillius, Björn ; Ebert, Martin ; Weinbruch, Stephan ; Schuetz, Lothar ; Levin, Zev ; Barrie, Leonard A. ; Bingemer, Heinz
Surface measurements of aerosol and ice nuclei (IN) at a Central European mountain site during an episode of dust transport from the Sahara are presented. Transport is simulated by the Eulerian regional dust model DREAM. Ice nuclei and mineral dust are significantly correlated. The highest correlation is found between IN concentration and aerosol surface area. The ice nucleating characteristics of the aerosol with respect to temperature and supersaturation are similar during the dust episode than during the course of the year. This suggests that dust is always a dominant constituent of ice nucleating aerosols in Central Europe.
Klein, Holger ; Nickovic, Slobodan ; Haunold, Werner ; Bundke, Ulrich ; Nillius, Björn ; Ebert, Martin ; Weinbruch, Stephan ; Schuetz, Lothar ; Levin, Zev ; Barrie, Leonard A. ; Bingemer, Heinz
Surface measurements of aerosol and ice nuclei (IN) at a Central European mountain site during an episode of dust transport from the Sahara are presented. Ice nuclei were sampled by electrostatic precipitation on silicon wafers and were analyzed in an isothermal static vapor diffusion chamber. The transport of mineral dust is simulated by the Eulerian regional dust model DREAM. Ice nuclei and mineral dust are significantly correlated, in particular IN number concentration and aerosol surface area. The ice nucleating characteristics of the aerosol as analyzed with respect to temperature and supersaturation are similar during the dust episode than during the course of the year. This suggests that dust may be a main constituent of ice nucleating aerosols in Central Europe.
The isotopic composition of methane in the stratosphere : high-altitude balloon sample measurements
(2011)
The isotopic composition of stratospheric methane has been determined on a large suite of air samples from stratospheric balloon flights covering subtropical to polar latitudes and a time period of 16 yr. 154 samples were analyzed for δ13C and 119 samples for δD, increasing the previously published dataset for balloon borne samples by an order of magnitude, and more than doubling the total available stratospheric data (including aircraft samples) published to date. The samples also cover a large range in mixing ratio from tropospheric values near 1800 ppb down to only 250 ppb, and the strong isotope fractionation processes accordingly increase the isotopic composition up to δ13C = −14‰ and δD = +190‰, the largest enrichments observed for atmospheric CH4 so far. When analyzing and comparing kinetic isotope effects (KIEs) derived from single balloon profiles, it is necessary to take into account the residence time in the stratosphere in combination with the observed mixing ratio and isotope trends in the troposphere, and the range of isotope values covered by the individual profile. The isotopic composition of CH4 in the stratosphere is affected by both chemical and dynamical processes. This severely hampers interpretation of the data in terms of the relative fractions of the three important sink mechanisms (reaction with OH, O(1D) and Cl). It is shown that a formal sink partitioning using the measured data severely underestimates the fraction removed by OH, which is likely due to the insensitivity of the measurements to the kinetic fractionation in the lower stratosphere. Full quantitative interpretation of the CH4 isotope data in terms of the three sink reactions requires a global model.
The isotopic composition of methane in the stratosphere : high-altitude balloon sample measurements
(2011)
The isotopic composition of stratospheric methane has been determined on a large suite of air samples from stratospheric balloon flights covering subtropical to polar latitudes and a time period of 16 yr. 154 samples were analyzed for δC and 119 samples for δD, increasing the previously published dataset for balloon borne samples by an order of magnitude, and more than doubling the total available stratospheric data (including aircraft samples) published to date. The samples also cover a large range in mixing ratio from tropospheric values near 1800 ppb down to only 250 ppb, and the strong isotope fractionation processes accordingly increase the isotopic composition up to δ13C=−14‰ and δD= +190‰, the largest enrichments observed for atmospheric CH4 so far. When analyzing and comparing kinetic isotope effects (KIEs) derived from single balloon profiles, it is necessary to take into account the residence time in the stratosphere in combination with the observed mixing ratio and isotope trends in the troposphere, and the range of isotope values covered by the individual profile. Temporal isotope trends can also be determined in the stratosphere and compare reasonably well with the tropospheric trends. The effects of chemical and dynamical processes on the isotopic composition of CH4 in the stratosphere are discussed in detail. Different ways to interpret the data in terms of the relative fractions of the three important sink mechanisms (reaction with OH, O(1D)) and Cl, respectively), and their limitations, are investigated. The classical approach of using global mean KIE values can be strongly biased when profiles with different minimum mixing ratios are compared. Approaches for more local KIE investigations are suggested. It is shown that any approach for a formal sink partitioning from the measured data severely underestimates the fraction removed by OH, which is likely due to the insensitivity of the measurements to the kinetic fractionation in the lower stratosphere. Attempts can be made to correct for the lower stratospheric sink bias, but full quantitative interpretation of the CH4 isotope data in terms of the three sink reactions requires a global model.
Pison, Isabelle C. ; Fortems-Cheiney, Audrey ; Schmidt, Martina ; Chevallier, Frédéric ; Ramonet, Michel ; Jordan, Armin ; Søvde, Ole Amund ; Engel, Andreas ; Fisher, Rebecca E. ; Lowry, David ; Nisbet, Euan G. ; Levin, Ingeborg ; Hammer, Samuel ; Necki, Jaroslaw ; Bartyzel, J. ; Reimann, Stefan ; Vollmer, Martin K. ; Steinbacher, Martin ; Aalto, Tuula ; Maione, Michela ; Arduini, Jgor ; O'Doherty, Simon ; Grant, Aoife ; Sturges, William T. ; Forster, Grant L. ; Lunder, Chris Rene ; Privalov, Viacheslav I. ; Paramonova, Nina N. ; Werner, A. ; Bousquet, Philippe
This paper presents an analysis of the recent tropospheric molecular hydrogen (H2) budget with a particular focus on soil uptake and European surface emissions. A variational inversion scheme is combined with observations from the RAMCES and EUROHYDROS atmospheric networks, which include continuous measurements performed between mid-2006 and mid-2009. Net H2 surface flux, then deposition velocity and surface emissions and finally, deposition velocity, biomass burning, anthropogenic and N2 fixation-related emissions were simultaneously inverted in several scenarios. These scenarios have focused on the sensibility of the soil uptake value to different spatio-temporal distributions. The range of variations of these diverse inversion sets generate an estimate of the uncertainty for each term of the H2 budget. The net H2 flux per region (High Northern Hemisphere, Tropics and High Southern Hemisphere) varies between −8 and +8 Tg yr−1. The best inversion in terms of fit to the observations combines updated prior surface emissions and a soil deposition velocity map that is based on bottom-up and top-down estimations. Our estimate of global H2 soil uptake is −59±9 Tg yr−1. Forty per cent of this uptake is located in the High Northern Hemisphere and 55% is located in the Tropics. In terms of surface emissions, seasonality is mainly driven by biomass burning emissions. The inferred European anthropogenic emissions are consistent with independent H2 emissions estimated using a H2/CO mass ratio of 0.034 and CO emissions within the range of their respective uncertainties. Additional constraints, such as isotopic measurements would be needed to infer a more robust partition of H2 sources and sinks.
Yver, Camille E. ; Pison, Isabelle C. ; Fortems-Cheiney, Audrey ; Schmidt, Martina ; Chevallier, Frédéric ; Ramonet, Michel ; Jordan, Armin ; Søvde, Ole Amund ; Engel, Andreas ; Fisher, Rebecca E. ; Lowry, David ; Nisbet, Euan G. ; Levin, Ingeborg ; Hammer, Samuel ; Necki, Jaroslaw ; Bartyzel, Jakub ; Reimann, Stefan ; Vollmer, Martin ; Steinbacher, Martin ; Aalto, Tuula ; Maione, Michela ; Arduini, Jgor ; O'Doherty, Simon ; Grant, Aoife ; Sturges, William T. ; Forster, Grant L. ; Lunder, Chris Rene ; Privalov, Viacheslav I. ; Paramonova, Nina N.
This paper presents an analysis of the recent tropospheric molecular hydrogen (H2) budget with a particular focus on soil uptake and surface emissions. A variational inversion scheme is combined with observations from the RAMCES and EUROHYDROS atmospheric networks, which include continuous measurements performed between mid-2006 and mid-2009. Net H2 surface flux, soil uptake distinct from surface emissions and finally, soil uptake, biomass burning, anthropogenic emissions and N2 fixation-related emissions separately were inverted in several scenarios. The various inversions generate an estimate for each term of the H2 budget. The net H2 flux per region (High Northern Hemisphere, Tropics and High Southern Hemisphere) varies between −8 and 8 Tg yr−1. The best inversion in terms of fit to the observations combines updated prior surface emissions and a soil deposition velocity map that is based on soil uptake measurements. Our estimate of global H2 soil uptake is −59 ± 4.0 Tg yr−1. Forty per cent of this uptake is located in the High Northern Hemisphere and 55% is located in the Tropics. In terms of surface emissions, seasonality is mainly driven by biomass burning emissions. The inferred European anthropogenic emissions are consistent with independent H2 emissions estimated using a H2/CO mass ratio of 0.034 and CO emissions considering their respective uncertainties. To constrain a more robust partition of H2 sources and sinks would need additional constraints, such as isotopic measurements.
Feng, Wuhu ; Chipperfield, Martyn P. ; Davies, Stewart ; Sen, Bhaswar ; Toon, Geoffrey C. ; Blavier, Jean-François ; Webster, Christopher R. ; Volk, C.-Michael ; Ulanovsky, Alexey ; Ravegnani, Fabrizio ; Gathen, Peter von der ; Jost, Hans-Jürg ; Richard, Erik C. ; Claude, Hans
We have used the SLIMCAT 3-D off-line chemical transport model (CTM) to quantify the Arctic chemical ozone loss in the year 2002/2003 and compare it with similar calculations for the winters 1999/2000 and 2003/2004. Recent changes to the CTM have improved the model's ability to reproduce polar chemical and dynamical processes. The updated CTM uses σ-θ as a vertical coordinate which allows it to extend down to the surface. The CTM has a detailed stratospheric chemistry scheme and now includes a simple NAT-based denitrification scheme in the stratosphere.
In the model runs presented here the model was forced by ECMWF ERA40 and operational analyses. The model used 24 levels extending from the surface to ~55 km and a horizontal resolution of either 7.5°×7.5° or 2.8°×2.8°. Two different radiation schemes, MIDRAD and the CCM scheme, were used to diagnose the vertical motion in the stratosphere. Based on tracer observations from balloons and aircraft, the more sophisticated CCM scheme gives a better representation of the vertical transport in this model which includes the troposphere. The higher resolution model generally produces larger chemical O3 depletion, which agrees better with observations.
The CTM results show that very early chemical ozone loss occurred in December 2002 due to extremely low temperatures and early chlorine activation in the lower stratosphere. Thus, chemical loss in this winter started earlier than in the other two winters studied here. In 2002/2003 the local polar ozone loss in the lower stratosphere was ~40% before the stratospheric final warming. Larger ozone loss occurred in the cold year 1999/2000 which had a persistently cold and stable vortex during most of the winter. For this winter the current model, at a resolution of 2.8°×2.8°, can reproduce the observed loss of over 70% locally. In the warm and more disturbed winter 2003/2004 the chemical O3 loss was generally much smaller, except above 620 K where large losses occurred due to a period of very low minimum temperatures at these altitudes.
Pätz, Hans-Werner ; Volz-Thomas, Andreas ; Hegglin, Michaela I. ; Brunner, Dominik ; Fischer, Herbert ; Schmidt, Ulrich
Two aircraft instruments for the measurement of total odd nitrogen (NOy) were compared side by side aboard a Learjet A35 in April 2003 during a campaign of the AFO2000 project SPURT (Spurengastransport in der Tropopausenregion). The instruments albeit employing the same measurement principle (gold converter and chemiluminescence) had different inlet configurations. The ECO-Physics instrument operated by ETH-Zürich in SPURT had the gold converter mounted outside the aircraft, whereas the instrument operated by FZ-Jülich in the European project MOZAIC III (Measurements of ozone, water vapour, carbon monoxide and nitrogen oxides aboard Airbus A340 in-service aircraft) employed a Rosemount probe with 80 cm of FEP-tubing connecting the inlet to the gold converter. The NOy concentrations during the flight ranged between 0.3 and 3 ppb. The two data sets were compared in a blind fashion and each team followed its normal operating procedures. On average, the measurements agreed within 6%, i.e. within the combined uncertainty of the two instruments. This puts an upper limit on potential losses of HNO3 in the Rosemount inlet of the MOZAIC instrument. Larger transient deviations were observed during periods after calibrations and when the aircraft entered the stratosphere. The time lag of the MOZAIC instrument observed in these instances is in accordance with the time constant of the MOZAIC inlet line determined in the laboratory for HNO3.
Pätz, Hans-Werner ; Volz-Thomas, Andreas ; Hegglin, Michaela I. ; Brunner, Dominik ; Fischer, Herbert ; Schmidt, Ulrich
Two aircraft instruments for the measurement of total odd nitrogen (NOy) were compared side by side aboard a Learjet A35 in April 2003 during a campaign of the AFO2000 project SPURT (Spurengastransport in der Tropopausenregion). The instruments albeit employing the same measurement principle (gold converter and chemiluminescence) had different inlet configurations. The ECO-Physics instrument operated by ETH-Zürich in SPURT had the gold converter mounted outside the aircraft, whereas the instrument operated by FZ-Jülich in the European project MOZAIC III (Measurements of ozone, water vapour, carbon monoxide and nitrogen oxides aboard Airbus A340 in-service aircraft) employed a Rosemount probe with 80 cm of FEP-tubing connecting the inlet to the gold converter. The NOy concentrations during the flight ranged between 0.3 and 3 ppb. The two data sets were compared in a blind fashion and each team followed its normal operating procedures. On average, the measurements agreed within 7%, i.e. within the combined uncertainty of the two instruments. This puts an upper limit on potential losses of HNO3 in the Rosemount inlet of the MOZAIC instrument. Larger transient deviations were observed during periods after calibrations and when the aircraft entered the stratosphere. The time lag of the MOZAIC instrument observed in these instances is in accordance with the time constant of the MOZAIC inlet line determined in the laboratory for HNO3.
Numerical simulation of flow, H₂SO₄ cycle and new particle formation in the CERN CLOUD chamber
(2011)
To study the effect of galactic cosmic rays on aerosols and clouds, the Cosmic Leaving OUtdoor Droplets (CLOUD) project was established. Experiments are carried out at a 26 m3 tank at CERN (Switzerland). In the experiments, the effect of ionising particle radiation on H2SO4 particle formation and growth is investigated. To evaluate the experimental configuration, the experiment was simulated using a coupled multidimensional CFD – particle model (CLOUD-FPM). In the model the coupled fields of gas/vapour species, temperature, flow velocity and particle properties were computed to investigate the tank's mixing state and mixing times. Simulation results show that the mixing state of the tank's contents largely depends on the characteristics of the mixing fans and a 1-fan configuration, as used in first experiments, may not be sufficient to ensure a homogeneously mixed chamber. To mix the tank properly, 2 fans are necessary. The 1/e response times for instantaneous changes of wall temperature and saturation ratio inside the chamber were found to be in the order of few minutes. Particle nucleation and growth was also simulated and particle number size distribution properties of the freshly nucleated particles (particle number, mean size, standard deviation of the assumed log-normal distribution) were found to be mixed over the tank's volume similar to the gas species.
Voigtländer, Jens ; Duplissy, Jonathan ; Rondo, Linda ; Kürten, Christoph Andreas ; Stratmann, Frank
To study the effect of galactic cosmic rays on aerosols and clouds, the Cosmics Leaving OUtdoor Droplets (CLOUD) project was established. Experiments are carried out at a 26.1 m3 tank at CERN (Switzerland). In the experiments, the effect of ionizing radiation on H2SO4 particle formation and growth is investigated. To evaluate the experimental configuration, the experiment was simulated using a coupled multidimensional computational fluid dynamics (CFD) – particle model. In the model the coupled fields of gas/vapor species, temperature, flow velocity and particle properties were computed to investigate mixing state and mixing times of the CLOUD tank's contents. Simulation results show that a 1-fan configuration, as used in first experiments, may not be sufficient to ensure a homogeneously mixed chamber. To mix the tank properly, two fans and sufficiently high fan speeds are necessary. The 1/e response times for instantaneous changes of wall temperature and saturation ratio were found to be in the order of few minutes. Particle nucleation and growth was also simulated and particle number size distribution properties of the freshly nucleated particles (particle number, mean size, standard deviation of the assumed log-normal distribution) were found to be distributed over the tank's volume similar to the gas species.
In this paper we present evidence that the observed increase in tropical upwelling after the year 2000 may be attributed to a change in the Brewer-Dobson circulation pattern. For this purpose, we use the concept of transit times derived from residual circulation trajectories and different in-situ measurements of ozone and nitrous dioxide. Observations from the Canadian midlatitude ozone profile record, probability density functions of in-situ N2O observations and a shift of the N2O-O3 correlation slopes, taken together, indicate that the increased upwelling in the tropics after the year 2000 appears to have triggered an intensification of tracer transport from the tropics into the extratropics in the lower stratosphere below about 500 K. This finding is corroborated by the fact that transit times along the shallow branch of the residual circulation into the LMS have decreased for the same time period (1993–2003). On a longer time scale (1979–2009), the transit time of the shallow residual circulation branch show a steady decrease of about −1 month/decade over the last 30 years, while the transit times of the deep branch remain unchanged. This highlights the fact that a change in the upwelling across the tropical tropopause is not a direct indicator for changes of the whole Brewer-Dobson circulation.
In this paper we present evidence that the observed increase in tropical upwelling after the year 2000 may be attributed to a change in the Brewer-Dobson circulation pattern. For this purpose, we use the concept of transit times derived from residual circulation trajectories and different in-situ measurements of ozone and nitrous dioxide. Observations from the Canadian midlatitude ozone profile record, probability density functions of in-situ N2O observations and a shift of the N2O-O3 correlation slopes, taken together, indicate that the increased upwelling in the tropics after the year 2000 appears to have triggered an intensification of tracer transport from the tropics into the extratropics in the lower stratosphere below about 500 K. This finding is corroborated by the fact that transit times along the shallow branch of the residual circulation into the LMS have decreased for the same time period (1993–2003). On a longer time scale (1979–2009), the transit time of the shallow residual circulation branch show a steady decrease of about −1 month/decade over the last 30 yr, while the transit times of the deep branch remain unchanged. This highlights that changes in the upwelling across the tropical tropopause are not sufficient as an indicator for changes in the entire Brewer-Dobson circulation.
The title complex, [PdCl2(C18H15P)2]·0.5C6H6, has the PdII ion in a square-planar coordination mode (r.m.s. deviation for Pd, P and Cl atoms = 0.024 Å) with the PPh3 and Cl ligands mutually trans. The benzene solvent molecule is located about a crystallographic inversion centre. The title complex is isostructural with trans-dichloridobis(triphenylphosphane)palladium(II) 1,4-dichlorobenzene sesquisolvate [Kitano et al. (1983 [triangle]). Acta Cryst. C39, 1015–1017].
We present a non-parametric and computationally efficient method that detects spatiotemporal firing patterns and pattern sequences in parallel spike trains and tests whether the observed numbers of repeating patterns and sequences on a given timescale are significantly different from those expected by chance. The method is generally applicable and uncovers coordinated activity with arbitrary precision by comparing it to appropriate surrogate data. The analysis of coherent patterns of spatially and temporally distributed spiking activity on various timescales enables the immediate tracking of diverse qualities of coordinated firing related to neuronal state changes and information processing. We apply the method to simulated data and multineuronal recordings from rat visual cortex and show that it reliably discriminates between data sets with random pattern occurrences and with additional exactly repeating spatiotemporal patterns and pattern sequences. Multineuronal cortical spiking activity appears to be precisely coordinated and exhibits a sequential organization beyond the cell assembly concept.
Introduction: In this article the personal study and life situation of parents who are also medical students at the Medical School of the Goethe University Frankfurt am Main is discussed. There is a special focus on the topics "studying with children" and "family-friendly university", which have been present in discussions about university development and in the daily life of academics, especially during the last decade. The workgroup "Individual Student Services" at the medical faculty at the Goethe University tries to meet the necessities of the individual study courses and to support the study success with a new counselling and student service concept.
Methods: The experience of parents studying medicine was recorded in semi-structured interviews (Date: April 2010), which were held as part of the sponsored pilot project on part-time medical studies ("Pilot Project Part-time Medical Studies"). Additionally, study results from the Medical School of the Goethe University Frankfurt am Main were integrated as well as a literature analysis.
Results: It was found that the teaching demands and support services, which have been suggested and needed for years now, have been partially implemented and are without sufficient support at the faculty level to date. Thus the current situation of medical students with children is still difficult and seems a big challenge for everyone involved.
Solution: As part of the "Individual Student Services" a new pilot project on part-time medical studies was established in November 2009. Only the use of new, unconventional and innovative ideas allows universities to adequately support the changing and heterogeneous student population and support them to successfully completing their medical studies.
Einleitung: In dem vorliegenden Artikel wird die persönliche Studien- und Lebenssituation von Studierenden mit Kindern am Fachbereich Medizin der Goethe-Universität Frankfurt am Main beleuchtet. Der spezielle Fokus liegt auf den Themen "Studium mit Kind" sowie "familiengerechte Hochschule", welche in Deutschland in der letzten Dekade sehr präsent sowohl in der Hochschulforschung als auch im akademischen Alltag sind. Hier versucht die Arbeitsstelle "Individuelle Studienbegleitung" am FB Medizin der Goethe-Universität durch ein neues Beratungs- und Servicekonzept mit wissenschaftlicher Begleitforschung den individuellen Studienverläufen gerecht zu werden und den Studienerfolg zu fördern.
Methoden: In erster Linie stammen die hier beschriebenen Erfahrungen der Medizinstudierenden mit Kind aus qualitativen Leitfadeninterviews (Stand April 2010), die im Rahmen des Modellprojektes Teilzeitstudium Medizin durchgeführt wurden. Ergänzend wurden die Studienergebnisse des Fachbereichs Medizin der Goethe-Universität Frankfurt am Main herangezogen und eine Literaturanalyse einbezogen.
Ergebnisse: Als Ergebnis kann festgehalten werden, dass die bereits seit mehreren Jahren erhobenen Forderungen und gewünschten Unterstützungsleistungen zwar zum Teil umgesetzt, aber noch nicht ausreichend an allen Fachbereichen implementiert wurden. Somit ist die aktuelle Situation von Studierenden mit Kindern in der Medizin nach wie vor schwierig und stellt für alle Beteiligten eine große Herausforderung dar.
Lösungsansatz: Im Rahmen der Arbeitsstelle "Individuelle Studienbegleitung" konnte im November 2009 das "Modellprojekt Teilzeitstudium Medizin" aufgebaut werden. Nur durch neue, unkonventionelle und innovative Ideen kann man die Sicherstellung der medizinischen Ausbildung erreichen und die heutige heterogene Studierendenschaft adäquat ansprechen sowie Studierende erfolgreich durch ihr Studium begleiten.
During meditation, practitioners are required to center their attention on a specific object for extended periods of time. When their thoughts get diverted, they learn to quickly disengage from the distracter. We hypothesized that learning to respond to the dual demand of engaging attention on specific objects and disengaging quickly from distracters enhances the efficiency by which meditation practitioners can allocate attention. We tested this hypothesis in a global-to-local task while measuring electroencephalographic activity from a group of eight highly trained Buddhist monks and nuns and a group of eight age and education matched controls with no previous meditation experience. Specifically, we investigated the effect of attentional training on the global precedence effect, i.e., faster detection of targets on a global than on a local level. We expected to find a reduced global precedence effect in meditation practitioners but not in controls, reflecting that meditators can more quickly disengage their attention from the dominant global level. Analysis of reaction times confirmed this prediction. To investigate the underlying changes in brain activity and their time course, we analyzed event-related potentials. Meditators showed an enhanced ability to select the respective target level, as reflected by enhanced processing of target level information. In contrast with control group, which showed a local target selection effect only in the P1 and a global target selection effect in the P3 component, meditators showed effects of local information processing in the P1, N2, and P3 and of global processing for the N1, N2, and P3. Thus, meditators seem to display enhanced depth of processing. In addition, meditation altered the uptake of information such that meditators selected target level information earlier in the processing sequence than controls. In a longitudinal experiment, we could replicate the behavioral effects, suggesting that meditation modulates attention already after a 4-day meditation retreat. Together, these results suggest that practicing meditation enhances the speed with which attention can be allocated and relocated, thus increasing the depth of information processing and reducing response latency.
In this study, it is demonstrated that moving sounds have an effect on the direction in which one sees visual stimuli move. During the main experiment sounds were presented consecutively at four speaker locations inducing left or rightward auditory apparent motion. On the path of auditory apparent motion, visual apparent motion stimuli were presented with a high degree of directional ambiguity. The main outcome of this experiment is that our participants perceived visual apparent motion stimuli that were ambiguous (equally likely to be perceived as moving left or rightward) more often as moving in the same direction than in the opposite direction of auditory apparent motion. During the control experiment we replicated this finding and found no effect of sound motion direction on eye movements. This indicates that auditory motion can capture our visual motion percept when visual motion direction is insufficiently determinate without affecting eye movements.
We describe the frog species Diasporus citrinobapheussp. n. from the Cordillera Central of western Panama. The new species differs from all other species in its genus in coloration, disk cover and disk pad shape, skin texture, advertisement call, and size. It is most similar to Diasporus tigrillo, from which it differs in dorsal skin texture, relative tibia length, number of vomerine teeth, ventral coloration, dorsal markings, and relative tympanum size, and to Diasporus gularis, from which it can be distinguished by the lack of membranes between the toes, adult size, posterior thigh coloration, and position of the choanae. We provide data on morpho- logy, vocalization, and distribution of the new species, as well as brief information on its natural history.
Alme, Johan ; Andres, Y. ; Appelshäuser, Harald ; Bablok, Sebastian ; Bialas, Norbert ; Bolgen, Rikard ; Bonnes, Uwe ; Bramm, Roland ; Braun-Munzinger, Peter ; Campagnolo, Roberto ; Christiansen, Peter ; Dobrin, Alexandru Florin ; Engster, Claude ; Fehlker, Dominik ; Foka, Yiota ; Frankenfeld, Ulrich ; Gaardhøje, Jens Joergen ; Garabatos, Chilo ; Glässel, Peter ; Gonzalez Gutierrez, Carmen ; Gros, Philippe ; Gustafsson, Hans-Åke ; Helstrup, Håvard ; Hoch, Michael ; Ivanov, Marian ; Janik, Rudolf ; Junique, Antoine ; Kalweit, Alexander Philipp ; Keidel, Ralf ; Kniege, Stefan ; Kowalski, Marek ; Larsen, Dag Toppe ; Lesenechal, Yannick ; Lenoir, Philippe ; Lindegaard, Niels ; Lippmann, Christian ; Mager, Magnus ; Mast, Manfred ; Matyja, Adam ; Munkejord, Magne ; Musa, Luciano ; Nielsen, Borge Svane ; Nikolic, Vedran ; Oeschler, Helmut ; Olsen, E.K. ; Oskarsson, Anders ; Osterman, Lennart ; Pikna, Miroslav ; Rehman, Attiq ur ; Renault, Gaël ; Renfordt, Rainer Arno Ernst ; Rossegger, Stefan ; Röhrich, Dieter ; Røed, Ketil ; Richter, Mattias ; Rueshmann, G. ; Rybicki, Andrzej ; Sann, Hans ; Schmidt, Hans-Rudolf ; Siska, Martin ; Sitar, Branislav ; Soegaard, Carsten ; Soltveit, Hans Kristian ; Soyk, Daniel ; Stachel, Johanna ; Stelzer, Herbert ; Stenlund, Evert Anders ; Stock, Reinhard ; Strmeň, Peter ; Szarka, Imrich ; Ullaland, Kjetil ; Vranić, Danilo ; Veenhof, Rob ; Westergaard, Joern ; Wiechula, Jens ; Windelband, Bernd
The design, construction, and commissioning of the ALICE Time-Projection Chamber (TPC) is described. It is the main device for pattern recognition, tracking, and identification of charged particles in the ALICE experiment at the CERN LHC. The TPC is cylindrical in shape with a volume close to 90 m3 and is operated in a 0.5 T solenoidal magnetic field parallel to its axis.
In this paper we describe in detail the design considerations for this detector for operation in the extreme multiplicity environment of central Pb–Pb collisions at LHC energy. The implementation of the resulting requirements into hardware (field cage, read-out chambers, electronics), infrastructure (gas and cooling system, laser-calibration system), and software led to many technical innovations which are described along with a presentation of all the major components of the detector, as currently realized. We also report on the performance achieved after completion of the first round of stand-alone calibration runs and demonstrate results close to those specified in the TPC Technical Design Report.
Körner, Christian ; Barrera, Miguel ; Dukanovic, Jovana ; Eydt, Katharina ; Harner, Max ; Rabl, Regina ; Vogel, Frank ; Rapaport, Doron ; Neupert, Walter ; Reichert, Andreas
Crista junctions (CJs) are tubular invaginations of the inner membrane of mitochondria that connect the inner boundary with the cristae membrane. These architectural elements are critical for mitochondrial function. The yeast inner membrane protein Fcj1, called mitofilin in mammals, was reported to be preferentially located at CJs and crucial for their formation. Here we investigate the functional roles of individual domains of Fcj1. The most conserved part of Fcj1, the C-terminal domain, is essential for Fcj1 function. In its absence, formation of CJ is strongly impaired and irregular, and stacked cristae are present. This domain interacts with full-length Fcj1, suggesting a role in oligomer formation. It also interacts with Tob55 of the translocase of outer membrane β-barrel proteins (TOB)/sorting and assembly machinery (SAM) complex, which is required for the insertion of β-barrel proteins into the outer membrane. The association of the TOB/SAM complex with contact sites depends on the presence of Fcj1. The biogenesis of β-barrel proteins is not significantly affected in the absence of Fcj1. However, down-regulation of the TOB/SAM complex leads to altered cristae morphology and a moderate reduction in the number of CJs. We propose that the C-terminal domain of Fcj1 is critical for the interaction of Fcj1 with the TOB/SAM complex and thereby for stabilizing CJs in close proximity to the outer membrane. These results assign novel functions to both the C-terminal domain of Fcj1 and the TOB/SAM complex.
New projects, services and collaborations have recently brought the infrastructural services for African Studies a big step forward. This report gives an account of new subject gateways and digitisation projects. It discusses recent European cooperation ventures in the field of librarianship. Additionally, new developments and services of the Africa Collection at Frankfurt University Library are presented, which help to address the changing needs of researchers and to handle information overload, while keeping up with the latest developments. Nevertheless, the fragmentation and compartmentalisation of the different services still hinder more integrated information services.
Foamy viruses (FVs) are distinct retroviruses classified as Spumaretrovirinae in contrast to the other retroviruses, the Orthoretrovirinae. As a unique feature of FVs, Gag is not sufficient for sub-viral particle (SVP) release. In primate and feline FVs (PFV and FFV), particle budding completely depends on the cognate FV Env glycoproteins. It was recently shown that an artificially added N-terminal Gag myristoylation signal (myr-signal) overcomes this restriction in PFV inducing an Orthoretrovirus-like budding phenotype. Here we show that engineered, heterologous N-terminal myr-signals also induce budding of the distantly related FFV Gag. The budding efficiency depends on the myr-signal and its location relative to the N-terminus of Gag. When the first nine amino acid residues of FFV Gag were replaced by known myr-signals, the budding efficiency as determined by the detection of extracellular SVPs was low. In contrast, adding myr-signals to the intact N-terminus of FFV Gag resulted in a more efficient SVP release. Importantly, budding of myr-Gag proteins was sensitive towards inhibition of cellular N-myristoyltransferases. As expected, the addition or insertion of myr-signals that allowed Env-independent budding of FFV SVPs also retargeted Gag to plasma membrane-proximal sites and other intracellular membrane compartments. The data confirm that membrane-targeted FV Gag has the capacity of SVP formation.
Schwalb, Christian H. ; Grimm, Christina ; Baranowski, Markus ; Sachser, Roland ; Porrati, Fabrizio ; Reith, Heiko ; Das, Pintu ; Müller, Jens ; Völklein, Friedemann ; Kaya, Alexander ; Huth, Michael
This paper introduces a new methodology for the fabrication of strain-sensor elements for MEMS and NEMS applications based on the tunneling effect in nano-granular metals. The strain-sensor elements are prepared by the maskless lithography technique of focused electron-beam-induced deposition (FEBID) employing the precursor trimethylmethylcyclopentadienyl platinum [MeCpPt(Me)3]. We use a cantilever-based deflection technique to determine the sensitivity (gauge factor) of the sensor element. We find that its sensitivity depends on the electrical conductivity and can be continuously tuned, either by the thickness of the deposit or by electron-beam irradiation leading to a distinct maximum in the sensitivity. This maximum finds a theoretical rationale in recent advances in the understanding of electronic charge transport in nano-granular metals.
Introduction. To evaluate clinical feasibility and reproducibility of cytometric bead assay (CBA) in nondiluted vitreous samples of patients with age-related macular degeneration (ARMD), diabetic macular edema (DME), and central retinal vein occlusion (CRVO). Methods. Twelve patients from a single clinics day qualified for intravitreal injections (ARMD n = 6, DME n = 3, CRVO n = 3) and underwent a combination treatment including a single-site 23 gauge core vitrectomy which yielded a volume of 0.6 mL undiluted vitreous per patient. Interleukin-6 (IL-6), vascular endothelial growth factor isoform A (VEGF-A), and monocyte chemo-attractant protein-1 (MCP-1) were assessed directly from 0.3 mL at the same day (fresh samples). To assess the reproducibility 0.3 ml were frozen for 60 days at -80°, on which the CBA was repeated (frozen samples). Results. In the fresh samples IL-6 was highest in CRVO (median IL-6 55.8 pg/mL) > DME (50.6) > ARMD (3.1). Highest VEGF was measured in CRVO (447.4) > DME (3.9) > ARMD (2.0). MCP-1 was highest in CRVO (595.7) > AMD (530.8) > DME (178). The CBA reproducibility after frozen storage was examined to be most accurate for MCP1 (P = 0.91) > VEGF (P = 0.68) > IL-6 (P = 0.49). Conclusions. CBA is an innovative, fast determining, and reliable technology to analyze proteins in fluids, like the undiluted vitreous, which is important to better understand ocular pathophysiology and pharmacology. There is no influence of intermittent storage at -80° for the reproducibility of the CBA.
Bierbach, David ; Klein, Moritz ; Sassmannshausen, Vanessa ; Schlupp, Ingo ; Riesch, Rüdiger ; Parzefall, Jakob ; Plath, Martin
Reproductive isolation among locally adapted populations may arise when immigrants from foreign habitats are selected against via natural or (inter-)sexual selection (female mate choice). We asked whether also intrasexual selection through male-male competition could promote reproductive isolation among populations of poeciliid fishes that are locally adapted to extreme environmental conditions [i.e., darkness in caves and/or toxic hydrogen sulphide (H(2)S)]. We found strongly reduced aggressiveness in extremophile P. oecilia mexicana, and darkness was the best predictor for the evolutionary reduction of aggressiveness, especially when combined with presence of H(2)S. We demonstrate that reduced aggression directly translates into migrant males being inferior when paired with males from non-sulphidic surface habitats. By contrast, the phylogenetically old sulphur endemic P. sulphuraria from another sulphide spring area showed no overall reduced aggressiveness, possibly indicating evolved mechanisms to better cope with H(2)S.
Integrin-mediated cell-matrix interaction in physiological and pathological blood vessel formation
(2011)
Physiological as well as pathological blood vessel formation are fundamentally dependent on cell-matrix interaction. Integrins, a family of major cell adhesion receptors, play a pivotal role in development, maintenance, and remodeling of the vasculature. Cell migration, invasion, and remodeling of the extracellular matrix (ECM) are integrin-regulated processes, and the expression of certain integrins also correlates with tumor progression. Recent advances in the understanding of how integrins are involved in the regulation of blood vessel formation and remodeling during tumor progression are highlighted. The increasing knowledge of integrin function at the molecular level, together with the growing repertoire of integrin inhibitors which allow their selective pharmacological manipulation, makes integrins suited as potential diagnostic markers and therapeutic targets.
Although throughout the history of anthropology the ethnography of urban societies was never an important topic, investigations on cities in Africa contributed to the early theoretical development of urban studies in social sciences. As the ethnography of rural migrants in towns made clear, cultural diversity and creativity are foundational and permanent elements of urban cultures in Africa (and beyond). Currently, two new aspects complement these insights: 1) Different forms of mobility have received a new awareness through the concept of transnationalism. They are much more complex, including not only rural–urban migration, but also urban–urban migration, and migrations with a destination beyond the continent. 2) Urban life-worlds also include the appropriation of globally circulating images and lifestyles, which contribute substantially to the current cultural dynamics of cities in Africa. These two aspects are the reasons for the high complexity of urban contexts in Africa. Therefore, whether it is still appropriate to speak about the “locality” of these life-worlds has become questionable. At the same time, these new aspects explain the self-consciousness of members of urban cultures in Africa. They contribute to the expansive character of these societies and to the impression that cities in Africa host the most innovative and creative societies worldwide.
My contribution focuses on the relationship between theory and praxis, since the task of a “critical archaeology” is to mediate between these two spheres. Its target audience is the public, not other scholars. Critical archaeology is not part of scientific practice, but rather is part of intellectual reasoning that is both value-laden and that exercises practical critique. Respect for the specific logics of theory and praxis is crucial for its success. A “critical archaeology” that merits its name must steer its way between the Scylla of a technocratic paternalism that limits praxis and the Charybdis of submission to theory under the presumption of the “relevance of praxis.”
BACKGROUND: The identification of beta-barrel membrane proteins out of a genomic/proteomic background is one of the rapidly developing fields in bioinformatics. Our main goal is the prediction of such proteins in genome/proteome wide analyses.
RESULTS: For the prediction of beta-barrel membrane proteins within prokaryotic proteomes a set of parameters was developed. We have focused on a procedure with a low false positive rate beside a procedure with lowest false prediction rate to obtain a high certainty for the predicted sequences. We demonstrate that the discrimination between beta-barrel membrane proteins and other proteins is improved by analyzing a length limited region. The developed set of parameters is applied to the proteome of E. coli and the results are compared to four other described procedures.
CONCLUSION: Analyzing the beta-barrel membrane proteins revealed the presence of a defined membrane inserted beta-barrel region. This information can now be used to refine other prediction programs as well. So far, all tested programs fail to predict outer membrane proteins in the proteome of the prokaryote E. coli with high reliability. However, the reliability of the prediction is improved significantly by a combinatory approach of several programs. The consequences and usability of the developed scores are discussed.
Schmidt von Braun, Serena ; Sabetti, Antonino ; Hanic-Joyce, Pamela J. ; Gu, Jun ; Schleiff, Enrico ; Joyce, Paul B. M.
Enzymes involved in tRNA maturation are essential for cytosolic, mitochondrial, and plastid protein synthesis and are therefore localized to these different compartments of the cell. Interestingly, only one isoform of tRNA nucleotidyltransferase (responsible for adding the 3′-terminal cytidine–cytidine–adenosine to tRNAs) has been identified in plants. The present study therefore explored how signals contained on this enzyme allow it to be distributed among the different cell compartments. It is demonstrated that the N-terminal portion of the protein acts as an organellar targeting signal and that differential use of multiple in-frame start codons alters the localization of the protein. Moreover, it is shown that the mature domain has a major impact on the distribution of the protein within the cell. These data indicate that regulation of dual localization involves not only specific N-terminal signals, but also additional factors within the protein or the cell.
Veith, Thomas ; Martin, Roman ; Wurm, Jan Philip ; Weis, Benjamin L. ; Duchardt-Ferner, Elke ; Safferthal, Charlotta ; Hennig, Raoul ; Mirus, Oliver ; Bohnsack, Markus ; Wöhnert, Jens ; Schleiff, Enrico
Eukaryotic ribosome biogenesis requires the concerted action of numerous ribosome assembly factors, for most of which structural and functional information is currently lacking. Nob1, which can be identified in eukaryotes and archaea, is required for the final maturation of the small subunit ribosomal RNA in yeast by catalyzing cleavage at site D after export of the preribosomal subunit into the cytoplasm. Here, we show that this also holds true for Nob1 from the archaeon Pyrococcus horikoshii, which efficiently cleaves RNA-substrates containing the D-site of the preribosomal RNA in a manganese-dependent manner. The structure of PhNob1 solved by nuclear magnetic resonance spectroscopy revealed a PIN domain common with many nucleases and a zinc ribbon domain, which are structurally connected by a flexible linker. We show that amino acid residues required for substrate binding reside in the PIN domain whereas the zinc ribbon domain alone is sufficient to bind helix 40 of the small subunit rRNA. This suggests that the zinc ribbon domain acts as an anchor point for the protein on the nascent subunit positioning it in the proximity of the cleavage site.
Machettira, Anu Bheemaiah ; Groß, Lucia E. ; Tillmann, Bodo ; Weis, Benjamin L. ; Englich, Gisela ; Sommer, Maik Sascha ; Königer, Martina ; Schleiff, Enrico
Organelles are surrounded by membranes with a distinct lipid and protein composition. While it is well established that lipids affect protein functioning and vice versa, it has been only recently suggested that elevated membrane protein concentrations may affect the shape and organization of membranes. We therefore analyzed the effects of high chloroplast envelope protein concentrations on membrane structures using an in vivo approach with protoplasts. Transient expression of outer envelope proteins or protein domains such as CHUP1-TM–GFP, outer envelope protein of 7 kDa–GFP, or outer envelope protein of 24 kDa–GFP at high levels led to the formation of punctate, circular, and tubular membrane protrusions. Expression of inner membrane proteins such as translocase of inner chloroplast membrane 20, isoform II (Tic20-II)–GFP led to membrane protrusions including invaginations. Using increasing amounts of DNA for transfection, we could show that the frequency, size, and intensity of these protrusions increased with protein concentration. The membrane deformations were absent after cycloheximide treatment. Co-expression of CHUP1-TM–Cherry and Tic20-II–GFP led to membrane protrusions of various shapes and sizes including some stromule-like structures, for which several functions have been proposed. Interestingly, some structures seemed to contain both proteins, while others seem to contain one protein exclusively, indicating that outer and inner envelope dynamics might be regulated independently. While it was more difficult to investigate the effects of high expression levels of membrane proteins on mitochondrial membrane shapes using confocal imaging, it was striking that the expression of the outer membrane protein Tom20 led to more elongate mitochondria. We discuss that the effect of protein concentrations on membrane structure is possibly caused by an imbalance in the lipid to protein ratio and may be involved in a signaling pathway regulating membrane biogenesis. Finally, the observed phenomenon provides a valuable experimental approach to investigate the relationship between lipid synthesis and membrane protein expression in future studies.