TY - JOUR A1 - Bartholomäus, Alexander A1 - Fedyunin, Ivan A1 - Feist, Peter A1 - Sin, Celine A1 - Zhang, Gong A1 - Valleriani, Angelo A1 - Ignatova, Zoya T1 - Bacteria differently regulate mRNA abundance to specifically respond to various stresses JF - Geology N2 - Environmental stress is detrimental to cell viability and requires an adequate reprogramming of cellular activities to maximize cell survival. We present a global analysis of the response of Escherichia coli to acute heat and osmotic stress. We combine deep sequencing of total mRNA and ribosome-protected fragments to provide a genome-wide map of the stress response at transcriptional and translational levels. For each type of stress, we observe a unique subset of genes that shape the stress-specific response. Upon temperature upshift, mRNAs with reduced folding stability up-and downstream of the start codon, and thus with more accessible initiation regions, are translationally favoured. Conversely, osmotic upshift causes a global reduction of highly translated transcripts with high copy numbers, allowing reallocation of translation resources to not degraded and newly synthesized mRNAs. KW - transcription KW - translation KW - deep sequencing KW - Escherichia coli KW - copy numbers Y1 - 2016 U6 - https://doi.org/10.1098/rsta.2015.0069 SN - 1364-503X SN - 1471-2962 VL - 374 PB - Royal Society CY - London ER - TY - JOUR A1 - Marce, Rafael A1 - George, Glen A1 - Buscarinu, Paola A1 - Deidda, Melania A1 - Dunalska, Julita A1 - de Eyto, Elvira A1 - Flaim, Giovanna A1 - Grossart, Hans-Peter A1 - Istvanovics, Vera A1 - Lenhardt, Mirjana A1 - Moreno-Ostos, Enrique A1 - Obrador, Biel A1 - Ostrovsky, Ilia A1 - Pierson, Donald C. A1 - Potuzak, Jan A1 - Poikane, Sandra A1 - Rinke, Karsten A1 - Rodriguez-Mozaz, Sara A1 - Staehr, Peter A. A1 - Sumberova, Katerina A1 - Waajen, Guido A1 - Weyhenmeyer, Gesa A. A1 - Weathers, Kathleen C. A1 - Zion, Mark A1 - Ibelings, Bas W. A1 - Jennings, Eleanor T1 - Automatic High Frequency Monitoring for Improved Lake and Reservoir Management JF - Frontiers in plant science N2 - Recent technological developments have increased the number of variables being monitored in lakes and reservoirs using automatic high frequency monitoring (AHFM). However, design of AHFM systems and posterior data handling and interpretation are currently being developed on a site-by-site and issue-by-issue basis with minimal standardization of protocols or knowledge sharing. As a result, many deployments become short-lived or underutilized, and many new scientific developments that are potentially useful for water management and environmental legislation remain underexplored. This Critical Review bridges scientific uses of AHFM with their applications by providing an overview of the current AHFM capabilities, together with examples of successful applications. We review the use of AHFM for maximizing the provision of ecosystem services supplied, by lakes and reservoirs (consumptive and non consumptive uses, food production, and recreation), and for reporting lake status in the EU Water Framework Directive. We also highlight critical issues to enhance the application of AHFM, and suggest the establishment of appropriate networks to facilitate knowledge sharing and technological transfer between potential users. Finally, we give advice on how modern sensor technology can successfully be applied on a larger scale to the management of lakes and reservoirs and maximize the ecosystem services they provide. Y1 - 2016 U6 - https://doi.org/10.1021/acs.est.6b01604 SN - 0013-936X SN - 1520-5851 VL - 50 SP - 10780 EP - 10794 PB - American Chemical Society CY - Washington ER - TY - THES A1 - Maier, Natalia T1 - Aufbau eines Testsystems zum Nachweis von Ethylglucuronid (EtG) in Haaren Y1 - 2016 ER - TY - JOUR A1 - Hanke-Gogokhia, Christin A1 - Wu, Zhijian A1 - Gerstner, Cecilia D. A1 - Frederick, Jeanne M. A1 - Zhang, Houbin A1 - Baehr, Wolfgang T1 - Arf-like Protein 3 (ARL3) Regulates Protein Trafficking and Ciliogenesis in Mouse Photoreceptors JF - The journal of biological chemistry N2 - Arf-like protein 3 (ARL3) is a ubiquitous small GTPase expressed in ciliated cells of plants and animals. Germline deletion of Arl3 in mice causes multiorgan ciliopathy reminiscent of Bardet-Biedl or Joubert syndromes. As photoreceptors are elegantly compartmentalized and have cilia, we probed the function of ARL3 (ADP-ribosylation factor (Arf)-like 3 protein) by generating rod photoreceptor-specific (prefix (rod)) and retina-specific (prefix (ret)) Arl3 deletions. In predegenerate (rod)Arl3(-/-) mice, lipidated phototransduction proteins showed trafficking deficiencies, consistent with the role of ARL3 as a cargo displacement factor for lipid-binding proteins. By contrast, (ret)Arl3(-/-) rods and cones expressing Cre recombinase during embryonic development formed neither connecting cilia nor outer segments and degenerated rapidly. Absence of cilia infers participation of ARL3 in ciliogenesis and axoneme formation. Ciliogenesis was rescued, and degeneration was reversed in part by subretinal injection of adeno-associated virus particles expressing ARL3-EGFP. The conditional knock-out phenotypes permitted identification of two ARL3 functions, both in the GTP-bound form as follows: one as a regulator of intraflagellar transport participating in photoreceptor ciliogenesis and the other as a cargo displacement factor transporting lipidated protein to the outer segment. Surprisingly, a farnesylated inositol polyphosphate phosphatase only trafficked from the endoplasmic reticulum to the Golgi, thereby excluding it from a role in photoreceptor cilia physiology. KW - animal model KW - gene knock-out KW - lipid-binding protein KW - photoreceptor KW - protein trafficking (Golgi) KW - retinal degeneration Y1 - 2016 U6 - https://doi.org/10.1074/jbc.M115.710954 SN - 0021-9258 SN - 1083-351X VL - 291 SP - 7142 EP - 7155 PB - American Society for Biochemistry and Molecular Biology CY - Bethesda ER - TY - JOUR A1 - Brzezinka, Krzysztof A1 - Altmann, Simone A1 - Czesnick, Hjördis A1 - Nicolas, Philippe A1 - Gorka, Michal A1 - Benke, Eileen A1 - Kabelitz, Tina A1 - Jähne, Felix A1 - Graf, Alexander A1 - Kappel, Christian A1 - Bäurle, Isabel T1 - Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling JF - eLife N2 - Plants as sessile organisms can adapt to environmental stress to mitigate its adverse effects. As part of such adaptation they maintain an active memory of heat stress for several days that promotes a more efficient response to recurring stress. We show that this heat stress memory requires the activity of the FORGETTER1 (FGT1) locus, with fgt1 mutants displaying reduced maintenance of heat-induced gene expression. FGT1 encodes the Arabidopsis thaliana orthologue of Strawberry notch (Sno), and the protein globally associates with the promoter regions of actively expressed genes in a heat-dependent fashion. FGT1 interacts with chromatin remodelers of the SWI/ SNF and ISWI families, which also display reduced heat stress memory. Genomic targets of the BRM remodeler overlap significantly with FGT1 targets. Accordingly, nucleosome dynamics at loci with altered maintenance of heat-induced expression are affected in fgt1. Together, our results suggest that by modulating nucleosome occupancy, FGT1 mediates stress-induced chromatin memory. Y1 - 2016 U6 - https://doi.org/10.7554/eLife.17061 SN - 2050-084X VL - 5 PB - eLife Sciences Publications CY - Cambridge ER - TY - JOUR A1 - Grossart, Hans-Peter A1 - Rojas-Jimenez, Keilor T1 - Aquatic fungi: targeting the forgotten in microbial ecology JF - Current opinion in microbiology N2 - Fungi constitute important and conspicuous components of aquatic microbial communities, but their diversity and functional roles remain poorly characterized. New methods and conceptual frameworks are required to accurately describe their ecological roles, involvement in global cycling processes, and utility for human activities, considering both cultivation independent techniques as well as experiments in laboratory and in natural ecosystems. Here we highlight recent developments and extant knowledge gaps in aquatic mycology, and provide a conceptual model to expose the importance of fungi in aquatic food webs and related biogeochemical processes. Y1 - 2016 U6 - https://doi.org/10.1016/j.mib.2016.03.016 SN - 1369-5274 SN - 1879-0364 VL - 31 SP - 140 EP - 145 PB - Elsevier CY - London ER - TY - JOUR A1 - Roggenbuck, Dirk A1 - Borghi, Maria Orietta A1 - Somma, Valentina A1 - Buettner, Thomas A1 - Schierack, Peter A1 - Hanack, Katja A1 - Grossi, Claudia A1 - Bodio, Caterina A1 - Macor, Paolo A1 - von Landenberg, Philipp A1 - Boccellato, Francesco A1 - Mahler, Michael A1 - Meroni, Pier Luigi T1 - Antiphospholipid antibodies detected by line immunoassay differentiate among patients with antiphospholipid syndrome, with infections and asymptomatic carriers JF - IEEE transactions on geoscience and remote sensing N2 - Background: Antiphospholipid antibodies (aPL) can be detected in asymptomatic carriers and infectious patients. The aim was to investigate whether a novel line immunoassay (LIA) differentiates between antiphospholipid syndrome (APS) and asymptomatic aPL+ carriers or patients with infectious diseases (infectious diseases controls (IDC)). Methods: Sixty-one patients with APS (56 primary, 22/56 with obstetric events only, and 5 secondary), 146 controls including 24 aPL+ asymptomatic carriers and 73 IDC were tested on a novel hydrophobic solid phase coated with cardiolipin (CL), phosphatic acid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylserine, beta2-glycoprotein I (beta 2GPI), prothrombin, and annexin V. Samples were also tested by anti-CL and anti-beta 2GPI ELISAs and for lupus anticoagulant activity. Human monoclonal antibodies (humoAbs) against human beta 2GPI or PL alone were tested on the same LIA substrates in the absence or presence of human serum, purified human beta 2GPI or after CL-micelle absorption. Results: Comparison of LIA with the aPL-classification assays revealed good agreement for IgG/IgM a beta 2GPI and aCL. Anti-CL and anti-beta 2GPI IgG/IgM reactivity assessed by LIA was significantly higher in patients with APS versus healthy controls and IDCs, as detected by ELISA. IgG binding to CL and beta 2GPI in the LIA was significantly lower in aPL+ carriers and Venereal Disease Research Laboratory test (VDRL) + samples than in patients with APS. HumoAb against domain 1 recognized beta 2GPI bound to the LIA-matrix and in anionic phospholipid (PL) complexes. Absorption with CL micelles abolished the reactivity of a PL-specific humoAb but did not affect the binding of anti-beta 2GPI humoAbs. Conclusions: The LIA and ELISA have good agreement in detecting aPL in APS, but the LIA differentiates patients with APS from infectious patients and asymptomatic carriers, likely through the exposure of domain 1. KW - Antiphospholipid syndrome KW - Antiphospholipid antibody KW - Phospholipid binding proteins KW - Beta2-glycoprotein I KW - Line immunoassay Y1 - 2016 U6 - https://doi.org/10.1186/s13075-016-1018-x SN - 1478-6354 SN - 1478-6362 VL - 18 PB - BioMed Central CY - London ER - TY - GEN A1 - Roggenbuck, Dirk A1 - Borghi, Maria Orietta A1 - Somma, Valentina A1 - Büttner, Thomas A1 - Schierack, Peter A1 - Hanack, Katja A1 - Grossi, Claudia A1 - Bodio, Caterina A1 - Macor, Paolo A1 - von Landenberg, Philipp A1 - Boccellato, Francesco A1 - Mahler, Michael A1 - Meroni, Pier Luigi T1 - Antiphospholipid antibodies detected by line immunoassay differentiate among patients with antiphospholipid syndrome, with infections and asymptomatic carriers T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Background Antiphospholipid antibodies (aPL) can be detected in asymptomatic carriers and infectious patients. The aim was to investigate whether a novel line immunoassay (LIA) differentiates between antiphospholipid syndrome (APS) and asymptomatic aPL+ carriers or patients with infectious diseases (infectious diseases controls (IDC)). Methods Sixty-one patients with APS (56 primary, 22/56 with obstetric events only, and 5 secondary), 146 controls including 24 aPL+ asymptomatic carriers and 73 IDC were tested on a novel hydrophobic solid phase coated with cardiolipin (CL), phosphatic acid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylserine, beta2-glycoprotein I (β2GPI), prothrombin, and annexin V. Samples were also tested by anti-CL and anti-β2GPI ELISAs and for lupus anticoagulant activity. Human monoclonal antibodies (humoAbs) against human β2GPI or PL alone were tested on the same LIA substrates in the absence or presence of human serum, purified human β2GPI or after CL-micelle absorption. Results Comparison of LIA with the aPL-classification assays revealed good agreement for IgG/IgM aß2GPI and aCL. Anti-CL and anti-ß2GPI IgG/IgM reactivity assessed by LIA was significantly higher in patients with APS versus healthy controls and IDCs, as detected by ELISA. IgG binding to CL and ß2GPI in the LIA was significantly lower in aPL+ carriers and Venereal Disease Research Laboratory test (VDRL) + samples than in patients with APS. HumoAb against domain 1 recognized β2GPI bound to the LIA-matrix and in anionic phospholipid (PL) complexes. Absorption with CL micelles abolished the reactivity of a PL-specific humoAb but did not affect the binding of anti-β2GPI humoAbs. Conclusions The LIA and ELISA have good agreement in detecting aPL in APS, but the LIA differentiates patients with APS from infectious patients and asymptomatic carriers, likely through the exposure of domain 1. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 436 KW - Antiphospholipid syndrome KW - Antiphospholipid antibody KW - Phospholipid binding proteins KW - Beta2 - glycoprotein I KW - Line immunoassay Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407211 SN - 1866-8372 IS - 436 ER - TY - JOUR A1 - Memczak, Henry A1 - Lauster, Daniel A1 - Kar, Parimal A1 - Di Lella, Santiago A1 - Volkmer, Rudolf A1 - Knecht, Volker A1 - Herrmann, Andreas A1 - Ehrentreich-Foerster, Eva A1 - Bier, Frank Fabian A1 - Stoecklein, Walter F. M. T1 - Anti-Hemagglutinin Antibody Derived Lead Peptides for Inhibitors of Influenza Virus Binding JF - PLoS one N2 - Antibodies against spike proteins of influenza are used as a tool for characterization of viruses and therapeutic approaches. However, development, production and quality control of antibodies is expensive and time consuming. To circumvent these difficulties, three peptides were derived from complementarity determining regions of an antibody heavy chain against influenza A spike glycoprotein. Their binding properties were studied experimentally, and by molecular dynamics simulations. Two peptide candidates showed binding to influenza A/Aichi/2/68 H3N2. One of them, termed PeB, with the highest affinity prevented binding to and infection of target cells in the micromolar region without any cytotoxic effect. PeB matches best the conserved receptor binding site of hemagglutinin. PeB bound also to other medical relevant influenza strains, such as human-pathogenic A/California/7/2009 H1N1, and avian-pathogenic A/MuteSwan/Rostock/R901/2006 H7N1. Strategies to improve the affinity and to adapt specificity are discussed and exemplified by a double amino acid substituted peptide, obtained by substitutional analysis. The peptides and their derivatives are of great potential for drug development as well as biosensing. Y1 - 2016 U6 - https://doi.org/10.1371/journal.pone.0159074 SN - 1932-6203 VL - 11 SP - 82 EP - 90 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Czesnick, Hjördis A1 - Lenhard, Michael T1 - Antagonistic control of flowering time by functionally specialized poly(A) polymerases in Arabidopsis thaliana JF - The plant journal N2 - Polyadenylation is a critical 3-end processing step during maturation of pre-mRNAs, and the length of the poly(A) tail affects mRNA stability, nuclear export and translation efficiency. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerase (PAPS) isoforms fulfilling specialized functions, as reflected by their different mutant phenotypes. While PAPS1 affects several processes, such as the immune response, organ growth and male gametophyte development, the roles of PAPS2 and PAPS4 are largely unknown. Here we demonstrate that PAPS2 and PAPS4 promote flowering in a partially redundant manner. The enzymes act antagonistically to PAPS1, which delays the transition to flowering. The opposite flowering-time phenotypes in paps1 and paps2 paps4 mutants are at least partly due to decreased or increased FLC activity, respectively. In contrast to paps2 paps4 mutants, plants with increased PAPS4 activity flower earlier than the wild-type, concomitant with reduced FLC expression. Double mutant analyses suggest that PAPS2 and PAPS4 act independently of the autonomous pathway components FCA, FY and CstF64. The direct polyadenylation targets of the three PAPS isoforms that mediate their effects on flowering time do not include FLC sense mRNA and remain to be identified. Thus, our results uncover a role for canonical PAPS isoforms in flowering-time control, raising the possibility that modulating the balance of the isoform activities could be used to fine tune the transition to flowering. Significance Statement The length of the poly(A) tail affects mRNA stability, nuclear export and translation efficiency. Arabidopsis has three isoforms of nuclear poly(A) polymerase (PAPS): PAPS1 plays a major role in organ growth and plant defence. Here we show that PAPS2 and PAPS4 redundantly promote flowering and act antagonistically to PAPS1, which delays flowering. We suggest that modulating the activity of these isoforms fine-tunes the transition to flowering. KW - polyadenylation KW - 3-end processing KW - poly(A) polymerase KW - flowering time KW - autonomous pathway KW - Arabidopsis thaliana Y1 - 2016 U6 - https://doi.org/10.1111/tpj.13280 SN - 0960-7412 SN - 1365-313X VL - 88 SP - 570 EP - 583 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Schneider, Florian D. A1 - Brose, Ulrich A1 - Rall, Björn C. A1 - Guill, Christian T1 - Animal diversity and ecosystem functioning in dynamic food webs JF - Nature Communications N2 - Species diversity is changing globally and locally, but the complexity of ecological communities hampers a general understanding of the consequences of animal species loss on ecosystem functioning. High animal diversity increases complementarity of herbivores but also increases feeding rates within the consumer guild. Depending on the balance of these counteracting mechanisms, species-rich animal communities may put plants under top-down control or may release them from grazing pressure. Using a dynamic food-web model with body-mass constraints, we simulate ecosystem functions of 20,000 communities of varying animal diversity. We show that diverse animal communities accumulate more biomass and are more exploitative on plants, despite their higher rates of intra-guild predation. However, they do not reduce plant biomass because the communities are composed of larger, and thus energetically more efficient, plant and animal species. This plasticity of community body-size structure reconciles the debate on the consequences of animal species loss for primary productivity. Y1 - 2016 U6 - https://doi.org/10.1038/ncomms12718 SN - 2041-1723 VL - 7 SP - 3129 EP - 3138 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - González-Fortes, Gloria M. A1 - Kolbe, Ben A1 - Fernandes, Daniel A1 - Meleg, Ioana N. A1 - Garcia-Vazquez, Ana A1 - Pinto-Llona, Ana C. A1 - Constantin, Silviu A1 - de Torres, Trino J. A1 - Ortiz, Jose E. A1 - Frischauf, Christine A1 - Rabeder, Gernot A1 - Hofreiter, Michael A1 - Barlow, Axel T1 - Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears JF - Molecular ecology N2 - Ancient DNA studies have revolutionized the study of extinct species and populations, providing insights on phylogeny, phylogeography, admixture and demographic history. However, inferences on behaviour and sociality have been far less frequent. Here, we investigate the complete mitochondrial genomes of extinct Late Pleistocene cave bears and middle Holocene brown bears that each inhabited multiple geographically proximate caves in northern Spain. In cave bears, we find that, although most caves were occupied simultaneously, each cave almost exclusively contains a unique lineage of closely related haplotypes. This remarkable pattern suggests extreme fidelity to their birth site in cave bears, best described as homing behaviour, and that cave bears formed stable maternal social groups at least for hibernation. In contrast, brown bears do not show any strong association of mitochondrial lineage and cave, suggesting that these two closely related species differed in aspects of their behaviour and sociality. This difference is likely to have contributed to cave bear extinction, which occurred at a time in which competition for caves between bears and humans was likely intense and the ability to rapidly colonize new hibernation sites would have been crucial for the survival of a species so dependent on caves for hibernation as cave bears. Our study demonstrates the potential of ancient DNA to uncover patterns of behaviour and sociality in ancient species and populations, even those that went extinct many tens of thousands of years ago. KW - ancient DNA KW - extinction KW - homing KW - sociality KW - Ursus arctos KW - Ursus spelaeus Y1 - 2016 U6 - https://doi.org/10.1111/mec.13800 SN - 0962-1083 SN - 1365-294X VL - 25 SP - 4907 EP - 4918 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Almathen, Faisal A1 - Charruau, Pauline A1 - Mohandesan, Elmira A1 - Mwacharo, Joram M. A1 - Orozco-terWengel, Pablo A1 - Pitt, Daniel A1 - Abdussamad, Abdussamad M. A1 - Uerpmann, Margarethe A1 - Uerpmann, Hans-Peter A1 - De Cupere, Bea A1 - Magee, Peter A1 - Alnaqeeb, Majed A. A1 - Salim, Bashir A1 - Raziq, Abdul A1 - Dessie, Tadelle A1 - Abdelhadi, Omer M. A1 - Banabazi, Mohammad H. A1 - Al-Eknah, Marzook A1 - Walzer, Chris A1 - Fayer, Bernard A1 - Hofreiter, Michael A1 - Peters, Joris A1 - Hanotte, Olivier A1 - Burger, Pamela A. T1 - Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary JF - Proceedings of the National Academy of Sciences of the United States of America N2 - Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and mitochondrial genotype information from 1,083 extant animals collected across the species’ range. We observe little phylogeographic signal in the modern population, indicative of extensive gene flow and virtually affecting all regions except East Africa, where dromedary populations have remained relatively isolated. In agreement with archaeological findings, we identify wild dromedaries from the southeast Arabian Peninsula among the founders of the domestic dromedary gene pool. Approximate Bayesian computations further support the “restocking from the wild” hypothesis, with an initial domestication followed by introgression from individuals from wild, now-extinct populations. Compared with other livestock, which show a long history of gene flow with their wild ancestors, we find a high initial diversity relative to the native distribution of the wild ancestor on the Arabian Peninsula and to the brief coexistence of early-domesticated and wild individuals. This study also demonstrates the potential to retrieve ancient DNA sequences from osseous remains excavated in hot and dry desert environments. KW - anthropogenic admixture KW - Camelus dromedarius KW - demographic history KW - paleogenetics KW - wild dromedary Y1 - 2016 U6 - https://doi.org/10.1073/pnas.1519508113 SN - 0027-8424 VL - 113 SP - 6707 EP - 6712 PB - National Acad. of Sciences CY - Washington ER - TY - THES A1 - Bartholomäus, Alexander T1 - Analyzing Transcriptional and Translational Control in E. coli using Deep-Seq Data Y1 - 2016 ER - TY - JOUR A1 - Rajasundaram, Dhivyaa A1 - Selbig, Joachim T1 - analysis JF - Current opinion in plant biology N2 - The development of ‘omics’ technologies has progressed to address complex biological questions that underlie various plant functions thereby producing copious amounts of data. The need to assimilate large amounts of data into biologically meaningful interpretations has necessitated the development of statistical methods to integrate multidimensional information. Throughout this review, we provide examples of recent outcomes of ‘omics’ data integration together with an overview of available statistical methods and tools. Y1 - 2016 U6 - https://doi.org/10.1016/j.pbi.2015.12.010 SN - 1369-5266 SN - 1879-0356 VL - 30 SP - 57 EP - 61 PB - Elsevier CY - London ER - TY - JOUR A1 - Saffert, Paul A1 - Adamla, Frauke A1 - Schieweck, Rico A1 - Atkins, John F. A1 - Ignatova, Zoya T1 - An Expanded CAG Repeat in Huntingtin Causes+1 Frameshifting JF - The journal of biological chemistry N2 - Maintenance of triplet decoding is crucial for the expression of functional protein because deviations either into the -1 or +1 reading frames are often non-functional. We report here that expression of huntingtin (Htt) exon 1 with expanded CAG repeats, implicated in Huntington pathology, undergoes a sporadic +1 frameshift to generate from the CAG repeat a trans-frame AGC repeat-encoded product. This +1 recoding is exclusively detected in pathological Htt variants, i.e. those with expanded repeats with more than 35 consecutive CAG codons. An atypical +1 shift site, UUC C at the 5 end of CAG repeats, which has some resemblance to the influenza A virus shift site, triggers the +1 frameshifting and is enhanced by the increased propensity of the expanded CAG repeats to form a stem-loop structure. The +1 trans-frame-encoded product can directly influence the aggregation of the parental Htt exon 1. KW - aggregation KW - Huntington disease KW - translation KW - translation regulation KW - trinucleotide repeat disease KW - frameshifting KW - seeding Y1 - 2016 U6 - https://doi.org/10.1074/jbc.M116.744326 SN - 0021-9258 SN - 1083-351X VL - 291 SP - 18505 EP - 18513 PB - American Society for Biochemistry and Molecular Biology CY - Bethesda ER - TY - THES A1 - Shikangalah, Rosemary Ndawapeka T1 - An ecohydrological impact assessment in urban areas BT - urban water erosion in Windhoek, Namibia N2 - Over the last decades, the world’s population has been growing at a faster rate, resulting in increased urbanisation, especially in developing countries. More than half of the global population currently lives in urbanised areas with an increasing tendency. The growth of cities results in a significant loss of vegetation cover, soil compaction and sealing of the soil surface which in turn results in high surface runoff during high-intensity storms and causes the problem of accelerated soil water erosion on streets and building grounds. Accelerated soil water erosion is a serious environmental problem in cities as it gives rise to the contamination of aquatic bodies, reduction of ground water recharge and increase in land degradation, and also results in damages to urban infrastructures, including drainage systems, houses and roads. Understanding the problem of water erosion in urban settings is essential for the sustainable planning and management of cities prone to water erosion. However, in spite of the vast existence of scientific literature on water erosion in rural regions, a concrete understanding of the underlying dynamics of urban erosion still remains inadequate for the urban dryland environments. This study aimed at assessing water erosion and the associated socio-environmental determinants in a typical dryland urban area and used the city of Windhoek, Namibia, as a case study. The study used a multidisciplinary approach to assess the problem of water erosion. This included an in depth literature review on current research approaches and challenges of urban erosion, a field survey method for the quantification of the spatial extent of urban erosion in the dryland city of Windhoek, and face to face interviews by using semi-structured questionnaires to analyse the perceptions of stakeholders on urban erosion. The review revealed that around 64% of the literatures reviewed were conducted in the developed world, and very few researches were carried out in regions with extreme climate, including dryland regions. Furthermore, the applied methods for erosion quantification and monitoring are not inclusive of urban typical features and they are not specific for urban areas. The reviewed literature also lacked aspects aimed at addressing the issues of climate change and policies regarding erosion in cities. In a field study, the spatial extent and severity of an urban dryland city, Windhoek, was quantified and the results show that nearly 56% of the city is affected by water erosion showing signs of accelerated erosion in the form of rills and gullies, which occurred mainly in the underdeveloped, informal and semi-formal areas of the city. Factors influencing the extent of erosion in Windhoek included vegetation cover and type, socio-urban factors and to a lesser extent slope estimates. A comparison of an interpolated field survey erosion map with a conventional erosion assessment tool (the Universal Soil Loss Equation) depicted a large deviation in spatial patterns, which underlines the inappropriateness of traditional non-urban erosion tools to urban settings and emphasises the need to develop new erosion assessment and management methods for urban environments. It was concluded that measures for controlling water erosion in the city need to be site-specific as the extent of erosion varied largely across the city. The study also analysed the perceptions and understanding of stakeholders of urban water erosion in Windhoek, by interviewing 41 stakeholders using semi-structured questionnaires. The analysis addressed their understanding of water erosion dynamics, their perceptions with regards to the causes and the seriousness of erosion damages, and their attitudes towards the responsibilities for urban erosion. The results indicated that there is less awareness of the process as a phenomenon, instead there is more awareness of erosion damages and the factors contributing to the damages. About 69% of the stakeholders considered erosion damages to be ranging from moderate to very serious. However, there were notable disparities between the private householders and public authority groups. The study further found that the stakeholders have no clear understanding of their responsibilities towards the management of the control measures and payment for the damages. The private householders and local authority sectors pointed fingers at each other for the responsibilities for erosion damage payments and for putting up prevention measures. The reluctance to take responsibility could create a predicament for areas affected, specifically in the informal settlements where land management is not carried out by the local authority and land is not owned by the occupants. The study concluded that in order to combat urban erosion, it is crucial to understand diverse dynamics aggravating the process of urbanisation from different scales. Accordingly, the study suggests that there is an urgent need for the development of urban-specific approaches that aim at: (a) incorporating the diverse socio-economic-environmental aspects influencing erosion, (b) scientifically improving natural cycles that influence water storages and nutrients for plants in urbanised dryland areas in order to increase the amount of vegetation cover, (c) making use of high resolution satellite images to improve the adopted methods for assessing urban erosion, (d) developing water erosion policies, and (e) continuously monitoring the impact of erosion and the influencing processes from local, national and international levels. N2 - In den letzten Jahrzehnten ist die Erdbevölkerung mit großer Geschwindigkeit gewachsen. Das hatte eine verstärkte Urbanisierung zur Folge, insbesondere in den Entwicklungsländern. Zurzeit lebt über die Hälfte der globalen Bevölkerung in Stadtgebieten, mit steigender Tendenz. Städtewachstum geht mit einem signifikanten Verlust von Vegetationsbedeckung, sowie mit Bodenverdichtung und -versiegelung einher. Diese Faktoren führen bei Starkregenereignissen zu einem hohen Oberflächenabfluss, und zu Problemen durch beschleunigte wasserbedingte Bodenerosion in Straßen und auf Baugelände. In Städten ist eine beschleunigte wasserbedingte Bodenerosion ist ein ernstzunehmendes Umweltproblem, denn sie verursacht eine Verschmutzung der Gewässer, eine verminderte Grundwasserneubildung und erhöhte Landdegradierung. Darüber hinaus kommt es zu erosionsbedingten Schäden in der städtischen Infrastruktur, inklusive der Entwässerungssysteme, sowie an Häusern und Straßen. Für ein nachhaltiges Planen und Management von erosionsanfälligen Städten ist es von essentieller Bedeutung, die Probleme der Wassererosion in städtischen Gebieten zu verstehen. Trotz der großen Anzahl wissenschaftlicher Studien über Wassererosion in ländlichen Gegenden bleibt unser Verständnis der zu Grunde liegenden Erosionsdynamiken in urbanen Trockengebieten unzureichend. Diese Studie zielt darauf ab, Wassererosion, sowie die dazu beitragenden sozio-ökologischen Faktoren, in einem typischen urbanen Trockengebiet zu erfassen. Hierzu wurde ein fachübergreifender Ansatz am Fallbeispiel der Stadt Windhoek, Namibia, gewählt. Die Arbeit umfasst eine detaillierte Literaturanalyse der aktuellen Forschungsansätze zur urbanen Wassererosion und den damit verbundenen Herausforderungen. Außerdem wurde eine feldstudienbasierte Methode entwickelt, mit der das Ausmaß der Wassererosion in der Stadt Windhoek quantifiziert und räumlich erfasst wurde. Schließlich wurden persönliche Befragungen mit halbstrukturierten Fragebögen durchgeführt, um die Wahrnehmung der verschiedenen Interessenvertreter zum Thema Erosion in Stadtgebieten zu analysieren. Die Literaturanalyse hat gezeigt, dass 64% der untersuchten Studien in der entwickelten Welt durchgeführt wurden und nur sehr wenige Regionen mit extremen Klimabedingungen, einschließlich Trockengebieten, untersucht wurden. Hinzu kommt, dass die verwendeten Methoden zur Erosionsquantifizierung und -beobachtung die für urbane Gebiete typischen Merkmale nicht beinhalten und dafür auch nicht ausgerichtet sind. Des Weiteren mangelt es der untersuchten Literatur an Ansätzen, die den Einfluss des Klimawandels und politische Aspekte in Bezug auf Erosion in Stadtgebieten thematisieren. In einer Feldstudie wurde das Ausmaß von Wassererosion in der trocken gelegenen Stadt Windhoek quantifiziert und räumlich erfasst. Beinahe 56% der Stadt waren von Wassererosion betroffen und wiesen Anzeichen beschleunigter Erosion in Form von Rinnen und Rillen auf. Letztere traten vor allem in den unterentwickelten, informellen und semi-formellen Stadtgebieten auf. Das Ausmaß der Erosion in Windhoek wurde unter anderem von der Vegetationsbedeckung und dem Vegetationstyp, von sozial-urbanen Faktoren, und zu einem geringeren Grad von dem geschätzten Gefälle bestimmt. Der Vergleich einer interpolierten feldstudienbasierten Erosionskarte mit Ergebnissen, die auf einer konventionellen Methode zur Erosionserfassung (der Allgemeinen Bodenabtragsgleichung (ABAG)) basieren, ergab eine starke Abweichung in den räumlichen Mustern. Das verdeutlicht die Unzulänglichkeit einer direkten Übertragung von traditionellen nicht-urbanen Methoden zur Erosionserfassung auf ein urbanes Umfeld und betont die Notwendigkeit, neue Methoden sowohl zur Erfassung als auch zum Management von Erosion für urbane Gebiete zu entwickeln. Aus der großen Variabilität des Erosionsausmaßes innerhalb der Stadt lässt sich folgern, dass Methoden zur Kontrolle von Wassererosion in Städten standortspezifisch sein sollten. Anhand von halbstrukturierten Fragebögen wurde in einem weiteren Teil der Arbeit die Wahrnehmung und das Verständnis der unterschiedlichen Interessenvertreter zum Thema urbane Wassererosion in Windhoek untersucht. Insgesamt wurden 41 Interessenvertreter zu ihrem Verständnis der Wassererosionsdynamiken, zu ihrer Wahrnehmung in Bezug auf mögliche Ursachen und zum Ausmaß der Erosionsschäden, sowie zu ihrer Einstellung zur Verantwortlichkeit für die Erosion in der Stadt befragt. Die Ergebnisse deuten darauf hin, dass es eine geringe Wahrnehmung für das Phänomen der Erosion als Prozess gibt, dafür aber eine im Vergleich erhöhte Wahrnehmung der Erosionsschäden und der Faktoren, die zu den Schäden beitragen. Ungefähr 69% der Interessenvertreter stuften die Erosionsschäden als moderat bis sehr ernsthaft ein. Dabei gab es erkennbare Differenzen zwischen der Gruppe der privaten Haushalte und der der öffentlichen Behörden. Des Weiteren hat die Untersuchung ergeben, dass die Interessenvertreter kein klares Verständnis ihrer Verantwortung in Bezug auf das Management der Kontrollmaßnahmen, sowie ihrer finanziellen Verantwortung für die Schäden haben. Die privaten Haushalte und die örtlichen Behörden wiesen sich gegenseitig die Zahlungsverantwortung für die Erosionsschäden und für vorbeugende Maßnahmen zu. Der Unwille der einzelnen Akteure, Verantwortung zu übernehmen, könnte eine Zwickmühle für die betroffenen Gebiete werden. Dies gilt insbesondere für die informellen Siedlungen, in denen von den örtlichen Behörden kein Landmanagement durchgeführt wird, das Land aber auch nicht Eigentum der Bewohnern ist. Abschließend hat die Studie ergeben, dass es für eine effektive Erosionsbekämpfung in der Stadt von ausschlaggebender Bedeutung ist, die verschiedenen, den Prozess der Urbanisierung auf negative Weise verstärkenden Dynamiken, auf ihren unterschiedlichen Skalen zu verstehen. Auf Grundlage der hier präsentierten Ergebnisse wird eine Entwicklung speziell auf Stadtgebiete ausgerichteter Ansätze mit folgenden Zielen dringend nahegelegt: (a) Einer Integration von diversen sozio-ökonomisch-ökologischen Aspekten, die sich auf Erosion auswirken; (b) Einer wissenschaftlich begründeten Verbesserung der natürlichen Kreisläufe, die sich positiv auf die Wasserspeicherung im Boden und die Nährstoffverfügbarkeit für Pflanzen auswirken, um dadurch einen höheren Vegetationsbedeckungsgrad zu erreichen; (c) Der Nutzung hoch aufgelöster Satellitendaten, um die Methoden zur Erosionserfassung für urbane Gebiete zu verbessern; (d) Der Entwicklung politischer Maßnahmen zur Bekämpfung von Wassererosion. KW - urban soil erosion KW - water erosion KW - risk mapping KW - urbane Bodenerosion KW - Wassererosion KW - Risikoabbildung Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-102356 ER - TY - JOUR A1 - Mayer, Magnus C. A1 - Schauenburg, Linda A1 - Thompson-Steckel, Greta A1 - Dunsing, Valentin A1 - Kaden, Daniela A1 - Voigt, Philipp A1 - Schaefer, Michael A1 - Chiantia, Salvatore A1 - Kennedy, Timothy E. A1 - Multhaup, Gerhard T1 - Amyloid precursor-like protein 1 (APLP1) exhibits stronger zinc-dependent neuronal adhesion than amyloid precursor protein and APLP2 JF - Journal of neurochemistry N2 - The amyloid precursor protein (APP) and its paralogs, amyloid precursor-like protein 1 (APLP1) and APLP2, are metalloproteins with a putative role both in synaptogenesis and in maintaining synapse structure. Here, we studied the effect of zinc on membrane localization, adhesion, and secretase cleavage of APP, APLP1, and APLP2 in cell culture and rat neurons. For this, we employed live-cell microscopy techniques, a microcontact printing adhesion assay and ELISA for protein detection in cell culture supernatants. We report that zinc induces the multimerization of proteins of the amyloid precursor protein family and enriches them at cellular adhesion sites. Thus, zinc facilitates the formation of de novo APP and APLP1 containing adhesion complexes, whereas it does not have such influence on APLP2. Furthermore, zinc-binding prevented cleavage of APP and APLPs by extracellular secretases. In conclusion, the complexation of zinc modulates neuronal functions of APP and APLPs by (i) regulating formation of adhesion complexes, most prominently for APLP1, and (ii) by reducing the concentrations of neurotrophic soluble APP/APLP ectodomains. KW - amyloid precursor protein KW - amyloid precursor-like protein KW - neuronal adhesion KW - number and brightness KW - zinc Y1 - 2016 U6 - https://doi.org/10.1111/jnc.13540 SN - 0022-3042 SN - 1471-4159 VL - 137 SP - 266 EP - 276 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Woodhouse, Jason Nicholas A1 - Makower, A. Katharina A1 - Yeung, Anna C. Y. A1 - Ongley, Sarah E. A1 - Micallef, Melinda L. A1 - Moffitt, Michelle C. A1 - Neilan, Brett A. T1 - Advances in genomics, transcriptomics and proteomics of toxin-producing cyanobacteria JF - Environmental microbiology reports N2 - A common misconception persists that the genomes of toxic and non-toxic cyanobacterial strains are largely conserved with the exception of the presence or absence of the genes responsible for toxin production. Implementation of -omics era technologies has challenged this paradigm, with comparative analyses providing increased insight into the differences between strains of the same species. The implementation of genomic, transcriptomic and proteomic approaches has revealed distinct profiles between toxin-producing and non-toxic strains. Further, metagenomics and metaproteomics highlight the genomic potential and functional state of toxic bloom events over time. In this review, we highlight how these technologies have shaped our understanding of the complex relationship between these molecules, their producers and the environment at large within which they persist. Y1 - 2016 U6 - https://doi.org/10.1111/1758-2229.12366 SN - 1758-2229 VL - 8 SP - 3 EP - 13 PB - Wiley-Blackwell CY - Hoboken ER - TY - THES A1 - Geyer, Juliane T1 - Adapting biodiversity conservation management to climate change Y1 - 2016 ER -