TY - JOUR A1 - Rödel, Claudia Jasmin A1 - Otten, Cecile A1 - Donat, Stefan A1 - Lourenço, Marta Sofia Rocha A1 - Fischer, Dorothea A1 - Kuropka, Benno A1 - Paolini, Alessio A1 - Freund, Christian A1 - Abdelilah-Seyfried, Salim T1 - Blood Flow Suppresses Vascular Anomalies in a Zebrafish Model of Cerebral Cavernous Malformations JF - Circulation Research N2 - RATIONALE: Pathological biomechanical signaling induces vascular anomalies including cerebral cavernous malformations (CCM), which are caused by a clonal loss of CCM1/KRIT1 (Krev interaction trapped protein 1), CCM2/MGC4607, or CCM3/PDCD10. Why patients typically experience lesions only in lowly perfused venous capillaries of the cerebrovasculature is completely unknown. OBJECTIVE: In contrast, animal models with a complete loss of CCM proteins lack a functional heart and blood flow and exhibit vascular anomalies within major blood vessels as well. This finding raises the possibility that hemodynamics may play a role in the context of this vascular pathology. METHODS AND RESULTS: Here, we used a genetic approach to restore cardiac function and blood flow in a zebrafish model of CCM1. We find that blood flow prevents cardiovascular anomalies including a hyperplastic expansion within a large Ccm1-deficient vascular bed, the lateral dorsal aorta. CONCLUSIONS: This study identifies blood flow as an important physiological factor that is protective in the cause of this devastating vascular pathology. KW - animal models KW - cerebral cavernous malformations KW - endothelial cell KW - hemodynamics KW - zebrafish Y1 - 2019 U6 - https://doi.org/10.1161/CIRCRESAHA.119.315076 SN - 0009-7330 SN - 1524-4571 VL - 125 IS - 10 SP - E43 EP - E54 PB - Lippincott Williams & Wilkins CY - Philadelphia ER - TY - JOUR A1 - Groth, Detlef A1 - Scheffler, Christiane A1 - Hermanussen, Michael T1 - Body height in stunted Indonesian children depends directly on parental education and not via a nutrition mediated pathway BT - Evidence from tracing association chains by St. Nicolas House Analysis JF - Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft für Anthropologie N2 - Background: Multiple linear correlations between parameters can be shown in correlation matrices. Correlations can be ranked, but can also be visualized in network graphs. Yet, translating a correlation matrix into a network graph is not trivial. In view of a popular child game, we propose to name this method St. Nicolas House Analysis. Material and methods: We present a new method (St. Nicolas House Analysis) that helps translating correlation matrices into network graphs. The performance of this and other network reconstruction methods was tested in randomly created virtual scale-free networks, networks consisting of bands or hubs, using balanced classification rate and the F1-Score for correctly predicting existing and non-existing edges. Thereafter we analyzed anthropometric data and information on parental education, obtained from an anthropometric survey in 908 Indonesian boys and 808 Indonesian girls. Seven parameters were analyzed: child height standard deviation score (hSDS), child BMI standard deviation scores (BMI_SDS), mid-upper-arm circumference (MUAC), mean thickness of subscapular and triceps skinfold (mean SF), and elbow breadth; as well as maternal and paternal education (years of schooling). The parameters were considered as the nodes of the network; the edges represent the correlations between the nodes. Results: Performance measures, balanced classification rate and the F1-score, showed that St. Nicolas’ House Analysis was superior to methods using sophisticated correlation value thresholds and methods based on partial correlations for analyzing bands and hubs. We applied this method also in an Indonesia data set. Ranking correlations showed the direct association between parental education and child growth. Conclusion: St. Nicolas House Analysis confirmed that growth of Indonesian school children directly depends on maternal education, with no evidence that this effect is mediated by the state of nutrition. Y1 - 2019 U6 - https://doi.org/10.1127/anthranz/2019/1027 SN - 0003-5548 VL - 76 IS - 5 SP - 445 EP - 451 PB - Schweizerbart CY - Stuttgart ER - TY - JOUR A1 - Duydu, Yalcin A1 - Basaran, Nursen A1 - Yalcin, Can Özgür A1 - Ustundag, Aylin A1 - Aydin, Sevtap A1 - Anlar, Hatice Gul A1 - Bacanli, Merve A1 - Aydos, Kaan A1 - Atabekoglu, Cem Somer A1 - Golka, Klaus A1 - Ickstadt, Katja A1 - Schwerdtle, Tanja A1 - Werner, Matthias A1 - Bolt, Hermann M. T1 - Boron-exposed male workers in Turkey BT - no change in sperm Y:X chromosome ratio and in offspring's sex ratio JF - Archives of toxicology : official journal of EUROTOX N2 - Boron-associated shifts in sex ratios at birth were suggested earlier and attributed to a decrease in Y- vs. X-bearing sperm cells. As the matter is pivotal in the discussion of reproductive toxicity of boron/borates, re-investigation in a highly borate-exposed population was required. In the present study, 304 male workers in Bandirma and Bigadic (Turkey) with different degrees of occupational and environmental exposure to boron were investigated. Boron was quantified in blood, urine and semen, and the persons were allocated to exposure groups along B blood levels. In the highest ("extreme") exposure group (n = 69), calculated mean daily boron exposures, semen boron and blood boron concentrations were 44.91 +/- 18.32 mg B/day, 1643.23 +/- 965.44 ng B/g semen and 553.83 +/- 149.52 ng B/g blood, respectively. Overall, an association between boron exposure and Y:X sperm ratios in semen was not statistically significant (p > 0.05). Also, the mean Y:X sperm ratios in semen samples of workers allocated to the different exposure groups were statistically not different in pairwise comparisons (p > 0.05). Additionally, a boron-associated shift in sex ratio at birth towards female offspring was not visible. In essence, the present results do not support an association between boron exposure and decreased Y:X sperm ratio in males, even under extreme boron exposure conditions. KW - Paternal exposure KW - Boron exposure KW - Y:X chromosome ratio KW - Sex ratio at birth Y1 - 2019 U6 - https://doi.org/10.1007/s00204-019-02391-z SN - 0340-5761 SN - 1432-0738 VL - 93 IS - 3 SP - 743 EP - 751 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Klopsch, Rebecca A1 - Baldermann, Susanne A1 - Hanschen, Franziska S. A1 - Voss, Alexander A1 - Rohn, Sascha A1 - Schreiner, Monika A1 - Neugart, Susanne T1 - Brassica-enriched wheat bread: Unraveling the impact of ontogeny and breadmaking on bioactive secondary plant metabolites of pak choi and kale JF - Food chemistry N2 - Consumption of Brassica vegetables is linked to health benefits, as they contain high concentrations of the following secondary plant metabolites (SPMs): glucosinolate breakdown products, carotenoids, chlorophylls, and phenolic compounds. Especially Brassica vegetables are consumed as microgreens (developed cotyledons). It was investigated how different ontogenetic stages (microgreens or leaves) of pak choi (Brassica rapa subsp. chinensis) and kale (Brassica oleracea var. sabellica) differ in their SPM concentration. The impact of breadmaking on SPMs in microgreens (7 days) and leaves (14 days) in pak choi and kale as a supplement in mixed wheat bread was assessed. In leaves, carotenoids, chlorophylls, and phenolic compounds were higher compared to those of microgreens. Breadmaking caused a decrease of SPMs. Chlorophyll degradation was observed, leading to pheophytin and pyropheophytin formation. In kale, sinapoylgentiobiose, a hydroxycinnamic acid derivative, concentration increased. Thus, leaves of Brassica species are suitable as natural ingredients for enhancing bioactive SPM concentrations in bread. KW - Ontogeny KW - Brassica KW - Glucosinolate breakdown product KW - Flavonoid KW - Carotenoid KW - Thermal processing Y1 - 2019 U6 - https://doi.org/10.1016/j.foodchem.2019.05.113 SN - 0308-8146 SN - 1873-7072 VL - 295 SP - 412 EP - 422 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Frommhold, Martin A1 - Heim, Arend A1 - Barabanov, Mikhail A1 - Maier, Franziska A1 - Mühle, Ralf-Udo A1 - Smirenski, Sergei M. A1 - Heim, Wieland T1 - Breeding habitat and nest-site selection by an obligatory "nest-cleptoparasite", the Amur Falcon Falco amurensis JF - Ecology and evolution N2 - The selection of a nest site is crucial for successful reproduction of birds. Animals which re-use or occupy nest sites constructed by other species often have limited choice. Little is known about the criteria of nest-stealing species to choose suitable nesting sites and habitats. Here, we analyze breeding-site selection of an obligatory "nest-cleptoparasite", the Amur Falcon Falco amurensis. We collected data on nest sites at Muraviovka Park in the Russian Far East, where the species breeds exclusively in nests of the Eurasian Magpie Pica pica. We sampled 117 Eurasian Magpie nests, 38 of which were occupied by Amur Falcons. Nest-specific variables were assessed, and a recently developed habitat classification map was used to derive landscape metrics. We found that Amur Falcons chose a wide range of nesting sites, but significantly preferred nests with a domed roof. Breeding pairs of Eurasian Hobby Falco subbuteo and Eurasian Magpie were often found to breed near the nest in about the same distance as neighboring Amur Falcon pairs. Additionally, the occurrence of the species was positively associated with bare soil cover, forest cover, and shrub patches within their home range and negatively with the distance to wetlands. Areas of wetlands and fallow land might be used for foraging since Amur Falcons mostly depend on an insect diet. Additionally, we found that rarely burned habitats were preferred. Overall, the effect of landscape variables on the choice of actual nest sites appeared to be rather small. We used different classification methods to predict the probability of occurrence, of which the Random forest method showed the highest accuracy. The areas determined as suitable habitat showed a high concordance with the actual nest locations. We conclude that Amur Falcons prefer to occupy newly built (domed) nests to ensure high nest quality, as well as nests surrounded by available feeding habitats. KW - cleptoparasitism KW - fire KW - habitat use KW - machine learning KW - magpie KW - nest-site selection KW - random forest Y1 - 2019 U6 - https://doi.org/10.1002/ece3.5878 SN - 2045-7758 VL - 9 IS - 24 SP - 14430 EP - 14441 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Lozada Gobilard, Sissi Donna A1 - Weigend, M. A1 - Fischer, E. A1 - Janssens, S. B. A1 - Ackermann, M. A1 - Abrahamczyk, Stefan T1 - Breeding systems in Balsaminaceae in relation to pollen/ovule ratio, pollination syndromes, life history and climate zone JF - Plant biology N2 - Pollen/ovule (P/O) ratios are often used as proxy for breeding systems. Here, we investigate the relations between breeding systems and P/O ratios, pollination syndromes, life history and climate zone in Balsaminaceae. We conducted controlled breeding system experiments (autonomous and active self-pollination and outcrossing tests) for 65 Balsaminaceae species, analysed pollen grain and ovule numbers and evaluated the results in combination with data on pollination syndrome, life history and climate zone on a phylogenetic basis. Based on fruit set, we assigned three breeding systems: autogamy, self-compatibility and self-incompatibility. Self-pollination led to lower fruit set than outcrossing. We neither found significant P/O differences between breeding systems nor between pollination syndromes. However, the numbers of pollen grains and ovules per flower were significantly lower in autogamous species, but pollen grain and ovule numbers did not differ between most pollination syndromes. Finally, we found no relation between breeding system and climate zone, but a relation between climate zone and life history. In Balsaminaceae reproductive traits can change under resource or pollinator limitation, leading to the evolution of autogamy, but are evolutionary rather constant and not under strong selection pressure by pollinator guild and geographic range changes. Colonisation of temperate regions, however, is correlated with transitions towards annual life history. Pollen/ovule-ratios, commonly accepted as good indicators of breeding system, have a low predictive value in Balsaminaceae. In the absence of experimental data on breeding system, additional floral traits (overall pollen grain and ovule number, traits of floral morphology) may be used as proxies. KW - Annual KW - autogamy KW - cleistogamy KW - evolution KW - fly pollination KW - Impatiens KW - outcrossing KW - perennial KW - self-incompatibility KW - temperate KW - tropical Y1 - 2018 U6 - https://doi.org/10.1111/plb.12905 SN - 1435-8603 SN - 1438-8677 VL - 21 IS - 1 SP - 157 EP - 166 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Staszek, Pawel A1 - Krasuska, Urszula A1 - Otulak-Koziel, Katarzyna A1 - Fettke, Jörg A1 - Gniazdowska, Agnieszka T1 - Canavanine-Induced Decrease in Nitric Oxide Synthesis Alters Activity of Antioxidant System but Does Not Impact S-Nitrosoglutathione Catabolism in Tomato Roots JF - Frontiers in plant science N2 - Canavanine (CAN) is a nonproteinogenic amino acid synthesized in legumes. In mammalians, as arginine analogue, it is an inhibitor of nitric oxide synthase (NOS) activity. The aim of this study was to investigate the impact of CAN-induced nitric oxide level limitation on the antioxidant system and S-nitrosoglutathione (GSNO) metabolism in roots of tomato seedlings. Treatment with CAN (10 or 50 mu M) for 24-72 h led to restriction in root growth. Arginine-dependent NOS-like activity was almost completely inhibited, demonstrating direct effect of CAN action. CAN increased total antioxidant capacity and the level of sulphydryl groups. Catalase (CAT) and superoxide dismutase (SOD) activity decreased in CAN exposed roots. CAN supplementation resulted in the decrease of transcript levels of genes coding CAT (with the exception of CAT1). Genes coding SOD (except MnSOD and CuSOD) were upregulated by CAN short treatment; prolonged exposition to 50-mu M CAN resulted in downregulation of FeSOD, CuSOD, and SODP-2. Activity of glutathione reductase dropped down after short-term (10-mu M CAN) supplementation, while glutathione peroxidase activity was not affected. Transcript levels of glutathione reductase genes declined in response to CAN. Genes coding glutathione peroxidase were upregulated by 50-mu M CAN, while 10-mu M CAN downregulated GSHPx1. Inhibition of NOS-like activity by CAN resulted in lower GSNO accumulation in root tips. Activity of GSNO reductase was decreased by short-term supplementation with CAN. In contrast, GSNO reductase protein abundance was higher, while transcript levels were slightly altered in roots exposed to CAN. This is the first report on identification of differentially nitrated proteins in response to supplementation with nonproteinogenic amino acid. Among nitrated proteins differentially modified by CAN, seed storage proteins (after short-term CAN treatment) and components of the cellular redox system (after prolonged CAN supplementation) were identified. The findings demonstrate that due to inhibition of NOS-like activity, CAN leads to modification in antioxidant system. Limitation in GSNO level is due to lower nitric oxide formation, while GSNO catabolism is less affected. We demonstrated that monodehydroascorbate reductase, activity of which is inhibited in roots of CAN-treated plants, is the protein preferentially modified by tyrosine nitration. KW - canavanine KW - cellular antioxidant system KW - GSNOR-GSNO reductase KW - nitrated proteins KW - nitric oxide-NO KW - nonproteinogenic amino acid KW - NOS-like activity KW - reactive nitrogen species (RNS) Y1 - 2019 U6 - https://doi.org/10.3389/fpls.2019.01077 SN - 1664-462X VL - 10 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Schorn, Sina A1 - Salman-Carvalho, Verena A1 - Littmann, Sten A1 - Ionescu, Danny A1 - Grossart, Hans-Peter A1 - Cypionka, Heribert T1 - Cell architecture of the giant sulfur bacterium achromatium oxaliferum BT - Extra-cytoplasmic localization of calcium carbonate bodies JF - FEMS Microbiology Ecology N2 - Achromatium oxaliferum is a large sulfur bacterium easily recognized by large intracellular calcium carbonate bodies. Although these bodies often fill major parts of the cells' volume, their role and specific intracellular location are unclear. In this study, we used various microscopy and staining techniques to identify the cell compartment harboring the calcium carbonate bodies. We observed that Achromatium cells often lost their calcium carbonate bodies, either naturally or induced by treatments with diluted acids, ethanol, sodium bicarbonate and UV radiation which did not visibly affect the overall shape and motility of the cells (except for UV radiation). The water-soluble fluorescent dye fluorescein easily diffused into empty cavities remaining after calcium carbonate loss. Membranes (stained with Nile Red) formed a network stretching throughout the cell and surrounding empty or filled calcium carbonate cavities. The cytoplasm (stained with FITC and SYBR Green for nucleic acids) appeared highly condensed and showed spots of dissolved Ca2+ (stained with Fura-2). From our observations, we conclude that the calcium carbonate bodies are located in the periplasm, in extra-cytoplasmic pockets of the cytoplasmic membrane and are thus kept separate from the cell's cytoplasm. This periplasmic localization of the carbonate bodies might explain their dynamic formation and release upon environmental changes. KW - sulfur-bacteria KW - calcium carbonate inclusions KW - extra-cytoplasmic pockets KW - calcite Y1 - 2019 U6 - https://doi.org/10.1093/femsec/fiz200 SN - 1574-6941 VL - 96 IS - 2 SP - 1 EP - 8 PB - Oxford University Press CY - Oxford ER - TY - THES A1 - Taube, Robert T1 - Characterisations of Fungal Communities in Temperate Lakes BT - with focus on diversity, abundance and methodological aspects of quantifying abundance Y1 - 2019 ER - TY - JOUR A1 - Numberger, Daniela A1 - Ganzert, Lars A1 - Zoccarato, Luca A1 - Mühldorfer, Kristin A1 - Sauer, Sascha A1 - Grossart, Hans-Peter A1 - Greenwood, Alex D. T1 - Characterization of bacterial communities in wastewater with enhanced taxonomic resolution by full-length 16S rRNA sequencing JF - Scientific reports N2 - Wastewater treatment is crucial to environmental hygiene in urban environments. However, wastewater treatment plants (WWTPs) collect chemicals, organic matter, and microorganisms including pathogens and multi-resistant bacteria from various sources which may be potentially released into the environment via WWTP effluent. To better understand microbial dynamics in WWTPs, we characterized and compared the bacterial community of the inflow and effluent of a WWTP in Berlin, Germany using full-length 16S rRNA gene sequences, which allowed for species level determination in many cases and generally resolved bacterial taxa. Significantly distinct bacterial communities were identified in the wastewater inflow and effluent samples. Dominant operational taxonomic units (OTUs) varied both temporally and spatially. Disease associated bacterial groups were efficiently reduced in their relative abundance from the effluent by the WWTP treatment process, except for Legionella and Leptospira species which demonstrated an increase in relative proportion from inflow to effluent. This indicates that WWTPs, while effective against enteric bacteria, may enrich and release other potentially pathogenic bacteria into the environment. The taxonomic resolution of full-length 16S rRNA genes allows for improved characterization of potential pathogenic taxa and other harmful bacteria which is required to reliably assess health risk. Y1 - 2019 U6 - https://doi.org/10.1038/s41598-019-46015-z SN - 2045-2322 VL - 9 PB - Nature Publ. Group CY - London ER - TY - THES A1 - Riedel, Simona T1 - Characterization of Mitochondrial ABC Transporter Homologues in Rhodobacter capsulatus T1 - Charakterisierung von Homologen zu mitochondrialen ABC Transportern in Rhodobacter capsulatus N2 - ABC-Transporter (ABC abgeleitet von ATP-Binding Cassette) gehören zur Klasse der Transmembran-Proteine und kommen in allen drei Domänen des Lebens vor. Ihr struktureller Aufbau ist dabei stets ähnlich, wohingegen konservierte Proteinsequenzen selten vorkommen. Die Transporter sind aus zwei lipophilen, membran-durchspannenden Domänen, welche auch TMDs (abgeleitet von Transmembrane spanning Domains) genannt werden, und zwei hydrophilen Domänen, die auch NBDs (abgeleitet von Nucleotide Binding Domains) genannt werden, aufgebaut. Die Vielzahl der durch ABC-Transporter beförderten Moleküle erklärt dabei die enorme Anzahl diverser TMDs. In den Mitochondrien des Menschen findet man vier ABC-Transporter (ABCB6, ABCB7, ABCB8 und ABCB10) mit funktionellen Homologen in Hefen und Pflanzen. In Bakterien hingegen können, mit Ausnahme von Rickettsiae und verwandten Bakterien, keine Homologen zu mitochondrialen ABC-Transportern identifiziert werden. Die transportierten Moleküle sowie die damit verbundenen Funktionen sind im Einzelnen bislang weitgehend unbekannt. ABCB7 und die entsprechenden Homologen in Hefen (Atm1) und in Pflanzen (ATM3) konnten mit der cytosolischen Eisen-Schwefel-Cluster-Biosynthese in Zusammenhang gebracht werden. Eine schwefelhaltige Verbindung der mitochondrialen Matrix wird mit Hilfe dieses Transporters der cytosolischen Eisen-Schwefel-Cluster-Assemblierung zur Verfügung gestellt. Die 2014 publizierten Kristallstrukturen von Atm1 (Hefe) und Atm1 aus Novosphingobium aromaticivorans offenbarten dabei eine hoch konservierte Glutathion-Bindetasche innerhalb der TMDs für ABCB7 Homologe. In der Modellpflanze Arabidopsis thaliana konnte ATM3 zusätzlich mit der Biosynthese des Molybdän-Cofaktors in Verbindung gebracht werden. In der vorliegenden Arbeit wurde das α-Proteobacterium Rhodobacter capsulatus als Modellorganismus genutzt, um mitochondriale ABC-Transporter Homologe zu untersuchen. Das Bakterium enthält zwei ABC-Transporter-Gene, rcc03139 und rcc02305, die mit den humanen mitochondrialen Transportern große Sequenzübereinstimmungen aufweisen (rcc03139: 41 % respektive 38 % Identität mit ABCB8 und ABCB10, rcc02305: 47 % identisch mit ABCB7 und ABCB6). Mit Hilfe erzeugter Interposon-Mutanten (Δrcc02305I und Δrcc03139I) konnte erstmals gezeigt werden, dass bakterielle Transporter funktionell sehr ähnliche Aufgaben wie die mitochondrialen ABC-Transporter übernehmen. Beispielsweise akkumulierten beide Interposon-Mutanten reaktive Sauerstoff-Spezies (ROS) ohne gleichzeitige Akkumulation von Glutathion oder Eisen. Weiterhin konnten wir zeigen, dass, ähnlich wie bereits für ATM3 postuliert, die Biosynthese des Molybdän-Cofaktors in Δrcc02305I verändert ist. Mit Hilfe einer lebensfähigen Doppelmutante, in der beide ABC-Transporter-Gene gleichzeitig deletiert wurden, konnten wir ausschließen, dass die beiden bakteriellen ABC-Transporter grundsätzlich redundante Funktionen haben. Durch die Analyse des Proteoms von Δrcc03139I im Vergleich zu der des Wildtyps, konnte eine extreme Beeinflussung der Tetrapyrrol Biosynthese sowie entsprechender Zielproteine identifiziert werden. Dies konnte zusätzlich durch die Quantifizierung einzelner Zwischenprodukte der Biosynthese bestätigt werden. Im Gegensatz dazu konnte anhand der Analyse des Proteoms in Verbindung mit analytischen Methoden in Δrcc02305I ein Ungleichgewicht in der Schwefelverteilung identifiziert werden. Zusammen mit der Entdeckung einer Pyridoxalphosphat (PLP) Bindestelle in Rcc02305 und anderen ABCB7-artigen Transportern, welche direkt mit dem Walker-A-Motiv der NBD überlappt, ermöglichte dies eine völlig neue Theorie, wie die schwefelhaltige Verbindung transportiert werden kann. Wir gehen davon aus, dass an PLP zunächst ein Persulfid produziert wird, welches unmittelbar mit dem Glutathion der transmembranen Bindetasche zu einem gemischten Polysulfid reagiert. Im Anschluss daran wird die ATP-Bindestelle frei und die Hydrolyse des ATPs löst eine Konformationsänderung aus, welche das gemischte Polysulfid ins Periplasma bzw. in den intermembranen Raum freigibt. N2 - ATP-binding cassette (ABC) transporters are present in all kingdoms of life and enable active transport of various different molecules across biological membranes. They all share an overall architecture of two lipophilic transmembrane spanning domains (TMDs) traversing the membrane and two hydrophilic nucleotide binding domains (NBDs) usually lacking sequence identity. The multiplicity in transported molecules is accompanied by extreme diversity in TMDs. Human mitochondria harbor four ABC transporters, namely ABCB6, ABCB7, ABCB8 and ABCB10 with functional homologues in yeast and plants. Except the ones found in Rickettsiae and related bacteria mitochondrial ABC transporters are absent in bacteria. In addition to converting energy mitochondria are important platforms for biosynthesizing various cofactors as iron sulfur clusters, molybdenum cofactor (Moco) or heme. ABCB7 (Atm1 in yeast) has been shown to connect mitochondrial with cytosolic iron sulfur cluster assembly by exporting a yet unknown sulfur containing molecule. In addition, TMDs of Atm1 display a glutathione binding pocket accessible from the matrix which has been identified in all ABCB7-like transporters and also exists in a bacterial ABC transporter homologue of Atm1 in Novosphingobium aromaticivorans. In addition, ATM3, a plant mitochondrial homologous ABC transporter to human ABCB7, has been associated with biosynthesizing Moco. In this study we used the α-proteobacterium Rhodobacter capsulatus as a model organism to characterize mitochondrial ABC transporter homologues. R. capsulatus contains two homologues to mitochondrial ABC transporters with the corresponding gene loci rcc03139 and rcc02305. They share 38 to 47 % sequence identities to human mitochondrial ABC transporters ABCB8/ABCB10 and ABCB7/ABCB6, respectively. We created interposon mutants lacking either rcc03139 or rcc02305, analyzed the physiological effects on R. capsulatus and compared the findings especially to eukaryotic deletion studies. A viable bacterial double mutant strain lacking both mitochondrial ABC transporters was constructed to investigate possible overlapping functions. Both R. capsulatus single mutants showed a severe accumulation of intracellular reactive oxygen species (ROS) in comparison to ∆nifDK which revealed to be additive in the double mutant. In the proteome of ∆rcc03139I abundancies of tetrapyrrole related proteins were significantly increased in comparison to the proteome of parental strain, which was further validated by reduced amounts of tetrapyrrole intermediates in ∆rcc03139. In contrast, in ∆rcc02305I total glutathione (GSH) was elevated when endogenous GSH biosynthesis was inhibited. In conjunction with proteomic studies we uncovered misbalanced sulfur distribution in ∆rcc02305I. Furthermore, strains lacking Rcc02305 accumulated cyclic pyranopterin monophosphate (cPMP), an intermediate of Moco biosynthesis, as it was already shown for the deletion strain of the eukaryotic counterpart ATM3 in plants. In contrast single mutant strain Δrcc03139I neither accumulated cPMP nor glutathione. Bioinformatic analysis of the amino acid sequence of Rcc02305 revealed a pyridoxal 5´phosphate (PLP) binding site which overlaps with Walker A within the NBDs of Rcc02305 and other ABCB7-like transporters. The PLP cofactor is well studied in C-DES (L-cysteine/cystine lyase from Synechocystis) for persulfide production and in L-cysteine desulfurases such as IscS and NFS1 for its role in formation of protein-bound persulfides. Based on our findings we are able to propose a new modality for the transport of the sulfur containing molecule: first of all, the transporter produces a highly reactive persulfide which is then subsequently trapped by glutathione polysulfide, already bound within the binding pocket in TMDs. Walker A becomes accessible for ATP and after hydrolysis the mixed polysulfide is released. Based on our studies we are convinced that both mitochondrial ABC transporter homologues fulfil distinct roles in R. capsulatus: Rcc02305 is a representative of Atm1/ABCB7-like transporters and important for proper sulfur distribution by exporting persulfides. In contrast Rcc03139 is a representative of ABCB6/ABCB10 related transporters and involved in biosynthesizing tetrapyrroles. KW - Rhodobacter capsulatus KW - ABC Transporter KW - ABCB7 KW - Mitochondrien KW - PLP-Walker A-Überlagerung KW - Rhodobacter capsulatus KW - ABC transporter KW - ABCB7 KW - mitochondria KW - PLP-Walker A-overlap Y1 - 2019 ER - TY - JOUR A1 - Hoffmann, Stefan A. A1 - Hao, Nan A1 - Shearwin, Keith E. A1 - Arndt, Katja Maren T1 - Characterizing transcriptional interference between converging genes in bacteria JF - ACS synthetic biology N2 - Antisense transcription is common in naturally occurring genomes and is increasingly being used in synthetic genetic circuitry as a tool for gene expression control. Mutual influence on the expression of convergent genes can be mediated by antisense RNA effects and by transcriptional interference (TI). We aimed to quantitatively characterize long-range TI between convergent genes with untranslated intergenic spacers of increasing length. After controlling for antisense RNA-mediated effects, which contributed about half of the observed total expression inhibition, the TI effect was modeled. To achieve model convergence, RNA polymerase processivity and collision resistance were assumed to be modulated by ribosome trailing. The spontaneous transcription termination rate in regions of untranslated DNA was experimentally determined. Our modeling suggests that an elongating RNA polymerase with a trailing ribosome is about 13 times more likely to resume transcription than an opposing RNA polymerase without a trailing ribosome, upon head-on collision of the two. KW - gene regulation KW - antisense transcription KW - transcriptional interference KW - mathematical modeling KW - Escherichia coli Y1 - 2019 U6 - https://doi.org/10.1021/acssynbio.8b00477 SN - 2161-5063 VL - 8 IS - 3 SP - 466 EP - 473 PB - American Chemical Society CY - Washington ER - TY - THES A1 - Schwuchow, Viola T1 - Charakterisierung der periplasmatischen Aldehyd-Oxidoreduktase (PaoABC) aus Escherichia coli N2 - Im Mittelpunkt dieser Arbeit standen Analysen zur Charakterisierung der periplasmatischen Aldehyd Oxidoreduktase aus E. coli. Kinetische Untersuchungen mit Ferricyanid als Elektronenakzeptor unter anaeroben Bedingungen zeigten für dieses Enzym eine höhere Aktivität als unter aeroben Bedingungen. Die getroffene Hypothese, dass PaoABC fähig ist Elektronen an molekularen Sauerstoff weiter zu geben, konnte bestätigt werden. Für den Umsatz aromatischer Aldehyde mit molekularem Sauerstoff wurde ein Optimum von pH 6,0 ermittelt. Dies steht im Gegensatz zur Reaktion mit Ferricyanid, mit welchem ein pH-Optimum von 4,0 gezeigt wurde. Die Reaktion von PaoABC mit molekularem Sauerstoff generiert zwar Wasserstoffperoxid, die Produktion von Superoxid konnte dagegen nicht beobachtet werden. Dass aerobe Bedingungen einen Einfluss auf das Auslösen der Expression von PaoABC haben, wurde in dieser Arbeit ebenfalls ermittelt. Im Zusammenhang mit der Produktion von ROS durch PaoABC wurde die Funktion eines kürzlich in Elektronentransfer-Distanz zum FAD identifizierten [4Fe4S]-Clusters untersucht. Ein Austausch der für die Bindung des Clusters zuständigen Cysteine führte zur Instabilität der Proteinvarianten, weswegen für diese keine weiteren Untersuchungen erfolgten. Daher wird zumindest ein struktur-stabilisierender Einfluss des [4Fe4S]-Clusters angenommen. Zur weiteren Untersuchung der Funktion dieses Clusters, wurde ein zwischen FAD und [4Fe4S]-Cluster lokalisiertes Arginin gegen ein Alanin ausgetauscht. Diese Proteinvariante zeigte eine reduzierte Geschwindigkeit der Reaktion gegenüber dem Wildtyp. Die Bildung von Superoxid konnte auch hier nicht beobachtet werden. Die Vermutung, dass dieser Cluster einen elektronen-sammelnden Mechanismus unterstützt, welcher die Radikalbildung verhindert, kann trotz allem nicht ausgeschlossen werden. Da im Umkreis des Arginins weitere geladene und aromatische Aminosäuren lokalisiert sind, können diese den notwendigen Elektronentransfer übernehmen. Neben der Ermittlung eines physiologischen Elektronenakzeptors und dessen Einfluss auf die Expression von PaoABC zeigt diese Arbeit auch, dass die Chaperone PaoD und MocA während der Reifung des MCD-Kofaktor eine gemeinsame Bindung an PaoABC realisieren. Es konnte im aktiven Zentrum von PaoABC ein Arginin beschrieben werden, welches auf Grund der engen Nachbarschaft zum MCD-Kofaktor und zum Glutamat (PaoABC-EC692) am Prozess der Substratbindung beteiligt ist. Im Zusammenhang mit dem Austausch dieses Arginins gegen ein Histidin oder ein Lysin wurden die Enzymspezifität und der Einfluss physiologischer Bedingungen, wie pH und Ionenstärke, auf die Reaktion des Enzyms untersucht. Gegenüber dem Wildtyp zeigten die Varianten mit molekularem Sauerstoff eine geringere Affinität zum Substrat aber auch eine höhere Geschwindigkeit der Reaktion. Vor allem für die Histidin-Variante konnte im gesamten pH-Bereich ein instabiles Verhalten bestimmt werden. Der Grund dafür wurde durch das Lösen der Struktur der Histidin-Variante beschreiben. Durch den Austausch der Aminosäuren entfällt die stabilisierende Wirkung der delokalisierten Elektronen des Arginins und es kommt zu einer Konformationsänderung im aktiven Zentrum. Neben der Reaktion von PaoABC mit einer Vielzahl aromatischer Aldehyde konnte auch der Umsatz von Salicylaldehyd zu Salicylsäure durch PaoABC in einer Farbreaktion bestimmt werden. Durch Ausschluss von molekularem Sauerstoff als terminaler Elektronenakzeptor, in einer enzym-gekoppelten Reaktion, erfolgte ein Elektronentransport auf Ferrocencarboxylsäure. Die Kombination aus beiden Methoden ermöglichte eine Verwendung von Ferrocen-Derivaten zur Generierung einer enzym-gekoppelten Reaktion mit PaoABC. Die Untersuchungen zu PaoABC zeigen, dass die Vielfalt der durch das Enzym katalysierten Rektionen weitere Möglichkeiten der enzymatischen Bestimmung biokatalytischer Prozesse bietet. KW - Eschericha coli KW - Periplasma KW - Aldehydoxidase KW - Aldehyd KW - Oxidoreduktase KW - Molybdän Y1 - 2019 ER - TY - JOUR A1 - Codutti, Agnese A1 - Bente, Klaas A1 - Faivre, Damien A1 - Klumpp, Stefan T1 - Chemotaxis in external fields: Simulations for active magnetic biological matter JF - PLoS Computational Biology : a new community journal N2 - The movement of microswimmers is often described by active Brownian particle models. Here we introduce a variant of these models with several internal states of the swimmer to describe stochastic strategies for directional swimming such as run and tumble or run and reverse that are used by microorganisms for chemotaxis. The model includes a mechanism to generate a directional bias for chemotaxis and interactions with external fields (e.g., gravity, magnetic field, fluid flow) that impose forces or torques on the swimmer. We show how this modified model can be applied to various scenarios: First, the run and tumble motion of E. coli is used to establish a paradigm for chemotaxis and investigate how it is affected by external forces. Then, we study magneto-aerotaxis in magnetotactic bacteria, which is biased not only by an oxygen gradient towards a preferred concentration, but also by magnetic fields, which exert a torque on an intracellular chain of magnets. We study the competition of magnetic alignment with active reorientation and show that the magnetic orientation can improve chemotaxis and thereby provide an advantage to the bacteria, even at rather large inclination angles of the magnetic field relative to the oxygen gradient, a case reminiscent of what is expected for the bacteria at or close to the equator. The highest gain in chemotactic velocity is obtained for run and tumble with a magnetic field parallel to the gradient, but in general a mechanism for reverse motion is necessary to swim against the magnetic field and a run and reverse strategy is more advantageous in the presence of a magnetic torque. This finding is consistent with observations that the dominant mode of directional changes in magnetotactic bacteria is reversal rather than tumbles. Moreover, it provides guidance for the design of future magnetic biohybrid swimmers. Author summary In this paper, we propose a modified Active Brownian particle model to describe bacterial swimming behavior under the influence of external forces and torques, in particular of a magnetic torque. This type of interaction is particularly important for magnetic biohybrids (i.e. motile bacteria coupled to a synthetic magnetic component) and for magnetotactic bacteria (i.e. bacteria with a natural intracellular magnetic chain), which perform chemotaxis to swim along chemical gradients, but are also directed by an external magnetic field. The model allows us to investigate the benefits and disadvantages of such coupling between two different directionality mechanisms. In particular we show that the magnetic torque can speed chemotaxis up in some conditions, while it can hinder it in other cases. In addition to an understanding of the swimming strategies of naturally magnetotactic organisms, the results may guide the design of future biomedical devices. Y1 - 2019 U6 - https://doi.org/10.1371/journal.pcbi.1007548 SN - 1553-734X SN - 1553-7358 VL - 15 IS - 12 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Plikk, Anna A1 - Engels, Stefan A1 - Luoto, Tomi P. A1 - Nazarova, Larisa B. A1 - Salonen, J. Sakari A1 - Helmens, Karin F. T1 - Chironomid-based temperature reconstruction for the Eemian Interglacial (MIS 5e) at Sokli, northeast Finland JF - Journal of paleolimnology N2 - The Last Interglacial (Eemian, MIS 5e) can be considered a test-bed for climate dynamics under a warmer-than-present climate. In this study we present a chironomid record from the high latitude Sokli site (N Finland), where a long continuous sediment sequence from the last interglacial has been preserved from glacial erosion. The chironomid-analysis shows a diverse fauna, with dominance of warm-water indicators and shifts in assemblage composition that can be attributed to temperature, lake depth, productivity and habitat availability. Quantitative mean July paleotemperature estimates based on the chironomid data indicate overall mean July air temperatures up to 1 degrees C warmer than present. Two cooling events can be discerned, the Tunturi event, dated to about 127.5kaBP, in the lower part of the sequence, and the Varrio event, dated to about 119kaBP, associated with the beginning of a cooling trend in the upper part of the record. Warm conditions already at the onset of the interglacial contrast with a recent chironomid-based last interglacial temperature reconstruction from Denmark, which suggests a late onset of Eemian warming. The relatively small increase in inferred temperatures compared to present day temperatures at Sokli differs from other high latitude Eemian sites, and likely reflects the influence of the Atlantic Meridional Overturning Circulation in maintaining already elevated temperatures in Fennoscandia during interglacials. KW - Paleoclimate KW - Abrupt events KW - Last Interglacial KW - AMOC KW - Transfer functions KW - Validation Y1 - 2019 U6 - https://doi.org/10.1007/s10933-018-00064-y SN - 0921-2728 SN - 1573-0417 VL - 61 IS - 3 SP - 355 EP - 371 PB - Springer Science CY - Dordrecht ER - TY - JOUR A1 - Zimmermann, Heike Hildegard A1 - Harms, Lars A1 - Epp, Laura Saskia A1 - Mewes, Nick A1 - Bernhardt, Nadine A1 - Kruse, Stefan A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Pestryakova, Luidmila Agafyevna A1 - Wieczorek, Mareike A1 - Trense, Daronja A1 - Herzschuh, Ulrike T1 - Chloroplast and mitochondrial genetic variation of larches at the Siberian tundrataiga ecotone revealed by de novo assembly JF - PLoS one N2 - Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/ L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix. Y1 - 2019 U6 - https://doi.org/10.1371/journal.pone.0216966 SN - 1932-6203 VL - 14 IS - 7 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Angeleska, Angela A1 - Nikoloski, Zoran T1 - Coherent network partitions JF - Discrete applied mathematics N2 - Graph clustering is widely applied in the analysis of cellular networks reconstructed from large-scale data or obtained from experimental evidence. Here we introduce a new type of graph clustering based on the concept of coherent partition. A coherent partition of a graph G is a partition of the vertices of G that yields only disconnected subgraphs in the complement of G. The coherence number of G is then the size of the smallest edge cut inducing a coherent partition. A coherent partition of G is optimal if the size of the inducing edge cut is the coherence number of G. Given a graph G, we study coherent partitions and the coherence number in connection to (bi)clique partitions and the (bi)clique cover number. We show that the problem of finding the coherence number is NP-hard, but is of polynomial time complexity for trees. We also discuss the relation between coherent partitions and prominent graph clustering quality measures. KW - Graph partitions KW - Network clustering KW - Coherence number KW - Coherent partition Y1 - 2019 U6 - https://doi.org/10.1016/j.dam.2019.02.048 SN - 0166-218X SN - 1872-6771 VL - 266 SP - 283 EP - 290 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Bhuvanesh, Thanga A1 - Machatschek, Rainhard Gabriel A1 - Lysyakova, Liudmila A1 - Kratz, Karl A1 - Schulz, Burkhard A1 - Ma, Nan A1 - Lendlein, Andreas T1 - Collagen type-IV Langmuir and Langmuir-Schafer layers as model biointerfaces to direct stem cell adhesion JF - Biomedical materials : materials for tissue engineering and regenerative medicine N2 - In biomaterial development, the design of material surfaces that mimic the extra-cellular matrix (ECM) in order to achieve favorable cellular instruction is rather challenging. Collagen-type IV (Col-IV), the major scaffolding component of Basement Membranes (BM), a specialized ECM with multiple biological functions, has the propensity to form networks by self-assembly and supports adhesion of cells such as endothelial cells or stem cells. The preparation of biomimetic Col-IV network-like layers to direct cell responses is difficult. We hypothesize that the morphology of the layer, and especially the density of the available adhesion sites, regulates the cellular adhesion to the layer. The Langmuir monolayer technique allows for preparation of thin layers with precisely controlled packing density at the air-water (A-W) interface. Transferring these layers onto cell culture substrates using the Langmuir-Schafer (LS) technique should therefore provide a pathway for preparation of BM mimicking layers with controlled cell adherence properties. In situ characterization using ellipsometry and polarization modulation-infrared reflection absorption spectroscopy of Col-IV layer during compression at the A-W interface reveal that there is linear increase of surface molecule concentration with negligible orientational changes up to a surface pressure of 25 mN m(-1). Smooth and homogeneous Col-IV network-like layers are successfully transferred by LS method at 15 mN m(-1) onto poly(ethylene terephthalate) (PET), which is a common substrate for cell culture. In contrast, the organization of Col-IV on PET prepared by the traditionally employed solution deposition method results in rather inhomogeneous layers with the appearance of aggregates and multilayers. Progressive increase in the number of early adherent mesenchymal stem cells (MSCs) after 24 h by controlling the areal Col-IV density by LS transfer at 10, 15 and 20 mN m(-1) on PET is shown. The LS method offers the possibility to control protein characteristics on biomaterial surfaces such as molecular density and thereby, modulate cell responses. KW - collagen-IV KW - basement membrane KW - Langmuir-Schafer films KW - stem cell adhesion KW - protein KW - ellipsometry Y1 - 2019 U6 - https://doi.org/10.1088/1748-605X/aaf464 SN - 1748-6041 SN - 1748-605X VL - 14 IS - 2 PB - Inst. of Physics Publ. CY - Bristol ER - TY - JOUR A1 - Naseri, Gita A1 - Behrend, Jessica A1 - Rieper, Lisa A1 - Müller-Röber, Bernd T1 - COMPASS for rapid combinatorial optimization of biochemical pathways based on artificial transcription factors JF - Nature Communications N2 - Balanced expression of multiple genes is central for establishing new biosynthetic pathways or multiprotein cellular complexes. Methods for efficient combinatorial assembly of regulatory sequences (promoters) and protein coding sequences are therefore highly wanted. Here, we report a high-throughput cloning method, called COMPASS for COMbinatorial Pathway ASSembly, for the balanced expression of multiple genes in Saccharomyces cerevisiae. COMPASS employs orthogonal, plant-derived artificial transcription factors (ATFs) and homologous recombination-based cloning for the generation of thousands of individual DNA constructs in parallel. The method relies on a positive selection of correctly assembled pathway variants from both, in vivo and in vitro cloning procedures. To decrease the turnaround time in genomic engineering, COMPASS is equipped with multi-locus CRISPR/Cas9-mediated modification capacity. We demonstrate the application of COMPASS by generating cell libraries producing n-carotene and co-producing p-ionone and biosensor-responsive naringenin. COMPASS will have many applications in synthetic biology projects that require gene expression balancing. Y1 - 2019 U6 - https://doi.org/10.1038/s41467-019-10224-x SN - 2041-1723 VL - 10 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Kahl, Sandra M. A1 - Lenhard, Michael A1 - Joshi, Jasmin Radha T1 - Compensatory mechanisms to climate change in the widely distributed species Silene vulgaris JF - The journal of ecology N2 - The adaptation of plants to future climatic conditions is crucial for their survival. Not surprisingly, phenotypic responses to climate change have already been observed in many plant populations. These responses may be due to evolutionary adaptive changes or phenotypic plasticity. Especially plant species with a wide geographic range are either expected to show genetic differentiation in response to differing climate conditions or to have a high phenotypic plasticity. We investigated phenotypic responses and plasticity as an estimate of the adaptive potential in the widespread species Silene vulgaris. In a greenhouse experiment, 25 European populations covering a geographic range from the Canary Islands to Sweden were exposed to three experimental precipitation and two temperature regimes mimicking a possible climate-change scenario for central Europe. We hypothesized that southern populations have a better performance under high temperature and drought conditions, as they are already adapted to a comparable environment. We found that our treatments significantly influenced the plants, but did not reveal a latitudinal difference in response to climate treatments for most plant traits. Only flower number showed a stronger plasticity in northern European populations (e.g. Swedish populations) where numbers decreased more drastically with increased temperature and decreased precipitation treatment. Synthesis. The significant treatment response in Silene vulgaris, independent of population origin - except for the number of flowers produced - suggests a high degree of universal phenotypic plasticity in this widely distributed species. This reflects the likely adaptation strategy of the species and forms the basis for a successful survival strategy during upcoming climatic changes. However, as flower number, a strongly fitness-related trait, decreased more strongly in northern populations under a climate-change scenario, there might be limits to adaptation even in this widespread, plastic species. KW - climate change KW - global change ecology KW - latitudinal gradient KW - local adaptation KW - phenotypic plasticity KW - plant performance KW - temperature increase Y1 - 2019 U6 - https://doi.org/10.1111/1365-2745.13133 SN - 0022-0477 SN - 1365-2745 VL - 107 IS - 4 SP - 1918 EP - 1930 PB - Wiley CY - Hoboken ER -