TY - JOUR A1 - Sheng, Gui-Lian A1 - Basler, Nikolas A1 - Ji, Xue-Ping A1 - Paijmans, Johanna L. A. A1 - Alberti, Federica A1 - Preick, Michaela A1 - Hartmann, Stefanie A1 - Westbury, Michael V. A1 - Yuan, Jun-Xia A1 - Jablonski, Nina G. A1 - Xenikoudakis, Georgios A1 - Hou, Xin-Dong A1 - Xiao, Bo A1 - Liu, Jian-Hui A1 - Hofreiter, Michael A1 - Lai, Xu-Long A1 - Barlow, Axel T1 - Paleogenome reveals genetic contribution of extinct giant panda to extant populations JF - Current biology N2 - Historically, the giant panda was widely distributed from northern China to southwestern Asia [1]. As a result of range contraction and fragmentation, extant individuals are currently restricted to fragmented mountain ranges on the eastern margin of the Qinghai-Tibet plateau, where they are distributed among three major population clusters [2]. However, little is known about the genetic consequences of this dramatic range contraction. For example, were regions where giant pandas previously existed occupied by ancestors of present-day populations, or were these regions occupied by genetically distinct populations that are now extinct? If so, is there any contribution of these extinct populations to the genomes of giant pandas living today? To investigate these questions, we sequenced the nuclear genome of an similar to 5,000-year-old giant panda from Jiangdongshan, Teng-chong County in Yunnan Province, China. We find that this individual represents a genetically distinct population that diverged prior to the diversification of modern giant panda populations. We find evidence of differential admixture with this ancient population among modern individuals originating from different populations as well as within the same population. We also find evidence for directional gene flow, which transferred alleles from the ancient population into the modern giant panda lineages. A variable proportion of the genomes of extant individuals is therefore likely derived from the ancient population represented by our sequenced individual. Although extant giant panda populations retain reasonable genetic diversity, our results suggest that this represents only part of the genetic diversity this species harbored prior to its recent range contractions. Y1 - 2019 U6 - https://doi.org/10.1016/j.cub.2019.04.021 SN - 0960-9822 SN - 1879-0445 VL - 29 IS - 10 SP - 1695 EP - 1700 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Chipman, Ariel D. A1 - Ferrier, David E. K. A1 - Brena, Carlo A1 - Qu, Jiaxin A1 - Hughes, Daniel S. T. A1 - Schroeder, Reinhard A1 - Torres-Oliva, Montserrat A1 - Znassi, Nadia A1 - Jiang, Huaiyang A1 - Almeida, Francisca C. A1 - Alonso, Claudio R. A1 - Apostolou, Zivkos A1 - Aqrawi, Peshtewani A1 - Arthur, Wallace A1 - Barna, Jennifer C. J. A1 - Blankenburg, Kerstin P. A1 - Brites, Daniela A1 - Capella-Gutierrez, Salvador A1 - Coyle, Marcus A1 - Dearden, Peter K. A1 - Du Pasquier, Louis A1 - Duncan, Elizabeth J. A1 - Ebert, Dieter A1 - Eibner, Cornelius A1 - Erikson, Galina A1 - Evans, Peter D. A1 - Extavour, Cassandra G. A1 - Francisco, Liezl A1 - Gabaldon, Toni A1 - Gillis, William J. A1 - Goodwin-Horn, Elizabeth A. A1 - Green, Jack E. A1 - Griffiths-Jones, Sam A1 - Grimmelikhuijzen, Cornelis J. P. A1 - Gubbala, Sai A1 - Guigo, Roderic A1 - Han, Yi A1 - Hauser, Frank A1 - Havlak, Paul A1 - Hayden, Luke A1 - Helbing, Sophie A1 - Holder, Michael A1 - Hui, Jerome H. L. A1 - Hunn, Julia P. A1 - Hunnekuhl, Vera S. A1 - Jackson, LaRonda A1 - Javaid, Mehwish A1 - Jhangiani, Shalini N. A1 - Jiggins, Francis M. A1 - Jones, Tamsin E. A1 - Kaiser, Tobias S. A1 - Kalra, Divya A1 - Kenny, Nathan J. A1 - Korchina, Viktoriya A1 - Kovar, Christie L. A1 - Kraus, F. Bernhard A1 - Lapraz, Francois A1 - Lee, Sandra L. A1 - Lv, Jie A1 - Mandapat, Christigale A1 - Manning, Gerard A1 - Mariotti, Marco A1 - Mata, Robert A1 - Mathew, Tittu A1 - Neumann, Tobias A1 - Newsham, Irene A1 - Ngo, Dinh N. A1 - Ninova, Maria A1 - Okwuonu, Geoffrey A1 - Ongeri, Fiona A1 - Palmer, William J. A1 - Patil, Shobha A1 - Patraquim, Pedro A1 - Pham, Christopher A1 - Pu, Ling-Ling A1 - Putman, Nicholas H. A1 - Rabouille, Catherine A1 - Ramos, Olivia Mendivil A1 - Rhodes, Adelaide C. A1 - Robertson, Helen E. A1 - Robertson, Hugh M. A1 - Ronshaugen, Matthew A1 - Rozas, Julio A1 - Saada, Nehad A1 - Sanchez-Gracia, Alejandro A1 - Scherer, Steven E. A1 - Schurko, Andrew M. A1 - Siggens, Kenneth W. A1 - Simmons, DeNard A1 - Stief, Anna A1 - Stolle, Eckart A1 - Telford, Maximilian J. A1 - Tessmar-Raible, Kristin A1 - Thornton, Rebecca A1 - van der Zee, Maurijn A1 - von Haeseler, Arndt A1 - Williams, James M. A1 - Willis, Judith H. A1 - Wu, Yuanqing A1 - Zou, Xiaoyan A1 - Lawson, Daniel A1 - Muzny, Donna M. A1 - Worley, Kim C. A1 - Gibbs, Richard A. A1 - Akam, Michael A1 - Richards, Stephen T1 - The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima JF - PLoS biology N2 - Myriapods (e. g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history. Y1 - 2014 U6 - https://doi.org/10.1371/journal.pbio.1002005 SN - 1545-7885 VL - 12 IS - 11 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - King, Turi E. A1 - Gonzalez-Fortes, Gloria M. A1 - Balaresque, Patricia A1 - Thomas, Mark G. A1 - Balding, David A1 - Delser, Pierpaolo Maisano A1 - Neumann, Rita A1 - Parson, Walther A1 - Knapp, Michael A1 - Walsh, Susan A1 - Tonasso, Laure A1 - Holt, John A1 - Kayser, Manfred A1 - Appleby, Jo A1 - Forster, Peter A1 - Ekserdjian, David A1 - Hofreiter, Michael A1 - Schuerer, Kevin T1 - Identification of the remains of King Richard III JF - Nature Communications Y1 - 2014 U6 - https://doi.org/10.1038/ncomms6631 SN - 2041-1723 VL - 5 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Mitzner, Rolf A1 - Rehanek, Jens A1 - Kern, Jan A1 - Gul, Sheraz A1 - Hattne, Johan A1 - Taguchi, Taketo A1 - Alonso-Mori, Roberto A1 - Tran, Rosalie A1 - Weniger, Christian A1 - Schröder, Henning A1 - Quevedo, Wilson A1 - Laksmono, Hartawan A1 - Sierra, Raymond G. A1 - Han, Guangye A1 - Lassalle-Kaiser, Benedikt A1 - Koroidov, Sergey A1 - Kubicek, Katharina A1 - Schreck, Simon A1 - Kunnus, Kristjan A1 - Brzhezinskaya, Maria A1 - Firsov, Alexander A1 - Minitti, Michael P. A1 - Turner, Joshua J. A1 - Möller, Stefan A1 - Sauter, Nicholas K. A1 - Bogan, Michael J. A1 - Nordlund, Dennis A1 - Schlotter, William F. A1 - Messinger, Johannes A1 - Borovik, Andrew S. A1 - Techert, Simone A1 - de Groot, Frank M. F. A1 - Föhlisch, Alexander A1 - Erko, Alexei A1 - Bergmann, Uwe A1 - Yachandra, Vittal K. A1 - Wernet, Philippe A1 - Yano, Junko T1 - L-edge x-ray absorption spectroscopy of dilute systems relevant to metalloproteins using an X-ray free-electron laser JF - The journal of physical chemistry letters N2 - L-edge spectroscopy of 3d transition metals provides important electronic structure information and has been used in many fields. However, the use of this method for studying dilute aqueous systems, such as metalloenzymes, has not been prevalent because of severe radiation damage and the lack of suitable detection systems. Here we present spectra from a dilute Mn aqueous solution using a high-transmission zone-plate spectrometer at the Linac Coherent Light Source (LCLS). The spectrometer has been optimized for discriminating the Mn L-edge signal from the overwhelming 0 K-edge background that arises from water and protein itself, and the ultrashort LCLS X-ray pulses can outrun X-ray induced damage. We show that the deviations of the partial-fluorescence yield-detected spectra from the true absorption can be well modeled using the state-dependence of the fluorescence yield, and discuss implications for the application of our concept to biological samples. Y1 - 2013 U6 - https://doi.org/10.1021/jz401837f SN - 1948-7185 VL - 4 IS - 21 SP - 3641 EP - 3647 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Herrero, Mario A1 - Thornton, Philip K. A1 - Mason-D'Croz, Daniel A1 - Palmer, Jeda A1 - Bodirsky, Benjamin Leon A1 - Pradhan, Prajal A1 - Barrett, Christopher B. A1 - Benton, Tim G. A1 - Hall, Andrew A1 - Pikaar, Ilje A1 - Bogard, Jessica R. A1 - Bonnett, Graham D. A1 - Bryan, Brett A. A1 - Campbell, Bruce M. A1 - Christensen, Svend A1 - Clark, Michael A1 - Fanzo, Jessica A1 - Godde, Cecile M. A1 - Jarvis, Andy A1 - Loboguerrero, Ana Maria A1 - Mathys, Alexander A1 - McIntyre, C. Lynne A1 - Naylor, Rosamond L. A1 - Nelson, Rebecca A1 - Obersteiner, Michael A1 - Parodi, Alejandro A1 - Popp, Alexander A1 - Ricketts, Katie A1 - Smith, Pete A1 - Valin, Hugo A1 - Vermeulen, Sonja J. A1 - Vervoort, Joost A1 - van Wijk, Mark A1 - van Zanten, Hannah H. E. A1 - West, Paul C. A1 - Wood, Stephen A. A1 - Rockström, Johan T1 - Articulating the effect of food systems innovation on the Sustainable Development Goals JF - The lancet Planetary health N2 - Food system innovations will be instrumental to achieving multiple Sustainable Development Goals (SDGs). However, major innovation breakthroughs can trigger profound and disruptive changes, leading to simultaneous and interlinked reconfigurations of multiple parts of the global food system. The emergence of new technologies or social solutions, therefore, have very different impact profiles, with favourable consequences for some SDGs and unintended adverse side-effects for others. Stand-alone innovations seldom achieve positive outcomes over multiple sustainability dimensions. Instead, they should be embedded as part of systemic changes that facilitate the implementation of the SDGs. Emerging trade-offs need to be intentionally addressed to achieve true sustainability, particularly those involving social aspects like inequality in its many forms, social justice, and strong institutions, which remain challenging. Trade-offs with undesirable consequences are manageable through the development of well planned transition pathways, careful monitoring of key indicators, and through the implementation of transparent science targets at the local level. Y1 - 2020 U6 - https://doi.org/10.1016/S2542-5196(20)30277-1 SN - 2542-5196 VL - 5 IS - 1 SP - E50 EP - E62 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Nathan, Ran A1 - Monk, Christopher T. A1 - Arlinghaus, Robert A1 - Adam, Timo A1 - Alós, Josep A1 - Assaf, Michael A1 - Baktoft, Henrik A1 - Beardsworth, Christine E. A1 - Bertram, Michael G. A1 - Bijleveld, Allert A1 - Brodin, Tomas A1 - Brooks, Jill L. A1 - Campos-Candela, Andrea A1 - Cooke, Steven J. A1 - Gjelland, Karl O. A1 - Gupte, Pratik R. A1 - Harel, Roi A1 - Hellstrom, Gustav A1 - Jeltsch, Florian A1 - Killen, Shaun S. A1 - Klefoth, Thomas A1 - Langrock, Roland A1 - Lennox, Robert J. A1 - Lourie, Emmanuel A1 - Madden, Joah R. A1 - Orchan, Yotam A1 - Pauwels, Ine S. A1 - Riha, Milan A1 - Röleke, Manuel A1 - Schlägel, Ulrike A1 - Shohami, David A1 - Signer, Johannes A1 - Toledo, Sivan A1 - Vilk, Ohad A1 - Westrelin, Samuel A1 - Whiteside, Mark A. A1 - Jaric, Ivan T1 - Big-data approaches lead to an increased understanding of the ecology of animal movement JF - Science N2 - Understanding animal movement is essential to elucidate how animals interact, survive, and thrive in a changing world. Recent technological advances in data collection and management have transformed our understanding of animal "movement ecology" (the integrated study of organismal movement), creating a big-data discipline that benefits from rapid, cost-effective generation of large amounts of data on movements of animals in the wild. These high-throughput wildlife tracking systems now allow more thorough investigation of variation among individuals and species across space and time, the nature of biological interactions, and behavioral responses to the environment. Movement ecology is rapidly expanding scientific frontiers through large interdisciplinary and collaborative frameworks, providing improved opportunities for conservation and insights into the movements of wild animals, and their causes and consequences. Y1 - 2022 U6 - https://doi.org/10.1126/science.abg1780 SN - 0036-8075 SN - 1095-9203 VL - 375 IS - 6582 SP - 734 EP - + PB - American Assoc. for the Advancement of Science CY - Washington ER - TY - JOUR A1 - Marks, Richard G. A1 - Musch, Sebastian A1 - Haußig, Hans-Michael A1 - Weiss, Aleš A1 - Albeck-Gidron, Rachel A1 - Sigalow, Emily A1 - Ariel, Yaakov S. A1 - Niculescu, Mira A1 - Landau, David A1 - Rageth, Nina A1 - Ichikawa, Hiroshi A1 - Rohland, Eva A1 - Czendze, Oskar A1 - Reich, Tamar Chana A1 - Schulz, Michael Karl A1 - Arnold, Rafael D. A1 - Anderl, Gabriele A1 - Gempp-Friedrich, Tilmann A1 - Liu, Yongqiang A1 - Battenberg, J. Friedrich A1 - Reichert, Carmen A1 - Riemer, Nathanael A1 - Krah, Markus A1 - Thulin, Mirjam ED - Riemer, Nathanael ED - Albeck-Gidron, Rachel ED - Krah, Markus T1 - PaRDeS : Zeitschrift der Vereinigung für Jüdische Studien = JewBus, Jewish Hindus & other Jewish Encounters with East Asian Religions T2 - PaRDeS N2 - PaRDeS. Zeitschrift der Vereinigung für Jüdische Studien e.V., möchte die fruchtbare und facettenreiche Kultur des Judentums sowie seine Berührungspunkte zur Umwelt in den unterschiedlichen Bereichen dokumentieren. Daneben dient die Zeitschrift als Forum zur Positionierung der Fächer Jüdische Studien und Judaistik innerhalb des wissenschaftlichen Diskurses sowie zur Diskussion ihrer historischen und gesellschaftlichen Verantwortung. N2 - PaRDeS. Journal of the Association of Jewish Studies e.V. The journal aims at documenting the fruitful and multifarious culture of Judaism as well as its relations to its environment within diverse areas of research. In addition, the journal is meant to promote Jewish Studies within academic discourse and discuss its historic and social responsibility. T3 - PaRDeS : Zeitschrift der Vereinigung für Jüdische Studien e.V. - 23 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-402536 SN - 978-3-86956-418-0 SN - 1614-6492 SN - 1862-7684 IS - 23 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Förstner, Bernd Rainer A1 - Böttger, Sarah Jane A1 - Moldavski, Alexander A1 - Bajbouj, Malek A1 - Pfennig, Andrea A1 - Manook, Andre A1 - Ising, Marcus A1 - Pittig, Andre A1 - Heinig, Ingmar A1 - Heinz, Andreas A1 - Mathiak, Klaus A1 - Schulze, Thomas G. A1 - Schneider, Frank A1 - Kamp-Becker, Inge A1 - Meyer-Lindenberg, Andreas A1 - Padberg, Frank A1 - Banaschewski, Tobias A1 - Bauer, Michael A1 - Rupprecht, Rainer A1 - Wittchen, Hans-Ulrich A1 - Rapp, Michael A. A1 - Tschorn, Mira T1 - The associations of positive and negative valence systems, cognitive systems and social processes on disease severity in anxiety and depressive disorders JF - Frontiers in psychiatry N2 - Background Anxiety and depressive disorders share common features of mood dysfunctions. This has stimulated interest in transdiagnostic dimensional research as proposed by the Research Domain Criteria (RDoC) approach by the National Institute of Mental Health (NIMH) aiming to improve the understanding of underlying disease mechanisms. The purpose of this study was to investigate the processing of RDoC domains in relation to disease severity in order to identify latent disorder-specific as well as transdiagnostic indicators of disease severity in patients with anxiety and depressive disorders. Methods Within the German research network for mental disorders, 895 participants (n = 476 female, n = 602 anxiety disorder, n = 257 depressive disorder) were recruited for the Phenotypic, Diagnostic and Clinical Domain Assessment Network Germany (PD-CAN) and included in this cross-sectional study. We performed incremental regression models to investigate the association of four RDoC domains on disease severity in patients with affective disorders: Positive (PVS) and Negative Valance System (NVS), Cognitive Systems (CS) and Social Processes (SP). Results The results confirmed a transdiagnostic relationship for all four domains, as we found significant main effects on disease severity within domain-specific models (PVS: & beta; = -0.35; NVS: & beta; = 0.39; CS: & beta; = -0.12; SP: & beta; = -0.32). We also found three significant interaction effects with main diagnosis showing a disease-specific association. Limitations The cross-sectional study design prevents causal conclusions. Further limitations include possible outliers and heteroskedasticity in all regression models which we appropriately controlled for. Conclusion Our key results show that symptom burden in anxiety and depressive disorders is associated with latent RDoC indicators in transdiagnostic and disease-specific ways. KW - Research Domain Criteria KW - depression KW - anxiety disoders KW - disease severity KW - transdiagnostic KW - RDoC Y1 - 2023 U6 - https://doi.org/10.3389/fpsyt.2023.1161097 SN - 1664-0640 VL - 14 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Zech, Hilmar G. A1 - Reichert, Markus A1 - Ebner-Priemer, Ulrich W. A1 - Tost, Heike A1 - Rapp, Michael A. A1 - Heinz, Andreas A1 - Dolan, Raymond J. A1 - Smolka, Michael N. A1 - Deserno, Lorenz T1 - Mobile data collection of cognitive-behavioral tasks in substance use disorders: Where are we now? JF - Neuropsychobiology N2 - Introduction: Over the last decades, our understanding of the cognitive, motivational, and neural processes involved in addictive behavior has increased enormously. A plethora of laboratory-based and cross-sectional studies has linked cognitive-behavioral measures to between-subject differences in drinking behavior. However, such laboratory-based studies inevitably suffer from small sample sizes and the inability to link temporal fluctuations in task measures to fluctuations in real-life substance use. To overcome these problems, several existing behavioral tasks have been transferred to smartphones to allow studying cognition in the field. Method: In this narrative review, we first summarize studies that used existing behavioral tasks in the laboratory and self-reports of substance use with ecological momentary assessment (EMA) in the field. Next, we review studies on psychometric properties of smartphone-based behavioral tasks. Finally, we review studies that used both smartphone-based tasks and self-reports with EMA in the field. Results: Overall, studies were scarce and heterogenous both in tasks and in study outcomes. Nevertheless, existing findings are promising and point toward several methodological recommendations: concerning psychometrics, studies show that - although more systematic studies are necessary - task validity and reliability can be improved, for example, by analyzing several measurement sessions at once rather than analyzing sessions separately. Studies that use tasks in the field, moreover, show that power can be improved by choosing sampling schemes that combine time-based with event-based sampling, rather than relying on time-based sampling alone. Increasing sampling frequency can further increase power. However, as this also increases the burden to participants, more research is necessary to determine the ideal sampling frequency for each task. Conclusion: Although more research is necessary to systematically study both the psychometrics of smartphone-based tasks and the frequency at which task measures fluctuate, existing studies are promising and reveal important methodological recommendations useful for researchers interested in implementing behavioral tasks in EMA studies. KW - Ecological momentary assessment KW - Behavioral tasks KW - Smartphone KW - Substance use KW - Addiction Y1 - 2022 U6 - https://doi.org/10.1159/000523697 SN - 0302-282X SN - 1423-0224 VL - 81 IS - 5 SP - 438 EP - 450 PB - Karger CY - Basel ER - TY - JOUR A1 - Gancheva, Sofiya A1 - Ouni, Meriem A1 - Jelenik, Tomas A1 - Koliaki, Chrysi A1 - Szendroedi, Julia A1 - Toledo, Frederico G. S. A1 - Markgraf, Daniel Frank A1 - Pesta, Dominik H. A1 - Mastrototaro, Lucia A1 - De Filippo, Elisabetta A1 - Herder, Christian A1 - Jähnert, Markus A1 - Weiss, Jürgen A1 - Strassburger, Klaus A1 - Schlensak, Matthias A1 - Schürmann, Annette A1 - Roden, Michael T1 - Dynamic changes of muscle insulin sensitivity after metabolic surgery JF - Nature Communications N2 - The mechanisms underlying improved insulin sensitivity after surgically-induced weight loss are still unclear. We monitored skeletal muscle metabolism in obese individuals before and over 52 weeks after metabolic surgery. Initial weight loss occurs in parallel with a decrease in muscle oxidative capacity and respiratory control ratio. Persistent elevation of intramyocellular lipid intermediates, likely resulting from unrestrained adipose tissue lipolysis, accompanies the lack of rapid changes in insulin sensitivity. Simultaneously, alterations in skeletal muscle expression of genes involved in calcium/lipid metabolism and mitochondrial function associate with subsequent distinct DNA methylation patterns at 52 weeks after surgery. Thus, initial unfavorable metabolic changes including insulin resistance of adipose tissue and skeletal muscle precede epigenetic modifications of genes involved in muscle energy metabolism and the long-term improvement of insulin sensitivity. Y1 - 2019 U6 - https://doi.org/10.1038/s41467-019-12081-0 SN - 2041-1723 VL - 10 PB - Nature Publ. Group CY - London ER -