@article{ShengBaslerJietal.2019, author = {Sheng, Gui-Lian and Basler, Nikolas and Ji, Xue-Ping and Paijmans, Johanna L. A. and Alberti, Federica and Preick, Michaela and Hartmann, Stefanie and Westbury, Michael V. and Yuan, Jun-Xia and Jablonski, Nina G. and Xenikoudakis, Georgios and Hou, Xin-Dong and Xiao, Bo and Liu, Jian-Hui and Hofreiter, Michael and Lai, Xu-Long and Barlow, Axel}, title = {Paleogenome reveals genetic contribution of extinct giant panda to extant populations}, series = {Current biology}, volume = {29}, journal = {Current biology}, number = {10}, publisher = {Cell Press}, address = {Cambridge}, issn = {0960-9822}, doi = {10.1016/j.cub.2019.04.021}, pages = {1695 -- 1700}, year = {2019}, abstract = {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.}, language = {en} } @article{ChipmanFerrierBrenaetal.2014, author = {Chipman, Ariel D. and Ferrier, David E. K. and Brena, Carlo and Qu, Jiaxin and Hughes, Daniel S. T. and Schroeder, Reinhard and Torres-Oliva, Montserrat and Znassi, Nadia and Jiang, Huaiyang and Almeida, Francisca C. and Alonso, Claudio R. and Apostolou, Zivkos and Aqrawi, Peshtewani and Arthur, Wallace and Barna, Jennifer C. J. and Blankenburg, Kerstin P. and Brites, Daniela and Capella-Gutierrez, Salvador and Coyle, Marcus and Dearden, Peter K. and Du Pasquier, Louis and Duncan, Elizabeth J. and Ebert, Dieter and Eibner, Cornelius and Erikson, Galina and Evans, Peter D. and Extavour, Cassandra G. and Francisco, Liezl and Gabaldon, Toni and Gillis, William J. and Goodwin-Horn, Elizabeth A. and Green, Jack E. and Griffiths-Jones, Sam and Grimmelikhuijzen, Cornelis J. P. and Gubbala, Sai and Guigo, Roderic and Han, Yi and Hauser, Frank and Havlak, Paul and Hayden, Luke and Helbing, Sophie and Holder, Michael and Hui, Jerome H. L. and Hunn, Julia P. and Hunnekuhl, Vera S. and Jackson, LaRonda and Javaid, Mehwish and Jhangiani, Shalini N. and Jiggins, Francis M. and Jones, Tamsin E. and Kaiser, Tobias S. and Kalra, Divya and Kenny, Nathan J. and Korchina, Viktoriya and Kovar, Christie L. and Kraus, F. Bernhard and Lapraz, Francois and Lee, Sandra L. and Lv, Jie and Mandapat, Christigale and Manning, Gerard and Mariotti, Marco and Mata, Robert and Mathew, Tittu and Neumann, Tobias and Newsham, Irene and Ngo, Dinh N. and Ninova, Maria and Okwuonu, Geoffrey and Ongeri, Fiona and Palmer, William J. and Patil, Shobha and Patraquim, Pedro and Pham, Christopher and Pu, Ling-Ling and Putman, Nicholas H. and Rabouille, Catherine and Ramos, Olivia Mendivil and Rhodes, Adelaide C. and Robertson, Helen E. and Robertson, Hugh M. and Ronshaugen, Matthew and Rozas, Julio and Saada, Nehad and Sanchez-Gracia, Alejandro and Scherer, Steven E. and Schurko, Andrew M. and Siggens, Kenneth W. and Simmons, DeNard and Stief, Anna and Stolle, Eckart and Telford, Maximilian J. and Tessmar-Raible, Kristin and Thornton, Rebecca and van der Zee, Maurijn and von Haeseler, Arndt and Williams, James M. and Willis, Judith H. and Wu, Yuanqing and Zou, Xiaoyan and Lawson, Daniel and Muzny, Donna M. and Worley, Kim C. and Gibbs, Richard A. and Akam, Michael and Richards, Stephen}, title = {The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima}, series = {PLoS biology}, volume = {12}, journal = {PLoS biology}, number = {11}, publisher = {PLoS}, address = {San Fransisco}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1002005}, pages = {24}, year = {2014}, abstract = {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.}, language = {en} } @article{KingGonzalezFortesBalaresqueetal.2014, author = {King, Turi E. and Gonzalez-Fortes, Gloria M. and Balaresque, Patricia and Thomas, Mark G. and Balding, David and Delser, Pierpaolo Maisano and Neumann, Rita and Parson, Walther and Knapp, Michael and Walsh, Susan and Tonasso, Laure and Holt, John and Kayser, Manfred and Appleby, Jo and Forster, Peter and Ekserdjian, David and Hofreiter, Michael and Schuerer, Kevin}, title = {Identification of the remains of King Richard III}, series = {Nature Communications}, volume = {5}, journal = {Nature Communications}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/ncomms6631}, pages = {8}, year = {2014}, language = {en} } @article{MitznerRehanekKernetal.2013, author = {Mitzner, Rolf and Rehanek, Jens and Kern, Jan and Gul, Sheraz and Hattne, Johan and Taguchi, Taketo and Alonso-Mori, Roberto and Tran, Rosalie and Weniger, Christian and Schr{\"o}der, Henning and Quevedo, Wilson and Laksmono, Hartawan and Sierra, Raymond G. and Han, Guangye and Lassalle-Kaiser, Benedikt and Koroidov, Sergey and Kubicek, Katharina and Schreck, Simon and Kunnus, Kristjan and Brzhezinskaya, Maria and Firsov, Alexander and Minitti, Michael P. and Turner, Joshua J. and M{\"o}ller, Stefan and Sauter, Nicholas K. and Bogan, Michael J. and Nordlund, Dennis and Schlotter, William F. and Messinger, Johannes and Borovik, Andrew S. and Techert, Simone and de Groot, Frank M. F. and F{\"o}hlisch, Alexander and Erko, Alexei and Bergmann, Uwe and Yachandra, Vittal K. and Wernet, Philippe and Yano, Junko}, title = {L-edge x-ray absorption spectroscopy of dilute systems relevant to metalloproteins using an X-ray free-electron laser}, series = {The journal of physical chemistry letters}, volume = {4}, journal = {The journal of physical chemistry letters}, number = {21}, publisher = {American Chemical Society}, address = {Washington}, issn = {1948-7185}, doi = {10.1021/jz401837f}, pages = {3641 -- 3647}, year = {2013}, abstract = {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.}, language = {en} } @article{HerreroThorntonMasonD'Crozetal.2020, author = {Herrero, Mario and Thornton, Philip K. and Mason-D'Croz, Daniel and Palmer, Jeda and Bodirsky, Benjamin Leon and Pradhan, Prajal and Barrett, Christopher B. and Benton, Tim G. and Hall, Andrew and Pikaar, Ilje and Bogard, Jessica R. and Bonnett, Graham D. and Bryan, Brett A. and Campbell, Bruce M. and Christensen, Svend and Clark, Michael and Fanzo, Jessica and Godde, Cecile M. and Jarvis, Andy and Loboguerrero, Ana Maria and Mathys, Alexander and McIntyre, C. Lynne and Naylor, Rosamond L. and Nelson, Rebecca and Obersteiner, Michael and Parodi, Alejandro and Popp, Alexander and Ricketts, Katie and Smith, Pete and Valin, Hugo and Vermeulen, Sonja J. and Vervoort, Joost and van Wijk, Mark and van Zanten, Hannah H. E. and West, Paul C. and Wood, Stephen A. and Rockstr{\"o}m, Johan}, title = {Articulating the effect of food systems innovation on the Sustainable Development Goals}, series = {The lancet Planetary health}, volume = {5}, journal = {The lancet Planetary health}, number = {1}, publisher = {Elsevier}, address = {Oxford}, issn = {2542-5196}, doi = {10.1016/S2542-5196(20)30277-1}, pages = {E50 -- E62}, year = {2020}, abstract = {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.}, language = {en} } @article{NathanMonkArlinghausetal.2022, author = {Nathan, Ran and Monk, Christopher T. and Arlinghaus, Robert and Adam, Timo and Al{\´o}s, Josep and Assaf, Michael and Baktoft, Henrik and Beardsworth, Christine E. and Bertram, Michael G. and Bijleveld, Allert and Brodin, Tomas and Brooks, Jill L. and Campos-Candela, Andrea and Cooke, Steven J. and Gjelland, Karl O. and Gupte, Pratik R. and Harel, Roi and Hellstrom, Gustav and Jeltsch, Florian and Killen, Shaun S. and Klefoth, Thomas and Langrock, Roland and Lennox, Robert J. and Lourie, Emmanuel and Madden, Joah R. and Orchan, Yotam and Pauwels, Ine S. and Riha, Milan and R{\"o}leke, Manuel and Schl{\"a}gel, Ulrike and Shohami, David and Signer, Johannes and Toledo, Sivan and Vilk, Ohad and Westrelin, Samuel and Whiteside, Mark A. and Jaric, Ivan}, title = {Big-data approaches lead to an increased understanding of the ecology of animal movement}, series = {Science}, volume = {375}, journal = {Science}, number = {6582}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {0036-8075}, doi = {10.1126/science.abg1780}, pages = {734 -- +}, year = {2022}, abstract = {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.}, language = {en} } @misc{MarksMuschHaussigetal.2018, author = {Marks, Richard G. and Musch, Sebastian and Haußig, Hans-Michael and Weiss, Aleš and Albeck-Gidron, Rachel and Sigalow, Emily and Ariel, Yaakov S. and Niculescu, Mira and Landau, David and Rageth, Nina and Ichikawa, Hiroshi and Rohland, Eva and Czendze, Oskar and Reich, Tamar Chana and Schulz, Michael Karl and Arnold, Rafael D. and Anderl, Gabriele and Gempp-Friedrich, Tilmann and Liu, Yongqiang and Battenberg, J. Friedrich and Reichert, Carmen and Riemer, Nathanael and Krah, Markus and Thulin, Mirjam}, title = {PaRDeS : Zeitschrift der Vereinigung f{\"u}r J{\"u}dische Studien = JewBus, Jewish Hindus \& other Jewish Encounters with East Asian Religions}, series = {PaRDeS}, journal = {PaRDeS}, number = {23}, editor = {Riemer, Nathanael and Albeck-Gidron, Rachel and Krah, Markus}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-418-0}, issn = {1614-6492}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-402536}, year = {2018}, abstract = {PaRDeS. Zeitschrift der Vereinigung f{\"u}r J{\"u}dische Studien e.V., m{\"o}chte die fruchtbare und facettenreiche Kultur des Judentums sowie seine Ber{\"u}hrungspunkte zur Umwelt in den unterschiedlichen Bereichen dokumentieren. Daneben dient die Zeitschrift als Forum zur Positionierung der F{\"a}cher J{\"u}dische Studien und Judaistik innerhalb des wissenschaftlichen Diskurses sowie zur Diskussion ihrer historischen und gesellschaftlichen Verantwortung.}, language = {de} } @article{FoerstnerBoettgerMoldavskietal.2023, author = {F{\"o}rstner, Bernd Rainer and B{\"o}ttger, Sarah Jane and Moldavski, Alexander and Bajbouj, Malek and Pfennig, Andrea and Manook, Andre and Ising, Marcus and Pittig, Andre and Heinig, Ingmar and Heinz, Andreas and Mathiak, Klaus and Schulze, Thomas G. and Schneider, Frank and Kamp-Becker, Inge and Meyer-Lindenberg, Andreas and Padberg, Frank and Banaschewski, Tobias and Bauer, Michael and Rupprecht, Rainer and Wittchen, Hans-Ulrich and Rapp, Michael A. and Tschorn, Mira}, title = {The associations of positive and negative valence systems, cognitive systems and social processes on disease severity in anxiety and depressive disorders}, series = {Frontiers in psychiatry}, volume = {14}, journal = {Frontiers in psychiatry}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-0640}, doi = {10.3389/fpsyt.2023.1161097}, pages = {10}, year = {2023}, abstract = {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.}, language = {en} } @article{ZechReichertEbnerPriemeretal.2022, author = {Zech, Hilmar G. and Reichert, Markus and Ebner-Priemer, Ulrich W. and Tost, Heike and Rapp, Michael A. and Heinz, Andreas and Dolan, Raymond J. and Smolka, Michael N. and Deserno, Lorenz}, title = {Mobile data collection of cognitive-behavioral tasks in substance use disorders: Where are we now?}, series = {Neuropsychobiology}, volume = {81}, journal = {Neuropsychobiology}, number = {5}, publisher = {Karger}, address = {Basel}, issn = {0302-282X}, doi = {10.1159/000523697}, pages = {438 -- 450}, year = {2022}, abstract = {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.}, language = {en} } @article{GanchevaOuniJeleniketal.2019, author = {Gancheva, Sofiya and Ouni, Meriem and Jelenik, Tomas and Koliaki, Chrysi and Szendroedi, Julia and Toledo, Frederico G. S. and Markgraf, Daniel Frank and Pesta, Dominik H. and Mastrototaro, Lucia and De Filippo, Elisabetta and Herder, Christian and J{\"a}hnert, Markus and Weiss, J{\"u}rgen and Strassburger, Klaus and Schlensak, Matthias and Sch{\"u}rmann, Annette and Roden, Michael}, title = {Dynamic changes of muscle insulin sensitivity after metabolic surgery}, series = {Nature Communications}, volume = {10}, journal = {Nature Communications}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/s41467-019-12081-0}, pages = {13}, year = {2019}, abstract = {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.}, language = {en} }