Comparative Analysis of Tandem Repeats from Hundreds of Species Reveals Unique Insights into Centromere Evolution

Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data. The assumption that the most abundant tandem repeat is the centromere DNA was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and in length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond ~50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution, including the appearance of higher order repeat structures in which several polymorphic monomers make up a larger repeating unit. While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animals and plants. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes

Integrating Data Science and Earth Science

This open access book presents the results of three years collaboration between earth scientists and data scientists, in developing and applying data science methods for scientific discovery. The book will be highly beneficial for other researchers at senior and graduate level, interested in applying visual data exploration, computational approaches and scientifc workflows

COSMOS-Europe : a European network of cosmic-ray neutron soil moisture sensors

We thank TERENO (Terrestrial Environmental Observatories), funded by the Helmholtz-Gemeinschaft for the financing and maintenance of CRNS stations. We acknowledge financial support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) of the research unit FOR 2694 Cosmic Sense (grant no. 357874777) and by the German Federal Ministry of Education of the Research BioökonomieREVIER, Digitales Geosystem – Rheinisches Revier project (grant no. 031B0918A). COSMOS-UK has been supported financially by the UK’s Natural Environment Research Council (grant no. NE/R016429/1). The Olocau experimental watershed is partially supported by the Spanish Ministry of Science and Innovation through the research project TETISCHANGE (grant no. RTI2018-093717-BI00). The Calderona experimental site is partially supported by the Spanish Ministry of Science and Innovation through the research projects CEHYRFO-MED (grant no. CGL2017-86839- C3-2-R) and SILVADAPT.NET (grant no. RED2018-102719-T) and the LIFE project RESILIENT FORESTS (grant no. LIFE17 CCA/ES/000063). The University of Bristol’s Sheepdrove sites have been supported by the UK’s Natural Environment Research Council through a number of projects (grant nos. NE/M003086/1, NE/R004897/1, and NE/T005645/1) and by the International Atomic Energy Agency of the United Nations (grant no. CRP D12014). Acknowledgements. We thank Peter Strauss and Gerhab Rab from the Institute for Land and Water Management Research, Federal Agency for Water Management Austria, Petzenkirchen, Austria. We thank Trenton Franz from the School of Natural Resources, University of Nebraska–Lincoln, Lincoln, NE, United States. We also thank Carmen Zengerle, Mandy Kasner, Felix Pohl, and Solveig Landmark, UFZ Leipzig, for supporting field calibration, lab analysis, and data processing. We furthermore thank Daniel Dolfus, Marius Schmidt, Ansgar Weuthen, and Bernd Schilling, Forschungszentrum Jülich, Germany. The COSMOS-UK project team is thanked for making its data available to COSMOS-Europe. Luca Stevanato is thanked for the technical details about the Finapp sensor. The stations at Cunnersdorf, Lindenberg, and Harzgerode have been supported by Falk Böttcher, Frank Beyrich, and Petra Fude, German Weather Service (DWD). The Zerbst site has been supported by Getec Green Energy GmbH and Jörg Kachelmann (Meteologix AG). The CESBIO sites have been supported by the CNES TOSCA program. The ERA5-Land data are provided by ECMWF (Muñoz Sabater, 2021). The Jena dataset was retrieved at the site of The Jena Experiment, operated by DFG research unit FOR 1451.Peer reviewedPublisher PD

Comparative Genomics of the Apicomplexan Parasites Toxoplasma gondii and Neospora caninum: Coccidia Differing in Host Range and Transmission Strategy

Toxoplasma gondii is a zoonotic protozoan parasite which infects nearly one third of the human population and is found in an extraordinary range of vertebrate hosts. Its epidemiology depends heavily on horizontal transmission, especially between rodents and its definitive host, the cat. Neospora caninum is a recently discovered close relative of Toxoplasma, whose definitive host is the dog. Both species are tissue-dwelling Coccidia and members of the phylum Apicomplexa; they share many common features, but Neospora neither infects humans nor shares the same wide host range as Toxoplasma, rather it shows a striking preference for highly efficient vertical transmission in cattle. These species therefore provide a remarkable opportunity to investigate mechanisms of host restriction, transmission strategies, virulence and zoonotic potential. We sequenced the genome of N. caninum and transcriptomes of the invasive stage of both species, undertaking an extensive comparative genomics and transcriptomics analysis. We estimate that these organisms diverged from their common ancestor around 28 million years ago and find that both genomes and gene expression are remarkably conserved. However, in N. caninum we identified an unexpected expansion of surface antigen gene families and the divergence of secreted virulence factors, including rhoptry kinases. Specifically we show that the rhoptry kinase ROP18 is pseudogenised in N. caninum and that, as a possible consequence, Neospora is unable to phosphorylate host immunity-related GTPases, as Toxoplasma does. This defense strategy is thought to be key to virulence in Toxoplasma. We conclude that the ecological niches occupied by these species are influenced by a relatively small number of gene products which operate at the host-parasite interface and that the dominance of vertical transmission in N. caninum may be associated with the evolution of reduced virulence in this species

Integrative analysis of multimodal mass spectrometry data in MZmine 3

3 Pág.We thank Christopher Jensen and Gauthier Boaglio for their contributions to the MZmine codebase. We thank Jianbo Zhang and Zachary Russ for their donations to MZmine development. The MZmine 3 logo was designed by the Bioinformatics & Research Computing group at the Whitehead Institute for Biomedical Research. T.P. is supported by Czech Science Foundation (GA CR) grant 21-11563M and by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement 891397. Support for P.C.D. was from US NIH U19 AG063744, P50HD106463, 1U24DK133658 and BBSRC-NSF award 2152526. T.S. acknowledges funding by Deutsche Forschungsgemeinschaft (441958208). M. Wang acknowledges the US Department of Energy Joint Genome Institute ( https://ror.org/04xm1d337 , a DOE Office of Science User Facility) and is supported by the Office of Science of the US Department of Energy operated under subcontract No. 7601660. E.R. and H.H. thank Wen Jiang (HILICON AB) for providing the iHILIC Fusion(+) column for HILIC measurements. M.F., K.D. and S.B. are supported by Deutsche Forschungsgemeinschaft (BO 1910/20). L.-F.N. is supported by the Swiss National Science Foundation (project 189921). D.P. was supported through the Deutsche Forschungsgemeinschaft (German Research Foundation) through the CMFI Cluster of Excellence (EXC-2124 — 390838134 project-ID 1-03.006_0) and the Collaborative Research Center CellMap (TRR 261 - 398967434). J.-K.W. acknowledges the US National Science Foundation (MCB-1818132), the US Department of Agriculture, and the Chan Zuckerberg Initiative. MZmine developers have received support from the European COST Action CA19105 — Pan-European Network in Lipidomics and EpiLipidomics (EpiLipidNET). We acknowledge the support of the Google Summer of Code (GSoC) program, which has funded the development of several MZmine modules through student projects. We thank Adam Tenderholt for introducing MZmine to the GSoC program.Peer reviewe

Entwicklung eines tokenbasierten Authentifizierungs- und Autorisierungssystems für eine verteilte Dateninfrastruktur

In der vorliegenden Arbeit wird ein Konzept und eine Implementierung zur Authen-tifizierung und Autorisierung von Benutzern und Ressourcen mit Hilfe des OAuth2-Protokolls in einer verteilten Dateninfrastruktur vorgestellt. Die Implementierung er-folgt in der Programmiersprache Java unter Zuhilfenahme des Spring-Frameworks.Das OAuth2-Protokoll wird ausführlich erläutert und die notwendigen Anpassungenan der bestehenden Dateninfrastruktur werden für alle definierten Entitäten des Pro-tokolls ausgeführt und dokumentiert. Es wird darauf eingegangen welche Sicherheits-maßnahmen sind erforderlich und wie diese am konkreten Beispiel zu implementierensind

Agamben in the Ogaden: Violence and sovereignty in the Ethiopian–Somali frontier

This paper asks what makes the periphery or the frontier a prime locus of the “inclusionary exclusion” that is, according to Giorgio Agamben, so constitutive of the state of exception. By applying Agamben’s analytics to the Ogaden e a frontier province of the Ethiopian state e we propose an interpretation of the political history of the Ethiopian Ogaden as a recurrent government by exception that spans the Imperial rule (c. 1890e1974), the socialist dictatorship of the Derg (1974e1991), and the current revolutionary democratic regime led by the Ethiopian Peoples’ Revolutionary Democratic Front (EPRDF) (1991etoday). Drawing attention to the historical continuities in the exercise of (Ethiopian) state sovereignty in its (Somali) frontier, we offer a genealogy of the violent incorporation of the Ogaden into the Ethiopian body politic. We identify recurring practices of sovereign power by successive Ethiopian regimes that are constitutive of the state of exception, namely a conflation between law and lawlessness, the politics of bare life and an encampment strategy. By doing so, this paper insists on the constitutive importance of land appropriation e Carl Schmitt’s Landnahme e in performances of sovereignty and territorialization at the margins of the postcolonial state