P. patens genomic and transcriptomic analyses

The model organism Physcomitrium patens, formerly Physcomitrella patens is a moss in the Funariaceae family. Due to P. patens ability to generate easily transgenic plants via homologous recombination, the interest of scientists worldwide was attracted. P. patens was the world's first completely sequenced non-seed plant genome (V1). Constant improvements of the genome assembly and the associated gene annotations resulted in the current P. patens pseudo-chromosomal genome version (V3). This genome version is the basis of all analyses performed in this thesis. Since P. patens became a U.S. Department of Energy Joint Genome Institute (DOE JGI) plant flagship genome 1 and a member of the JGI Gene Atlas project 2, hundreds of P. patens RNA-seq samples were generated. During my time as a PhD student, I analysed the JGI Gene Atlas RNA-seq samples and several dozen other RNA-seq samples from different projects. These RNA-seq samples contained data from five different P. patens ecotypes/accessions (Gransden, Kaskaskia, Reute, Villersexel, and Wisconsin).To efficiently analyse this data, I developed a powerful RNA-seq pipeline to perform differentially expressed gene (DEG) calling. The performance of the RNA-seq pipeline was tested by comparing its results to commercial software solutions and multiple RNA-seq samples from different species. My newly generated gene expression results, together with previous published expression data from a variety of other projects, were stored at our novel online tool PEATmoss. Furthermore, my gene version lookup tables were implemented in a database structure. This, allows PEATmoss users to find gene models of different gene annotation versions and to use them in PEATmoss. With an updated version of my RNA-seq pipeline, I identified and analysed sequence variations in P. patens accessions. A clear clustering by individual accessions could be shown. I could demonstrate, that due to decades of vegetative propagation in laboratories, somatic mutations have accumulated in Gransden laboratory plants. In addition, we used restriction fragment length polymorphism (RFLP) to offer a simple method for quick identification of unknown P. patens plants. 1 https://jgi.doe.gov/our-science/science-programs/plant-genomics/plant-flagship-genomes/ 2 https://jgi.doe.gov/doe-jgi-plant-flagship-gene-atlas

Dermaptera from Cyprus and Turkey.

Forficula smyrnensis Serville, 1839 wird erstmals von Zypern, Forficula lurida Fischer, 1853 und Labidura riparia (Pallas, 1773) werden aus der Türkei nachgewiesen. Eine Liste der bisher von Zypern und der Türkei bekannten Dermapteren wird vorgelegt. Darminhaltsuntersuchungen von Forficula lurida und Labidura riparia deuten auf eine carnivore Ernährungsweise hin; dagegen wurden bei Forficula smyrnensis ausschließlich pflanzliche Nahrungsreste gefunden.StichwörterForficula, Labidura, Turkey, Cyprus, Asia Minor, gut contents, feeding.Forficula smyrnensis Serville, 1839 is recorded for the first time from Cyprus, and Forficula lurida Fischer, 1853 and Labidura riparia (Pallas, 1773) are again recorded from Turkey. A list of Cypriot and Turkish Dermaptera previously recorded is given. The gut contents of Forficula lurida and Labidura riparia suggests carnivorous feeding habits, whereas in Forficula smyrnensis only plant fragments found.KeywordsForficula, Labidura, Turkey, Cyprus, Asia Minor, gut contents, feeding

Earwigs-online: Vor- und Nachteile einer selbst entwickelten Internetdatenbank.

Die Website www.earwigs-online.de widmet sich ausschließlich den Dermaptera (Ohrwürmer) und basiert auf einer Reihe von Datenbanken, die über die letzten 10 Jahre entwickelt wurden. Die Vernetzung und Programmierung erfolgte entsprechend den Kenntnissen und Bedürfnissen des alleinigen Nutzers, d.h. des Autors. Als weitere wichtige Elemente wurden automatische Verschlagwortung und eine digitale Bibliothek aufgenommen. Derzeit umfassen die Datenbanken rund 16.000 Einträge zur Verbreitung, 4.000 Literaturstellen, 7.200 Schlagworte, 5.000 Taxonnamen und eine digitale Bibliothek mit 1.000 Zusammenfassungen und Artikeln. Bei der Arbeit mit den Datenbanken kristallisierten sich eine Reihe von Vor- und Nachteilen heraus. Nachteilig an einem vereinzelten Projekt sind die Belastungen durch die Programmierung, Datensicherung und Internetanbindung, geringere bzw. keine (finanzielle) Unterstützung durch Projektträger und Arbeitgeber, sowie die Nichtverfügbarkeit der Daten in größeren Portalen. Als vorteilig erwiesen sich die Verfügbarkeit aller Daten zu jeder Zeit, die schnelle Veröffentlichbarkeit und die freie Kombinierbarkeit der Daten. Der gewichtigste Vorteil ist sicher die reine Existenz dieser Datenbank: Da Dermapteren in Wissenschaft, Medizin und Landwirtschaft nicht im Focus des Interesses stehen, ist es unwahrscheinlich, dass größere Projekte und Institutionen den Aufbau dieser Datenbanken betrieben hätten. Die Fülle der jetzt verfügbaren Daten wäre sicher nicht zugänglich.StichwörterDermaptera, Ohrwurm, Datenbank, Earwigs-online, Internetdatenbank, Digitale Bibliothek.The website www.earwigs-online.de is dedicated exclusively to the Dermaptera (earwigs) and is based on a series of databases developed during the last ten years. The programming and integration of the databases proceeded together with the developing knowledge and requirements of the sole user, namely the author. Important incorporated features are an automatic facility for selecting key words and a digital library with 1,000 abstracts and articles. At present the databases contain approximately 16,000 entries on distribution, 4,000 literature citations, 7,200 key words and 5,000 names of taxa. As work proceeded, a number of advantages and disadvantages became clear. Disadvantages in a single project are the burdens of programming, safeguarding data and providing a link with the internet, together with small or absent financial support by sponsors and employers, as well as the non-availability of the data in larger portals. It proved advantageous to have the data constantly available, and to be able to publish these quickly in a freely combined form. The most important advantage is certainly the very existence of this database. Earwigs are not the focus of interest in zoology, medicine or agriculture. It is therefore unlikely that larger projects and institutions would have created these databases. A wealth of data would have remained unavailable.KeywordsDermaptera, Ohrwurm, Datenbank, Earwigs-online, Internetdatenbank, Digitale Bibliothek

A TEMPORAL AND SPATIAL ANALYSIS OF EROSION PROCESSES IN CALANCHI BADLANDS. A CASE STUDY FROM THE UPPER ORCIA VALLEY WITH STATE-OF-THE-ART METHODOLOGIES

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From amino acid mixtures to peptides in liquid sulphur dioxide on early Earth

The formation of peptide bonds is one of the most important biochemical reaction steps. Without the development of structurally and catalytically active polymers, there would be no life on our planet. However, the formation of large, complex oligomer systems is prevented by the high thermodynamic barrier of peptide condensation in aqueous solution. Liquid sulphur dioxide proves to be a superior alternative for copper-catalyzed peptide condensations. Compared to water, amino acids are activated in sulphur dioxide, leading to the incorporation of all 20 proteinogenic amino acids into proteins. Strikingly, even extremely low initial reactant concentrations of only 50 mM are sufficient for extensive peptide formation, yielding up to 2.9% of dialanine in 7 days. The reactions carried out at room temperature and the successful use of the Hadean mineral covellite (CuS) as a catalyst, suggest a volcanic environment for the formation of the peptide world on early Earth

Inflammatory bowel disease following anti-interleukin-1-treatment in systemic juvenile idiopathic arthritis

BACKGROUND: Inflammatory bowel disease can develop in the context of some rheumatic diseases in childhood, including juvenile idiopathic arthritis (JIA). Inflammatory bowel disease (IBD) is frequently associated with other immune-mediated diseases; however, systemic onset JIA (sJIA) has not previously been connected to IBD. Treatment of sJIA has significantly changed in recent years, possibly causing changes in inflammatory patterns. Therefore, data from the German Center for Pediatric and Adolescent Rheumtology from 2010 until 2015 were analyzed by retrospective chart review. FINDINGS: Eighty-two patients with confirmed diagosis of sJIA were found. Of these, three were identified with a diagnosis of IBD confirmed by colonoscopy (two cases of Crohn's disease, one case of ulcerative colitis) 0.8 - 4.3 years after diagnosis. All three were treated with IL-1 antagonists (anakinra in two cases, canakinumab in one case) and were well controlled for sJIA symptoms at time of diagnosis of IBD CONCLUSIONS: IBD seems to be a rare, but possible complication of sJIA. Treatment with IL-1 antagonists might be a relevant factor for a switch in the clinical phenotype of the underlying inflammatory process

Sex chromosome dominance in a UV sexual system

Abstract: the alternation between multicellular haploid gametophytes and diploid sporophytes is a defining feature of most plant and algal life cycles. In such organisms, male and female sexes are determined in the haploid gametophyte with a female (U) or male (V) sex chromosome. Once the U and V chromosomes unite at fertilisation, sex determination no longer occurs, raising key questions about the fate of UV sex chromosomes in the diploid sporophyte stage of the life cycle. Here, we unravel the genetic and molecular interactions between the U and V chromosomes by assessing transcriptional and chromatin states across the life cycle of the brown algaEctocarpusalongsideouroborosmutants that decouple life cycle stage from ploidy. We reveal how sex chromosome genes are developmentally regulated across the life cycle, with genes involved in female sex determination in particular undergoing strong down-regulation in the sporophyte. Diploidouroborosmutants containing both a U and V sex chromosome behave as functional male gametophytes yet still exhibit feminized transcription, suggesting that presence of the V chromosome alone is insufficient to fully suppress female developmental program. Although the silencing of sex chromosome genes in the diploid sporophyte does not appear to correlate with localised changes in chromatin state, small RNAs may play a role in the repression of a female sex-linked gene. Finally, we show how histone H3K79me2 is globally re-configured in the diploid phase of the life cycle, including the sex determining region of the UV sex chromosomes. Contrary to its pattern in the haploid gametophyte, H3K79me2 no longer associates with repressed genes in the diploid sporophyte, suggesting that the function of this histone mark inEctocarpusmay be more complex than previously appreciated

Interactions between U and V sex chromosomes during the life cycle of Ectocarpus

In many animals and flowering plants, sex determination occurs in the diploid phase of the life cycle with XX/XY or ZW/ZZ sex chromosomes. However, in early diverging plants and most macroalgae, sex is determined by female (U) or male (V) sex chromosomes in a haploid phase called the gametophyte. Once the U and V chromosomes unite at fertilization to produce a diploid sporophyte, sex determination no longer occurs, raising key questions about the fate of the U and V sex chromosomes in the sporophyte phase. Here, we investigate genetic and molecular interactions of the UV sex chromosomes in both the haploid and diploid phases of the brown alga Ectocarpus. We reveal extensive developmental regulation of sex chromosome genes across its life cycle and implicate the TALE-HD transcription factor OUROBOROS in suppressing sex determination in the diploid phase. Small RNAs may also play a role in the repression of a female sex-linked gene, and transition to the diploid sporophyte coincides with major reconfiguration of histone H3K79me2, suggesting a more intricate role for this histone mark in Ectocarpus development than previously appreciated.</p