Ignicoccus und Nanoarchaeum: 3D-Struktur und Proteom

Die ungewöhnliche Ultrastruktur sowie die interarchaeelle Beziehung von Ignicoccus hospitalis und Nanoarchaeum geben nach wie vor Rätsel auf. In dieser Arbeit wurden Zellen mit FIB/SEM und Elektronentomographie in 3D visualisiert und analysiert. In den FIB/SEM Analysen zeigte Ignicoccus ein komplexes endogenes Membransystem zusätzlich zu einer äußeren Membran. Dieses System besteht aus röhrenförmigen Ausbuchtungen des Cytoplasmas und sehr wenigen „freien Vesikeln“. Die Zellen sind daher kompartimentiert, aber auch polarisiert. Die Beziehung der einzelnen Kompartimente zueinander wurde umfangreich diskutiert, auch unter dem Aspekt von Ähnlichkeiten zum eukaryotischen endogenen Membransystem. Zusätzlich wurden potentielle Polyphosphatspeicher im Cytoplasma charakterisiert. Die Elektronentomographie Daten zeigten durch ihre hohe Auflösung zusätzliche strukturelle Besonderheiten: eine umfangreiche Matrix aus Filamenten im ‚Inter-membrane compartment‘, ringförmige Strukturen als Mittler zwischen der inneren und äußeren Membran und eine Fusion der Cytoplasmen, wenn Nanoarchaeum an Ignicoccus anheftet. Weiterhin wurden in weitreichenden Proteomanalysen ca. 80% der vorhergesagten Proteine für Ignicoccus gefunden und 85% für Nanoarchaeum. In den Transkriptomanalysen war der Abdeckungswert sogar ca. 97% und beweist so die Hypothese eines ‚streamlined genomes‘ in Ignicoccus. Vergleichende Studien zeigten nur geringen Einfluss von Nanoarchaeum auf Ignicoccus (sowohl auf Protein- als auch mRNA-Ebene). Tendenziell wurden Energiemetabolismus und CO2-Fixierung hochreguliert, während Transkription und Zellteilung reprimiert wurden. Letzlich wurden verschiedene Proteine (vor allem Homologe des eukaryotischen Vesikeltransportsystems) in Ignicoccus lokalisiert. Anhand der Ergebnisse werden Spekulationen über mögliche Funktionen diskutiert

Visual Interactive Comparison of Part-of-Speech Models for Domain Adaptation

Interactive visual analysis of documents relies critically on the ability of machines to process and analyze texts. Important techniques for text processing include text summarization, classification, or translation. Many of these approaches are based on part-of-speech tagging, a core natural language processing technique. Part-of-speech taggers are typically trained on collections of modern newspaper, magazine, or journal articles. They are known to have high accuracy and robustness when applied to contemporary newspaper style texts. However, the performance of these taggers deteriorates quickly when applying them to more domain specific writings, such as older or even historical documents. Large training sets tend to be scarce for these types of texts due to the limited availability of source material and costly digitization and annotation procedures. In this paper, we present an interactive visualization approach that facilitates analysts in determining part-of-speech tagging errors by comparing several standard part-of-speech tagger results graphically. It allows users to explore, compare, evaluate, and adapt the results through interactive feedback in order to obtain a new model, which can then be applied to similar types of texts. A use case shows successful applications of the approach and demonstrates its benefits and limitations. In addition, we provide insights generated through expert feedback and discuss the effectiveness of our approach

Functional compartmentalization and metabolic separation in a prokaryotic cell

The prokaryotic cell is traditionally seen as a “bag of enzymes,” yet its organization is much more complex than in this simplified view. By now, various microcompartments encapsulating metabolic enzymes or pathways are known for Bacteria. These microcompartments are usually small, encapsulating and concentrating only a few enzymes, thus protecting the cell from toxic intermediates or preventing unwanted side reactions. The hyperthermophilic, strictly anaerobic Crenarchaeon Ignicoccus hospitalis is an extraordinary organism possessing two membranes, an inner and an energized outer membrane. The outer membrane (termed here outer cytoplasmic membrane) harbors enzymes involved in proton gradient generation and ATP synthesis. These two membranes are separated by an intermembrane compartment, whose function is unknown. Major information processes like DNA replication, RNA synthesis, and protein biosynthesis are located inside the “cytoplasm” or central cytoplasmic compartment. Here, we show by immunogold labeling of ultrathin sections that enzymes involved in autotrophic CO2 assimilation are located in the intermembrane compartment that we name (now) a peripheric cytoplasmic compartment. This separation may protect DNA and RNA from reactive aldehydes arising in the I. hospitalis carbon metabolism. This compartmentalization of metabolic pathways and information processes is unprecedented in the prokaryotic world, representing a unique example of spatiofunctional compartmentalization in the second domain of life

MultiMediate'23: Engagement Estimation and Bodily Behaviour Recognition in Social Interactions

Automatic analysis of human behaviour is a fundamental prerequisite for the creation of machines that can effectively interact with- and support humans in social interactions. In MultiMediate'23, we address two key human social behaviour analysis tasks for the first time in a controlled challenge: engagement estimation and bodily behaviour recognition in social interactions. This paper describes the MultiMediate'23 challenge and presents novel sets of annotations for both tasks. For engagement estimation we collected novel annotations on the NOvice eXpert Interaction (NOXI) database. For bodily behaviour recognition, we annotated test recordings of the MPIIGroupInteraction corpus with the BBSI annotation scheme. In addition, we present baseline results for both challenge tasks.Comment: ACM MultiMedia'2

Drawn Stories, Moving Images. Comic Books and their Screen Adaptations

The comic transcends the merely entertaining, and fans of comics become engaged and invested in the field through a range of activities. Major cities host regular comic conventions, attracting hundreds of thousands of attendees each year, who search for special issues of their favourite comic-book series, meet artists, attend workshops and buy merchandise. Many fans do not stop at just attending conventions; they do so dressed as their favourite comic characters or wearing badges, buttons, T-shirts or sweaters with images of those characters on them. In other words: many fans do ot merely consume comic books; rather, they arrange a considerable part of their lives around them and in some cases even embody their heroes, that is, they copy their behaviour and their language. The comic universe, the comic books and the range of activities emerging out of them and around them become a meaningful universe for fans

Super Resolution Fluorescence Microscopy and Tracking of Bacterial Flotillin (Reggie) Paralogs Provide Evidence for Defined-Sized Protein Microdomains within the Bacterial Membrane but Absence of Clusters Containing Detergent-Resistant Proteins

Biological membranes have been proposed to contain microdomains of a specific lipid composition, in which distinct groups of proteins are clustered. Flotillin-like proteins are conserved between pro—and eukaryotes, play an important function in several eukaryotic and bacterial cells, and define in vertebrates a type of so-called detergent-resistant microdomains. Using STED microscopy, we show that two bacterial flotillins, FloA and FloT, form defined assemblies with an average diameter of 85 to 110 nm in the model bacterium Bacillus subtilis. Interestingly, flotillin microdomains are of similar size in eukaryotic cells. The soluble domains of FloA form higher order oligomers of up to several hundred kDa in vitro, showing that like eukaryotic flotillins, bacterial assemblies are based in part on their ability to self-oligomerize. However, B. subtilis paralogs show significantly different diffusion rates, and consequently do not colocalize into a common microdomain. Dual colour time lapse experiments of flotillins together with other detergent-resistant proteins in bacteria show that proteins colocalize for no longer than a few hundred milliseconds, and do not move together. Our data reveal that the bacterial membrane contains defined-sized protein domains rather than functional microdomains dependent on flotillins. Based on their distinct dynamics, FloA and FloT confer spatially distinguishable activities, but do not serve as molecular scaffolds

Emergence of fractal geometries in the evolution of a metabolic enzyme

Fractals are patterns that are self-similar across multiple length-scales. Macroscopic fractals are common in nature; however, so far, molecular assembly into fractals is restricted to synthetic systems. Here we report the discovery of a natural protein, citrate synthase from the cyanobacterium Synechococcus elongatus, which self-assembles into Sierpiński triangles. Using cryo-electron microscopy, we reveal how the fractal assembles from a hexameric building block. Although different stimuli modulate the formation of fractal complexes and these complexes can regulate the enzymatic activity of citrate synthase in vitro, the fractal may not serve a physiological function in vivo. We use ancestral sequence reconstruction to retrace how the citrate synthase fractal evolved from non-fractal precursors, and the results suggest it may have emerged as a harmless evolutionary accident. Our findings expand the space of possible protein complexes and demonstrate that intricate and regulatable assemblies can evolve in a single substitution