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

Efficacy of Budesonide Orodispersible Tablets as Induction Therapy for Eosinophilic Esophagitis in a Randomized Placebo-Controlled Trial.

BACKGROUND & AIMS: Swallowed topical-acting corticosteroids are recommended as first-line therapy for eosinophilic esophagitis (EoE). Asthma medications not optimized for esophageal delivery are sometimes effective, although given off-label. We performed a randomized, placebo-controlled trial to assess the effectiveness and tolerability of a budesonide orodispersible tablet (BOT), which allows the drug to be delivered to the esophagus in adults with active EoE. METHODS: We performed a double-blind, parallel study of 88 adults with active EoE in Europe. Patients were randomly assigned to groups that received BOT (1 mg twice daily; n = 59) or placebo (n = 29) for 6 weeks. The primary end point was complete remission, based on clinical and histologic factors, including dysphagia and odynophagia severity ≤2 on a scale of 0-10 on each of the 7 days before the end of the double-blind phase and a peak eosinophil count <5 eosinophils/high power field. Patients who did not achieve complete remission at the end of the 6-week double-blind phase were offered 6 weeks of open-label treatment with BOT (1 mg twice daily). RESULTS: At 6 weeks, 58% of patients given BOT were in complete remission compared with no patients given placebo (P < .0001). The secondary end point of histologic remission was achieved by 93% of patients given BOT vs no patients given placebo (P < .0001). After 12 weeks, 85% of patients had achieved remission. Six-week and 12-week BOT administration were safe and well tolerated; 5% of patients who received BOT developed symptomatic, mild candida, which was easily treated with an oral antifungal agent. CONCLUSIONS: In a randomized trial of adults with active EoE, we found that budesonide oral tablets were significantly more effective than placebo in inducing clinical and histologic remission. Eudra-CT number 2014-001485-99; ClinicalTrials.gov ID NCT02434029

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

Peroxisomal core structures segregate diverse metabolic pathways

Peroxisomes are single membrane-bounded oxidative organelles with various metabolic functions including β-oxidation of fatty acids. Peroxisomes of many species confine certain metabolic enzymes into sub-compartments sometimes visible as electron dense cores. Why these structures form is largely unknown. Here, we report that in the smut fungus Ustilago maydis detergent resistant core structures are enriched for different enzymes excluding several key enzymes of the β-oxidation pathway. This confinement contributes to generation of peroxisome subpopulations that differ in their enzyme content. We identify short amino acid motifs necessary and sufficient for protein self-assembly into aggregates in vitro. The motifs trigger enrichment in cores in vivo and are active in mammalian cells. Perturbation of core assembly via variation of such motifs affects peroxisome function in U. maydis strains challenged with fatty acids. Thus, protein core structures serve to compartmentalize the lumen of peroxisomes thereby preventing interference of biochemical reactions. Metabolic compartmentalization of peroxisomes via assembly of specific proteins may occur in other organisms as well

Membrane binding properties of the cytoskeletal protein bactofilin

Bactofilins are a widespread family of cytoskeletal proteins that are essential for bacterial morphogenesis, chromosome organization, and motility. They assemble into non-polar filaments independently of nucleotides and typically associate with the cytoplasmic membrane. Their membrane interaction is thought to involve a short N-terminal peptide, but the underlying mechanism is unclear. Here, we clarify the complete membrane-targeting sequence (MTS) of the Caulobacter crescentus bactofilin BacA and identify residues critical for its function. Using molecular dynamics simulations, we show that its affinity for membranes arises from hydrophobic residue-driven water exclusion and electrostatic interactions with negatively charged phospholipid headgroups. Bioinformatic analysis suggests that this mode of membrane binding is conserved across diverse bacterial phyla. Importantly, we observe that BacA polymerization and membrane binding stimulate each other, and both of these processes are necessary for recruiting the membrane-bound client protein PbpC, a cell wall synthase that interacts with BacA via its N-terminal cytoplasmic region. PbpC can functionally replace the MTS of BacA when overproduced, demonstrating that client proteins contribute to the bactofilin-membrane association. Thus, bactofilin assembly and localization are determined by a complex interplay of different factors, thereby enabling the adaptation of these processes to the needs of the systems they control