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Characterizing the hologenome of Lasallia pustulata and tracing genomic footprints of lichenization
(2017)
The lichen symbiosis – consisting of fungal mycobionts and photoautotroph photobionts (green algae or cyanobacteria) – is globally successful. It covers an estimated 6% of the global surface with habitats ranging from deserts to the arctic. This success is reflected in the diversity of the mycobionts, with around 21% of all fungal species participating in lichen symbioses that can be facultative or obligate. Lichenization is furthermore evolutionary old, with fossil evidence for lichens reaching back 415 million years. For an individual fungal lineage, the Lecanoromycetes, the lichenization happened around 300 million years ago. This longstanding symbiotic relationship and the diversity of observed symbiotic dependency make them promising models to study the genomic consequences that follow the establishment of symbioses. Despite this, only little is known about the genomic effects of lichenization and extreme symbiotic dependency. To fill this gap we sequenced the hologenome of the lichen Lasallia pustulata, where the mycobiont could so far not been cultivated, suggesting that it might be more dependent on its symbionts.
As the poor culturability of lichen symbionts renders their genomes inaccessible to standard sequencing practices, we evaluated the extent to which different metagenome sequencing- and de novo assembly-strategies can be used to sequence and reconstruct the genomes of the individual symbionts. We find that the abundances of individual genomes present in the L. pustulata hologenome vary substantially, with the mycobiont being most abundant. Using in silico generated data sets and real Illumina sequencing data for L. pustulata we observe that the skewed abundances prevent a contiguous assembly of the underrepresented genomes when using only short-read sequencing. We conclude that short-read sequencing can offer first insights into lichen hologenomes. The fragmentation of the reconstructions hinders downstream analyses into the genomic consequences of lichenization though, as these are focused on identifying the gain and loss of genes.
We thus demonstrate a hybrid genome assembly strategy that is based on both short- and long-read sequencing. We show that this strategy is capable of creating highly contiguous genome reconstructions, not only for the L. pustulata mycobiont but also its photobiont Trebouxia sp., along with substantial amounts of the bacterial microbiome. A subsequent analysis of the microbiome of L. pustulata – performed over nine different samples collected in Germany and Italy – showed a stable taxonomic composition across the geographic range. We find that Acidobacteriaceae, which are known to thrive in nutrient poor habitats, are the dominant taxa. These would make them well adapted for the co-habitation with L. pustulata, which largely grows on rocks. Whether the Acidobacteriaceae are functionally involved in the lichen symbiosis is unclear so far.
As further comparative genomic studies rely on comprehensive genome annotations, we evaluate the completeness and fidelity of the gene annotations for the mycobiont L. pustulata as well as four further Lecanoromycetes. This reveals that un- and mis-annotated genes impact all evaluated genomes, with artificially joined genes and unannotated genes having the largest impact. In addition to these factors we find that the sequence composition – especially G/C-rich inverted repeats – lead to sequencing errors that interfere with the gene prediction. We minimize the effects of these artifacts through a rigorous curation.
Given the extremely sparse taxon sampling of available green alga genomes, we focus our search for the genomic footprints of lichenization on the mycobionts. We compare the genomes of the Lecanoromycetes to their closest relatives, the Eurotiomycetes and Dothideomycetes. This reveals that the last common ancestor of the Lecanoromycetes has lost around 10% of its genes after they split from the non-lichenized ancestor they share with the Eurotiomycetes. These losses are furthermore enriched, showing an excessive loss of genes involved with the degradation of polysaccharides. The loss of these genes fits a change from an ancestral saprotrophic lifestyle that depends on degrading complex plant matter, to the symbiotic lifestyle that relies on simpler nutrients provided by the photobionts. While the last common ancestor of the Lecanoromycetes additionally gained around 400 genes these could so far not be further characterized due to a lack of functionally annotated reference data.
As the mycobiont L. pustulata could so far not been grown in axenic culture, we initially expected to find an extensive genomic remodeling compared to the other mycobionts that easily grow in culture. We do not find evidence for this. Analyzing both the contraction of gene families and the loss of genes, we observe that L. pustulata and Umbilicaria muehlenbergii – its close relative that is easily grown in culture – share most of these. Furthermore, L. pustulata does not show an excessive loss of evolutionary old and well-conserved genes. These effects are mirrored on the functional level, as neither gene family contractions nor gene losses show a functional enrichment. This is partially due to the lack of functional reference data, analogous to the genes gained in the Lecanoromycetes, rendering their characterization hard. Thus, further studies on the genomic consequences of lichenization and differences in symbiotic dependence will have to be conducted, including larger taxon sets. This will be even more important for the photobionts, as the Chlorophyta are even more sparsely sampled today, hindering an effective functional and evolutionary study.
Inhalt
1. Strauß, Johann (Vater:/Sr.) (* 14.3.1804 – † 25.9.1849) [3]
2. Strauß, Johann (Sohn:/Jr.) (* 25.10.1825 – † 3.6.1899) [6]
3. Die Operetten-Adaptionen [12]
3.1 Die Fledermaus (Operette in 3 Akten, Johann Strauß, Sohn) :/:/ UA: 5.4.1874 [12]
3.2 Eine Nacht in Venedig (Operette in 3 Akten, Johann Strauß, Sohn) :/:/ UA: 3.10.1883 [17]
3.3 Der Zigeunerbaron (Operette in 3 Akten, Johann Strauß, Sohn) :/:/ UA: 24.10.1885 [18]
3.4 Wiener Blut (Johann Strauß, Sohn) :/:/ UA: 25.10.1899 [19]
3.5 Frühlingsluft (Jose. Strauß) :/:/ UA: 9.5.1903 [
Les Blank
(2017)
Hans-Joachim Schlegel
(2017)
Chromosomal translocations - leading to the expression of fusion genes - are well-studied genetic abberrations associated with the development of leukemias. Most of them represent altered transcription factors that affect transcription or epigenetics, while others - like BCR-ABL - are enhancing signaling. BCR-ABL has become the prototype for rational drug design, and drugs like Imatinib and subsequently improved drugs have a great impact on cancer treatments. By contrast, MLL-translocations in acute leukemia patients are hard to treat, display a high relapse rate and the overall survival rate is still very poor. Therefore, new treatment modalities are urgently needed. Based on the molecular insights of the most frequent MLL rearrangements, BET-, DOT1L-, SET- and MEN1/LEDGF-inhibitors have been developed and first clinical studies were initiated. Not all results of these studies have are yet available, however, a first paper reports a failure in the DOT1L-inhibitor study although it was the most promising drug based on literature data. One possible explanation is that all of the above mentioned drugs also target the cognate wildtype proteins. Here, we want to strengthen the fact that efforts should be made to develop drugs or strategies to selectively inhibit only the fusion proteins. Some examples will be given that follow exactly this guideline, and proof-of-concept experiments have already demonstrated their feasibility and effectiveness. Some of the mentioned approaches were using drugs that are already on the market, indicating that there are existing opportunities for the future which should be implemented in future therapy strategies.
Tissue size regulation is critical for the normal functioning of the organ as well as to prevent unwanted pathogenesis such as cancer. The Hippo signaling pathway is well known for its robust regulation of tissue growth by the negative regulation of its nuclear effectors YAP1 and WWTR1. In this study, I have described the role of Yap1/Wwtr1 in zebrafish development, with a primary emphasis on the cardiovascular system.
I have generated zebrafish yap1 and wwtr1 mutants by CRISPR/CAS9. The mutant alleles are likely to be nonfunctional due to a premature stop codon and they show evidence of nonsense-mediated decay. Given that Yap1 and Wwtr1 are closely related proteins and have overlapping functions, I am given the opportunity to perform combinatorial analysis of the mutations on zebrafish development. Together with molecular probing tools, high-throughput sequencing and high-resolution imaging, I showed that
1. Double yap1;wwtr1 mutants exhibit severe posterior elongation phenotype, but somitogenesis appears to proceed as usual.
2. Yap1 and Wwtr1 may play an important role in PCV development and secondary angiogenic sprouting. However, key experiments will be needed to elucidate the direct role of Yap1 and Wwtr1 on these processes.
3. wwtr1-/- larvae hearts have a reduction in trabeculation, but in mosaic WT hearts, mutant cardiomyocytes prefer to populate the trabecular layer. My studies revealed that the mutant compact wall could not support trabeculation, which explains the hypotrabeculation phenotype of wwtr1-/- hearts. Additionally, Wwtr1 is required for myocardial Notch activity and can inhibit compact wall cardiomyocytes from entering the trabecular layer.
In summary, the Hippo signaling pathway, through Yap1/Wwtr1 has important regulatory functions in growth control. My work has revealed a surprising role for Yap1/Wwtr1 in tissue morphogenesis such as posterior tail morphogenesis and specific developmental processes of the cardiovascular system. It will be of interest to elucidate the regulation of Yap1/Wwtr1 in individual cells that translates into the complex cellular behaviors that drives morphogenesis.
Galunisertib, a Transforming growth factor-βRI (TGF-βRI) kinase inhibitor, blocks TGF-β-mediated tumor growth in glioblastoma. In a three-arm study of galunisertib (300 mg/day) monotherapy (intermittent dosing; each cycle =14 days on/14 days off), lomustine monotherapy, and galunisertib plus lomustine therapy, baseline tumor tissue was evaluated to identify markers associated with tumor stage (e.g., histopathology, Ki67, glial fibrillary acidic protein) and TGF-β-related signaling (e.g., pSMAD2). Other pharmacodynamic assessments included chemokine, cytokine, and T cell subsets alterations. 158 patients were randomized to galunisertib plus lomustine (n = 79), galunisertib (n = 39) and placebo+lomustine (n = 40). In 127 of these patients, tissue was adequate for central pathology review and biomarker work. Isocitrate dehydrogenase (IDH1) negative glioblastoma patients with baseline pSMAD2+ in cytoplasm had median overall survival (OS) 9.5 months vs. 6.9 months for patients with no tumor pSMAD2 expression (p = 0.4574). Eight patients were IDH1 R132H+ and had a median OS of 10.4 months compared to 6.9 months for patients with negative IDH1 R132H (p = 0.5452). IDH1 status was associated with numerically higher plasma macrophage-derived chemokine (MDC/CCL22), higher whole blood FOXP3, and reduced tumor CD3+ T cell counts. Compared to the baseline, treatment with galunisertib monotherapy preserved CD4+ T cell counts, eosinophils, lymphocytes, and the CD4/CD8 ratio. The T-regulatory cell compartment was associated with better OS with MDC/CCL22 as a prominent prognostic marker.
Die Erfassung von subjektiven Theorien von bildungsfernen Personen gestaltet sich schwierig, wenn die Personen nicht in der Lage sind, ihre Theorien formal zu abstrahieren. In dieser Publikation wird ein Verfahren beschrieben, mit welchen Schritten dennoch subjektive Theorien zur aufgestellten Forschungsfrage extrahiert werden können. Das Verfahren basiert auf einer systematischen Auswertung von transkribierten Interviews.
Human brain dynamics and functional connectivity fluctuate over a range of temporal scales in coordination with internal states and environmental demands. However, the neurobiological significance and consequences of functional connectivity dynamics during rest have not yet been established. We show that the coarse-grained clustering of whole-brain dynamic connectivity measured with magnetic resonance imaging reveals discrete patterns (dynamic connectivity states) associated with wakefulness and sleep. We validate this using EEG in healthy subjects and patients with narcolepsy and by matching our results with previous findings in a large collaborative database. We also show that drowsiness may account for previous reports of metastable connectivity states associated with different levels of functional integration. This implies that future studies of transient functional connectivity must independently monitor wakefulness. We conclude that a possible neurobiological significance of dynamic connectivity states, computed at a sufficiently coarse temporal scale, is that of fluctuations in wakefulness.
NEK family kinases are serine/threonine kinases that have been functionally implicated in the regulation of the disjunction of the centrosome, the assembly of the mitotic spindle, the function of the primary cilium and the DNA damage response. NEK1 shows pleiotropic functions and has been found to be mutated in cancer cells, ciliopathies such as the polycystic kidney disease, as well as in the genetic diseases short-rib thoracic dysplasia, Mohr-syndrome and amyotrophic lateral sclerosis. NEK1 is essential for the ionizing radiation DNA damage response and priming of the ATR kinase and of Rad54 through phosphorylation. Here we report on the structure of the kinase domain of human NEK1 in its apo- and ATP-mimetic inhibitor bound forms. The inhibitor bound structure may allow the design of NEK specific chemo-sensitizing agents to act in conjunction with chemo- or radiation therapy of cancer cells. Furthermore, we characterized the dynamic protein interactome of NEK1 after DNA damage challenge with cisplatin. Our data suggest that NEK1 and its interaction partners trigger the DNA damage pathways responsible for correcting DNA crosslinks.
CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin
(2017)
Many pathogenic bacteria produce pore-forming toxins to attack and kill human cells. We have determined the 4.5 Å structure of the ~2.2 MDa pore complex of pneumolysin, the main virulence factor of Streptococcus pneumoniae, by cryoEM. The pneumolysin pore is a 400 Å ring of 42 membrane-inserted monomers. Domain 3 of the soluble toxin refolds into two ~85 Å β-hairpins that traverse the lipid bilayer and assemble into a 168-strand β-barrel. The pore complex is stabilized by salt bridges between β-hairpins of adjacent subunits and an internal α-barrel. The apolar outer barrel surface with large sidechains is immersed in the lipid bilayer, while the inner barrel surface is highly charged. Comparison of the cryoEM pore complex to the prepore structure obtained by electron cryo-tomography and the x-ray structure of the soluble form reveals the detailed mechanisms by which the toxin monomers insert into the lipid bilayer to perforate the target membrane.
Membrane proteins frequently assemble into higher order homo- or hetero-oligomers within their natural lipid environment. This complex formation can modulate their folding, activity as well as substrate selectivity. Non-disruptive methods avoiding critical steps, such as membrane disintegration, transfer into artificial environments or chemical modifications are therefore essential to analyze molecular mechanisms of native membrane protein assemblies. The combination of cell-free synthetic biology, nanodisc-technology and non-covalent mass spectrometry provides excellent synergies for the analysis of membrane protein oligomerization within defined membranes. We exemplify our strategy by oligomeric state characterization of various membrane proteins including ion channels, transporters and membrane-integrated enzymes assembling up to hexameric complexes. We further indicate a lipid-dependent dimer formation of MraY translocase correlating with the enzymatic activity. The detergent-free synthesis of membrane protein/nanodisc samples and the analysis by LILBID mass spectrometry provide a versatile platform for the analysis of membrane proteins in a native environment.
Summary: Persistence with osteoporosis therapy is vital for fracture prevention. This non-interventional study of postmenopausal women receiving denosumab in Germany, Austria, Greece, and Belgium found that persistence with denosumab remains consistently high after 24 months in patients at high risk of fracture.
Purpose: Continued persistence with osteoporosis therapy is vital for fracture prevention. This non-interventional study of clinical practice evaluated medication-taking behavior of postmenopausal women receiving denosumab in Germany, Austria, Greece, and Belgium and factors influencing persistence.
Methods: Subcutaneous denosumab (60 mg every 6 months) was assigned according to prescribing information and local guidelines before and independently of enrollment; outcomes were recorded during routine practice for up to 24 months. Persistence was defined as receiving the subsequent injection within 6 months + 8 weeks of the previous injection and adherence as administration of subsequent injections within 6 months ± 4 weeks of the previous injection. Medication coverage ratio (MCR) was calculated as the proportion of time a patient was covered by denosumab. Associations between pre-specified baseline covariates and 24-month persistence were assessed using multivariable logistic regression.
Results: The 24-month analyses included 1479 women (mean age 66.3–72.5 years) from 140 sites; persistence with denosumab was 75.1–86.0%, adherence 62.9–70.1%, and mean MCR 87.4–92.4%. No covariate had a significant effect on persistence across all four countries. For three countries, a recent fall decreased persistence; patients were generally older with chronic medical conditions. In some countries, other covariates (e.g., older age, comorbidity, immobility, and prescribing reasons) decreased persistence. Adverse drug reactions were reported in 2.3–6.9% patients.
Conclusions: Twenty-four-month persistence with denosumab is consistently high among postmenopausal women in Europe and may be influenced by patient characteristics. Further studies are needed to identify determinants of low persistence.
Gleichstellungs-Monitor 2016
(2017)
Der Kaiserschnitt ist wahrscheinlich eine der am häufigsten durchgeführten operativen Eingriffe weltweit. Noch vor einem Jahrhundert galt er als Notoperation, um das Leben des Kindes und der Mutter zu retten, heute hat er zu einer gängigen Geburtspraxis etabliert, fast jedes dritte Kind kommt mittlerweile per Sectio zu Welt. Dieser signifikante Anstieg trat in den letzten Jahren viele polarisierende Diskussionen los, die nach den Ursachen dieses Wandels forschen. Die Weltgesundheitsorganisation kritisiert, dass der unnötige Anstieg in Lateinamerika und Asien bereits epidemische Ausmaße erreicht habe. Im Mittelpunkt der Forschung stehen die diversen Indikationen, die maternalen und neonatalen Kurz- und Langzeitfolgen sowie die Vor- und Nachteile verschiedener anästhetischer Verfahren während des Eingriffs.
Ziel dieser Arbeit war es, das Forschungsaufkommen zum Thema Sectio zwischen 1900 und 2013 sowohl nach quantitativen als auch nach qualitativen Aspekten zu beleuchten, wobei auf die Daten im Web of Science zurückgegriffen wurde. Nach Festlegung eines Suchterminus mit maximaler Trefferanzahl wurde ein Datenpool von 12.608 Publikationen gewonnen, dessen bibliographische Daten im Rahmen von unterschiedlichen Fragestellungen untersucht und ausgewertet wurden. Um die Ergebnisse anschaulich zu repräsentieren, wurden diverse Diagrammarten gewählt, für globale Sachverhalte wurde Kartenanamorphoten verwendet.
Für das ausgewählte Datenkontingent ist die Sprache Englisch dominierend, es wurden 92,8 % aller identifizierten Publikationen (≙ 11.706 von 12.608) in dieser Sprache abgefasst. Hierbei stellt der Article die am häufigsten gewählte Erscheinungsform (57,4 %) dar.
Die Publikationsanzahl hat im Laufe des betrachteten Jahrhunderts stetig zugenommen. Dieser Zuwachs erfolgte vor allem in den letzten drei Dekaden, was zum einen am gestiegenen Forschungsinteresse am Thema Kaiserschnitt und zum anderen an der gestiegenen Publikationsanzahl liegt. Zudem wurde im Jahre 1991 bei der Datenbankabfrage die Topics-Suche eingeführt. Einzelne Publikationsmaxima können darauf zurückgeführt werden, dass die
Wissenschaft gesteigertes Interesse an wegweisenden Entwicklungen rund um das Thema Kaiserschnitt zeigte.
Das Land, das am meisten Publikationen (29 %) hervorbrachte, ist die USA – dort befinden sich auch die meisten Institutionen (1.517), die zum Thema Kaiserschnitt Forschung betreiben und es ist das Land mit dem höchsten h-Index (84). Resultierend aus diesen Daten kann den USA eine herausragende Position bezüglich der behandelnden Thematik zugeschrieben werden. Doch auch in europäischen Ländern wie Großbritannien und Deutschland kann eine hohe Forschungsaktivität nachgewiesen werden. Bei Betrachtung der Zitationsrate der Länder lag Schweden vorne (20,4), obwohl dort deutlich weniger publiziert wurde. Neben der renommierten Harvard University war auch die Partners Healthcare, Boston an der Forschung maßgeblich beteiligt.
Bei der Zeitschriftenanalyse ist das American Journal of Obstetrics and Gynecology mit 1.432 Publikationen das meistpublizierende Fachjournal, mit 16.446 Zitierungen ist es auch gleichzeitig das meistzitierte. Die höchste Zitationsrate von 19,97 wurde der Zeitschrift Obstetrics&Gynecology zuteil, gefolgt von Anesthesia&Analgesia.
Es konnte eine signifikante Korrelation festgestellt werden zwischen der Publikationsanzahl und dem Zeitraum, in denen diese veröffentlicht wurden
Bei den Autorenanalysen wurde die Leistung anhand von Publikationsvolumen, Zitationsrate und h-Index beurteilt. Als produktivster Autor wurde Prof. Aaron Caughey identifiziert, er publizierte 70mal zum Thema Kaiserschnitt, zum Großteil jedoch als Letztautor. Den höchsten h-Index erreicht der Wissenschaftler Kenneth Leveno mit einem Wert von 23, die höchste Zitationsrate Baha Sibai mit 42,26.
Es konnte ebenfalls aufgezeigt werden, dass die Kooperationsbeziehungen in den letzten Jahren an Bedeutung gewonnen haben und vor allem ab Beginn des 21. Jahrhunderts signifikant angestiegen sind. Zurückzuführen ist diese Entwicklung auf die vereinfachte und schnelle Kommunikation aufgrund der weiterentwickelten Technik und die vorangeschrittene Globalisierung. Die USA
ist der bedeutendste Kooperationspartner unter den Ländern, intensive Zusammenarbeit kann für Großbritannien und Kanada festgestellt werden.