Establishment of the body axes in Xenopus laevis through goosecoid, myosin 1d and bicaudal c

The bilaterian body plan consists of three body axes: the anteroposterior (AP; head-trunk/tail), the dorsoventral (DV; back-belly) and the left-right (LR; placement of inner organs) axis. Axis formation occurs during early embryogenesis and is critical for further development and viability of the embryo. In this comprehensive study three highly conserved determinants were functionally analyzed in the context of axis development. The first chapter of this work covers the autoregulatory, homeodomain containing, repressor gene goosecoid (gsc), whose most prominent expression marks the Spemann-(Mangold) organizer (SO). The SO is the primary dorsal signaling center and is instructive for tissue patterning along the DV and AP axes. Transplanting the SO or misexpressing gsc on the opposite ventral side of an embryo is sufficient to establish a new/secondary AP axis. However, its function during normal development in the SO remained enigmatic as the gsc loss of function (LOF) lead to no severe early developmental defects. To elucidate the function of gsc, timed gain of function (GOF) experiments were performed. Gsc efficiently repressed the planar cell polarity (PCP)/Wnt signaling pathway leading to severe gastrulation and neurulation defects. This novel Gsc function was correlated with two vertebrate specific domains, suggesting an evolutionary new function of Gsc with the emergence of jaws/neural crests in vertebrates. The second chapter of this study addresses the functions of Myosin1d (Myo1d) and Bicaudal c1 (Bicc1) during the LR axis determination in vertebrates. In this group LR symmetry breakage takes place at a ciliated epithelium called LR organizer (LRO). The initial cue for the asymmetric LR axis development is a cilia-driven leftward fluid flow. These cilia have to be correctly polarized through PCP/Wnt signaling. Interestingly, the invertebrate Drosophila melanogaster also displays a distinct LR axis but uses a cilia independent, yet not fully understood, mechanism. It depends on a myo1d homologous gene, myo31DF, and PCP. To unravel a potential common evolutionary origin of the bilaterian LR axis myo1d was analyzed during Xenopus laevis lateralization. Myo1d LOF experiments disturbed LR axis formation by compromising PCP dependent outgrowth and polarization of LRO cilia. These experiments link the PCP/Myosin based mechanism of flies to the newly evolved cilia/flow dependent mode of vertebrate LR axis determination suggesting actomyosin as common ancestral LR determinant. Contrary to Myo1d, Bicc1 was already described for its function during polarization of flow producing LRO cilia. However bicc1s expression is most prominent in the sensory LRO cells (sLRO). These cells detect the fluid flow and translate it into left-sided signaling of the morphogen Nodal1 and consequently asymmetric LR axis formation. These cells downregulate the expression of the secreted Nodal1 antagonist DAN domain family member 5 (dand5) in response to flow. Bicc1s function was re-evaluated with respect to its function in sLRO cells. Ex vivo and in vivo experiments involving GOF as well as LOF experiments showed that Bicc1 regulates both dand5 and nodal1 via a direct and indirect post-transcriptional mechanism, respectively. In the process of dand5 regulation several other LR determinants and regulatory events were linked with the Bicc1 dependent mechanism: Dicer1 dependent microRNA repression of dand5 and a proposed cation channel Polycystin 2 mediated Bicc1 modification. These results highlight the importance of a tightly controlled Dand5 protein level as decisive for the overall outcome of the LR symmetry breakage in vertebrates.Der Körperbauplan von Bilateria setzt sich aus drei Körperachsen zusammen: Der anteroposterioren (AP; Längsachse), der dorsoventralen (DV; Rücken-Bauch) und der links-rechts (LR, Anordnung der inneren Organe) Achse. Die Körperachsenbildung findet während der frühen Embryonalentwicklung statt und ist entscheidend für die weitere Entwicklung und die Lebensfähigkeit des Embryos. In dieser umfassenden Arbeit wurden drei hoch konservierte Determinanten auf ihre Funktion während der Achsenentwicklung analysiert. Das erste Kapitel dieser Arbeit beschreibt die Funktion des autoregulatorischen Repressors und Homeoboxgens goosecoid (gsc), dessen bekannteste Expression den Spemann-(Mangold) Organisator (SO) markiert. Der SO ist das primäre dorsale Signalzentrum und bekannt für seine instruktive gewebespezifizierende Funktion entlang der AP- und der DV-Achse. Transplantation des SO oder Missexpression von gsc auf der gegenüberliegenden, ventralen, Seite des Embryos, ist ausreichend, um eine neue/zweite AP Körperachse zu erzeugen. Trotzdem blieb seine Funktion im SO während der normalen Entwicklung rätselhaft, da ein Funktionsverlust zu keinen massiven frühen Entwicklungsproblemen führte. Um die Funktion von gsc herauszufinden wurden zeitlich und räumlich terminierte Überexpressionen durchgeführt. Gsc reprimierte effizient den Planaren Zellpolaritäts (PCP)/Wnt Signalweg was zu ernsthaften Gastrulations- und Neurulationsdefekten führte. Die neu beschriebene Funktion von Gsc konnte mit zwei Wirbeltier-spezifischen Domänen korreliert werden. Dies suggerierte eine evolutionär neue Funktion von Gsc mit der Entstehung von Kiefern und Neuralleistenzellen in Wirbeltieren. Das zweite Kapitel dieser Arbeit behandelt die Funktion von Myosin1d (Myo1d) und Bicaudal c1 (Bicc1) während der LR Achsenentwicklung in Wirbeltieren. In dieser Tiergruppe wird die LR Symmetrie durch ein ciliertes Epithel, den sogenannten LR Organisator (LRO), gebrochen. Das erste Signal für die asymmetrische LR Entwicklung ist ein durch Cilien erzeugter linksgerichteter Flüssigkeitsstrom. Dafür müssen diese Cilien durch den PCP Signalweg korrekt polarisiert sein. Interessanterweise zeigt das wirbellose Tier Drosophila melanogaster auch eine eindeutige LR-Achse, für die sie allerdings einen Zilien-unabhängigen Mechanismus verwenden. Dieser ist bis heute noch nicht eindeutig geklärt, beruht aber auf dem myo1d orthologen Gen myo31DF und dem PCP Signalweg. Um einen potentiellen evolutionären Ursprung der LR Achsenentwicklung in Bilateria zu entschlüsseln, wurde myo1d während der Lateralisierung in Xenopus laevis analysiert. Funktionsverlust Experimente von Myo1d resultierten dabei in einer gestörten LR Achsenentwicklung, basierend auf einer Störung des PCP abhängigen Auswachsens und der Polarisierung der LRO-Cilien. Diese Experimente verbinden den PCP/Myosin abhängigen Mechanismus von Fliegen mit dem neu evolvierten Cilien/Flüssigkeitsstrom abhängigen Mechanismus der LR Achsenentwicklung in Wirbeltieren. Somit wird ein Actomyosin abhängiger Mechanismus als gemeinsamer ursprünglicher LR Achsendeterminant für Bilateria impliziert. Im Gegensatz zu Myo1d wurde für Bicc1 schon eine Funktion während der Polarisierung der LRO Cilien beschrieben. Dennoch ist die markanteste Expression von bicc1 in den sensorischen LRO Zellen (sLRO), welche den Flüssigkeitsstrom detektieren und in ein linksseitiges Signal des Morphogens Nodal1 umwandeln. Dieses Signal resultiert dann in der Entstehung der asymmetrischen LR Achse. Als Antwort auf den Flüssigkeitsstrom wird die Expression von dem sekretierten Nodal1-Antagonisten DAN domain family member 5 (dand5) in den sLRO Zellen runter reguliert. Die Funktion von Bicc1 sollte im Bezug auf die Funktion in den sLRO Zellen reevaluiert werden. Ex vivo und in vivo Funktionsverlust und Funktionsgewinn Experimente zeigten, dass Bicc1 sowohl dand5 direkt als auch nodal1 indirekt post-transkriptional reguliert. Desweiteren wurden auch andere LR Determinanten mit dem Mechanismus der Bicc1 abhängigen dand5 Regulation vernetzt: Die Dicer1 abhängige microRNA vermittelte Repression von dand5 und die mögliche Modifikation von Bicc1 in Abhängigkeit vom Kationen-Kanal Polycystin 2 (Pkd2). Diese Ergebnisse verdeutlichen maßgeblich die Bedeutung eines engmaschig kontrollierten Dand5 Proteinlevels für das Ergebnis des LR Symmetriebruchs in Wirbeltieren

Sub-Telomere Directed Gene Expression during Initiation of Invasive Aspergillosis

Aspergillus fumigatus is a common mould whose spores are a component of the normal airborne flora. Immune dysfunction permits developmental growth of inhaled spores in the human lung causing aspergillosis, a significant threat to human health in the form of allergic, and life-threatening invasive infections. The success of A. fumigatus as a pathogen is unique among close phylogenetic relatives and is poorly characterised at the molecular level. Recent genome sequencing of several Aspergillus species provides an exceptional opportunity to analyse fungal virulence attributes within a genomic and evolutionary context. To identify genes preferentially expressed during adaptation to the mammalian host niche, we generated multiple gene expression profiles from minute samplings of A. fumigatus germlings during initiation of murine infection. They reveal a highly co-ordinated A. fumigatus gene expression programme, governing metabolic and physiological adaptation, which allows the organism to prosper within the mammalian niche. As functions of phylogenetic conservation and genetic locus, 28% and 30%, respectively, of the A. fumigatus subtelomeric and lineage-specific gene repertoires are induced relative to laboratory culture, and physically clustered genes including loci directing pseurotin, gliotoxin and siderophore biosyntheses are a prominent feature. Locationally biased A. fumigatus gene expression is not prompted by in vitro iron limitation, acid, alkaline, anaerobic or oxidative stress. However, subtelomeric gene expression is favoured following ex vivo neutrophil exposure and in comparative analyses of richly and poorly nourished laboratory cultured germlings. We found remarkable concordance between the A. fumigatus host-adaptation transcriptome and those resulting from in vitro iron depletion, alkaline shift, nitrogen starvation and loss of the methyltransferase LaeA. This first transcriptional snapshot of a fungal genome during initiation of mammalian infection provides the global perspective required to direct much-needed diagnostic and therapeutic strategies and reveals genome organisation and subtelomeric diversity as potential driving forces in the evolution of pathogenicity in the genus Aspergillus

Vertebrate Left-Right Asymmetry: What Can Nodal Cascade Gene Expression Patterns Tell Us?

Laterality of inner organs is a wide-spread characteristic of vertebrates and beyond. It is ultimately controlled by the left-asymmetric activation of the Nodal signaling cascade in the lateral plate mesoderm of the neurula stage embryo, which results from a cilia-driven leftward flow of extracellular fluids at the left-right organizer. This scenario is widely accepted for laterality determination in wildtype specimens. Deviations from this norm come in different flavors. At the level of organ morphogenesis, laterality may be inverted (situs inversus) or non-concordant with respect to the main body axis (situs ambiguus or heterotaxia). At the level of Nodal cascade gene activation, expression may be inverted, bilaterally induced, or absent. In a given genetic situation, patterns may be randomized or predominantly lacking laterality (absence or bilateral activation). We propose that the distributions of patterns observed may be indicative of the underlying molecular defects, with randomizations being primarily caused by defects in the flow-generating ciliary set-up, and symmetrical patterns being the result of impaired flow sensing, on the left, the right, or both sides. This prediction, the reasoning of which is detailed in this review, pinpoints functions of genes whose role in laterality determination have remained obscure

A Conserved Role of the Unconventional Myosin 1d in Laterality Determination

Anatomical and functional asymmetries are widespread in the animal kingdom [ 1, 2 ]. In vertebrates, many visceral organs are asymmetrically placed [ 3 ]. In snails, shells and inner organs coil asymmetrically, and in Drosophila, genitalia and hindgut undergo a chiral rotation during development. The evolutionary origin of these asymmetries remains an open question [ 1 ]. Nodal signaling is widely used [ 4 ], and many, but not all, vertebrates use cilia for symmetry breaking [ 5 ]. In Drosophila, which lacks both cilia and Nodal, the unconventional myosin ID (myo1d) gene controls dextral rotation of chiral organs [ 6, 7 ]. Here, we studied the role of myo1d in left-right (LR) axis formation in Xenopus. Morpholino oligomer-mediated myo1d downregulation affected organ placement in \u3e50% of morphant tadpoles. Induction of the left-asymmetric Nodal cascade was aberrant in \u3e70% of cases. Expression of the flow-target gene dand5 was compromised, as was flow itself, due to shorter, fewer, and non-polarized cilia at the LR organizer. Additional phenotypes pinpointed Wnt/planar cell polarity signaling and suggested that myo1d, like in Drosophila [ 8 ], acted in the context of the planar cell polarity pathway. Indeed, convergent extension of gastrula explant cultures was inhibited in myo1d morphants, and the ATF2 reporter gene for non-canonical Wnt signaling was downregulated. Finally, genetic interference experiments demonstrated a functional interaction between the core planar cell polarity signaling gene vangl2 and myo1d in LR axis formation. Thus, our data identified myo1d as a common denominator of arthropod and chordate asymmetry, in agreement with a monophyletic origin of animal asymmetry

Bicc1 and Dicer regulate left-right patterning through post-transcriptional control of the Nodal inhibitor Dand5

Rotating cilia at the vertebrate left-right organizer (LRO) generate an asymmetric leftward flow, which is sensed by cells at the left LRO margin. Ciliary activity of the calcium channel Pkd2 is crucial for flow sensing. How this flow signal is further processed and relayed to the laterality-determining Nodal cascade in the left lateral plate mesoderm (LPM) is largely unknown. We previously showed that flow down-regulates mRNA expression of the Nodal inhibitor Dand5 in left sensory cells. De-repression of the co-expressed Nodal, complexed with the TGFß growth factor Gdf3, drives LPM Nodal cascade induction. Here, we show that post-transcriptional repression of dand5 is a central process in symmetry breaking of Xenopus, zebrafish and mouse. The RNA binding protein Bicc1 was identified as a post-transcriptional regulator of dand5 and gdf3 via their 3'-UTRs. Two distinct Bicc1 functions on dand5 mRNA were observed at pre- and post-flow stages, affecting mRNA stability or flow induced translational inhibition, respectively. To repress dand5, Bicc1 co-operates with Dicer1, placing both proteins in the process of flow sensing. Intriguingly, Bicc1 mediated translational repression of a dand5 3'-UTR mRNA reporter was responsive to pkd2, suggesting that a flow induced Pkd2 signal triggers Bicc1 mediated dand5 inhibition during symmetry breakage

Soil erosion modelling: a bibliometric analysis

Soil erosion can present a major threat to agriculture due to loss of soil, nutrients, and organic carbon. Therefore, soil erosion modelling is one of the steps used to plan suitable soil protection measures and detect erosion hotspots. A bibliometric analysis of this topic can reveal research patterns and soil erosion modelling characteristics that can help identify steps needed to enhance the research conducted in this field. Therefore, a detailed bibliometric analysis, including investigation of collaboration networks and citation patterns, should be conducted. The updated version of the Global Applications of Soil Erosion Modelling Tracker (GASEMT) database contains information about citation characteristics and publication type. Here, we investigated the impact of the number of authors, the publication type and the selected journal on the number of citations. Generalized boosted regression tree (BRT) modelling was used to evaluate the most relevant variables related to soil erosion modelling. Additionally, bibliometric networks were analysed and visualized. This study revealed that the selection of the soil erosion model has the largest impact on the number of publication citations, followed by the modelling scale and the publication's CiteScore. Some of the other GASEMT database attributes such as model calibration and validation have negligible influence on the number of citations according to the BRT model. Although it is true that studies that conduct calibration, on average, received around 30% more citations, than studies where calibration was not performed. Moreover, the bibliographic coupling and citation networks show a clear continental pattern, although the co-authorship network does not show the same characteristics. Therefore, soil erosion modellers should conduct even more comprehensive review of past studies and focus not just on the research conducted in the same country or continent. Moreover, when evaluating soil erosion models, an additional focus should be given to field measurements, model calibration, performance assessment and uncertainty of modelling results. The results of this study indicate that these GASEMT database attributes had smaller impact on the number of citations, according to the BRT model, than anticipated, which could suggest that these attributes should be given additional attention by the soil erosion modelling community. This study provides a kind of bibliographic benchmark for soil erosion modelling research papers as modellers can estimate the influence of their paper