Mechanisms governing the pioneering and redistribution capabilities of the non-classical pioneer PU.1

Establishing gene regulatory networks during differentiation or reprogramming requires master or pioneer transcription factors (TFs) such as PU.1, a prototype master TF of hematopoietic lineage differentiation. To systematically determine molecular features that control its activity, here we analyze DNA-binding in vitro and genome-wide in vivo across different cell types with native or ectopic PU.1 expression. Although PU.1, in contrast to classical pioneer factors, is unable to access nucleosomal target sites in vitro, ectopic induction of PU.1 leads to the extensive remodeling of chromatin and redistribution of partner TFs. De novo chromatin access, stable binding, and redistribution of partner TFs both require PU.1's N-terminal acidic activation domain and its ability to recruit SWI/SNF remodeling complexes, suggesting that the latter may collect and distribute co-associated TFs in conjunction with the non-classical pioneer TF PU.1

A Trigger Enzyme in Mycoplasma pneumoniae: Impact of the Glycerophosphodiesterase GlpQ on Virulence and Gene Expression

Mycoplasma pneumoniae is a causative agent of atypical pneumonia. The formation of hydrogen peroxide, a product of glycerol metabolism, is essential for host cell cytotoxicity. Phosphatidylcholine is the major carbon source available on lung epithelia, and its utilization requires the cleavage of deacylated phospholipids to glycerol-3-phosphate and choline. M. pneumoniae possesses two potential glycerophosphodiesterases, MPN420 (GlpQ) and MPN566. In this work, the function of these proteins was analyzed by biochemical, genetic, and physiological studies. The results indicate that only GlpQ is an active glycerophosphodiesterase. MPN566 has no enzymatic activity as glycerophosphodiesterase and the inactivation of the gene did not result in any detectable phenotype. Inactivation of the glpQ gene resulted in reduced growth in medium with glucose as the carbon source, in loss of hydrogen peroxide production when phosphatidylcholine was present, and in a complete loss of cytotoxicity towards HeLa cells. All these phenotypes were reverted upon complementation of the mutant. Moreover, the glpQ mutant strain exhibited a reduced gliding velocity. A comparison of the proteomes of the wild type strain and the glpQ mutant revealed that this enzyme is also implicated in the control of gene expression. Several proteins were present in higher or lower amounts in the mutant. This apparent regulation by GlpQ is exerted at the level of transcription as determined by mRNA slot blot analyses. All genes subject to GlpQ-dependent control have a conserved potential cis-acting element upstream of the coding region. This element overlaps the promoter in the case of the genes that are repressed in a GlpQ-dependent manner and it is located upstream of the promoter for GlpQ-activated genes. We may suggest that GlpQ acts as a trigger enzyme that measures the availability of its product glycerol-3-phosphate and uses this information to differentially control gene expression

A MIMO-OFDM testbed, channel measurements, and system considerations for outdoor-indoor WiMAX

The design, implementation, and test of a real-time flexible 2×2 (Multiple Input Multiple Output-Orthogonal Frequency Division Multiplexing) MIMO-OFDM IEEE 802.16 prototype are presented. For the design, a channel measurement campaign on the 3.5GHz band has been carried out, focusing on outdoor-indoor scenarios. The analysis of measured channels showed that higher capacity can be achieved in case of obstructed scenarios and that (Channel Distribution Information at the Transmitter) CDIT capacity is close to (Channel State Information at the Transmitter) CSIT with much lower complexity and requirements in terms of channel estimation and feedback. The baseband prototype used an (Field Programmable Gate Array) FPGA where enhanced signal processing algorithms are implemented in order to improve system performance. We have shown that for MIMO-OFDM systems, extra signal processing such as enhanced joint channel and frequency offset estimation is needed to obtain a good performance and approach in practice the theoretical capacity improvements

Daten, Kombinatorik, Wahrscheinlichkeit 3/4. Arbeitsheft Daten, Kombinatorik, Wahrscheinlichkeit 3/4

Peter-Koop A, Streit-Lehmann J, Bassin L, Pinker-Schmidl L. Daten, Kombinatorik, Wahrscheinlichkeit 3/4. Arbeitsheft Daten, Kombinatorik, Wahrscheinlichkeit 3/4 . Welt der Zahl. Braunschweig: Westermann; 2022

The Stability of Cytadherence Proteins in Mycoplasma pneumoniae Requires Activity of the Protein Kinase PrkC▿ †

Mycoplasma pneumoniae belongs to the mollicutes, a group of bacteria that have strongly reduced genomes but that are nevertheless capable of independent life. With only three transcription factors, the regulatory features of these bacteria are very limited. Thus, posttranslational regulation might be important for M. pneumoniae. In addition to the highly specific HPr kinase, the M. pneumoniae prkC gene encodes the serine/threonine protein kinase C. In order to study the function(s) of this kinase, we isolated an M. pneumoniae mutant affected in PrkC. This mutation resulted in nonadherent growth and loss of cytotoxicity. Examination of the phosphorylation profile of the prkC mutant suggested that phosphorylation of cytadherence proteins was affected by the loss of this kinase. In contrast, inactivation of the prpC gene affecting the protein phosphatase that antagonizes PrkC-dependent phosphorylation resulted in more intensive phosphorylation of the cytadherence proteins HMW1 and HMW3 of the major adhesin P1 and of the surface protein MPN474. Moreover, loss of PrkC affects not only the phosphorylation state of the cytadherence proteins but also their intracellular accumulation. However, the expression of the corresponding genes was not affected by PrkC, suggesting that PrkC-dependent phosphorylation results in stabilization of the cytadherence proteins. The HMW proteins and P1 are part of the so-called terminal organelle of M. pneumoniae that is involved in gliding motility, cell division, and adhesion to host epithelial tissues. Our observations suggest that the posttranslational modification of cytadherence proteins by PrkC is essential for the development and function of the M. pneumoniae terminal organelle

Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1

The transcription factor PU.1 is crucial for the development of many hematopoietic lineages and its binding patterns significantly change during differentiation processes. However, the 'rules' for binding or not-binding of potential binding sites are only partially understood. To unveil basic characteristics of PU.1 binding site selection in different cell types, we studied the binding properties of PU.1 during human macrophage differentiation. Using in vivo and in vitro binding assays, as well as computational prediction, we show that PU.1 selects its binding sites primarily based on sequence affinity, which results in the frequent autonomous binding of high affinity sites in DNase I inaccessible regions (25-45% of all occupied sites). Increasing PU.1 concentrations and the availability of cooperative transcription factor interactions during lineage differentiation both decrease affinity thresholds for in vivo binding and fine-tune cell type-specific PU.1 binding, which seems to be largely independent of DNA methylation. Occupied sites were predominantly detected in active chromatin domains, which are characterized by higher densities of PU.1 recognition sites and neighboring motifs for cooperative transcription factors. Our study supports a model of PU.1 binding control that involves motif-binding affinity, PU.1 concentration, cooperativeness with neighboring transcription factor sites and chromatin domain accessibility, which likely applies to all PU.1 expressing cells

Kombinierte Programmevaluierung der Christian Doppler Labors und Josef Ressel Zentren 2016

Die vorliegende Evaluierung wird im Auftrag des Bundesministeriums für Wissenschaft, Forschung und Wirtschaft (BMWFW) durchgeführt, deren Förderprogramme „Förderung der Einrichtung und des Betriebs von Christian Doppler Labors“ und „Förderung und Einrichtung des Betriebs von Josef Ressel Zentren“ von der CDG abgewickelt werden. Die gesamte Evaluierung orientiert sich am Vor-bild der Nutzen-, Programm- und Systemevaluierung aus dem Jahr 2011 (vgl. Economica/IWI 2012). Zusätzlich werden in der aktuellen Evaluierung die Josef Ressel Zentren sowie ergänzende Module (Finanzierung der Grundlagenforschung, Patentanalyse) einbezogen. Zielsetzung ist es, das Förderprogramm bzw. die beiden zu evaluierenden Programme hinsichtlich ihrer Wirkungsebenen Output (Kennzahlenebene), Outcome (Ebene der operationalisierbaren Ziele) und Impact (Ebene der wirtschafts- und gesellschaftspolitischen Ziele) mittels der Economica/IWI. Methodik zu untersuchen. Aufbauend auf den Ergebnissen der Kenndatenerhebung erfolgt in einem zweiten Schritt die Untersuchung der Zielerreichung der Programme im Rahmen der Programmevaluierung. Schließlich wird ein Vergleich der aktuellen Ergebnisse mit jenen aus 2011 vorgenommen