Protein tyrosine phosphatases in glioma biology

Gliomas are a diverse group of brain tumors of glial origin. Most are characterized by diffuse infiltrative growth in the surrounding brain. In combination with their refractive nature to chemotherapy this makes it almost impossible to cure patients using combinations of conventional therapeutic strategies. The drastically increased knowledge about the molecular underpinnings of gliomas during the last decade has elicited high expectations for a more rational and effective therapy for these tumors. Most studies on the molecular pathways involved in glioma biology thus far had a strong focus on growth factor receptor protein tyrosine kinase (PTK) and phosphatidylinositol phosphatase signaling pathways. Except for the tumor suppressor PTEN, much less attention has been paid to the PTK counterparts, the protein tyrosine phosphatase (PTP) superfamily, in gliomas. PTPs are instrumental in the reversible phosphorylation of tyrosine residues and have emerged as important regulators of signaling pathways that are linked to various developmental and disease-related processes. Here, we provide an overview of the current knowledge on PTP involvement in gliomagenesis. So far, the data point to the potential implication of receptor-type (RPTPδ, DEP1, RPTPμ, RPTPζ) and intracellular (PTP1B, TCPTP, SHP2, PTPN13) classical PTPs, dual-specific PTPs (MKP-1, VHP, PRL-3, KAP, PTEN) and the CDC25B and CDC25C PTPs in glioma biology. Like PTKs, these PTPs may represent promising targets for the development of novel diagnostic and therapeutic strategies in the treatment of high-grade gliomas

Measurement of cos⁡2β\cos{2\beta} in B0→D(∗)h0B^{0} \to D^{(*)} h^{0} with D→KS0π+π−D \to K_{S}^{0} \pi^{+} \pi^{-} decays by a combined time-dependent Dalitz plot analysis of BaBar and Belle data

We report measurements of $\sin{2\beta}$ and $\cos{2\beta}$ from a time-dependent Dalitz plot analysis of $B^{0} \to D^{(*)} h^{0}$ with $D \to K_{S}^{0} \pi^{+} \pi^{-}$ decays, where the light unflavored and neutral hadron $h^{0}$ is a $\pi^{0}$, $\eta$, or $\omega$ meson. The analysis is performed with a combination of the final data sets of the \babar\ and Belle experiments containing $471 \times 10^{6}$ and $772 \times 10^{6}$ $B\bar{B}$ pairs collected at the $\Upsilon\left(4S\right)$ resonance at the asymmetric-energy B factories PEP-II at SLAC and KEKB at KEK, respectively. We measure $\sin{2\beta} = 0.80 \pm 0.14 \,(\rm{stat.}) \pm 0.06 \,(\rm{syst.}) \pm 0.03 \,(\rm{model})$ and $\cos{2\beta} = 0.91 \pm 0.22 \,(\rm{stat.}) \pm 0.09 \,(\rm{syst.}) \pm 0.07 \,(\rm{model})$. The result for the direct measurement of the angle is $\beta = \left( 22.5 \pm 4.4 \,(\rm{stat.}) \pm 1.2 \,(\rm{syst.}) \pm 0.6 \,(\rm{model}) \right)^{\circ}$. The last quoted uncertainties are due to the composition of the $D^{0} \to K_{S}^{0} \pi^{+} \pi^{-}$ decay amplitude model, which is newly established by a Dalitz plot amplitude analysis of a high-statistics $e^{+}e^{-} \to c\bar{c}$ data sample as part of this analysis. We find the first evidence for $\cos2\beta>0$ at the level of $3.7$ standard deviations. The measurement excludes the trigonometric multifold solution $\pi/2 - \beta = (68.1 \pm 0.7)^{\circ}$ at the level of $7.3$ standard deviations and therefore resolves an ambiguity in the determination of the apex of the CKM Unitarity Triangle. The hypothesis of $\beta = 0^{\circ}$ is ruled out at the level of $5.1$ standard deviations, and thus CP violation is observed in $B^{0} \to D^{(*)} h^{0}$ decays.Comment: To be submitted to Physical Review

Identification of microorganisms in Aerobic Granular Sludgeactively involved in biological phosphorus removal

One of the aims of the treatment of domestic and industrial wastewater is the removal of phosphorus prior to discharge into the environment. Since phosphorus concentrations in wastewater exceed the requirement of bacterial growth, biological phosphorus removal is based on the ability of a group of microorganisms, named “Polyphosphate Accumulating Organisms” (PAO), to form large quantities of polyphosphate in their cells. In this study, we are focussing on the bacteria actively involved in the phosphorus removal in a lab scale bioreactor operated with aerobic granular sludge technology. This process based on dense microbial biofilms is a cost-effective and land-saving alternative to the conventional wastewater treatment with activated sludge. The identification of the microorganisms belonging to PAO relies on their distinct phenotype assessed with fluorescent probes targeting the intracellular polyphosphate structures. Sequencing of the 16S rRNA gene amplicons of PAO selected with flow-cytometry will be used to reveal the phylogenetic affiliation of the different actors involved in the phosphorus removal. This is of particular significance since low abundant microorganisms may play an important role in the phosphorus removal performance of aerobic granular sludge. We hypothesize that the maintenance of different populations involved in the same functional process is explained by multiple ecological niches present in such biofilm structures

Identification of bacteria from wastewater for the oxidation of micropollutants

The term "micropollutants" includes xenobiotic compounds of various origins which can be found in aquatic environments at concentration levels of nano- to micrograms per liter and which present a negative effect on ecosystems. Many aromatic micropollutants present in municipal wastewater are due to human activities, such as pharmaceuticals or biocides, and are not easily removed by conventional biological treatments in wastewater treatment plants (WWTPs). Fungal laccases and other multicopper oxidases are known to efficiently oxidize a wide spectrum of aromatic compounds, while a few in vitro studies on bacterial enzymes have also suggested the potential to use bacterial oxidases to increase the removal efficiency of micropollutants in WWTPs. In the present study, we chose to focus on the oxidative activities displayed by bacteria present in WWTPs. One aim of this work was to develop a screening method to isolate microorganisms producing oxidases with a potential activity on aromatic micropollutants. The microorganisms were selected on solid rich medium for their ability to oxidize 2,6-dimethoxyphenol (DMP), a chromogenic compound which becomes brown upon oxidation. DMP was chosen among other chromogenic substrates as it was not affecting bacterial growth, is nicely oxidized at neutral pH and is mimicking the basic structure of aromatic micropollutants. Selected bacterial isolates were identified as members of different genera (Pseudomonas, Comamonas, Enterobacter, …) and their ability to oxidize DMP was confirmed in liquid cultures as well as using an in vitro enzymatic assay with crude extracts. Preliminary observations suggested that DMP oxidation is linked with the stationary phase of bacterial growth. Further characterization of the physiology and biochemistry of the oxidases is under investigation for a subset of isolates

The capture technology matters: Composition of municipal wastewater solids drives complexity of microbial community structure and volatile fatty acid profile during anaerobic fermentation

The production of volatile fatty acids (VFAs) represents a relevant option to valorize municipal wastewater (MWW). In this context, different capture technologies can be used to recover organic carbon from wastewater in form of solids, while pre-treatment of those solids has the potential to increase VFA production during subsequent fermentation. Our study investigates how VFA composition produced by fermentation is influenced (i) by the choice of the capture technology, as well as (ii) by the use of thermal alkaline pre-treatment (TAP). Therefore, the fermentation of solids originating from a primary settler, a micro-sieve, and a high-rate activated sludge (HRAS) system was investigated in continuous lab-scale fermenters, with and without TAP. Our study demonstrates that the capture technology strongly influences the composition of the produced solids, which in turn drives the complexity of the fermenter's microbial community and ultimately, of the VFA composition. Solids captured with the primary settler or micro-sieve consisted primarily of polysaccharides, and led to the establishment of a microbial community specialized in the degradation of complex carbohydrates. The produced VFA composition was relatively simple, with acetate and propionate accounting for >90% of the VFAs. In contrast, the HRAS system produced biomass-rich solids associated with higher protein contents. The microbial community which then developed in the fermenter was therefore more diversified and capable of converting a wider range of substrates (polysaccharides, proteins, amino acids). Ultimately, the produced VFA composition was more complex, with equal fractions of isoacids and propionate (both ~20%), while acetate remained the dominant acid (~50%). Finally, TAP did not significantly modify the VFA composition while increasing VFA yields on HRAS and sieved material by 35% and 20%, respectively. Overall, we demonstrated that the selection of the technology used to capture organic substrates from MWW governs the composition of the VFA cocktail, ultimately with implications for their further utilization.ISSN:0048-9697ISSN:1879-102

Imaging the aerobic granular sludge microbial community using light-sheet fluorescence micros

One of the aims of wastewater treatment is the removal of phosphorus before the water is discharged into the environment. Since phosphorus concentrations in wastewater exceed the requirement of bacterial growth, biological phosphorus removal is based on the ability of a group of microorganisms, named “Polyphosphate Accumulating Organisms” (PAO), to store large quantities of intracellular phosphate in form of polyphosphate. In this study, we are focusing on the PAO actively involved in bioreactors operated with Aerobic Granular Sludge (AGS) technology. This process based on dense microbial biofilms is a cost-effective and landsaving alternative to the conventional biological wastewater treatment with activated sludge. This promising technology has received a significant commercial interest, but questions remain unanswered regarding the system performances in the context of full-scale applications. Like many natural microbial communities, the microbial structure of the AGS is complex. Its spatial organization is shaped by the diffusion of nutrients from the external environment and by the diffusion of microbial by-products formed in the biofilm. Understanding how the AGS microbial community works requires the elucidation of its spatial architecture and development. Light-sheet fluorescence microscopy is a powerful tool for examining microbial communities by overcoming the limitations of the classical three-dimensional confocal fluorescence microscopy. This technique shapes the excitation laser into a thin sheet providing an optical sectioning in order to illuminate the sample on a single plane. Then the emission signal is collected by a perpendicular lens. The large datasets generated are analyzed with a pipeline on the FIJI platform[1] to extract quantitative information. Preliminary results indicate that AGS are composed of heterogeneous biofilm aggregates. Interestingly, our observations are contrasting the AGS model structure previously described[2]. We would like to highlight the necessity of multiple observations when highly variable structures, like AGS, are analyzed in order to capture data which are representative of the studied system. [1] Schindelin et al. in Nat. Methods 28;9(7):676-82 (2012) [2] Winkler et al. in Water Res. 15;46(16):4973-80 (2012)   Poster 3 Conférence: Swiss Microbial Ecology Meeting 2019 (Lausanne) Titre: Anaerobic Biodegradation of organohalide pollutants: a crucial step towards the elucidation of proteins involved Auteurs: Lorenzo Cimmino, Adrian Schmid, Christof Holliger, Julien Maillard Abstract: Halogenated organic compounds (so-called organohalides) represent one of the major class of groundwater pollutants. The exploration of how organohalides are used as energy source is important in terms of ecosystem remediation but is also essential for the complete understanding of microbial metabolic interactions in the environment. Organohalide respiration (OHR) is a bacterial anaerobic process in which chlorinated compound, e.g. tetrachloroethene (PCE), is used as terminal electron acceptor. In the present work, Desulfitobacterium hafniense TCE1 and Dehalobacter restrictus, our model organohalide-respiring bacteria (OHRB) harbouring the pceABCT gene cluster, will be considered for the study of PCE respiration. To date, the function of PceA, the key catalytic enzyme in the process, and PceT, the dedicated molecular chaperone for PceA maturation, are well defined. However, the roles of PceB and PceC are not yet elucidated and the biochemistry of OHR electron transfer is still relatively elusive. Based on the genetic composition of the pce gene cluster, the hypothesis of a possible PceABC respiratory complex is tempting but the question remains largely unanswered. The present work represents an evaluation of the stoichiometry of PceA, PceB and PceC proteins via quantitative proteomics applied to the membranes fractions of our model organisms. In a second phase, the use of Blue-Native electrophoresis technology will be considered to investigate whether PceC participates in a membrane-bound protein complex toge

Polyphosphate - a key biopolymer in aerobic granular sludge technology

Polyphosphate is the key biopolymer in wastewater treatment (WWT) processes applying enhanced biological phosphorus removal (EBPR) by polyphosphate-accumulating organisms (PAO). Alternating anaerobic (no oxygen and no nitrate) and aerobic phases is used to promote a net phosphorus removal from the wastewater as PAO are capable to take up and store phosphate as intracellular polyphosphate during the aerobic growth phase. In the anaerobic phase, PAO replenish their carbon and energy source in form of polyhydroxyalkanoates (PHA) from volatile fatty acids (VFA) present or formed in the wastewater. The energy and reducing equivalents needed to form PHA come from glycogen and polyphosphate, the polymers that are replenished during the aerobic phase. A few PAO have been already identified, among which Candidatus Accumulibacter phosphatis is a major player in WWT microbial communities enriched with VFA. However, depending on the carbon source the microbial community can strongly fluctuate and other PAO might play a major role in phosphorus removal. We are studying the dynamics of microbial communities in lab-scale aerobic granular sludge sequencing batch reactors subjected to changes of carbon source going from simple VFA to a mixture of VFA, glucose and amino acids. Both metagenomic approaches targeting polyphosphate kinase (ppk) genes and functional analysis of PAO using fluorescence techniques staining the polyphosphate polymer allow us to investigate the key metabolic genes in the synthesis of polyphosphate and expand the knowledge on the diversity of PAO in such engineered systems