Quickscan III

13 October 2018
#Wheat #Phosphoproteomics #High temperature
Wheat is one of the most important human food sources, but this crop is very sensitive to temperature changes. While this has been investigated on various levels to some extent, very little is known about early signaling events associated with an increase in temperature. Here, Lam Dai Vu, Tingting Zhu and colleagues in the Ive De Smet group (VIB-UGent Center for Plant Systems Biology) and the Kris Gevaert group (VIB-UGent Center for Medical Biotechnology) present the impact of a short-term and mild increase in temperature on the phosphoproteome, allowing us to capture phosphorylation-mediated signaling mechanisms.
Vu, Zhu et al., Journal of Experimental Botany 2018

#RNF41 #Interactome
RNF41 is an E3 ubiquitin ligase involved in a diverse set of cellular processes including signaling of various receptors, intracellular trafficking and apoptosis. The Jan Tavernier and Sven Eyckerman Labs (VIB-UGent Center for Medical Biotechnology) jointly established a high-confidence interactome map of RNF41 thereby providing a unique tool for further elucidation of the role of RNF41. This first RNF41 interactome was generated by using three MS-based orthogonal assays, Virotrap, BioID and AP-MS, combined with datasets from previously performed microarray MAPPIT and Y2H screens.
Masschaele et al., Journal of Proteome Research 2018

#Microglia #A20
Microglial cells are the resident mononuclear phagocytes of the CNS and have a functional role in both immune defense and CNS maintenance. These cells may however also acquire a detrimental pro-inflammatory phenotype that actively contributes to the chronicity of inflammatory brain diseases, including the neuroinflammatory disease multiple sclerosis (MS). Sofie Voet of the Geert van Loo Lab (VIB-UGent Center for Inflammation Research) showed that the anti-inflammatory protein A20 plays a critical role in the control of microglia activation in CNS homeostasis, but also in MS-like disease by regulating inflammasome activation and Interleukin-1b secretion.
Voet et al., Nature Communications 2018

#Programmed cell death #Senescence #Flower
The transience of flowers is proverbial. Flower life span is tightly regulated and defines the time frame in which flowers can be pollinated to produce fruit and seed. Zhen Gao and colleagues from the Moritz Nowack lab (VIB-UGent Center for Plant Systems Biology) show that age-induced programmed cell death in the pollen-receiving floral stigma contributes to the termination of floral receptivity in Arabidopsis. This knowledge might provide new leads to modulate flower longevity as a means to stabilize seed set and fruit yield in crops.
Gao et al., Nature Plants 2018

#OxidativeStress #RedoxRegulation
The Joris Messens Lab (VIB-VUB Center for Structural Biology), in collaboration with the Frank Van Breusegem Lab (VIB-UGent Center for Plant Systems Biology) and the Kris Gevaert Lab (VIB-UGent Center for Medical Biotechnology), identified the proteome of oxidized methionines in Arabidopsis thaliana leaves exposed to high light stress. To understand the influence of the post-translational modifications on protein function, glutathione transferase Tau23 and Phi9, which detoxify herbicides, were structurally and kinetically characterized. Our findings showed that under oxidizing conditions, both enzymes maintain functionality using different compensatory mechanisms. In addition, redox regulatory systems restore the activity of both enzymes. These studies provide insights on how enzymes remain functional under oxidizing conditions and help plants survive oxidative stress.
Tossounian et al., BBA General subjects 2017
Tossounian et al., Protein Science 2018

#Glucocorticoids #Compound A #Lymphoid malignancies
Glucocorticoids (GCs) are a cornerstone in the treatment of lymphoid malignancies, but prolonged GC treatment is hampered by deleterious side effects and GC resistance. To tackle and overcome these GC-related problems, Dorien Clarisse and Karolien De Bosscher (VIB-UGent Center for Medical Biotechnology), assessed the combination of classical GCs with a plant-derived anti-inflammatory, Compound A, as a treatment for lymphoid malignancies.
Yet, this combination neither enhances GC-induced apoptosis, nor prolongs GC responsiveness of lymphoid malignant cells.
Clarisse et al., PLoS One 2018

#PromethION #Visualization
The Christine Van Broeckhoven Lab (VIB-UAntwerp Center for Molecular Neurology) is employing the long-read sequencing platforms MinION and PromethION from Oxford Nanopore Technologies, which provide invaluable additions to the toolbox of genetic research. However, software tailored to the dominant short read technologies is not always appropriate for these long reads. To address this issue, we developed NanoPack, a set of tools for processing, creating statistical summaries and visualizing long-read sequencing data. Our software enables in-depth quality control and comparison across datasets.
De Coster et al., Bioinformatics 2018

#Glucocorticoid Receptor #STAT1 #TNF-induced inflammation
Researchers from the Claude Libert Lab (VIB-UGent Center for Inflammation Research) found that the Glucocorticoid Receptor (GR), as a homodimer, controls the expression of another transcription factor, STAT1. When this control fails in the intestinal epithelium, an interferon response develops spontaneously because of permanent stimulation by the microbes. This response sensitizes the epithelium to cell death, and the whole organism to sepsis. This data reveals a new level of interplay between microbiota and gene expression control in the intestinal epithelium.
Ballegeer, Van Looveren et al., Journal of Clinical Investigation 2018

#Alzheimer’s disease #ABCA7
ABCA7 is one of the most compelling new risk genes for Alzheimer’s disease (AD), but previously identified loss-of-function mutations in ABCA7 could not account for the observed genome-wide association. The lab of Kristel Sleegers, part of the Neurodegenerative Brain Diseases Group (VIB-UAntwerp Center for Molecular Neurology), discovered that this association is explained by tandem repeat expansions in ABCA7. These expansions alter ABCA7 alternative splicing and AD biomarkers in cerebrospinal fluid and strongly increase the risk of disease.
De Roeck et al., Acta Neuropathy 2018

#Spatial learning #Retrosplenial cortex
The retrosplenial cortex (RSC) is involved in spatial learning, and RSC neurons exhibit discrete sequence activity that resembles hippocampal place cell activity. A team jointly led by Vincent Bonin (NERF, VIB-KU Leuven-imec) and Bruce McNaughton (University of Lethbridge) found that RSC spatial coding improves with experience and relies on instructive signals from the hippocampus. This data supports the theory that the hippocampus endows the RSC (and possibly other cortical areas) with an index-like, continuous representation of the spatial context of events that could support coordinated retrieval of recent memory.
Mao et al., PNAS 2018

#Superior colliculus #Visual processing
The superior colliculus plays an important role in the orienting responses of the eye, head and body. The team of Karl Farrow (NERF, VIB-KU Leuven-imec) used two-photon calcium imaging to record the activity of collicular neurons in mice and determine whether their receptive field properties show any systematic organization around the monocular-binocular border, where information from the two eyes meets. Nasal and temporal motion selectivity were found to be separated in retinotopic space, illustrating the important coherence between the spatial organization of inputs and response properties within the visual system.
de Malmazet et al., Current Biology 2018

#Synaptic identity #LRR proteins
The group of Joris de Wit (VIB-KU Leuven Center for Brain & Disease Research) showed that hippocampal pyramidal neurons express multiple Leucine-rich repeat adhesion molecules with specific synaptic distributions. FLRT2, LRRTM1 and Slitrk1 have different effects on synaptic architecture and function, and act in input-specific combinations and in a context-dependent manner to specify synaptic properties. These findings help to unravel the regulation of neuronal connectivity and may lead to a better understanding of how mutations related to autism and schizophrenia affect circuit connectivity and brain function.
Schroeder et al., Neuron 2018

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