Biology subjects

Weber, A.

Publications and source records attributed to Weber, A..

7 recordsLinked to original sources

bioRxiv2018

Optimised DNA extraction and library preparation for minute arthropods: application to target enrichment in chalcid wasps used for biocontrol.

Enriching subsets of the genome prior to sequencing allows focusing effort on regions that are relevant to answer specific questions. As experimental design can be adapted to sequence many samples simultaneously, using such approach also contributes to reduce cost. In the field of ecology and evolution, target enrichment is increasingly used for genotyping of plant and animal species or to better understand the evolutionary history of important lineages through the inference of statistically robust phylogenies. Limitations to routine target enrichment by research laboratories are both the complexity of current protocols and low input DNA quantity. Thus, working with tiny organisms such as micro-arthropods can be challenging. Here, we propose easy to set up optimisations for DNA extraction and library preparation prior to target enrichment. Prepared libraries were used to capture 1432 Ultra-Conserved Elements (UCEs) from microhymenoptera (Chalcidoidea), which are among the tiniest insects on Earth and the most commercialized worldwide for biological control purposes. Results show no correlation between input DNA quantities (1.8-250ng, 0.4 ng with an extra whole genome amplification step) and the number of sequenced UCEs. Phylogenetic inferences highlight the potential of UCEs to solve relationships within the families of chalcid wasps, which has not been achieved so far. The protocol (library preparation + target enrichment), allows processing 96 specimens in five working days, by a single person, without requiring the use of expensive robotic molecular biology platforms, which could help to generalize the use of target enrichment for minute specimens.

evolutionary biology↗

bioRxiv2018

Biochemical mechanisms driving rapid fluxes in C4 photosynthesis

Biochemical mechanisms driving rapid fluxes in C4 photosynthesis Biochemical mechanisms driving... Modeling Plant growth RNA-seq Enzyme measurements Quantum yield measurements Data availability Material and Methods References Sufficient flux through pathways is critical to their function within the metabolic network. A high flux cycle called C4 photosynthesis evolved in some plants to combat the slow speed and low specificity of the plants carbon fixation enzyme Rubisco1. In these plants, flux through the C4 photosynthetic cycle eclipses flux through Rubisco making it the highest flux in planta2,3. Engineering efforts are underway ...

plant biology↗

bioRxiv2018

The proto CpG island methylator phenotype of sessile serrated adenoma/polyps

Sessile serrated adenomas/polyps (SSA/Ps) are the putative precursors of the {small tilde}20% of colon cancers with the CpG island methylator phenotype (CIMP), but their molecular features are poorly understood. We used high-throughput analysis of DNA methylation and gene expression to investigate the epigenetic phenotype of SSA/Ps. Fresh-tissue samples of 17 SSA/Ps and (for comparison purposes) 15 conventional adenomas (cADNs)--each with a matched sample of normal mucosa-- were prospectively collected during colonoscopy (total no. samples analyzed: 64). DNA and RNA were extracted from each sample. DNA was subjected to bisulfite next-generation sequencing to assess methylation levels at {small tilde}2.7 million CpG sites located predominantly in gene regulatory regions and spanning 80.5Mb ({small tilde}2.5% of the genome); RNA was sequenced to define the samples transcriptomes. An independent series of 61 archival lesions was used for targeted verification of DNA methylation findings. Compared with normal mucosa samples, SSA/Ps and cADNs exhibited markedly remodeled methylomes. In cADNs, hypomethylated regions were far more numerous (18,417 vs 4288 in SSA/Ps) and rarely affected CpG islands/shores. SSA/Ps seemed to have escaped this wave of demethylation. Cytosine hypermethylation in SSA/Ps was more pervasive (hypermethylated regions: 22,147 vs 15,965 in cADNs; hypermethylated genes: 4938 vs 3443 in cADNs) and more extensive (region for region), and it occurred mainly within CpG islands and shores. Given its resemblance to the CIMP typical of SSA/Ps putative descendant colon cancers, we refer to the SSA/P methylation phenotype as proto-CIMP. Verification studies of six hypermethylated regions (3 SSA/P-specific and 3 common) demonstrated the high potential of DNA methylation markers for predicting the diagnosis of SSA/Ps and cADNs. Surprisingly, proto-CIMP in SSA/Ps was associated with upregulated gene expression (n=618 genes vs 349 that were downregulated); downregulation was more common in cADNs (n=712 vs 516 upregulated genes). The epigenetic landscape of SSA/Ps differs markedly from that of cADNs. These differences are a potentially rich source of novel tissue-based and noninvasive biomarkers that can add precision to the clinical management of the two most frequent colon-cancer precursors.

cancer biology↗

bioRxiv2018

Arabidopsis species deploy distinct strategies to cope with drought stress

O_LIBackground and Aims Water limitation is an important determinant of the distribution, abundance and diversity of plant species. Yet, little is known about how the response to limiting water supply changes among closely related plant species with distinct ecological preferences. Comparison of the model annual species A. thaliana to its close perennial relatives A. lyrata and A. halleri, can help disentangle the molecular and physiological changes contributing to tolerance and avoidance mechanisms, because these species must maintain tolerance and avoidance mechanisms to increase long-term survival, but they are exposed to different levels of water stress and competition in their natural habitat.\nC_LIO_LIMethods We conducted a dry-down experiment that mimics a period of missing precipitation. We quantified the covariation of progressive decrease in soil water content (SWC) with various physiological and morphological plant traits across a set of representative genotypes in Arabidopsis thaliana, A. lyrata and A. halleri. To quantify the degree of plant stress, transcriptome changes were also monitored.\nC_LIO_LIKey Results The analysis of trait co-variation demonstrates that the three species differ in the strategies they deploy to respond to drought stress. A. thaliana showed drought avoidance reaction but failed to survive wilting. A. lyrata efficiently combined avoidance and tolerance mechanisms. By contrast, A. halleri showed some degree of tolerance to wilting but it did not seem to protect itself from the stress imposed by drought. Transcriptome data collected just before plant wilting and after recovery corroborated the phenotypic analysis, with A. lyrata and A. halleri showing a stronger activation of recovery- and stress-related genes, respectively.\nC_LIO_LIConclusions We conclude that these three Arabidopsis species have evolved distinct strategies to face drought stress, and discuss the extent to which these strategic differences reflect their respective ecological priorities.\nC_LI

plant biology↗

bioRxiv2018

The fungal ligand chitin directly binds and signals inflammation dependent on oligomer size and TLR2

Chitin is a highly abundant polysaccharide and linked to fungal infection and asthma. Unfortunately, its polymeric structure has hampered the identification of immune receptors directly binding chitin and signaling immune activation and inflammation, because purity, molecular structure and molarity are not well definable for a polymer typically extracted from biomass. Therefore, by using defined chitin (N-acetyl-glucosamine) oligomers, we identified six subunit long chitin chains as the smallest immunologically active motif and the innate immune receptor Toll-like receptor (TLR) 2 as the primary fungal chitin receptor on human and murine immune cells. Chitin oligomers directly bound TLR2 with nanomolar affinity and showed both overlapping and distinct signaling outcomes compared to known mycobacterial TLR2 ligands. Conversely, chitin oligomers shorter than 6 subunits were inactive or showed antagonistic effects on chitin/TLR2-mediated signaling, hinting to a size-dependent sensing/activation system unexpectedly conserved in plants and humans. Since blocking the chitin-TLR2 interaction effectively prevented chitin-mediated inflammation in vitro and in vivo, our study highlights the chitin TLR2 interaction as a potential target for developing novel therapies in chitin-related pathologies and fungal disease.

immunology↗

bioRxiv2018

Natural variation in stomata size contributes to the local adaptation of water-use efficiency in Arabidopsis thaliana

Stomata control gas exchanges between the plant and the atmosphere. How natural variation in stomata size and density contributes to resolve trade-offs between carbon uptake and water-loss in response to local climatic variation is not yet understood. We developed an automated confocal microscopy approach to characterize natural genetic variation in stomatal patterning in 330 fully-sequenced Arabidopsis thaliana accessions collected throughout the European range of the species. We compared this to variation in water-use efficiency, measured as carbon isotope discrimination ({delta}13C). We detect substantial genetic variation for stomata size and density segregating within Arabidopsis thaliana. A positive correlation between stomata size and {delta}13C further suggests that this variation has consequences on water-use efficiency. Genome-wide association analyses indicate a complex genetic architecture underlying not only variation in stomata patterning but also to its co-variation with carbon uptake parameters. Yet, we report two novel QTL affecting {delta}13C independently of stomata patterning. This suggests that, in A. thaliana, both morphological and physiological variants contribute to genetic variance in water-use efficiency. Patterns of regional differentiation and co-variation with climatic parameters indicate that natural selection has contributed to shape some of this variation, especially in Southern Sweden, where water availability is more limited in spring relative to summer. These conditions are expected to favor the evolution of drought avoidance mechanisms over drought escape strategies.

plant biology↗

bioRxiv2017

Pharmacological Macrophage Attenuation by Imatinib Reverts Hepatic Steatosis and Inflammation in Obese Mice

AimsNon-alcoholic fatty liver disease (NAFLD) has become one of the most common liver diseases worldwide. As macrophages play a key role in NAFLD, therapies targeting macrophages have been postulated. Indeed, strategies depleting macrophages or blocking monocyte recruitment into the liver improve NAFLD, however, are not feasible in clinical practice. Our goal was to assess whether attenuation of macrophages can be achieved by imatinib, an anti-leukemia drug with known anti-inflammatory and anti-diabetic properties, and how this impacts NAFLD.\n\nMaterials and MethodsMurine macrophages were polarized in vitro to different activation states in the presence or absence of imatinib; mice on high fat diet orally treated with imatinib or vehicle; and human monocytes of diabetic patients and healthy controls treated with or without imatinib for translational application.\n\nResultsImatinib specifically attenuated pro-inflammatory murine macrophages in vitro and in vivo. In livers of obese mice, imatinib caused Kupffer cells to adopt an attenuated phenotype via modulation of the TNF-pathway. This immune-modulation resulted in markedly improved hepatic steatosis along with beneficial effects on liver function, lipids and systemic inflammation. The immune-dampening effect of imatinib also prevailed in human monocytes, indicating translational applicability.\n\nConclusionsImmune-modulation of myeloid cells as exemplified by imatinib may be a novel therapeutic strategy in patients with NAFLD.

immunology↗