Biology subjects

Meyer, V.

Publications and source records attributed to Meyer, V..

3 recordsLinked to original sources

bioRxiv2018

Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation

Current molecular biology laboratories rely heavily on the purification and manipulation of nucleic acids. Yet, commonly used centrifuge-and column-based protocols require specialised equipment, often use toxic reagents and are not economically scalable or practical to use in a high-throughput manner. Although it has been known for some time that magnetic beads can provide an elegant answer to these issues, the development of open-source protocols based on beads has been limited. In this article, we provide step-by-step instructions for an easy synthesis of functionalised magnetic beads, and detailed protocols for their use in the high-throughput purification of plasmids, genomic DNA and total RNA from different sources, as well as environmental TNA and PCR amplicons. We also provide a bead-based protocol for bisulfite conversion, and size selection of DNA and RNA fragments. Comparison to other methods highlights the capability, versatility and extreme cost-effectiveness of using magnetic beads. These open source protocols and the associated webpage (https://bomb.bio) can serve as a platform for further protocol customisation and community engagement.

molecular biology↗

bioRxiv2018

Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks

A significant challenge in our understanding of biological systems is the high number of genes with unknown function in many genomes. The fungal genus Aspergillus contains important pathogens of humans, model organisms, and microbial cell factories. Aspergillus niger is used to produce organic acids, proteins, and is a promising source of new bioactive secondary metabolites. Out of the 14,165 open reading frames predicted in the A. niger genome of only 2% have been experimentally verified and over 6,000 are hypothetical. Here we show that gene co-expression network analysis can be used to overcome this limitation. A meta-analysis of 155 transcriptomics experiments generated co-expression networks for 9,579 genes ([~]65%) of the A. niger genome. By populating this dataset with over 1,200 gene functional experiments from the genus Aspergillus and performing gene ontology enrichment, we could infer biological processes for 9,263 of A. niger genes, including 2,970 hypothetical genes. Experimental validation of selected co-expression sub-networks uncovered four transcription factors involved in secondary metabolite synthesis, which were used to activate production of multiple natural products. This study constitutes a significant step towards systems-level understanding of A. niger, and the datasets can be used to fuel discoveries of model systems, fungal pathogens, and biotechnology.

systems biology↗

bioRxiv2018

Photosynthesis under very high oxygen concentrations in dense microbial mats and biofilms

Using microsensors O2 concentrations were measured in photosynthetically active microbial mats of up to 3 mM, corresponding to a partial pressure of 3 bar. This could damage mats by internal gas formation, and be inhibitory by formation of reactive oxygen species (ROS) and reduced effectivity of RuBisCo. The reliability of the electrochemical microsensors was checked by creating elevated O2 concentrations in a water volume placed inside a pressure tank. A microsensor mounted with the tip in the gassed water bath showed a response linearly proportional to 5.5 mM corresponding to 4 bar pure O2 pressure. After release of the pressure the O2 concentration reduced quickly to 2.5 mM, then stabilized and subsequently reduced slowly over 14 hours to approximately 2 mM. We concluded that the very high O2 concentrations measured in phototrophic microbial mats are real and O2 oversaturation in mats is a stable phenomenon. As consequence of high O2 concentrations, net production of H2O2 occurred. The accumulation was, however, limited to the respiratory zone under the photosynthetic layer. Despite the high gas pressure inside mats, no disruption of the mat structure was apparent by bubble formation inside the mats,and bubbles were only observed at mat surfaces. Additions of H2O2 to high concentrations in the water column were efficiently removed in the photosynthetically active zone. As the removal rate was linearly proportional to the H2O2 influx, this removal occurred possibly not enzymatically but by abiotic processes. Phototrophic microorganisms can produce O2 at high rates under strongly elevated O2 levels, despite the decreased efficiency due to the unfavorable kinetics of RuBisCo and energy costs for protection. Under non-limiting light conditions, this apparent dilemma is, however, not disadvantageous.\n\nImportanceBiofilms are often used in photobioreactors for production of biomass, food or specialty chemistry. Photosynthesis rates can be limited by high O2 levels or high O2/CO2 ratios which are especially enhanced in biofilms and mats, due to mass transfer limitations. High O2 may lead to reactive O2 species (ROS) and reduce the efficiency of RuBisCo. Moreover, gas formation may destabilize their structure. Here we show that extremely high levels of O2 are possible in mats and biofilms without ebullition, and while maintaining very high photosynthetic activity.

microbiology↗