Biology subjects

Murk, A.

Publications and source records attributed to Murk, A..

4 recordsLinked to original sources

bioRxiv2024

A system for functional studies of the major virulence factor of malaria parasites

PfEMP1 is a variable antigen displayed on erythrocytes infected with the malaria parasite Plasmodium falciparum. PfEMP1 mediates binding of the infected cell to the endothelium of blood vessels, a cause of severe malaria. Each parasite encodes [~]60 different PfEMP1 variants but only one is expressed at a time. Switching between variants underlies immune evasion in the host and variant-specific severity of disease. PfEMP1 is difficult to study due to expression heterogeneity between parasites which also renders genetic modification approaches ineffective. Here, we used selection linked integration (SLI) to generate parasites all expressing the same PfEMP1 variant and genome edit the expressed locus. Moving this system from the reference strain 3D7 to IT4 resulted in PfEMP1 expressor parasites with effective receptor binding capacities. We also introduce a second version of SLI (SLI2) to introduce additional genome edits. Using these systems, we study PfEMP1 trafficking, generate cell lines binding to the most common endothelial receptors, survey the protein environment from functional PfEMP1 in the host cell and identify new proteins needed for PfEMP1 mediated sequestration. These findings show the usefulness of the system to study the key virulence factor of malaria parasites.

microbiology↗

bioRxiv2021

High resolution species detection: accurate long read eDNA metabarcoding of North Sea fish using Oxford Nanopore sequencing

To monitor the effect of nature restoration projects in North Sea ecosystems, accurate and intensive biodiversity assessments are vital. DNA based techniques and especially environmental DNA (eDNA) metabarcoding is becoming a powerful monitoring tool. However, current approaches are based on genetic target regions <500 nucleotides, which offer limited taxonomic resolution. We developed a method for eDNA metabarcoding, based on nanopore sequencing of a longer amplicon, enabling improved identification of fish species. We designed a universal primer pair targeting a 2kb region of fish mitochondria, and compared it to the commonly used MiFish primer pair that targets only [~]170bp. In sillico and mock community testing showed that the 2kb fragments improved the accurate identification of genetically closely related species. eDNA was amplified, and sequenced using the Oxford Nanopore MinION in combination with the sequence read processing pipeline Decona. Analyzing eDNA from a North Sea aquarium showed that sequences from both primer pairs could be assigned to most species, but both approaches also identified unique species in the aquarium eDNA. Next, both primer pairs were used on multiple eDNA samples from the North Sea. Here, similar location specific fish communities were obtained from both approaches. More species were identified through the MiFish approach in the field samples. Interestingly, this difference was not observed in the aquarium, suggesting that 2kb fragment based metabarcoding potentially detects more recent occurrences of animals. This new method has the potential to improve and expand the molecular toolbox for eDNA based monitoring approaches.

molecular biology↗

bioRxiv2021

Relative Risk Assessment of Ecological Areas with the Highest Potential Impact of Underwater Released Exhaust CO2 from Innovative Ships

Applying underwater released exhaust gas as air lubrication along the ships hull to reduce the energy consumption is under development. However, this direct emission to the water could pose a risk to the local marine environment, especially in shipping-dense areas. Specifically, CO2, a dominant component in the exhaust gas, has the potency to enhance algal blooms and cause acidification. This study provides the first relative risk assessment of ships with underwater release exhaust gas systems on a global scale, taking into account local water conditions and shipping intensity. Risk was characterized for 262 marine ecoregions by plotting the expected CO2 emission from ships to water against the estimated vulnerability to acidification and algal blooms. The vulnerability of each ecoregion was assessed based on background dissolved inorganic carbon (DIC) level, chlorophyll-a concentrations and total alkalinity. The results reveal that areas with relatively high vulnerability are mainly located above 30{degrees} N latitude. The Yellow Sea, Southern China Sea, and North Sea come out as relatively high risk areas. Looking in more detail to European high-risk ecoregions, the highest risk levels are found in areas with dense shipping lanes and maritime chokepoints, e.g. the Strait of Dover and the Strait of Gibraltar. This was the first attempt to make such a risk assessment and the outcome is only indicative. In a next phase additional parameters, such as water currents and biological composition of the ecosystem should be included. Key PointsO_LIThe first global environmental risk assessment was made for innovative ships that apply underwater released exhaust gas as air lubrication C_LIO_LIEcoregions with relatively high vulnerability to acidification and algal blooms are mainly located above 30{degrees} N latitude C_LIO_LIThe risk for the marine ecosystem of the underwater released exhaust CO2 from ships is limited to specific shipping-dense areas C_LI

ecology↗

bioRxiv2019

Adding insult to injury: Effects of chronic oxybenzone exposure and elevated temperature on two reef-building corals

We studied the effect of chronic oxybenzone exposure and elevated temperature on coral health. Microcolonies of Stylophora pistillata and Acropora tenuis were cultured in 20 flow-through aquaria, of which 10 were exposed to oxybenzone at a field-relevant concentration of ~0.06 g L-1 at 26 {degrees}C. After two weeks, half of the corals experienced a heat wave culminating at 33 {degrees}C. All S. pistillata colonies survived the heat wave, although heat reduced growth and zooxanthellae density, irrespective of oxybenzone. A. tenuis survival was reduced to 0% at 32 {degrees}C, and oxybenzone accelerated mortality. Oxybenzone and heat significantly reduced photosynthetic yield in both species, causing a 5% and 22-33% decrease, respectively. In addition, combined oxybenzone and temperature stress altered the abundance of five bacterial families in the microbiome of S. pistillata. Our results suggest that oxybenzone adds insult to injury by further weakening corals in the face of global warming. Highlights[tpltrtarr] Chronic effect study on corals combining oxybenzone and elevated temperature [tpltrtarr]Oxybenzone affected photosystem II of coral photosymbionts and altered coral microbiome [tpltrtarr]Temperature effects were stronger than oxybenzone effects [tpltrtarr]Sensitivities were species-dependent [tpltrtarr]Oxybenzone adds insult to injury by weakening corals in the face of global warming

pharmacology and toxicology↗