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Understanding the molecular mechanisms of gene regulation and metabolism in the malaria parasite Plasmodium falciparum using functional genomics and metabolomics

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Malaria is one of the most devastating diseases of humankind, affecting nearly one in ten people worldwide and resulting in over 1.5 million deaths annually. This disease is caused by the Plasmodium parasite, of which Plasmodium falciparum is the deadliest form. While the past century has seen significant progress in anti-malarial drug development, many of these drugs are losing efficacy due to the rise of drug-resistant parasites. One of the major challenges facing the field is the identification of new drug targets for efficacious, affordable treatment. My lab focuses on transcriptional regulation and metabolism as potential avenues to disrupt the progression of this deadly parasite. To accomplish this, our research combines tools from functional genomics, molecular biology, computational biology, biochemistry, and metabolomics to understand the fundamental molecular mechanisms underlying the development of this parasite. The focus is predominantly on the red blood cell stage of development, which is the stage in which all of the clinical manifestations of the malaria disease occur.

Transcriptional regulation in malaria parasites:

My lab is interested in role of transcriptional regulation in parasite development. To study this, we focus on the only known family of DNA binding proteins encoded by the Plasmodium genome, the Apicomplexan AP2 (ApiAP2) protein family. These proteins are highly conserved among all Apicomplexan parasites and find their origin in plants. (Why is there a plant connection you ask? Intriguingly, malaria parasites contain an amazing non-photosynthetic chloroplast-like organelle called the apicoplast which was acquired via a secondary endosymbiotic event so there are many features of plant cells in these intriguing single celled eukaryotic parasites!) To address the specific in vivo roles for the 27 members of the ApiAP2 protein family, we are pursuing several lines of inquiry. These approaches include modulating expression levels of these proteins, generating knockdowns and knockouts, as well as in vivo protein tagging for chromatin immunoprecipitation. We are also using luciferase reporter assays to measure the stage-specificity of expression controlled by the identified target DNA motifs, and we are using mass spectrometry-based proteomics to determine protein-protein interactions for these transcriptional regulatory complexes. Our goal is to define the dynamic transcriptional regulatory network of the malaria parasite and to determine which ApiAP2 proteins are the master regulators governing the various stages of parasite development including the blood stage, the mosquito stage and the liver stage with the goal of targeting these proteins as a way to kill parasites.

Or you can just use your home .m2 cache directory that you share e.g. with your Eclipse/IDEA:

The $MAVEN_CONFIG dir (default to /root/.m2 ) could be configured as a volume so anything copied there in a Dockerfile at build time is lost. For that reason the dir /usr/share/maven/ref/ exists, and anything in that directory will be copied on container startup to $MAVEN_CONFIG .

To create a pre-packaged repository, create a pom.xml with the dependencies you need and use this in your Dockerfile . /usr/share/maven/ref/settings-docker.xml is a settings file that changes the local repository to /usr/share/maven/ref/repository , but you can use your own settings file as long as it uses /usr/share/maven/ref/repository as local repo.

To add your custom settings.xml file to the image use

For an example, check the tests dir

Maven needs the user home to download artifacts to, and if the user does not exist in the image an extra user.home Java property needs to be set.

For example, to run as user 1000 mounting the host' Maven repo

The maven images come in many flavors, each designed for a specific use case.

This is the defacto image. If you are unsure about what your needs are, you probably want to use this one. It is designed to be used both as a throw away container (mount your source code and start the container to start your app), as well as the base to build other images off of.

This image does not contain the common packages contained in the default tag and only contains the minimal packages needed to run maven . Unless you are working in an environment where only the maven image will be deployed and you have space constraints, we highly recommend using the default image of this repository.

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