Open PhD student position at the Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Ãeské Budìjovice, Czech Republic A PhD position is open to study viruses of protists, with an emphasis on Giant Viruses and Polinton-like viruses, using high-throughput isolation methods, genomics, transcriptomics, proteomics, and experimental approaches. Protists are susceptible to infection by viruses just like all cellular life forms. However, little is known about their defense systems. Polinton-like viruses (PLVs) exist both as transposon-like elements in protist genomes and as bona fide DNA viruses that parasitize protist-infecting Giant Viruses (GVs), limiting their spread and safeguarding protist populations. Despite their remarkable abundance in some aquatic environments and expansions in certain protists, how PLVs infect cells, interact with the GV replication machinery, and the conditions under which they might reactivate from their host's genome remains obscure. To address these knowledge gaps, we propose to combine state-of-the-art genomics, transcriptomics, and proteomics to track individual infection stages in model protist-GV-PLVs systems. To achieve this, we will first isolate freshwater protists and subsequently their GVs and PLVs. The anticipated outcomes will enhance our understanding of antiviral defense systems in microeukaryotes and microbial interactions at large. About the employer: The Department of Aquatic Microbial Ecology (Institute of Hydrobiology, Biology Centre of the Czech Academy of Science) is an internationally recognized high-class institution for studying freshwater microbes. There are five well-equipped microbiological laboratories: a general wet-lab, two labs for bacterial and eukaryotic cultivation, and two for molecular biology. Instrumentation: A fully automated fluorescence microscope with image analysis for high-throughput evaluation of CARD-FISH stained samples, three fluorescence microscopes equipped with image analysis systems, inverted microscopes, a micromanipulator and microinjector, a spectrofluorometer, basic equipment for cultivation and molecular biology, ultra-low temperature freezers, a flow cytometer. Full equipment for lake sampling is available. Seven Linux servers and five Network-attached storage (NAS) units (total 1216 threads, 9 TB RAM, ca. 1000 TB of storage) are available with all relevant software installed for omics data analyses. One MinION (Oxford Nanopore) machine is available for performing long-read sequencing of DNA. Two Nvidia Tesla T4 graphics processing units (GPU) are integrated on servers for performing base calling of long reads, including calling of modified bases for epigenomics analyses. Requirements: Min. education level: Master's degree Field of education: Microbiology, Biotechnology, Molecular Biology, Bioinformatics Applicants for the PhD position must have, or are expected to receive by July 2025, an M.Sc. degree in Biological Sciences (e.g. Microbiology, Biotechnology, Molecular Biology, Bioinformatics) and must show a strong interest in virus biology and eukaryotic genomics. Work is expected to be 60% computational and 40% laboratory based Prior experience in Linux/Perl/R/Python programming might be favourably considered but is not a prerequisite for selection Minimum practical experience with basic molecular biology methods is highly desirable Candidates must be proficient in English. How to apply: Please submit a detailed CV (including your grades), a brief statement of your research interests and work performed (max. 1 page), and the name and contact information for at least one referee via the REPLY button below. Preferably combine all this information into a single PDF file. The position will remain open until a suitable candidate is found, applications will be evaluated monthly starting December 20, 2024. The target starting date is July 2025, with a later (1-2 months) date being negotiable. For more information about this position, please contact Dr. Paul-Adrian Bulzu (bulzupaul@gmail.com) or follow the link: https://jobs.bc.cas.cz/en/detail/233 *Paul-Adrian Bulzu, PhD* Laboratory of Microbial Ecology and Evolution Department of Aquatic Microbial Ecology Institute of Hydrobiology Biology Centre CAS Na Sadkach 7 370 05 Ceske Budejovice Czech Republic Tel: 00420 38777 5819 twitter: @SmallThingsLab bulzupaul@gmail.com (to subscribe/unsubscribe the EvolDir send mail to golding@mcmaster.ca)