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Preannouncement of a PhD Position - Laboratory of evolutionary genetics, Domazet-Lošo research group

17.11.2020.

Within Marie Skłodowska-Curie Innovation Training Network PEST-BIN Ruđer Bošković Institute (IRB), Zagreb, Croatia will announce in December 2020 opening of a 3-years PhD position.

General info

PEST-BIN is a Marie Skłodowska-Curie Innovation Training Network (ITN), funded by the European Commission, Horizon 2020 Program. Commencing its activities in January 2021, the Network will provide PhD training to 15 Early Stage Researchers (ESRs).

Consortium objectives

Antibiotic resistance has been named as one of the greatest threats to global health by the World Health Organization. There are increasing numbers of bacterial infections not responding to known antibiotics. The humanity needs to pioneer disruptive technologies to re-gain the upper hand. To do so, PEST-BIN mobilizes six universities, three research institutes, a hospital and five private companies with one common mission: to pioneer novel technologies to fight bacterial infections.

Our network will combine very diverse tools: from nano-engineering, antibiotic discovery and production, via proteomics-based diagnostics to big data analysis using artificial intelligence (AI) – all of which will be contribute to new, interdisciplinary technologies. All PEST-BIN ESRs will be trained in an intersectoral environment – experiencing a tight collaboration among academia, healthcare and the private sector.

PhD project description

Prof. Domazet-Lošo research group is interested in the evolutionary genomics and macroevolutionary dynamics of bacteria. Within PEST-BIN network we will focus specifically on biofilm formation capacity of the selected bacterial pathogens. In the first phase, entire biofilms will be sampled at different time-points, covering inoculation to aging period of biofilm growth. These samples, taken in replicates, will provide starting material for RNA and protein isolation.

Total RNA will be sequenced by NGS approaches with the goal to get an overview of the transcription dynamics during biofilm growth. Same timepoints will be used for quantification of proteins and phosphoproteins by LC/MS. Transcriptome, proteome and phospho-proteome data will be than linked to evolutionary measures. For instance, by phylostratigraphic approach we will estimate the phylogenetic age of all genes in the genomes of studied pathogens. Other evolutionary measures include nonsynonymous and synonymous divergence of coding sequences and codon usage bias. Transcriptome/proteome data and evolutionary estimates will be linked by transcriptome age index (TAI) class of tools.

We will seek to find critical transition stages in biofilms of the pathogenic bacteria by an array of tools that include correspondence, principal component, clustering and enrichment analysis. We expect that this approach will allow us to mine candidate genes that play critical role in infection outcomes related to biofilms. PhD candidate research secondments are planned at the Technical University of Denmark and the University of Zagreb.

Additional requirements: A strong interest in evolutionary microbiology, evolutionary genomics or evolutionary bioinformatics. A capacity to work in a cross-disciplinary collaborative biomedical research environment.

Benefits and salary

The successful candidates will receive an attractive salary in accordance with the MSCA regulations for Early Stage Researchers (http://ec.europa.eu/research/mariecurieactions/). The exact salary will be confirmed upon appointment and is dependent on the country correction factor (to allow for the difference in cost of living in different EU Member States). The salary includes a living allowance, a mobility allowance and a family allowance (if already married). The guaranteed PhD funding is for 36 months. All ESRs will have e personal career development plan and benefit from continuing education, secondments and training/networking events within PEST-BIN. All ESR will be guided by an academic and non-academic supervisor, experiencing a truly intersectoral working environment.

Eligibility

Applicants can be of any nationality. PEST-BIN supports a balanced gender representation by promoting genuine equal access opportunities throughout the recruitment process.
Applicants are required to undertake transnational mobility (i.e. move from one country to another) when taking up their appointment. At the time of recruitment by the host beneficiary, ESRs must not have resided or carried out their main activity (work, studies, etc.) in the country of their host beneficiary for more than 12 months in the 3 years immediately prior to the date of appointment.

To be considered an ESR, at the time of recruitment by the host the candidates must be in the first four years (full- time equivalent) of their research careers. This is measured from the date when they obtained the degree which formally entitles them to embark on a doctorate (typically a MSc degree).

Applicants must have a diploma (or obtain a diploma before their employment starts) granting access to doctoral studies (typically a MSc degree).

Applicants must be able to demonstrate their ability to understand and express themselves in both written and spoken English at a level that is sufficiently high for them to derive the full benefit from the network training.

Pre-application

It is expected that the position will be officially announced mid-December 2020 and open for application for 60 days. Please visit this site again for full information on application procedure, deadline and required documentation.

Pre-application enquiries are welcome immediately; please sent a cover letter including your motivation, experience and interests (up to two pages), a full CV including ID photo, and email addresses of two referees to Prof. dr. Tomislav Domazet-Lošo.

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