The Faculty of Biology of

Adam Mickiewicz University in Poznań

is looking for

6 PhD students

to participate in research projects of the international PhD program of

KNOW “RNA Research Centre in Poznań”

 

About KNOW

The KNOW program is funded by Polish government to promote research at the best Polish research centers. The acronym KNOW stands for Leading National Research Centers (pl. Krajowe Naukowe Ośrodki Wiodące). The consortium „RNA Research Centre in Poznań” formed by the Faculty of Biology and the Institute of Bioorganic Chemistry was awarded the KNOW status in May 2014 (information on the webpage of Polish Ministry of Science and Education, and on the webpage of Adam Mickiewicz University ). There are only two research centers in Poland awarded with KNOW status in the field of biological sciences.

About research projects of the KNOW PhD program

The KNOW RNA Research Centre in Poznań is looking for candidates to participate in research projects of the international PhD program (student scholarships in these projects are 3.000 PLN/month).The short descriptions of the six research projects are listed below, with more details in the linked documents.

  1. The role and transcriptional/posttranscriptional regulation of newly identified barely microRNAs from miR444 gene family”, (prof. Zofia Szweykowska-Kulinska). MicroRNAs are small eukaryotic molecules that regulate gene expression at the posttranscriptional level. The regulatory roles of miRNAs have been demonstrated mainly in plant development. Recent studies also have shown a crucial regulatory role of microRNAs in plant response to environmental cues. Barley is an economically important monocotyledonous crop plant. However, little is known about barley miRNAs, their precursors and MIR gene structures. The aim of this study is to reveal the role and expression pattern of microRNAs in barley in different stress conditions (link).
  2. The role of DDX5 helicase in the 3′ end processing of canonical core histone transcripts in human cells“, (prof. Krzysztof Sobczak). DDX5 is well known ATP-dependent RNA helicase, which is involved in many cellular processes, especially in those requiring secondary structure remodeling, like pre-mRNA splicing, pre-rRNA or miRNA processing. Recently, we showed that this enzyme interacts with U7 snRNP, that is involved in the 3′ end processing of core canonical histone transcripts in Metazoa cells. The PhD student will elucidate the function of DDX5 protein in the U7 snRNA:histone pre-mRNA duplex assambly/disassembly in human cells (link).
  3. Structural studies of the core complex responsible for miRNA biogenesis in plants”, (prof. Artur Jarmolowski). MicroRNAs (miRNAs) are small non-coding RNAs of about 21nt in length, which participate in a wide variety of physiological cellular processes by regulating the gene expression at a sequence-specific manner. In plants both main miRNA biogenesis steps, pri-miRNA processing and pre-miRNA processing, occur inside the cell nucleus, and are performed by a complex comprising of at least five different proteins. The aim of this project is to use different biophysical approaches to determine the structure of protein complexes involved in plant miRNA biogenesis (link).
  4. The coding sequence of mRNA as a target for translation regulation by the Hfq protein”, (prof. Mikolaj Olejniczak). The synthesis of proteins by ribosomes programmed with mRNA template is finely tuned and subject to regulation at several steps of this process. One of the mechanisms of translation regulation in bacteria involves trans-encoded small noncoding RNAs (sRNAs), which are essential for the bacterial cell’s adaptation to changing environmental conditions and affect the virulence of bacterial pathogens. The aim of this project is to explain the function of a chaperone protein Hfq in sRNA-dependent translation regulation (link).
  5. Identification of tRNA and tRNA-like encoding genes in genomic sequences”, (prof. Wojciech Karlowski). In recent years new functions associated with tRNA molecules have been recognized that are independent of their role of carriers of amino acids and decoding factors in the process of protein biosynthesis. Hydrolysis of tRNAs within the anticodon loop induced by stress conditions or viral infections is a source of tRNA halves. Another class of tRNA-derived short RNAs (5’‒ and 3’‒ tRFs) enerated by cleavages within loops D and T comprises tRNA fragments corresponding to the 5’‒ and 3’‒ terminal sequences of mature tRNAs, respectively. There is a growing body of evidence that these RNAs are not products of random tRNA degradation, but instead play biological functions as posttranscriptional regulators of gene expression. The association of certain tRFs with proteins involved in microRNA‒ and siRNA‒dependent gene silencing suggests that there exists a link between these classes of non-coding RNAs. On the other hand, in genomic DNA, there are regions resembling tRNA‒encoding genes either in their ability to adopt a tRNA‒like secondary structure and/or the presence of RNA polymerase III type II promoters. Such tRNA‒like structures in viral genomes were shown to affect RNA’s stability, translation, replication and genome encapsulation. The aim of the project is an identification of genomic sequences possessing certain tRNA-like features in the available genomes of prokaryotic, eukaryotic and viral origin. Such regions could be a source of transcripts whose expression and/or processing depends on components of tRNA-biogenesis pathways including RNA polymerase III and enzymes involved in tRNA maturation.
    • identification of type II RNA polymerase III promoters consisting of correctly spaced Box A and Box B elements that are not associated with the bona fide tRNA genes
    • identification of regions capable of folding into structures similar to entire tRNA or mimicking parts of the tRNA
    • identification of tRNA genes or tRNA‒like elements overlapping RNA polymerase II‒ dependent genes (encoding proteins or long non-coding RNAS)
    • analysis of evolution and conservation patterns of tRNA–like elements in eukaryotic and prokaryotic genomes

    (link).

  6. Evolving artificial gene networks inspired by RNA world biochemistry”, (prof. Borys Wrobel). This project concerns biologically inspired computation, which is a discipline of science and engineering that aims to understand and build complex systems using computational models based on the design principles found in nature. The PhD student will be involved in designing and building software that he/she will then use to evolve and analyse artificial genetic networks (detailed description of the project (link).

How to apply

Applications should consist of a cover letter and a CV, including a list of grades in college (and their average). A copy of the Master of Sciences diploma or its equivalent should be included. If the candidate will soon graduate, then information about the planned graduation date can be provided, which should be confirmed by the thesis advisor. In the application the candidates should specify, to which project they apply. If more than one project is of interest, then a list of 3 projects in their preferred order should be provided. Also, the name and contact information of a potential referee should be enclosed. The applications should be send to rnaschool@amu.edu.pl by June 15th. In case of further inquiries, please, contact us at the same e-mail address.

In assessing the candidates the following will be considered: the average of grades in college, scientific interests and achievements (scholarships, conferences, papers, etc.), research experience, international experience, and a good command of English. The preferred candidates will be the college graduates in the fields of molecular biology, biotechnology, bioinformatics, or related, depending on the specific requirements of the projects (see above).

Selected candidates will be invited for an interview, which may be in person or by Skype. Candidates selected for the interview will be asked to give a presentation in English concerning their previous research experience.

Faculty of Biology of Adam Mickiewicz University in Poznań

The Faculty of Biology is located in the modern building of Collegium Biologicum at the Morasko campus in Poznań. Its researchers have at their disposal several well-equipped research facilities. The research at the Faculty is funded by grants from European Union and from national agencies, such as National Science Centre, and Foundation for Polish Science. At present, the Faculty employs more than 200 researchers and 120 PhD students.