Education - Ph.D. studies - Institute of Genetics

Ph.D. Topics of the Institute of Genetics

The cell mediated immunity of Drosophila melanogaster

Group: Laboratory of Immunology
Supervisor: István ANDÓ

Drosophila melanogaster has been recognized as a premier genetic model system for understanding gene function, developmental networks and molecular basis for genetic disorders. Drosophila has blood cells or hemocytes that are important for innate immune functions as well as pattern formation, tissue remodeling and wound healing. Throughout evolution, a large number of molecules have retained their biochemical specificities and maintained analogous functions with organization in similar pathways. The immune response in Drosophila shows remarkable similarities with the innate immunity of vertebrates, suggesting that they share a common evolutionary ancestry. Drosophila lacks adaptive immunity but it can eliminate microbes in minutes with well developed innate immunity generating a concerted action of humoral and cellular mechanisms. The humoral immunity involves the secretion of inducible antimicrobial peptides by the fat body and hemocytes and induction of proteolytic cascades which lead to melanization and coagulation. The cellular reactions are mediated by hemocytes, cells, directly interacting with microorganisms and parasites. The cellular reactions are initiated immediately after the recognition of the foreign particles and manifested as phagocytosis of microorganisms and cell debris or encapsulation of tissues and parasites. In the past decade we have established the tools and methodology to define the cellular elements of the Drosophila immune system. These involved the generation of immunological markers for Drosophila hemocytes, isolation of genes encoding for the markers, the generation of transgenic stocks having marker molecules for “in vivo” detection and analysis, generation of mutant and transgenic stocks with impaired hemocyte morphology and function as well as “in vitro”culture of Drosophila cell lines and hemocytes. These constructs allowed also genetic screens to identify signaling pathways of hemocyte development. We are defining further the molecules expressed in a cell type specific manner with the aim to identify hemocyte subpopulations, compartments and lineages and to find out their lineage- and functional- significance.

Functional characterization of symbiotic plant genes and proteins

Group: Laboratory of Medicago Genetics
Supervisor: Gabriella ENDRE

There has been a long-standing research activity in our laboratory to identify and study plant genes that play essential roles in the nitrogen fixing symbiosis. As a main result the first symbiotic receptor was identified from Medicago by map-based cloning strategy in this lab (Endre et al. 2002 Nature 417: 962-966). Besides classical and molecular genetic work, the wide varieties of techniques of molecular biology are being used to further characterize the identified genes and their protein products. Research experience covers structural genomics, forward genetics, plant tissue culture, transformations, yeast two hybrid system, protein expression and purification. Describing the elements and functions of the signal transduction pathway leading to the symbiotic nodule development may reveal new interesting discoveries, of which some may be contributing to our understanding to general molecular pathways in plant development.

Exploring genomic resources and biodiversity in a model legume to identify key traits in a model legume plant

Group: Laboratory of Medicago Genetics
Supervisor: Gabriella ENDRE

The aim of the project is to better understand the molecular basis of legume-specific biological problems which should contribute to the establishment of environmentally-friendly and sustainable agriculture. The use of legume plants in sustainable agriculture will only be possible if legume biological problems can be addressed with modern tools. The objective of this project is the use of the genomic tools available in Medicago truncatula to fasten the molecular characterization of new loci which affect important agronomical traits in legumes. The project has two major goals: 1) exploring insertion mutant lines in the model legume: forward genetic screen; 2) exploring the natural diversity in the model legume. In the first part a Tnt1 insertional Medicago mutant collection will be used (our laboratory was involved in the generation of this collection, and is maintaining the seed collection), in the second part Linkage Disequilibrium (LD) mapping studies and association genetics analyses will be used to study biodiversity using Medicago ecotypes.

Studying legume genes identified by microarray experiments under abiotic stress conditions

Group: Laboratory of Medicago Genetics
Supervisor: Ernő KISS, Gabriella ENDRE

Due to climatic changes, salinity and drought are subjects of great interest because of their negative impact on plant production. In the present work, we investigate the effect of these abiotic stresses on pattern of gene expression of M. sativa. The possible modulation influence of the presence of symbiotic bacteria on stress responses of the host plant was also analyzed and compared to the non-symbiotic condition.

Functional analysis of the Drosophila embryonic germ cell transcriptome by RNAi

Group: Laboratory of Drosophila Germ Cell Differentiation
Supervisor: Miklós ERDÉLYI

Germ cells, the ultimate stem cells are able to renew themselves while giving rise to the new generation. Although developmental potency of the primordial germ cells (PGCs) is restricted to the germ lineage, PGCs can acquire pluripotency in vitro. Moreover, there are evidences supporting the theory of the PGC origin of embryonic germ cells. It may be hypothesized that germ cells and embryonic stem cells are under similar genetic regulation, therefore germ cell and stem cell research can mutually benefit from each other’s results. In Drosophila, the early PGCs (pole cells) develop under the control of factors that localize in the germ plasm, the most posterior part of the egg. This peculiar mode of the segregation of the germ line factors within the egg makes Drosophila an excellent model of PGC research. Germ plasm is rich in RNAs of maternal origin, suggesting that at least in part the germ line factors are inherited in the form of localized RNA. The goal of our research is the comprehensive functional analysis of the early Drosophila germ cell transcriptome. RNA interference (RNAi) is used to explore the function of germ plasm enriched and PGC specific transcripts. We inject gene specific dsRNAs into early embryos whose germ cells were fluorescently labeled. Early PGC phenocopies are recorded by automated video microscopy. Several germ cell specific genes have been identified this way. Currently we work on detailed genetic, and cell biological analysis of the newly identified germ line factors.

Analysis of mutagenesis and carcinogenesis in yeast and human systems

Group: Laboratory of Immunology
Supervisor: Lajos HARACSKA

The stability of our genetic material is endangered both by DNA-damaging agents from the environment and by endogenous problems during DNA replication arising from spontaneous damage. To maintain the integrity of the genome, a variety of repair mechanisms have envolved that remove damaged bases from DNA. However, as a result of mutation in repair systems, limited cellular repair capacity or timing, DNA damage sometimes is not repaired before replication takes place. When the DNA replication machinery encounters an unrepaird DNA lesion in template strand, it faces a challenge, because the machinery is often unable to replicate past the lesion. We are researching the mechanisms that come into play when replication stalls at DNA lesions and that eventually lead to error-free or error-prone replication of damaged DNA. The error-prone replication of damaged DNA increases mutagenesis and leads to carcinogenesis, whereas error-free replication contributes to genetic stability.

In situ dissection of cis-acting elements in the bithorax complex of Drosophila melanogaster

Group: Laboratory of Chromatin Structure and Gene Expression
Supervisor: László SIPOS

Many genes that respond to developmental cues must maintain their responding states long after the cues have disappeared. In Drosophila, the maintenance of repressed states of many developmentally important genes is accomplished by a protein called POLYCOMB and by interacting proteins of the Polycomb-Group. Homologous proteins are found in mammals where they appear to have analogous functions. The long-term repression by the Polycomb-Group is accompanied by a change in chromosome structure making it less accessible to transcription factors and polymerases.
The Polycomb-Group proteins act through DNA-sites called Polycomb Response Elements (PREs). The best examples of such sites are in the Drosophila bithorax-complex, a cluster of genes that control segmental differentiation. Although PREs are known to interact with each other over large distances, they were studied mostly in transgenic constructs inserted into random sites of the Drosophila genome.
Because of technical limitations, PREs have not been recognized or studied in their original location and context. However, we have recently developed a novel method of gene conversion, which made uniquely possible and convenient to dissect PREs, and to follow their functioning in situ. Our emphasis is to define the logic of how these sites are switched to the repressing mode and how the repression is imposed on neighboring sequences.

Regulation of DNA damage bypass in yeasts

Group: Laboratory of DNA Repair
Supervisor: Ildikó UNK

Unrepaired DNA damages can have fatal consequences to cells: during genome duplication they can block the replication machinery leading to the collapse of the replication fork, gross chromosomal rearrangements, ultimately to cell death. To ensure survival cells apply DNA lesion bypass processes that can result in either error-free or error-prone bypass of DNA damages. In the error-free way the newly synthesized strand preserves the original information of the parental strand leading to genomic stability, conversely, error-prone lesion bypass introduces mutations opposite the lesion causing elevated mutagenesis, genomic instability, and in humans it can ultimately result in carcinogenesis. The opposing effects of different lesion bypass pathways necessitate tight regulation that should give preference to error-free pathways over the error-prone lesion bypass. However, how this regulation is achieved is not known.
Our aim is to investigate the molecular mechanism of the regulation of DNA lesion bypass, with special emphasis on PCNA. PCNA plays an essential role during DNA replication, and it is also indispensable for both the error-free and mutagenic bypass processes. Using genetic and biochemical tools we want to identify proteins that interact with PCNA and mediate its regulatory role during DNA lesion bypass.