Individual Research Projects

12 new PhD positions in the EU Horizon 2020 Marie Sklodowska- Curie MSCA-ITN Project RENALTRACT – On-line application (deadline 30-7-2015)

On the 25th of February 2015 the European Commission approved the new EU Horizon 2020 Marie Skłodowska-Curie Innovative Training Network Project RENALTRACT (The RENALTRACT training program is a cross-disciplinary collaborative research effort focusing on the complex embryonic programs that govern the formation and assembly of the renal tract system and their alteration leading to renal tract malformations, Project 642937).

RENALTRACT is a consortium coordinated by the CNRS, which consists of high profile universities, research institutions and companies located in Finland, France, Germany and UK. This project is set to formally start on the 1st of September 2015.

RENALTRACT now offers 12 open PhD positions (“Early Stage Researchers”). The MSCA programme offers a highly competitive living allowance (salary). Benefits include mobility allowance and a family allowance (under eligibility condition); duration 36 months.

All details about the project, the 12 positions, the recruitment procedure, the eligibility criteria and financial terms are provided on this page as well. The deadline for applications is 30 July 2015.

Project ESR1

PhD position description : The PhD thesis project will be centered to target the cellular and molecular mechanisms of a key process in establishing the functionnal kidney, namely how the exretory and secrretory nephron is assembled. The project will address the detailes of how the cell-cell and tissue interactions between ureteric bud and metanephric mesenchyme advances kidney organogenesis. We showed earlier that the Wnt signals mediate kidney tubule induction and the project builds on this fundamental disovery.

Supervisor : Seppo VAINIO

Host : University of Oulu : http://www.oulu.fi/english/

Project ESR2

PhD position description : Renal stem cells form a unique population of cells that give rise to all nephrons. To ensure proper growth of the developing organ, renal stem cells need to balance pathways that promote self-renewal, proliferation and differentiation. How this delicate balance is achieved is only partially understood. The present project aims at identifying the genetic and epigenetic factors governing these fundamental decisions. We have generated several mouse models of transcription factors and epigenetic modifiers that appear to be essential for kidney development. The successful candidate will perform a detailed histological and molecular analysis of these mutant mice. In addition, he/she will carry out ChIP-Seq analysis to identify direct downstream target genes of these factors and determine how the epigenetic landscape is affected by the removal of these factors. Taken together, this research project will provide important insights into the regulation of stem cell biology, the interaction of transcription factors with the epigenetic machinery and should lead to a better understanding of CAKUT in human patients.

Supervisor : Andreas SCHEDL

Host : Nice University : http://unice.fr/

CNRS : http://www.cnrs.fr/index.php

Project ESR3

PhD position description : Due to its relatively simple organization and its experimental accessibility, the Xenopus pronephros has emerged as an attractive model to study the early events in kidney development. The objective of the ESR3 project will be to identify and characterize genes that are regulated by Pax8 at the early steps of kidney development using high-throughput transcriptomic analysis. Pax8/2 genes are crucial regulators of development and function at multiple stages of vertebrate kidney organogenesis. In Xenopus, depletion of the pax8 transcription factor gene leads to a complete absence of pronephric tubules. Pax8 is required for kidney field specification and cell proliferation of pronephric precursors. ESR3 will select genes differentially expressed upon Pax8 knockdown in kidney field explants and performed in vivo functional analysis of the selected genes.

Supervisor : Muriel UMBHAUER

Host : Pierre et Marie Curie University : http://www.upmc.fr/en/index.html

CNRS : http://www.cnrs.fr/index.php

Project ESR4

PhD position description : Identifying novel candidate genes including transcription factors regulating kidney development. ESR4@UG will analyse the effect of candidate genes on nephrogenesis using the Drosophila ‘kidney’ (Malpighian tubule). As Drosophila is a test bed for vertebrate genes, mammalian candidate genes will be assessed either with gain-of-function (mammalian genes and/or their Drosophila orthologues) or loss-of-function (mutants or cell- or tissue- specific targeted RNAi for Drosophila homologues of mammalian genes), to screen for developmental and adult morphological phenotypes using genetics, confocal microscopy and physiology.

Supervisor : Shireen DAVIES

Host : University of Glasgow : http://www.gla.ac.uk

Project ESR5

PhD position description : The mature ureter possesses a simple two-layered tissue architecture with an inner epithelial layer, the urothelium, adapted to prevent urine re-entering the body, and an outer multi-layered mesenchymal coating of fibroblasts and smooth muscle cells that confer rigidity and flexibility to the ureteric tube. Either tissue arises from undifferentiated progenitors during embryogenesis. Coordinated survival, growth and differentiation of the two tissue compartments require continued exchange of signals between them, the lack of which leads to functional obstruction and hydroureter formation. We have previously analyzed the role of Wnt, Shh and Ephrin signaling in mouse ureter development in our team. The new PhD student shall complement these efforts by identifying and characterizing additional signalling pathways that regulate early ureter development in the mouse. The PhD student will use a combination of tissue specific gene targeting studies in vivo and embryological manipulation of ureteric explant cultures in vitro to characterize the phenotypic changes associated with the loss and gain of different signalling pathways. Microarray analysis shall be used to characterize the genome wide changes of the transcriptional program triggered by the loss of these signalling pathways. Appropriate candidate effectors will be further analysed for functional implication in ureter development.

Supervisor : Andreas KISPERT

Host : Medizinische Hochschule Hannover

Project ESR6

PhD position description : The PhD research will combine mouse genetics, molecular cellular biology with focus on ureter with the aim of understanding the molecular logic that regulates the differentiation of smooth muscle progenitor cells. That involves investigating gene expression changes in mutant backgrounds with the support of -omics approaches. The experiments might provide new genes causing, modifying or predisposing to congenital anomalies of the kidney and urinary tract (CAKUT).

Supervisor : Laurent FASANO

Host : Aix-Marseille University : http://edu.univ-amu.fr/en

CNRS : http://www.cnrs.fr/index.php

Project ESR7

PhD position description : We aim to find out why people are sometimes born with kidneys, ureters and bladders. These are the main causes of children needing long term renal dialysis and kidney transplantation. We are also working on translational therapies, including growth factors and precursor cells, for kidney, bladder and, more recently, neural disease. This project will focus on the roles of heparanase molecules in functional bladder differentiation, using mouse and Xenopus models, with a focus on neuro-muscular cell biology and physiology.

Supervisor : Adrian S. WOOLF

Host : University of Manchester http://www.manchester.ac.uk/

Project ESR8

PhD position description : The PhD researcher will be engaged in a project exploring the complex genetic origins of congenital anomalies of the kidney and urinary tract (CAKUT) involving next-generation sequencing and systems biology approaches. The project will be based on a recently established large-scale clinical-genetic collaboration within the EURenOmics Consortium for high-throughput research in rare kidney diseases.  The researcher will relay genetic findings in diseased children to Renaltract laboratory partners for functional verification and vice versa search for human variants in genes emerging from in vitro and animal model research. The emerging knowledge base will be used to model the cumulative impact of variants in multiple renal developmental genes by integrative gene network analysis. Hence, the position is particularly suitable for a young researcher interested in molecular genetics, genetic statistics/bioinformatics and systemics biology.

Supervisor : Franz SCHAEFER

Host : Universitäts-klinikum Heidelberg : http://www.heidelberg-university-hospital.com/index.php?id=2&L=en

Project ESR9

PhD position description : The PhD research will identify novel renal tract (RTM)-related biomarkers in urine. For this aim proteome analysis will be performed with the use of capillary electrophoresis coupled to mass spectrometry and the use of multivariate statistical analysis. Previously identified urinary proteomic biomarkers associated with ureteropelvic junction obstruction, vesicoureteral reflux, and chronic kidney disease will be validated. Sequence analysis will help to get insights into the patho-physiology and furthermore into the involved proteases with the use of the cleavage site of the peptides. All information will be merged with that available from the literature to generate a first model of molecular changes associated with RTMs.

Supervisor : Petra ZUERBIG

Host : Mosaiques Diagnostics GmbH http://mosaiques-diagnostics.de/diapatpcms/mosaiquescms/front_content.php?idcat=155

Project ESR10

PhD position description : Heterozygous mutations in the gene encoding the factor HNF1B represent the most common known monogenic cause of developmental renal disease and are cause of a complex syndrome known as Renal Cyst And Diabetes (RCAD), characterized by abnormalities of the kidney (cysts, hypoplasia), genital tracts and pancreas hypoplasia. Using a unique mouse model that reproduces at the heterozygous state the main pathological features of the RCAD disease the aim of the project is to identify the key factors that modulate cyst initiation and normal renal tubule morphogenesis. The PhD researcher will examine in particular the implication of miRNA-mRNA targets in these processes, by performing high-throughput miRNA-Sequencing and mRNA-Sequencing of mouse embryonic kidneys at different developmental/postnatal stages. A subset of differentially expressed miRNAs will be selected for further validation by renal cell transfections reporter assays and using the Xenopus system. By combining the use of different model organisms, these studies are expected not only to provide a better understanding of the molecular basis underlying the RCAD disease but further reveal how miRNAs and transcription factors are integrated into gene regulatory networks controlling normal kidney development and function.

Supervisor : Silvia CEREGHINI

Host : Pierre et Marie Curie University : http://www.upmc.fr/en/index.html

CNRS : http://www.cnrs.fr/index.php

Project ESR11

PhD position description : Simple models for nephrolithiasis and renal sequelae of errors of metabolism (IEM). This project will include technics as for project ESR4@UG, but additionally with metabolomics and informatics. ESR11 will model genetic mutations on nephrolithiasis, using a Drosophila tubule kidney stone model. ESR11 will perform a screen for gene candidates for nephrolithiasis and seek homologous human candidate gene loci; and also identify renal sequelae of inborn errors of metabolism by identifying Drosophila  homologues of human IEM disease genes. These will be mutated in flies, and analogous renal sequelae sought. These will be studied with metabolomics and proteomic techniques (in collaboration with industrial partner MOS).

Supervisor : Julian DOW

Host : University of Glasgow : http://www.gla.ac.uk/

Project ESR12

PhD position description : The PhD researcher will join an interdisciplinary team of biologists, clinicians and engineers to develop and perform a large-scale drug screen in zebrafish. The research project will combine zebrafish genetics and chemical biology with state-of-the-art automated microscopy techniques and computational analysis methods. The project aims to identify disease-modulating substances by performing a high content screening assay using transgenic and genetic zebrafish model for ciliopathies associated with nephronophthisis-related cystic kidney disease (NPHP).

Supervisor : Jochen GEHRIG

Host : Acquifer : www.acquifer.de