PROJECT A: Pathophysiology of cholestatic liver diseases: mechanisms and targets for

therapy (pilihan 2)
Department of Gastroenterology and Hepatology
Coordinators: prof. dr. H. Moshage PhD, prof. dr. K.N. Faber PhD
Type of research: Basic Sciences, laboratory
Field: Hepatology, Cell Biology
Capacity: 2 IRF students
Background
Chronic liver diseases are characterized by the progressive loss of hepatocytes, the functional
liver cells, as a result of cell death. Several toxic factors present in the chronically injured
liver contribute to cell death, e.g. reactive oxygen species, pro-apoptotic cytokines like TNF
and bile acids. Cell death is the consequence of either necrosis (or passive cell death) or
apoptosis (programmed cell destruction). In contrast to necrosis, apoptosis is an active and
strongly regulated process and therefore amenable to intervention. At the same time, during
chronic liver diseases, there is proliferation of connective tissue cells in the liver, the so-
called stellate cells and activation of liver-specific macrophages: the Kupffer cells. The
proliferation and activation of stellate cells and Kupffer cells leads to liver inflammation and
fibrosis.
To treat the detrimental effects of chronic liver diseases, i.e. death of hepatocytes, activation
of Kupffer cells and proliferation of stellate cells, we need to know the exact actions of toxic
factors, present during liver diseases, on hepatocytes, Kupffer cells and stellate cells.
A major cause of chronic liver diseases is chronic cholestasis: the accumulation of bile in the
liver, due to disturbances in the enterohepatic circulation of bile. Therefore, it is very
important to elucidate the mechanisms of bile homeostasis and to be able to correct any
disturbances in bile homeostasis. Recently, an important role of vitamin A has been
discovered in maintaining bile homeostasis.
Goals of our studies are
1) to elucidate the effects of relevant toxic factors present in the chronically injured live
2) to prevent cell death induced by these factors by manipulating signal transduction
pathways
3) to elucidate the mechanisms of regulation of bile flow and, in particular, the role of
vitamin A in this regulation.
Approach
The research of the department is very much focused on laboratory work. It involves both in
vivo and in vitro (cultured hepatocytes, Kupffer cells and stellate cells). The student
participates actively in the research of the department and will be supervised by PhD
students/technicians and Master students of the department. Techniques used will include:
hepatocyte/stellate cell isolation and culture, assays for apoptosis (caspase activity, nuclear
condensation), intervention in intracellular apoptosis and signal-transduction pathways,
assays for cell proliferation, mRNA isolation and real time PCR, Western blotting and
immunofluorescence microscopy

PROJECT I: Stopping the Flow: Aspartate metabolism in Malaria (pilihan 3)
Supervisor: dr. Groves pHD
Area: Biotechnology
Vacancy: Internship in cellular, molecular and structural biology
Title: Stopping the Flow: Aspartate metabolism in Malaria
Introduction
Malaria is an infectious disease that remains a clear and present threat to human health. It has
been estimated that the disease is responsible for more than half a million deaths annually.
Currently no effective vaccine exists to protect against malarial infections, although efforts to
develop one are ongoing. Several anti-malarial medications are available, but the spread of
multidrug-resistant parasites severely limits their efficacy. There is a pressing need for
academic research to discover new drugs to treat infections of the human malaria parasite (P.
falciparum). Highly attractive avenues for the antimalarial drug discovery are metabolic
pathways. We have recently exploited the structural properties of enzymes such as aspartate
aminotransferase (AspAT) and demonstrated the vulnerability of the parasite to interference
with metabolism of the amino acid aspartate.
Short Project Description
The aim of the proposed project is to investigate enzymes required by the malaria parasite to
create, control and utilize aspartate. The PhD student will apply modern molecular techniques
to analyze malarial enzymes using state-of-the-art biochemical and biophysical techniques.
The PhD student will also use X-ray crystallography to determine the atomic structure and
properties of the enzymes as well as their molecular interactions with new drug leads.
Additionally, these structural analyses will provide a deeper understanding of the molecular
mode of action of the proteins. The PhD student will also be directly responsible for
establishing in vitro assays and screening small molecules for activity. Compounds shown to
have an in vitro effect will then be screened on cellular level on cultured parasites and the
effects assessed using mass spectrometry. She/he will also be involved in testing and
optimizing the new drugs using biochemistry, biophysics and structural biology.
Networking and Training Opportunities
This is a collaborative project between Prof C. Wrenger (Unit of Drug Discovery,
Department of Parasitology at ICB-USP, Sao Paulo) and Dr. M. Groves (Drug Design Unit,
Department of Pharmacy, University of Groningen, Holland). The PhD student will have the
possibility to gain research experience in Brazil and Europe. The University of Groningen has
an international reputation in drug design and attracts students from all over the world. The
University offers a stimulating venue for student research exchange and gives students the
opportunity to broaden their social scientific network. The PhD student will benefit from
training in state-of-the-art techniques and join a highly active and productive international
collaboration.
This highly interdisciplinary PhD offers the candidate the possibility to become an expert in a
wide range of state-of-the-art cell biology, molecular biology, biochemistry, biophysics and
structural biology techniques.
Living in Groningen
Groningen is the economical and cultural capital of the north of the Netherlands. Groningen
is a culturally diverse city that has hosted many musical and theatrical events, boasts several
theatres and museums, many art galleries, bookshops and a wide range of markets, shops and
restaurants with dishes from all over the world. A remarkable characteristic of Groningen is
its relatively young population. One out of every five people in the city is a student, and over
half the population is younger than 35 years old. This has resulted in a wide range of
restaurants, bars, sporting activities, culture, accommodation and recreation at reasonable
prices.
Prior Publications from the collaborating Groups:
1. Wrenger C, Mller IB, Silber AM, Jordanova R, Lamzin VS & Groves MR (2012)
Aspartate aminotransferase bridging carbohydrate and energy metabolism
in Plasmodium falciparum. Curr Drug Metabolism.
2. Wrenger C, Mller IB, Butzloff S, Jordanova R, Lunev & Groves MR. (2012)
Crystallization and preliminary X-ray diffraction of malate dehydrogenase from
Plasmodium falciparum Acta Cryst., Vol F68, 659-62.
3. Butzloff S, Groves MR, Wrenger C & Mller IB. (2012) Cytometric quantification
of singlet oxygen in the human malaria parasite Plasmodium falciparum. Cytometry
A. Vol 81, 698-703.
4. Wrenger, C, Mller, IB, Schifferdecker, AJ, Jain, R., Jordanova, R. & Groves,
MR (2011) Specific inhibition of the aspartate aminotransferase of Plasmodium
falciparum. J Mol Biol. Vol. 405, 956-71.
5. Jain R, Jordanova R, Mller IB, Wrenger C, & Groves MR (2010) Purification,
crystallization and preliminary X-ray analysis of the aspartate aminotransferase of
Plasmodium falciparum. Acta Cryst F Vol 66, 409-12.
6. Knckel J, Jordanova R, Mller IB, Wrenger C & Groves MR (2009) Mobility of
the conserved glycine 155 is required for formation of the active plasmodial Pdx1
dodecamer. Biochim. Biophys. Acta. Vol 1790, 347-50.
7. Mller IB, Knckel J, Groves MR, Jordanova R, Ealick SE, Walter RD & Wrenger
C. (2008) The assembly of the plasmodial PLP synthase complex follows a defined
course. PLoS ONE. Vol. 19, e1815.
Contact:
Dr. M.R. Groves
m.r.groves@rug.nl
http://www.rug.nl/staff/m.r.groves/

PROJECT N: Nephrology (pilihan 1)
Research Dept. Nephrology, Univ Med Center Groningen, The Netherlands Department
of Internal Medicine, Division of Nephrology.
Graduate School of Medical Sciences;
Groningen Research Institute for Drug Exploration (GUIDE)
Coordinators: Prof. G.J. Navis MD PhD (g.j.navis@umcg.nl)
Dr. J. van den Born PhD (j.van.den.born@umcg.nl)
In Nephrology Dept. various projects are running using diverse methodologies (see 1-6). You
are invited to express your interests in one of these fields (being either clinical,
epidemiological, human- or animal in vivo- or in vitro experimental) to indicate what sub-
project interests you most. Please motivate your interest for the specific topic.
1. Patients with renal disease and progressive renal function loss, are being studied with
respect to the mechanisms via which the urinary protein leakage results in renal
function loss. Both non-diabetic- and diabetic renal disease are studied. Most of these
patients are included in clinical trials to study the efficacy of regimens to lower
proteinuria and to prevent progressive renal function loss.
2. Our center also has a large population of renal transplant recipients. These patients are
monitored very closely, and regimens aimed at increasing the duration of graft
function as well as patient survival are being studied currently. A major focus point is
on the involvement of viral infections in chronic renal transplant dysfunction.
3. General population cohorts are studied to detect which parameters lead to initiation of
progressive renal function loss and its complications. The cohorts PREVEND and
Lifelines from the general population are good examples. The natural course is
followed to study possible causes of morbidity and mortality in relation to renal
parameters.
4. Lifestyle and the kidney. Many lifestyle factors are involved in the risk of long term
renal function loss. These include smoking as well as nutritional habits, such as
excess caloric intake leading to obesity and diabetes, excess sodium intake and
sedentary lifestyle. The mechanisms of renal damage induced by these lifestyle
factors are being studied in patients as well as experimental animals, and the effect of
lifestyle intervention measures on the course of renal disease is being studied.
Nutritional monitoring is part of this project
5. Various animal (rat) models of proteinuria and progressive renal disease are being
studied, in order to unravel the mechanisms of renal damage and to optimize
antiproteinuric and renoprotective treatments. Focus points are the RAAS Vitamin
D FGF23 axis; progression of structural tubulo-interstitial changes; and the
interplay of proteinuria and dyslipidemia.
6. Innate immunity and the kidney. Within this research line we try to unravel the role of
innate immune system (complement system, leukocytes, chemokines) in chronic renal
damage in proteinuric and transplanted kidneys. By intervention of novel heparin(oid)
related drugs we aim to reduce the contribution of inflammation in chronic renal
tissue remodelling. Research is largely done in experimental models of renal disease.