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Universidade Nacional da Irlanda em Galway -- Ciência sem Fronteiras
PhD Project Template
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Use one form per project
Please complete & submit to international@nuigalway.ie as soon as possible, and by 27/11/2012
In your email, begin the subject line with [SWB] (be sure to use square brackets) to ensure that
your email is filed correctly. Emails will be automatically filed
PI name & contact details:
Dr. Heinz Peter Nasheuer,
Biochemistry,
National University of Ireland, Galway
University Road
Galway
Ireland
Email: h.nasheuer@nuigalway.ie
phone: +353-91-49 2430
fax: +353-91-49 5504
School:
School of Natural Sciences
Has project been agreed with head (or
nominee) of proposed registration school?
Research Centre / group affiliation:
Research group / centre website:
PI website / link to CV:
Centre for Chromosome Biology;
Cell Cycle Control Group
http://www.chromosome.ie/researchers/nasheuer/
http://www.chromosome.ie/researchers/nasheuer/
Brief summary of PI research / research group / centre activity (2 or 3 lines max):
The research group has three major topics of interest:
 Cell cycle-dependent regulation and mechanisms of human DNA replication and repair pathways
 DNA replication of human polyoma viruses defining small molecules and novel small cellular
non-coding RNA as inhibitors of viral DNA replication
 Systems biology of protein-protein interactions in living cells using advanced microscopic
techniques
Title & brief description of PhD project (suitable for publication on web):
Cellular Small Non-Coding RNAs Highly Active in Inhibiting Polyoma Viral DNA Replication.
The human polyoma virus BKV is a small, non-enveloped, icosahedral virus and its genomes is
organized in circular double-stranded DNA. Additional human polyomaviruses have recently been
discovered (KI, WU and the Merkel cell polyoma-virus). Preliminary findings suggest that these
viruses associated with the oral cavity and respiratory system and may cause Merkel cell
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carcinomas. BKV is often activated after kidney transplantations and in patients with bone marrow
or hematopoietic stem cell transplantations causing Polyomavirus-Associated Nephropathy (PVAN)
of kidneys, and hemorrhagic cystitis (BKV-Associated Hemorrhagic Cystitis, BKV-HC), respectively.
The replication of polyomaviruses is well characterised and therefore, the finding that small cellular
non-coding RNAs, which were first described by the Nasheuer Group and named small replicationregulatory RNAs (srRNAs), inhibit virus replication in vitro and in vivo was astonishing. In the light of
the treatment of infections of humans by new viruses and to control activation of polyomavirus
during drug treatment of patients, the understanding of the molecular mechanism underlying the
inhibition of polyomavirus replication by srRNAs is very important for biomedical research and will
have an impact to support human health and wellbeing. The aim of the proposal is to determine
highly inhibitory native mouse cellular small ncRNAs regulating viral DNA replication. Current
hypotheses suggest that native srRNAs arise from transcription of satellite repeats in mammalian
heterochromatin and modulate viral DNA replication.
Firstly, libraries of small, size-fractionated RNAs will be prepared from mouse cells and cDNA
libraries will then be produced following described protocols previously used in the Nasheuer
laboratory. Next these cDNA will be directly sequenced using next generation sequencing
techniques. These sequence databases will be computationally analyzed for RNAs fulfilling the
principles determined for srRNA regulatory activity. Candidate srRNAs will then be synthesized and
tested in BKV DNA replication assays. If a large number of candidate srRNAs is detected, we will
synthesize and then pool these RNA sequences to assay them in the BKV DNA replication in vitro.
The specific RNA sequences in pools with significant inhibitory activity will then be individually
analyzed in viral DNA replication in vitro and in vivo. Following these analyses the cellular functions
of native srRNAs highly active in the inhibition of viral DNA replication will be characterized. To this
end the intracellular distribution and expression of selected, representative native srRNAs during
the cell cycle of mouse cells will be investigated to gain understanding of srRNA functions. To
analyse the expression of native srRNAs, quantitative reverse transcription PCR (qRTPCR) will be
performed. Preliminary analyses of the cellular distribution of srRNAs suggest that these inhibitory
RNAs are present in the nucleus of mouse cells. To analyse the srRNA localisation in detail we will
perform fluorescence in situ hybridization experiments of cells. These studies of native srRNAs will
provide new insight about the mechanism of BKV replication in mammalian cells where srRNA may
act as physiological protection mechanism to defend cells against viral infections analogous to the
bacterial CRISPR/Cas immune system against phages but mammalian cells using a different
mechanism.
Unique selling points of PhD project in NUI Galway:
NUI Galway projects should emphasise features that are not typically available in Brazil – specific equipment,
multi-disciplinarity, aspects of structured programme, links with industry, placements, links with other research
groups etc.
The student will gain experience in multiple areas of genome stability and the biology of small noncoding RNA learning state-of-the-art biochemical, cell and molecular biological techniques such as
RNA sequencing, advanced fluorescence and immunofluorescence microscopy analyses including
RNA fluorescence in situ hybridization, as well as bioinformatical analysis of RNA sequences.
The PI is a member of the Centre for Chromosome Biology (CCB) at NUI Galway in Ireland and very
closely cooperates with research groups at NUI Galway and with international laboratories to
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Universidade Nacional da Irlanda em Galway -- Ciência sem Fronteiras
advance the knowledge in the mechanisms of genome instability. CCB comprises a highly interactive
network of researchers who are interested in topics focusing the biology of genomes.
The Centre has gained international attention through its recent findings on the regulation of
trinucleotide repeats and the involvement of small noncoding RNA in the inhibition of viral DNA
replication.
The Centre currently consist of 11 groups with more than 90 researchers and support staff. Their
interests are focused on all molecular aspects underlying chromosome replication, segregation,
repair, evolution, chromatin regulation and transcription. To investigate chromosome biology
processes involved the Centre has available a range of technologies available at the molecular,
cellular and organismal level.
http://www.chromosome.ie/
Name & contact details for project queries, if different from PI named above:
as above
Please indicate the graduates of which disciplines that should apply:
Graduates with a background molecular gentics/biology, biochemistry, cell biology, or related
disciplines should apply.
Ciência sem Fronteiras / Science Without Borders Priority Area:
Please indicate the specific programme priority area under which the proposed PhD project fits- choose only
one (tick box):
Engineering and other technological areas
Pure and Natural Sciences (e.g. mathematics, physics, chemistry)/Physical Sciences (Mathematics,
Physics, Chemistry, Biology and Geosciences)
Health and Biomedical Sciences / Clinical, Pré-clinical and Health Sciences
X
Information and Communication Technologies (ICTs), Computing
Aerospace
Pharmaceuticals
Sustainable Agricultural Production
Oil, Gas and Coal
Renewable Energy
Minerals, Minerals Technology
Biotechnology
Nanotechnology and New Materials
Technologies for Prevention and Mitigation of Natural Disasters
Bioprospecting and Biodiversity
Marine Sciences
Creative Industry
New technologies in constructive engineering
Please indicate which of the following applies to this project (referring to Science Without Borders
arrangements):
Suitable only as a Full PhD (Y/N):
Available to candidates seeking a Sandwich PhD arrangement (Y/N): _____
Suitable for either:
Y