PhD PROGRAMME IN BIOMOLECULAR SCIENCES
ANNOUNCEMENT OF SELECTION: 31st cycle – Academic Year 2015/2016

DEADLINE FOR APPLICATIONS: August 27, 2015, hrs. 4:00 PM (Italian time) CLOSED
Link to the Application online
Positions: 17
(6 additional, see below)
Scholarships: 16 (6 additional, see below) of which 6 on topics related to the research activities carried out at the Centre for Integrative Biology; 9 on specific research topics and 1 directed

Directed scholarship

n. 1 scholarship funded by CIBIO – Centre for Integrative Biology to be carried out at the Armenise-Harvard laboratory of Cancer Biology and Genetics and directed to the topic: “In vitro and in vivo characterization of prostate cancer secretome and its roles in tumour progression and androgen deprivation resistance”.
Principal investigator: dr. Andrea Lunardi ( http://web.unitn.it/en/cibio/38106/armenise-harvard-laboratory-of-cancer-biology-genetics )

Scholarships on specific research topics (that require specific competence assessed during the oral examination)

1 scholarship funded by The Microsoft Research – University of Trento Centre for Computational and Systems Biology (COSBI), reserved for the topic: “Modeling of human neurodegenerative and metabolic diseases from multi-source data types”. In this project the candidate is expected to build algorithmic and network based model of molecular events associated with neurodegenerative/metabolic diseases relying on experimental data and public domain data. This study will help in understanding the molecular pathways altered in the disease and generate biological hypotheses on disease development and progression. The design and realization of the study will be done at COSBI (see http://www.cosbi.eu). Preferred skills: a master in Bioinformatics, Systems Biology or closely related disciplines with knowledge in data manipulation procedures is preferred. Some experience in neuroscience/metabolism will be a plus.
Principal investigator: Prof. Corrado Priami

n. 1 scholarship funded by CIBIO – Centre for Integrative Biology, which project will be carried out at the Neurodegenerative Diseases andTranscriptional Neurobiology laboratories. Scholarship is reserved for the topic: “The impact of chloride signaling dysregulation in neurodegeneration”. Neurodegenerative diseases, are characterized by accumulation of toxic proteins into aggregates. Proteins acquire their biologically active and thermodynamically stable native conformation through a sequence of structural rearrangements and are sensitive to micro-environment. Changes in the pH and ion composition of intracellular space may result in aggregation. Altered chloride homeostasis has been observed in neurological disorders and genetic mutations impairing Cl transport are responsible for epilepsy, neuropatic pain, and Alzheimer’s disease. Small changes in chloride concentration can have big impact on the transmembrane gradients, membrane currents and potential. In this project, we will test the hypothesis that altered [Cl] causes neurodegeneration through altered protein folding. To test our hypothesis, we will pursue these specific aims:
- To characterize the effect of unbalanced Cl concentration on protein misfolding and aggregation in neurodegenerative diseases.
- To determine the impact of altered Cl metabolism on neurotoxicity.
- To establish alterations of Cl homeostasis in living animals.
Expertise in molecular and cellular biology along with skills in gel electrophoresis and protein immunoprecipitation are requested, along with an excellent knowledge of neurodegenerative diseases. The ability to use the fluorescent and confocal microscope is a plus. The optimal candidate should be proficient in English.
Principal investigators:
dr. Maria Pennuto ( http://web.unitn.it/en/cibio/31509/laboratory-of-neurodegenerative-diseases )
dr. Manuela Basso ( http://web.unitn.it/en/cibio/32974/laboratory-of-transcriptional-neurobiology )

n. 1 scholarship funded by Fondazione Bruno Kessler (FBK), and reserved for the topic: “Cloud computing bioinformatics solutions for predictive analytics of big omics data in pharmacogenomics”. The research activity will take place at the Predictive Models for Biomedicine & Environment Lab (FBK/MPBA  http://mpba.fbk.eu/en/home), Complex Data Analytics Research Line of FBK, possibly in collaboration with international pharmacogenomics companies. Skills requested: machine learning for biomolecular profiling, bioinformatics for functional genomics (microarray or NGS) and solutions for developing bioinformatics pipelines in HPC or cloud infrastructures. Previous experience of collaboration with international research labs will be positively considered.
Principal investigator: dr. Cesare Furlanello

Additional positions and reserved scholarships

Scholarships on reserved topics, and related positions, that may be made available after the issue of the announcement and within a week before the assessment of qualifications, will be listed below. Only those applicants who have submitted the application by the deadline of August 27, 2015, will be allowed to participate in the supplementary.  The suitability of the candidates for reserved scholarships will be evaluated during the oral examination.

N. 1 additional position and n. 1 reserved scholarship: funded by CIBIO – Centre for Integrative Biology.
Posted on August 10, 2015.
1 scholarship, part of a European Research Council (ERC-CoG, 5 yrs, http://cordis.europa.eu/project/rcn/197873_en.html) titled "Synthetic Lethal Phenotype Identification through Cancer Evolution Analysis (SPICE)" that requires specific competence assessed during the oral examination.
In this project the PhD student is expected to develop a computational strategy to identify synthetic lethal combinations through the integration of genomic and transcriptomic sequencing data from hundreds of human tumors leveraging the Demichelis laboratory expertise in cancer evolution analysis. The overall purpose of the SPICE research project is the development of an innovative methodology to nominate genomic biomarkers of lethal cancer and to identify co-targeting solutions based on synthetic lethal combinations. The project conjugates computational and experimental work to in vitro validate the most promising candidates. The PhD student will interact with the experimental side of the SPICE project and with national and international collaborators. Preferred skills: combination of Computer Science or Bioinformatics with Biotechnology or Biology training is ideal; knowledge of programming languages is mandatory; experience in cancer genomics and or human genetics is desired.
Principal investigator: Prof. Francesca Demichelis ( demichelislab.unitn.it )

N. 1 additional position and n. 1 reserved scholarship: funded by CIBIO-Centre for Integrative Biology on The Creutzfeldt-Jakob Disease Foundation’s project.
Posted on August 21, 2015.
Scolarship reserved to the topic: “Pharmacological chaperones for the cellular prion protein”. The candidate will be involved in a research project aimed to identify novel small molecule ligands for the cellular prion protein, and characterize their biological effects against prion diseases in vitro and in vivo. Minimum requirements: a master in Pharmaceutical Biotechnologies, or related disciplines; some experience with basic techniques of biochemistry and cellular biology. Previous experience with cellular models of prion diseases will be a plus.

N. 1 additional position and n. 1 reserved scholarship: funded by CIBIO - Center for Integrative Biology on a project financed by the Italian Ministry of Education, University and Research (MIUR).
Posted on August 24, 2015.
Scolarship reserved for the research project entitled: “MicroRNAs: roles and mode of actions in brain wiring”. This project aims to uncover the microRNAs that are key in the establishment of neuronal networks during development and their mode of action in this process. The candidate is expected to use a wide arrays of well-established but also innovative and cutting-age techniques for the accomplishment of this project such as Next Generation Sequencing and live imaging.
The project will be carried out at CIBIO within The Giovanni Armenise-Harvard Foundation Laboratory of axonal neurobiology. To get more information on the laboratory, please visit the webpage:
http://www.unitn.it/en/cibio/11875/laboratories.
The successful candidate should be highly motivated, display initiative, problem solving skills and independence. Candidates with a Master’s degree in Biotechnology or related disciplines and with knowledge in Neuroscience and/or RNA biology are encouraged to apply.
Principal investigator: Dr. Marie-Laure Baudet (marielaure.baudet@unitn.it).

N. 1 additional position and n. 1 reserved scholarship: funded by CIBIO-Centre for Integrative Biology.
Posted on September 3, 2015.
Scholarship reserved to the topic: “Metal ions in the origins of life”.
The project seeks to explore the role of metal ions on the origins of life. Modern day organisms make use of metal ions for fundamental metabolic reactions. For example, 1/3 of all proteins are believed to exploit a coordinated metal ion for activity, and cellular respiration and DNA and protein metabolism are all metal dependent. However, it is presently unclear if this dependence on metal ions was there from the very beginning of the emergence of a protocell or a later adaptation of a non-metal dependent primitive organism. This project seeks to determine the plausibility of prebiotic peptides and nucleic acids to exploit environmental metal ions for activity that leads to the emergence of cellular life.
The project will be carried out at CIBIO within The Armenise-Harvard Laboratory of Synthetic and Reconstructive Biology .
The ideal candidate would have a degree in chemistry or biochemistry; however, candidates with sufficient laboratory experience regardless of the degree will be considered. Experience with metals (e.g. bioinorganic chemistry) and molecular biology is desirable. 
Principal investigator: prof. Sheref Samir Mansy

N. 1 additional position and n. 1 reserved scholarship: funded by CIBIO-Centre for Integrative Biology.
Posted on September 8, 2015.
Scholarship reserved to the topic: "Outer Membrane Vesicles (OMVs) from “Vaccinobacter”: a Synthetic Biology approach for effective vaccines against infectious diseases and cancer"
Vaccination is one of the most effective intervention in the history of medicine. However, there are a number of infectious diseases for which vaccines do not exist yet. Furthermore, chronic diseases such as cancer are still awaiting valid solutions to turn vaccination into an effective prophylactic and/or therapeutic intervention. The main objective of our Laboratory of Synthetic and Structural Vaccinology (SSV) is to create novel vaccine platforms based on the exploitation of the Outer Membrane Vesicles (OMVs) naturally released by Gram-negative bacteria. Because of the intrinsic capacity of OMVs to potently stimulate innate immunity and thanks to the possibility of OMVs to be manipulated with heterologous antigens the vesicles have the potential to become the scaffold of highly innovative and effective vaccines.   
Research directions.
The main activities of the SSV Laboratory can be summarized as follows:
1.    Genome editing of Escherichia coli to create a new strain specialized in OMVs production – OMVs carry a conspicuous number of endogenous proteins mainly belonging to outer membrane and periplasmic compartments. It is expected that the alteration of the protein repertoire of OMVs could profoundly affect the immune response elicited in mammals both in qualitative and quantitative terms. Innovative approaches for genome editing are being applied to selectively remove/add genes and gene pathways to ultimately create an E. coli  strain capable of releasing abundant quantities of OMVs carrying a minimal amount of endogenous proteins and novel immune-stimulatory components.
2.    Development of novel genetic tools to decorate OMVs with foreign antigens – The main objective of this activity is to find gene technology strategies to deliver the desired protein antigens to the OMV compartments. Such technologies will include gene fusions, domain engineering and grafting of transport machineries. 
3.    Development of novel OMV-based vaccines against bacterial pathogens and cancer – OMVs will be decorated with selected bacterial and cancer antigens and immunogenicity and protective activity of OMVs are being evaluated in vitro and in vivo. In particular, the mechanisms of stimulation of innate immunity is being analyzed using cell lines engineered with specific Patterns Recognition Receptors (PRRs). Furthermore, the elicitation of antibodies, CD4 and CD8 T cells will be evaluated in appropriate animal models. Finally,  mouse models for infectious diseases and cancer will be set-up and used to establish the protective properties of OMV-based vaccines and to correlate protection to humoral and cell-mediated immunity.
The candidate will be mostly, but not exclusively, involved in Activity 2. As a consequence, the candidate should demonstrate theoretical and experimental competence in molecular biology, cell biology and in immunology. In particular, she/he should be familiar with the basic techniques of molecular biology such as PCR, gene cloning in eukaryotic/prokaryotic systems, growth of bacteria/cell lines, and analysis of protein expression by using SDS-PAGE and Western Blot. Experience in purification of recombinant proteins will be highly appreciated, as well as competences in basic immunology techniques and FACS analysis.  Fluency in English, both written and spoken, is required.
Principal Investigator:  Prof. Guido Grandi

N. 1 additional position and n. 1 reserved scholarship: funded by CIBIO-Centre for Integrative Biology.
Posted on September 8, 2015.
Scholarship reserved to the topic: "Extracellular vesicles as prognostic and treatment indicators in neural tumors: toward a “liquid biopsy” of solid tumors".
This project is focused on the evaluation of the feasibility of the use of extracellular vesicles derived from peripheral blood (EVs, exosomes and ectosomes) enriched in tumor-derived ones as indicators of the disease course and of the treatment effectiveness in up to two types of solid tumors of neural origin. A standardized, easy to apply (in the clinical setting) way of extracting EVs from the human blood will be established. In parallel, experiments with cell lines and primary cell spheroids will allow us to study the in vitro release and composition (in terms of mRNAs and proteins) of the tumor cell EVs, to detect enrichments with respect to the mother cell composition by high throughput methods. Subsequently we will test methods to enrich in tumor-derived EVs the EVs obtained by cancer patients, to which the same high throughput analyses will be applied to identify proteins and mRNAs which could act as markers of the disease course and/or of the response to treatment in high risk patients. The two solid tumors of neural origin will be chosen among neuroblastoma, glioblastoma multiforme, melanoma, small cell lung carcinoma depending on the establishment of collaboration agreements with local and Italian hospitals for the blood samples of patients.
The ideal candidate for this project is a master graduate in biology or biotechnology with experience in work with solid tumors in a clinical setting and with the knowledge of the basic methods of cell and molecular biology applied to tumor cells and tissue samples.
Principal Investigator: prof. Alessandro Quattrone ( Laboratory of Translational Genomics )

The Academic year starts November 1, 2015.

Announcement of selection: Rector's Decree n. 311 of 18.05.2015, published in this webpage on May 22, 2014 – available in the “Download Box”*
*please note that only the Italian version of the call is legally binding, the English version is provided for information only.

Candidates are recommended to complete the online application well in advance before the deadline, in order to avoid possible technical problems or overcharge of the connection and/or of the application systems.

Assessment schedule: Assessment of qualifications: September 9, 2015; Oral exams: September 21 - 22 - 23, 2015 at: CIBIO Meeting Room, building Povo 2, Via Sommarive, 9 - 38123 Povo (Trento - Italy)