8 PhD SCHOLARSHIPS ANNOUCEMENT

Doctoral Programme in Nuclear Magnetic Resonance Applied to Chemistry, Materials and Biosciences – PTNMRPhD (PD/00065/2013)

1. IDENTIFICATION OF SCHOLARSHIPS

The Faculty of Sciences and Technology at Universidade Nova de Lisboa (FCT-UNL), as coordinating institution of the Doctoral Programme in Nuclear Magnetic Resonance Applied to Chemistry, Materials and Biosciences – PTNMRPhD (PD/00065/2013), opens a call for the 8 PhD Scholarships, funded by national funds through Fundação para a Ciência e a Tecnologia, IP, and Ministério da Ciência, Tecnologia e Ensino Superior (FCT/MCTES), and  Fundo Social Europeu - Programa Operacional do Capital Humano (PO CH)

2. SCIENTIFIC AREA

Exact Sciences and Engineering

3. CANDIDATES

Candidates must hold a Master’s degree or legal equivalent, or a Bachelor’s degree with a total number of academic credits equal or above 240 (pre-Bologna degrees) in the area of chemistry, biological sciences, life sciences, material sciences, physics, or related areas with a  minimum grade-point average of 14/20 (Portuguese Scale or equivalent by conversion in case of foreign candidates).

Candidates that have already benefited from a previous PhD scholarship from FCT are not eligible.

For the scholarship type “Mixed” candidates must have permanent residence in Portugal (whatever the candidate’s nationality).

Other requirements:

- Motivation to work in NMR applied to Biologival Sciences, Chemistry, Physics or Materials;

- Fluent in English as this is the Program official language.

- Motivation to perform research work;

 

4. DEADLINES AND APPLICATION CRITERIA

4.1. Applications for candidates are open from the 17 of December 2018 to the 7 of January 2019

4.2. Application are submitted on-line exclusively through the PTNMRPhD website (https://sites.fct.unl.pt/ptnmrphd/), accompanied with all documents required and within the deadline.

4.3. Criteria for Admission

Admission criteria will be verified by means of a written application that should include the following documents:

a)    Detailed Curriculum vitae including degrees, grades obtained, courses attended, research experience and publications;

b)    Personal statement. The personal statement (maximum 2 pages) should include a description of academic interests and career goals, a description of scientific interests and a summary of previous research experience including laboratory work. A final full paragraph should present the reasons for applying to the Program;

c)    Copy of personal identification card (Passport);

d)    Copy of Diplomas/Certificates of relevant examinations (e.g. BSc or MSc degree)

e)    For academic degrees obtained outside Portugal it is mandatory to present the copy of registration of the recognition of the academic degree and the conversion of the final classification to the Portuguese scale (process regulated by Decree-Law no. 341/2007, of October 12), or alternatively, to obtain equivalence / recognition of academic degrees (process regulated by Decree-Law no. 283/83 of June 21)[1];

f)     Proof of permanent and habitual residence in Portugal, if applicable (Mandatory if applying to Mixed Scholarships);

g)    Updated statement proving the professional situation of the candidate, indicating the nature of the bond, duties and weekly teaching hours, if applicable, being able to replace it with a declaration of honor, if you do not carry out any professional or service activity;

h)   Two names and contacts for references. These persons will be asked to send a closed reference letter;

i)     Explicit indication of three working plans from the list presented in point 5, in order of preference (2 from the main list and 1 from the additional list).

 

 

5. RESEARCH PROJECTS/SUPERVISORS/HOST INSTITUTIONS

Main Research Projects:

Research Project 1

Title: Structural studies of liquid phase proteins related to human disease

Scientific Area of PhD: Chemistry

Scholarship Type: Mixed

Summary: Protein liquid-liquid phase separation (LLPS) may lead to the formation of cellular membraneless proteinaceous organelles that constitute an effective responsive strategy for biological compartmentalization. These have been shown important for cellular homeostasis and disease, constituting a different liquid medium that recruits specific proteins and excludes others, and where particular reactions are promoted and others inhibited. In this project, using state-of-the-art NMR combined with other biophysical techniques (fluorescence microscopy, optical spectroscopies and calorimetry), we will unravel the molecular factors determining protein LLPS, and study the effects on structure and dynamics of proteins inside the liquid droplets. This will provide important information on biomolecular function and disease mechanisms, paving the way for future pharmaceutical and biotechnological applications.

Instituição de Acolhimento: Faculdade de Ciências e Tecnologia, UNL

Morada: Quinta da Torre, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal

Orientador Científico: Eurico Cabrita, FCT-Universidade Nova de Lisboa

Co-orientador 1: Douglas Laurents, CSIC Madrid, Espanha

 

Research Project 2

Title: Studying the immunomodulatory action of novel chromone-based compounds by NMR metabolomics and metabolic flux analysis

Scientific Area of PhD: Chemistry

Scholarship Type: National

Summary: This work aims at investigating the immunomodulatory action of nature-inspired chromone-based compounds, with a view to contribute for the development of novel anti-inflammatory therapies. NMR metabolomics and NMR-based stable-isotope metabolic flux analysis will be employed to assess how immune-inflammatory cells (e.g. macrophages) reprogram their metabolism and change their phenotypes upon different treatments. This approach is expected to greatly advance current understanding of chromones biological activity, as well as to open new prospects in the field of anti-inflammatory immunotherapy.

Instituição de Acolhimento: Universidade de Aveiro

Morada: Departamento de Química, CICECO, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal

Orientador Científico:  Iola Duarte, CICECO – Aveiro Institute of Materials, Department of Chemistry, Universidade de Aveiro

Co-orientador 1: Artur Silva, QOPNA, Department of Chemistry, Universidade de Aveiro

Co-orientador 2: John Jones, Center for Neuroscience and Cell Biology (CNC), Universidade de Coimbra

 

Research Project 3

Tittle: Dissecting the supramolecular dynamics of the virulent Tir during infection

Scientific Area of PhD: Molecular Biosciences

Scholarship Type: Mixed

Summary: The translocated intimin receptor, Tir, is essential for EHEC and EPEC virulence. Once injected into host cells, as the first step of infection, Tir goes from the cytosol into plasma membranes to attach the pathogen to the surface and hijack host cellular processes. The dynamics and structural assembly of Tir in eukaryotic cells have a huge impact on virulence, but it remains largely unexplored, in particular from a quantitative/structural point of view. The project concerns the molecular and atomic description of Tir and its self-organisation in membranes using hybrid structural approaches (NMR/SAXS).

 

Instituição de Acolhimento: Instituto de Tecnologia Química e Biológica António Xavier, UNL

Morada: ITQB - Instituto de Tecnologia Química e Biológica, Av. da República (EAN). Apartado 127. 2781-901 Oeiras, PORTUGAL

Orientador Científico: Tiago Neto Cordeiro, ITQB - Instituto de Tecnologia Química e Biológica

Co-orientador:  Markus Weingarth, Bijvoet Center, Univ Utrecht

 

 

Research Project 4

Title: Bacterial Peroxidases – a bacterial mechanism against the immune system

Scientific Area of PhD: Chemistry

Scholarship Type: Mixed

Summary:  Pathogenic bacteria, such as Neisseria gonorrhoeae that causes the sexually transmitted disease gonorrhea, are constantly exposed to reactive oxygen species (ROS) and have developed defense mechanisms to cope with oxidative stress. Bacterial peroxidase is one of these enzymes. This enzyme catalyzes the reduction of hydrogen peroxide to water, with the required electrons being donated by small electron shuttle proteins. We intent to isolate and determine the structure of a small cytochrome c and characterize its interaction with the bacterial peroxide using different techniques (cell microscopy, RT-PCR, microcalorimetry, NMR). These results will contribute to the understanding of the involvement of Neisseria gonorrhoeae bacterial peroxidase has a first line defense mechanism against exogenously produced hydrogen peroxide in the host environment.

Instituição de Acolhimento: Faculdade de Ciências e Tecnologia, UNL

Morada: Quinta da Torre, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal

Orientador Científico: Sofia Pauleta, FCT-Universidade Nova de Lisboa

Co-orientador 1:  Lucia Banci, CERM, University of Florence

Co-orientador 2: Corinne Aubert, CNRS Marseille, France

 

Research Project 5

Title: NMR-aided development of new olefin metathesis catalysts for pharmaceutical applications

Scientific Area of PhD: Chemistry

Scholarship Type: National

Summary:  Homogeneous OM catalysts are powerful synthetic tools, Ru catalysts in particular due to their tolerance to functional groups, but their separation from the reaction media is difficult and hampers industrial application. New supported catalysts that combine the versatility of homogeneous catalysts with ease of separation and catalyst recyclability will be developed. NMR will be a key technique in catalysts characterization (liquid and solid state), surface characterization, catalyst active species and decomposition pathways (DNP).

Instituição de Acolhimento: Instituto Superior Técnico, Universidade de Lisboa

Morada: Departamento de Química, IST, Av. Rovisco Pais, 1, 1049-001 Lisboa, Portugal

Orientador Científico: Maria João Ferreira, Instituto Superior Técnico, Universidade de Lisboa

Co-orientador 1: Mariana Sardo, CICECO, Universidade de Aveiro

Co-orientador 2: Ana Margarida Martins, Instituto Superior Técnico, Universidade de Lisboa

 

Research Project 6

Title: NMR and EPR study of the interaction of 3-hydroxy-4-pyridinone chelates with Biological Membranes

Scientific Area of PhD: Biomedical Sciences

Scholarship Type: National

Summary:  Ligands of the 3-hydroxy-4-pyridinone class and their metal ion chelates find application in the fields Drug Design and Plant Nutrition. NMR and EPR will be used to gather information about their interactions with of biological membranes.The knowledge of the interactions of drugs/nutrients with biological membranes could allow for a better understanding of the mechanisms of delivery, transport, bio-distribution and retention of these substances in the organized media of cellular membrane. This understanding contributes to the discovery, design, and screening of novel therapeutic/nutrient agents.

Instituição de Acolhimento: ICBAS, Universidade do Porto

Morada: R. Jorge de Viterbo Ferreira 228, 4050-313 Porto

Orientador Científico: Maria da Conceição Rangel

Co-orientador 1: Eurico Cabrita, FCT-UNL

Co-orientador 2: Galya Ivanova, REQUIMTE-UP

 

Research Project 7

Title: NMR study of low molecular weight components of Non-transferrin bound Iron

Scientific Area of PhD: Biomedical Sciences

Scholarship Type: National

Summary:  All human cells require iron for survival, and its safe transport is ensured by serum transferrin. Non Transferrin Bound Iron is generally regarded as a source of oxidative stress, both in the circulating component and inside the cell. NTBI is able to circumvent the tightly regulated iron uptake system, promoting intracellular iron accumulation.

We propose to apply modern NMR methodologies to study the low molecular weight component of NTBI in the blood serum of hereditary hemochromatosis and diabetes patients. EPR spectroscopy will also be employed and LC-MS, which has proved useful in the speciation of iron citrate complexes,
will be used as a complementary methodology. We also propose to apply NMR methodologies to study protein paramagnetic metal ion centers to study the interaction of HSA with iron.

Instituição de Acolhimento: ICBAS, Universidade do Porto

Morada: R. Jorge de Viterbo Ferreira 228, 4050-313 Porto

Orientador Científico: Maria da Conceição Rangel

Co-orientador 1: Anjos Macedo, FCT-UNL

Co-orientador 2: André Neto da Silva, REQUIMTE-UP

Research Project 8

Title: The role of conformational changes and protein dynamics of a hub protein in the infection cycle of the Influenza virus studied by in-cell NMR.

Scientific Area of PhD: Chemistry

Scholarship Type: Mixed

Summary: Influenza epidemics and pandemics are constant threats to human health and recent emergence of influenza A H5N1 and H1N1 strains has heightened these concerns. Rapid emergence of drug-resistant viral mutations has limited the use of current medicines in the market like the neuraminidase (NA) inhibitors and rendered the matrix protein 2 (M2) blockers ineffective. Therefore, there is an urgent need of novel anti-influenza drugs directed to alternative biological targets. In order to better understand the central role of one of the main viral proteins in viral proliferation, and following in vitro NMR and computational work being carried out in the laboratory, in this project in-cell NMR will be used to study the role of conformational changes and protein dynamics in the multiple interactions of this hub protein with host proteins of the infected cells.

Instituição de Acolhimento: Universidade de Coimbra (UC)

Morada: R. Larga, 3004-535 Coimbra

Supervisor: Rui M. M. Brito (Departamento de Química, Universidade de Coimbra)

Co-Supervisor: Lucia Banci (Magnetic Resonance Center – CERM, University of Florence, Italy)

 

Additional Research Projects:

Additional Research Project 1

Title: Probing the nano-structuring of ionic liquid based fluids using ¹²⁹Xe NMR spectroscopy: towards structure-properties relationships.

Área do Grau de doutor: Química

Bolsa: Nacional

Summary:  The complex nanostructure of ionic liquid based fluids will be studied using ¹²⁹Xe NMR spectroscopy. ¹²⁹Xe chemical shifts are highly sensitive to molecular medium making xenon an excellent NMR probe. Fluids with potential theranostic value will be studied, such as nanoemulsions for medical applications, seeking to establish the relation between molecular structure, organization and the properties of the fluid. Molecular Dynamics simulations will provide molecular level interpretation of the results. Other spectroscopic, thermodynamic and rheological properties will also be addressed.

Instituição de Acolhimento: Instituto Superior Técnico, Universidade de Lisboa

Morada: IST, Av. Rovisco Pais, 1, 1049-001 Lisboa, Portugal

Orientador Científico: Eduardo Filipe, CQE, IST

Co-orientador 1: José Ascenso, CQE,IST

Co-orientador 2: Ana Sofia Ferreira, FCT-UNL

 

Additional Research Project 2

Title: Exploring the molecular bases of ‘unnatural’ reactivity of engineered cytochormes c

Área do Grau de doutor: Ciências Biomoleculares

Bolsa: Mista

Summary:  Heme proteins in general and cytochromes c in particular play key roles in numerous processes essential for life. In addition to their unquestionable biological role, it has recently emerged that they can be tuned to perform reactions not found in nature. Biomolecular NMR spectroscopy is uniquely suited to investigate the structural and dynamic factors underpinning these ‘unnatural’ reactions, providing guidance for the rational design of efficient bio-based catalysts.

Instituição de Acolhimento: Instituto de Tecnologia Química e Biológica António Xavier, UNL

Morada: ITQB - Instituto de Tecnologia Química e Biológica, Av. da República (EAN). Apartado 127. 2781-901 Oeiras, PORTUGAL

Orientador Científico: Ricardo O. Louro, ITQB-NOVA

Co-orientador 1: TBA, CERM

 

Additional Research Project 3

Title: Structural characterization of natural products from microalgae with anti-tumor activity

Área do Grau de doutor: Química

Bolsa: Nacional

Summary:  Cancer is a global health problem causing approximately 7.9 million deaths each year, 70% of which in the developing world. Research carried out over the years has identified numerous natural compounds that due to its low toxicity and potential anticancer activity could be used for prevention and combat of cancer. New therapies using natural compounds or their derivatives should be developed to replace highly toxic drugs and help to increase the patients' quality of life. Microalgae appear to be an excellent under-exploited source of novel compounds displaying bioactivity against human cancer cells. The aim of this work is to find and characterize microalgal-derived compounds with low toxicity and anticancer activity against the most common types of cancer, with a focus on those striking developing countries (lung, stomach, breast, liver and cervical). Taking advantage of the large live collection of microalgae at the University of Coimbra (ACOI), multi-nuclear and multidimensional NMR will be used to characterize the compounds present in extracts of microalgae cultures with the most promising anti-tumor activity.

Instituição de Acolhimento: Universidade de Coimbra (UC)

Morada: R. Larga, 3004-535 Coimbra

Supervisor: Rui M. M. Brito (Departamento de Química, Universidade de Coimbra)

Co-orientador 1: Eurico Cabrita (FCT-UNL)

 

Additional Research Project 4

Title: Fe/S Cluster Biosynthesis System

Scientific Area of PhD: Chemistry

Scholarship Type: Mixed

Summary:  Strict anaerobic bacteria present in their genome a cluster of genes that have been proposed to be involved in Iron-Sulfur cluster biosynthesis, with no resemblance to other prokaryotic system but instead are homologous to the eukaryotic ones. In eukaryotes, these systems are involved in various severe diseases and there is an urge to understand the mechanism of action of these proteins/enzymes. The homologous prokaryotic proteins will be biochemical and structurally characterized using different techniques and, the network of interactions will be identified and characterized (cell microscopy, RT-PCR, microcalorimetry, NMR).

Instituição de Acolhimento: Faculdade de Ciências e Tecnologia, UNL

Morada: Quinta da Torre, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal

Orientador Científico: Sofia Pauleta, FCT-Universidade Nova de Lisboa

Co-orientador 1:  Lucia Banci, CERM, University of Florence

Co-orientador 2: Corinne Aubert, CNRS Marseille, France

 

6. SELECTION AND RANKING OF APPLICANTS

The process of selection and ranking of applicants is coordinated by the Directive Board. Selection follows a two-step procedure involving a written application (stage 1 – 70%) and an interview (stage 2– 30%).

Selected applicants will be admitted for the full PhD program (period of 4 years).

Stage 1: The general guidelines from FCT/MEC on individual PhD grants will be followed for the stage 1.

Assessment of written applications by a sub-committee of the Directive Board will consider the CV (80%), and letter of intent (10%) and the two reference letters (10%).

CV evaluation considers the classifications of degree (European scale of comparability should be used), internationalization/mobility, specialization courses, laboratory experience and scientific publications (if any).

A shortlist of elected candidates will proceed to Stage 2. All candidates shall be informed of Stage 1 classification.

Stage 2: Selected candidates will be interviewed. This step serves to evaluate the intellectual and scientific ability of the candidates, think critically, research interests together with career goals after the PhD and expectations for joining this specific programme, and command of English.

 7. SELECTION COMMITTEE

The selection committee is the following: Prof. Eurico Cabrita (President), Prof. Ana Gil (Univ. Aveiro), Prof. Rui Brito (Univ. de Coimbra), Prof. Anjos Macedo (FCT-UNL), Prof. José do Rosário Ascenso (IST-UL), Prof. Conceição Rangel (UP) and Dr. Pedro Lamosa (ITQB-UNL).

8. RESULTS AND NOTIFICATION OF CANDIDATES


8.1. Admission and exclusion lists and final list will be available through the electronic page of the program; https://sites.fct.unl.pt/ptnmrphd/.

8.2. All communication with candidates such as admission to the 2^nd stage of selection or exclusion will be communicated to the email address of the candidate Curriculum Vitae.

8.3. The final list will be communicated to all candidates.

9. DURATION OF THE BALANCE SHEET, MONTHLY MAINTENANCE ALLOWANCE

According to Article 9 of the RBI (Regulamento das Bolsas de Investigação), the scholarship lasts for one year, renewable at least for a maximum period of 4 years, and is expected to start in February 2019.

The monthly maintenance allowance (SMM) to be granted is set out in the Table attached to the RBI, taking into account the type of Scholarship. The payment of the SMM as well as the payment of the expenses resulting from the possible adhesion of the fellow to the voluntary social insurance scheme (1º Escalão) will be made monthly by bank transfer to the account identified by the fellow in the context of the process of the Scholarship contract.

The candidates selected will exercise the functions of scholarship holder on an exclusive dedication under the terms established in the Researcher's Statute.

10. NON-DISCRIMINATION AND EQUAL ACCESS POLICY

The PTNMR Doctoral Program promotes a policy of non-discrimination and equal access, so that no candidate can be privileged, benefited, impaired or deprived of any right or exemption from any duty age, sex, sexual orientation, marital status, family status, economic situation, education, social origin or condition, genetic heritage, reduced working capacity, disability, chronic illness, nationality, ethnic origin or race , territory of origin, language, religion, political or ideological convictions, and trade union membership.