CCMAR is one of the institutions in which the programme INPhINIT will offer fellowships to complete a PhD. Here is how it works:

• The programme INPhINIT offers 35 attractive fellowships to complete a PhD in 100 renown institutions of Portugal and Spain in the disciplines of life sciences and health, experimental sciences, physics, chemistry and mathematics.
• Applicants must have resided in Portugal for less than 12 months in the last 3 years.
• Applicants must apply to obtain a fellowship and will thus have the possibility to choose to come to CCMAR, inserted in one of the.10 proposed research projects in the fields of phytoplankton and seagrass ecology, protection and sustainable exploitation of marine resources and marine biochemistry and biotechnology.
• All projects are available in this search engine, including the 10 CCMAR projects described below.
• Feel free to contact project supervisors to obtain more information. And if you decide to apply, best of luck!!

CCMAR PROJECTS:

Phytoplankton and seagrass ecology:

• Phytoplankton diversity, Resilience and Recuperation Time to Extreme Events in the Azores Area
  • Supervisor: Fatima Abrantes
  • Summary: Understanding the future climate-related risks for biodiversity may improve by studying the response of ocean micro-organisms to past extreme climate and environmental events. A combined study of different phytoplankton, zooplankton and benthic microfossils, should allow the investigation of biodiversity variability and the plankton-benthic coupling conditions through past extreme climate events. Furthermore, a sedimentary sequence containing a record of “extreme” environmental events and the transition to “normal” sedimentation gives information on the resilience and recuperation time of different microorganisms. Existing records for the Azores area reveal that rapid climatic changes are well marked in the region, while a recovered core reveals the presence of pellets of volcanic material and volcanic ash intercalated in hemipelagic sediments, a record of volcanic activity. Cores from cruises DANA14 & KNR197 are located at the winter north limit of the present day Azores Front (AzF). Considering the high primary production associated with the southern limit of the front, the abundance of microorganisms in the sediments is expected to be high and the estimated sedimentation rate should permit high resolution for the periods of interest. To reach the objectives imply dating by AMS 14C particularly below and above volcanic debris. To better define an age model and identify the periods of interest, stable oxygen isotope data will be generated. The sediments physical characterization, organic elements content and microfossil analysis will be preformed. The laboratory work, results evaluation as well as paper preparation will be mainly the responsibility of the candidate.  
    We are looking for enthusiastic and highly motivated individuals with a good biological or geological background, or a master in marine sciences or equivalent. Study to be done in close collaboration with colleagues from GEUS & Aarhus University, DK WHOI, USA, with potential visits to their institution.

• The spread of emerging marine biotoxins: risks to seafood safety supervised
  • Supervisor: Pedro Reis Costa
  • Summary:The expansion in range of harmful algae blooms (HABs) species is one of the changes likely to occur in response to climate change, in particular the spread of Gambierdiscus and Ostreopsis. Ciguatera fish poisoning (CFP) is one of the largest scale seafood poisonings affecting tens of thousands people every year worldwide. Although ciguatera endemic areas are tropical and subtropical Indo-Pacific Ocean and Caribbean Sea, human poisoning episodes have been recently reported after consumption of fish caught in Europe, including Portuguese waters. The emergence of Gambierdiscus spp and associated CFP in Madeira Archipelago, suggest that this could be an important sentinel site to study expansion and increased occurrence of this HAB at a site that did not experience problems in the past. The benthic dinoflagellate Ostreopsis spp that has been pointed out as an example of the tropicalization of the Mediterranean Sea have been increasingly reported in Portuguese south coast and Madeira islands. Ostreopsis produce palytoxins, highly toxic natural compounds that may via aerosol cause human respiratory disorders, and have been associated with mortality events of benthic marine communities.The overall objective of this PhD project is to investigate 1) how toxins produced by small epibenthic dinoflagellates, endemic from tropical and subtropical regions, can be transferred up to the marine food web in European waters, 2) how the toxins are metabolized by fish/shellfish and biotransformed into more potent compounds, and 3) pose a risk for human consumption.This PhD project will benefit from synergies with two ongoing projects, supported by EFSA and FCT, aiming to 1) determine the incidence of ciguatera fish poisoning in Europe and the epidemiological characteristics of the cases, 2) assess the presence of emerging toxins in food in Europe and 3) harmonized and validate methodologies for the screening and the quantification of emerging toxins in contaminated food matrices. Specific tasks and duties include: a)Investigate the distribution and seasonal variability of the toxic dinoflagellates Gambierdiscus spp., Ostreopsis spp in Madeira and Algarve waters hotspots; b) Investigate the processes and pathways of marine food web transfer from toxin producers up to top predators; c) To disseminate the activities, results and guidelines within the scientific community, stakeholders and general public.

• Primary production and climate variability in the south-east pacific at orbital and millennial time scales
  • Supervisor: Fatima Abrantes
  • Summary: Coastal upwelling systems associated to the ocean’s eastern boundaries (EBUs) are the most productive of the global ocean with low latitude EBUS’s being potential major centers of carbon sequestration. To improve our understanding of the processes regulating primary producers dynamics in the EBUs and their potential reaction to global warming is an obligation.Instrumentally based empirical studies propose that global warming will induce stronger coastal upwelling, while modeling simulations are not in agreement. Different approaches point to different scenarios for each and different EBU, implying that model’s parameterization needs to be improved and specific for each region. To do so, it is essential to generate time series that can document the amplitude, rate, and timing of the natural variability in each EBU behind the 150-200 yr of instrumental data, that is, to extended to longer climate cycles and the sediment record.The Peru-Chile Upwelling System is the most productive of the modern ocean, and the one that suffers the most drastic inter annual variability associated to the El Niño-Southern Oscillation Cycle. As such, it constitutes an excellent site to investigate this EBU reaction to past climate variability. We propose a quantitative diatom study of three Sites collected during IODP Leg 202 along the SW American coast (1233, 1234 & 1237), at orbital scale for the last 250 ky and millennial scale for the climatic events of major importance.The student will be responsible for doing the diatom quantification and assemblage definition in the three sites.  Compare obtained data with other important proxies such as: Planktonic and Benthic foraminifers’ quantification and assemblages, stable isotopes, biomarkers, pollens and others that have are to be done by the IODP Leg202 researchers. We are looking for enthusiastic and highly motivated individuals with a good biological or geological background, or a master in marine sciences or equivalent.

• Seagrasses as mitigators of ocean acidification impacts on commercial shellfish production
  • Supervisors: João Miguel Sousa da Silva (supervisor) / Rui Orlando Pimenta Santos (co-supervisor)
  • Summary:The hypothesis that seagrasses may provide refugia for calcifiers like oysters and clams, by increasing pH and the aragonite saturation state will be tested in Ria Formosa coastal lagoon in southern Portugal. Intertidal and shallow subtidal seagrass meadows are often adjacent to commercial clam and oyster farms. Using a combination of field and manipulative mesocosms experiments, the candidate will evaluate the influence of seagrass metabolism in the pH and aragonite saturation state of adjacent clam and oyster beds and explore the ratios of biomass and areal extent of seagrass/bivalves to determine the area of seagrass required to mitigate and/or offset the effects of OA on the target bivalve species.The outcomes are expected to support resource managers in the sustainable management of natural systems like Ria Formosa, with two potential positive consequences, seagrass conservation and mitigation of OA effects in the local bivalve production, with economic and societal benefits.Specific tasks and duties include: a) Field work. Determining the diel and seasonal variability of pH levels and aragonite saturation state within seagrass meadows and in unvegetated clam and oyster beds. This task involves extensive field work in shallow-water environments, with boat support. b) Mesocosm experiments. CCMAR operates a state-of-the-art mesocosm structure (http://mesocosm.eu/mesocosm/marine-plant-mesocosm-system/), where manipulative experiments with seagrasses and bivalves will be carried out. c) Laboratorial assays. Seagrass metabolism will be evaluated in dedicated chambers and water samples will be processed for carbonate chemistry analysis. Bivalves used in the experiments will be analysed for developmental abnormalities. The candidate will thus receive training and perform some analysis in external laboratories.  d) Data analysis, manuscript preparation and reporting. e)Dissemination of results to local stakeholders and scientific audiences.

     

Protection and sustainable exploitation of marine resources:

• Building a bridge between habitat mapping and marine spatial planning
  • Supervisor: Jorge M.S. Gonçalves
  • Summary: Assessing and mapping of marine habitats is crucial to the development and implementation of management plans and conservation strategies. The broad aim of this research will be to develop a methodological framework in assessing, mapping and modeling the distribution of vulnerable habitats such as coral gardens, and its associated threats such as longline and trammel / gill net fisheries in order to promote a better marine spatial planning and management. In this PhD project we will use historical data (SSS / MB, ROV imagery, fishing inquiries and AIS / VMS) from previous projects (eg MeshAtlantic) and data from new surveys that will be carried out in ongoing projects (eg HABMAR and MARSW) . The suite of methods that will be employed are mainly related to species distribution models, geostatistics, multivariate analysis and multiactor participatory processes. The project is truly cross-disciplinary, incorporating new advances on marine habitat mapping, on the spatial distribution of fishing catches and economic yield per unit of effort and on conservation management. The student will have the advantage of spending time in different research environments (CCMAR and secondment in AZTI or IMR). The supervising team will be led by Jorge Gonçalves and the student will be integrated in the CCMAR's Doctoral School.Responsibilities include: a) Project management, b) Write scientific papers and present communications at conferences, c) Mentoring undergraduate students. Requirements: Good communication and networking skill, critical and independent thinkin, basic knowledge about GIS, geostatistiscs, marine invertebrate taxonomy and image analysis and annotation.

• Regulation of shell formation and disease resistance in marine bivalves
  • Supervisors: João Cardoso and Deborah Power
  • Summary: The successful candidate will work in a very competitive scientific area. The candidate will be integrated into an international working environment and will be supervised by Drs Joao Cardoso and Deborah Power. The workplan integrates experimental, bioinformatics, molecular, cell culture, functional approaches and tissue histology. We will focus on the characterization of mantle enzymes, ion transporters and channels, shell matrix proteins and genes that are involved in innate immunity (TLR, Lysozymes, PGRP, etc). We will also explore the potential involvement of putative peptides and orphan receptors (eg: G-protein couple receptor family) that are likely to regulate mantle function but for which little is currently known. Molecular Biology will involve bivalve tissue collection and RNA extraction, cDNA synthesis and PCR and quantitative-PCR analysis and establishment of gene knock-out or knock-down technologies for bivalves (ex: RNAi or CRISPR on bivalves or bivalve cells) to infer about target gene function in shell development/maintenance and diseases resistance/susceptibility. Cell cultures will involve transfection of mammalian cell lines with candidate target receptors to identify putative regulatory signalling (peptide and receptors). Functional assays will involve biochemical assays to characterize enzyme activity in the mantle. Histology will be perform to characterise mantle morphology and involve tissue processing, staining procedures and in situ tissue expression analysis of target genes (ISH or IHC). Most of the techniques used are fully established and routinely in used. Transcriptome mantle data for bivalves from China and Portugal are available. Responsibilities include: a) Collect and maintain animals in laboratory environment, b) Plan and conduct scientific investigations and experiments according to the PhD workplan; c) Collecting, preparing and/or testing samples (molecular, biochemical and histological/histochemistry analysis/bioinformatics of sequence data); d) Recording and analysing data (including statistical analysis); e) Keeping up to date with relevant scientific and technical developments; f) Scientific writing of manuscripts about the outcome of the studies performed, reports, reviews and public oral/poster presentations at conferences. g) Help with the supervision of undergraduate students; h) Participate and collaborate in the lab routine; i) Participate in public outreach activities; j) Complementary courses will be provided in “soft skills” eg. Person management, project management, business skills, graphic skills for scientific illustration etc. Requirements: Degree in Biology, Biochemistry or related areas; good skills of English spoken and written.

Biochemistry and biotechnology of marine organisms:

• Ultra-sensitive bioelectronic transducers as a screening tool to monitor the activity of marine compounds on cells and tissues
  • Supervisors: Deborah Power and Henrique Gomes
  • Summary:The approach used in the PhD project will overcome the limitations of currently available microelectrode arrays (MEA) technology. The specific objectives of the project and tasks to be undertaken by the PhD recruited will be to: 1- fabricate transducers with high spatio-temporal resolution and an intrinsic noise level below 1 microvolt. To achieve this, two strategies will be explored; (i) fabrication of nano-structured surface coatings using ZnO nanorods or nano-wires,  (ii) conducting polymer surfaces such as PEDOT:PSS. Both materials strategies will be implemented into soft and biocompatible substrates. Among the substrates to be explored are (i) cellulose (ii) poly-lactic-glycolic acid (PLGA) and an elastomer such as ultra-soft polydimethyl siloxane (PDMS). The final goal is to solve the fabrication issues so that devices can be built on a flexible and biocompatible scaffold. 2. To validate the developed sensors using electrophysiological extracellular measurements in vitro with several different immortalized cells lines such as glioma seeded onto the electrophysiological sensing platform. The signal patterns generated by cell populations will be recorded and correlated with cellular activity. 3. To demonstrate that the device can be scaled up and validated to establish it as a screening tool for marine compounds of potential interest. Responsibilities include: a) Plan and conduct scientific investigations and experiments according to the PhD workplan; b) Collecting, preparing and/or testing samples (molecular, biochemical and histological/histochemistry analysis/bioinformatics of sequence data); c) Recording and analysing data (including statistical analysis); d) Keeping up to date with relevant scientific and technical developments; e) Scientific writing to publish the outcome of the studies performed, reports, reviews and public oral/poster presentations at conferences; f) Supervise undergraduate students; g) Participate in public outreach activities; h) Complementary courses will be provided to promote development of “soft skills” eg. Person management, project management, business skills, graphic skills for scientific illustration etc. Requirements: Degree in Biosciences or electronics or related areas.

• XtremeBeauty: Development and optimization of innovative cosmetic ingredients based on natural marine products
  • Supervisor: Luísa Custódio
  • Summary: The PhD candidate will identify innovative cosmetic ingredients in marine organisms and salt marsh plants, focusing on promising species already identified in previous FCT funded R&D projects. He/she will prepare eco-friendly extracts and evaluate them in vitro for bioactivities relevant for the cosmetic industry, such as antioxidant, anti-inflammatory, skin sagging and photo protection, using cell free and also cell basedassyas, along with enzymatic techniques. Selected extracts are appraised for acute toxicity on mammalian cell lines, fully chemically characterized (by for example, GC/MS, HPLC and LC/MS), and used for the development of nanoparticle-based cosmetic formulations that will be re-tested by selected in vitro assays and evaluated for skin safety, according to EU norms. Experimental work will be developed in CCMAR and in Faculty of Pharmacy (Lisbon). Responsibilities include: a) To prepare natural extracts and evaluate them in vitro for selected biological activities; b) To prepare nanoparticle-based cosmetic formulations and evaluate their topical safety and efficacy; c) To analyse data and write scientific papers to be submitted to peer reviewed international journals; d) To disseminate results by appropriate means, such as international conferences. Requirements:To have an excellent Master degree in Biology or related area, be fluent in English - written and spoken, be motivated, enthusiastic, hard-working and responsible, be able and willing to cope with an interdisciplinary working group.

• XtremeCrops: Development and optimisation of innovative sustainable production systems using extremophile halophytes
  • Supervisor: Luísa Custódio
  • Summary: You will optimize the cultivation conditions for selected edible and medicinal halophytes, in saline conditions. Selected species will be cultivated in a greenhouse, irrigated with water with different salinities, including with effluents from marine aquaculture facilities, and / or fertilized with aquaculture sludges. Selected species will be further cultivated in an IMTA system in IMPA, in aquaponics combined with the production of marine fish (e.g. Dicentrarchus labrax and Sparus aurata). The target is to (a priori) select halophytes with favorable biochemical profiles aiming commercial uses in the food, pharma and / or cosmetic areas, and subsequently to investigate the maximization of metabolite production through adjustments to the production process. You will be able to learn and apply different aspects of the cultivation process (germination, measurement of plant growth) and biochemical techniques, including those used for the determination of the nutritional profile of food; in vitro techniques (cell free, enzymatic, cell based assays) for the evaluation of human health improvement properties (antioxidant, anti-inflammatory, anti-diabetic, neuroprotective) and cosmetic applications (skin sagging, anti-melanogenic) and for the metabolic characterization of natural products (GC/MS, HPLC, LC/MS). Responsibilities include: a) To optimise the growing conditions for selected edible and medicinal halophyte species in saline conditions; b) To determine the nutritional profile of produced biomass; c) To prepare natural extracts from produced biomass and determine relevant biological properties targeting commercial applications in different commercial areas; d) To analyse data and write scientific papers published in peer-reviewed international journals; e) To disseminate results by appropriate means, such as international conferences. Requirements: excellent Master degree in Biology or related area; fluency in English, written and spoken; to be motivated, enthusiastic, hard-working and responsible.

• Biosensors as a tool to unveil the molecular basis of structure-function relationships of molecules from marine organisms: a case study with Transthyretin (TTR)    
  • Supervisor: Rui Borges
  • Summary: The work plan involves the production, purification and characterization of TTR protein variants (fish, human and engineered mutants), their immobilization on QCM biosensors, and its use to monitor and characterize TTR binding, including QCM protocol and instrument development. The results will be complemented and assessed with independent assays using standard biochemical techniques and also with time-correlated single photon counting with DNA nanolever biosensor (switchSENSE). This new technique, although not as robust or versatile as QCM, promises a much lower detection limit. Other parallel studies include evaluating the stability of the TTR proteins and their complexes. To demonstrate the QCM ability to monitor chemical pollutants in the sea, the developed protocol will be used to study the interaction between TTR and EDC, by measuring the affinity and kinetics of TTR binding to model hormones and EDCs in various conditions (e.g. buffers, temperature).To develop the methodology for screening/identification, the QCM will be used to pull down known binding partners of TTR from complex but previously characterized proteins mixes (e.g. tissue extracts). The complexes will be eluted from the QCM and submitted to mass spectrometry analysis for identification. The methodology will then be expanded to increasingly complex samples from marine origins, aiming at its use with environmental samples. Finally, to bridge marine with biomedical applications, we will use our QCM/calorimeter for the complete thermodynamic characterization of the TTR binding with selected partners from the previous studies, aiming to find new compounds that stabilize TTR and evaluate their mode of action. To successful develop and apply the methodologies involved, the PhD candidate should have a solid training both in biological and fundamental sciences, with a keen interest in instrumental development, such as a background in Biological Engineering or related areas.