Join the IIM | PhD Opportunities (FPU 2020)

Supervisors: Fiz Pérez ? fiz.perez@iim.csic.es | Mercedes de la Paz ? mercedes.delapaz@iim.csic.es | ? Group Webpage

Nitrous oxide (N₂O) and methane (CH₄) are biologically produced trace gases that exerts a strong climate influence as powerful greenhouse gases which also affect stratospheric ozone depletion (N₂O) and the oxidative capacity of the atmosphere (CH₄). Because the ocean emits one third of the global N₂O natural emissions to the atmosphere, the observations has been targeted mainly toward low oxygen oceanic regions, limited in extension but characterised by intense N₂O production. However, the capacity to uptake N₂O and its injection into the deep ocean circulation in ventilated regions such as the North Atlantic Ocean and the subpolar gyre have received until now little attention. This knowledge is urgently needed to refine our estimations of the global oceanic N₂O budgets.

The PhD project will combine available and new N₂O and CH₄ measurements from previous and future planned oceanographic cruises carried in the OVIDE repeated hydrographic section, which connects Lisbon with Greenland. Those observations are framed within the international program GO-SHIP (https://www.go-ship.org/), in which the group is involved since 2002. Furthermore, the research group contributes to relevant international programs (RECCAP https://www.globalcarbonproject.org/index.htm), that aim to quantify the role of the ocean to the global greenhouse budgets (CO₂, N₂O and CH₄). In addition, the candidate will be trained in high precision trace gas chromatographic analysis in the facilities of the IIM-CSIC, one of the few national laboratories validated for measuring oceanic N₂O and CH₄(SCOR WG143). The incorporation of the candidate within this research group, will bring him/her the opportunity to be involved in oceanographic investigations of global scale relevance.

The interdisciplinary approach proposed in this project will combine participation in oceanographic cruises, advanced training in high precision gas chromatography and other biogeochemical parameters. Additionally, training in marine biogechemistry coupled with  water masses analysis will help to decipher main mechanisms taking part of the N₂O cycle and its distribution in the North Atlantic. The candidate will be also given training in professional skills, including attendance an international summer schools, international conferences, stays in foreign institution and other training strategies.

Requirements:

We seek an enthusiastic, self-motivated candidate, with a strong aptitude for the use of analytical instrumentation. It will be an asset to have good numerical skills and interests in ocean biogeochemistry and global change. This project is suited for a candidate graduated in chemistry, physics, oceanography/marine sciences or a suitable branch of environmental sciences. Good academic record is required (GPA above the required level of the call), and desirable good English level and writing abilities.

Supervisors: Carmen G. Castro ? cgcastro@iim.csic.es | Francisco G. Figueiras ? paco@iim.csic.es   ? Group Webpage

Marine phytoplankton supports approximately half of the global Earth primary production. The structure and composition of the microbial plankton community modulate the fluxes of biogenic matter and energy, and consequently determine the trophic structure of the marine ecosystems and the role of the Ocean as climate regulator. Among marine ecosystems, coastal upwelling regions are particularly important due to their high levels of primary production. The Western Iberian coast, located in the northern boundary of the NW Africa upwelling system, is one of these regions.

In this PhD Thesis, the structure, composition and functioning of the microbial plankton community will be studied in the western Iberian coastal upwelling system. This will be achieved by analyzing valuable, quality-verified data previously collected in oceanographic campaigns in the region within the framework of several research projects. Microbial plankton composition and biomass, size-fractionated primary production, net community production and respiration will be studied all together for the first time in this coastal upwelling system, and to our knowledge in any coastal upwelling system. The idea is to tackle different time scales of variability from the seasonal to the short-term variability. Seasonality will be characterized with an annual sampling in shelf waters. A sampling conducted in the Ría the Vigo, a bay where upwelling and downwelling are enhanced due to the geomorphology, will be used to characterize the microbial response to intensification of upwelling and downwelling events. The short-term evolution of recently upwelled water will be addressed through tracking a water parcel in which a drifting buoy was deployed.

The PhD candidate will have the opportunity of being in a multidisciplinary marine work environment, excellent marine lab infrastructure, and extensive options of further collaborations with other national and international groups. 

Requirements:

Candidates should hold a Marine Sciences, Biology, Chemistry or Environmental Sciences degree, english proficiency and a GPA above the required level of the call.

Supervisor:  Ricardo Prego ? prego@iim.csic.es |   ? Group Webpage

The Anthropocene has been proposed as a new geo-stratigraphic epoch where humans have become a global factor affecting the ecosystems. Estuaries constitute a biogeochemical reservoir where natural sources mix with human pressures.

The proposed thesis will assess the imprint of anthropogenic changes in the estuarine zone of Galician Rias focusing in three subject: (i) hydropower damps and drinking water reservoirs; (ii) emergent contaminant loads, as Rare Earth Elements; and (iii) disused mining impact.

About that matters, the biogeochemical studies in rias are very scarce and have been published mainly in the current century. Studies carried out in the Marine Biogeochemistry group (IIM-CSIC) suggested the Anthopocene trace from the mid-20th century. This is mainly related with the Galicia industrialization after the Spanish Civil War.

The doctorate work will be based in two projects currently under development in the MBGC group and the data-base of two completed projects. The predoctoral training plan will follow four steps:

• • Bibliographic review on estuarine waters and sediments: search for publications in Scopus, CSIC library, and MB collection.
  • Knowledge of equipment and techniques: participation in project sampling and analysis activities. Learn clean-room techniques with the help of technician.
  • Processing and study data, learning techniques for writing scientific articles and preparing six manuscript on three aforementioned subjects.
  • Participation in two international congress and a stay with another foreing international group.

Requirements:

Candidates should hold a degree in Chemistry or Environmental Sciences degree, english proficiency and a GPA above the required level of the call.

Supervisors: Antonio Cobelo ? acobelo@iim.csic.es ? Marine Biochemistry Group  | Jose MF. Babarro ? jbabarro@iim.csic.es ? EsMaBa Group

The anthropogenic use of a new range of trace elements whose inherent properties are required for use in an ever expanding list of new technologies is rapidly increasing, inducing significant changes in the processes associated with their natural environmental cycle at the Earth surface. These new set of chemical elements, here defined as Technology-Critical Elements (TCEs), include Ga, Ge, In, Te, Nb, Ta, Tl, several platinum group elements (PGEs: Pt, Pd, Rh) and most of the rare earth elements (REEs: Y, La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Yb, Lu).

However, there are still significant gaps in our knowledge and understanding of these technology-critical elements (TCEs), from their environmental levels and fate to their potential (eco)toxicological impact. Of further concern is that, despite the current widespread use of these TCEs, current knowledge does not support the application of robust risk assessment processes and, as a consequence, they are not included in regulations (in contrast to those available for other metals with a longer record of use).

We therefore propose here the development of a PhD Thesis based on a holistic approach to assess the concentrations, bioaccumulation and trophic transfer of TCEs in the marine environment, covering: (i) their determination and speciation in water and sediments, (ii) a study on their bioaccumulation potential, (iii) their trophic transfer in the food web, and (iv) a risk assessment based on their concentrations and bioaccumulation/biomagnification characteristics. The Vigo Ria is chosen as an excellent model coastal system for this study, as it has been widely studied in term of its ecology, biogeochemical cycles and contamination, and supports a significant degree of anthropogenic pressure including urban, industrial and aquaculture activities.

This PhD thesis project is expected to result in significant social and economic benefits as the findings and conclusions derived from the project results and conclusions will help in our identification of whether certain technology-critical elements can be considered as potential metals of concern. These metals are not currently included in environmental regulations, and therefore the results of this study will provide new and valuable information in order to enhance the environmental safety including human exposure to these metals through seafood.

Requirements:

Candidates should hold a Marine Sciences, Biology, Chemistry or Environmental Sciences degree and a GPA above the required level of the call.

Supervisor:  Alexsandre Alonso ? alex@iim.csic.es    |      ? Group Webpage

Movement plays a vital role in any ecological or evolutionary process and therefore has profound effects on the structure and dynamics of populations. Thus, a holistic understanding of the spatial ecology of marine populations is essential to inform marine conservation initiatives. This is especially true for elasmobranch species which have life-history features that make them more vulnerable to multiple impacts. In the last two decades, our knowledge of the spatial ecology of marine animals have experienced an extraordinary increase, in part due to the technological development of telemetry techniques. In particular, acoustic telemetry has become a popular means of tracking fish and aquatic invertebrates in the wild with high spatial and temporal resolution. Within this context, a PhD project is offered to investigate how the interaction between natural and anthropogenic factors affects the spatial ecology of coastal populations and their impact on conservation.

We use in this project the data recorded by a fixed net of acoustic receivers displayed within the National Parks of Illas Atlánticas de Galicia (NPIAG, NW Spain). This acoustic array is included in the European Tracking Network (www.europeantrackingnetwork.org ) as long-term observatory program to monitor movements and behaviour of fish. The project is focused on important coastal elasmobranchs that inhabit shallow waters of the National Park (Raja undulata and Scyliorhinus canicula).

The main objectives of this PhD proposal are:

• • To depict temporal patterns of occurrence of these species within the studied marine protected area (NPIAG) and to identify main drivers.
  • To study behaviour patterns and its relationship with fate of individuals.
  • Eco-evo implications of individual variability of behaviour.

The candidate will take advantage of current projects developed by the research group in the field of spatial ecology and behaviour of marine animals and from the ongoing COST action that supports the ETN initiative with opportunity for courses, workshops and international collaborations. With the support of an experienced technical staff, the candidate will take part in the management of the monitoring program. This includes maintenance of acoustic array, carry out tagging surveys, data management and data analysis. The candidate will also have the opportunity to supervise undergraduate students.

We are seeking a highly motivated candidate with excellent marks in both the graduate and master studies. The candidate will have to manage a large database, analyze and model data, and publish articles in high-ranking journals. Thus, a high sense of organization, knowledge on programming languages such as R, and a good level of English are particularly appreciated

Requirements:

Applicants must hold a first degree in relevant subjects (for example, biology, biotechnology, marine biology, environmental science) and a GPA above the required level of the call. Knowledge on programing (R, Python) will be valued.

Supervisor:  Jose Pintado   pintado@iim.csic.es  | ? Group Webpage

Bacterial communities associated with Ulva spp. play an important functional role both in morphogenesis and reproduction, considering Ulva and its associated microbiota a singular functional entity or holobiont. Moreover, Ulva spp. host antibiotic-producing bacteria (APB, e.g. Phaeobacter sp.) with known antagonism against fish pathogens.

Using a multi-disciplinary approach, including -omic techniques, the research will contribute to the understanding of the role those APB, and the conditions that favour their predominance in Ulva spp., which would have implications in disease control in fish-algae IMTA-RAS systems (Integrated Multi-Trophic Aquaculture-Recirculating Aquaculture Systems).

Requirements:

Applicants must hold a first degree in biology, marine biology, environmental science, or similar with a GPA above the required level of the call. Background in microbioloy and genomics and/or metabolomics will be valuable.

Supervisors:  Beatriz Novoa ? beatriznovoa@iim.csic.es | Antonio Figueras ? antoniofigueras@iim.csic.es | ? Group Webpage

The general objective of this PhD project is to understand the involvement of immune and metabolic genes in the priming of the antiviral response.

The project will continue with the study of genes that were characterized in our  group  to understand their role in the priming of the innate immunity. Also, we will study other genes, not typically understood as immune genes, but with a critical role on metabolism. We will analyze the interphase between metabolism and immunity to improve our understanding of the potential innate immunity memory using the zebrafish as a model species and the advantage of conducting the assays in a whole organism. We will apply transcriptomic and next generation sequencing approaches to identify the molecular basis of the immune response against viruses.

Requirements:

Degree in Biology, Biotechnology or Biochemistry with a a GPA above the required level of the call. Master studies completed.

Supervisors:  Mónica Carrera ? mcarrera@iim.csic.es | Manuel Pazos ? mpazos@iim.csic.es  | ? Group Webpage

The PhD project will be framed on the Spanish AEI/EU-FEDER project SYS-ALLERGOMICS (Proteomics and structural-based systems biology of fish allergy in raw and processed seafood). A main goal of the project is to study the intracellular mechanism of T-cell activation in response to the different forms of fish allergens in order to i) set valid peptides for their used as vaccines, and,  ii) develop a fish product as a potential hypoallergenic seafood product.

The tasks will involve Proteomics and Mass Spectrometry analysis of the fish and mice samples generated in the context of the SYS-ALLERGOMICS project. Particularly, the student will be skilled in sample preparation, protein identification and quantification by using Mass Spectrometry instruments, together with the analysis of post-translational modifications (PTMs) relevant for fish allergy. The candidate will work in close collaboration with partners of the project consortium with expertise in Proteomics-based Systems Biology and Fish Technology (IIM-CSIC / Vigo, Spain: Dr. Mónica Carrera, Dr. Manuel Pazos), Structural Biology of Allergens (IQFR-CSIC / Madrid, Spain: Dr. María Gasset) and Systems Inmunology (CINBIO-UVIGO /Vigo, Spain: Dr. Susana Magadán, ). In addition, the candidate will do the presentation of reports/articles and communications. 

Requirements:

The applicant must have a degree in Biology, Biochemistry, Chemistry, or in related sciences with a GPA above the required level of the call. Fluent English, independence and motivation will be a plus.

Supervisors:  Isabel Medina? medina@iim.csic.es  | Santiago Aubourg ? saubourg@iim.csic.es | ? Group Webpage 

This PhD Project aims the beneficial effect that diets rich in algae and seafood can have during aging, with a particular emphasis on the effect on neuroinflammation and, therefore, on related neurological and neurodegenerative disorders.

Current research on the role of foods of marine origin in mental health, focuses on the intake of marine lipids and especially omega-3 polyunsaturated fatty acids (PUFA n-3), in improving inflammation, oxidative stress and aging of immune cells, components that represent important mechanisms underlying aging. In this scenario, the formation of oxidized metabolites derived from n-3 PUFAs, such as EPA and DHA, is addressed as a crucial mechanism in the progression of inflammation and brain aging. The new proresolution lipid mediators of inflammation, derived from EPA and DHA and including lipoxins, resolvins, protectins and maresins not only delay the excessive inflammatory process, but also promote resolution by improving elimination of apoptotic cells and inflamed brain tissue debris. Due to the instability of these metabolites and the complexity of their precise analysis, this area of research is a complex challenge.

Therefore, the present thesis aims the formation of lipid mediators derived from oxidative modifications that occur in cell and tissue coming from animal models, and that can be associated with neurodegenerative disorders. The potential regulatory role that the consumption of foods of marine origin can play on these disorders will be evaluated. For this, Liquid Chromatography applications coupled to Mass Spectrometry will be developed to address the epilipidoma resulting from enzymatic and non-enzymatic lipid oxidative modifications, in samples from cell cultures and animal experimentation. And the results will be integrated with the information available on signaling pathways focused on lipids and oxidative modifications of proteins. The project will highlight the convenience of the intake of fish and products of marine origin during aging, as significant components of personalized nutrition for targeting a majority segment of the European population.

Requirements:

Graduates in Biochemistry, Chemistry, Biology, or Pharmacy with expertise in Analytical Chemistry or equivalent and a GPA above the required level of the call. Experience in Instrumental Techniques based on Mass Spectrometry for Protein and Lipid analysis.

Supervisors: Eva Balsa ? ebalsa@iim.csic.es | David Henriques ? davidh@iim.csic.es  | ? Group Webpage

Biotechnology industry uses biological systems, for example, yeasts, bacteria or algae, to obtain different products such as food ingredients, pharmaceuticals, etc. Biological systems are complex systems that make optimization and control of bioprocesses a challenging task. Mathematical models can help to decipher such complexity and to guide bioprocess operation design.

In this study, we will explore the use of multi-phase and multi-objective optimization as the underlying hypothesis to explain cellular metabolism in a changing environment. Furthermore, we will develop numerical methods and software tools to automatize the development of optimization-based dynamic genome-scale models.

The modelling framework and software tools will be tested and used to describe yeast fermentation processes of interest for the food industry

Requirements:

BSc and MSc in Mathematics, Physics, Industrial Engineering, Bioingeneering, Biotechnology or similar with a GPA above the required level of the call. 

Supervisors: Eva Balsa ? ebalsa@iim.csic.es ? Bio-process Engineering Group | Xosé Antón Vázquez Álvarez  ? jvazquez@iim.csic.es  ? ReVal Group

This thesis aims at the model-based dynamic optimisation of industrially relevant fermentation processes based on the growth of bacteria from different origins using substrates recovered from food waste.

We are currently considering three types of bacterial groups: 1) lactic acid bacteria, 2) probiotic marine bacteria and 3) bacteria producing biopolymers and metabolites of interest. Regarding substrates, and in line with the Marine Biorefinery concept, we work with sources rich in sugars –glucose– (eg, mussel cooking effluents) and sources rich in organic nitrogen –peptones– (eg, fishery and aquaculture by-products).

We will perform experiments in 300 mL Erlenmeyer flask scale and subsequently scaled to 2 L bioreactors. Experiments will account fo the effect of temperature and different substrate concentrations (glucose and peptones) on bacterial growth and the concomitant production of metabolites.

Dynamic models will be developed to predict the various fermentation processes and subsequently, used into a dynamic optimisation framework to maximise efficiency and productivity in batch and fed-batch conditions.

Requirements:

BSc and MSc in Biotechnology, Bioprocess Engineering, Bioengineering, Chemical Engineering, Biochemistry... with a GPA above the required level of the call.

Supervisor:  Marta López Cabo ? marta@iim.csic.es | Juan Rodriguez Herrera ? juanherrera@iim.csic.es  |  ? Group Webpage

The main objective of the PhD thesis will be to assess quatitatively the risk resulting from the consumption of Ready-To-Eat (RTE) foods contaminated by Listeria monocytogenes at the processing plants in the food industry, following and integrated value chain approach. The following sub-objectives will be addressed:

• • Identification and characterization of current high-risk scenarios for listeriosis in the food industry
  • Characterization of bacterial communities co-living with L. monocytogenes in polymicrobial biofilms in the food industry.
  • To identify bacteria and other environmental factors enhancing the presence of L. monocytogenes in polymicrobial biofilms in high-risk scenarios.
  • Characterization of transfer by contact of biofilm cells of L. monocytoenes from surfaces to foods (cross-contamination) in high-risk scenarios.
  • Evaluation of the safety of foods cross-contaminated by biofilm cells of L. moncytogenes and C. jejuni at proxessing and retail levels following an integrated chain approach.

Requirements:

BSc and MSc in Biology, Microbiology, Food Technology or Biotechnology with a GPA above the required level of the call.

Supervisors: Luís Taboada Antelo ? ltaboada@iim.csic.es  | Carlos Vilas ? carlosvf@iim.csic.es |? Group Webpage

Thermal processes in the food industry are mainly used to extend shelf-life of the products either by inactivating or reducing the growth rate of potentially harmful microorganisms that might be present in the foodstuff. However, such thermal processes have a negative effect on the quality of the product since, for instance, they induce degradation of nutrients or sensory parameters such as color or texture. They are also highly time and energy consuming processes. Besides, current control strategies are limited to simple Proportional Integral Derivative (PID) temperature actuators to keep track of a pre-selected time-temperature profile in the processing unit. Such profile is, in general, very conservative to ensure food safety which results into quality losses and excessive energy consumption and process duration. Moreover, PID controllers cannot properly handle scenarios where an over-demand of energy prevents the system to follow the predefined profile. Such a conflicting situation, quite familiar to most food processors, is often solved by re-processing of the whole batch, requiring additional time and energy consumption.

Accurate control and supervision of the thermal treatment in the event of unexpected disturbances during production is compulsory to avoid potential microbiological outbreaks or the loss of the whole batch. This calls for the derivation of real-time advanced control strategies.

To this aim, an important aspect to be considered is the ability to keep track in real-time of process indicators (such as microbial lethality, product color/texture, nutrient content, etc.). Direct measurements of such indicators either cannot be obtained on-line measured on-line or they require invasive methods that prevent the product to be consumed. In this regard, mathematical models describing the process can be used in combination with non-invasive process measurements to keep track of the indicators that cannot be directly measured. Such combination of mathematical models and process measurements is usually referred to as software sensors. Besides, the control strategies must also consider the intrinsic variability associated with the process and the food matrix since it might cause that only part of the products in a batch comply with the safety requirements.

The final objective of the thesis is the integration of software sensors into advanced real-time controllers to optimize (maximize quality, minimize process duration and energy consumption) thermal processes of the food industry where product variability is relevant.

The main tasks to be carried out in our multi-disciplinary, highly proactive, motivating and internationally recognized research group are:

• • Analysis of available market hardware sensors for the evaluation of relevant Key Performance Indicators in thermal processes.
  • Development of mathematical models describing process and product dynamics as well as the evolution of quality and safety indicators.
  • Calibration of mathematical models from experimental data and characterization of the variability of relevant parameters.
  • Combination of hardware sensors and mathematical models for the development of software sensors able to evaluate variables that cannot be directly measured.

Requirements:

BSc and MSc in Mathematics, Physics, Industrial Engineering or Food Technology with a GPA above the required level of the call. Understanding of mechanistic modeling strategies. Computer programming skills in high level languages (Matlab, Python) and experience in the numerical solution of differential equations will be highly valuated.