Join the IIM | AEI’s Post-Doc Financial Aid (Juan de la Cierva 2020)

Supervisors: Álex Alonso ? alex@iim.csic.es  

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Understanding how aquatic animals respond to environmental variability is becoming increasingly important in face of the rapidly changing marine environment. This is specially so in the case of the spatial ecology on the individuals because movements determine individual fitness and population dynamics and can therefore connect ecological and evolutionary processes.

In the context of a rapidly and drastically changing marine environment, however, it is crucial to identify the environmental and biological drivers that determine spatial and behavioural patterns to evaluate not only how animals use space but also to assess their vulnerability to environmental and anthropogenic stressors.

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 post-doc project is offered to investigate how the interaction between natural and anthropogenic factors affect the spatial ecology of coastal populations and their impact on conservation.

The candidate will benefit from the telemetry data recorded by a fixed net of acoustic receivers deployed within the Illas Atlánticas de Galicia National Park (NPIAG, NW Spain) since 2019. This acoustic array is included in the European Tracking Network (ETN) as a  long-term observatory programme to monitor movements and behaviour in fish.

The project is focused on important coastal elasmobranchs that inhabit shallow waters of the National Park (mainly Raja undulata; but also Raja brachyura, Raja clavata and Scyliorhinus canicula).

With the support of an experienced technical staff, the candidate will be independent to lead their own research plan. Candidate project proposals are:

• • Social connectivity of coastal species and their role in conservation.
  • Role of trophic position on spatial ecology of coastal fish.
  • Individual variation of fish behavioural traits and their drivers.

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. The candidate will also be in charge of the management of the monitoring program. This includes maintenance of acoustic array, carry out tagging surveys, data management and data analysis. They will also have the opportunity to supervise master students.

The candidate is expected to succesfully manage large datasets of acoustic telemetry data, 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:

Tendering researchers must hold a PhD degree, preferably on spatial ecology or ecological modelling. Knowledge of programming in R, data analysis and statistical modelling and a good level of English are particularly appreciated.

Supervisor:  Fran Saborido Rey ? fran@iim.csic.es

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Marine ecosystems are facing rapid changes making it urgent to understand how exploited fishes respond to environmental variability, including fishing pressure. In this context, it is equally important to understand the temporal demographic changes, as well as the spatial variation. While the former has been well studied, spatial analysis has received considerably less attention. But it is crucial to assess stock resilience and vulnerability to environmental and anthropogenic stressors.

Flemish Cap is a fishing ground located east of the Grand Bank of Newfoundland in international waters. It is an especially sensitive to climate change area due to its particular oceanographic and geographic characteristics. Atlantic cod and redfish stocks are very relevant for fisheries as well as for the demersal ecosystem because of the key-role of these species in the trophic web that have shown significant spatio-temporal fluctuations in several biological traits, suggesting they are sensitive to external variations.

We have a long time-series (33 years) on biological data of these species from the annual scientific survey and more importantly key life-history parameters related with mortality, growth, maturation and productivity. This time-series is being expanded backwards using dendrochronology techniques to reconstruct growth and maturity historical retrospective data series. Estimation of fish productivity is a key issue to understand recruitment process, and hence stock-recruitment relationship, a cornerstone in fisheries management. Several life history traits are involved in productivity and most are highly influenced by environmental factors and by fisheries.

The starting hypothesis of this project is that climate processes are a major determinant of the structure and function of the demersal fisheries (Atlantic cod and redfish) of Flemish Cap, producing spatio-temporal changes.

Research will investigate trends in productivity related traits during last decades in the Flemish Cap ecosystem and will try to disentangle the mixed effects of fisheries and the environment in the main key fish species in this ecosystem. Spatial variations will be linked with habitat use and trophic web. Regime shifts will be estimated, and the vulnerability of the species, in the context of the ecosystem functioning analyzed to provide a better understanding of the resilience of the exploited species.

The candidate will benefit from i) the extensive time series produced from the annual research survey that covers the entire Flemish Cap ecosystem and that it is still ongoing (should join the survey every year); ii) the modern facilities at the Life History Service, including computing; iii) will co-supervise a PhD in a related topic.

Requirements:

We seek an enthusiastic, self-motivated candidate holding a PhD degree, preferably on spatial ecology or ecological modelling, with deep knowledge on fish life history.

The degree must have been obtained not earlier than January 2016. Knowledge of programming in R, data analysis and statistical modelling and a good level of English are particularly appreciated.

Supervisors: Fran Saborido Rey ? fran@iim.csic.es | Laura Casas ? lauracasas@iim.csic.es

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The status of marine fish stocks needs to be assessed to ensure fishing practices that exploit the stocks at sustainable levels. On the other hand, the field of ecological genomics seeks to understand the genetic mechanisms underlying responses of organisms to their natural environments, being a truly interdisciplinary field.

We are currently working, through several research projects, in the application of DNA High Throughput Sequencing (HTS) methodologies to resolve some of the current fisheries management challenges and complement traditional methods to assist fisheries assessment.

These methodologies include the close-kin mark-recapture (CKMR) method which provides a new way to estimate abundance - and other key demographic parameters - using genetics to affordably and reliably identify parent–offspring pairs (POPs; and conceivably other types of kin) and then analyze the number and pattern of pairs in a mark-recapture framework. Moreover, CKMR also provides direct evidence on which animals are contributing surviving offspring, a parameter with important implications for the productivity and resilience of any species.

Novel HTS methods offer as well the possibility to infer other important parameters, including stock boundaries and connectivity or fine-scale population structure and molecular sexing, which are essential for fisheries management.

A good example is Labrus bergylta, a temperate protogynous species of commercial interest across Europe. Research performed by our research group during the last decade has shown the existence of two genetically diverging colour morphs with clear differences in life-history that would require a separate management. These morphs are also being used to explore the genetic basis underpinning reproductive isolation in the marine environment, where physical barriers are absent, and to infer genomic changes shaping early stages of differentiation that enable speciation with gene flow.

Our current projects are deepening into the molecular basis of this evolutionary trend and its implications for managing stocks and biodiversity.

The candidate will join these and other related projects and will benefit from i) the extensive sampling access based in our annual research survey, as well sampling facilities; ii) the modern facilities at the Life History Service, including molecular biology labs and high-performance computing; iii) will co-supervise master students and potentially a PhD in the same subject.

Requirements:

We seek an enthusiastic, self-motivated candidate holding a PhD degree, preferably on spatial ecology or ecological modelling, with deep knowledge on fish life history.

The degree must have been obtained not earlier than January 2016. Knowledge of programming in R, data analysis and statistical modelling and a good level of English are particularly appreciated.

Supervisor:  Sonia Dios Vidal ? sdios@iim.csic.es  

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A research line is proposed within the framework of STRAUSS Project: Effects of Ocean Waves in the Rías Baixas Upwelling System: surface dynamics on selected biological case studies.

The general objective of the project is to analyze the impact that ocean waves have on key natural resources (mussels and clams) of the Rías Baixas upwelling system in order to manage them in future scenarios under the Climatic Change context.

Molluscs farming in Galicia have a high socioeconomic impact both directly and indirectly through related activities. In this sense, the interaction between the open ocean currents and the coastal-generated waves may have a significant impact on cultivated marine resources.

In the case of mussels, their performance relies on the ability to attach on cultivation ropes through the byssus. This could be disturbed by the waves and generated movements of cultivation ropes causing significant losses of biomass by byssus breakage. For clams, turbulence linked to currents and waves may be also significant for the sea bed where these molluscs are harvested. For both mussels and clams, this could be especially critical during abrupt hydrodynamic events that generate excessive agitation in either the water column or seafloor. Mussels could need to expend more energy to produce stronger byssus, and clams could be stressed enough to cope with any additional environmental threat.

Several tasks within the project will address the impact of waves in the ecosystem through these selected case studies (mussels and clams). Mussels sampling will be conducted seasonally in 4 distinct raft locations in the Ría de Arousa and after abrupt events of wave forcing. Clams will be tested with seasonal samplings in the field (Cabo do mar shellfish bank), targeted actions following abrupt events and with controlled-laboratory experiments.

For mussels, specific gene expression of foot protein 3, which is a component of the adhesive plaque of the byssus, will allow inferring risk assessments for the maintenance of the biomass in the cultivation systems in combination with other spatial and temporal parameters of interest within the project.

For clams, histological analysis will be carried out for evaluation of pathological alterations and/or presence of pathogens, mainly for the presence and number of rickettsias colonies, which live naturally in intracellular colonies in the gills of clams, but can undergo an exacerbated growth under adverse conditions.

For both mussels and clams, an evaluation of the immune condition and oxidative stress will be carried out to establish the relation between wave forcing (mainly during abrupt events) and the mollusk cellular stress response.

The laboratory counts with all the equipment needed to carry out the tasks proposed and also with specific services within IIM such as the Marine Environment Sampling and Image Unit (for field sampling); Flow Cytometry Service (for oxidative stress analysis) and Life History Service (for histological procedures). A technician and an experienced postdoctoral researcher will support the tasks progression.

Requirements:

Applicants must hold a PhD degree in relevant subjects such as Biology, Biotechnology or Marine Science.

Supervisors:  Marta López Cabo ?  marta@iim.csic.es  | Juan Rodríguez Herrera ?  juanherrera@iim.csic.es 

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The postdoctoral researcher will be involved in the ongoing research project of the group , ASEQURA, intended to quantitatively assess the risk from consumption of Ready-to-Eat foods contaminated by L. monocytogenes at processing plants following an integrated value chain approach.

Specifically, the relevance of cross-contamination of foods with L. monocytogenes biofilm cells for risk assessment will be analyzed following the steps below:

1. Characterization of L. monocytogenes-carrying polymicrobial biofilms formed in hot-spots in processing chains of high-risk foods.

Targeted seafood will be searched for L. monocytogenes at processing plants and retail points to determine prevalence at different stages of production. Biofilm models will be designed by combining L. monocytogenes with prevailing accompanying genera or species. To this end, strains will be selected based on the response to process variables of concern, persistence, expression of virulence determinants and involvement in reported outbreaks.

Next, the effects of accompanying bacteria and environmental factors on population dynamics of biofilm cells will be examined under conditions simulating those in hot-spots, and outcomes will be used to select highest-risk cases.

2. Quantification of the transfer of biofilm cells of case studies to targeted foods on high-risk pathways of processing chains previously identified.

The effects of accompanying bacteria, relevant environmental factors and food industrial operations on biofilm cell transfer will be determined, and outcomes will populate risk assessment.

3. Monitorization of population dynamics of L. monocytogenes in targeted foods cross-contaminated by biofilm cells to evaluate the safety of targeted foods.

This will be conducted at the processing stage, from transfer sites all along the processing chain, with a particular focus on critical control points, and also at retail level, from final production to consumption.

4. Proposal of risk management measures to be implemented in the future to reduce the incidence of listeriosis.

Finally, measures with most impact on risk mitigation will be prioritized.

Requirements:

Applicants must hold a PhD in Applied Microbiology. Experience in predictive microbiology and in microscopic and molecular microbiology techniques will be valuable.

Supervisor:  Camino Gestal ? cgestal@iim.csic.es 

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A research line is proposed within the framework of OCTOMICS project: "Octopus aquaculture: searching for a successful production driven by nutrigenomic and epigenetic interaction studies".

The common octopus (Octopus vulgaris) is a highly-valued species of great commercial interest in Spain, and it is an excellent candidate for aquaculture diversification. However, the massive mortalities during the early life-cycle stages (paralarvae) hamper its commercial production. In recent years, the interest in cephalopod culture has increased, arising new relevant data on octopus paralarvae.

Epigenetic mechanisms are important gene expression regulators with heritable modifications. Among them, DNA methylation is the process of adding a methyl group to cytosines. The environment in which an individual experience during early life stages, even prior to its birth, is determinant for its future metabolism and health. Through epigenetic marks, environmental cues can be transmitted to the genomic machinery of a cell and regulate patterns of gene transcription. Nutrients influence epigenetic mechanisms by altering the regulation of specific genes involved in metabolic pathways resulting in a nutritional programming. Thus, nutrients of the diet and temperature can have a direct effect in the development, by changing the epigenome.

DNA methylation is also known to be important in affecting cellular differentiation during development by regulating gene expression in the genome. Preliminary results show a plasticity throughout O. vulgaris life cycle, changing profiles from paralarvae to adult stages. This pattern of methylation could also be sensitive to alterations in nutritional and environmental conditions during the early development, thus impacting on its health, growth and survival. Our findings show a global demethylation phenomenon occurring along O. vulgaris early development being directly driven by the age of the paralarvae, but also the influence of a diet to favor this methylation loss.

The general objective of the project is to characterize the epigenetic marks associated with different developmental stages of the early development. Several tasks within the project will address the impact of incubation temperature of embryos, as well as the culture temperature and diet of paralarvae to the DNA methylation status of the early developmental stages of the common octopus.

The use of the RRBS (Reduced Representation Bisulfite Sequencing) high-throughput method for DNA methylation analysis (methylome), allow developing an integrative approach for studying DNA methylation differences independent of a reference genome. This technology can be used in the common octopus and might offer new insights to the identification of epigenetic marks affecting the expression of genes that could be triggered by environmental and nutritional stimuli, which could be useful biomarkers to be used to the improvement of the octopus’ aquaculture.

The IIM-CSIC is registered as “User and Breeding Centre on Animal Experimentation”. The laboratory counts with all the molecular equipment needed to carry out the tasks proposed, including qPCR machines, and aquarium facilities. The research group counts with qualified personnel to perform bioinformatics analysis of massive sequencing.

We have access as users to the “Centro de Supercomputación de Galicia (CESGA)”, which will allow the useful bioinformatics analysis of methylomic data. A lab. technician and the research group currently involved in the project will support the tasks progression.

Requirements:

Applicants must hold a PhD degree in relevant subjects such as Biology, Biotechnology or Marine Science. Background in bioinformatic tools will be valuable.

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

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We are looking for a Post-doctoral candidate to work at the Chemistry of Marine Products group at the Institute of Marine Research (IIM), Spanish National Research Council (CSIC), located in Vigo, Spain.

The candidate will work within of the Spanish AEI/EU-FEDER project SYS-ALLERGOMICS: "Proteomics and structural-based systems biology of fish allergy in raw and processed seafood" (Check our website for more details).

The tasks will involve Proteomics and Mass Spectrometry analysis of the fish and mice samples generated in the context of the SYS-ALLERGOMICS project.

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.

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.

Within of the consortium the candidate will work in close collaboration with partners with expertise in Proteomics-based Systems Biology and Fish Technology (IIM-CSIC - Dr. Mónica Carrera & Dr. Manuel Pazos - Vigo, Spain), Structural Biology of Allergens (IQFR-CSIC - Dr. María Gasset - Madrid, Spain) and Systems Immunology (CINBIO-UVIGO - Dr. Susana Magadán - Vigo, Spain). In addition, the candidate will do the presentation of reports/articles and communications. 

Requirements:

The applicant must have a PhD in Biology, Biochemistry, Chemistry, or in related sciences. Fluent English, independence and motivation will be a plus.