BLUE YOUNG TALENT PLUS ‐ BYTplusbyt.ciimar.up.pt/wp-content/uploads/2019/03/BYT... · ambientes e taxas de impacto e riscos de especiação e extinção. No entanto, além de algumas

BLUE YOUNG TALENT PLUS ‐ BYTplus

CENTRO INTERDISCIPLINAR DE INVESTIGAÇÃO MARINHA E AMBIENTAL ‐ CIIMAR

PROPOSTA DE PROJETO DE MESTRADO 2019 ‐ 2020

ORIENTADOR(A)/SUPERVISOR: Agostinho Antunes (Líder de Grupo – CIIMAR/Professor FCUP)

GRUPO: Genómica Evolutiva e Bioinformática

LOCAL DE REALIZAÇÃO DO TRABALHO: CIIMAR/FCUP

TEMA/Theme: SeXomics ‐ Sexo e o meio ambiente: Descodificação genómica e a perpetuação da vida animal num mundo em mudança / SeXomics ‐ Sex and the environment: Genomic decoding and the perpetuation of animal life in a changing world

RESUMO:

RESUMO/SUMMARY

A maioria dos animais reproduzem‐se sexualmente, mas existe uma notável diversidade de mecanismos determinantes do sexo, mesmo entre espécies intimamente relacionadas. Por exemplo, em algumas espécies as mudanças de sexo podem ocorrer dentro da vida de um indivíduo e incluem hermafroditas e o sexo pode ser controlado no nível do cromossoma ou através de pistas ambientais. Estes processos têm importantes implicações evolutivas e ecológicas nos padrões de variação genética, grau de endogamia, taxa de adaptação a novos ambientes e taxas de impacto e riscos de especiação e extinção. No entanto, além de algumas espécies‐modelo, sabemos pouco sobre por que e como diferentes sistemas sexuais evoluíram, particularmente em vertebrados inferiores e invertebrados. Estudos comparativos têm sido dificultados pela falta de dados biológicos e genómicos acessíveis sobre sistemas sexuais, mecanismos de determinação de sexo e diversificação na árvore animal da vida e pela falta de compreensão dos processos ambientais e genómicos envolvidos na evolução dos sistemas de acasalamento. Tais dados permitirão não só analisar em profundidade a evolução dos sistemas sexuais, como também analisar mais detalhadamente o risco de mudança ambiental na distribuição, invasividade e extinção de espécies.

OBJECTIVOS/OBJECTIVES:

Aqui, propomos caracterizar os padrões genéticos de genes associados à reprodução em espécies de metazoárias sob diferentes pressões

selectivas ambientais, e diversificação sexual associada à adaptação ambiental nos níveis de escala ampla / fina. Estas questões incluem:

(1) A determinação do sexo no ambiente coloca as espécies em alto risco de extinção, especialmente num mundo em mudança do clima;

(2) Alguns sistemas sexuais são mais transitórios do que outros; e (3) Como os mecanismos de determinação do sexo afectam os padrões

de evolução genómica?

Propomos a utilização de análises de sequenciação de última geração de subgenomes reprodutivos (gene / nível cromossómico) e 2)

análises proteómicas para testar interacções proteicas funcionais e putativas com poluentes ambientais para obter dados críticos de

padrões de evolução de espécies, diversificação e mal funcionamento genético associado. Os dados genómicos fornecerão valor e

ferramentas importantes para pesquisas ambientais e biomédicas, possivelmente levando a novas aplicações, incluindo terapias genéticas

e regenerativas mais eficientes, desenho de novas drogas, novos mecanismos de controlo de pragas, etc.

ÁREA CIENTÍFICA: Genómica, Genética, Evolução Molecular, Bioinformática.

LICENCIATURAS ADMITIDAS: Biologia, Bioquímica, Ciências dos Computadores. Outras licenciaturas afins na área

poderão eventualmente ser consideradas.

PRINCIPAIS METODOLOGIAS/MAIN METHODOLOGIES:

Identificação de substituições sinónimas (silenciosas) e não‐sinónimas (substituições aminoacídicas) para testar evidências de seleção a nível molecular

utilizando testes estatísticos robustos. Interações funcionais importantes em sistemas enzimáticos (complexo recetor‐ligando) e interações proteína‐proteína

serão estudados em detalhe atómico. A integração final destes resultados irá permitir a simulação de vários aspetos das complexas interações biológicas que

influenciam a evolução do sexo, que poderão ser validados através de testes funcionais experimentais com proteínas recombinantes. O significado evolutivo

de determinadas mutações poderá ser de particular interesse para a saúde humana e investigação farmacêutica. Finalmente, os dados também serão usados

para reavaliar a evolução e as relações filogenéticas entre várias espécies de metazoários, o que pode fornecer valor sobre a capacidade das espécies de

sobreviver, adaptar e/ou ter sucesso em ambientes degradados e em mudança afectados por poluentes ambientais ou mudança climática.

Tarefas a desempenhar pelo estudante que se integrará na equipa deste projeto de investigação (PTDC/CTA‐AMB/31774/2017) financiado pela FCT:

Análise laboratorial e bioinformática de genes envolvidos na reprodução e sexo em metazoários (vertebrados e invertebrados). O trabalho experimental

incluirá a recolha de organismos e extração de DNA/RNA, PCR, sequenciação e outras metodologias de genómica molecular. Interpretação dos resultados

obtidos utilizando métodos filogenéticos e de adaptação molecular. Participação na elaboração de manuscritos.

REFERÊNCIAS/REFERENCES:

BORGES R, JOHNSON WE, O’BRIEN SJ, VASCONCELOS V, ANTUNES A. 2012. The emergence and the duplication events in the melanopsin gene family (OPN4m and

OPN4x) during vertebrate evolution. PLoS One 7(12): e52413. (Factor de impacto: 4.092).

PHILIP S, MACHADO JP, MALDONADO E, VASCONCELOS V, O'BRIEN SJ, JOHNSON WE, ANTUNES A. (2012). Fish lateral line innovation: insights into the evolutionary

genomic dynamics of a unique mechanosensory organ. Molecular Biology and Evolution 29(12):3887‐3898. (Factor de impacto: 14.308).

SUNAGAR K, JOHNSON WE, O’BRIEN SJ, VASCONCELOS V, ANTUNES A. (2012) Evolution of CRISPs associated with toxicoferan‐reptilian venom and mammalian

reproduction. Molecular Biology and Evolution 29(7): 1807‐1822. (Factor de impacto: 14.308).

DUTERTRE S, JIN A, VETTER I, HAMILTON B, SUNAGAR K, LAVERGNE V, DUTERTRE V, FRY BG, ANTUNES A, VENTER D, ALEWOOD P, LEWIS R (2014) Evolution of

separate predation‐ and defence‐evoked venoms in carnivorous snails. Nature communications 5:3521. (Factor de impacto: 10.015).

ZHANG G, LI C, LI Q, LI B, LARKIN DM, LEE C, STORZ JF, ANTUNES A, GREENWOLD MJ, MEREDITH RW, ET AL. 2014. Comparative genomics reveals insights into avian

genome evolution and adaptation. Science. 346(6215):1311‐1320. (Factor de impacto: 31.480).

KHAN I, YANG Z, MALDONADO E, LI C, ZHANG G, GILBERT MTP, JARVIS ED, O’BRIEN SJ, JOHNSON WE, ANTUNES A. (2015) Olfactory receptor subgenomes linked with

broad ecological adaptations in Sauropsida. Molecular Biology and Evolution 32(11):2832‐43. (Factor de impacto: 14.308).

BORGES R, KHAN I, JOHNSON WE, GILBERT MTP, ZHANG G, JARVIS ED, O’BRIEN SJ, ANTUNES A. (2015) Gene loss, adaptive evolution and the co‐evolution of plumage

coloration genes with opsins in birds. BMC Genomics 16(1):751. (Factor de impacto: 3.990).

SILVA L, ANTUNES A. (2017) Vomeronasal Receptors in Vertebrates and the Evolution of Pheromones Detection. Annual Review of Animal Bioseciences 5:53‐370.

(Factor de impacto: 4.348).

BORGES R, JOHNSON WE, O’BRIEN SJ, HEESY C, ANTUNES A. (2018) Adaptive genomic evolution of opsins reveals that early mammals flourished in nocturnal

environments. BMC Genomics 19: 121. (Impact factor: 3.867).

MARRA NJ, STANHOPE MJ, JUE N, WANG M, SUN Q, BITAR PP, RICHARDS VP, KOMISSAROV A, RAYKO M, KLIVER S, STANHOPE BJ, WINKLER C, O’BRIEN SJ, ANTUNES A,

JORGENSEN S, SHIVJI MS (2019) White shark genome: ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability. PNAS.

Outros trabalhos do grupo publicados:

http://www.ncbi.nlm.nih.gov/pubmed/?term=Agostinho+Antunes

Referências na comunicação social:

http://www.rtp.pt/noticias/mundo/sequencia‐de‐genomas‐de‐48‐especies‐revela‐como‐evoluiram‐os‐passaros_n789258#

http://noticias.up.pt/descodificacao‐do‐genoma‐do‐grande‐tubarao‐branco‐tem‐adn‐da‐u‐porto/

https://www.publico.pt/2019/02/21/ciencia/noticia/genoma‐tubaraobranco‐deixounos‐longevidade‐1862747#gs.i3XgfDqg

BLUE YOUNG TALENT PLUS - BYTplus

CENTRO INTERDISCIPLINAR DE INVESTIGAÇÃO MARINHA E AMBIENTAL - CIIMAR

PROPOSTA DE PROJETO DE MESTRADO 2019 - 2020

ORIENTADOR(A)/SUPERVISOR: Filipe Fernandes Coutinho

GRUPO/GROUP: NUTRIMU - CIIMAR

CO-ORIENTADOR(A)/CO-SUPERVISOR: Cláudia R. Serra

GRUPO/GROUP: NUTRIMU - CIIMAR

LOCAL DE REALIZAÇÃO DO TRABALHO/PLACE OF WORK: CIIMAR and FCUP

TEMA/THEME: Cyanobacterial outer membrane vesicles as a novel technology for European sea bass juveniles vaccination against Mycobacterium marinum

RESUMO:

RESUMO/SUMMARY This work aims at implementing outer membrane vesicles (OMV) as novel platforms in vaccine technology. The goal will be to explore OMV derived from non-pathogenic bacteria (cyanobacteria) as an antigen delivery vehicle to immunize the European seabass against the opportunistic pathogen Mycobacterium marinum that causes mycobacteriosis, for which no vaccine or satisfactory treatment is available. This work will be dedicated to test the immunostimulatory capacity of OMVs loaded with Mycobacterium marinum-proteins. It will be divided in four tasks: Task 1 - Fish husbandry Optimal husbandry conditions following European sea bass requirements will be applied for cultivation at CIIMAR facilities. ESB juveniles (5-10 g) will be obtained from commercial farms and after a quarantine period, will be maintained at CIIMAR facilities in a thermoregulated (22-25ºC) marine (35‰ salinity) water recirculation system, on a 12h light/12h dark photoperiod. Task 2 - Fish immunization Aiming to induce specific and prolonged adaptive immune responses in European sea bass, 5 distinct combinations of OMV populations, each packaged with a specific M. marinum-proteins, will be administered to triplicate groups of fish. Juveniles European sea bass will be immunized intraperitoneally with 100 μL of OMV with the following characteristics: i) OMV carrying secreted-type antigens; ii) OMV carrying mycomembrane-associated antigens; iii) OMV carrying both secreted-type and mycomembrane associated antigens; iv) empty OMV; or v) no OMV, injected with the same volume of a sterile phosphate-buffered saline solution as the control group. Prior to vaccination, fish will be anesthetized with a 0.3 mg/L of ethylene glycol monophenyl ether. On day 0 and once a week thereafter (at days 7, 14, 21, 28 - until day 70 post-vaccination) 6 fish from each experimental group will be anesthetized for blood samples collection. At the end of the trial head-kidney from three fish per tank will also be sampled and stored in RNAlater for further analysis. Task 3 – CyannoVaccine-specific immunoglobulins Blood samples will be used to determine the serum concentration of specific antibodies promoted by the vaccine, by measuring the presence of specific immunoglobulins against M. marinum antigenic proteins. For such analysis, an indirect ELISA method will be used as described in Gao et al., 2014. Task 3 – Immune response The expression of several immune-related genes (pro-inflammatory cytokines, IL-1β, TNF-α and IL-6) in head-kidney will be analysed by real-time PCR to evaluate fish immune response (Azeredo et al., 2017). By the end of these tasks the OMV combination which induces the most effective adaptive immune response will be identified.

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Biological Sciences


Select the best CyanoVaccine candidate, through the identification of the OMV combination that induces the most effective adaptive immune response.


Husbandry of European sea bass juveniles

Immunization of European sea bass juveniles by intraperitoneal injection of engineered outer membrane vesicles (OMV)

Measurement of serum specific immunoglobulins against M. marinum antigenic proteins by indirect ELISA

Determination of the expression of several immune-related genes in head-kidney by real-time PCR


Azeredo R, Pérez-Sánchez J, Sitjà- Bobadilla A, Fouz B, Tort L, Aragão C, et al., 2015. European sea bass (Dicentrarchus labrax) immune status and disease resistance are impaired by arginine dietary supplementation. PLoS ONE 10(10): e0139967.

Gao BL, Liu J, Dong LX, Zhang L, Qin JH, Wang JP, 2014. Broad specific enzyme-linked immunosorbent assay for determination of residual phenothiazine drugs in swine tissues. Anal Biochem. 454:7–13.

Brudal E, Lampe EO, Reubsaet L, Roos N, Hegna IK, Thrane IM, Koppang EO, Winther-Larsen HC, 2015. Vaccination with outer membrane vesicles from Francisella noatunensis reduces development of francisellosis in a zebrafish model. Fish & Shellfish Immunology 42: 50-57.




ORIENTADOR(A)/SUPERVISOR: Emília Sousa

GRUPO/GROUP: Natural Products and Medicinal Chemistry

CO‐ORIENTADOR(A)/CO‐SUPERVISOR: Diana Resende

GRUPO/GROUP: Natural Products and Medicinal Chemistry

LOCAL DE REALIZAÇÃO DO TRABALHO/PLACE OF WORK: Faculdade de Farmácia da Universidade do

Porto

TEMA/THEME: Exploring the sea for new antimalarial agents

RESUMO:

RESUMO/SUMMARY Malaria is still among the main public health problems in least developed regions of the world and, despite severe efforts amongst the scientific community in order to control and eradicate this disease, new antimalarial compounds will not become available in the upcoming years. [1,2] New evidences of a multidrug-resistant P. falciparum parasite lineage in some countries in Southeast Asia represents a serious threat to global malaria control and eradication. [1] Recently our group synthesized a series of alkaloids based on the structure of known antimalarial drugs or lead drug candidates. Some of the compounds exhibited excellent antimalarial activity against the sensitive strain P. falciparum 3D7 (IC50 = 0.05 ‐ 0.2 µM), thus representing potential new chemotypes for further optimization towards novel and affordable antimalarial drugs.


The main purpose of this work is to obtain analogues of the active alkaloids by structure‐based design performing

molecular modifications to obtain more efficient analogues and screening for their antimalarial activities.

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Medicinal Chemistry


Organic synthesis, purification and isolation procedures and structural elucidation of organic substances. The structure elucidation will be performed by spectroscopic methods (UV, IR, 1H and 13C NMR), and mass spectrometry. In collaboration with other research groups, the synthesized compounds will be tested for their antimalarial

activity. Analogues of the most promising compounds with potential as drug candidates or industrial applications

will be prepared by molecular modifications in order to perform structure‐activity relationship studies.


[1] World health organization ‐ World malaria report 2018. Available online:

https://www.who.int/malaria/publications/world‐malaria‐report‐2018/en/

[2] Bule MH, Ahmed I, Maqbool F, Zia MA. International Journal of Pharmacology 2017, 13(7), 818‐831.




ORIENTADOR(A)/SUPERVISOR: Ana Paula Mucha

GRUPO/GROUP: ECOBIOTEC

CO‐ORIENTADOR(A)/CO‐SUPERVISOR: Marisa Almeida

GRUPO/GROUP: ECOBIOTEC

LOCAL DE REALIZAÇÃO DO TRABALHO/PLACE OF WORK: CIIMAR

TEMA/THEME: Assessment of microbial communities associated with lost fishing gears

RESUMO:

RESUMO/SUMMARY

Fishing‐related debris represents more than 50% of the weight of the floating macroplastics pollution found in

marine environment. Plastic debris provides a substrate for microbes that lasts much longer than most natural

floating substrates and has been implicated as a transportation vector for biological pollutants such as

opportunistic pathogens. Nevertheless, biological pollution loads in lost fishing gear (mainly composed of plastics)

have not yet been sufficiently explored, being this the aim of this work.

Obtained results will contribute for a better understanding of the ecological implications of fishing‐related debris.

An important contribution will be made for the understanding of the role of lost fishing gears as a substrate for

microbial colonization, with special emphasis on potential opportunistic pathogens and pollutant‐degrading

bacteria.


To assess microbial communities associated with lost fishing gear, with special emphasis on 1) the presence of

harmful microorganisms such as opportunistic pathogens, and 2) the identification of pollutant‐degrading bacteria,

which can indicate the possibility of microorganism playing a role in reducing lost fishing gears impacts.

ÁREA CIENTÍFICA/SCIENTIFIC AREA:

Environmental Sciences


Laboratory manipulative experiments will be carried out using fragments of fishing gear exposed to natural sea

water under different dynamic conditions (different levels of agitation), both in the presence and in the absence

of marine sediment (sand with different grain size), to simulate microbial colonization that the gear can undergo

in water column and after their seafloor deposition.

The microbial communities extracted from fragments of lost fishing gear will be identified by using next

generation sequencing technology (NGS). Special attention will be dedicated to the presence of specific microbial

groups. One of these groups are the opportunistic pathogens, as plastic debris have been implicated as vector for

transportation of harmful microorganisms. The other group are pollutant‐degrading bacteria, or groups of

microorganism presenting degradative genes, that can point to a possible role of microorganisms in reducing lost

fishing gears impacts.


Zettler, E. R., Mincer, T. J., & Amaral‐Zettler, L. A. (2013). Life in the “plastisphere”: microbial communities on

plastic marine debris. Environmental science & technology, 47(13), 7137‐7146.

Almeida, C. M. R., Oliveira, T., Reis, I., Gomes, C. R., & Mucha, A. P. (2017). Bacterial community dynamic

associated with autochthonous bioaugmentation for enhanced Cu phytoremediation of salt‐marsh sediments.

Marine environmental research, 132, 68‐78.




ORIENTADOR(A)/SUPERVISOR: Carla Sofia Garcia Fernandes

GRUPO/GROUP: NATURAL PRODUCTS AND MEDICINAL CHEMISTRY

CO‐ORIENTADOR(A)/CO‐SUPERVISOR: Maria Elizabeth Tiritan

GRUPO/GROUP: NATURAL PRODUCTS AND MEDICINAL CHEMISTRY

LOCAL DE REALIZAÇÃO DO TRABALHO/PLACE OF WORK: FFUP (Rua de Jorge Viterbo Ferreira n.º 228,

4050‐313 PORTO)

TEMA/THEME: Síntese de Péptidos de Origem Marinha e Análogos com Potencial Atividade Antimicrobiana/ Synthesis of Marine‐derived Peptides and Analogues with Potential Antimicrobial Activity

RESUMO:

RESUMO/SUMMARY Os oceanos são uma fonte rica de compostos bioativos estruturalmente únicos sob a perspetiva de potenciais agentes terapêuticos. Nos últimos anos, os produtos naturais marinhos têm despertado grande interesse, essencialmente devido ao leque alargado de atividades biológicas e farmacológicas que demonstram exibir. Para além disso, são interessantes modelos para modificações moleculares e / ou síntese total, de modo a obter compostos mais potentes e em maior quantidade. Os péptidos marinhos constituem um grupo particularmente interessante devido à sua química e diversas atividades biológicas, incluindo antimicrobiana. Neste contexto, esta proposta tem como objetivo sintetizar péptidos marinhos e análogos para posterior avaliação de atividade antimicrobiana. A pureza enantiomérica dos péptidos obtidos será avaliada por cromatografia líquida utilizando fases estacionárias quirais. The oceans are a rich source of structurally unique bioactive compounds under the prospect of potential therapeutic agents. In recent years, natural marine products have aroused great interest, mainly due to their wide range of biological and pharmacological activities. Additionally, they are interesting models for molecular modifications and / or total synthesis to obtain more potent compounds and in higher quantity. Marine peptides are a particularly interesting group because of their chemistry and various biological activities, including antimicrobial. In this context, this proposal aims to synthesize marine‐derived peptides and analogues for further evaluation of antimicrobial activity. The enantiomeric purity of the obtained peptides will be evaluated by liquid chromatography using chiral stationary phases.

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Química Medicinal/Medicinal Chemistry


1. Sintetizar uma pequena biblioteca de péptidos e análogos para posterior avaliação da atividade antimicrobiana 2. Elucidar a estrutura dos compostos sintetizados 3. Determinar a pureza enantiomérica dos péptidos obtidos 1. Synthesize a small library of marine‐derived peptides and analogues for further evaluation of antimicrobial activity 2. Structure elucidation of the synthesized compounds 3. Determination of the enantiomeric purity of the obtained peptides


‐ Síntese orgânica de péptidos ‐ Elucidação estrutural por 1H RMN, 13C RMN, IV, MS e cristalografia de raios X ‐ Avaliação da pureza enantiomérica por cromatografia líquida ‐ Organic Synthesis of Peptides ‐ Structural elution by 1H NMR, 13C NMR, IR, MS and X‐ray crystallography ‐ Evaluation of the enantiomeric purity by liquid chromatography


‐ Phyo, Y.; Ribeiro, J.; Fernandes, C.; Kijjoa, A.; Pinto, M.M.M. Marine Natural Peptides: Determination of Absolute Configuration using Liquid Chromatography Methods and Bioactivities, Molecules, 2018, 23(2), 306, doi:10.3390/molecules23020306. ‐ Cheung, R.C.; Ng, T.B.; Wong, J.H. Marine peptides: Bioactivities and applications. Mar. Drugs 2015, 13, 4006–4043. ‐ Gogineni, V.; Hamann, M.T. Marine natural product peptides with therapeutic potential: Chemistry, biosynthesis, and pharmacology. Biochim. Biophys. Acta, 2018, 1862, 81–196. ‐ Anjum, K.; Abbas, S.Q.; Akhter, N.; Shagufta, B.I.; Shah, S.A.A.; Hassan, S.S.U. Emerging biopharmaceuticals from bioactive peptides derived from marine organisms. Chem. Biol. Drug Des., 2017, 90, 12–30.

BLUEYOUNGTALENTPLUS-BYTplus

CENTROINTERDISCIPLINARDEINVESTIGAÇÃOMARINHAEAMBIENTAL-CIIMAR

PROPOSTADEPROJETODEMESTRADO2019-2020

ORIENTADOR(A)/SUPERVISOR:CatarinaMagalhães

GRUPO/GROUP:EcoBioTec

CO-ORIENTADOR(A)/CO-SUPERVISOR:PedroDuarte

GRUPO/GROUP:NorwegianPolarInstitute

CO-ORIENTADOR(A)/CO-SUPERVISOR:MariaPaolaTomasino

GRUPO/GROUP:EcoBioTec

LOCALDEREALIZAÇÃODOTRABALHO/PLACEOFWORK:CIIMAR,EcoBioTec

TEMA/THEME:Biogeography of Arctic Eukaryotic Microbiome: a combining approach of metabarcoding, metagenomics and microscopic cell counts.

RESUMO:

RESUMO/SUMMARYGlobal worming and climate change has been manifested in the decrease of the Arctic Ocean see ice extent and

thickness (Parkinson and Comiso 2013). The thinner sea-ice regime that the Arctic has been facing changed Arctic’s primary productivity and biogeochemistry (Barber et al. 2015). In fact the dramatically sea-ice retreat in the Arctic Ocean promoted an increase in productivity, and massive under-ice phytoplankton blooms (Assmy et al.

2017). Thus a remaining question is whether those communities are likely to change in the Artic and which feedbacks might be expected from this changing eukaryotic microbiome that could accelerate or mitigate climate change impacts.


Understand the dynamics of the microbial communities responsible for the productivity of the Arctic ecosystem

will be worthwhile in order to draw future trends on an Arctic Climate Change Scenario. This master project will aim to present a comprehensive analysis of the biogeographic patters of Arctic phytoplankton diversity and distribution along two oceanographic transects in the Marginal Ice Zone around Svalbard. By combining 5 years of

unique Arctic data sets (metabarcoding/metagenomic/microscope identification) from previous (2016-2018) and future (2019-2020) Arctic expeditions, this study will fill critical gaps concerning the response of the main Arctic

primary producers, in terms of diversity and distribution dynamics, to Arctic climate driven changes.

ÁREACIENTÍFICA/SCIENTIFICAREA:

PRINCIPAISMETODOLOGIAS/MAINMETHODOLOGIES:

Fieldwork will be performed in the future campaigns (2019-2020) at the Marginal Ice Zone and Kongsfjorden integrated into a long term international monitoring program lead by Norwegean Polar Institute for Climate Change Studies in the Arctic. Phytoplankton samples will be concentrated through filtration and preserved (-80ºC) on board

to be used for later DNA extraction, and genomic and metagenomic analysis using specific methodologies (Sousa et al. 2019). Microscope phytoplankton counts and identification will be performed on board in fresh samples and also

in the lab in preserved samples. Sequence analyses will be performed by using illumina technology and Bioinformatic tools will be apply to analyze all the data generated from next generation sequencing (metabarcoding and metagenomics) (Sousa et al. 2019). Statistical tools will be also use to integrate phytoplankton diversity and

distribution in time and space with contextualized environmental data.


Parkinson CL, Comiso JC. 2013. On the 2012 record low Arctic sea ice cover: combined impact of preconditioning

and an August storm. Geophys Res Lett 40:1356-1361 Barber et al. 2015. Selected physical, biological and biogeochemical implications of a rapidly changing Arctic Marginal Ice Zone. Progr Oceanogr 139:122-150

Assmy P et al. 2017. Leads in Arctic pack ice enable early phytoplankton blooms below snow-covered sea ice. Sci. Rep. 7:40850

Sousa AG et al. 2018. Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime. Microb Ecol. DOI: 10.1007/s00248-018-01314-2.




ORIENTADOR(A)/SUPERVISOR: Maria de Fátima Carvalho

GRUPO/GROUP: EcoBioTec

CO-ORIENTADOR(A)/CO-SUPERVISOR: Pedro Leão; Ralph Urbatzka

GRUPO/GROUP: Cyanobacterial Natural Products; Blue biotechnology and ecotoxicology

LOCAL DE REALIZAÇÃO DO TRABALHO/PLACE OF WORK: EcoBioTec

TEMA/THEME: Deep-sea pharmacies: Exploring deep-sea Actinobacteria for the production of novel natural products with pharmaceutical applications

RESUMO:

RESUMO/SUMMARY Actinobacteria are a large group of Gram-positive bacteria, highly prolific in the production of bioactive secondary metabolites with a wide range of biological and pharmaceutical properties. Most of known actinobacterial species are of terrestrial origin, but it has been recently shown that they are also “true” habitants of the oceans and are a proven source of novel relevant secondary metabolites, such as antibiotics, antitumor, anti-inflammatory and antiviral compounds, biosurfactants, etc. (Dharmaraj, 2010; Olano et al., 2009). The deep sea is a unique environment characterized by extreme conditions, such as high pressure, low temperature, lack of light and variable salinity and oxygen concentrations, causing unique evolutionary pressures on microorganisms. Deep-sea ecosystems are known to contain a high diversity of actinobacteria, a great proportion of which are predicted to be novel species and genera (Bull and Stach, 2007). This proposal intends to investigate the cultivable actinobacterial community associated with deep-sea samples collected in Madeira and Azores archipelagos and explore their potential to produce bioactive compounds with pharmaceutical relevance.


In this proposal it is intended to:

(i) isolate actinobacteria from various deep-sea samples collected in Madeira and Azores islands;

(ii) identify the isolated strains;

(iii) investigate the potential of the isolated actinobacteria to produce compounds with antimicrobial, anticancer,

anti-inflammatory and antiobesity activities;

(iv) identify secondary metabolites produced by the strains exhibiting bioactivity.

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Ciências Biológicas e afins


Several deep-sea samples recently collected in expeditions in the Madeira and Azores archipelagos are currently

available in the laboratory for the isolation of actinobacteria. The cultivable community of actinobacteria

associated with these samples will be isolated in different selective media and identified through 16S rRNA gene

sequencing. A preliminary assessment of the production of bioactive compounds by the isolates will be performed

by culturing each isolate in selective liquid medium, followed by extraction of culture medium with an organic

solvent and screening for antimicrobial, anticancer, anti-inflammatory and antiobesity activities in the obtained

extracts. The most promising bioactive extracts will be further studied in order to identify the compound(s)

responsible for the bioactivity and their chemical structures.


- Bull, A. T. and Stach, J.E. (2007). Marine actinobacteria: new opportunities for natural product search and

discovery. Trends in microbiology, 15(11): 491-499.

- Dharmaraj, S. (2010). Marine Streptomyces as a novel source of bioactive substances. World Journal of

Microbiology and Biotechnology, 26 (12): 2123–2139.

- Olano, C., Méndez, C. and Salas, J.A. (2009). Antitumor compounds from marine actinomycetes. Marine Drugs,

7(2): 210–248.

BLUE YOUNG TALENT PLUS‐ BYTplus



ORIENTADOR(A)/SUPERVISOR: Filipe Castro

GRUPO/GROUP: AGE

CO‐ORIENTADOR(A)/CO‐SUPERVISOR: Raquel Ruivo

GRUPO/GROUP: ‐


TEMA/THEME: When less is more: the role of gene loss in phenotypic diversification

RESUMO:

RESUMO/SUMMARY Genomes are dynamic biological units, with processes of gene duplication and loss triggering evolutionary novelty. Mammalian radiation entailed the successful colonization of multiple and ecologically diverse habitats. This evolutionary path was accompanied by the appearance of novel phenotypic traits in association with genomic changes such as gene duplication. Yet, Gene Inactivation has emerged as well‐known driver of evolutionary change. The power of this evolutionary mechanism has been described in diverse vertebrate and non‐vertebrate lineages. Here, we will investigate the gene composition of multiple genetic pathways (e.g. lipid and sugar metabolism) in mammals. We will combine comparative genomics with functional assays to determine when and how have key adaptations emerged in vertebrate ancestry and whether gene loss has been an effective adaptive process.


To investigate and identify evolutionary processes of gene loss in Vertebrate genomes and their role in

phenotypic diversification.


The work plan will be entail a strong component of Bioinformatics (e.g. gene mining, gene annotation,

phylogenetics, selection) in combination with Molecular and Cell Biology techniques (e.g. next generation

sequencing technologies).

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Comparative Genomics and Evolution

LICENCIATURAS ADMITIDAS /ADMITABLE DEGREES: Biology and Biochemistry


Marlétaz F, Firbas PN, Maeso I, Tena JJ, Bogdanovic O, Perry M, Wyatt CDR, de la Calle‐Mustienes E, Bertrand S, Burguera D, Acemel RD, van Heeringen SJ, Naranjo S, Herrera‐Ubeda C, Skvortsova K, Jimenez‐Gancedo S, Aldea D, Marquez Y, Buono L, Kozmikova I, Permanyer J, Louis A, Albuixech‐Crespo B, Le Petillon Y, Leon A, Subirana L, Balwierz PJ, Duckett PE, Farahani E, Aury JM, Mangenot S, Wincker P, Albalat R, Benito‐Gutiérrez È, Cañestro C, Castro F, D'Aniello S, Ferrier DEK, Huang S, Laudet V, Marais GAB, Pontarotti P, Schubert M, Seitz H, Somorjai I, Takahashi T, Mirabeau O, Xu A, Yu JK, Carninci P, Martinez‐Morales JR, Crollius HR, Kozmik Z, Weirauch MT, Garcia‐Fernàndez J, Lister R, Lenhard B, Holland PWH, Escriva H, Gómez‐Skarmeta JL, Irimia M. Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature. 2018 Dec;564(7734):64‐70. doi: 10.1038/s41586‐018‐0734‐6. Genes for de novo biosynthesis of omega‐3 polyunsaturated fatty acids are widespread in animals. Kabeya N, Fonseca MM, Ferrier DEK, Navarro JC, Bay LK, Francis DS, Tocher DR, Castro LFC, Monroig Ó. Sci Adv. 2018 May 2;4(5):eaar6849. doi: 10.1126/sciadv.aar6849.




ORIENTADOR(A)/SUPERVISOR: Carolina Castro

GRUPO/GROUP: NUTRIMU

CO‐ORIENTADOR(A)/CO‐SUPERVISOR: Helena Peres


LOCAL DE REALIZAÇÃO DO TRABALHO/PLACE OF WORK: FCUP and CIIMAR

TEMA/THEME: Potential of solid‐state fermented wineries and olive oil by‐products as functional ingredients for European sea bass feeds

RESUMO:


The aim of this study is to access the potential of the solid state fermentation extract of GM and OP mixture as functional ingredient in feeds for European sea bass (Dicentrarchus labrax), an important European aquaculture species. The prospective beneficial effects of the solid state fermentation extract of GM and OP mixture will be evaluated in E. sea bass in terms of zootechnical performance, physiological, immunological and oxidative status.

RESUMO/SUMMARY Wineries and olive oil industries are important agro‐industrial activities in Portugal that produce large amounts and varieties of by‐products (such as grape marc (GM) and olive pomace (OP)). Reuse and valorization of these agro‐industrial by‐products are crucial both from economic and environmental perspectives. Solid‐state fermentation(SSF) using fungi is a low‐cost biotechnology that allows to convert these inexpensive agro‐industrial by‐products into add‐value and innovative ingredients. As a source of important bioactive molecules (such as antioxidant and phenolic compounds) that are reported to induce beneficial effects on animal health and well‐being (Fontana et al., 2013; Ghanbari et al., 2012), these ingredients have the potential to be used as functional ingredient for fish feeds. However, the potential of solid‐state fermented ingredients from winery and olive oil by‐products as functional ingredient in fish feeds was up to now little explored.


The first stage of this project will comprise characterization of extract obtained by solid state fermentation of the GM and OP mixture, namely the antioxidant activity, type and level of phenolic compounds present on the final product (methodology described in Dulf et al., 2015).

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Aquaculture; Fish nutrition

The second stage of this project will involve a growth trial to test the efficacy of the solid state fermentation extract of GM and OP mixture on fish growth, voluntary feed intake, feed efficiency and health status.

A control diet will be formulated without containing the fermented extract of GM and OP mixture. Three other diets will be formulated similarly to the control diet but including increasing levels of the extract. The extract levels to be included will be determinated according to antioxidant activity, type and levels of phenolic compounds present in the extract. Each diet will be tested in triplicated.

The growth trial will be run at the Marine Zoology Station in a recirculation water system, following the experimental design described in Magalhães et al. (2016).

At the end of the trial blood and intestine from 3 fish per tank will be sampled to characterize:

‐ Hematological profile by assessement of erythrocyte (haematocrit; haemoglobin concentration; erythrocytes number; mean cell volume; mean cell haemoglobin; mean haemoglobin concentration) and leukocyte (total and differential leukocyte numbers) parameters as described in Machado et al. (2019).

‐ immune response by quantifying nitric oxide, total Ig and peroxidase, lysozyme and alternative complement pathway activities in plasma, according to Machado et al. (2019); and expression of genes coding for key markers of mucosal immunity (IgT), Tcell markers (CD4; CD8), pro‐inflammatory (IL‐1β; IL‐6; TNF‐α) and anti‐inflammatory (IL‐10;COX‐2;TGF‐β) cytokines in intestine by RT‐PCR (Machado et al., 2019);

‐ intestine oxidative status by measuring activity of antioxidant enzymes (superoxide‐dismutase, SOD; catalase, CAT; glutathione‐peroxidase, GPX; glutathione‐reductase, GR) and non‐enzymatic oxidative stress indicators (lipid‐peroxidation, TBARS; reduced and oxidized‐glutathione, GSH; GSSG), as described by Castro et al. (2015).

Data on zootechnical parameters, such as growth rate, weight gain, feed intake, protein efficiency and body

condition indices will be obtained. Nitrogen and energy budgets will be obtained at the end of the growth trial.


Castro, C., Peréz‐Jiménez, A., Coutinho, F., Díaz‐Rosales, P., Serra, C.A., Panserat, S., Corraze, G., Peres, H., Oliva‐

Teles, A. 2015. Dietary carbohydrate and lipid sources affect differently the oxidative status of European sea bass

(Dicentrarchus labrax) juveniles. Br. J. Nutr. 114:1584‐93.

Dulf, F.V., Vodnar, D.C., Dulf, E., Tosa, M.I. 2015. Total Phenolic Contents, Antioxidant Activities, and Lipid

Fractions from Berry Pomaces Obtained by Solid‐State Fermentation of Two Sambucus Species with Aspergillus

niger. J. Agric. Food Chem. 63: 3489−3500.

Fontana, A. R., Antoniolli, A., Bottini, R. 2013. Grape pomace as a sustainable source of bioactive compounds:

extraction, characterization, and biotechnological applications of phenolics. J. Agric. Food Chem. 61: 8987‐9003.

Ghanbari R., ,Anwar, F., Alkharfy, K.M., Gilani, A.H., Saari, N. 2012. Valuable nutrients and functional bioactives in

different parts of olive (Olea europaea L.)‐a review. Int. J. Mol. Sci. 13:3291‐340.

Machado, M., Castro, C., Oliva‐Teles, A., Costas, B. 2019. Interactive effects of dietary vegetable oil and

carbohydrate incorporation on the innate immune response of European seabass (Dicentrarchus labrax) juveniles

subjected to acute stress. Aquaculture 498: 171‐180.

Magalhães, R., Lopes, T., Martins, N., Díaz‐Rosales, P., Couto, A., Pousão‐Ferreira, P., Oliva‐Teles, A., Peres, H.

2016. Carbohydrases supplementation increased nutrient utilization in white seabream (Diplodus sargus) juveniles

fed high soybean meal diets. Aquaculture. 463: 43‐50.




ORIENTADOR(A)/SUPERVISOR: Inês Guerreiro


CO-ORIENTADOR(A)/CO-SUPERVISOR: Aires Oliva-Teles



TEMA/THEME: Regulation of appetite by glucose in gilthead seabream (Sparus aurata).

RESUMO:

RESUMO/SUMMARY Control of feed intake and energy metabolism is crucial for proper growth and development. However, in fish, understanding on the endocrine control of appetite and body weight is not as developed as in mammals (1, 2). In aquaculture such knowledge is of vital importance, to maximize animal growth while optimizing feed conversion. Appetite regulation and metabolic utilization of diets may be affected by glucose availability. Moreover, it is known that glucose has a central role in energy homeostasis and that glucose plasmatic levels are regulated by endocrine mediators, gut-derived factors, and nutritional factors (3). Ghrelin and leptin are key hormones involved in appetite regulation; while ghrelin is involved in orexigenic responses, leptin is involved in anorexigenic responses (1). Thus, understanding how glucose interact with appetite regulating hormones, namely ghrelin and leptin, is of particular relevance when considering new aquafeeds that include high levels of plant feedstuffs rich in carbohydrates. Gilthead seabream was the chosen species since it is the most produced fish in the Mediterranean and despite its economic importance, knowledge on appetite regulation is still limited.


This work aims to assess glucose effect on appetite regulating hormones in gilthead seabream.

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Aquaculture – Fish nutrition and physiology


Gilthead seabream will be acclimatized to the experimental conditions for 2 weeks in CIIMAR. During this time fish will be fed a commercial diet, 2 times a day, until visual satiation. Then, after 1 day of feed deprivation, fish will be intraperitoneal injected with glucose or saline solution and after 3h (corresponding to glucose peak) and 24h (post-prandial basal level) will be sampled, to assess endocrine factors involved in appetite. Fish will be sampled for blood, brain, liver, stomach, intestine and adipose tissue. The following parameters will be determined: plasma metabolites indicators of nutrient metabolism; liver composition; expression of genes related with glucose metabolism, orexigenic (orexins; NPY; ghrelin) and anorexigenic molecules (CRH; CART; CCK; leptin). This work will result in one manuscript.


(1) Hoskins, L.J., & Volkoff, H. (2012). Gen Comp Endocrinol 176, 327-335

(2) Rønnestad, I. et al. (2017). Front Endocrinol 8:73, doi: 10.3389/fendo.2017.00073

(3) Riley Jr., L.G. et al. (2009). Comp Biochem Physiol A 154, 541-546




ORIENTADOR(A)/SUPERVISOR: Benjamin Costas


CO‐ORIENTADOR(A)/CO‐SUPERVISOR: Rita Azeredo



TEMA/THEME: The potential use of tryptophan supplementation for animal health management

RESUMO:

RESUMO/SUMMARY The concept of maintaining animal health through the best possible nutrition is well accepted in modern animal farming and functional amino acids appear to be good candidates to improve health and survival. Tryptophan in particular have known roles in the improvement of the immune response to infection and recent evidence indicates that several immune mechanisms are influenced by its availability. In this context, this project mainly aims to provide a better understanding of the underpinning neuro‐endocrine and immune machinery of fish fed tryptophan supplements during inflammatory conditions and to deliver a deeper understanding of the basic mechanisms involved during acute and chronic inflammatory processes. This is particularly important for the aquaculture industry, where few therapeutic possibilities are available against infectious episodes.


The main goal of this proposal is to allow a better understanding of the role of tryptophan on the inflammatory

response, immune modulation and disease resistance in fish. In particular, it is intended to verify the neuro‐

endocrine and immune modulatory effects of tryptophan during inflammation, and to what extent tryptophan

have a significant impact on disease resistance in fish. Understanding the role of this particular amino acid during

inflammation could be of major importance to the nutritional immunology community and for the design of

dietary therapeutic interventions.

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Biological and Veterinary Sciences


Fish trials and fish handling procedures

Hematology

Assessment of immune and oxidative stress parameters

Gene expression


N/A




ORIENTADOR(A)/SUPERVISOR: Helena Silva (PhD)

GRUPO/GROUP: Evolutionary Genomics and Blue Biotechnology ‐ Emergent Biotechnologies and Seafood

Processing (IPMA)

CO‐ORIENTADOR(A)/CO‐SUPERVISOR:

GRUPO/GROUP:

LOCAL DE REALIZAÇÃO DO TRABALHO/PLACE OF WORK: IPMA, I.P. ‐ Algés

TEMA/THEME: Molecular zoogeography of bivalve molluscs

RESUMO:

RESUMO/SUMMARY

Numerous species of bivalves are exploited commercially for food. Their origin and distribution is of major relevance and of economic importance. Though their distribution is relatively well known in many production areas, there are still the need for easy and quick geographic identification of some species of bivalves. Some molecular biology methodologies seem promising for this purpose. Some sampling in specific areas will be needed, DNA extraction, amplification, and purification prior sequencing will be done. Morphological identification of specimens will also accompany the molecular biology work.

OBJECTIVOS/OBJECTIVES: The object of this work is to explore molecular biology methodologies for

characterization and geographic identification of bivalve molluscs from known production areas.

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Molecular Biology/Biology

PRINCIPAIS METODOLOGIAS/MAIN METHODOLOGIES: Basic molecular biology techniques, PCR, Real‐Time PCR.

Analysis and treatment of results, use of Genetic Databases like BOLD and Blast. Anatomic identification of

bivalves.





ORIENTADOR(A)/SUPERVISOR: Joana Soares

GRUPO/GROUP: Endocrine Disruption and Emergent Contaminants (EDEC)

CO‐ORIENTADOR(A)/CO‐SUPERVISOR: Miguel Machado Santos

GRUPO/GROUP: Endocrine Disruption and Emergent Contaminants (EDEC)

LOCAL DE REALIZAÇÃO DO TRABALHO/PLACE OF WORK: CIIMAR (Interdisciplinary Centre of Marine and

Environmental Research)

TEMA/THEME: Application of embryo bioassay as a high throughput approach to toxicological screening

of emerging contaminants

RESUMO:

RESUMO/SUMMARY

Presently, concerns have increased on the toxicological risk of emerging pollutants, such as high-tech materials, nanoparticles, pharmaceuticals, etc. Ultimately, the aquatic ecosystems are the final destination of these compounds, that can thus threat the integrity of a vast array of organisms [Soares et al., 2018]. Many of these chemicals are not new, but the knowledge on their behaviour, toxicity as well as ecological impact is still scarce, urging the need to improve this chemicals environmental risk assessment [Santos et al., 2018]. Concomitantly, the current paradigm of toxicity testing relies on the use of extensive juvenile/animals. This approach is time-consuming, expensive, and inadequate to face the increasing need of high-throughput testing of an increasing number of new chemicals. One of the most promising alternatives is the use of embryo bioassays. Importantly, available toxicological data dealing with biologically active compounds and priority chemicals indicates that impairment in early development is expected to provoke delayed effects at the adult stage, providing useful ecotoxicological information [Soares et al., 2009]

It is in this context that the current project proposal emerges. We propose to improve environmental risk assessment of emerging pollutants through the application of sensitivity embryo bioassays with aquatic animals, linking the biological effects with affected pathways.

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Endocrine Disruption and Ecotoxicology


The following specific aims will be addressed:

a) Screen emerging pollutants ecotoxicological effects using embryo bioassays, b) Develop biochemical and molecular tools to characterize the mode of action of emerging

pollutants, c) Improve emerging pollutants ecotoxicological risk assessment.


Embryo zebrafish bioassays will be used as they have already been significantly validated at international levels, and already incorporate the screening of sublethal effects in key stages of embryonic development. Furthermore, our group work has a long experience on embryo development and full-life cycle studies with Danio rerio as well as of markers of development. We will select for toxicity testing representative groups of emerging pollutants that raise major concern. Embryo exposure to the toxicants will be performed through water and microinjection. For those chemicals where sufficient toxicological data is available in international literature, we will contrast the information with our results to demonstrate the sensitivity of these embryo bioassays in the hazard and risk characterization of emerging pollutants. After determining the effects of the tested chemicals on the embryonic development, the screening of the chemicals mode of action will be performed, using both biochemical and molecular tools (i.e., oxidative stress, Real time PCR, immunocitochemistry).


Soares, J., Neuparth, T., Lyssimachou, A., Lima, D., André, A., Reis-Henriques, M.A., Castro, L.F.C., Carvalho, A.P., Monteiro, N.M., Santos, M.M., 2018. 17α-ethynilestradiol and tributyltin mixtures modulates the expression of NER and p53 DNA repair pathways in male zebrafish gonads and disrupt offspring embryonic development. Ecological Indicators 95(2), 1008-1018. doi: 10.1016/j.ecolind.2017.04.054.

Soares, J., Coimbra, A.M., Reis-Henriques, M.A., Monteiro, N.M., Vieira, M.N., Oliveira, J.M.A., Guedes-Dias, P., Fontaínhas-Fernandes, A., Sila Parra, S., Carvalho, A.P., Santos, M.M., 2009. Disruption of zebrafish (Danio rerio) embryonic development after full life-cycle parental exposure to low levels of ethinylestradiol. Aquatic Toxicology 95(4), 330-338. doi: 10.1016/j.aquatox.2009.07.021.

Santos, M.M., Ruivo, R., Capitão, A., Fonsexa, E., Castro, L.F.C., 2018. Identifying the gaps: resources and perspectives on the use of nuclear receptor based-assays to improve hazard assessment of emerging contaminants. Journal of Hazardous Materials 15, 508-511. doi: 10.1016/j.jhazmat.2018.04.076.




ORIENTADOR(A)/SUPERVISOR: Leonardo J. Magnoni

GRUPO/GROUP: LANUCE

CO‐ORIENTADOR(A)/CO‐SUPERVISOR: Francisco Guardiola

GRUPO/GROUP: Nutrition and immunobiology


TEMA/THEME: The effect of sustained swim training on the welfare of gilthead seabream (Sparus aurata)

RESUMO:

RESUMO/SUMMARY

Swimming is a key behavioural component contributing to the fitness of most species. Several

studies have shown that induced sustained swimming in cultured fish enhances growth and increases

survival rates 1,2. Nevertheless, most studies showing the beneficial effects of induced swimming have

been conducted on salmonid fish 3-5. However, the implementation of these conditions has frequently

been overlooked in other cultured species. Reduced swimming performance of cultured Atlantic salmon

versus wild counterparts has been associated with decreased disease resistance 7. Interestingly, exercise

promotes health in mammals, associated with the skeletal muscle´s secretory function 9.

This research proposed will investigate if sustained swim training increases welfare of gilthead

seabream by reducing stress and improving immune response.


The research proposed here will investigate if sustained swim training (SST) at optimal speeds in

gilthead seabream (Sparus aurata):

Improve immune function.

Increase the survival and welfare by boosting robustness (reducing stress).


Biology, Aquatic sciences, Animal welfare, Animal physiology


The following tasks are proposed:

Determination of the swimming capacity.

Following the methodology described for other species 6.

Growth trial.

Fish will be housed in tanks divided into two spaces holding control or swimming groups 8. Flow will be

set based on the previous test. Fish will be fed a commercial diet ad libitum twice a day. Flow will be

stopped to quantify voluntary feed intake . Growth performance will be evaluated every 30 days. After 60

days half of the fish in SST groups will be transferred to 3 tanks (detraining, set at similar flow as the

control). After 30 days all the groups will be sampled. Fish will be anaesthetized and blood will be

collected to analyse parameters related to stress and innate immune responses. These parameters will

include HCT, Hb and WBCV (blood); cortisol, lactate and glucose levels , as well as ACH50, peroxidase

and lysozyme activities (plasma). Mucus will be sampled to analyze viscosity and innate immune

parameters. Fish will be euthanized and head-kidney, liver and skeletal muscle will be collected.

Differential expression of key genes will be assessed in tissues by qPCR, including markers of stress and

immune responses (e.g. GRPs, MtHsp, IgM, ILs, TNF-α) .


1 Palstra, A. & Planas, J. Fish under exercise. Fish Physiol. Biochem. 37, 259‐272, doi:doi:10.1007/s10695‐011‐9505‐0 (2011).

2 Davison, W. & Herbert, N. A. in Swimming Physiology of Fish: Towards Using Exercise to Farm a Fit Fish in Sustainable Aquaculture (eds Arjan P. Palstra & Josep V. Planas) 177‐202 (Springer Berlin Heidelberg, 2013).

3 Walker, M. G. & Emerson, L. Sustained swimming speeds and myotomal muscle function in the trout, Salmo gairdneri. Journal of Fish Biology 13, 475‐481, doi:doi:10.1111/j.1095‐8649.1978.tb03457.x (1978).

4 Houlihan, D. F. & Laurent, P. Effects of Exercise Training on the Performance, Growth, and Protein Turnover of Rainbow Trout (Salmo gairdneri). Canadian Journal of Fisheries and Aquatic Sciences 44, 1614‐1621, doi:10.1139/f87‐195 (1987).

5 Totland, G. K. et al. Growth and composition of the swimming muscle of adult Atlantic salmon (Salmo salar L.) during long‐term sustained swimming. Aquaculture 66, 299‐313, doi:10.1016/0044‐8486(87)90115‐3 (1987).

6 Tudorache, C., Viaene, P., Blust, R., Vereecken, H. & De Boeck, G. A comparison of swimming capacity and energy use in seven European freshwater fish species. Ecol. Freshw. Fish 17, 284‐291, doi:10.1111/j.1600‐0633.2007.00280.x (2008).

7 Castro, V. et al. Disease resistance is related to inherent swimming performance in Atlantic salmon. BMC Physiology 13, 1, doi:10.1186/1472‐6793‐13‐1 (2013).

8 Palstra, A. P. et al. Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming Fish. PLoS ONE 8, e53171, doi:10.1371/journal.pone.0053171 (2013).

9 Pedersen, K. A. in Comprehensive Physiology (ed R. Terjung) (2013).




ORIENTADOR(A)/SUPERVISOR: Luisa Valente

GRUPO/GROUP: LANUCE

CO‐ORIENTADOR(A)/CO‐SUPERVISOR: Benjamin Costas



TEMA/THEME: Valorisation of agro‐food by products: the potential hydrolysates in functional feeds

RESUMO:

RESUMO/SUMMARY Protein hydrolysates were recently identified as sustainable alternatives to replace fish meal in diets for marine fish species (3,4). They are high-quality protein sources and contain bioactive peptides able to stimulate fish growth and immunity, also having antimicrobial activity. The use of these compounds can increase fish disease resistance, reducing the need for antibiotics, and contribute to a circular economy concept targeting zero waste. Size-fractioned protein hydrolysates from agro food by products will be produced by innovative methods under the project MOBFOOD (http://lanuce.ciimar.up.pt/projects/mobfood). Such hydrolysates will be included in diets for European sea bass, an important marine fish species and fed to juveniles during 3 months. At the end of the trial, the impact of the diets on the immunological status of the fish will be evaluated and compared to a commercial diet.


Evaluate the bioactive properties of selected protein hydrolysates and its potential as feed ingredients for

European sea bass. Different hydrolysates from agro‐food by‐products will be produced by innovative methods

under the project MOBFOO and fully characterised. The most appropriate ones for sea bass will be selected and included in equilibrated diets for this species. After 3 months, the immunological status of the fish fed the hydrolysates will be compared with those fed commercial feeds.


Biochemistry; Biological Sciences; Veterninary Sciences


- Chemical evaluation of the hydrolysate: peptide characterisation (molecular weight by fast protein liquid chromatography (FPLC), hydrophobicity by high performance LC (HPLC) and peptide sequencing by LC with mass spectrometry (LC-MS), nutritional value (amino acid composition, protein and lipid content and fatty acid profile)

- In vitro bacteriostatic and bactericidal activities of hydrolysates against bacteria with impact on D. labrax diseases

- In vivo experiments with juvenile D. labrax for immune status evaluation: plasma activity of lysozyme, peroxidase, ACH50 and IgM) and haematological profile (haematocrit and blood cell counting)


1. Cuesta, A., Meseguer, J., Esteban, M. Vet Immunol Immunopathol 2004, 101(3‐4), 203‐210.

2. Machado, M., Azeredo, R., Díaz‐Rosales, P., Afonso, A., Peres, H., Oliva‐Teles, A., Costas, B. Fish & Shellfish

Immunol 2015 42(2), 353‐362.

3. Skalli, A., Zambonino‐Infante, J.‐L., Kotzamanis, Y., Fabregat, R., Gisbert, E. Aquacult Nutr 2014, 20(2), 118‐

131.

4. Xu, H., Mu, Y., Liang, M., Zheng, K., & Wei, Y. Aquacult Res 2017, 48(6), 2945‐2953.




ORIENTADOR(A)/SUPERVISOR: Luis Filipe Rangel

GRUPO/GROUP: Laboratório de Patologia Animal

CO‐ORIENTADOR(A)/CO‐SUPERVISOR: Maria João Santos


LOCAL DE REALIZAÇÃO DO TRABALHO/PLACE OF WORK: Faculdade de Ciências da UP / CIIMAR

TEMA/THEME: Influência dos parasitas coccídeos na ocorrência de outras infeções por micro e macroparasitas em peixes de interesse económico

RESUMO:

RESUMO/SUMMARY O desenvolvimento da piscicultura passa pelo seu sucesso económico, ou seja, por reduzir os custos e maximizar os lucros. Um dos grandes entraves ao desenvolvimento da piscicultura são as doenças, nomeadamente as parasitoses que provocam mortalidade ou retardam o desenvolvimento e o crescimento dos peixes. Os microparasitas coccídeos, por exemplo, retardam o desenvolvimento dos peixes ao reduzirem a absorção dos nutrientes. As pisciculturas compensam esse atraso com o aumento do tempo de engorda, com a consequente redução do lucro. No entanto, desconhece‐se que outros efeitos estes parasitas coccídeos poderão provocar na saúde dos peixes. As pisciculturas, como são sistemas fechados, potenciam o aparecimento de constantes infecções parasitárias. Para além do aumento do tempo de engorda dos peixes, os coccídeos poderão estar a contribuir para o aumento da carga parasitária com eventuais graves prejuízos.


O objectivo principal deste trabalho é o de avaliar se uma maior intensidade de infecção por coccídeos, e

consequente menor absorção de nutrientes, torna os peixes mais susceptíveis à infeção por outros grupos de

parasitas.

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Parasitologia / Patologia


A metodologia a utilizar será a seguinte:

i) Pesquisa de micro e macroparasitas nas espécies de peixes selecionadas;

ii) Determinação das prevalências e intensidade de infecção de cada espécie de parasita por hospedeiro;

iii) Comparação das prevalências e intensidades de infecção de todos os parasitas em relação aos parasitas

coccídeos;

iv) Caracterização morfológica e molecular das espécies parasitas novas para a ciência.


Gjurcevic, E., Kuzir, S., Bazdaric, B., Matanovic, K., Debelic, I., Marino, F., Drasner, K. and Rosenthal, B. M. (2017).

New data on Eimeria dicentrarchi (Apicomplexa: Eimeriidae), a common parasite of farmed European sea bass

(Dicentrarchus labrax) from the mid‐eastern Adriatic. Veterinary Archives 87, 77‐86.

Molnar, K. (2006): Phylum Apicomplexa. In Fish Diseases and Disorders, Volume 1: Protozoan and Metazoan

Infections (2nd ed.), (Woo, P. T. K., Ed.), CAB International, Wallingford, pp. 183‐204.

Steinhagen, D., Oesterreich, B. and Korting, W. (1997). Carp coccidiosis: clinical and hematological observations of

carp infected with Goussia carpelli. Diseases of Aquatic Organisms, 30, 137‐143.




ORIENTADOR(A)/SUPERVISOR: Marcos RubalGarcía

GRUPO/GROUP: Coastal Biodiversity

CO‐ORIENTADOR(A)/CO‐SUPERVISOR: Puri Veiga Sánchez

GRUPO/GROUP:Coastal Biodiversity

LOCAL DE REALIZAÇÃO DO TRABALHO/PLACE OF WORK:LBC (CIIMAR) and Lab 2.54 (Biology Department

of Faculty of Sciences, UP)

TEMA/THEME: Abundance, distribution and phenology of native and non‐indigenous canopy macroalgae along north Portugal

RESUMO:

RESUMO/SUMMARY Marine forests constitute the largest biogenic structures found in benthic marine systems of the world’s cold‐water and temperate coastal habitats (Steneck et al., 2002). Canopy forming seaweeds are ecosystem engineers that are dramatically declining worldwide. Urban and industrial pollution can cause local extinction of canopies while at a larger spatial scale, eutrophication, and global warming are the main responsibles of canopy decline. These impacts are leading to shifts in habitat structure from canopy forming species to alternative states, in the worst case to barren grounds composed of filamentous and encrusting species (Micheli et al., 2005; Connell et al., 2008). Due to the ecological importance of assemblages dominated by canopies and the decline of their populations within the past decades, it is imperative a better knowledge of their distribution abundance and fitness to develop a conservation strategy. This proposal is integrated in the project “Sargaço como recurso de alto valor numa mudança global. Vale a pena investir neste recurso?” com referência POCI-01-0145-FEDER-029818 co‐financed by COMPETE 2020, Portugal 2020 and the European Union through the ERDF, and by FCT through national funds.

ÁREA CIENTÍFICA/SCIENTIFIC AREA:Marine Biology, Ecology, Aquatic sciences


The aims of this proposal are:

i) To explore differences on the abundance and distribution of native and non indigenous canopies

ii) To explore differences on the reproductive phenology of native and non indigenous canopies

iii) To explore the differences on the fitness of native and non indigenous canopies


Field sampling of abundance and distribution of the main intertidal canopy macroalgae

Determination of the reproductive status of the main intertidal canopy macroalgae

Determination of the fitness of the main intertidal canopy macroalgae


CONNELL S., RUSSELL B., TURNER D., SHEPHERD A., KILDEA T., MILLER D., AIROLDI L. & CHESHIRE A., 2008 — Recovering a lost baseline: missing kelp forests from a metropolitan coast. Marine ecology progress series 360: 63‐72. MICHELI F., BENEDETTI‐CECCHI L., GAMBACCINI S., BERTOCCI I., BORSINI C., OSIO G.C. & ROMANO F., 2005 — Cascading human impacts, marine protected areas, and the structure of Mediterranean reef assemblages. Ecological monographs 75(1): 81‐102. STENECK R.S., GRAHAM M.H., BOURQUE B.J., CORBETT D., ERLANDSON J.M., ESTES J.A. & TEGNER M.J., 2002 — Kelp forest ecosystems: biodiversity, stability, resilience and future. Environmental conservation 29(4): 436‐459.




ORIENTADOR(A)/SUPERVISOR: Marisa Almeida


CO-ORIENTADOR(A)/CO-SUPERVISOR: Sandra Ramos



TEMA/THEME: Potential of lost fishing gears for adsorption of pollutants

RESUMO:

RESUMO/SUMMARY

Fishing-related debris represents more than 50% of the weight of the floating macroplastics pollution found in

marine environment. Plastic is an inert material, but environmental dynamics can induce modifications on its

surface, making it suitable to adsorb pollutants. Nevertheless, chemical pollution loads in lost fishing gear (mainly

composed of plastics) have not yet been sufficiently explored, being this the aim of this work.

Obtained results, regarding pollutants adsorption will contribute for a better understanding of the ecological

implications of fishing-related debris.


To evaluate, under laboratory manipulative experiments, the potential of lost gears for adsorption of organic and

inorganic pollutants

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Environmental science


Different fishing gears will be fragmented and exposed to natural sea water doped with different organic (e.g.

PAHs) and inorganic (trace metals) pollutants at environmental relevant levels.

These experiments will be carried out under different dynamic conditions (different levels of agitation), both in

the presence and in the absence of marine sediment (sand with different grain size).

Gear fragments and samples of water and sand will be collected over time, for the quantification of the selected

pollutants, after appropriate extraction.





ORIENTADOR(A)/SUPERVISOR: Miguel Santos

GRUPO/GROUP: Endocrine Disruptors and Emerging Contaminants (EDEC)

CO-ORIENTADOR(A)/CO-SUPERVISOR: Filipe Castro

GRUPO/GROUP: Animal Genetics and Evolution

LOCAL DE REALIZAÇÃO DO TRABALHO/PLACE OF WORK: CIIMAR/FCUP

TEMA/THEME: Ecotoxicology of Deep-sea environments: combined effects of deep-sea mining and multi-stressors

RESUMO:

RESUMO/SUMMARY The commercial plans to exploit mineral resources on deep-ocean beds, including those in the vicinity of hydrothermal-

vents, raise increasing concern about the damage that such actions might cause to the sensitive and poorly-understood

ecosystems that live there (Santos et al., 2018). It has been suggested that mining is currently the only anthropogenic

activity projected to have a major impact on vent ecosystems and other deep-sea areas, although the potential scale of

such impacts are unknown at present (Van Dover, 2011). In fact, recent data shows that anthropogenic chemicals

accumulate in deep-sea animals at high levels, although the impact that such accumulation may have in sensitive taxa is

still unknown (Mengerink et al., 2014). Recent evidences also show that deep-sea organisms are already experiencing

impact of climate change associated stressors. Here, we aim to address the potential hazard of deep-sea mining

associated stressors (i.e., sediment plumes, light, noise, chemical contamination) with environmental and other

anthropogenic stressors, through a combination of approaches.


1) To evaluate the combined effects of deep-sea mining associated stressors with environmental and

anthropogenic stressors through; a) High –pressure laboratory experiments (using hyperbaric chambers) to

simulate the impact of multi-stressors in taxa under deep sea conditions; b) determine the physiological and

molecular signatures of in vivo stressors exposure through biochemical and molecular tools.

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Ciências ambientais


1. Ecotoxicological assays under hyperbaric conditions

2. Ecology

3. Molecular Biology


Van Dover, C.L., 2011. Tighten regulations on deep-sea mining. Nature 470 (7332), 31–33.

https://doi.org/10.1038/470031a.

Mengerink, K.J., Van Dover, C.L., Ardron, J., Baker, M., Escobar-Briones, E., Gjerde, K., Koslow, J.A., Ramirez-Llodra, E.,

Lara-Lopez, A., Squires, D., Sutton, T., Sweetman, A.K., Levin, L.A., 2014. A call for deep-ocean stewardship. Science 344

(6185), 696–698. https://doi.org/10.1126/science.1251458.

Santos, MM et al., 2018. The last frontier: coupling technological developments with scientific challenges to improve

hazard assessment of deep-sea mining. Science of the Total Environment 627, 1505–1514.

https://doi.org/10.1016/j.scitotenv.2018.01.221

Santos, M.M., Ruivo, R., Capitão, A., Fonseca, E., Castro, L.F.C. (2018). Identifying the gaps: Resources and perspectives

on the use of nuclear receptor based-assays to improve hazard assessment of emerging contaminants. Journal of

Hazardous Materials, 358, 508-511. DOI: 10.1016/j.jhazmat.2018.04.076

Lopes CL, Bastos L, Caetano M, Martins I, Santos MM and Iglesias I, 2019. Development of physical modelling tools in

support of risk scenarios: A new framework focused on deep-sea mining. The Science of the total environment 650:2294-

2306.

https://doi.org/10.1038/470031a

https://doi.org/10.1016/j.scitotenv.2018.01.221




ORIENTADOR(A)/SUPERVISOR: Maria João Santos


CO‐ORIENTADOR(A)/CO‐SUPERVISOR: Luis Filipe Rangel


LOCAL DE REALIZAÇÃO DO TRABALHO/PLACE OF WORK: Faculdade de Ciências da UP / CIIMAR

TEMA/THEME: Será algum dos sexos do escaravelho da palmeira mais debilitado do que outro pelos seus parasitas?

RESUMO:

RESUMO/SUMMARY A praga do escaravelho das palmeiras, causada pelo insecto Rhynchophorus ferrugineus, está neste momento completamente descontrolada em Portugal e na Europa. Entrou em Portugal pelo Algarve nos anos 90 e desde aí tem progredido paulatinamente, estando já distribuida em todo o território do continente de Portugal, e até já atingiu a Madeira. Todo e qualquer controlo que se consiga alcançar será uma “lança em África”. Começou‐se por tentar controlar esta praga recorrendo a químicos, que rapidamente se mostraram ineficazes. Actualmente já se pratica o seu controlo biológico por disseminação de Nemátodes parasitas de insectos. A pesquisa de parasitas do escravelho revelou já que além de nemátodes existem também algumas espécies de ácaros que ocorrem com alguma frequência nestes insetos. O problema deste trabalho inclui dois temas: Quais são os parasitas mais maléficos para o escaravelho? E haverá distinção por sexo do hospedeiro nesse efeito? Pretendemos analisar parasitologicamente escaravelhos da palmeira em diferentes estados de desenvolvimento e relacionar a ocorrência de parasitas com o tamanho do inseto, separando machos de fêmeas sempre que o estado de desenvolvimento o permita. Na tentiva de explorar melhor o Controlo Biológico com eventualmente outras espécies parasitas distintas das que já se utilizam, e sobretudo mais resistentes.


1) Determinar quais são os parasitas mais maléficos para o escaravelho da palmeira

2) Determinar se existem diferenças entre sexos do inseto, e determinar qual dos sexos é o sexo fraco

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Parasitologia / Patologia


Fazer a análise parasitológica de 60 escaravelhos da palmeira e medir peso e dimensão do inseto.

Determinar prevalências e abundâncias (médias ± SD, intervalo) para cada estado de desenvolvimento (larva,

pupa, ou adulto)

Relacionar os níveis de infeção com o sexo do hospedeiro, e determinar o sexo fraco

Relacionar os níveis de infeção com a condição física do hospedeiro e determinar qual o parasita mais maléfico


Hajek A. E. 2004. Natural enemies, an introduction to biological control. Cambridge University Press

Masilamany, D., Ahadiyat, A. Masan, P., Chuah T‐S. 2015. Mites (Acari) associated with Rhynchophorus

ferrugineus (Coleoptera: Curculionidae) in Malaysia, with a revised list of the mites found on this weevil. Journal

of Asia‐Pacific Entomology 18: 169‐174.

Manachini, B. Schillaci, D. Ariza, V. B. 2013. Biological Responses of Rhynchophorus ferrugineus (Coleoptera:

Curculionidae) to Steinernema carpocapsae (Nematoda: Steinernematidae). Biological and Microbial Control.

106(4): 1582Ð1589.




ORIENTADOR(A)/SUPERVISOR: Nádia Eusébio

GRUPO/GROUP: Cyanobacterial Natural Products

CO-ORIENTADOR(A)/CO-SUPERVISOR: Pedro Leão

GRUPO/GROUP: Cyanobacterial Natural Products


TEMA/THEME: Genetic and chemical diversity of a novel halogenase class

RESUMO:

RESUMO/SUMMARY

Natural products have been a fruitful and reliable source of chemical diversity that have been broadly used for medicinal treatments [1], which is the case of the well-known penicillin that changed the course of health history. Nevertheless, a decrease in the rate of discovery of natural compounds in classical source organisms may be compromising the discovery of new important natural products. Based on our recent discovery of a new cyanobacterial class of halogenase, this project proposes to address this challenge by using these enzymes to guide natural product discovery. A unique bioresource (LEGE Culture Collection) [2] will be key to discovering biosynthetic gene clusters that contain these new enzymes. Orthogonal biochemical exploration approaches will identify the encoded natural products in cyanobacterial metabolomes. The new compounds will be structurally elucidated and their bioactivity will be profiled.


The aims of this project are: i) Understanding the architecture of biosynthetic gene clusters containing the new halogenases; ii) Biosynthetic-hypothesis guided discovery of new natural products.



To achieve such goals, we will categorize all the new halogenase-homolog-containing biosynthetic gene clusters

from LEGE strains and publicly available cyanobacterial genomes through comparative analysis of their gene

content and organization.

Biosynthetic hypotheses will be formulated for each biosynthetic gene cluster and different strategies will be used

to reveal the encoded natural product (MS/MS metabolomics, construction of mutants, heterologous expression

in E. coli and Streptomyces).

New compounds will be isolated using different chromatographies (flash, HPLC, etc.) and characterized mostly by

1D/2D NMR and HRMS methods.

Bioactivity assays for pure compounds will include antimicrobial, antifungal, antialgal and cytotoxic activities.


1. Newman, D.J. and G.M. Cragg, Natural Products as Sources of New Drugs from 1981 to 2014. Journal of Natural

Products, 2016. 79(3): p. 629-661.

2. Ramos, V., et al., Cyanobacterial diversity held in microbial biological resource centers as a biotechnological

asset: the case study of the newly established LEGE culture collection. Journal of Applied Phycology, 2018. 30(3): p.

1437-1451.




ORIENTADOR(A)/SUPERVISOR: Pedro Leão

GRUPO/GROUP: Cyanobacterial Natural Products (CNP)

CO‐ORIENTADOR(A)/CO‐SUPERVISOR: Kathleen Abt


LOCAL DE REALIZAÇÃO DO TRABALHO/PLACE OF WORK: CIIMAR (Terminal Cruzeiros Porto Leixões)

TEMA/THEME: Discovery of new natural products from Nodosilinea cyanobacteria

RESUMO:

RESUMO/SUMMARY Cyanobacteria are very talented chemists among bacteria [1]; their natural products are often extremely toxic (e.g. microcystin ‐ a potent cyanotoxin [2]) or potent against pharmacological targets (e.g. dolastatin 10, which was developed into the anticancer drug bentuximab vedotin [3]). Genome sequences of cyanobacteria indicate that there are many more natural products waiting to be discovered from these organisms[4]. In this proposal, the student will focus on cyanobacteria of the marine genus Nodosilinea, abundant in the Portuguese coast and from which we have already isolated the bartolosides [5]. The student will perform a large‐scale metabolomics study to identify new‐to‐science compounds in extracts from Nodosilinea strains and then use algal‐culturing techniques to obtain large amounts of biomass from which the new molecules will be isolated. Pure natural products will have their structures elucidated by Nuclear Magnetic Resonance (1D and 2D), Mass spectrometry (HRMS/MS) and other spectroscopic techniques. The student will then search the genome sequences of the Nodosilinea strains to try to link the new natural products to the corresponding biosynthetic pathway. Finally, the student will test the pure compounds in various bioassays (ranging from antibacterial to anticancer) to evaluate the pharmacological potential of the new natural products.


1. Perform a comparative metabolomics analysis of ca. 40 Nodolsilinea strains;

2. Identify, using comparartive metabolomics tools, at least two new natural products;

3. Isolate and elucidate the structure of at least one new natural product;

4. Identity at least one putative new biosynthetic gene cluster

5. Perform a biological activity profiling for at least one new natural product.

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Biochemistry / Pharmaceutical Sciences


LC‐HRMS/MS and comparative metabolomics analysis;

Algal culturing and handling;

MS‐guided isolation (chromatographies such as column, flash or HPLC, iterated with MS analysis);

Structure elucidation (de novo, using 1D and 2D NMR, as well as HRMS/MS, among other spectroscopies);

Genome mining (annotation of genome data, generation of biosynthetic hypothesis, mining genome data);

Biological assays (microplate‐ and agar‐based antibacterial, antifungal assays, cytotoxicity assays in cancer cell

lines).


1. Nunnery JK, Mevers E, Gerwick WH. 2010. Biologically active secondary metabolites from marine

cyanobacteria. Current Opinion in Biotechnology. 21(6):787–93

2. Schatz D, Keren Y, Vardi A, Sukenik A, Carmeli S, et al. 2007. Towards clarification of the biological role of

microcystins, a family of cyanobacterial toxins. Environmental Microbiology. 9(4):965–70

3. Gerwick WH, Moore BS. 2012. Lessons from the Past and Charting the Future of Marine Natural Products Drug

Discovery and Chemical Biology. Chem Biol. 19(1):85–98

4. Dittmann E, Gugger M, Sivonen K, Fewer DP. 2015. Natural Product Biosynthetic Diversity and Comparative

Genomics of the Cyanobacteria. Trends in Microbiology. 23(10):642–52

5. Leão PN, Nakamura H, Costa M, Pereira AR, Martins R, et al. 2015. Biosynthesis‐Assisted Structural Elucidation

of the Bartolosides, Chlorinated Aromatic Glycolipids from Cyanobacteria. Angew. Chem. Int. Ed. 54(38):11063–67




ORIENTADOR(A)/SUPERVISOR: Paula Enes


CO-ORIENTADOR(A)/CO-SUPERVISOR: Ana Couto


LOCAL DE REALIZAÇÃO DO TRABALHO/PLACE OF WORK: FCUP and CIIMAR

TEMA/THEME: Insect meals as fish meal substitutes in diets for European sea bass (Dicentrarchus labrax): effects on gut function and health

RESUMO:

RESUMO/SUMMARY In aquaculture, finding alternative ingredients to fish meal (FM) is urgently needed. Insect meal (IM), recently authorized for use in aquafeeds, has high protein and lipid contents and a balanced amino acid profile, thus being a promising aquafeed commodity. However, insects are also rich in chitin, that may negatively interfere with fish performance, nutrient digestibility and be an allergen. European sea bass (ESB) was chosen as model species due to its high commercial importance in European aquaculture. This project aims at producing low FM diets for ESB that cost-effectively support growth without compromising gut function and health. For that, novel and promising aquafeed commodities, Hermetia illucens meal, Hermetia exuviae, Tenebrio molitor meal and Acheta domesticus meal, will be the nutritional strategies used. Since a healthy digestive system is fundamental for ideal performance, the impact of IM on fish gut function and health will be evaluated by assessing its effects on gut morphology, digestive and antioxidant enzymes activities, gut immunology and gut microbiota diversity.

OBJECTIVOS/OBJECTIVES: This study aims to evaluate the effect of dietary replacement of FM by IM on ESB gut function and health through assessing its effects on:

- Activity of luminal (total alkaline proteases; α- amylase, lipase and chitinolytic) and brush border membrane enzymes (alkaline phosphatase, maltase and leucine-aminopeptidase);

- Gut morphology; - Gut antioxidant status; - Gut immunology and; - Gut microbiota.

ÁREA CIENTÍFICA/SCIENTIFIC AREA: AQUACULTURE – FISH NUTRION

PRINCIPAIS METODOLOGIAS/MAIN METHODOLOGIES: Digestive enzymes Activity of the luminal enzymes total alkaline proteases, α-amylase, lipase and chitinases (1), and activity of the brush border membrane enzymes, alkaline phosphatase, maltase and leucine-aminopeptidase (2) will be determined in whole-gut to assess IM effect on fish digestive function. Histomorphology Histological samples will be used to diagnose potential disturbances, temporary or permanent, caused by the ingestion of IM, since these novel commodities may have harmful effects on gut mucosa, and cause intestinal dysfunction. Distal gut samples will be processed and sectioned using standard histological techniques, and sections will be stained with haematoxylin-eosin. Blind evaluation of histological preparations will be performed with particular attention given to any inflammatory change (3). Antioxidant status Oxidative status will be evaluated in whole-gut by assessing the activity of antioxidant enzymes (catalase, superoxide dismutase, glutathione peroxidase, glutathione reductase, glucose 6-phosphate dehydrogenase), and by measuring oxidative damage markers such as total and oxidised glutathione (tGSH and GSSG) and lipid peroxidation products (TBARS) (4). Immune response The expression of several genes encoding proteins with regulatory roles in immune responses, such as cytokines (IL-1β, IL-6 and TNF-α), antimicrobial peptides (hepcidin and beta-defensin), T cell markers, and molecules related to T cell activities such as receptors (TcR-β, TcR-γ), surface markers (CD4, CD8-α), soluble factors (IL-10) and T cell-related molecules (recombination activating genes, RAGs) will be assessed by real-time PCR (SYBR Green, Bio-Rad) in fish distal gut. Microbial diversity analysis The taxonomic diversity of ESB allochthonous (digesta) and autochthonous (mucosa) gut microbiota concerning each feeding condition will be assessed by polymorphism analyses of 16S rRNA genes by denaturing gradient gel electrophoresis-DGGE (5). DGGE profiles will be analyzed by Quantity One software (Bio-Rad) to generate similarity dendograms and densitometric analyses to identify bands shown to be either over- or under-represented due to the different diet regimes. Distinct representative DGGE bands will be excised, corresponding 16S rRNA amplicons purified and sequenced to identify microbiota OTUs (Operational Taxonomic Units) and correlate their relevance with the different diet regimes.

REFERÊNCIAS/REFERENCES: (1) Bergmeyer, H.U., 1965. Methods of enzymatic analysis. Verlag Chemie, Academic Press. (2) Couto, A. Kortner, T.M, Penn, M., Ostby, G., Bakke, A.M., Krogdahl, A., Oliva-Teles, A., 2015. Saponins and

phytosterols in diets for European sea bass (Dicentrarchus labrax) juveniles: effects on growth, intestinal morphology and physiology. Aquaculture Nutrition 21, 180-193.

(3) Krogdahl, A., Bakke-McKellep, A.M., Baeverfjord, G., 2003. Effects of graded levels of standard soybean meal on intestinal structure, mucosal enzyme activities, and pancreatic response in Atlantic salmon (Salmo salar L.). Aquaculture Nutrition 9, 361-371.

(4) Perez-Jimenez, A., Peres, H., Rubio, V.C., Oliva-Teles, A., 2012. The effect of dietary methionine and white tea on oxidative status of gilthead sea bream (Sparus aurata). British Journal of Nutrition 108, 120-1209.

(5) Serra, C.R, Júnior, F.M., Couto, A., Oliva-Teles, A., Enes, P., 2018. Gut microbiota and gut morphology of gilthead sea bream (Sparus aurata) juveniles are not affected by chromic oxide as digestibility marker. Aquaculture Research 49, 1347-1356.




ORIENTADOR(A)/SUPERVISOR: Cláudia R. Serra GRUPO/GROUP: NUTRIMU - CIIMAR

CO-ORIENTADOR(A)/CO-SUPERVISOR: Paula Enes GRUPO/GROUP: NUTRIMU - CIIMAR


TEMA/THEME: Characterization of novel Probiotics isolated from European sea bass (Dicentrarchus labrax)

gut microbiota for improving insect meal utilization and gut health

RESUMO:

RESUMO/SUMMARY In aquaculture, finding alternative ingredients to fish meal (FM) is urgently needed. Insect meal (IM), recently authorized for use in aquafeeds, has high protein and lipid contents and a balanced amino acid profile, thus being a promising aquafeed commodity. However, insects are also rich in chitin, that may negatively interfere with fish performance, nutrient digestibility and be an allergen. To overcome chitin impairments, this proposal intends to characterize bacterial strains that were isolated from the gastrointestinal tract of European sea bass (ESB), for their use as novel Probiotics (PRO) in aquaculture. To be industrially valuable, these PRO bacteria, besides being safe, must be capable of producing chitinases to improve the use of high IM-containing diets, thus supporting cost-effective fish growth without compromising welfare and health status.

OBJECTIVOS/OBJECTIVES: This work will be dedicated to the in vitro screening and characterization of putative PRO bacteria, isolated from the gastrointestinal tract of ESB juveniles fed IM and chitin-enriched diets. Bacterial strains will be tested for important traits, namely: ability to utilize chitin (component of IM); biosafety issues, including absence of antibiotic resistances and toxigenic potential; gut-survival capacity and suitability for bioreactors upscale. The final goal is to find the best PRO candidates that can thereafter be evaluated in vivo considering their potential to modulate fish gut microbiota, aiming to improve dietary chitin utilization and avoid potential allergen effects.


The work is divided in 3 Tasks using MICROBIOLOGY, MOLECULAR BIOLOGY and BIOCHEMISTRY methodologies: Task1: Identification and characterization of putative PRO based on functional properties (chitin utilization) PRO bacteria previously selected will be characterized for morphology by phase-contrast microscopy (1,2). Each isolate will be evaluated regarding its growth performance on minimal medium (3), supplemented with 1% (w/v) of chitin, followed by quantification of chitin utilization. Bacteria known to possess chitinolytic extracellular activities will be used as positive controls (4). Detailed taxonomic identification will be performed for the isolates with promising extracellular chitinolytic activities. Standard molecular and biochemical methods will be used to disclose the identification and the key metabolic properties of the isolates (e.g. 16S rRNA gene sequencing analysis; biochemical fingerprint, using the API20 and API 50 CHB systems from bioMerieux). Pathogenic species will be discarded.



1) Nicholson, W. L., Setlow, P. (1990) Sporulation, germination and outgrowth. In: Harwood C.R., Cutting, S.M. (Eds.) Molecular Biological Methods for Bacillus. John Wiley & Sons Ltd., Chichester, UK, pp. 391-450. 2) Barbosa, T.M., Serra, C.R., La Ragione, R.M., Woodward, M.J., Henriques, A.O. (2005) Screening for Bacillus isolates in the broiler gastrointestinal tract. Applied and Environmental Microbiology 71, 968-978. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546680/ 3) Harwood, C.R., Cutting, S.M. (1990) Chemically defined growth media and supplements. In: Harwood, C.R., Cutting, S.M. (Eds.) Molecular biological methods for Bacillus. John Wiley & Sons Ltd., Chichester, UK, p. 548. 4) Brzezinska, M. S., Jankiewicz, U., Burkowska, A., & Walczak, M. (2014). Chitinolytic microorganisms and their possible application in environmental protection. Current microbiology, 68(1), 71-81. URL: https://link.springer.com/article/10.1007/s00284-013-0440-4 5) Panel, E. F. (2012). Guidance on the assessment of bacterial susceptibility to antimicrobials of human and veterinary importance. EFSA Journal, 10(6), 2740. URL: https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/j.efsa.2012.2740 6) Panel, E. F. (2014). Guidance on the assessment of the toxigenic potential of Bacillus species used in animal nutrition. EFSA Journal, 12(5), 3665. URL: https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/j.efsa.2014.3665

Task 2: PRO Biosafety assessment Following recommendations of EFSA (European Food Safety Authority), PRO bacteria will be checked for “absence of food poisoning toxins, absence of surfactant activity, and absence of enterotoxic activity” using standard methods. Carriage of antibiotic resistance will be studied by testing PRO susceptibility to different classes of antibiotics. Minimal inhibitory concentrations (MIC) will be determined using E-tests and/or the NCCLS reference broth microdilution method. If resistant to any of the antibiotics, capacity to spread via genetic exchange will be tentatively determined by checking for the presence of mobile genetic elements and their relationship with antibiotic resistance genes biosafety regulations and industrial standards. Isolates presenting antibiotic resistance and/or toxigenic potential, following standard procedures (5,6) will be discarded. Task 3: Gut-survival aptitude To assess gut adaptation, resistance to transit through the gut will be evaluated by determining the acid and bile tolerance of isolates as previously reported (2).




ORIENTADOR(A)/SUPERVISOR: Puri Veiga Sánchez


CO‐ORIENTADOR(A)/CO‐SUPERVISOR: Marcos Rubal García


LOCAL DE REALIZAÇÃO DO TRABALHO/PLACE OF WORK: LBC (CIIMAR) and Lab 2.54 (Biology Department


TEMA/THEME: Effects of habitat homogenization caused by harvesting of mussels on their biodiversity associated

RESUMO:

RESUMO/SUMMARY Intertidal rocky shores provide goods and services to mankind as food or recreation (1). Moreover, many of their species are ecosystem engineers because they modify, create or maintain useful habitat for other organisms (2), enhancing biodiversity (3, 4). However, intertidal shores suffer effects of different anthropogenic stressors such as harvesting that may reduce the amount and value of their services (1), with consequences to human wellbeing (5). The mussel Mytilus galloprovincilis is a widespread filter‐feeding animal along the Atlantic rocky shores . It is considered an ecosystem engineer because its clumps facilitate the establishment and persistence of many invertebrates (6). Despite its importance, only one study have evaluated its associated biodiversity in the Iberian Peninsula (3). Moreover, this mussel is a species with commercial interest (7, 8) providing valuable ecosystem services such as food, mediation of toxic waste and other nuisances, habitat and supporting services (9). The aim of this master proposal is to explore the effects of habitat homogenization caused by mussel harvesting on their associated biodiversity, using an experimental approach. This proposal, is integrated in the project ECOS ‐ “New tools to evaluate the ecological status of rocky shores and its relationship with ecosystem services” co‐financed by COMPETE 2020, Portugal 2020 and the European Union through the ERDF, and by FCT through national funds.



i) To elucidate the effects of habitat homogenisation caused by harvesting on biodiversity associated

with Mytilus galloprovincialis clumps.

ii) To integrate results obtained to provide useful information for conservation and management

purposes.


To test the effect of mussel harvesting, a field manipulative experiment will be done at two rocky shores in North

Portugal. At each shore, twelve experimental plots of 20 x 20 cm, dominated by M. galloprovincialis, will be chosen

and permanently marked.

The effect of habitat homogenisation caused by harvesting will be evaluated by considering two different treatments:

a) harvesting, collecting the biggest individuals but maintaining the smaller ones (more homogenous habitat, only

with small‐sized mussels) and b) control (no harvesting, more heterogeneous habitat, with big and small‐sized

mussels).

Experimental plots will be maintained in the field for a period. At the end of this period, biodiversity associated with

each plot will be studied and compared between treatments using multivariate and univariate analysis of variance.

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Marine Biology, Ecology, Aquatic sciences


1. Wyles KJ, Pahl S, Thompson RC. 2014. Perceived risks and benefits of recreational visits to the marine

environment: Integrating impacts on the environment and impacts on the visitor. Ocean & Coastal Management

88: 53–63.

2. Jones CG, Lawton JH, Shachak M. 1994. Organisms as ecosystem engineers. Oikos 69: 373–386.3. Gestoso I,

Arenas F, Rubal M, Veiga P, Peña M, Olabarria C. 2013. Marine Environmental Research 90: 85–95.

3. Gestoso I, Arenas F, Rubal M, Veiga P, Peña M, Olabarria C. 2013. Shifts from native to non‐indigenous mussels:

enhanced habitat complexity and its effects on faunal assemblages. Marine Environmental Research 90: 85–95.

4. Veiga P, Rubal M, Sousa‐Pinto I. 2014. Structural complexity of macroalgae influences epifaunal assemblages

associated with native and invasive species. Marine Environmental Research 101: 115–123.

5. Worm B, Barbier EB, Beaumont N, Duffy JE, Folke C, Halpern BS, Jackson JBC, Lotze HK, Micheli F, Palumbi SR,

Sala E, Selkoe KA, Stachowicz JJ, Watson R. 2006. Impacts of biodiversity loss on ocean ecosystem services. Science

314: 787–790.

6. Arribas LP, Donnarumma L, Palomo MG, Scrosati A. 2014. Intertidal mussels as ecosystem engineers: their

associated invertebrate biodiversity under contrasting wave exposures. Marine Biodiversity 44: 203–211.

7. Rius M, Cabral HN. 2004. Human harvesting of Mytilus galloprovincialis Lamarck, 1819, on the central coast of

Portugal. Scientia Marina 68: 545–551.

8. Bertocci I, Dominguez R, Freitas C, Sousa‐Pinto I. 2012. Patterns of variation of intertidal species of commercial

interest in the Parque Litoral Norte (north Portugal) MPA: Comparison with three reference shores. Marine

Environmental Research 77: 60–70.

9. TEEB. 2015. The Economics of Ecosystems & Biodiversity: Ecosystem Services. Hosted by UNEP TEEB office,

Geneva, Switzerland.




ORIENTADOR(A)/SUPERVISOR: Rui Faria

GRUPO/GROUP: Animal Genetics and Evolution ‐ AGE

CO‐ORIENTADOR(A)/CO‐SUPERVISOR: Filipe Castro

GRUPO/GROUP: Animal Genetics and Evolution ‐ AGE


TEMA/THEME: A base genética de evolução paralela no intertidal/The genetic basis of parallel evolution across the intertidal

RESUMO:

RESUMO/SUMMARY

During this MSc project we will try to address the following question: Why does some intertidal species evolve (and maintain) so many life-forms? To answer this question, we will focus on Littorina fabalis, a marine Gastropod for which several ecotypes/forms have been described in the Iberian Peninsula and Northern Europe. By using population genomics approaches, we will try to understand if these ecotypes have a single origin or evolved multiple times (parallel evolution); and try to identify the genetic basis of ecotype evolution.


1. Identify the genomic regions influenced by selection underlying ecotype divergence in multiple

locations

2. Quantify the amount of shared genetic variation underlying ecotype divergence among locations

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Evolutionary Biology, population genomics, adaptation, speciation


Molecular lab:

DNA extraction, pools of DNA/tissues, library preparation and Next generation sequencing

Data analyses:

Quality control of NGS reads, read mapping, variant calling, detection of signatures of selection


Morales HE, Faria R, Johannesson K, Larsson T, Panova M, Westram AM, Butlin JK. Genomic architecture of parallel ecological divergence: beyond a single environmental contrast. https://www.biorxiv.org/content/10.1101/447854v1

Faria R, Chaube P, Morales H, Larsson T,Lemmon AR, Lemmon EM, Rafajlovic M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK (2018) Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology, https://doi.org/10.1111/mec.14972 Carvalho J, Sotelo G, Galindo J, Faria R (2016). Genetic characterization of flat periwinkles (Littorinidae) from the Iberian Peninsula reveals interspecific hybridization and different degrees of differentiation. Biological Journal of the Linnean Society 118, 503-519.




ORIENTADOR(A)/SUPERVISOR: Sandra Ramos


CO-ORIENTADOR(A)/CO-SUPERVISOR: Marisa Almeida



TEMA/THEME: Potential of lost fishing gears for the release of microplastics

RESUMO:

RESUMO/SUMMARY

Fishing-related debris represents more than 50% of the weight of the floating macroplastics pollution found in

marine environment. Plastic is an inert material, but environmental dynamics can induce modifications on its

surface, which can lead to the release of microplastics. Nevertheless, release of microplastics from lost fishing

gear (mainly composed of plastics) have not yet been sufficiently explored, being this the aim of this work.

Obtained results will contribute for a better understanding of the ecological implications of fishing-related debris.


To evaluate, under laboratory manipulative experiments, the potential of lost gears for the release of

microplastics

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Environmental science


Different fishing gear, collected at the hotspots of ghost nets along the NW Coast of Portugal will be fragmented

and exposed to natural sea water under different dynamic conditions (different levels of agitation), both in the

presence and in the absence of marine sediment (sand with different grain size), to simulate the degradation

processes that the gear can suffer in water column and after their seafloor deposition.

Samples of water and sand will be collected over time, for the quantification of microplastics.





ORIENTADOR(A)/SUPERVISOR: Sandra Antónia Cordeiro Figueiredo


CO-ORIENTADOR(A)/CO-SUPERVISOR: Pedro Nuno da Costa Leão; Ralph Urbatzka

GRUPO/GROUP: Cyanobacterial Natural Products (CNP); Blue Biotechnology and Ecotoxicology (BBE)

LOCAL DE REALIZAÇÃO DO TRABALHO/PLACE OF WORK: CNP, CIIMAR

TEMA/THEME: Discovery of cyanobacterial natural products with anticancer activity

RESUMO:

RESUMO/SUMMARY Cyanobacteria are aquatic photosynthetic microorganisms capable of producing unprecedent natural products

with pronounced pharmacological activities [1, 2]. In fact, different studies have reported their anti-infective [3,

4], anti-inflammatory [5] and mainly cytotoxic activity [6-8]. Other marine compounds have already been

approved for the treatment of cancer in clinic, such as Brentuximab vedotin (Adcetris®). In this project we intend

to exploit this huge metabolic potential of cyanobacteria using different strains from the LEGE culture collection

available in CIIMAR. Initially, the compounds will be isolated by LC-MS-guided isolation, combining different

chromatographic techniques, such as Flash Chromatography and Preparative HPLC. Subsequently the structure of

the pure compounds will be elucidated using different analytical techniques (e.g., MS/MS, NMR, IR). Then, these

new and pure NPs will be subjected to different screening assays to evaluate their bioactivity. Finally, preliminary

studies of the mechanism of action of the most promising compounds will be done using techniques, such as flow

cytometry, fluorescence microscopy and western blotting.


The main goal of this project is to obtain new cyanobacterial natural products and test their anticancer activity.

More specifically, the objectives are the isolation and elucidation of secondary metabolites from cyanobacteria

and subsequent screening against different cancer cell lines and study of their mechanism of action

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Natural Sciences


• Culturing of cyanobacteria;

• Mass spectrometry;

• Chromatographic methods (e.g., Flash Chromatography and HPLC);

• Spectroscopy (e.g., NMR, IR);

• Techniques of cancer cell culture;

• Flow cytometry;

• Fluorescence microscopy;

• Western blotting.


[1] R.K. Singh, S. Prakash Tiwari, A.K. Rai, T.M. Mohapatra, J. Antibiot. 64 (2011) 401–412.

[2] J.K. Nunnery, E. Mevers, W.H. Gerwick, Curr. Opin. Biotechnol. 21 (2010) 787–793.

[3] T.L. Simmons, N. Engene, L.D. Ureña, L.I. Romero, E. Ortega-Barría, L. Gerwick, W.H. Gerwick, Viridamides A and B, J. Nat. Prod. 71 (2008) 1544–1550.

[4] R.G. Linington, B.R. Clark, E.E. Trimble, A. Almanza, L.-D. Ureña, D.E. Kyle, W.H. Gerwick, J. Nat. Prod. 72 (2009) 14–7.

[5] F.A. Villa, K. Lieske, L. Gerwick, Eur. J. Pharmacol. 629 (2010) 140–6.

[6] W. Wrasidlo, A. Mielgo, V.A. Torres, S. Barbero, K. Stoletov, T.L. Suyama, R.L. Klemke, W.H. Gerwick, D.A. Carson, D.G. Stupack, Proc. Natl. Acad. Sci. 105 (2008) 2313–8.

[7] K. Taori, V.J. Paul, H. Luesch, J. Am. Chem. Soc. 130 (2008) 1806–7.

[8] J.S. Mynderse, R.E. Moore, M. Kashiwagi, T.R. Norton, Science. 196 (1977) 538–40.



PROPOSTA DE PROJETO DE MESTRADO 2019 – 2020

ORIENTADOR(A)/SUPERVISOR: Guilherme Scotta Hentschke

GRUPO/GROUP: Blue Biotechnology and Ecotoxicology ‐ BBE

CO‐ORIENTADOR(A)/CO‐SUPERVISOR: Vitor M. O. Vasconcelos

GRUPO/GROUP: Blue Biotechnology and Ecotoxicology ‐ BBE

LOCAL DE REALIZAÇÃO DO TRABALHO/PLACE OF WORK: Centro Interdisciplinar de Investigação Marinha

e Ambiental ‐ CIIMAR

TEMA/THEME: Biodiversidade e Potencial Biotecnológico de Cianobactérias da região el Jadida, em Marrocos.

RESUMO:


Objetivo Geral: Conhecer a diversidade de cianobactérias terrestres, marinhas e de água doce da região de El

Jadida em Marrocos.

Objetivos Específicos: 1) isolar estirpes a partir das populações encontradas, 2) identificar taxonomicamente as

populações encontradas na natureza, bem como as estirpes isoladas através de técnicas de NGS; 3) descrever

novos géneros e espécies de cianobactérias, 4) avaliar o potencial biotecnológico das estirpes isoladas.

RESUMO/SUMMARY

INTRODUÇÃO: A grande diferenciação dos habitats e a diversidade ecológica tropical e subtropical levaram

à uma maior taxa de especiação nessas áreas. Para as cianobactérias, muitas espécies ainda devem ser

descritas para essas regiões, especialmente em locais pouco estudados. Neste contexto, Marrocos

representa uma fonte com excelente potencial para descoberta de novos taxons de cianobactérias com

interesse biotecnológico. OBJETIVOS: Conhecer a diversidade de cianobactérias marinhas, terrestres e de água

doce da região de El Jadida, em Marrocos. METODOLOGIA: O projeto será desenvolvido no CIIMAR, no âmbito

dos projetos EBB e EMERTOX. Para identificação de géneros e espécies, será utilizada abordagem polifásica, com

estudos morfológicos (população da natureza e estirpes isoladas) e moleculares (16S rDNA e 16S‐23S ITS). As

análises de potencial biotecnológico serão realizadas através de análise de genes responsáveis pela produção de

metabolitos secundários, incluindo toxinas.

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Biotecnologia

PRINCIPAIS METODOLOGIAS/MAIN METHODOLOGIES: Todo o projeto será desenvolvido no CIIMAR, no âmbito

dos projetos EBB e EMERTOX.

1) Coleta de material: As coletas serão realizadas em julho de 2019, em ambientes terrestres, marinhos e

água doce na região de El Jadida em Marrocos. A solicitação para autorização de colheitas já foi enviada às

autoridades competentes do país através do projeto EMERTOX de modo a cumprir o protocolo de

Nagoya.

2) Isolamento de estirpes: As estirpes serão isoladas utilizando‐se meios de cultivo BG‐11 (Ripka et al. 1979)

e Z8 (Kotai, 1972), sólidos e líquidos, em câmara de fluxo laminar, e mantidas sob condições controladas

(Ramos et al. 2018).

3) Estudo da biodiversidade: As espécies serão identificadas através de análises morfológicas, da filogenia

do 16S rDNA e das estruturas secundárias da região 16S‐23S rDNA ITS (Hentschke et al. 2016) bem como

através estudos de metagenómica (Ramos et al., 2017).

a. Análises morfológicas: As populações da natureza e as estirpes isoladas serão analisadas sob

microscópio óptico, fotografadas e medidas com auxílio de software especializado.

b. Análises filogenéticas: As regiões 16S rDNA e 16S‐23S rDNA ITS serão amplificadas e sequenciadas

como descrito em (Hentschke et. al. 2016). Para identificação em nível genérico, as sequências de

16S rDNA serão alinhadas com sequências autênticas obtidas no GenBank e analisadas

filogeneticamente através dos métodos de máxima verossimilhança e inferência Bayesiana.

c. Análise de estruturas secundárias do 16S‐23S rDNA: as helices d1‐d1’, Box B, V2 e V3 serão

construídas com a ferramenta Mfold (Zucker, 2003) e utilizadas para identificação em nível

específico.

d. Estudos de metagenómica de cianobactérias (Ramos et al., 2017)

4) Avaliação do potencial biotecnológico: será feita a busca por genes codificadores de metabolitos de

interesse biotecnológico (Martins e Vasconcelos, 2015), e toxinas (Moreira et al., 2014).


Hentschke et al. 2016. Phylogenetic placement of Dapisostemon gen. nov. and Streptostemon, two tropical heterocytous genera (Cyanobacteria). Phytotaxa 245 (2): 129–143. Kótai, J. 1972. Instructions for Preparation of Modified Nutrient Solution Z8 for Algae,Blindern B–11/69 Martins, J., Vasconcelos, V., 2015. Cyanobactins from cyanobacteria: genetic and chemical current state of knowledge. Marine Drugs 13: 6910‐6946 Moreira C., et al. 2014. Methods to detect cyanobacteria and their toxins in the environment. Applied Microbiology and Biotechnology. 98:8073‐8082 Ramos et al. 2018. Cyanobacterial diversity held in microbial biological resource centers as a biotechnological asset: the case study of the newly established LEGE culture collection. J. of Appl. Phycol. 30: 1437–1451. Ramos et al., 2017. Cyanobacterial diversity in microbial mats from the hypersaline lagoon system of Araruama, Brazil: an in‐depth polyphasic study. Frontiers in Microbiology. 8:1233 Ripka, R., et al. 1979. Generic Assignements. Strain Histories and Properties of Pure Cultures of Cyanobacteria. Journal of General Microbiology 11: 1‐61. Zucker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research 31: 3406–3415.




ORIENTADOR(A)/SUPERVISOR: Cristina Calheiros GRUPO/GROUP: EcoBiotec

CO‐ORIENTADOR(A)/CO‐SUPERVISOR: Ana Paula Mucha / Marisa Almeida

GRUPO/GROUP: EcoBiotec

LOCAL DE REALIZAÇÃO DO TRABALHO/PLACE OF WORK: Centro Interdisciplinar de Investigação Marinha

e Ambiental. Terminal de Cruzeiros de Leixões, 4450‐208 Matosinhos

TEMA/THEME: Floating wetland islands as ecotechnology to promote ecosystems establishment

RESUMO:

RESUMO/SUMMARY According to the United Nations World Water Development Report (WWAP, 2015), the sustainable water management is a key issue to follow a green growth pathway and establish a green economy. Besides that, “Upscaling NBS (Nature Based Solutions) will be central to achieving the 2030 Agenda for Sustainable Development” (WWAP,2018). When considering specific water bodies that are subject to certain types of contamination or pressures, like some rivers, ponds, boat marinas and aquaculture production sites, the water quality assessment and mitigation plan pose a major strategic action. Floating wetlands islands (FWI) are an innovative variant of the traditional constructed wetlands, being a man‐made ecosystem intending to mimic the depurative processes that naturally occur in wetlands. Innovative work has been carried out at CIIMAR in relation to the establishment of FWI in a port marina context, using cork platforms vegetated with different plant species. Although the FWI technology is potentially robust, the biological and physicochemical processes underlying their operation are not completely understood nor have been the subject of detailed research.


The present project aims assess the application of Nature Based Solutions, such floating wetland islands‐FWI to promote water quality enhancement and ecosystem restoration in aquatic environments, such port marina, acting as a mitigation tool on degraded and threatened sites, supporting its societal and economical applicability. This technology integrates a multidisciplinary knowledge in terms of their design where FWI are set to sustain vegetation and other forms of life taking advantage of the root system developed in order to promote water quality improvement and ecosystem rehabilitation.


Environmental Biotechnology


Field and laboratory work will be carried out by the student.

It will be given the opportunity to learn techniques related to water quality characterization. The biocenosis of

organisms associated with the FWI will be carried out by magnifying glass and optical microscopy. Mapping of the

biotic communities associated to FWI is intended to be assessed to understand their dynamics through molecular

biology tools.


Natalia Pavlineri, Nikolaos Th. Skoulikidis, Vassilios A. Tsihrintzis.Constructed Floating Wetlands: A review of research, design, operation and management aspects, and data meta‐analysis. Chemical Engineering Journal 308 (2017) 1120–1132 (WWAP, 2015) WWAP (United Nations World Water Assessment Programme). 2015. The United Nations World Water Development Report 2015: Water for a Sustainable World. Paris, UNESCO. (WWAP, 2018) WWAP (United Nations World Water Assessment Programme). 2018. The United Nations World Water Development Report 2018: Nature‐based solutions for water. Paris, UNESCO.




ORIENTADOR(A)/SUPERVISOR: Leandro Sampaio

GRUPO: Coastal Biodiversity

CO‐ORIENTADOR(A/CO‐SUPERVISOR): Puri Veiga Sánchez

GRUPO: Coastal Biodiversity

LOCAL DE REALIZAÇÃO DO TRABALHO/PLACE OF WORK: LBC (CIIMAR) and Lab 2.54 (Biology Department


TEMA/Theme: Recolonisation and succession of defaunated mussel beds on rock substrate with dissimilar slopes.

RESUMO/SUMMARY Organisms living in the marine rocky intertidal zone often compete for space and bare substrate provides a

huge opportunity to expand their domains. Multiple physical and biological factors affect the migration, settlement and recruitment of species and consequently the recovery of a new area (1).

For sessile species, access to suitable substrate is a crucial factor, because once established, they can no longer change their position and, therefore, cannot evade predation and competition. Therefore, the composition of early sessile colonisers can determine the successional pathways of the assemblage. Differently, mobile species actively move among habitat areas, resulting in rapid colonisation of recently vacant substrate (2).

Most successional models distinguish between early‐colonising species, with characteristics like abundant offspring and high growth rates, and late colonizing species, with characteristics like strong competitive abilities and slow grow rates (3, 4). But the successional patterns ultimately depend on how early settlers interact and affect positively (by facilitation) or negatively (by inhibition) the later settlers (5).

Mussel beds are biogenic habitats recognised as biodiversity hotspots, which sometimes experience significant losses due to a variety of factors, including anthropogenic pressure. However, the colonisation process within complex biogenic habitats is unclear, and successional patterns still need to be properly documented (6), particularly taking into account the role that substrate slope plays in the colonization effort.

ÁREA CIENTÍFICA/SCIENTIFIC AREA: Ecology, Zoology, Marine Biology.



i) To study the effect of rock slope and free substrate availability on sessile and mobile fauna

recolonisation of a vacant area.

ii) Investigate the macrofaunal successional patterns in rocky intertidal complex biogenic habitats.

iii) Compare results to known successional models characterizing rocky intertidal zones.


The study will be conducted at rocky shores with high mussel cover and 20x20cm quadrats will be defaunated at

low or mid intertidal levels. 10x10 cm plots inside defaunated areas will be collected at specific times: 7, 15, 30 and

90 days, plus rock slope will be registered to measure its role in the colonization effort. Samples will be brought to

the laboratory to be sorted and identified to the lowest taxonomic level. Composition and specific diversity will be

measured and analysis of data will be done through multivariate and univariate analysis of variance. This proposal

allow us to obtain a model of the successional patterns derived from the recolonisation of a defaunated small scale

area at the core of complex biogenic habitats that harbor many marine invertebrate species seeking refuge from

predation, shelter from hydrodynamism or nursery areas for growth.


1. Curelovich, J.N., Lovrich, G.A., Cueto, G.R., Calcagno, J.A. 2018. Recruitment and zonation in a sub‐Antarctic rocky intertidal community. Journal of the Marine Biological Association of the United Kingdom, 98 (2): 411‐422. https://dx.doi.org/10.1017/S0025315416001284

2. Valdivia, N., Buschbaum, C., Thiel, M. 2014. Succession in intertidal mussel bed assemblages on different shores: Species mobility matters. Marine Ecology Progress Series, 497: 131‐142. https://dx.doi.org/10.3354/meps10593.

3. Connell, J.H., Slatyer, R.O. 1977. Mechanisms of succession in natural communities and their role in community stability and organization. The American Naturalist, 111: 1119−1144. https://doi.org/10.1086/283241.

4. Sampaio, L. 2001. Processo sucessional de recolonização dos fundos dragados da Ria de Aveiro após o desassoreamento: comunidades macrobentónicas. Dissertação de Mestrado. Universidade de Aveiro. 87 p + Anexos.

5. Jones, C.G., Lawton, J.H., Shachak, M. 1994. Organisms as ecosystem engineers. Oikos, 69: 373−386.

https://dx.doi.org/10.2307/3545850

6. Underwood, A.J., Chapman, M.G. 2006. Early development of subtidal macrofaunal assemblages: Relationships to period and timing of colonization. Journal of Experimental Marine Biology and Ecology, 330 (1): 221‐233. https://doi.org/10.1016/j.jembe.2005.12.029.

Documents

BLUE YOUNG TALENT PLUS ‐ BYTplusbyt.ciimar.up.pt/wp-content/uploads/2019/03/BYT... · ambientes e taxas de impacto e riscos de especiação e extinção. No entanto, além de algumas