Study of Perkinsus olseni infection mechanisms: identification and regulation of parasite genes differentially expressed in response to host and environmental stress

Tese dout., Biologia, Universidade do Algarve, 2008

Notable differences in gene expression between injured turbot (Scophthalmus maximus) and brill (Scophthalmus rhombus) skin

Dissertação de mestrado, Engenharia Biológica, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

mRNA-Seq and microarray development for the Grooved carpet shell clam, Ruditapes decussatus: a functional approach to unravel host -parasite interaction

Background The Grooved Carpet shell clam Ruditapes decussatus is the autochthonous European clam and the most appreciated from a gastronomic and economic point of view. The production is in decline due to several factors such as Perkinsiosis and habitat invasion and competition by the introduced exotic species, the manila clam Ruditapes philippinarum. After we sequenced R. decussatus transcriptome we have designed an oligo microarray capable of contributing to provide some clues on molecular response of the clam to Perkinsiosis. Results A database consisting of 41,119 unique transcripts was constructed, of which 12,479 (30.3%) were annotated by similarity. An oligo-DNA microarray platform was then designed and applied to profile gene expression in R. decussatus heavily infected by Perkinsus olseni. Functional annotation of differentially expressed genes between those two conditionswas performed by gene set enrichment analysis. As expected, microarrays unveil genes related with stress/infectious agents such as hydrolases, proteases and others. The extensive role of innate immune system was also analyzed and effect of parasitosis upon expression of important molecules such as lectins reviewed. Conclusions This study represents a first attempt to characterize Ruditapes decussatus transcriptome, an important marine resource for the European aquaculture. The trancriptome sequencing and consequent annotation will increase the available tools and resources for this specie, introducing the possibility of high throughput experiments such as microarrays analysis. In this specific case microarray approach was used to unveil some important aspects of host-parasite interaction between the Carpet shell clam and Perkinsus, two non-model species, highlighting some genes associated with this interaction. Ample information was obtained to identify biological processes significantly enriched among differentially expressed genes in Perkinsus infected versus non-infected gills. An overview on the genes related with the immune system on R. decussatus transcriptome is also reported.

Identification and study of novel genes expressed in the heart precursor cells

Understanding heart development on a molecular level is a requirement for uncovering the causes of congenital heart diseases. Several genes have been implicated as critical for heart development. However, the inducers of these genes as well as their targets and pathways, remain largely unknown. We have identified a promoter element of chick cCer able to drive EGFP expression in a population of cells that consistently exit from the anterior primitive streak region, from as early as stage HH3+, and that later will populate the heart. Using this promoter element as a tool allowed us to identify novel genes previously not known to potentially play a role in heart development. In order to identify and study genes expressed and involved in the correct development and differentiation of the vertebrate heart precursor cell (HPC) lineages, a differential screening using Affymetrix GeneChip® system technologies was performed. Remarkably, this screening led to the identification of more than 700 transcripts differentially expressed in the heart forming regions (HFR). Bioinformatic tools allowed us to filter the large amount of data generated from this approach and to select a few transcripts for in vivo validation. Five genes were selected for further characterization by whole mount in situ hybridization leading to the validation of their expression in the HPC. From those, Adtk1 and Ccbe1 were selected for functional analysis. Regarding to ccbe1, a more detailed WISH analysis was performed and showed that Ccbe1 is expressed specifically on the cardiac progenitors regions at HH4, more specifically in primary heart field and at later stages is present in the second heart field. Further functional analyses by knockdown and overexpression revealed an important role for Ccbe1 in early heart tube formation. Moreover, the results presented in this thesis suggested that Ccbe1 is a key gene during heart development and might be limited to multipotent and highly proliferative progenitors and downregulated upon cellular commitment into more specific cardiac phenotypes. Other of the genes identified, Adtk1 was also subjected to further functional studies. Knockdown of Adtk1 using morpholino oligonucleotides suggested that it might be necessary for the migration and fusion of the heart tube as well as for neural tube closure.

Chick heart/hemangioblast progenitor 12 (chep 12: study of a novel gene expressed in the heart/hemangioblast percursors cells

Dissertação de mest., Ciências Biomédicas, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2009

An integrated and comparative approach to genetic selection of the aquaculture species Dicentrarchus labrax

The European sea bass, Dicentrarchus labrax, is one of the most important marine species cultivated in Southern Europe and has not benefited from selective breeding. One of the major goals in the sea bass (D. labrax) aquaculture industry is to understand and control the complexity of growth associated traits. The aim of the methodology developed for the studies reported in the thesis was not only to establish genetic and genomic resources for sea bass, but to also develop a conceptual strategy to efficiently create knowledge in a research environment that can easily be transferred to the aquaculture industry. The strategy involved; i) establishing an annotated sea bass transcriptome and then using it to, ii) identify new genetic markers for target QTL regions so that, iii) new QTL analysis could be performed and marker based resolution of the DNA regions of interest increased, and then iv) to merge the linkage map and the physical map in order to map the QTL confidence intervals to the sea bass genome and identify genes underlying the targeted traits. Finally to test if genes in the QTL regions that are candidates for divergent growth phenotypes have modified patterns of transcription that reflects the modified whole organism physiology SuperSAGE-SOLiD4 gene expression was used with sea bass with high growth heterogeneity. The SuperSAGE contributed to significantly increase the transcriptome information for sea bass muscle, brain and liver and also led to the identification of putative candidate genes lying in the genomic region of growth related QTL. Lastly all differentially expressed transcripts in brain, liver and muscle of the European sea bass with divergent specific growth rates were mapped to gene pathways and networks and the regulatory pathways most affected identified and established the tissue specific changes underlying the divergent SGR. Owing to the importance of European sea bass to Mediterranean aquaculture and the developed genomics resources from the present thesis and from other studies it should be possible to implement genetic selection programs using marker assisted selection.

Molecular structure and functional analysis of runx3 in zebrafish

Tese de doutoramento, Ciências Biomédicas, Universidade do Algarve, Departamento de Ciências Biomédicas e Medicina, 2014

Identification of novel molecular determinants of tissue mineralization in fish

The identification of genes involved in signaling and regulatory pathways, and matrix formation is paramount to the better understanding of the complex mechanisms of bone formation and mineralization, and critical to the successful development of therapies for human skeletal disorders. To achieve this objective, in vitro cell systems derived from skeletal tissues and able to mineralize their extracellular matrix have been used to identify genes differentially expressed during mineralization and possibly new markers of bone and cartilage homeostasis. Using cell systems of fish origin and techniques such as suppression subtractive hybridization and microarray hybridization, three genes never associated with mechanisms of calcification were identified: the calcium binding protein S100-like, the short-chain dehydrogenase/reductase sdr-like and the betaine homocysteine S-methyltransferase bhmt3. Analysis of the spatial-temporal expression of these 3 genes by qPCR and in situ hybridization revealed: (1) the up-regulation of sdr-like transcript during in vitro mineralization of gilthead seabream cell lines and its specificity for calcified tissues and differentiating osteoblasts; (2) the up-regulation of S100-like and the down-regulation of bhmt3 during in vitro mineralization and the central role of both genes in cartilaginous tissues undergoing endo/perichondral mineralization in juvenile fish. While expression of S100-like and bhmt3 was restricted to calcified tissues, sdr-like transcript was also detected in soft tissues, in particular in tissues of the gastrointestinal tract. Functional analysis of gene promoters revealed the transcriptional regulation of the 3 genes by known regulators of osteoblast and chondrocyte differentiation/mineralization: RUNX2 and RAR (sdr-like), ETS1 (s100-like; bhmt3), SP1 and MEF2c (bhmt3). The evolutionary relationship of the different orthologs and paralogs identified within the scope of this work was also inferred from taxonomic and phylogenetic analyses and revealed novel protein subfamilies (S100-like and Sdr-like) and the explosive diversity of Bhmt family in particular fish groups (Neoteleostei). Altogether our results contribute with new data on SDR, S100 and BHMT proteins, evidencing for the first time the role for these three proteins in mechanisms of mineralization in fish and emphasized their potential as markers of mineralizing cartilage and bone in developing fish.

The transcriptome of metamorphosing flatfish

Background Flatfish metamorphosis denotes the extraordinary transformation of a symmetric pelagic larva into an asymmetric benthic juvenile. Metamorphosis in vertebrates is driven by thyroid hormones (THs), but how they orchestrate the cellular, morphological and functional modifications associated with maturation to juvenile/adult states in flatfish is an enigma. Since THs act via thyroid receptors that are ligand activated transcription factors, we hypothesized that the maturation of tissues during metamorphosis should be preceded by significant modifications in the transcriptome. Targeting the unique metamorphosis of flatfish and taking advantage of the large size of Atlantic halibut (Hippoglossus hippoglossus) larvae, we determined the molecular basis of TH action using RNA sequencing. Results De novo assembly of sequences for larval head, skin and gastrointestinal tract (GI-tract) yielded 90,676, 65,530 and 38,426 contigs, respectively. More than 57 % of the assembled sequences were successfully annotated using a multi-step Blast approach. A unique set of biological processes and candidate genes were identified specifically associated with changes in morphology and function of the head, skin and GI-tract. Transcriptome dynamics during metamorphosis were mapped with SOLiD sequencing of whole larvae and revealed greater than 8,000 differentially expressed (DE) genes significantly (p < 0.05) up- or down-regulated in comparison with the juvenile stage. Candidate transcripts quantified by SOLiD and qPCR analysis were significantly (r = 0.843; p < 0.05) correlated. The majority (98 %) of DE genes during metamorphosis were not TH-responsive. TH-responsive transcripts clustered into 6 groups based on their expression pattern during metamorphosis and the majority of the 145 DE TH-responsive genes were down-regulated. Conclusions A transcriptome resource has been generated for metamorphosing Atlantic halibut and over 8,000 DE transcripts per stage were identified. Unique sets of biological processes and candidate genes were associated with changes in the head, skin and GI-tract during metamorphosis. A small proportion of DE transcripts were TH-responsive, suggesting that they trigger gene networks, signalling cascades and transcription factors, leading to the overt changes in tissue occurring during metamorphosis.

Identification of novel molecular determinants of tissue mineralization in fish

Tese de doutoramento, Ciências Biomédicas, Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, 2015

Identificação de indicadores moleculares de bem-estar durante o cultivo de dourada (Sparus aurata, Linnaeus 1758), utilizando técnicas de proteómica

Dissertação de Mestrado, Biologia Marinha, Especialização em Biotecnologia Marinha, Faculdade de Ciências do Mar e do Ambiente, Universidade do Algarve, 2008

A proteomic study of the effects of nutrient restriction in utero on postnatal metabolism

It is widely recognized that protein restriction in utero may cause metabolic and endocrine adaptations, which may be of benefit to the neonate on a short-term basis but may cause adverse long-term conditions such as obesity, Type 2 diabetes, metabolic syndrome, hypertension and cardiovascular diseases. Adequate foetal and early post natal nutrient and energy supply is therefore essential for adult animal health, performance and life span. In this project it was investigated the progressive adaptations of the hepatic proteome in male mink offspring exposed to either a low protein (FL) or an adequate protein (FA) diet in utero fed either on a low protein (LP) or on an adequate (AP) diet from weaning until sexual maturity. Specifically, the aim was to determine the metabolic adaptations at selected phases of the animal’s first annual cycle and establish the metabolic priorities occurring during those phases. The three different morphological stages studied during the first year of development included, end of bone growth at 4 months of age, maximal fat accretion at 6 months of age and sexual maturity at 12 months of age. A reference proteome of mink liver coming from these different animal groups were generated using 2D electrophoresis coupled to MALDI-TOF analysis and the way in which dietary treatment affect their proteome was established. Approximately 330 proteins were detected in the mink liver proteome. A total of 27 comparisons were carried out between all different animal groups which resulted in 20 differentially expressed proteins. An extensive survey was conducted towards the characterization of these proteins including their subcellular localization, the biological processes in which they are involved and their molecular functions. This characterization allowed the identification of proteins in various processes including the glycolysis and fatty acid metabolism. The detailed analysis of the different dietary treatment animal groups was indicative of differences in metabolism and also to changes associated with development in mink.

MEF2C: expression, regulation and interaction with target genes in health and diseases

Tese de doutoramento, Ciências Biomédicas, Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, 2015

Análise e caracterização da expressão e papel funcional dos potenciais genes da família 2 GPCRs no protostómio Caenorhabditis elegans

Dissertação de Mestrado, Biotecnologia, Faculdade de Engenharia de Recursos Naturais, Universidade do Algarve, 2009

Study of the expression of different genes of long-chain polyunsaturated fatty acids (LC-PUFA) metabolism during the early paralarval development of the common octopus (Octopus vulgaris)

Dissertação de mestrado, Aquacultura e Pescas, Faculdade de Ciências e Tecnologias, Universidade do Algarve, 2015