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«13 Porto, Portugal 1 2 Index Programme Invited lectures Oral communications Posters List of participants 3 4 ProgramME 5 6 PROGRAMME | 4 JUNE 9:00 ...»

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2

XXXVIII

Jornadas

portuguesas de

Genetica

4-5 June 2013

Porto, Portugal

1

2

Index

Programme

Invited lectures

Oral communications

Posters

List of participants

3

4

ProgramME

5

6

PROGRAMME | 4 JUNE

9:00 – 9:30 - Registration

9:30 – 9:45 – Welcome session

9:45 – 10:45 - INVITED LECTURE IN CELL GENETICS

Statistical proteomes: can they shake current concepts of the gene?

Manuel Santos, CESAM, Universidade de Aveiro Cell Genetics 10:45-11:00 – An evolutionary perspective on metazoan NAD salvage pathways Raquel M. Silva 11:00-11:15 – Screening for novel germline genes using Drosophila melanogaster Paulo Navarro-Costa 11:15-11:45 – Coffee Break and Poster Session 11:45 – 12:00 - Genome mistranslation induces proteome aggregation and oxidative stress in zebrafish embryos Marisa Reverendo 12:00 – 12:15 - Epigenetic regulation of Mammalian Replication Origins Sofia Madeira 12:15 – 12:30 - Temporal dynamics of Erk and Gli3 Signaling Pathways evidence parallelisms in SHH morphogen interpretation in multiple tissues of the chick embryo Hugo Marcelino 12:30 – 14:00 – Lunch 14:00 – 15:00 - INVITED LECTURE IN EVOLUTION, GENOMICS AND POPULATION GENETICS Strategies to uncover the drought tolerance mechanism of the biodiesel plant Jatropha curcas (purging nut) Margarida Oliveira, ITQB, Universidade Nova de Lisboa Evolution, Genomics and Population Genetics 15:00 – 15:15 - Evolutionary conservation of the eumetazoan gene regulatory landscape André F. Rendeiro 15:15 – 15:30 - The genetic basis of Drosophila adaptation to viral infection with DCV Élio Sucena 7 15:30 – 15:45 - Elusive functional impact of adaptive mitochondrial protein evolution in a lineage of arctic hares (genus Lepus) assessed from comparative mitogenomic analyses Joana Vilela 15:45 – 16:45 - Coffee Break and Poster Session 16:45 – 17:00 - The genetic structure and admixture of the NE Portuguese communities of Jewish origin: news from the autosomal markers Célia Neto 17:00 – 17:15 - Population Structure of the African Sahel inferred from Genome-Wide SNP Screening Petr Triska 17:15 – 18:30 – Poster session PROGRAMME | 5 JUNE 9:30 – 10:30 - INVITED LECTURE IN CONSERVATION GENETICS Conservação e melhoramento dos recursos genéticos na era da genómica Albano Beja Pereira, CIBIO Conservation Genetics

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11:00-11:15 – Chloroplast genome variability in marginal grapevine (Vitis vinifera L.) cultivars from Vinhos Verdes DOC Region Isaura Castro 11:15-11:45 – Coffee Break and Poster Session 11:45 – 12:00 - Cytogenetic characterization of hybrids wheat containing the system msH1 Luis Rocha

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12:15 – 14:00 – Lunch 14:00 – 15:00 - INVITED LECTURE IN GENETIC DISORDERS AND HEALTH Clearance of extracellular misfolded proteins in systemic amyloidosis: experience with transthyretin Maria João Saraiva, IBMC, Universidade do Porto Genetic Disorders and Health 15:00 – 15:15 - A C. elegans mutant of an intellectual disability-associated gene shows behavioral deficits and GABAergic/cholinergic circuit abnormalities Carlos Bessa

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16:30 – 16:45 - Exome-Sequencing in familial thyroid carcinoma: genetic and functional characterization Catarina Salgado 16:45 – 17:00 – Closing Remarks

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RNA Biology Laboratory, Department of Biology, University of Aveiro, 3810-193 Aveiro The concept of statistical proteins was proposed in 1965 by Carl Woese in his theory of the origin of the genetic code and the translational machinery (Woese, 1965). Woese defined statistical proteins as mixtures of polypeptides whose primary structures are related to some theoretical average primary structure. In extant organisms they are synthesized through low level mistranslations of mRNA arising from tRNA misacylation, ribosome misreading, RNA editing and RNA modification. Canonical gene translation produces homogeneous mixtures of polyptpetides, but statistical proteins are heterogeneous arrays of polypetides whose cellular functions may also be heterogeneous, complicating the already complex relationship between genes and phenotypes. We have discovered that the main human fungal pathogen Candida albicans has a statistical proteome (Gomes et al, 2007). Its genome encodes 6202 protein genes - a similar number of genes to other fungi -, but ambiguous gene translation by the ribosome results in millions of different proteins that are not degraded by the C. albicans protein quality control machinery. In this fungus, there is no correlation between gene number and protein number despite the lack of alternative splicing. I will illustrate in my talk that statistical proteins are produced through global re-programming of the genetic code and have specific functions. They increase dramatically phenotypic and genetic diversity, expand adaptation capacity in changing ecological landscapes and influence virulence, biofilm formation and drug resistance. That is, statistical proteins allow C. albicans to produce phenotypic diversity in the absence of alternative splicing and without increasing gene number.

References: Woese C. R. (1965). On the evolution of the genetic code. PNAS, 54, 1546-1552.





Gomes A.C., Miranda I., Silva R.M., Moura G.R., Thomas B., Akoulitchev A. and Santos M.A. (2007) A genetic code alteration generates a proteome of high diversity in the human pathogen Candida albicans.

Genome Biology, 8, pp. R206.

Acknowledgments: This work was supported by FCT/FEDER project PTDC/BIA-MIC/099826/2008 and the EU FP7 Sybaris consortium.

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1 Genomics of Plant Stress lab, ITQB-UNL, Av. República, 2780-157 Oeiras, Portugal; 2IBET, Quinta do Marquês, 2784-505, Oeiras, Portugal; 3Plant Molecular Ecophysiology lab, ITQB-UNL, Av. República, 2780-157 Oeiras, Portugal;4 Functional Genomics Lab, Fraunhofer IGB, Nobelstr. 12, 70569, Stuttgart, Germany; 5 University of Stuttgart IGVT, Noberstr. 12, 70569, Stuttgart, Germany Jatropha curcas is an emerging source of biodiesel due to the high quality oil content of its seeds. Historically, these plants have been spread around the world by the Portuguese during the discoveries period. Jatropha curcas plants are very resilient to low water availability and are amenable for cultivation in areas with poor soil quality. Because the molecular mechanisms of drought stress response of J. curcas are still poorly described, we started our studies by comparing the behaviour of two accessions adapted to two contrasting climates (semi-arid and wet tropical). Seedlings of these plants were submitted to drought stress by water withhold in laboratory conditions (49 days), followed by recovery (1 week), and were evaluated for several morphological and physiological parameters[1]. In parallel, samples were collected for RNA isolation and 22 cDNA libraries were constructed and sequenced using Next Generation Sequencing (NGS) technology.

Sequences were annotated to the publicly available Jatropha genome database (http://www.kazusa.or.jp/jatropha/) and expression values were normalized using the reads/Kb/Million (RPKM) method. Seedlings of both accessions behaved similarly at morpho-physiological level, both under stress and control conditions. However, differences were clear when comparing control conditions versus drought in maximum stress.

Hierarchical clustering analysis of the transcriptomic data allowed forming 3 major clades, encompassing leaf samples, root samples and a third group joining root and leaf samples under maximum stress (day 49). For day 49 we found approximately 2000 genes in roots and 2000 in leaves that are responsive to drought. These genes have been described as involved in known pathways of stress response. We have been conducting RT-qPCR for specific genes, and further confirming the RNAseq data. Moreover, we found a very high drought stress recovery capacity, with the plants showing full recovery after only 3 days of re-watering, in terms of growth, physiology and transcriptomic data. We also found interesting changes at the photosynthetic metabolism, with decrease in the chlorophyll a/b ratio under severe stress, supported by the transcriptomic and RT-qPCR data. At present, we are further characterizing the drought responsive system of J. curcas by analysing changes at the hormonal level. The most recent data will be presented.

Acknowledgments: Quinvita for providing the seeds and Funding by FCT (PTDC/AGR-GPL/ 101435/2008).

[1] Sapeta H, Costa JM, Lourenço T, Maroco J, van der Linde P, Oliveira MM. (2013) - Environm. Exp. Bot.

85: 76-84.

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CIBIO Na ultima década o desenvolvimento tecnológico permitiu desenvolver novas técnicas de sequenciação baixando dramaticamente os custos de sequenciação de DNA. A sequenciação total do genoma de cada vez mais espécies domésticas é uma realidade que possibilita uma maior e melhor visão da variabilidade molecular destas. Nos últimos dois anos têm surgido no mercado SNPchips que permitem genotipar dezenas de milhares de mutações distribuídas ao longo do genoma. Porém, na sua maioria, estes chips testam SNPs cuja frequência alélica na maior das populações ainda não foi calculada, aumentando o risco de enviasamento na extrapolação entre populações. Nesta palestra irei demonstrar como em alternativa a re-sequenciação de alguns genes candidatos pode revelar-se uma alternativa viavel. Mais ainda, darei exemplos practicos de como a resequenciação tem ajudado a descobrir novas mutações que alteram a estruturas de proteínas importantes. Finalmente, darei exemplos acerca dos perigos e vantagens do uso de SNPchips e darei exemplos de como detectar genes/alelos que podem estar sobre selecção.

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Instituto de Biologia Molecular e Celular – IBMC; Instituto de Ciências Biomédicas Abel Salazar – ICBAS Universidade do Porto Increasing evidence indicates that accumulation of misfolded proteins in the form of oligomers, protofibrils or amyloid fibrils, and their consequences in triggering intracellular signaling cascades with toxic consequences represent unifying events in many of slowly progressive neurodegenerative disorders. Studies with small compounds or molecules, known to recognize and disrupt amyloidogenic structures, have proven efficient in promoting clearance of protein aggregates in experimental models of systemic and localized forms of amyloidoses. Doxycycline and EGCG were efficient in removing aggregates in pre-clinical studies in a transgenic mouse model for transthyretin (TTR) systemic amyloidosis and represent an opportunity to address mechanisms and key players in deposit removal. Extracellular chaperones, such as clusterin and metalloproteinases play an important role in this process.

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An evolutionary perspective on metazoan NAD salvage pathways João Carneiro1,2, Sara Duarte-Pereira1, Luísa Azevedo1,2, L. Filipe C. Castro3, Paulo Aguiar4, Irina S. Moreira5, António Amorim1,2 and Raquel M. Silva1 1 IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto; 2Faculty of Sciences of the University of Porto; 3Interdisciplinary Centre for Marine and Environmental Research (CIIMAR), CIMAR Associate Laboratory, University of Porto; 4CMUP - Centro de Matemática da Universidade do Porto; 5REQUIMTE - Rede de Química e Tecnologia, Faculty of Sciences, University of Porto Nicotinamide Adenine Dinucleotide (NAD) is a cofactor in redox reactions and a substrate for NAD-consuming enzymes, such as PARPs and sirtuins. The maintenance of NAD levels is crucial, thus, organisms use distinct pathways for NAD production and salvage depending on alternative precursors.

NAD salvage enzymes have gained increased attention due to their roles in aging, infection and disease and, more recently, as therapeutic targets in cancer [1]. Nicotinamide phosphoribosyltransferase (NAMPT) and Nicotinamidase (PNC) are the functional homologues in different NAD salvage pathways and, until now, NAMPT was thought to be restricted to vertebrates and both NAMPT and PNC homologues had not been found in the same lineages.

By combining molecular and structural biology with comparative and evolutionary approaches, we provide, for the first time, experimental evidence that both enzymes are expressed simultaneously in invertebrate species, identify active site residues of invertebrate enzymes and emphasize sequence and structural conservation patterns in metazoan NAMPTs and PNCs. The results indicate that both NAMPTs and PNCs can be concurrently functional in the same species, which indicates that these enzymes are not redundant after all [2].

[1] Chiarugi A, et al. The NAD metabolome - a key determinant of cancer cell biology. Nat Rev Cancer, 12:741-52 (2012).

[2] Carneiro J, et al. The Evolutionary Portrait of Metazoan NAD Salvage. PLoS ONE. Accepted (2013).

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Introduction: Sexual reproduction, the main Eukaryotic reproductive strategy, requires a germline – the immortal cell lineage responsible for gamete production. We hypothesize that Eukaryotes rely on a conserved core set of (epi)genetic determinants for segregation and development of the germline.

Objective: To identify and characterize novel evolutionarily-conserved germline genes.

Methods: We selected 52 novel genes as potentially important for germline development.

These genes were selected based on two different strategies: group A (n=34) on a transcriptomics-based approach for conserved genes enriched in male germline cells of 3 divergent Eukaryote species (Homo sapiens, Drosophila melanogaster and Arabidopsis thaliana); group B (n=18) on a data mining strategy of publically available data sets as to identify germline genes previously associated with human reproductive disorders. A Drosophila in vivo RNA interference (RNAi) assay was used to functionally analyze the selected 52 genes in order to identify those associated with germline defects.



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