Athanasios Exadactylos

Molecular cloning of four glutathione peroxidase (GPx) homologs and expression analysis during stress exposure of the marine teleost Sparus aurata.

Glutathione peroxidase (GPx; EC 1.11.1.9) is an important family of enzymes that protects organisms from oxidative damage. Four full-length GPx cDNAs were cloned and characterized by rapid amplification of cDNA ends polymerase chain reaction (RACE-PCR) from the liver of gilthead sea bream (Sparus aurata), an economically important species for Mediterranean aquaculture. Structural and functional annotations were performed for all paralogs, which suggested possible differences in function and subcellular localization. The phylogenetic analysis, based on the amino acid sequences, revealed four groups corresponding to teleostean GPx1a, GPx1b, GPx4a, and GPx4b and three groups for mammalian GPx1, GPx2 and GPx4. The tree topology indicated past duplication events for fish genes, unlike their mammalian homologs. Transcriptional analysis in ten tissues by reverse transcription quantitative polymerase chain reaction (RT-qPCR) evidenced a tissue-specific pattern for each GPx homolog. Fish experimental groups were exposed to stress factors such as fasting and confinement. Relative expression analysis in fish liver demonstrated that GPx1 genes were not regulated by dietary restriction; GPx4b was differentially expressed opposed to regularly fed fish. On the other hand, both GPx1 and GPx4 genes were up-regulated in fish post exposed to confinement, considered as a response to acute stress. The results underline the role of GPx genes as indicators of stress and welfare status in gilthead sea bream aquaculture.

DNA damage and differential gene expression associated with physical stress in gilthead seabream (Sparus aurata).

Fish stress may result in inhibition of reproduction, development and growth. Thus, appropriate indices should be developed to accurately define the physiological plasticity of fish, in terms of coping with stress. Sea bream individuals were subjected to physical stress (fasting and confinement). DNA fragmentation of liver cells was assessed, in addition to gene expression of selected genes and plasma cortisol levels determination. Stress response was characterized with significant temporal alterations. Increased DNA fragmentation was observed as an aftereffect of physical stress and consequently gene expression of tp53 was stimulated. The expression pattern of glucocorticoid receptor (nr3c1) was directly correlated with plasma cortisol. Furthermore, glucokinase (gk) gene expression was considerably upregulated under acute stress, depicting putative energetic demands. Finally, igf1 downregulation during stress, reflects the suppression of the GH/IGF axis and the substantial stress effects on growth. To conclude, most of the indices described in the present study could be synergistically used, in order to robustly quantify physical stress in marine teleosts.

Abiotic Stress of Seagrasses: Recent Advances in Transcriptomics, Genomics, and Systems Biology

Seagrasses are a unique taxonomic rank of Plantae, totally submerged to marine environment. They evolved from terrestrial plants so this progression provoked alterations in genome, providing adaptation abilities to aquatic environment. The development of high-throughput technologies, such as omics, bridges the gap between genome and phenotype, shedding some light on molecular mechanisms that regulate seagrass tolerance to abiotic stress.

Identification of the abiotic stress-related transcription in little Neptune grass Cymodocea nodosa with RNA-seq

Seagrasses exhibit vital ecological roles in the marine environment. Nevertheless, the genomic resources available for seagrasses are still scarce. In the present study, the transcriptome of Cymodocea nodosa was sequenced with a view to study the molecular mechanisms underlying abiotic stress responses. The sequenced transcriptome for the species was near-complete and a high percentage of the transcripts was computationally annotated. An experimental simulation of marine plant exposure to extreme temperature (34°C), salinity (50psu) and their combination was conducted. A dynamic transcriptome 24h response (short-term) from stress initialization was recorded. The most noteworthy alteration in gene expression was observed in heat-stressed plants. Transcripts associated with development, photosynthesis, osmotic balance and stress-response were differentially expressed, under the set experimental conditions. Results indicate a potential negative interaction of heat and osmotic stress on seagrasses transcriptome.

A computer algebra system approach in gene expression analysis

The primary purpose of this study is to provide an immediate connection to analytics of biological functions and visualisation. We introduce a visual framework in the environment of a main computer algebra system (CAS), Mathematica, to picture variations and evolution schemes in gene expression. Our computational approach constructs snapshots for gene expression profiles, with the advantage of being selfevident, concise and clear. A variety of colours is employed, beyond the conventional heat map colours. We provide dynamic options to facilitate comparisons among treatments, several colour choices to perform reference gene selection tests and, thus reveal the variation of gene expression through time and/or among treatments, or genes. The performance of the programming techniques in selected case studies concerning genes involved in embryonic development of common sole (Solea solea), is presented. This work could assist researchers in biosciences with suggestions to specific gene expression mapping.