Gel-based proteomics is a powerful approach to study the physiology of Staphylococcus aureus under various growth restricting conditions. We analyzed 679 protein spots from a reference 2-dimensional gel of cytosolic proteins of S. aureus COL by mass spectrometry resulting in 521 different proteins. 4,692 time dependent protein synthesis profiles were generated by exposing S. aureus to nine infection-related stress and starvation stimuli (H2O2, diamide, paraquat, NO, fermentation, nitrate respiration, heat shock, puromycin, mupirocin). These expression profiles are stored in an online resource called Aureolib (http://www.aureolib.de). Moreover, information on target genes of 75 regulators and regulatory elements were included in the database. Cross-comparisons of this extensive data collection of protein synthesis profiles using the tools implemented in Aureolib lead to the identification of stress and starvation specific marker proteins. Altogether, 226 protein synthesis profiles showed induction ratios of 2.5-fold or higher under at least one of the tested conditions with 157 protein synthesis profiles specifically induced in response to a single stimulus. The respective proteins might serve as marker proteins for the corresponding stimulus. By contrast, proteins whose synthesis was increased or repressed in response to more than four stimuli are rather exceptional. The only protein that was induced by six stimuli is the universal stress protein SACOL1759. Most strikingly, cluster analyses of synthesis profiles of proteins differentially synthesized under at least one condition revealed only in rare cases a grouping that correlated with known regulon structures. The most prominent examples are the GapR, Rex, and CtsR regulon. In contrast, protein synthesis profiles of proteins belonging to the CodY and σB regulon are widely distributed. In summary, Aureolib is by far the most comprehensive protein expression database for S. aureus and provides an essential tool to decipher more complex adaptation processes in S. aureus during host pathogen interaction.

Gene coding Insulin-like growth factor 2 (IGF2) is one of genes relating the growth of many fish species, including striped catfish. In this study, cDNA coding to protein IGF2 was isolated from total RNA extracted from liver tissue of catfish, then was amplified through reverse transcription PCR and standard PCR with IGF2 specific primer pair to generate the 642bp-in-size PCR product. The sequence of this cDNA-IGF2 is similar up to 95% to the cDNA-IGF2 gene sequence of catfish included in family Ictalurus. Based on that sequence, 3 primer pairs were designed to amplify 3 regions of IGF2 gene from genomic DNA extracted from fins of catfish, which have 900bp, 1500bp and 1200bp in length. That 3 regions were sequenced and assembled to give the final sequence with 3387bp in length of IGF2 gene, which includes 4 exons coding to IGF2 protein, and is similar up to 96% to sequence of mRNA coding to IGF2 protein of channel catfish Ictalurus punctatus and that of blue catfish Ictalurus furcatus. Determining the structure of IGF2 gene of striped catfish Pangasianodon hypophthalmus enable us to further examine its function and genetic variation.

Molecular biological research plays an important role in aquaculture, contributes to the improvement ofbroodstocks efficiently. Recently, with the development of next-generation sequencing (NGS) technology,genomic studies have been rapidly increased, in which data organisation and management hold a crucialposition. After obtaining NGS sequencing data of Vietnamese catfish (Pangasianodon hypophthalmus), wehave analysed and annotated the catfish genome, from which we have constructed a database for efficientusage. The database is built upon open source software following a three-layer model (interface, Web serviceand database) with a convenient interface through Web browsers. Users can look up sequence and annotationdata as well as visualize sequences through the Jbrowse genome browser. This database is important resourcefor functional genome and genetic improvement of the catfish.

Striped catfish (Pangasianodon hypophthalmus) is an economically important fish in Vietnam. The catfish fillets contain high fatty acid composition. The FABP family is involved in lipid transport and metabolism as well as in the regulation of gene expression and cell development. In this study, the catfish genome database was searched for fabp gene family; then, gene structure, classification and phylogenetic relationships were analyzed. In striped catfish genome, we found 10 fabp genes that are homologous to other fish species and other 5 novel fabp genes that have not been clearly annotated. These newly identified fabp genes cluster separately from the known members of the fabp family on the phylogenetic tree, and further studies are needed to understand their roles and functions. We examined transcriptional gene expression of fabp3, fabp7 and fabp10a genes in muscle, liver and brain tissues of the stripped catfish. The results showed that fabp10a gene was not strongly expressed in all 3 types of tissues; fabp3 gene was most strongly expressed in liver tissue and fabp7 was highly up-regulated in brain tissue. The results of this study provide a resource for further research on the function of fabp genes and their genetic diversity in striped catfish.