host began to downregulate the expression of the PTPs to antagonize the repression. Clearly, there is a need for further studies to elucidate the precise roles of the PTP family members in the TCR signaling pathway in fish. Conclusions Several recent studies have exploited novel high throughput deep sequencing technology as a new method to advance further understanding of the mechanism of fish defense against infection. We used the A. hydrophila infected large yellow croaker as a model to study the immune response of fish to bacter ial infection. Our analysis of the transcriptome and gene expression in A. hydrophila infected large yellow croa ker revealed changes in multiple signaling pathways involved in immunity in the large yellow croaker.

The multiple TLR mediated signaling cascades may be involved in early response to bacterial infection, causing the production of proinflammatory cytokines, chemo kines, and other cytokines, which may result in the inflammatory response and affect other signal pathways such as JAK STAT and MAPK. However, the TCR sig naling pathway, a pivotal process in cellular immunity, was suppressed in the early period of A. hydrophila infection. The immune related genes and signaling path ways involved in bacterial infection were identified and thereby provided valuable leads for further investigations into the immune response of fish. Methods Fish and infection experiments Large yellow croakers were pur chased from a mariculture farm in Lianjian, Fuzhou, China. The fish were maintained at 25 C in aerated water tanks with a flow through seawater supply.

After 7 days of acclimation, these fish were used for the infection experiments. Twenty fish Drug_discovery were injected intramuscularly with A. hydrophila at a dose of 1 �� 108 cfu 200 g of fish. The strain of A. hydrophila used in our manuscript was kindly provided by professor Xuan xian Peng. A second group of 20 fish was injected with sterilized 0. 9% NaCl at a dose of 0. 2 ml 200 g of fish as a control. The spleen tissues sampled at 12 h after infection with A. hydrophila were used for transcriptome analysis. The spleen tissues sampled at 24 h after injec tions with A. hydrophila or 0. 9% NaCl were used for gene expression profiling analysis. All experiments were conducted in Third Institute of Oceanography, SOA, China.

The protocols used meet the Regulations for the Administration of Affairs Concerning Experimental Animals established by the Fujian Provincial Depart ment of Science and Technology on the Use and Care of Animals. RNA isolation Total RNA was extracted from 50 to 100 mg of tissue with TRIZOL Reagent according to the manufacturers instructions. The RNA samples were incubated for 30 min at 37 C with 10 units of DNaseI to remove resi dual genomic DNA. The quality and quantity of the purified RNA were determined by measuring the absor bance at 260 nm 280 nm using a Nano drop ND 1000 spectrophotometer. The samples had an average RIN value of 8. 9 according to Labon chip an