Type I restriction-modification system and its resistance in electroporation efficiency in Flavobacterium columnare

Flavobacterium columnare, the causative agent of columnaris disease, infects freshwater fish worldwide. However, the pathogenicity of this bacterium is poorly understood due possibly to the lack of an efficient in-frame knockout technique. In order to improve electroporation efficiency, the type I restriction-modification system (R-M system) was cloned and its role in electroporation was examined in F. columnare G(4) strain. The complete sequence of type I R-M system in the bacterium, designated as Fcl, contains all three subunits of type I R-M system, named as fclM, fclS, fclR, respectively, with the identification of a hypothetical gene, fclX. Constitutive transcription of the three genes was observed in F. columnare G(4) by RT-PCR. The ORF of fclM and fclS was cloned into the plasmid pACYC184 and transformed into Escherichia coli TOP10. The resultant E. coli strain, designated as E. coli TOPmt, was transformed with the integrative plasmid pGL006 constructed for F. columnare G(4). The integrative plasmid was re-isolated from TOPmt and incubated with the lysate of F. columnare G(4). The re-isolated integrative plasmid, designated as pGL006', showed higher resistance than pGL006. With pGL006', the electroporation efficiency of the strain G(4) increased 2.6 times, while that of F. columnare G(18) was not obviously improved. Furthermore, a method to improve the electroporation efficiency of F. columnare G(4) was developed using the integrative plasmid methylated by E. coli TOPmt which contains the fclM and fclS gene of F. columnare G(4). Further analyses showed that the fcl gene cluster may be a unique type I R-M system in F. columnare G(4). It will be of significant interest to examine the composition and diversity of R-M systems in strains of F. columnare in order to set up a suitable genetic manipulation system for the bacterium.

Identification of immunogenic proteins of Flavobacterium columnare by two-dimensional electrophoresis immunoblotting with antibacterial sera from grass carp, Ctenopharyngodon idella (Valenciennes)

Flavobacterium columnare is a Gram-negative bacterium causing columnaris disease of freshwater fish worldwide, and development of efficacious vaccines has been a continuous challenge in aquaculture. In this study, 14 proteins were identified from cellular components of F. columnare using an immunoblotting approach in two-dimensional electrophoresis map gels with antibacterial sera from grass carp, Ctenopharyngodon idella (Valenciennes), and then anti-grass carp-recombinant Ig (rIg) polyclonal antibodies. These proteins were characterized conclusively by matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF/TOF MS). The 14 proteins are immunogenic molecules of F. columnare, including chaperonins DnaK, GroEL and trigger factor, and translation elongation factor G, translation elongation factor Tu, 30S ribosomal subunit protein S1, dihydrolipoamide succinyltransferase, succinyl-CoA synthetase, SpoOJ regulator protein, alcohol dehydrogenase, fructose-bisphosphate aldolase, 3-hydroxybutyryl-CoA dehydrogenase and two conserved hypothetical proteins. These identified immunogenic proteins may provide candidate molecules for the development of vaccines against columnaris disease.

Three goose-type lysozymes in the gastropod Oncomelania hupensis: cDNA sequences and lytic activity of recombinant proteins

Three goose-type (g-type) lysozymes, designated as OHLysG1, OHLysG2 and OHLysG3 were identified from expressed sequence tags (ESTs) of a gastropod Oncomelania hupensis, the intermediate host of Schistosoma japonicum. The full cDNA sequences of OHLysG1, OHLysG2 and OHLysG3 consisted of 735, 909 and 808 nucleotides, with an open reading frame of 198, 214 and 249 codons containing a 21, 7 and 8 amino acid (aa) signal peptide at the N-terminus, respectively. The three g-type lysozymes shared conserved features with other g-type lysozymes, such as the substrate binding sites, the catalytic residues critical for the fundamental structure and function of g-type lysozymes. It seems possible that g-type lysozymes in molluscs shared one conserved cysteine with those in birds and mammals, and six conserved cysteines were observed for mollusc g-type lysozymes, with two unique cysteines present in the g-type lysozymes of O. hupensis. The three lysozyme genes were expressed mainly in hepatopancreas, with relatively low expression level observed in head-foot muscle and intestine. When comparing S. japonicum-infected and uninfected snails, significant increase (P<0.05) was observed for all the three lysozymes in infected snails, with the highest increase detected in hepatopancreas, and lowest in intestine, implying their defensive role in the host-parasite, i.e. snail-trematode system. The three recombinant lysozymes expressed in Escherichia coli strain M15 showed lytic activity against Aeromonas hydrophila, Vibrio fluvialis, Aeromonas sobria and Micrococcus lysodeikticus. In conclusion, the finding of three g-type lysozymes in O. hupensis provides structural and functional evidence of multiple g-type lysozymes in gastropod, which may have evolutional implication in the snail-trematode system.

Establishment, characterization and viral susceptibility of a new cell line derived from goldfish, Carassius auratus (L.), tail fin

A continuous cell line [goldfish tail fin (GFTF)] derived from a goldfish tail fin, Carassius auratus, was established and characterized. GFTF cells predominantly consist of fibroblast-like cells that were maintained and subcultured more than 50 times over a period of 15 months. Cells grew at temperatures between 15 and 37°C, with an optimum temperature of 25°C. The growth rate of GFTF cells increased proportionally with the foetal bovine serum (FBS) concentration (5-20%), with optimum growth at 20% FBS. The chromosome numbers were 88-112, with a modal peak of 104 chromosomes. Five known fish viruses were tested to determine susceptibility. Results demonstrated that GFTF is susceptible to snakehead rhabdovirus, spring viraemia of carp virus and channel catfish virus (CCV). In addition, GFTF demonstrated a higher sensitivity to, and increased viral production of, CCV than that observed in the control cell line, channel catfish ovary cells. This suggests that GFTF cells would be useful as a diagnostic tool for viral diseases in this fish species, as well as for the isolation and study of goldfish viruses in the future. Furthermore, these cells were transfected with pEGFP-N1 vector DNA and some fluorescent signals were observed, suggesting that GFTF cells could be a useful tool for transgenic and genetic manipulation studies.

Characterization of two C-type lectin-like domain (CTLD)-containing proteins from the cDNA library of Chinese mitten crab Eriocheir sinensis

Chinese mitten crab Eriocheir sinensis is one of the most important aquaculture crustacean species in China. A cDNA library was constructed from mixed tissues of E. sinensis challenged with LPS. Eight genes involved in immune response were identified from 319 single colonies. Among them, two different C-type lectin-like domain (CTLD)-containing proteins were firstly identified in Chinese mitten crab. The full-length cDNA sequences of two C-type lectin-like domain (CTLD)-containing proteins named EsCTLDcp-1 and EsCTLDcp-2 were cloned by 5' RACE. The deduced amino acid sequences of EsCTLDcp-1 and EsCTLDcp-2 possessed several conserved features of C-type lectin subfamily. The tissue distribution of EsCTLDcp-1 and EsCTLDcp-2 was examined by Real-time PCR. In the normal Chinese mitten crab, the expression of EsCTLDcp-2 was detected in all tested tissues such as haemolymph, muscle, intestine, gill, heart, gonad and hepatopancreas, whereas in muscle, intestine, gill, heart and hepatopancreas for EsCTLDcp-1. The highest expressions of EsCTLDcp-1 and EsCTLDcp-2 were both observed in hepatopancreas. LPS significantly induced the expression of EsCTLDcp-1 and EsCTLDcp-2 in the hepatopancreas at the different time points. The induced fold change of EsCTLDcp-1 and EsCTLDcp-2 increased significantly from 2 h for EsCTLDcp-1 and 4 h for EsCTLDcp-2, and reached a maximum at 12 h, then dropped at 24 h. A differential pattern was found in Chinese mitten crab challenged with Chinese mitten crab pathogen Aeromonas hydrophila. The expression of EsCTLDcp-1 increased significantly at 2 h post-challenge crabs with A. hydrophila, then decreased at 4 h and 8 h, after that increased at 12 h and 24 h. The expression of EsCTLDcp-2 was decreased at the all time points. All these data suggest a differential role of EsCTLDcp-1 and EsCTLDcp-2 in the crab innate immune response to bacterial infection.

Ig heavy chain genes and their locus in grass carp Ctenopharyngodon idella

The cDNA and genomic sequences of IgD and IgZ were characterized in grass carp Ctenopharyngodon idella in the present study, and with the identification of a BAC clone covering zeta, mu, and delta genes, the IgH locus containing these Ig genes and other V, D, J genes was also illustrated in this fish. Secretory and membrane-bound IgZ were identified, with two transmembrane exons spliced within the CH4 exon, as reported in IgM of mammals and IgZ in other teleost fish. The first and second constant domains of IgZ shows more than 90% nucleotide identity with respective domains of grass carp IgM. The IgD has a structure of delta1-(delta2-delta3-delta4)(2)-delta5-delta6-delta7-TM-UTR, with the repeat of delta2-delta3-delta4; but intron was not found between the two repeat, i.e. between the first delta2-delta3-delta4 (delta2.1-delta3.1-delta4.1) and the second delta2-delta3-delta4 (delta2.2-delta3.2-delta4.2), and the intron between delta3.1 and delta4.1 was much shorter than the intron between delta3.2 and delta4.2. The genomic organization of the IgH locus has a pattern of Vn-Dn-Jn-Czeta-Dn-Jn-Cmu-Cdelta, as reported in other teleost fish. Thirteen V(H), fourteen D, and twelve J(H) genes were observed in this locus, with the similarity of three D segments and four J(H) segments being the same in the upstream of Czeta and Cmu. The transcriptional enhancer located at the mu-delta intergenic region was also analyzed and it seems possible that this enhancer is functional as verified in zebrafish and channel catfish.

Conservation and variation in mitochondrial genomes of gastropods Oncomelania hupensis and Tricula hortensis, intermediate host snails of Schistosoma in China

The complete mitochondrial genomes of intermediate host snails for Schistosoma in China were sequenced, including the sub-species Oncomelania hupensis hupensis in two types, and O. hupensis robertsoni, intermediate hosts for S. japonicum, and Tricula hortensis, the intermediate host of S. sinensium. Four genomes have completely the same gene order as in other caenogastropods, containing 13 protein-coding genes and 22 transfer RNAs. The gene size, start codon and termination codon are mostly the same for all protein-coding genes. However, pairwise sequence alignments revealed quite different degrees of variation. The ribbed-shelled O. hupensis hupensis and the smooth-shelled but with varix O. hupensis hupensis had a lower level of genetic distance (3.1% for protein-coding genes), but the coden usages differed obviously in the mitochondrial genomes of these two types of snails, implying that their genetic difference may be larger than previously recognized. The mean genetic distance between O. hupensis hupensis and O. hupensis robertsoni was 12% for protein-coding genes, indicating a higher degree of genetic difference. In consideration of the difference in morphology and distribution, we considered that O. hupensis hupensis and O. hupensis robertsoni can be considered as separate species. The ribbed-shelled O. hupensishupensis and smooth-shelled O. hupensis robertsoni were phylogenetically clustered together within a same clade, which was then clustered with T. hortensis, confirming their close relationship. However, species or sub-species in the Oncomelania from southeastern Asian countries should be included in future study in order to resolve the phylogenetic relationship and origination of all snails in the genus.

The first non-mammalian CXCR5 in a teleost fish: molecular cloning and expression analysis in grass carp (Ctenopharyngodon idella)

Background

Chemokines, a group of small and structurally related proteins, mediate chemotaxis of various cell types via chemokine receptors. In mammals, seven different CXC chemokine receptors denoted as CXCR1 to CXCR7 have been reported. However, the chemokine receptor CXCR5 has not been reported in other vertebrates.

Results

In the present study, the genomic sequence of CXCR5 was isolated from the grass carp Ctenopharyngodon idella. The cDNA sequence of grass carp CXCR5 (gcCXCR5) consists of 1518 bp with a 43 bp 5' untranslated region (UTR) and a 332 bp 3' UTR, with an open reading frame of 1143 bp encoding 381 amino acids which are predicted to have seven transmembrane helices. The characteristic residues (DRYLAIVHA) and conserved cysteine residues are located in the extracellular regions and in the third to seventh transmembrane domains. The deduced amino acid sequence shows 37.6-66.6% identities with CXCR5 of mammals, avian and other fish species. The grass carp gene consists of two exons, with one intervening intron, spaced over 2081 bp of genomic sequence. Phylogenetic analysis clearly demonstrated that the gcCXCR5 is clustered with those in other teleost fish and then in chicken and mammals. Real-time PCR analysis showed that gcCXCR5 was expressed in all tested organs/tissues and its expression level was the highest in trunk kidney, followed by in the spleen. The expression of gcCXCR5 was significantly modulated by immunostimulants such as peptidoglycan (PGN), lipopolysaccharide (LPS), polyinosinic-polycytidylic acid sodium salt (Poly I:C) and phytohaemagglutinin (PHA).

Conclusion

The cDNA and genomic sequences of CXCR5 have been successfully characterized in a teleost fish, the grass carp. The CXCR5 has in general a constitutive expression in organs/tissues examined, whereas its expression was significantly up-regulated in immune organs and down-regulated in brain, indicating its potential role in immune response and central nervous system.

Difference in genes between a high virulence strain G(4) and a low virulence strain G(18) of Flavobacterium columnare by using suppression subtractive hybridization

Flavobacterium columnare is the causative agent of columnaris disease. Different genetic groups of F. columnare show to some extent different degrees of virulence. To identify genetic differences between the high virulence strain G(4) and the low virulence strain G(18) of F. columnare, suppression subtractive hybridization was used. A total of 46 genes were identified from the virulent strain G(4), 35 of which showed some degree of homology with known proteins and can be classified into 11 categories: DNA replication or recombination proteins, inorganic ion transport proteins, outer membrane proteins, enterotoxin, binding proteins, YD repeat proteins, transposase, chaperon, signal transduction-related proteins, regulatory proteins, metabolism-related proteins. Several putative virulence factors identified in other bacteria could also be identified in the virulent strain G(4), such as ferrous iron transport protein, TonB-dependent receptor, transposases, as well as ABC transporter permease protein. The flanking region of a putative transposase ISFclI was analysed, and a putative Rhs element was located at the downstream of the putative transposase. The analysis of isfclI gene in 24 strains of F. columnare isolated in China revealed that 11 strains have isfclI, and all the strains from Zhaoqing, Anhui and Qingjiang have isfclI.

Structure and expression pattern of teleost caspase recruitment domain (CARD) containing proteins that are potentially involved in NF-kappaB signalling

Caspase-associated recruitment domain (CARD) proteins play critical roles in regulation of caspase activation, or regulation of NF-kappaB activation. In the present study, 9 CARD-genes, which may be involved in NF-kappaB activation, were identified in teleost fish. Phylogenetic analysis showed that the orthologs to mammalian RIPK2, NOD1, PYCARD, CARD9, CARD10, CARD11, CARD14, NOD2 and BCL10 were evident in teleost fish, but clear orthologs to mammalian CARD6 and CARD8 were not found in teleost fish. In zebrafish, most CARD-genes were expressed in embryos and larvae. In adult zebrafish, zfRIPK2, zfNOD1, zfPYCARD, zfCARD9 and zfNOD2 transcripts were constitutively expressed in kidney, gill, intestine, liver, brain and spleen whilst zfCARD11, zfCARD14 and BCL10 exhibited limited tissue distribution. A CARD-related gene (zfCARD-rel), containing a single CARD domain, was identified in the zebrafish genome and the EST databases and its transcripts were detected only in spleen and kidney. Phylogenetic analysis suggested that zfCARD-rel might be the ortholog of mammalian CARD8 or the short isoform of NLRP1. Overexpression of zfCARD-rel had a significantly inhibitory effect on NF-kappaB activity, demonstrating the zfCARD-rel protein might serve as a negative regulator of cell death and inflammatory response.

Molecular characterization and expression analysis of nuclear oligomerization domain proteins NOD1 and NOD2 in grass carp Ctenopharyngodon idella

Nuclear oligomerization domains (NODs) are cytosolic pattern recognition receptors (PRRs) to detect bacterial component. In this study, the molecular cloning and genomic characterization of grass carp NOD1 (gcNOD1) and grass carp NOD2 (gcNOD2) were reported. The complete open reading frame of gcNOD1 contains 2814 bp, encoding a 937-amino acid polypeptide. The gcNOD2 cDNA sequence encodes 982-amino acid polypeptide. Both gcNOD1 and gcNOD2 possess three conserved domains: carboxy terminal leucine rich repeat (LRR) domains, a central NOD, NBS or NACHT domain, and an amino terminal CARD domain (two in the case of NOD2). At the genomic level, gcNOD1 consists of 11 exons, with 10 intervening introns, spanning approximately 9 kb of genomic sequence. Whereas gcNOD2 has a length of approximately 5 kb with 9 intervening introns. Real time PCR analysis showed gcNOD1 and gcNOD2 were ubiquitously expressed in adult tissues. The highest transcript level of gcNOD1 was detected in brain, but in head kidney for gcNOD2. Grass carp reovirus significantly induced the expression of gcNOD1 and gcNOD2 in spleen (from days 1 to 6). However, expression profiles differed in time course response. Induction experiments with lipopolysaccharide (LPS), peptidoglycan (PGN) and polyI:C revealed the differential expression and regulation of gcNOD1 and gcNOD2 in blood, head kidney, trunk kidney and spleen. All these data suggest a potential role of NOD1 and NOD2 in fish innate immune protection to bacterial and virus infections.

Molecular characterization and expression analysis of the IFN-gamma related gene (IFN-gammarel) in grass carp Ctenopharyngodon idella

Interferon gamma (IFN-gamma), the only member of the type II class of interferons, has been identified in teleost fish. In addition to the IFN-gamma gene, fish possess an IFN-gamma related gene (IFN-gammarel) neighbouring the authentic IFN-gamma gene in the genome. In the present study, the cDNA sequence encoding 167 amino acids of IFN-gammarel and its genomic organization were identified in grass carp Ctenopharyngodon idella. The predicted protein sequence of grass carp IFN-gammarel (gcIFN-gammarel) showed 63% and 50% identities to zebrafish and common carp IFN-gammarel (previously termed as IFN-gamma1), respectively. The IFN-gammarel gene consists of 4 exons, with 3 intervening introns, spanning approximately 2kb of genomic sequence. The gcIFN-gammarel gene did not contain any polymorphic DNA repeats in the introns. Realtime PCR analysis showed that grass carp reovirus induced a high and long lasting (from days 1 to 7) expression of gcIFN-gammarel in spleen. The expression of gcIFN-gammarel in blood, head kidney, trunk kidney and spleen was also increased by bacterial peptidoglycan (PGN), lipopolysaccharide (LPS) and the interferon inducer polyI:C. The highest induction of gcIFN-gammarel expression by PGN was observed in spleen, then in blood and head kidney. Further analysis of the expression patterns of gcIFN-gammarel and PGN receptors, nucleotide oligomerization domains (NOD) 1 and 2, may suggest that IFN-gammarel was possibly activated in a NOD2-dependent mechanism.

The search for the IFN-gamma receptor in fish: Functional and expression analysis of putative binding and signalling chains in rainbow trout Oncorhynchus mykiss

Interferons (IFNs), consisting of three major subfamilies, type I, type II (gamma) and type III (lambda) IFN, activate vertebrate antiviral defences once bound to their receptors. The three IFN subfamilies bind to different receptors, IFNAR1 and IFNAR2 for type I IFNs, IFNgammaR1 and IFNgammaR2 for type II IFN, and IL-28R1 and IL-10R2 for type III IFNs. In fish, although many types I and II IFN genes have been cloned, little is known about their receptors. In this report, two putative IFN-gamma receptor chains were identified and sequenced in rainbow trout (Oncorhynchus mykiss), and found to have many common characteristics with mammalian type II IFN receptor family members. The presented gene synteny analysis, phylogenetic tree analysis and ligand binding analysis all suggest that these molecules are the authentic IFNgammaRs in fish. They are widely expressed in tissues, with IFNgammaR1 typically more highly expressed than IFNgammaR2. Using the trout RTG-2 cell line it was possible to show that the individual chains could be differentially modulated, with rIFN-gamma and rIL-1beta down regulating IFNgammaR1 expression but up regulating IFNgammaR2 expression. Over-expression of the two receptor chains in RTG-2 cells revealed that the level of IFNgammaR2 transcript was crucial for responsiveness to rIFN-gamma, in terms of inducing gammaIP expression. Transfection experiments showed that the two putative receptors specifically bound to rIFN-gamma. These findings are discussed in the context of how the IFNgammaR may bind IFN-gamma in fish and the importance of the individual receptor chains to signal transduction.

Immunoglobulin joining (J) chain and its expression in the Chinese soft-shelled turtle (Pelodiscus sinensis)

The immunoglobulin (Ig) joining (J) chain plays an important role in the formation of polymeric Igs and their transport into secretions. In the present study, the cDNA sequence of J chain has been cloned from the Chinese soft-shelled turtle (Pelodiscus sinensis) by reverse transcription (RT)-PCR and rapid amplification of cDNA ends (RACE). The cDNA sequence is 2347 bp in length and contains an open reading frame of 480 bp encoding 160 aa including the signal sequence. The deduced amino acid sequence has a high degree of homology with that of an already reported turtle J chain (80.7%), and of chicken (71.3%). By using real-time quantitative RT-PCR analysis, a significant up-regulation of J-chain transcripts was observed in spleen, kidney and blood of turtles injected with inactivated Aeromonas hydrophila, indicating the immune role of J chain in response to bacterial infection.

Zebrafish peptidoglycan recognition protein SC (zfPGRP-SC) mediates multiple intracellular signaling pathways

Insect PGRPs can function as bacterial recognition molecules triggering proteolytic and/or signal transduction pathways, with the resultant production of antimicrobial peptides. To explore if zebrafish peptidoglycan recognition protein SC (zfPGRP-SC) has such effects, RNA interference (siRNA) and high-density oligonucleotide microarray analysis were used to identify differentially expressed genes regulated by zfPGRP-SC. The mRNA levels for a set of genes involved in Toll-like receptor signaling pathway, such as TLRs, SARM, MyD88, TRAF6 and nuclear factor (NF)-kappa B2 (p100/p52), were examined by quantitative RT-PCR (QT-PCR). The results from the arrays and QT-PCR showed that the expression of 133 genes was involved in signal transduction pathways, which included Toll-like receptor signaling, Wnt signaling, BMP signaling, insulin receptor signaling, TGF-beta signaling, GPCR signaling, small GTPase signaling, second-messenger-mediated signaling, MAPK signaling, JAK/STAT signaling, apoptosis and anti-apoptosis signaling and other signaling cascades. These signaling pathways may connect with each other to form a complex network to regulate not just immune responses but also other processes such as development and apoptosis. When transiently over-expressed in HEK293T cells, zfPGRP-SC inhibited NF-kappaB activity with and without lipopolysacharide (LPS) stimulation.

Comparative study and expression analysis of the interferon gamma gene locus cytokines in Xenopus tropicalis

Using bioinformatics approach, the genome locus containing interleukin (IL)-22, IL-26, and interferon gamma (IFN-gamma) genes has been identified in the amphibian, Xenopus tropicalis. Like that in other vertebrates such as fish, birds, and mammals, the Xenopus IL-22, IL-26, and IFN-gamma are clustered in the same chromosome and the adjacent genes are conserved. The genomic structures of the Xenopus IL-22, IL-26, and IFN-gamma gene were identical to that of their mammalian counterparts. The Xenopus IL-22 and IL-26 genes contained five exons and four introns while the Xenopus IFN-gamma gene consisted of four exons and three introns. The Xenopus IL-22, IL-26, and IFN-gamma share 14.1-41.6%, 14.6-31.2%, and 23.7-36.5% identity to their counterparts in other species, respectively. Reverse-transcription polymerase chain reaction (PCR) and real-time quantitative PCR analyses revealed that the expression of IL-22, IL-26, and IFN-gamma genes was significantly upregulated after simulation with bacterial polyliposaccharide and/or synthetic double-stranded poly(I:C), suggesting these cytokines like those in other vertebrates play an important role in regulating immune response in Xenopus.

Genetic variation of fish parasite populations in historically connected habitats: undetected habitat fragmentation effect on populations of the nematode Procamallanus fulvidraconis in the catfish Pelteobagrus fulvidraco

Habitat fragmentation may have some significant effects on population genetic structure because geographic distance and physical barriers may impede gene flow between populations. In this study, we investigated whether recent habitat fragmentation affected genetic structure and diversity of populations of the nematode Procamallanus fulvidraconis in the yellowhead catfish, Pelteobagrus fulvidraco. The nematode was collected from 12 localities in 7 floodplain lakes of the Yangtze River. Using 11 intersimple sequence repeat markers, analysis of molecular variance showed that genetic diversity occurred mainly within populations (70.26%). Expected heterozygosity (He) of P. fulvidraconis was barely different between connected (0.2105) and unconnected lakes (0.2083). Population subdivision (Fst) between connected lakes (0.2177) was higher than in unconnected lakes (0.1676). However, the connected and unconnected lakes did not cluster into 2 clades. A Mantel test revealed significant positive correlation between genetic and geographic distances (R = 0.5335, P < 0.01). These results suggest that habitat fragmentation did not cause genetic differentiation among populations or a reduction of diversity in isolated populations of P. fulvidraconis. At least 2 factors may increase the dispersal range of the nematode, i.e., flash flooding in summer and other species of fish that may serve as the definitive hosts. Moreover, lake fragmentation is probably a recent process; population size of the nematode in these lakes is large enough to maintain population structure.

Cloning, characterization and expression analysis of SIMP (source of immunodominant MHC-associated peptides) in grass carp Ctenopharyngodon idella

SIMP (source of immunodominant MHC-associated peptides) plays a key role in N-linked glycosylation with the active site of oligosaccharyltransferase, being the source of MHC-peptides in the MHC I presentation pathway. In the present study, the SIMP gene has been cloned from grass carp Ctenopharyngodon idella by rapid amplification of cDNA ends (RACE). The full length of the cDNA sequence is 4384bp, including a 1117bp 5' UTR (untranslated region), a 2418bp open reading frame, and a 849bp 3' UTR. The deduced amino acids of the grass carp SIMP (gcSIMP) are a highly conserved protein with a STT3 domain and 11 transmembrane regions. The gcSIMP spans over more than 24,212bp in length, containing 16 exons and 15 introns. Most encoding exons, except the first and the 15th, have the same length as those in human and mouse. The gcSIMP promoter contains many putative transcription factor binding sites, such as Oct-1, GCN4, YY1, Sp1, Palpha, TBP, GATA-1, C/EBP beta, and five C/EBP alpha binding sites. The mRNA expression of gcSIMP in different organs was examined by real-time PCR. The gcSIMP was distributed in all the organs examined, with the highest level in brain, followed by the level in the heart, liver, gill, trunk kidney, muscle, head kidney, thymus, and the lowest level in spleen. Furthermore, the recombinant gcSIMP has been constructed successfully and expressed in Escherichia coli by using pQE-40 vector, and the polyclonal antibody for rabbit has been successfully obtained, which was verified to be specific. Identification of gcSIMP will help to explore the function in fish innate immunity.

Proteomic analysis of the sarcosine-insoluble outer membrane fraction of Flavobacterium columnare

Outer membrane proteins (OMPs) of bacteria are key molecules interacting with the host environment. Flavobacterium columnare, a pathogen-causing columnaris disease of fish worldwide, was studied in order to understand the composition of its OMPs. The sarcosine-insoluble membrane fraction of the OMPs was analysed using sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) in combination with reverse-phase high-performance liquid chromatography-tandem mass spectrometry (RP-HPLC MS/MS). Thirty-six proteins were identified, including proteins involved in cell wall/membrane biogenesis, specific transport of various nutrients and in essential metabolism. The present study is the first report on the OMPs of F. columnare, and may serve as the basis for understanding the pathogenesis of the bacterium.