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Aquaporins (AQPs) are key proteins that regulate fluid homeostasis in cells via modulating osmotic water transport. In the present study, we identified three variants of Aqp1ab transcript (mmAQP1ab x1, mmAQP1ab x2, and mmAQP1ab x3) in mud loaches (Misgurnus mizolepis), and their expression patterns were examined in response to heavy metal and immunostimulant exposure. Mud loach Aqp1ab gene has a somewhat different organizational structure (i.e. five exons interrupted by four introns) compared to most other teleostean Aqp1ab orthologues, which have four exons. The 5'-flanking regulatory region of Aqp gene showed diverse transcription factor binding motifs, particularly those associated with stress/immune responses. Developmental expression patterns indicated that Aqp1ab mRNA was maternally inherited, presumably important for fine-tuning gene expression during embryonic and early larval developments. Expression of mud loach Aqp1ab mRNA was significantly and differentially modulated in several tissues (intestine, kidneys, spleen, and liver) in response to various heavy metal treatments. In addition, Aqp1ab gene expression was highly induced in response to immune challenge (LPS and polyI:C injections). Collectively, our results suggested that AQPs are multifunctional effectors playing diverse roles in cellular pathways relevant to immune and/or stress adaptation responses, in addition to their involvement in osmoregulation.

Complete genome sequences of two cycas necrotic stunt virus (CNSV) isolates from Paeonia suffruticosa and Daphne odora were determined. Phylogenetic trees and pairwise comparisons using complete RNA1- and RNA2-encoded polyproteins showed that the two CNSV isolates are divergent (83.19%-89.42% in polyprotein 1 and 73.61%-85.78% in polyprotein 2). A comparative analysis based on taxonomic criteria for the species demarcation of nepoviruses confirmed that they are not new species but distinct variants. This is the first report of the complete genome sequences of CNSV detected in P. suffruticosa and D. odora, and the first report of CNSV infecting P. suffruticosa.

Transgenic Arabidopsis thaliana plants expressing cyanobacterial decarboxylation genes GLCD1 (GLYCOLATE DEHYDROGENASE I), HDH (HYDROXYACID DEHYDROGENASE), ODC (OXALATE DECARBOXYLASE) alone, and HDH::ODC simultaneously were successfully developed. Plants independently expressing GLCD1, HDH, ODC, and HDH::ODC were referred to as GD, HD, OX, and HX plants, respectively. The single-copy homozygous GD, HD, OX, and HX plants exhibited appreciable expression of chimeric genes. Phenotypic characterization demonstrated that rosette diameter of GD, HD, OX, and HX was 20, 22, 17, and 16% higher than wild-type (WT) plants. Total numbers of leaves were 32, 35, 37, and 34% more than WT plants after 32 days of sowing. Similarly, all transgenic plants produced more cauline branches than WT plants. All transgenic plants gained more height as compared to WT when recorded after 42 days of growth except HX transgenic plants. Plants vegetative dry biomass was 43% (GD), 35% (HD), 42% (OX), and 36% (HX) higher than WT plants. This is the first report on characterization of cyanobacterial decarboxylation pathway genes, which will pave the way for transformation of complete pathway in plants for better biomass accumulation.

The optimal transfection conditions for efficient transgene delivery into a specific cell type should be empirically determined, particularly in cases involving unusual cell types. We compared the conditions for effective introduction of transgenes into Siberian sturgeon (Acipenser baerii) cell lines by evaluating the cytotoxicity and transfection efficiency of three commercially available transfection reagents: Lipofectamine 2000, X-tremeGENE HP DNA Transfection Reagent, and GeneJuice Transfection Reagent. Plasmid vectors containing the gene encoding enhanced green fluorescent protein were mixed with each of the transfection reagents using reagent-to-plasmid ratios of 1:1, 2:1, and 4:1. Then, the complexes were used to transfect three Siberian sturgeon cell lines derived from the heart, head kidney, and gonad. Cytotoxicity and transfection efficiency were measured via flow cytometry after propidium iodide staining. No significant cytotoxicity was observed at the optimal treatment conditions in all cases, with the exception of Lipofectamine 2000-treated gonad-derived cells. Although the transfection efficiencies in A. baerii cells were generally low, X-tremeGENE HP DNA Transfection Reagent showed the highest transfection efficiency at ratios of 2:1 or 4:1, depending on the cell type. Hence, X-tremeGENE HP DNA Transfection Reagent can be used to effectively transfer foreign genes into three A. baerii cell lines.

Russian sturgeon (Acipenser gueldenstaedtii) is commercially important in Korea because its caviar is highly prized. Although the early ontogeny of the species has been described, behavioral modifications in response to various light intensities or diel photoperiodicity patterns have not been studied extensively. The objective of the present study was to examine the behavioral characteristics of hatchery-produced A. gueldenstaedtii prelarvae over a diel photoperiodic cycle. During a diel light cycle comprising 16 h of daylight (450 lx), 4 h of dim light (10 lx), and 4 h of darkness (

Maternal genes are important in directing early development and determining egg quality in fish. We here report the de novo transcriptome from four tissue libraries of the cyprinid loach, Misgurnus anguillicaudatus, and for the first time identified maternal gene transcripts in unfertilized eggs and suggest their immune system involvement. Expression profiles and functional enrichment revealed a total 24,116 transcripts were expressed as maternal transcripts in unfertilized eggs, which were involved in a wide range of biological functions and pathways. Comparison expression profiles and analysis of tissue specificity revealed that the large numbers of maternal transcripts were stored in unfertilized eggs near the late phase of ovarian maturation and before ovulation. Functional classification showed a total of 279 maternal immune-related transcripts classified with immune system process GO term and immune system KEGG pathway. qPCR analysis showed that transcript levels of identified maternal immune-related candidate genes were dynamically modulated during development and early ontogeny of M. anguillicaudatus. Taken together, this study could not only provide knowledge on the protective roles of maternal immune-related genes during early life stage of M. anguillicaudatus but could also be a valuable transcriptomic/genomic resource for further analysis of maternally provisioned genes in M. anguillicaudatus and other related teleost fishes.

BackgroundTranslationally controlled tumor protein (TCTP) is a conserved, multifunctional protein involved in numerous cellular processes in eukaryotes. Although the functions of TCTP have been investigated sporadically in animals, invertebrates, and plants, few lineage-specific activities of this molecule, have been reported. An exception is in Arabidopsis thaliana, in which TCTP (AtTCTP1) functions in stomatal closuer by regulating microtubule stability. Further, although the development of next-generation sequencing technologies has facilitated the analysis of many eukaryotic genomes in public databases, inter-kingdom comparative analyses using available genome information are comparatively scarce.MethodologyTo carry out inter-kingdom comparative analysis of TCTP, TCTP genes were identified from 377 species. Then phylogenetic analysis, prediction of protein structure, molecular docking simulation and molecular dynamics analysis were performed to investigate the evolution of TCTP genes and their binding proteins.ResultsA total of 533 TCTP genes were identified from 377 eukaryotic species, including protozoa, fungi, invertebrates, vertebrates, and plants. Phylogenetic and secondary structure analyses reveal lineage-specific evolution of TCTP, and inter-kingdom comparisons highlight the lineage-specific emergence of, or changes in, secondary structure elements in TCTP proteins from different kingdoms. Furthermore, secondary structure comparisons between TCTP proteins within each kingdom, combined with measurements of the degree of sequence conservation, suggest that TCTP genes have evolved to conserve protein secondary structures in a lineage-specific manner. Additional tertiary structure analysis of TCTP-binding proteins and their interacting partners and docking simulations between these proteins further imply that TCTP gene variation may influence the tertiary structures of TCTP-binding proteins in a lineage-specific manner.ConclusionsOur analysis suggests that TCTP has undergone lineage-specific evolution and that structural changes in TCTP proteins may correlate with the tertiary structure of TCTP-binding proteins and their binding partners in a lineage-specific manner.

Background Russian sturgeon (Acipenser gueldenstaedtii) is an emerging candidate species in the Korean aquaculture domain owing to its highly valued caviar. Although the embryonic development of this species was previously described, the complete image data on the morphological differentiation of developing embryos have not been yet fully available. Further, with the viewpoint of larval production in hatchery, the effects of temperature on embryonic viability and the temporal window of hatching event have not been extensively studied. Hence, the objective of this study was to provide a complete set of photographic image data on the embryogenesis and also to examine the effects of incubation temperatures on embryonic viability and hatching event in farm-bred Russian sturgeon. Results Typical characteristics of embryonic development including uneven, holoblastic cleavages with unequal blastomeres, followed by the formation of germ layer, neurulation, and organogenesis until hatching, were documented. Under different temperature conditions (12, 16, or 20 °C), viability of embryos incubated at 12 °C was significantly lower as relative to those of 16 and 20 °C incubated embryos. Hatchability of embryos was higher, and the timing of hatching event was more synchronized at 20 °C than at 12 and 16 °C. Conclusion Data from this study suggest that the incubation of Russian sturgeon embryos at 20 °C would be desirable in the hatchery practice with respect to the good hatchability of embryos and the synchronization of hatching events. Additionally, the updated image data for complete embryonic development could be a useful reference guide for not only developmental researches but also artificial propagation of Russian sturgeon in farms.

This study was conducted to establish and characterize the clonal-cell lines from Siberian sturgeon Acipenser baerii head-kidney tissues and to evaluate its applicability as a research tool. From the culture of A. baerii head-kidney derived cells, 10 cell lines were established first and then eight clonal-cell lines were derived from clonal growth and colony expansion of two cell lines that showed significant high colony-forming ability. All eight clonal-cell lines were morphologically similar and grew stably under monolayer culture but their growth rates were significantly different. They possessed diploid DNA contents, expressed epithelial cell-related genes and showed strong anchorage dependency to substrates. When a clonal-cell line was transfected separately with three plasmid vectors including fluorescent reporter genes driven by cytomegalovirus, marine medaka Oryzias dancena β-actin or A. baerii β-actin promoter, the cell lines expressed fluorescent signals regardless of promoter types. The cells harbouring foreign genes could be expanded to stable cell lines under drug selection and then they additionally could form the extensively proliferating colonies at low-density culture. Finally, the clonal-cell lines showed the susceptibility to viral haemorrhagic septicaemia virus (VHSV). Collectively, the clonal-cell lines from A. baerii head kidney were established and these cell lines will be able to provide an excellent in vitro system for various biological studies in this fish species.

Background Liver-expressed antimicrobial peptide-2 (LEAP-2) is an important component of innate immune system in teleosts. In order to understand isoform-specific involvement and regulation of LEAP-2 genes in mud loach (Misgurnus mizolepis, Cypriniformes), a commercially important food fish, this study was aimed to characterize gene structure and expression characteristics of two paralog LEAP-2 isoforms. Results Mud loach LEAP-2 isoforms (LEAP-2A and LEAP-2B) showed conserved features in the core structure of mature peptides characterized by four Cys residues to form two disulfide bonds. The two paralog isoforms represented a tripartite genomic organization, known as a common structure of vertebrate LEAP-2 genes. Bioinformatic analysis predicted various transcription factor binding motifs in the 5′-flanking regions of mud loach LEAP-2 genes with regard to development and immune response. Mud loach LEAP-2A and LEAP-2B isoforms exhibited different tissue expression patterns and were developmentally regulated. Both isoforms are rapidly modulated toward upregulation during bacterial challenge in an isoform and/or tissue-dependent fashion. Conclusion Both LEAP-2 isoforms play protective roles not only in embryonic and larval development but also in early immune response to bacterial invasion in mud loach. The regulation pattern of the two isoform genes under basal and stimulated conditions would be isoform-specific, suggestive of a certain degree of functional divergence between isoforms in innate immune system in this species.

Background Teleosts represent unique features in the regulation of muscle development and growth, with a great deal of myogenic plasticity. Muscle actins are major components to compose muscle fibers, and they play essential roles in cellular mobility and other related functions. In order to understand isoform-dependent roles of muscle actins in the mud loach (Misgurnus mizolepis), this study was aimed to characterize gene structure and expression pattern of the three muscle actin isoforms (α-skeletal, α-cardiac, and α-smooth muscle actins) isolated from this benthic fish species. Results Mud loach α-actin isoforms (ACTA1, ACTC1, and ACTA2) were fairly conserved in their primary structures and shared a high-sequence identity one another. At genomic level also, all the three isoforms exhibited the same exon-intron organization pattern characterized by eight translated exons. However, in mRNA expression patterns, these three actin isoforms were found to display an apparent isoform-dependency in tissue distribution (i.e., ACTA1 in the skeletal muscles, ACTC1 in the heart, and ACTA2 in the intestines) and developmental regulation (i.e., increased expression of ACTA1 and ACTC1 with the progress of myogenesis, and the significant elevation of ACTA2 during organ development in early larvae). Conclusion Data from this study suggest that three muscle actin isoforms have undergone certain functional differentiation with regard to their roles in the development and adult musculature, in spite of high structural similarity. Genetic information on muscle actins obtained in this study could provide a useful base to extend our understanding on evolutionary diversification of the myogenic regulation in teleosts.

Two distinct cDNAs encoding aquaporins (mmAQPs 1a and 3a) were isolated and characterized from mud loach Misgurnus mizolepis. The identified mud loach AQP cDNAs encode for polypeptides of 260 and 302 amino acids. Topology predictions confirmed six putative membrane-spanning domains connected by five loops and the N- and C-terminal domains being cytoplasmic. The mud loach AQPs 1a and 3a showed broad distribution in multiple tissues including immune-responsive tissues as well as osmoregulatory tissues. Hence, the diversity of AQP distribution and expression possibly indicated its differential functions in the regulation of fluid movement in response to environmental stimuli. The transcription of mmAQP genes was differentially modulated by immune challenges. In particular, the mmAQP3a expression level in the liver was more responsive to immune challenges than that of mmAQP1a. Taken together, fish stimulation or infection resulted in significant modulation of mud loach AQP genes, suggesting potential functional roles of these proteins in piscine pathophysiological process.

Background Metal-responsive transcription factor-1 (MTF-1) is a key transcriptional regulator playing crucial roles in metal homeostasis and cellular adaptation to diverse oxidative stresses. In order to understand cellular pathways associated with metal regulation and stress responses in Pacific abalone (Haliotis discus hannai), this study was aimed to isolate the genetic determinant of abalone MTF-1 and to examine its expression characteristics under basal and experimentally stimulated conditions. Results The abalone MTF-1 shared conserved features in zinc-finger DNA binding domain with its orthologs; however, it represented a non-conservative shape in presumed transactivation domain region with the lack of typical motifs for nuclear export signal (NES) and Cys-cluster. Abalone MTF-1 promoter exhibited various transcription factor binding motifs that would be potentially related with metal regulation, stress responses, and development. The highest messenger RNA (mRNA) expression level of MTF-1 was observed in the testes, and MTF-1 transcripts were detected during the entire period of embryonic and early ontogenic developments. Abalone MTF-1 was found to be Cd inducible and highly modulated by heat shock treatment. Conclusion Abalone MTF-1 possesses a non-consensus structure of activation domains and represents distinct features for its activation mechanism in response to metal overload and heat stress. The activation mechanism of abalone MTF-1 might include both indirect zinc sensing and direct de novo synthesis of transcripts. Taken together, results from this study could be a useful basis for future researches on stress physiology of this abalone species, particularly with regard to heavy metal detoxification and thermal adaptation.

Hibiscus syriacus (L.) (rose of Sharon) is one of the most widespread garden shrubs in the world. We report a draft of the H. syriacus genome comprised of a 1.75 Gb assembly that covers 92% of the genome with only 1.7% (33 Mb) gap sequences. Predicted gene modeling detected 87,603 genes, mostly supported by deep RNA sequencing data. To define gene family distribution among relatives of H. syriacus, orthologous gene sets containing 164,660 genes in 21,472 clusters were identified by OrthoMCL analysis of five plant species, including H. syriacus, Arabidopsis thaliana, Gossypium raimondii, Theobroma cacao and Amborella trichopoda. We inferred their evolutionary relationships based on divergence times among Malvaceae plant genes and found that gene families involved in flowering regulation and disease resistance were more highly divergent and expanded in H. syriacus than in its close relatives, G. raimondii (DD) and T. cacao. Clustered gene families and gene collinearity analysis revealed that two recent rounds of whole-genome duplication were followed by diploidization of the H. syriacus genome after speciation. Copy number variation and phylogenetic divergence indicates that WGDs and subsequent diploidization led to unequal duplication and deletion of flowering-related genes in H. syriacus and may affect its unique floral morphology.

Three distinct superoxide dismutases (SODs)—copper/zinc-SOD (SOD1), manganese-SOD (SOD2), and extracellular copper/zinc-SOD (SOD3)—were identified from a primitive chondrostean fish, Acipenser baerii, enabling the comparison of their transcriptional regulation patterns during development, prelarval ontogeny, and immune stimulation. Each A. baerii SOD isoform (AbSOD) shared conserved structural features with its vertebrate orthologs, however, phylogenetic analyses hypothesized a different evolutionary history for AbSOD3 relative to AbSOD1 and AbSOD2 in the vertebrate lineage. The AbSOD isoforms showed different tissue distribution patterns, AbSOD1 was predominantly expressed in most tissues. The expression of the AbSOD isoforms showed isoform-dependent dynamic modulation according to embryonic development and prelarval ontogenic behaviors. Prelarval microinjections revealed that lipopolysaccharide only induced AbSOD3 expression, while Aeromonas hydrophila induced the expression of AbSOD2 and AbSOD3. In fingerlings, the transcriptional response of each AbSOD isoform to bacterial infection was highly tissue-specific, and the three isoforms exhibited different response patterns within a given tissue type, AbSOD3 was induced the most sensitively, and its induction was the most pronounced in the kidneys and skin. Collectively, these findings suggest isoform-dependent roles for the multigene SOD family in antioxidant defenses against the oxidative stress associated with development and immune responses in these endangered sturgeon fish.

Oriental melon (Cucumis melo L. var. makuwa) is one of six subspecies of melon and is cultivated widely in East Asia, including China, Japan, and Korea. Although oriental melon is economically valuable in Asia and is genetically distinct from other subspecies, few reports of genome-scale research on oriental melon have been published. We generated 30.5 and 36.8 Gb of raw RNA sequence data from the female and male flowers, leaves, roots, and fruit of two oriental melon varieties, Korean landrace (KM) and Breeding line of NongWoo Bio Co. (NW), respectively. From the raw reads, 64,998 transcripts from KM and 100,234 transcripts from NW were de novo assembled. The assembled transcripts were used to identify molecular markers (e.g., single-nucleotide polymorphisms and simple sequence repeats), detect tissue-specific expressed genes, and construct a genetic linkage map. In total, 234 single-nucleotide polymorphisms and 25 simple sequence repeats were screened from 7,871 and 8,052 candidates, respectively, between the KM and NW varieties and used for construction of a genetic map with 94 F2 population specimens. The genetic linkage map consisted of 12 linkage groups, and 248 markers were assigned. These transcriptome and molecular marker data provide information useful for molecular breeding of oriental melon and further comparative studies of the Cucurbitaceae family.

【Several transgenic marine medaka Oryzias dancena strains harboring a green fluorescent protein (GFP) reporter construct regulated by an endogenous ${\beta}$ -actin promoter were established and their expression characteristics in relation to transgene copy numbers were examined in 21 transgene genotypes. Most of the transgenic strains displayed transgene insertion patterns typical of microinjection-mediated introduction of foreign DNA into fish embryos, characterized by the random integration of multiple transgene copies (ranging from 1 - 282 copies per cell), often accompanied by the formation of concatemer(s), as assessed by genomic Southern blot hybridization analysis and qPCR. Transgenic strains showed ubiquitous and continued temporal and spatial expression patterns of the transgenic GFP during most of their life cycle, from the embryonic stage to adulthood, enabling assessment of the expression pattern of the endogenous ${\beta}$ -actin gene. However, a comparative evaluation of transgene copy numbers and expression levels showed that copy number-dependent expression, the stability of the ubiquitous distribution and expression efficiency per transgene copy varied among the transgenic strains. Fluorescence expression levels were positively correlated with absolute transgene copy numbers, whereas the expression efficiency per transgene copy was inversely related to the number of transgene integrant copies. Data from this study will guide the selection of potentially desirable transgenic strains with ubiquitous expression of a fluorescent transgene, not only in this marine medaka species but also in other related model fish species.】

ADP-glucose pyrophosphorylase is crucial in starch metabolism. The open reading frame of IbAGPaseS gene is comprised of 1539-base pairs and encodes a polypeptide of 512 amino acid residues. The deduced IbAGPaseS protein sequence was homologous with that of other AGPase proteins of various plant species. Also, the IbAGPaseS gene appears to be a member of multiple gene families and further, the differences in the copy numbers among the ten cultivars were considered to lead to differences in starch contents. IbAGPaseS was expressed in whole tissues and revealed high activity in thick-pigmented roots and developing tuberous roots. RT-PCR analysis indicated that the main role of IbAGPaseS is starch biosynthesis accumulating sink tissues during sweet potato root development. The IbAGPaseS cDNA was introduced to sweet potato under the control of the CaMV 35S promoter using Agrobacterium-mediated gene transfer techniques, thereby affecting the expression levels of carbohydrate regulated genes and sporamin gene. These results suggest that IbAGPaseS affects carbohydrate gene regulation.

To examine the interrelationship between transgenic insertion patterns and transgene expression profiles in established transgenic fish lines, four s table transgenic marine medaka Oryzias dancena germlines harboring β-actin regulator-driven RFP reporter constructs were selected. The established transgenic strains were characterized with regard to their transgenic genotypes (insertion pattern, concatemer formation, and transgene copy number based on genomic Southern blot hybridization and qPCR assay) and expression characteristics at the mRNA (qRT-PCR), protein (western blot), and phenotypic (fluorescent appearance) levels. From comparative examinations, it was found that transgenic expression at both the transcription and translation levels could be signifi cantly downregulated in transgenic strains, potentially through methylation-mediated transgene silencing that was particularly associated with the formation of a long tail-to-head tandem concatemer in the chromosomal integration site(s). When this occurred, an inverse relationship between the transgene copy number and fluorescence intensity was observed in the resultant transgenic fish. However, with the other transgenic genotype, transgenic individuals with an identical Southern blot hybridization pattern, containing a tandem concatemer(s), had very different expression levels (highly robust vs. low expression strengths), which was possibly related to the differential epigenetic modifications and/or degrees of methylation. The concatemer-dependent downregulation of transgene activity could be induced in transgenic fish, but the overall pattern was strain-specific. Our data suggest that neither a low (or single) transgene copy number nor tandem transgene concatemerization is indicative of strong or silenced transgene expression in transgenic fish carrying a ubiquitous transgene. Hence, a sufficient number of transgenic lineages, with different genotypes, should be considered to ensure the establishment of the best-performance transgenic line(s) for practical applications.

The functional utility of a transgenic marine medaka Oryzias dancena strain carrying the red fluorescent protein (RFP) gene driven by an endogenous choriogenin H (chgH) promoter was evaluated for its ability to detect waterborne 17α-ethinylestradiol (EE2), a synthetic estrogen derivative. The chgH:rfp transgenic marine medaka larvae showed an age-dependent tendency in the efficiency of EE2-mediated transgene expression, in which transgenic larvae older than 6 days post-hatching displayed a more effective response in their transgene expression to EE2 than did younger hatchlings. During experimental exposures to high concentrations of EE2 (200 to 1,000 ng/L), the transgenic responses in the hatchlings were broadly dose- and duration-dependent. With exposures using lower doses of EE2 (25, 50 and 100 ng/L), EE2-induced transgenic RFP was also observed in the transgenic larvae, although the lower doses required exposure of longer duration. Under the EE2 exposure and microscope assay conditions used in our study, transgenic marine medaka larvae exhibited a similar degree of EE2-mediated RFP phenotype expression at various salinity levels (0, 15 and 30 ppt).

Sucrose is produced in mesophyll cells and transferred into phloem cells before it is delivered long-distance to sink tissues. However, little is known about how sucrose transport is regulated in plants. Here, we identified a T-DNA insertional mutant of Oryza sativa DNA BINDING WITH ONE FINGER 11 (OsDOF11), which is expressed in the vascular cells of photosynthetic organs and in various sink tissues. The osdof11 mutant plants are semi-dwarf and have fewer tillers and smaller panicles as compared with wild-type (WT) plants. Although sucrose enhanced root elongation in young WT seedlings, this enhancement did not occur in osdof11 seedlings due to reduced sucrose uptake. Sugar transport rate analyses revealed that less sugar was transported in osdof11 plants than in the WT. Expression of four Sucrose Transporter (SUT) genes-OsSUT1, OsSUT3, OsSUT4, and OsSUT5-as well as two Sugars Will Eventually be Exported Transporters (SWEET) genes, OsSWEET11 and OsSWEET14, was altered in various organs of the mutant, including the leaves. Chromatin immunoprecipitation assays showed that OsDOF11 directly binds the promoter regions of SUT1, OsSWEET11, and OsSWEET14, indicating that the expression of these transporters responsible for sucrose transport via apoplastic loading is coordinately controlled by OsDOF11. We also observed that osdof11 mutant plants were less susceptible to infection by Xanthomonas oryzae pathovar oryzae, suggesting that OsDOF11 participates in sugar distribution during pathogenic invasion. Collectively, these results suggest that OsDOF11 modulates sugar transport by regulating the expression of both SUT and SWEET genes in rice.

Background Metallothionein (MT) is a multifunctional protein playing important roles in homeostatic regulation and detoxification of metals. Mollusk species have been considered as useful sentinel platforms for MT-based biomarker approaches, and they have been reported to display an extraordinary structural diversity of MT proteins. However, potential diversity of molluskan MTs has not been fully explored and recent updates have suggested the need of revision of evolutionary hypothesis for molluskan MTs. Results Based on bioinformatic analysis and phylogenetic evidences, novel divergence mechanisms and paths were hypothesized in both gastropod and bivalve MT groups. Our analyses are suggestive of the taxon- or lineage-specific domain multiplication/duplication from the ancestral or prototypic MT. Diversification and selection of molluskan MTs might be driven by the needs for acquiring metal selectiveness, specialized novel function, and improved capacity of metal detoxification under environmentally stressed conditions. Conclusion The structural diversity and variations of molluskan MTs are significantly larger than previously understood. Undoubtedly, molluskan MTs have undergone dynamic divergent processes in their evolutionary histories, giving rise to the great diversity of domain structures in extant MT isoforms. Novel evolutionary paths for molluskan MTs newly proposed in this review could shed additional light onto the revision of the hypothesis for evolutionary differentiation of MTs in the molluskan lineage.

We investigated the effects of hydrogen peroxide on mucous cells and lysozymes in gill tissue of olive flounder. Morphological analysis revealed significant changes in the number of mucous cells after exposure to 300 and 500 mg L−1 hydrogen peroxide; however, there was no detectable difference in the 100 mg L−1 group. Lysozyme activities declined gradually in the gill mucus, but in contrast activities in serum increased significantly following the completion of treatment. The hepatic c- and g-type lysozyme levels showed significant responses, indicating that the liver is a major lysozyme producer in response to stress condition; however, in the head kidney, there were no significant changes in the g-type lysozyme level in all the groups, while the only detectable difference with the c-type gene in the 300 mg L−1. While the treatments showed no significant changes compared with the control for either branchial lysozyme, there were significant differences in c-type lysozyme between the 3rd treatment and 5 day. Taken together, our data indicate that hydrogen peroxide treatment may lead to modulation of the innate immune response of olive flounder; therefore, the application of hydrogen peroxide in a field system will require more attention to dose and timing effects.

We have identified six putative aquaporin (AQP) genes from marine medaka Oryzias dancena (named odAQPs 1, 3, 8, 10, 11 and 12). The marine medaka AQP cDNAs encode polypeptides of 259-298 amino acids, respectively. Topology predictions showed six transmembrane domains, five connecting loops, and cytoplasmic N- and C-terminal domains, all of which is conserved among AQP molecules. Although asparagine-proline-alanine (NPA) motifs are highly conserved in most odAQP isoforms, several AQPs revealed variant types of motifs such as asparagine-proline-proline (NPP), asparagine-proline-valine (NPV) or/and asparagine-proline-serine (NPS) motifs. The phylogenic analysis showed that marine medaka AQPs had closet relationship with Japanese ricefish (medaka; Oryzias latipes) counterparts. Reverse transcription (RT)-PCR analyses showed that marine medaka AQP transcripts would be expressed in not only osmoregulatory tissues but also nonosmoregulatory tissues, and also that the expression levels of certain AQP isoforms in nonosmoregulatory tissues were readily comparable or even higher than those in typically known osmoregulatory organs. Although the overall tissue distribution patterns of AQPs were not significantly different between 0- and 30-ppt acclimated fish, the expression levels under different salinities were largely variable among isoforms and tissues. This is the first report to investigate tissue expression profiles of teleostean AQPs 11 and 12 during the long-term acclimation to freshwater and salted water.

Plant receptor-like kinases (RLKs) are proteins that are involved in the regulation of development, hormone signaling, abiotic, and biotic stress responses. It has been suggested that cysteine-rich receptor-like kinases (CRKs), which are one of the largest RLK groups, is significant in pathogen defense and programmed cell death. The CRK1 gene is isolated and characterized from tomato (Solanum lycopersicum L.). The SlCRK1 has two C-X8-C-X2-C motifs: a trans-membrane region and a kinase domain similar to other CRKs. The semi-quantitative RT-PCR exhibits the specific expression of SlCRK1 in the flower, but not in the root, leaf, seed, and fruit of the tomato. In addition, SlCRK1 exhibits pollen-specific expression in the floral organ. SlCRK1 has pollen-specific cis-acting elements in the promoter region, and its promoter has pollen-specific activity in the homozygous transgenic plants of tomato and Arabidopsis as confirmed through histochemical GUS assays. Moreover, the expression of SlCRK1 is not detected via stress treatment or hormone treatment. In this study, SlCRK1 from tomato is characterized and its promoter can be useful in developing transgenic plants with foreign genes that should be expressed in pollens.

Background The transgenic approach using estrogen-responsive regulator in fish has been given much attention as a potential means to detect and/or address estrogen-related aquatic pollutions. In order to address the development stage- and reproduction status-dependent expression patterns of the chgH-rfp transgene (red fluorescent protein transgene driven by choriogenin H promoter) in marine medaka Oryzias dancena, naturally occurring red fluorescent protein (RFP) signals under non-exposed conditions as well as the transgenically induced RFP signals under estrogen-exposed conditions were assayed. Results Female transgenics begun to show naturally occurring RFP signals from the age of 7 weeks post hatching (WPH) without experimental estrogen exposure. Afterward, these RFP signals in female transgenics became robust with the progress of ovarian maturation. On the other hand, male transgenics did not show any naturally occurring RFP signal under non-exposed conditions irrespective of developmental stages and maturation statue. Upon exposures using estradiol-17β (E2) and 17α-ethinylestradiol (EE2), RFP signals were significantly induced specifically in the livers of transgenic males. Conclusions Male chgH-rfp transgenics were able to keep the “off” state of RFP expression during their entire life cycle unless exposed to exogenous estrogens. Owing to their tight regulation capability of estrogen-responsive transgene, transgenesis of chgH-rfp in male marine medaka could offer a useful model system for future ecotoxicogenomic studies regarding estrogenicity-related issues in aquatic and marine environments.

환경스트레스 저항성 오이 형질전환체 생산을 위해서 오이 “Eunsung” 품종의 자엽절 절편을 Nit유전자를 포함하는 pPZP211와 pCAMBIA2300 발현벡터로 각각 형질전환된 Agrobacterium과 공동 배양하였다. 공동배양 후 형질전환체 선발, 형질전환체 유도, 신장, 유식물체 생산 등은 자엽절 절편을 이용하는 CTM방법(Jang et al. 2011)에 따라 수행하였다. 발현벡터에 따라 선발배지에 100 mg/L paromomycin을 첨가하여 선발과정을 거쳤으며, 선발배지에서 3 cm크기의 shoot를 유도한 후 PCR, Southern, RT-PCR 및 Northern분석을 통해 형질전환 여부를 확인하였다. 공동배양 한 2,547개의 자엽절 절편으로부터 105개체(4.12%)가 선발배지로부터 얻어졌으며, 그들 중 45개체(1.77%)만이 Nit유전자의 PCR product를 얻을 수 있었다. 오이 genome에 Nit유전자의 도입여부를 확인하기 위하여 45개체에 대한 Southern분석을 수행한 결과 각각 39개체(1.53%)서 확인할 수 있었으며, 이중 오직 6개체(0.24%)에서만 Nit유전자가 안정적으로 발현되고 있음을 RT-PCR과 Northern분석을 통해 확인하였다. 이러한 결과는 Nit유전자가 오이 genome에 안정적으로 도입 및 발현되고 있음을 보여 주고 있음을 알 수 있었다.

The genomic organization, tissue distribution, and developmental expression of two paralogous GAPDH isoforms were characterized in the mud loach Misgurnus mizolepis (Cypriniformes). The mud loach gapdh isoform genes (mlgapdh-1 and mlgapdh-2) had different exon-intron organizations: 12 exons in mlgapdh-1 (spanning to 4.88 kb) and 11 in mlgapdh-2 (11.78 kb), including a non-translated exon 1 in each isoform. Southern blot hybridization suggested that the mud loach might possess the two copies of mlgapdh-1 and a single copy of mlgapdh-2. The mlgapdh-1 transcript levels are high in tissues requiring high energy flow, such as skeletal muscle and heart, whereas mlgapdh-2 is expressed abundantly in the brain. Both isoforms are differentially regulated during embryonic and larval development, during which their expression is upregulated with the progress of development. Lipopolysaccharide challenge preferentially induced mlgapdh-2 transcripts in the liver. Therefore, the two isoforms have diversified functionally; mlgapdh-1 is associated more closely with energy metabolism, while mlgapdh-2 is related more to stress/immune responses, in the mud loach.

Homeodomain-leucine zipper (HD-Zip) family proteins are unique to plants, but little is known about their role in defense responses. CaHB1 is a nuclear factor in peppers, belonging to subfamily II of HD-Zip proteins. Here, we determined the role of CaHB1 in the defense response. CaHB1 expression was induced when pepper plants were challenged with Phytophthora capsici, a plant pathogen to which peppers are susceptible, or environmental stresses such as drought and salt stimuli. CaHB1 was also highly expressed in pepper leaves following application of SA, whereas ethephon and MeJA had a moderate effect. To further investigate the function of CaHB1 in plants, we performed gain-of-function study by overexpression of CaHB1 in tomato. CaHB1-transgenic tomatoes showed significant growth enhancement including increased leaf thickness and enlarged cell size (1.8-fold larger than control plants). Microscopic analysis revealed that leaves from CaHB1-transgenic plants had thicker cell walls and cuticle layers than those from controls. Moreover, CaHB1-transgenic plants displayed enhanced resistance against Phytophthora infestans and increased tolerance to salt stress. Additionally, RT-PCR analysis of CaHB1-transgenic tomatoes revealed constitutive up-regulation of multiple genes involved in plant defense and osmotic stress. Therefore, our findings suggest roles for CaHB1 in development, salt stress, and pathogen defense.

An anesthetic protocol was optimized for microinjection-related handling of Siberian sturgeon (Acipenser baerii; Acipenseriformes) prolarvae, an extant primitive fish species commonly grown in aquaculture. Comparative examinations of three selected anesthetics (clove oil, lidocaine, and MS-222) with a dosage regime of 50, 100, 200, and 400 mg/L indicated that MS-222 was the most efficient agent for Siberian sturgeon prolarvae, as evidenced by the fast induction of anesthesia with quick and uniform recovery. Meanwhile, clove oil should be avoided, due to prolonged recovery times varying widely between individuals. None of the tested anesthetics significantly affected prolarval viability at any of the dosage regimes tested in this study. Based on an analysis of the duration of an unconscious state in air, we recommend a dose of 200 mg/L MS-222 for microinjection. Recovery time after use of this dose was influenced by the prolarval age and the development of gills, in which prolarvae older than 3 days after hatching required longer recovery times than did younger prolarvae. Post-recovery behavioral assessment showed no apparent difference between MS-222-anesthetized and non-anesthetized prolarvae in their swimming behavior and phototactic responses. Applicability of currently developed anesthetic protocol using MS-222 in larval microinjection was demonstrated with the injection of a visible dye to the anesthetized prolarvae, followed by the analysis of post-recovery viability. Taken together, the present anesthetic protocol based on 200 mg/L of MS-222 could provide researchers with practical usefulness with good safety margins for the micromanipulation and other related handlings of Siberian sturgeon prolarvae.

Purpose: Transglutaminase 2 (TGase 2) is expressed by tumor necrosis factor-α in various carcinoma. The role of TGase 2 expression in salivary gland tumors is not clear yet. Established slaivary gland tumor (SGT)cell line has been used to study the pathogenesis of salivary gland adenocarcinoma on a cellular level in vitro. The pupose of this study were to examine mRNA expression of TGase 2 in SGT cell line compared to other tumor cell lines, and to apply these results to the pathogenesis of salivary gland tumor. Materials and Methods: After SGT, SCC-15, HN 4, and HeLa tumor cell lines were cultured under preconfl uency, and 3 days after postconfl uency, the cells were harvested for total RNA extraction and cDNA preparation. Result: Reverse transcription polymerase chain reaction for semiquantitative mRNA analysis was done. TGase 2 mRNA expression was not induced by confl uency in all the cell lines. TGase 2 mRNA expression was variable but markedly enhanced in SGT cell line. Conclusion: mRNA expression of TGase 2 should play an important role in the pathogenesis of SGT cell line originated from ductal cell.

The genomic structure including the 5′-upstream regulatory region of the fast skeletal myosin light chain 2 gene (mlc2f) was characterized in the marine medaka (Oryzias dancena; Beloniformes). Molecular phylogenic analysis inferred that the marine medaka mlc2f should belong to the teleost mlc2fa group characterized by seven-exon organization. Bioinformatic analysis of the regulatory region represented the various transcription factor binding motifs especially including myogenic regulatory factor binding sites such as myocyte enhancer factor-2 site and E-box. Real-time RT-PCR assays revealed that the mlc2f mRNA was highly predominant in skeletal muscles and also that the muscular mlc2f expression was little modulated by environmental salinity ranging from 0 to 30 ppt. The mlc2f mRNA expression was differentially modulated during embryonic development of this species, in which the expression of mlc2f was stimulated from the retinal pigmentation stage and then markedly activated until hatching. From the microinjection-based introduction of a green fluorescent protein gene (gfp) driven by a 2.95-kb marine medaka mlc2f promoter into the marine medaka embryos, the onset of transgenic GFP expression was in accordance with that of endogenous mlc2f gene. Although all the microinjected embryos and resultant F0 fish showed a mosaic distribution of GFP expression with some ectopic expression pattern, the overall expression of transgenic GFP was enriched in the skeletal muscles. However, transgenic hemizygous F1 fish produced from the germline positive founders showed uniform, fast-skeletal muscle-specific expression of GFP, which resembled the pattern of the endogenous mlc2f gene expression. The expression of transgenic GFP was observable mainly in head region and weakly in caudal peduncle of the hatched larvae. The GFP expression was gradually intensified in these sites and became spread over other skeletal muscle parts with larval ages, such that the fish at 21 days post hatching acquired uniform GFP expression over nearly whole skeletal muscles. Data from this study suggest that the mlc2f promoter-driven transgenesis holds promising potential to monitor the differentiation of the fast skeletal muscles of this species in a real-time fashion and also to drive efficiently the expression of foreign proteins in the marine medaka skeletal muscles.

We characterized the cytoskeletal beta-actin (β-ACT) gene (actb) and its 5´-upstream regulatory region in the Javanese ricefish Oryzias javanicus. The gene and protein structures were deduced from amino acid sequences of the actb gene and conserved in the teleost lineage. The O. javanicus actb gene has common transcription factor binding motifs in its regulatory region found in teleostean orthologues. Following quantitative reverse transcription-PCR, actb gene transcripts were detected in all tissues examined; however, the basal expression levels were different. During early development, O. javanicus actb mRNA levels showed a gradual increase and peaked between late somitogenesis and the heartbeat stage. Microinjection of O. javanicus embryos with the actb gene promoter-driven red fluorescent protein (RFP) gene reporter vector showed a ubiquitous distribution of RFP signals, although most exhibited a mosaic pattern of transgene expression. A small number of microinjected embryos displayed a wide distribution of RFP signals over their entire body, which resembled the expression pattern of endogenous actb. Data from this study provide a basis to develop a transgenic system with ubiquitous expression of foreign genes in O. javanicus.

The simple sequence repeats (SSRs) are short tandem arrayed sequence motifs consisting of 2–6 bp, which are not only involved in causing human fatal diseases but also have various applications in plant genetic studies. Thanks to the advancements made in sequencing technology, now we can easily generate genomic/transcriptomic sequences in a shorter period of time. Therefore, trend to identify SSR markers needs up gradation to handle these high-throughput data. Unfortunately, existing web programs for identifying SSR markers are useful but they are unable to process high-throughput data. To overcome this disadvantage, we have constructed a web-based tool, RISA (http://sol.kribb.re.kr/RISA/), with a goal of one-click service to identify SSR markers from high-throughput data (up to 200 Mbp). RISA controls automatic input and output pipeline by demon which combines the SSR classification and investigation by Robert Kofler (SciRoKo) to search SSRs and Primer3 to identify primers specific to SSRs simultaneously. In our test, 45,495 qualified primer sets specific to 47,070 SSRs were identified by RISA from whole Arabidopsis lyrata genome (about 207 Mbp) in 15 minutes. In results, it includes SSR statistics generated from user’s queries and SSR markers information along with primers suitable for their amplification. To support handling of large amount of results, RISA provides various filtering options such as motif length, repeat units, total length and PCR product size. Therefore, we propose that RISA minimizes labour-intensive works or any other considerations which can be required during the development of SSR markers without having deep understanding of computer system and/or algorithms.

Stable transgenic germlines carrying the red fluorescence protein (RFP) gene (rfp) driven by fast skeletal myosin light chain-2 gene (mlc2f) promoter were established in a truly euryhaline fish species, the marine medaka (Oryzias dancena; Beloniformes). Transgenic lines contained transgene copy numbers varying from a single copy to more than 230 copies per genome. Although the transgenic founders displayed mosaic and/or ectopic expression of the RFP signal, the resultant F1 transgenics and their progeny showed consistently stable transmission of the transgenic locus and uniform RFP signal through several subsequent generations. In adult transgenics, an authentic brilliant red fluorescence was achieved over the skeletal muscles of the transgenic individuals, which might be sufficient for ornamental display. Expression analysis of the transgenic mRNAs indicated that rfp transcripts were predominantly expressed in the skeletal muscles. Different transgenic lines displayed different levels of transgene expression at the mRNA, protein, and phenotypic levels. However, the efficiency of transgene expression was independent of the transgene copy number. The RFP protein levels were consistently stable in the transgenic fish muscles through several generations, up to F5. The results of this study suggest that transgenic marine medaka that acquire strong fluorescent signals in their skeletal muscles can be developed as a promising, novel ornamental fish for display in both freshwater and seawater aquaria.

Background The oriental melon (Cucumis melo L. var. makuwa) is one of the most important cultivated cucurbits grown widely in Korea, Japan, and northern China. It is cultivated because its fruit has a sweet aromatic flavor and is rich in soluble sugars, organic acids, minerals, and vitamins. In order to elucidate the genetic and molecular basis of the developmental changes that determine size, color, and sugar contents of the fruit, we performed de novo transcriptome sequencing to analyze the genes expressed during fruit development. Results We identified a total of 47,666 of representative loci from 100,875 transcripts and functionally annotated 33,963 of the loci based on orthologs in Arabidopsis thaliana. Among those loci, we identified 5,173 differentially expressed genes, which were classified into 14 clusters base on the modulation of their expression patterns. The expression patterns suggested that the differentially expressed genes were related to fruit development and maturation through diverse metabolic pathways. Analyses based on gene set enrichment and the pathways described in the Kyoto Encyclopedia of Genes and Genomes suggested that the expression of genes involved in starch and sucrose metabolism and carotenoid biosynthesis were regulated dynamically during fruit development and subsequent maturation. Conclusion Our results provide the gene expression patterns related to different stages of fruit development and maturation in the oriental melon. The expression patterns give clues about important regulatory mechanisms, especially those involving starch, sugar, and carotenoid biosynthesis, in the development of the oriental melon fruit.

Alpha-dioxygenases (α-DOX) catalyzing the primary oxygenation of fatty acids to oxylipins were recently found in plants. Here, the biological roles of the pepper α-DOX (Ca-DOX) gene, which is strongly induced during non-host pathogen infection in chili pepper, were examined. Virus-induced gene silencing demonstrated that down-regulation of Ca-DOX enhanced susceptibility to bacterial pathogens and suppressed the hypersensitive response via the suppression of pathogenesis-related genes such as PR4, proteinase inhibitor II and lipid transfer protein (PR14). Ca-DOX-silenced pepper plants also exhibited more retarded growth with lower epidermal cell numbers and reduced cell wall thickness than control plants. To better understand regulation of Ca-DOX, transgenic Arabidopsis plants harboring the β-glucuronidase (GUS) reporter gene driven from a putative Ca-DOX promoter were generated. GUS expression was significantly induced upon avirulent pathogen infection in transgenic Arabidopsis leaves, whereas GUS induction was relatively weak upon virulent pathogen treatment. After treatment with plant hormones, early and strong GUS expression was seen after treatment of salicylic acid, whereas ethylene and methyl jasmonate treatments produced relatively weak and late GUS signals. These results will enable us to further understand the role of α-DOX, which is important in lipid metabolism, defense responses, and growth development in plants.

Paclitaxel is produced by various species of yew trees and has been extensively used to treat tumors. In our research, a taxadiene synthase (TS) gene from Taxus brevifolia was used to transform the roots of cultured ginseng (Panax ginseng C.A. Meyer) to produce taxadiene, the unique skeletal precursor to taxol. The TS gene was successfully introduced into the ginseng genome, and the de novo formation of taxadiene was identified by mass spectroscopy profiling. Without any change in phenotypes or growth difference in a TS-transgenic ginseng line, the transgenic TSS3-2 line accumulated 9.1 mu g taxadiene per gram cf dry weight In response to the treatment of methyl jasmonate for 3 or 6 days, the accumulation was 14.6 and 15.9 mu g per g of dry weight, respectively. This is the first report of the production of taxadiene by engineering ginseng roots with a taxadiene synthase gene. [BMB Reports 2012; 45(10): 589-594]

The marine medaka Oryzias dancena choriogenin H gene (odChgH) and its mRNA expression during estradiol- (E2) exposure were characterized. At the amino acid level, the choriogenin H protein is predicted to possess the conserved repetitive N-terminal region, as well as zona pellucida (ZP) and Trefoil factor family (TFF) domains. At the genomic level, odChgH has an eight-exon organization with a distribution pattern of transcription factor binding sites in the 5'-upstream region, which is commonly found in other estrogen-responsive genes. The tissue distribution pattern of odChgH mRNA was found to be gender-specific, whereby females showed a higher expression level and wider tissue distribution than did males. During embryonic development, odChgH mRNA was robustly detected from the stage of visceral blood vessel formation. Experimental E2 exposure of males resulted in odChgH mRNA being induced not only in the liver, but also in other several tissues. The E2-mediated induction was fairly dose-dependent. The basal expression levels of hepatic odChgH mRNA were lower in males that were acclimated to 30 ppt salinity than in those acclimated to 0 or 15 ppt salinity. In contrast, the inducibility of odChgH mRNA during E2 exposure was greater in seawater-acclimated fish than in brackish water- or freshwater-acclimated fish.

Transgenic marine medaka (Oryzias dancena) germlines were generated by the microinjection of the red fluorescent protein (RFP) reporter gene (rfp) driven by the endogenous choriogenin H gene (chgH) promoter. The selected transgenic lines contained multiple copies of the transgene (3-42 copies per cell) in their genomes. Although all the founders were mosaic, the transgene was stably transmitted from the F1 generation to all subsequent generations following a Mendelian pattern. Different transgenic lines showed different responsiveness to estradiol-17β (E2) exposure at the mRNA and protein levels, and the expression efficiency was dependent upon the transgene copy number. The induction of RFP was significantly affected by the developmental stage of transgenic larvae: later-stage larvae (older than 7 days post-hatching) showed higher sensitivity to E2 exposure than earlier-stage larvae. The response of transgenic expression to E2 was fairly dependent upon the E2 dose (200-3,200 ng/L) and exposure period (1-7 days), according to both a microscopic examination of RFP intensity and a qRT-PCR assay. The transgenic marine medaka showed similar transgenic responses to E2 under freshwater, brackish, and seawater conditions. In addition to E2, the transgenic RFP signal was also successfully induced during 1-week exposure to various other natural (1 μg/L estrone and 10 μg/L estriol) and synthetic (xeno)estrogens (0.1 μg/L 17α-ethynylestradiol, 1 μg/L diethylstilbestrol, and 10 mg/L bisphenol A). The efficiency of transgene expression varied greatly among the chemicals tested. The results of this study suggest that the chgH-rfp transgenic marine medaka species will be useful in the in vivo detection of waterborne estrogens under a wide range of salinity conditions.

Reed (Phragmites communis) is a potential bioenergy plant. We report on its first Agrobacterium-mediated transformation using mature seed-derived calli. The Agrobacterium strains LBA4404, EHA105, and GV3101, each harboring the binary vector pIG121Hm, were used to optimize T-DNA delivery into the reed genome. Bacterial strain, cocultivation period and acetosyringone concentration significantly influenced the T-DNA transfer. About 48% transient expression and 3.5% stable transformation were achieved when calli were infected with strain EHA105 for 10 min under 800 mbar negative pressure and cocultivated for 3 days in 200 lM acetosyringone containing medium. Putative transformants were selected in 25 mg l 1 hygromycin B. PCR, and Southern blot analysis confirmed the presence of the transgenes and their stable integration. Independent transgenic lines contained one to three copies of the transgene. Transgene expression was validated by RT-PCR and GUS staining of stems and leaves.

Two paralogous isoform cDNAs of warm-temperature-acclimation-associated 65-kDa protein (Wap65-1 and Wap65-2) were isolated from the cypriniform species, mud loach (Misgurnus mizolepis), and characterized. The deduced amino acid sequences of the two mud loach Wap65 isoforms (mlWap65-1 and mlWap65-2) share moderate levels of sequence homology with their corresponding orthologues from teleosts and with human hemopexin, a possible mammalian homologue. Both isoforms display conserved features, including essential motifs and/or residues that are important for the protein structure of hemopexin. In overall, mlWap65-2 is more homologous to human hemopexin than is mlWap65-1. Both mud loach Wap65 transcripts are predominantly expressed in liver, although the transcripts are ubiquitously detectable in most tissues with variable basal expression. Both mlWap65 isoforms are differentially regulated during embryonic development, and the changes in transcript levels during embryogenesis are greater for mlWap65-2 than for mlWap65-1. The transcription of the mlWap65 genes is differentially modulated by various stimuli, including thermal changes, immune challenge (lipopolysaccharide injection or bacterial infection), and heavy metal exposure (cadmium, copper, or nickel). The isoform mlWap65-1 is more responsive to warm temperature treatments than mlWap65-2, whereas mlWap65-2 is much more strongly stimulated by immune and heavy metal challenges than is mlWap65-1. Taken together, the results of this study suggest that mud loach Wap65 isoforms are potentially involved in multiple cellular pathways and that the two mud loach Wap65 isoforms undergo functional partitioning or subfunctionalization.

We determined the complete mitogenome sequences for four Coreoleuciscus splendidus strains (Teleostei: Cypriniformes) inhabiting the Han and Geum river drainages in the West Korea Subdistrict, and the Seomjin and Nakdong river drainages in the South Korea Subdistrict in the Korean peninsula. The gene contents and arrangement of C. splendidus were homogeneous to those of typical vertebrates. Phylogenetic analysis with the partitioned nucleotide matrix of concatenated mitochondrial genes revealed that C. splendidus formed a monophyletic group with gobionine species in the cyprinid lineage. The four river strains separated into two phylogenetically distinct groups, which were in accordance with the biogeographical distribution pattern in Korea according to subdistrict. The estimated divergence time among western and southern subdistrict populations was 37.9 ± 6.5 million years ago (Mya), whereas those between the two river strains in each subdistrict were estimated to be 3.2–3.4 Mya. The presence of such distinct historical lineages has great implications for biogeography of ichthyofauna in Korea and future management and conservation plans of C. splendidus populations.

Plants express resistance (R) genes to recognize invaders and prevent the spread of pathogens. To analyze nucleotide binding site, leucine-rich repeat (NB-LRR) genes, we constructed a fast pipeline to predict and classify the R gene analogs (RGAs) by applying in-house matrices. With predicted ~37,000 RGAs, we can directly compare RGA contents across entire plant lineages, from green algae to flowering plants. We focused on the highly divergent NBLRRs in land plants following the emergence of mosses. We identified entire loss of Toll/Interleukin-1 receptor, NBLRR (TNL) in Poaceae family of monocots and interestingly from Mimulus guttatus (a dicot), which leads to the possibility of species-specific TNL loss in other sequenced flowering plants. Using RGA maps, we have elucidated a positive correlation between the cluster sizes of NB-LRRs and their numbers. The cluster members were observed to consist of the same class of NB-LRRs or their variants, which were probably generated from a single locus for an R gene. Our website ( http://sol.kribb.re.kr/PRGA/ ), called plant resistance gene analog (PRGA), provides useful information, such as RGA annotations, tools for predicting RGAs, and analyzing domain profiles. Therefore, PRGA provides new insights into R-gene evolution and is useful in applying RGA as markers in breeding and or systematic studies.

We characterized a cytoplasmic actin gene locus in greenling Hexagrammos otakii (Scorpaeniformes). Genomic clones isolated from the greenling DNA library contained two homologous cytoplasmic actin gene copies (HObact2.1 and HObact2.2) in a tail-to-head orientation. Their gene structure is characterized by six translated exons and one non-translated exon. Exon-intron organization and the nucleotide sequences of the two actin gene isoforms are very similar. However, only the HObact2.1 isoform contains microsatellite-like, dinucleotide repeats in the 5'-flanking region (named HOms2002) and intron 1 following the non-translated exon 1 (named HOms769). One microsatellite locus (HOms769) was highly polymorphic while the other (HOms2002) was not. Based on bioinformatic analysis, different transcription factor binding motifs are related to stress and immune responses in the two actin isoforms. Semiquantitative and real-time reverse transcription-PCR assays showed that both isoform transcripts were detectable ubiquitously in all the tissues examined. However, the basal expression levels of each isoform varied across tissues. Overall, the two isoforms showed a similar, but not identical, expression pattern. Our data suggest that the cytoplasmic actin genes may be the result of a recent duplication event in the greenling genome, which has not experienced significant subfunctionalization in their housekeeping roles.

A trap identification system for isolating functional sequences to allow the constitutive expression of foreign protein from Edwardsiella tarda was developed. Using the green fluorescent protein (GFP) reporter-based trap system, various functional sequences to drive heterologous expression of the GFP were selectable in Escherichia coli host. However from the bioinformatic sequence analysis, all the segments predicted as regulatory regions were not native promoters actually existing upstream of endogenous E. tarda genes. Instead, a number of non-authentic sequences, possibly resulted from the random shuffling and/or intermolecular ligation were also proven to be able to display a potent GFP expression in the recombinant E. coli. Further analysis with selected clones showed that both authentic and non-authentic sequences could function in as a constitutive promoter, leading quite a consistent and stable GFP expression after repetitive subcultures. Microscopic examination also confirmed the uniform pattern of GFP expression in every host bacterium. Semi-quantitative assay of GFP showed that there was no clear relationship between expression levels and organizational features of the promoters trapped. Functional promoter-like elements achieved in the present study could be a good starting material for multivalent genetic engineering of E. tarda in order to produce recombinant vaccines in a cost-effective fashion.

The gene encoding hepcidin, an antimicrobial peptide, was isolated and characterized in the mud loach Misgurnus mizolepis (Cypriniformes). Mud loach hepcidin shows a considerable degree of structural homology to other vertebrate hamp1 orthologues at both the gene and protein levels, particularly with respect to its tripartite genomic organization, typical transcription-factor-binding motifs in its promoter, and conserved cysteine residues in the mature cationic peptide. The mud loach possesses at least two allelic forms of hamp1, which are expected to be translated into the same hepcidin preproprotein. The two alleles are transmitted from parental fish to offspring with a Mendelian inheritance pattern, as demonstrated with polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) genotyping. Southern blot hybridization analysis showed a high degree of polymorphisms in the restriction patterns of individuals. Mud loach hamp1 mRNA is predominantly expressed in the liver, although many other tissues showed detectable levels of hamp1 transcripts in RT-PCR assay. Lipopolysaccharide and bacterial challenges induced significant hamp1 expression, whereas hamp1 was not clearly stimulated by polyinosinic:polycytidylic acid [poly(I:C)] injection. Iron overload and Cu exposure also elevated hamp1 transcripts in various tissues. The transcriptional activation of mud loach hamp1 in response to these stimuli varied among tissue types, and the liver appears predominantly involved in hepcidin-mediated iron regulation. However, hepcidin expression in the kidney and spleen was preferentially modulated by inflammation-mediated signals produced by immune challenges. Our results suggest that mud loach hepcidin has two basic functions, in iron regulation and antimicrobial activity, and that its transcription is also modulated by other environmental perturbations, including heavy metal exposure.

Two hepcidin paralogs (ojhamp1 and ojhamp2) were isolated and characterized from a euryhaline Javanese ricefish (Oryzias javanicus: Beloniformes). The ojhamp1 cDNA encoded 90 or 91 amino acids (aa) of a typical HAMP1 preproprotein. This preproprotein is believed to cleave and yield the 66 or 67 aa-proprotein, followed by the 26 aa-mature peptide, composed of 8 conserved cysteine residues and the QSHL amino terminal motif. The ojhamp2 cDNA encoded 89 aa of HAMP2 preproprotein, cleaved to yield a 65 aa proprotein, and subsequently the 25 aa-mature peptide. The mature OJHAMP1 possessed a cationic isoelectric point (pI), whereas OJHAMP2 had an anionic charge. At the genomic level, both ojhamp1 and ojhamp2 share a conserved tripartite structure (three exons interrupted by two introns) with other vertebrate hepcidin genes. However, the ojhamp1 was shown to exist as two distinct mRNA species, encoding 90 or 91 aa, due to alternative splicing at the junction site between intron I and exon II. Both ojhamp1 and ojhamp2 transcripts were detected in a wide range of tissue types with varying levels of basal expression, although the highest expression was observed in the liver for both isoforms. Transcriptional response to bacterial challenge using Edwardsiella tarda showed that ojhamp1 was moderately upregulated in the liver but remained unchanged in the kidney. However, the ojhamp2 was significantly suppressed in both the kidney and liver, suggesting a potential diversification between the two paralogs.

Chinese medaka Oryzias sinensis (Teleostei: Beloniformes) is distributed in China and the western areas of Korea. It differs from the Japanese medaka O. latipes in its morphology and biogeographical distribution in Korea. In this study, we analyzed the complete nucleotide sequence of the mitochondrial genome (mitogenome) of O. sinensis and determined its genomic structure. The complete mitogenome is a circular molecule of 16,654 bp and its structural organization is conserved across diverse vertebrate taxa. On a phylogenetic tree inferred from the nucleotide matrix, partitioned into four regions (i.e., the first and second codon positions of protein-coding genes, and the ribosomal RNA and transfer RNA genes), O. sinensis clustered consistently with O. latipes specimens from China and Korea, with a relatively short branch length, but was separated from O. latipes specimen from Japan. Our findings will allow the resolution of the taxonomic problems of closely related Oryzias species, such as O. sinensis and O. latipes in a future study.