Characterization of the complete mitochondrial genome of the white grouper Epinephelus aeneus (Perciformes, Serranidae) and a comparative analysis with other Serranidae species.

The complete mitochondrial genome of the white grouper Epinephelus aeneus, which belongs to the family Serranidae, was determined. The complete mitochondrial genome measured 16,578 bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. The mitochondrial gene arrangement of E. aeneus was typical of vertebrates. Phylogenetic analysis conducted using the mitochondrial genomes of 13 related species showed that E. aeneus clustered with other Serranidae species. This mitochondrial genome provides an important resource for addressing taxonomic issues and developing conservation strategies.

The full-length mitochondrial genome of the crocodile icefish, Chionobathyscus dewitti (Teleostei: Perciformes: Channichthyidae).

The full-length mitochondrial genome of the crocodile icefish, Chionobathyscus dewitti (Teleostei: Perciformes: Channichthyidae) was analyzed by the primer walking method. The mitogenome was 17,451 bp in total length, comprising 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Its gene order was congruent with those of the other crocodile icefish but different with those of typical vertebrates. In the phylogenetic tree, C. dewitti showed the closest relationship to Chaenocephalus aceratus in the same family.

The complete mitochondrial genome of Cynoglossus interruptus and its novel rearrangement (Pleuronectiformes: Cynoglossidae).

The complete mitochondrial genome was determined for the Cynoglossus interruptus belonging to the family Cynoglossidae. The length of the complete mitochondrial genome is 17,262 bp, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. The gene rearrangement related to tRNAGln and a control region gene were found, forming the gene order of CR-Ile-Gln-Met. Phylogenetic analysis using mitochondrial genomes of 12 species showed that C. interruptus formed a well-supported monophyletic group with other Cynoglossus species.

The full-length mitochondrial genome of the Fernholm's hagfish, Myxine fernholmi (Myxini; Myxiniformes; Myxinidae).

The full-length mitochondrial genome of the Fernholm's hagfish, Myxine fernholmi (Myxini; Myxiniformes; Myxinidae) was analyzed by the primer walking method. Its mitogenome was 18,862 bp in total length and was composed of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. The gene content and order were congruent with those of typical vertebrates. In the phylogenetic tree, M. fernholmi showed the closest relationship to M. glutinosa in the same genus and subfamily and well separated from the other hagfish in the subfamily Eptatretinae.

Characterization of the complete mitochondrial genome of Dactylopterus volitans (Syngnathiformes, Dactylopteridae).

The complete mitochondrial genome was determined for the flying gurnard Dactylopterus volitans belonging to the family Dactylopteridae. The total length of the D. volitans mitochondrial genome is 16,632 bp, which consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. It has the typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis using mitochondrial genomes of 20 species showed that D. volitans formed a well-supported monophyletic group with other Dactylopteridae species.

Gene rearrangements in the mitochondrial genome of robust tonguefish, Cynoglossus robustus (Pleuronectiformes: Cynoglossidae) and a comparative analysis with other Cynoglossus fishes.

The complete mitochondrial genome was determined for the Robust tonguefish Cynoglossus robustus belonging to the family Cynoglossidae. The length of the complete mitochondrial genome is 16,720 bp, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. Rearrangements of the tRNAGln and a control region gene were found and tRNAGln is translocated from the light to the heavy strand. Phylogenetic analysis using mitochondrial genomes of 12 species showed that C. robustus formed a well-supported monophyletic group with other Cynoglossus species.

The genome of common long-arm octopus Octopus minor.

Background: The common long-arm octopus (Octopus minor) is found in mudflats of subtidal zones and faces numerous environmental challenges. The ability to adapt its morphology and behavioral repertoire to diverse environmental conditions makes the species a promising model for understanding genomic adaptation and evolution in cephalopods. Findings: The final genome assembly of O. minor is 5.09 Gb, with a contig N50 size of 197 kb and longest size of 3.027 Mb, from a total of 419 Gb raw reads generated using the Pacific Biosciences RS II platform. We identified 30,010 genes; 44.43% of the genome is composed of repeat elements. The genome-wide phylogenetic tree indicated the divergence time between O. minor and Octopus bimaculoides was estimated to be 43 million years ago based on single-copy orthologous genes. In total, 178 gene families are expanded in O. minor in the 14 bilaterian species. Conclusions: We found that the O. minor genome was larger than that of closely related O. bimaculoides, and this difference could be explained by enlarged introns and recently diversified transposable elements. The high-quality O. minor genome assembly provides a valuable resource for understanding octopus genome evolution and the molecular basis of adaptations to mudflats.

Effect of phlorotannins on myofibroblast differentiation and ECM protein expression in transforming growth factor ß1­induced nasal polyp­derived fibroblasts.

Phlorotannins (PTNs), a group of phenolic compounds from seaweeds, have diverse bioactivities. However, there has been no report on their antifibrotic effects during nasal polyp (NP) formation. In the present study, the effect of PTNs on transforming growth factor (TGF)­ß1­induced profibrotic responses in nasal polyp­derived fibroblasts (NPDFs) were determined and the relevant signaling pathways were investigated. The expression levels of collagen type­1 (Col­1) and fibronectin in NP tissues were measured by western blot analysis and immunohistochemistry. The NPDFs were treated with TGF­ß1 (1 ng/ml) in the presence or absence of PTNs (5­30 µg/ml). The expression levels of α­smooth muscle actin (α­SMA), Col­1, fibronectin, and phosphorylated­small mothers against decapentaplegic (Smad)2/3 in NPDFs were measured by western blot analysis. The contractile activity of the NPDFs was determined by a collagen gel contraction assay. Col­1 and fibronectin proteins were found to be expressed in NP tissues. PTNs had no significant cytotoxic effect on TGF­ß1­induced NPDFs. TGF­ß1 induced the expression α­SMA, Col­1 and fibronectin, and stimulated fibroblast­mediated contraction of collagen gel. However, pre­treatment with PTNs inhibited the expression of these proteins. The inhibitory effects were mediated through the suppression of Smad2/3 signaling pathways in TGF­ß1­induced NPDFs. These resulted suggested that PTNs may be important in inhibiting myofibroblast differentiation and extracellular matrix protein accumulation in NP formation through the Smad2/3 signaling pathway.

Spermidine Protects against Oxidative Stress in Inflammation Models Using Macrophages and Zebrafish.

Spermidine is a naturally occurring polyamine compound that has recently emerged with anti-aging properties and suppresses inflammation and oxidation. However, its mechanisms of action on anti-inflammatory and antioxidant effects have not been fully elucidated. In this study, the potential of spermidine for reducing pro-inflammatory and oxidative effects in lipopolysaccharide (LPS)-stimulated macrophages and zebrafish was explored. Our data indicate that spermidine significantly inhibited the production of pro-inflammatory mediators such as nitric oxide (NO) and prostaglandin E2 (PGE2), and cytokines including tumor necrosis factor-α and interleukin-1ß in RAW 264.7 macrophages without any significant cytotoxicity. The protective effects of spermidine accompanied by a marked suppression in their regulatory gene expression at the transcription levels. Spermidine also attenuated the nuclear translocation of NF-κB p65 subunit and reduced LPS-induced intracellular accumulation of reactive oxygen species (ROS) in RAW 264.7 macrophages. Moreover, spermidine prevented the LPS-induced NO production and ROS accumulation in zebrafish larvae and was found to be associated with a diminished recruitment of neutrophils and macrophages. Although more work is needed to fully understand the critical role of spermidine on the inhibition of inflammation-associated migration of immune cells, our findings clearly demonstrate that spermidine may be a potential therapeutic intervention for the treatment of inflammatory and oxidative disorders.

Anti-inhibitory potential of an ethanolic extract of Distromium decumbens on pro-inflammatory cytokine production in Pseudomonas aeruginosa lipopolysaccharide-stimulated nasal polyp-derived fibroblasts.

Marine algae are rich sources of biologically active compounds that may present useful leads in the development of pharmaceuticals, nutraceuticals, and functional foods. The main aim of this study was to identify the possible anti-inflammatory effects of Distromium decumbens in nasal polyp-derived fibroblasts (NPDFs) and its associated mechanism of action. NPDFs were stimulated by Pseudomonas aeruginosa lipopolysaccharide (PA-LPS) and treated with an ethanolic extract of Distromium decumbens (DDE). The production of interleukin-6 (IL-6) and IL-8 in the supernatant, the phosphorylation of mitogen-activated protein kinase (MAPK) molecules [extracellular signal-related kinase 1/2 (ERK1/2), c-Jun N-terminal kinase and p38 MAPK] and Akt, and the activation of nuclear factor-κB (NF-κB) were assayed in the PA-LPS-stimulated NPDFs untreated or treated with DDE. The expression levels of IL-6 and IL-8 in PA-LPS-exposed NPDFs were detected using enzyme-linked immunosorbent assays. The mechanisms by which DDE regulates cellular signaling cascades were investigated using electrophoretic mobility shift assays and western blot analysis. Functional validation was performed by measuring the inhibitory effects of DDE on neutrophil migration in vitro. DDE reduced the expression of IL-6 and IL-8 stimulated by PA-LPS in NPDFs. The activation of ERK1/2, Akt and NF-κB by PA-LPS was inhibited by DDE. Inhibitors of ERK1/2, Akt and NF-κB inhibited the expression of IL-6 and IL-8. In addition, DDE significantly attenuated PA-LPS-induced migration of differentiated HL-60 cells. The present findings suggest that DDE potently inhibits inflammation through the ERK1/2, Akt and NF-κB signaling pathways in NPDFs.

Benzyl isothiocyanate inhibits inflammasome activation in E. coli LPS-stimulated BV2 cells.

Inflammasomes are multi-protein complexes that play a crucial role in innate immune responses. Benzyl isothiocyanate (BITC) is a naturally occurring compound found in cruciferous vegetables, and BITC exhibits potential as a chemopreventive agent. However, whether BITC exerts inflammasome-mediated regulatory effects on neuroinflammation is unknown. In this study, we examined the effects of BITC on inflammasome-mediated interleukin-1ß (IL-1ß) production in E. coli lipopolysaccharide (LPS)-stimulated BV2 microglial cells. IL-1ß production is tightly regulated at the post-translational level through the inflammasoume. We measured the levels of IL-1ß produced from the LPS-exposed BV2 microglial cells using enzyme-linked immunosorbent assays (ELISAs). The BITC regulatory mechanisms in inflammasome-mediated cellular signaling pathways were examined by RT-PCR, western blot analysis and electrophoretic mobility shift assays. BITC inhibited the secretion of IL-1ß induced by LPS in the BV2 microglial cells. BITC inhibited inflammasome activation and NLR family, pyrin domain containing 3 (NLRP3)-mediated caspase-1 activation, and decreased the levels of inflammasome activation pro-inflammatory mediators, including mitochondrial reactive oxygen species (ROS) and adenosine triphosphate (ATP) secretion in the LPS-stimulated BV2 microglial cells. Furthermore, we demonstrated that nuclear factor-κB (NF-κB) activation induced by LPS was inhibited by BITC, which may contribute to the attenuated secretion of IL-1ß. These BITC-mediated inhibitory effects on IL-1ß expression may thus regulate neuroinflammation through the inflammasome-mediated signaling pathway.

Anti-allergic effects of a nonameric peptide isolated from the intestine gastrointestinal digests of abalone (Haliotis discus hannai) in activated HMC-1 human mast cells.

The aim of the present study was to examine whether the intestine gastrointestinal (GI) digests of abalone [Haliotis discus hannai (H. discus hannai)] modulate inflammatory responses and to elucidate the mechanisms involved. The GI digests of the abalone intestines were fractionated into fractions I (>10 kDa), II (5-10 kDa) and Ⅲ (<5 kDa). Of the abalone intestine GI digests (AIGIDs), fraction Ⅲ inhibited the passive cutaneous anaphylaxis (PCA) reaction in mice. Subsequently, a bioactive peptide [abalone intestine GI digest peptide (AIGIDP)] isolated from fraction Ⅲ was determined to be 1175.2 Da, and the amino acid sequence was found to be PFNQGTFAS. We noted that the purified nonameric peptide (AIGIDP) attenuated the phorbol­12­myristate 13-acetate plus calcium ionophore A23187 (PMACI)-induced histamine release and the production of pro-inflammatory cytokines, such as tumor necrosis factor-α (TNF-α), interleukin (IL)-1ß and IL-6 in human mast cells (HMC-1 cells). In addition, we also noted that AIGIDP inhibited the PMACI­induced activation of nuclear factor­κB (NF-κB) by suppressing IκBα phosphorylation and that it suppressed the production of cytokines by decreasing the phosphorylation of JNK. The findings of our study indicate that AIGIDP exerts a modulatory, anti-allergic effect on mast cell-mediated inflammatory diseases.

Effects of Polygonatum sibiricum rhizome ethanol extract in high-fat diet-fed mice.

CONTEXT: The rhizome of Polygonatum sibiricum Redoute (Liliaceae) has long been used to treat diabetes-associated complications. However, the pharmacological mechanism of P. sibiricum on metabolic disorders is not clear. OBJECTIVE: This study investigates the effect of an ethanol extract of P. sibiricum rhizomes (designated ID1216) on obesity conditions including weight loss in high-fat (HF) diet-fed mice and explores the potential underlying mechanisms. METHODS: To identify the metabolic impact of the P. sibiricum rhizome extract, HF diet-fed mice were administered ID1216 orally at doses of 250 and 1000 mg/kg/d for 10 weeks, and various factors related to metabolic syndrome were analyzed. We also examined the effects of ID1216 on the expression of genes involved in adipogenesis and lipolysis in 3T3-L1 cells, as well as genes associated with energy homeostasis in C2C12 myocytes. RESULTS: ID1216 administration led to significant decreases in body weight gain (37.5%), lipid accumulation in adipose tissues (52.8%), and the levels of plasma triglycerides (26.4%) and free fatty acids (28.1%) at a dose of 250 mg/kg/d, compared with the vehicle-treated group, as well as improved insulin resistance. In addition, ID1216 was found to regulate the expression of genes related to adipogenesis and fatty acid oxidation in 3T3-L1 cells and enhance the expression of genes that modulate energy homeostasis in C2C12 myocytes. CONCLUSIONS: ID1216 may be a promising therapeutic agent for improving obesity conditions through the sirtuin-1 and peroxisome proliferator-activated receptor γ coactivator-1α pathway.

Anti-amyloidogenic effects of ID1201, the ethanolic extract of the fruits of Melia toosendan, through activation of the phosphatidylinositol 3-kinase/Akt pathway.

Amyloid beta (Aß) peptides, which are generated from amyloid precursor protein (APP), are thought to play a major role in the pathogenesis of Alzheimer's disease (AD). This study investigated the anti-amyloidogenic effects of the ethanolic extract of Meliae Fructus (ID1201) using human embryonic kidney 293 cells with stably expressed human wild-type or Swedish mutant APP695 and ß-secretase 1. ID1201 treatment enhanced the non-amyloidogenic metabolism of APP; increases in soluble APPα levels and decreases in soluble APPß and Aß levels resulted from the α-secretase activation through the phosphatidylinositol 3-kinase (PI3K)/Akt pathway. In addition, ID1201-treated 5×familial AD (FAD) mice with 5 mutations in APP and presenilin 1 showed reduced levels of Aß and amyloid plaques in the brain relative to those of 5×FAD mice with vehicle treatments. These results indicate that ID1201 possesses anti-amyloidogenic effects via the activation of the PI3K/Akt pathway, suggesting that it is a potential therapeutic agent for AD.

Productivity and abundance of bacteria and phytoplankton in Incheon Dock, western coast of Korea.

The monthly variations of abundance and productivity of bacteria and phytoplankton were investigated in 2002 at Incheon Dock in Korea, almost closed marine ecosystem. Incheon Dock has unique marine environment with scarcely a current and waves such as in a lake. The bacterial abundance was 0.4-6.3 x 10(6) cells x ml(-1), while the bacterial productivity showed in the range of 0.7-26.3 mgC m(-3) hr(-1). The phytoplankton chlorophyll-a concentrations fell between 2.1 and 18.1 microg x l(-1), where nanoplankton fractions contributed in 32.5-96.78% (average: 73.2%). The algal bloom occurred in March and August, and primary productivity measured by using 14C method, showed a fluctuation ranging from 49.4 to 4,359.4 mgC m(-2) day(-1). The primary productivity of nanotoplankton accounted for 79% of total phytoplankton. Meanwhile, the ratio of bacterial productivity over primary productivity was between 2.0 and 7.7. This study showed that the abundance and productivity of bacteria and phytoplankton were higher at Incheon Dock than those at other coastal areas in Korea. Especially the assimilation number was higher at Incheon Dock than that at lake Shihwa which is a severely eutrophicated area. This result indicates that Incheon Dock has unique ecosystem oceanographically and topographically and it differs from other coastal areas in terms of the low trophic level organisms being abundant and highly productive.

Isolation of tetraprenyltoluquinols from the brown alga Sargassum thunbergii.

Thunbergols A (4) and B (5), tetraprenyltoluquinols, along with three known compounds (1-3) have been isolated from the brown alga Sargassum thunbergii. The structures of these two new compounds were determined to be 9-(3,4-dihydro-2,8-dimethyl-6-hydroxy-2H-1-benzopyran-2-yl)-6-methyl-2-(4-methyl-3-pentenyl)-(2E,6E)-nonadienoic acid (4) and 10-(2,3-dihydro-5-hydroxy-7-methyl-1-benzofuran-2-yl)-10-hydroxy-6-methyl-2-(4-methyl-3-pentenyl)-(2E,6E)-undecadienoic acid (5), respectively, by combined spectroscopic methods. Both of them exhibited significant scavenging activities on radical and potently inhibited generation of ONOO(-) from morpholinosydnonimine (SIN-1).

Morphological variation of dinoflagellate Prorocentrum lima (Ehrenberg) Dodge with geographical difference.

Prorocentrum lima (Ehrenberg) Dodge, one of the cosmopolitan dinoflagellates, is basically benthic and is found on the surface of macroalgae and detritus. The identification of this species requires detailed morphological observation because of its close similarity to other benthic Prorocentrum species. The purpose of this study is to detect the morphological variability of P. lima using culture clones collected from several areas to find an adequate way of subdividing the species. In this study, 33 clones of P. lima were collected from Saipan, Tahiti, Indonesia, Japan and Bermuda, and their thecal valves and periflagellar area were observed by means of light microscopy with differential interference contrast optics and scanning electron microscopy. In general cells have two centrally located pyrenoids and a posterior nucleus. The surface of both valves has many valve pores except the center. Evenly spaced marginal pores are located along the edge of the valves. P. lima samples studied herein were subdivided into four major types (ellipsoidal, general, short, and elongate ovoid) according to their shapes, length-to-width ratio and number of valve pores. The length-to-width ratios of ellipsoidal, general, short, and elongate ovoid types were 1.32, 1.33-1.43, 1.20-1.27, and 1.53-1.60 microm respectively. Also there were slight differences in the number of valve pores. The number of valve pores examined in this study ranges from 40 to 97: ellipsoidal, general, and short ovoid types range from 40 to 91, while an elongate ovoid type ranges from 80 to 97. The combination of valve shape, number of valve pores and length-to-width ratio provides useful information on the morphological variation of P. lima.