Shewanella goraebulensis sp. nov., isolated from sea water.

A novel Gram-stain-negative, facultatively anaerobic and rod-shaped bacterial strain, designated as DAU312T, was isolated from the sea water of the eastern coast of the Republic of Korea. Optimal growth was observed at 25 °C, pH 7.0-8.0 and with NaCl concentrations of 2.0 % (w/v). Catalase and oxidase activities were detected. On the basis of 16S rRNA gene sequences, strain DAU312T showed the highest similarity (99.2 %) to the type strain Shewanella electrodiphila MAR441T. The complete genome sequence of strain DAU312T contains 4 893 483 bp and 40.5 mol% G+C. Phylogenetic analyses based on 16S rRNA gene sequences and the up-to-date bacterial core genes showed that strain DAU312T, S. electrodiphila MAR441T and S. olleyana were all part of the same monophyletic clade. Their average nucleotide identity, digital DNA-DNA hybridization and two-way average amino acid identity values with each other and type strains of close Shewanella species were 83.4-77.5 %, 27.3-22.0 % and 89.8-81.2 %, respectively. The major cellular fatty acids (>10 %) were iso-C15 : 0, summed feature 3 (C16 : 1 ω7с and/or C16 : 1 ω6с) and C16 : 0. Phosphatidylethanolamine and phosphatidylglycerol were the main polar lipids. The respiratory quinones were Q-7, Q-8, MK-7 and MMK-7. Based on these polyphasic taxonomic findings, the name Shewanella goraebulensis sp. nov. is suggested for strain DAU312T, which is considered to represent a novel species of the genus Shewanella. The type strain is DAU312T (=KCTC 72427 T=JCM 35744T=KCCM 43478T).

Analysis of the complete mitochondrial genome sequence of Japanese butterflyfish, Chaetodon nippon (Chaetodontiformes, Chaetodontidae).

Japanese butterflyfish (Chaetodon nippon) belong to the family Chaetodontidae and order Chaetodontiformes. It has circular mitochondrial genome of 16,507 bp in length with 55.4% of A + T content and has 37 genes, including 22 tRNA, 2 rRNA, and 13 protein-coding genes, in addition to a control region. The results of phylogenetic analysis indicated that the C. nippon, C. wiebeli, C. auripes, C. auriga, C. octofasciatus, C. speculum, and C. modestus are closely related to each other. The findings of this study will provide useful genetic information for further phylogenetic and taxonomic classifications of Chaetodontidae.

Complete mitochondrial genome of brown-banded butterflyfish Chaetodon modestus (Chaetodontiformes, Chaetodontidae) and phylogenetic analysis.

The complete mitochondrial genome of the Chaetodon modestus (Temminck and Schlegel, 1844) was first determined in this study, which is 16,490 bp in length, containing 13 protein-coding genes, two rRNA genes, and 22 tRNA. Out of 37 mitochondrial genes, except for ND6 and eight tRNA (Pro, Glu, Ser, Tyr, Cys, Asn, Ala, Gln) genes were encoded on the L-strand, the others were encoded on the H-strand. The overall base composition includes A (28.0%), T (28.7%), G (16.7%), ad C (26.6%). The phylogenetic tree was built using the maximum-likelihood approach to provide a relationship within Chaetodontidae, which might be valuable for species management.

The complete mitochondrial genome of threadfin butterflyfish, Chaetodon auriga (Chaetodontiformes: Chaetodontidae) and phylogenetic analysis.

Chaetodon auriga (Forsskal, 1775) belongs to the family Chaetodontidae and the order Chaetodontiformes. Here, we report the complete mitochondrial genome of C. auriga assembled using the Illumina MiSeq platform. The circular mitochondrial genome of C. auriga is 16,527 bp long, has an A + T content of 54.53%, and contains 37 genes (13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes), and a non-coding region. The overall nucleotide composition was A: 28.19%, T: 26.34%, G: 16.27%, and C: 29.20%. The mitochondrial genome of C. auriga contributes to revealing the phylogenetic relationships among species of the Chaetodontidae family.

Complete mitochondrial genome of scorpionfish Scorpaena neglecta (Actinopterygii).

Scorpaena neglecta (Temminck and Schlegel, 1843) is a marine fish, in the family Scorpaenidae, order Scorpaeniformes, class Actinopterygii of the phylum Chordata. The first species of Scorpaena with a complete mitochondrial genome is described in the present study. The circular mitochondrial genome of S. neglecta has 17,202 bp with 54.75% A + T content and encodes 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), and two ribosomal RNA (rRNA). The phylogenetic tree indicates S. neglecta clustered into one branch and is closely related to other Scorpaenidae species. The mitochondrial genome structure and gene content of S. neglecta will support the study of evolution and phylogenetic relationships among Scorpaenidae species.

Complete mitochondrial genome of marine Petrale sole Eopsetta jordani (Pleuronectiformes: Pleuronectidae) flatfish.

Petrale sole Eopsetta jordani (Pleuronectiformes: Pleuronectidae) is a species of flounder, found in the northeastern Pacific Ocean and the Bering Sea of the United States and Canada. The complete mitochondrial DNA (mtDNA) of E. jordani has 16,483 bp with an overall A + T content of 61% and consists of 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and a non-coding control region. It has incomplete stop codon genes in ND2, COII, ATPase6, COIII, ND3, and ND4. Phylogenetic analysis indicated that E. jordani is not monophyletic with cogeneric Eopsetta grigorjewi and is separated from other species in the same family by a large distance. Present study results provide useful data for further research on genetic diversity and evolution of the Eopsetta and the Pleuronectidae.

Characterization of the complete mitochondrial genome of demersal flatfish Eopsetta grigorjewi (Pleuronectiformes: Pleuronectidae) from South Korea.

Eopsetta grigorjewi (Pleuronectiformes: Pleuronectidae) is a demersal flatfish found in South Korea, Japan, Taiwan, China, and the Yellow Sea. E. grigorjewi complete mitochondrion DNA (mtDNA) consists of 16,921 bp and a 54% A + T content. It includes 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA), 13 protein-coding genes, and 1 non-coding regulatory area. ND2, ND3, ND4, COII, COIII, ATPase6, and CytB all have incomplete stop codon genes. The evolutionary analysis of 13 species from the same family indicated a close relationship. This work will be valuable for future research on molecular evolution and the creation of biomarker databases for determining the originality of E. grigorjewi.

Complete mitochondrial genome of sea peach Halocynthia aurantium (stolidobranchia: Pyuridae) from Korea.

Halocynthia aurantium (Stolidobranchia: Pyuridae) is a species of tunicate of commercial value that is commonly found in the northern Pacific Ocean and in the Bering Sea. Here, we determined the complete mitogenome of sea peach H. aurantium using 150 PE high-throughput sequencing. The assembled mitogenome is 14,979 bp in length (overall A + T contents 56.2%), and contains 13 protein-coding genes, 21 transfer RNAs, two ribosomal RNAs. Phylogenetic analysis of the mitogenome sequence of H. aurantium fully resolved it in a clade with H. roretzi. These data and results will be useful for future studies on the evolution of the Halocynthia and the Pyuridae.

M2 Macrophages Mediate the Resistance of Gastric Adenocarcinoma Cells to 5-Fluorouracil through the Expression of Integrin ß3, Focal Adhesion Kinase, and Cofilin.

Tumor microenvironment components dictate the growth and progression of various cancers. Tumor-associated macrophages are the most predominant cells in TME and play a major role in cancer invasiveness. Gastric cancer is one of the most common cancers in Asia, and recently, various cases of resistance to fluorouracil treatment have been reported. In this study, we investigated the role of alternatively activated macrophages in the resistance of AGS gastric cancer cells to fluorouracil. THP-1 cells were polarized using recombinant human IL-4, then were cocultured with AGS cells treated with fluorouracil. Cell viability, Western blot, immunofluorescence, and cell invasion were performed for this investigation. Our results demonstrated that polarized macrophages initiated the survival of treated AGS cells and induced the resistance in AGS by upregulating the expression of integrin ß3, focal adhesion protein (FAK), and cofilin proteins. These results reveal that integrin ß3, focal adhesion protein (FAK), and cofilin proteins are potential targets for the improvement of fluorouracil efficacy in gastric cancer treatment.

Gene Signature for Sorafenib Susceptibility in Hepatocellular Carcinoma: Different Approach with a Predictive Biomarker.

BACKGROUND/AIM: Uniform treatment of hepatocellular carcinoma (HCC) with molecular targeted drugs (e.g., sorafenib) results in a poor overall tumor response when tumor subtyping is absent. Patient stratification based on actionable gene expression is a method that can potentially improve the effectiveness of these drugs. Here we aimed to identify the clinical application of actionable genes in predicting response to sorafenib. METHODS: Through quantitative real-time reverse transcription PCR, we analyzed the expression levels of seven actionable genes (VEGFR2, PDGFRB, c-KIT, c-RAF, EGFR, mTOR, and FGFR1) in tumors versus noncancerous tissues from 220 HCC patients treated with sorafenib. Our analysis found that 9 responders did not have unique clinical features compared to nonresponders. A receiver operating characteristic curve evaluated the predictive performance of the treatment benefit score (TBS) calculated from the actionable genes. RESULTS: The responders had significantly higher TBS values than the nonresponders. With an area under the curve of 0.779, a TBS combining mTOR with VEGFR2, c-KIT, and c-RAF was the most significant predictor of response to sorafenib. When used alone, sorafenib had a 0.7-3% response rate among HCC patients, but when stratifying the patients with actionable genes, the tumor response rate rose to 15.6%. Furthermore, actionable gene expression is significantly correlated with tumor response. CONCLUSIONS: Our findings on patient stratification based on actionable molecular subtyping potentially provide a therapeutic strategy for improving sorafenib's effectiveness in treating HCC.

A Nine-Gene Signature for Predicting the Response to Preoperative Chemoradiotherapy in Patients with Locally Advanced Rectal Cancer.

Preoperative chemoradiotherapy (PCRT) and subsequent surgery is the standard multimodal treatment for locally advanced rectal cancer (LARC), albeit PCRT response varies among the individuals. This creates a dire necessity to identify a predictive model to forecast treatment response outcomes and identify patients who would benefit from PCRT. In this study, we performed a gene expression study using formalin-fixed paraffin-embedded (FFPE) tumor biopsy samples from 156 LARC patients (training cohort n = 60; validation cohort n = 96); we identified the nine-gene signature (FGFR3, GNA11, H3F3A, IL12A, IL1R1, IL2RB, NKD1, SGK2, and SPRY2) that distinctively differentiated responders from non-responders in the training cohort (accuracy = 86.9%, specificity = 84.8%, sensitivity = 81.5%) as well as in an independent validation cohort (accuracy = 81.0%, specificity = 79.4%, sensitivity = 82.3%). The signature was independent of all pathological and clinical features and was robust in predicting PCRT response. It is readily applicable to the clinical setting using FFPE samples and Food and Drug Administration (FDA) approved hardware and reagents. Predicting the response to PCRT may aid in tailored therapies for respective responders to PCRT and improve the oncologic outcomes for LARC patients.

The complete mitochondrial genome of pitted stingray Bathytoshia brevicaudata (Myliobatiformes: Dasyatoidea).

The complete mitochondrial genome of pitted stingray, Bathytoshia brevicaudata (Myliobatiformes: Dasyatoidea) was investigated by next-generation sequencing. The analyzed mitochondrial genome was 17,640 nucleotides in length and had 59.2% for AT contents. This genome contains 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes. and 1 putative control region. Five protein-coding genes (ATPase6, COII, ND2, ND3, ND4) including incomplete stop codons and four tRNAs have atypical codons. The phylogenetic inference including 13 species of the same family revealed a close relationship with Pteroplatytrygon violacea. This is the first mitochondrial genome report from genus Bathytoshia.

Extracellular synthesis of gold nanoparticles using the marine bacterium Paracoccus haeundaensis BC74171T and evaluation of their antioxidant activity and antiproliferative effect on normal and cancer cell lines.

Green chemistry is beneficial for the production of eco-friendly and stable nanoparticles using biological agents. The present study was performed to explore the potential of the marine bacterium Paracoccus haeundaensis BC74171T for the extracellular synthesis of gold nanoparticles (AuNPs). Cell-free supernatant-mediated AuNPs were characterized by different techniques and analyzed for their antioxidant activity and antiproliferative effect on normal and cancer cells. Visual observations indicated the formation of AuNPs by the development of a ruby red color and were confirmed by a UV-vis absorbance peak at about 535 nm. The synthesized AuNPs were spherical in shape and had an average size of 20.93 ± 3.46 nm, as determined by transmission electron microscopy and a dynamic light scattering particle size analyzer, respectively. From Fourier transform infrared spectroscopy, the interaction of functional groups was determined and the presence of biomaterial on the AuNP surface was confirmed. Concentration-dependent antioxidant activity of AuNPs was observed by the 2,2-diphenyl-1-picrylhydrazyl method. The AuNPs synthesized do not show growth inhibition on HaCaT and HEK293 normal cells, while they show concentration-dependent growth inhibition in the case of A549 and AGS cancer cells. Thereby, this study proves that AuNP synthesis using P. haeundaensis is a facile method and that the AuNPs synthesized are non-toxic to human cells, which indicates that they can be useful in biomedical applications.

Cristazine, a novel dioxopiperazine alkaloid, induces apoptosis via the death receptor pathway in A431 cells.

The fungus Chaetomium sp. is a causative agent of infections in humans and is ubiquitous in the natural environment. The secondary metabolites of this genus exhibit many biological activities, including antifungal activity and toxicity in mitochondria. In this study, we isolated cristazine from the fungus C. cristatum, which has the potential to inhibit the growth of human epidermoid carcinoma (A431) cells in a dose- and time-dependent manner. Its inhibitory activity was examined using a cell viability assay and cell death was elucidated by western blot analysis. Cristazine triggered apoptotic cell death via the Type I death receptor pathway including the activation of caspases and other target proteins. However, cristazine did not have any effect on mitochondrial apoptotic proteins such as Bid, cytochrome c, and apoptosis-inducing factor. Cristazine inhibited the cell cycle progression by arresting the G1 /S phase and up-regulating the inhibitory proteins of cyclin-dependent kinases. Thus, cristazine has great potential for inducing apoptosis in A431 cells via both cell cycle arrest and the inhibition of cell growth.

Anti-Inflammatory Activity of ß-thymosin Peptide Derived from Pacific Oyster (Crassostrea gigas) on NO and PGE2 Production by Down-Regulating NF-κB in LPS-Induced RAW264.7 Macrophage Cells.

ß-thymosin is known for having 43 amino acids, being water-soluble, having a light molecular weight and ubiquitous polypeptide. The biological activities of ß-thymosin are diverse and include the promotion of wound healing, reduction of inflammation, differentiation of T cells and inhibition of apoptosis. Our previous studies showed that oyster ß-thymosin originated from the mantle of the Pacific oyster, Crassostrea gigas and had antimicrobial activity. In this study, we investigated the anti-inflammatory effects of oyster ß-thymosin in lipopolysaccharide (LPS)-induced RAW264.7 macrophage cells using human ß-thymosin as a control. Oyster ß-thymosin inhibited the nitric oxide (NO) production as much as human ß-thymosin in LPS-induced RAW264.7 cells. It also showed that oyster ß-thymosin suppressed the expression of prostaglandin E2 (PGE2), inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2). Moreover, oyster ß-thymosin reduced inflammatory cytokines such as tumor necrosis factor-α (TNF-α), interleukin-1ß (IL-1ß) and interleukin-6 (IL-6). Oyster ß-thymosin also suppressed the nuclear translocation of phosphorylated nuclear factor-κB (NF-κB) and degradation of inhibitory κB (IκB) in LPS-induced RAW264.7 cells. These results suggest that oyster ß-thymosin, which is derived from the mantle of the Pacific oyster, has as much anti-inflammatory effects as human ß-thymosin. Additionally, oyster ß-thymosin suppressed NO production, PGE2 production and inflammatory cytokines expression via NF-κB in LPS-induced RAW264.7 cells.

The complete mitochondrial genome of bobo croaker Pseudotolithus elongatus (Perciformes: Sciaenidae).

The complete mitochondrial genome of Pseudotolithus elongatus (Perciformes: Sciaenidae) is determined based on NGS technology. The assembled mitogenome is a 16,497 bp in length containing a typical set of the 13 protein-coding genes, 22 tRNAs, 2 rRNA genes, and the 1 putative control region. The overall base composition is A (27.8%), T (25.3%), G (16.1%), and C (30.8%) with an A-T content of 53.1%. The phylogenetic analysis of 36 mitogenomes from the GenBank indicated that P. elongatus is closely related to the Aplodinotus grunniens. This mitogenome information of the P. elongatus would be useful to understand evolutionary and phylogenetic analysis of the family Sciaenidae fishes.

Induction of apoptosis and G1 phase cell cycle arrest by Aster incisus in AGS gastric adenocarcinoma cells.

In recent decades, various bioactive compounds from plants have been investigated for their potential use in the treatment of diseases in humans. Aster incisus extract (AIE) is the extract of a common plant that is mostly found in Asia. It has traditionally been used for medicinal purposes in South Korea. In this study, we evaluated the potential anticancer effects of a methanolic extract of Aster incisus in a normal human cell line (HaCaT keratinocytes) and in 4 different types of human cancer cell lines (A549, lung cancer; Hep3B, liver cancer; MDA­MB­231, breast cancer; and AGS, gastric cancer). The HaCaT, A549, Hep3B, MDA­MB­231 and AGS cells were treated with various concentrations of AIE and following treatment, cell survival was evaluated. Additional analyses, such as WST-1 assay, western blot analysis, DAPI staining, flow cytometry, immunofluorescence staining and wound healing assay were performed to elucidate the mechanisms and pathways involved in the cell death induced by AIE. Treatment with AIE induced morphological changes and considerably reduced the viability of the both normal and cancer cell lines. Further analysis of the AGS gastric cancer cells revealed that AIE led to the induction of apoptosis and a high accumulation of cells in the G1 cell phase following treatment with AIE in a dose-dependent manner. The results also revealed that AIE successfully suppressed the migration of the AIE-treated AGS cells. The results of western blot analysis indicated that AIE increased the expression of pro-apoptotic proteins, particularly Bid, Bad, Bak, cytochrome c, apoptosis inducing factor (AIF), cleaved caspase­3, -8 and -9 and cleaved poly(ADP-ribose) polymerase (PARP). Additionally, AIE decreased the expression of the anti-apoptotic proteins, Bcl-2 and Bcl-xL. On the whole, the findings of this study demonstrate that AIE induces apoptosis through the activation of the caspase­dependent pathway mediated by the mitochondrial pathway and by arresting the cell cycle in AGS cells.

Acer okamotoanum Nakai Leaf Extract Inhibits Adipogenesis Via Suppressing Expression of PPAR γ and C/EBP α in 3T3-L1 Cells.

The genus Acer contains several species with various bioactivities including antioxidant, antitumor and anti-inflammatory properties. However, Acer okamotoanum Nakai, one species within this genus has not been fully studied yet. Therefore, in this study, we investigated the anti-adipogenic activities of leaf extract from A. okamotoanum Nakai (LEAO) on 3T3-L1 preadipocytes. Adipogenesis is one of the cell differentiation processes, which converts preadipocytes into mature adipocytes. Nowadays, inhibition of adipogenesis is considered as an effective strategy in the field of anti-obesity research. In this study, we observed that LEAO decreased the accumulation of lipid droplets during adipogenesis and down-regulated the expression of key adipogenic transcription factors such as peroxisome proliferator-activated receptor γ (PPAR γ) and CCAAT/enhancer binding protein α (C/EBP α). In addition, LEAO inactivated PI3K/Akt signaling and its downstream factors that promote adipogenesis by inducing the expression of PPAR γ. LEAO also activated ß-catenin signaling, which prevents the adipogenic program by suppressing the expression of PPAR γ. Therefore, we found that treatment with LEAO is effective for attenuating adipogenesis in 3T3-L1 cells. Consequently, these findings suggest that LEAO has the potential to be used as a therapeutic agent for preventing obesity.

Morphological changes of bacterial cells upon exposure of silver-silver chloride nanoparticles synthesized using Agrimonia pilosa.

Facile, eco-friendly synthesis of metal nanoparticles has been proposed as a cost effective method. In the present study, we propose the facile synthesis of silver-silver chloride (Ag-AgCl) nanoparticles (NPs) using the medicinally important Agrimonia pilosa plant extract without addition of capping or stabilizing agents. The Ag-AgCl NPs synthesis was observed at 40 °C after 10 min incubation; the synthesis of Ag-AgCl NPs was indicated by color change and confirmed by UV-vis spectroscopic peak at 454 nm. TEM analysis confirmed Ag-AgCl NPs were 10-20 nm in size and spherical, and oval in shape. Elemental composition was determined by energy dispersive X-ray analysis, and crystalline structure was confirmed by X-ray diffraction spectroscopy. Different phytocomponents present in the plant extract were analyzed by Gas Chromatography-Mass spectrometry, and the interaction of biomolecules in reduction process was analyzed by Fourier transform infrared spectroscopy studies. The synthesized Ag-AgCl NPs showed significant antibacterial efficiency, analyzed by well diffusion assay against pathogenic bacteria including Bacillus cereus, Listeria monocytogenes, Staphylococcus aureus, Staphylococcus saprophyticus, Escherichia coli, Pseudomonas putida. Minimum inhibitory concentration and minimum bactericidal concentration were evaluated by microbroth dilution, and spread plate method, respectively. The possible mechanism of bacterial growth inhibition is due to changes in bacterial cell wall morphology that was studied by FE-SEM analysis.

Anti-Inflammatory Effects of Aster incisus through the Inhibition of NF-κB, MAPK, and Akt Pathways in LPS-Stimulated RAW 264.7 Macrophages.

Aster incisus is a common flower found in almost all regions of South Korea. In the current study, we investigated the potential antioxidant and anti-inflammatory properties of the Aster incisus methanol extract in LPS-stimulated RAW 264.7 cells. We analyzed the phytochemicals contained in the extract by GC-MS. GC-MS results showed that the Aster incisus extract contains 9 known compounds. Later on, DPPH assay, WST-1 assay, nitric oxide (NO) assay, Western blot, and RT-PCR were conducted to investigate the anti-inflammatory effects of the extract. Our WST-1 assay results revealed that Aster incisus did not affect the viability of all tested cell lines up to a concentration of 200 µg/ml; therefore, lower concentrations (50 µg/ml and 150 µg/ml) were used for further assays. Aster incisus scavenged DPPH and inhibited the production of NO. Aster incisus also reduced significantly the production of inflammation-related enzymes (iNOS, Cox-2) and cytokines (TNFα, IL-1ß, and IL-6) and the gene expression of the proinflammatory cytokines. Additionally, further Western blot results indicated that Aster incisus inhibited the expression of p-PI3K, p-IκBα, p-p65 NF-κB, p-ERK1/2, p-SAPK/JNK, and p-Akt. Our results demonstrated that Aster incisus suppressed the expression of the inflammation mediators through the regulation of NF-κB, MAPK, and Akt pathways.