Genome sequence of pacific abalone (Haliotis discus hannai): the first draft genome in family Haliotidae

Background: Abalones are large marine snails in the family Haliotidae and the genus Haliotis belonging to the class Gastropoda of the phylum Mollusca. The family Haliotidae contains only one genus, Haliotis, and this single genus is known to contain several species of abalone. With 18 additional subspecies, the most comprehensive treatment of Haliotidae considers 56 species valid [1]. Abalone is an economically important fishery and aquaculture animal that is considered a highly prized seafood delicacy. The total global supply of abalone has increased 5-fold since the 1970s and farm production increased explosively from 50 mt to 103 464 mt in the past 40 years. Additionally, researchers have recently focused on abalone given their reported tumor suppression effect. However, despite the valuable features of this marine animal, no genomic information is available for the Haliotidae family and related research is still limited. To construct the H. discus hannai genome, a total of 580-G base pairs using Illumina and Pacbio platforms were generated with 322-fold coverage based on the 1.8-Gb estimated genome size of H. discus hannai using flow cytometry. The final genome assembly consisted of 1.86 Gb with 35 450 scaffolds (>2 kb). GC content level was 40.51%, and the N50 length of assembled scaffolds was 211 kb. We identified 29 449 genes using Evidence Modeler based on the gene information from ab initio prediction, protein homology with known genes, and transcriptome evidence of RNA-seq. Here we present the first Haliotidae genome, H. discus hannai, with sequencing data, assembly, and gene annotation information. This will be helpful for resolving the lack of genomic information in the Haliotidae family as well as providing more opportunities for understanding gastropod evolution.

Vitellibacter todarodis sp. nov., isolated from intestinal tract of a squid (Todarodes pacificus)

A Gram-stain-negative, non-motile, aerobic and rod-shaped or ovoid bacterial strain, designated MYP2-2^T, was isolated from the intestinal tract of a squid (Todarodes pacificus) collected from the East Sea, South Korea, and subjected to a polyphasic taxonomic study. Strain MYP2-2^T grew optimally at 30-35 °C and in the presence of 2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain MYP2-2^T belonged to the genus Vitellibacter. Strain MYP2-2^T exhibited 16S rRNA gene sequence similarities of 95.4-96.6 % to the type strains of Vitellibacter species and of less than 94.5 % to the type strains of other recognized species examined. Strain MYP2-2^T contained menaquinone MK-6 as the predominant respiratory quinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain MYP2-2^T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain MYP2-2^T was 41.6 mol%. Differential phenotypic properties, together with its phylogenetic distinctiveness, revealed that strain MYP2-2^T is separated from recognized species of the genus Vitellibacter. On the basis of the data presented, strain MYP2-2^T is considered to represent a novel species of the genus Vitellibacter, for which the name Vitellibacter todarodis sp. nov. is proposed. The type strain is MYP2-2^T (=KCTC 62141^T=NBRC 113025^T).

Paracoccus alimentarius sp. nov., isolated from a Korean foodstuff, salted pollack

A Gram-stain-negative, aerobic, non-motile and coccoid or ovoid bacterial strain, designated LB2^T, was isolated from a Korean foodstuff, salted pollack. Strain LB2^T grew optimally at 25-30 °C, at pH 7.0-8.0 and in the presence of 0-2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain LB2^T belonged to the genus Paracoccus, coherently clustering with the type strain of Paracoccus sulfuroxidans. Strain LB2^T exhibited 16S rRNA gene sequence similarity values of 98.0 and 97.0 % to the type strains of P. sulfuroxidans and Paracoccus halophilus, respectively, and of less than 96.9 % to the type strains of other Paracoccus species. Strain LB2^T contained Q-10 as the predominant ubiquinone. Major fatty acids of strain LB2^T were cyclo C19 : 0ω8c, C18 : 1ω7c and C16 : 0 (when grown on MA) or C18 : 1ω7c and C16 : 0 (on TSA). The major polar lipids detected in strain LB2^T were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminolipid and one unidentified glycolipid. The DNA G+C content of strain LB2^T was 61.4 mol% and its DNA-DNA relatedness values with the type strains of P. sulfuroxidans and P. halophilus were 26 and 18 %, respectively. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain LB2^T is separated from recognized Paracoccus species. On the basis of the data presented, strain LB2^T is considered to represent a novel species of the genus Paracoccus, for which the name Paracoccus alimentarius sp. nov. is proposed. The type strain is LB2^T (=KCTC 62138^T=NBRC 113023^T).

Tenacibaculum haliotis sp. nov., isolated from the gut of an abalone Haliotis discus hannai

A Gram-stain-negative, non-flagellated, gliding, non-spore-forming bacterial strain, designated RA3-2T, was isolated from the gut of an abalone (Haliotis discus hannai) collected from the sea around Jeju island, South Korea, and subjected to a polyphasic taxonomic study. RA3-2T grew optimally at 20 °C and in the presence of 2.0-3.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences indicated that RA3-2T fell within the clade comprising the type strains of species of the genus Tenacibaculum, clustering with the type strains of Tenacibaculum soleae, Tenacibaculum ovolyticum and Tenacibaculum dicentrarchi; showing 16S rRNA gene sequence similarity values of 96.2-96.8 %. The novel strain exhibited 16S rRNA gene sequence similarity values of 93.5-96.9 % to the type strains of the other species of the genus Tenacibaculum. RA3-2T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C15 : 0 3-OH as the major fatty acids. The major polar lipids of RA3-2T were phosphatidylethanolamine, two unidentified lipids, one unidentified aminophospholipid and one unidentified glycolipid. The DNA G+C content of RA3-2T was 31.7 mol%. The differential phenotypic properties, together with the phylogenetic data, revealed that RA3-2T is separated from other species of the genus Tenacibaculum with validly published names. On the basis of the data presented, RA3-2T is considered to represent a novel species of the genus Tenacibaculum, for which the name Tenacibaculum haliotis sp. nov. is proposed. The type strain is RA3-2T (=KCTC 52419T=NBRC 112382T).

Antimicrobial effect of the 60S ribosomal protein L29 (cgRPL29), purified from the gill of pacific oyster, Crassostrea gigas

We purified an ∼6.4-kDa antimicrobial peptide from an acidified gill extract of the Pacific oyster, Crassostrea gigas, by cation-exchange and C₁₈ reversed-phase high performance liquid chromatography (HPLC). The identified peptide was composed of 54 amino acids and had a molecular weight of 6484.6 Da. Comparison of the amino acid sequence and molecular weight with those of other known proteins or peptides revealed that the peptide had high identity with the 60S ribosomal protein L29, and so was named cgRPL29. The full-length cgRPL29 cDNA of the Pacific oyster comprised 325-bp, including a 5'-untranslated region (UTR) of 100-bp, a 3'-UTR of 57-bp, and an open reading frame of 168-bp encoding 55 amino acids, with a Met residue at the N-terminus. The cgRPL29 mRNA tissue distribution suggested that it is constitutively expressed in a non-tissue-specific manner. Secondary structural prediction and homology modeling indicated cgRPL29 have an unordered structure containing two partial α-helical regions. This is to our knowledge the first report of the antimicrobial effect of the 60S ribosomal protein L29 from marine invertebrates.

CO2 low-level laser therapy has an early but not delayed pain effect during experimental tooth movement

OBJECTIVES

To test the hypothesis that the use of low-level laser therapy (LLLT) reduces elevated pain by controlling the release of neurochemicals during orthodontic tooth movement.

SETTING AND SAMPLE POPULATION

Department of Orthodontics and Dentofacial Orthopedics, Okayama University. Sixty-five Sprague Dawley rats were subjected to tooth movement and LLLT.

MATERIALS AND METHODS

Adult Sprague Dawley rats were used in this study. Groups included day 0 controls, irradiation only controls and with or without irradiation sacrificed at 1, 3, 5, 7 and 14 days after tooth movement (n=5 each, total n=65). Tooth movement was achieved by insertion of an elastic module between molar teeth. Immunohistochemistry for CD-11b, GFAP and c-fos in the brain stem was performed. Stains were quantified by constructing a three-dimensional image using IMARIS, and counted using NEURON TRACER and WinROOF software. Two-way ANOVA followed by a Tukey's post hoc test (P<.05) was used for statistical comparison between groups.

RESULTS

C-fos expression was significantly increased at one and three days after tooth movement. LLLT significantly diminished this increase in c-fos expression only at one day after tooth movement CD-b11 and GFAP expression also significantly increased after tooth movement. No significant change was observed for CD-11b and GFAP expression in the central nervous system upon LLLT.

CONCLUSION

Low-level laser therapy may reduce early neurochemical markers but have no effect on delayed pain neurochemical markers after tooth movement.

Colwellia mytili sp. nov., isolated from mussel Mytilus edulis

A Gram-stain-negative, aerobic, motile and rod-shaped bacterial strain, designated RA2-7T, was isolated from a mussel (Mytilus edulis) collected from the South Sea, South Korea, and subjected to a taxonomic study using a polyphasic approach. Strain RA2-7T grew optimally at 20 °C, at pH 7.0-8.0 and in the presence of 2.0-3.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain RA2-7T belonged to the genus Colwellia. Strain RA2-7T exhibited 16S rRNA gene sequence similarity values of 98.3, 98.0 and 97.5 % to the type strains of Colwellia sediminilitoris, Colwellia aestuarii and Colwellia polaris, respectively, and of 94.5-96.5 % to the type strains of the other species of the genus Colwellia. Strain RA2-7T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the major fatty acids. The major polar lipids detected in strain RA2-7T were phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain RA2-7T was 39.0±0.04 mol% and its DNA-DNA relatedness values with the type strains of C. sediminilitoris, C. aestuarii and C. polaris were 14-19 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain RA2-7T is separated from recognized species of the genus Colwellia. On the basis of the data presented, strain RA2-7T is considered to represent a novel species of the genus Colwellia, for which the name Colwellia mytili sp. nov. is proposed. The type strain is RA2-7T (=KCTC 52417T=NBRC 112381T).

Ten-Year Experience With Bowel Transplantation at Seoul St. Mary's Hospital

A retrospective review of intestinal transplantation (ITx) at Seoul St. Mary's Hospital was made by collecting clinical data over the past 10 years. Fifteen consecutive cases from 2004 were analyzed. Five children and 10 adults (6 months to 69 years of age) were included. Primary diseases in adults included 4 mesenteric vessel thromboses, 2 strangulations, and 1 each of visceral myopathy, malignant gastrointestinal stromal tumor (GIST), mesenteric lymphangiectasis, and injury. Pediatric cases involved 2 Hirschsprung disease, 2 visceral myopathy, and 1 necrotizing enterocolitis. Three of 7 stomas were closed using a serial transverse enteroplasty procedure before transplantation. The ITx were performed using 3 living-donor Itx, 12 deceased-donor ITx, 14 isolated Itx, and 1 modified multivisceral transplantation. Daclizumab, basiliximab, alemtusumab, or basiliximab with rabbit antithymocyte globulin (rATG) was used for the induction; tacrolimus monotherapy was used as the basic maintenance immunosuppressant; and m-TOR inhibitor was used for renal dysfunction patients. Seven cases of acute cellular rejection were treated with rATG. Three cases of antibody-mediated rejection were treated with rituximab alone or with rituximab and bortezomib combination. There were 4 cases of early mortality within 6 months after Itx. Causes of death were declamping shock, cardiac tamponade with acute cellular rejection, dysmotility, and sepsis. Surgical complications consisted of 1 feeding jejunostomy displacement, and a minor leakage at a colo-colostomy site. One-year survival of the patient and graft was 73.33% (Kaplan-Meier survival curve). Although the total number of ITx is small, its social impact has been remarkable in changing the related laws and reimbursement policy in Korea.

Highly anisotropic thermal conductivity of discotic nematic liquid crystalline films with homeotropic alignment

Homeotropic alignment and photo-crosslinking of discotic nematic liquid crystals yield free-standing films with high in-plane thermal conductivity and thermal conductivity anisotropy.

Transcriptome Analysis Revealed Changes of Multiple Genes Involved in Haliotis discus hannai Innate Immunity during Vibrio parahemolyticus Infection

Abalone (Haliotis discus hannai) is one of the most valuable marine aquatic species in Korea, Japan and China. Tremendous exposure to bacterial infection is common in aquaculture environment, especially by Vibrio sp. infections. It’s therefore necessary and urgent to understand the mechanism of H. discus hannai host defense against Vibrio parahemolyticus infection. However studies on its immune system are hindered by the lack of genomic resources. In the present study, we sequenced the transcriptome of control and bacterial challenged H. discus hannai tissues. Totally, 138 MB of reference transcriptome were obtained from de novo assembly of 34 GB clean bases from ten different libraries and annotated with the biological terms (GO and KEGG). A total of 10,575 transcripts exhibiting the differentially expression at least one pair of comparison and the functional annotations highlight genes related to immune response, cell adhesion, immune regulators, redox molecules and mitochondrial coding genes. Mostly, these groups of genes were dominated in hemocytes compared to other tissues. This work is a prerequisite for the identification of those physiological traits controlling H. discus hannai ability to survive against Vibrio infection.

Solid Polymer Electrolytes Based on Functionalized Tannic Acids from Natural Resources for All-Solid-State Lithium-Ion Batteries

Solid polymer electrolytes (SPEs) for all-solid-state lithium-ion batteries are prepared by simple one-pot polymerization induced by ultraviolet (UV) light using poly(ethylene glycol) methyl ether methacrylate (PEGMA) as an ion-conducting monomeric unit and tannic acid (TA)-based crosslinking agent and plasticizer. The crosslinking agent and plasticizer based on natural resources are obtained from the reaction of TA with glycidyl methacrylate and glycidyl poly(ethylene glycol), respectively. Dimensionally stable free-standing SPE having a large ionic conductivity of 5.6×10(-4)  Scm(-1) at room temperature can be obtained by the polymerization of PEGMA into P(PEGMA) with a very small amount (0.1 wt %) of the crosslinking agent and 2.0 wt % of the plasticizer. The ionic conductivity value of SPE with a crosslinked structure is one order of magnitude larger than that of linear P(PEGMA) in the waxy state.

Construction of chimeric human epidermal growth factor containing short collagen-binding domain moieties for use as a wound tissue healing agent

Among the various human growth factors, epidermal growth factor (hEGF, consisting of 53 amino acids) has various effects on cell regeneration, stimulation of proliferation, migration of keratinocytes, formation of granulation tissues, and stimulation of fibroblast motility, which are important for wound healing. Owing to their multiple activities, EGFs are used as pharmaceutical and cosmetic agents. However, their low productivity, limited target specificity, and short half-life inhibit their application as therapeutic agents. To overcome these obstacles, we fused the collagen-binding domain (CBD) of Vibrio mimicus metalloprotease to EGF protein. About 18 or 12 amino acids (aa) (of the 33 total amino acids), which were essential for collagen-binding activity, were combined with the N- and C-termini of EGF. We constructed, expressed, and purified EGF (53 aa)-CBD (18 aa), EGF (53 aa)-CBD (12 aa), CBD (18 aa)-EGF (53 aa), and CBD (12 aa)-EGF (53 aa). These purified recombinant proteins increased the numbers of cells in treated specimens compared with non-treated specimens and control hEGF samples. The collagen-binding activities were also evaluated. Furthermore, CBD-hybridized hEGF induced phosphorylation of the EGF receptor. These results suggested that these fusion proteins could be applicable as small therapeutic agents in wound tissue healing.

Roseovarius scapharcae sp. nov., isolated from ark shell Scapharca broughtonii

A Gram-stain-negative, non-motile, aerobic and ovoid or rod-shaped bacterium, designated MA4-5T, was isolated from ark shell (Scapharca broughtonii) collected from the South Sea, South Korea. The novel strain grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 2.0 % (w/v) NaCl. Neighbour-joining and maximum-likelihood phylogenetic trees based on 16S rRNA gene sequences showed that strain MA4-5T forms a coherent cluster with the type strains of Roseovarius albus, Roseovarius aestuarii and Roseovarius nubinhibens, sharing 97.0-99.2 % sequence similarity. It exhibited 16S rRNA gene sequence similarity of 93.1-96.1 % to the type strains of other Roseovarius species. Strain MA4-5T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids of strain MA4-5T were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain MA4-5T was 53.8 mol% and its mean DNA-DNA relatedness values with the type strains of R. albus, R. aestuarii and R. nubinhibens were 11-26 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, indicated that strain MA4-5T is separate from recognized species of the genus Roseovarius. On the basis of the data presented, strain MA4-5T is considered to represent a novel species of the genus Roseovarius, for which the name Roseovarius scapharcae sp. nov. is proposed. The type strain is MA4-5T ( = KCTC 42703T = NBRC 111226T).

Follistatin-like 3 is a mediator of exercise-driven bone formation and strengthening

Exercise is vital for maintaining bone strength and architecture. Follistatin-like 3 (FSTL3), a member of follistatin family, is a mechanosensitive protein upregulated in response to exercise and is involved in regulating musculoskeletal health. Here, we investigated the potential role of FSTL3 in exercise-driven bone remodeling. Exercise-dependent regulation of bone structure and functions was compared in mice with global Fstl3 gene deletion (Fstl3-/-) and their age-matched Fstl3+/+ littermates. Mice were exercised by low-intensity treadmill walking. The mechanical properties and mineralization were determined by μCT, three-point bending test and sequential incorporation of calcein and alizarin complexone. ELISA, Western-blot analysis and qRT-PCR were used to analyze the regulation of FSTL3 and associated molecules in the serum specimens and tissues. Daily exercise significantly increased circulating FSTL3 levels in mice, rats and humans. Compared to age-matched littermates, Fstl3-/- mice exhibited significantly lower fracture tolerance, having greater stiffness, but lower strain at fracture and yield energy. Furthermore, increased levels of circulating FSTL3 in young mice paralleled greater strain at fracture compared to the lower levels of FSTL3 in older mice. More significantly, Fstl3-/- mice exhibited loss of mechanosensitivity and irresponsiveness to exercise-dependent bone formation as compared to their Fstl3+/+ littermates. In addition, FSTL3 gene deletion resulted in loss of exercise-dependent sclerostin regulation in osteocytes and osteoblasts, as compared to Fstl3+/+ osteocytes and osteoblasts, in vivo and in vitro. The data identify FSTL3 as a critical mediator of exercise-dependent bone formation and strengthening and point to its potential role in bone health and in musculoskeletal diseases.

A novel esterase from Paenibacillus sp. PBS-2 is a new member of the β-lactamase belonging to the family VIII lipases/esterases

Screening of a gene library from Paenibacillus sp. PBS-2 generated in Escherichia coli led to the identification of a clone with lipolytic activity. Sequence analysis showed an open reading frame encoding a polypeptide of 378 amino acid residues with a predicted molecular mass of 42 kDa. The esterase displayed 69% and 42% identity with the putative β-lactamases from Paenibacillus sp. JDR-2 and Clostridium sp. BNL1100, respectively. The esterase contained a Serx- x-Lys motif that is conserved among all β-lactamases found to date. The protein PBS-2 was produced in both soluble and insoluble forms when E. coli cells harboring the gene were cultured at 18°C. The enzyme is a serine protein and was active against p-nitrophenyl esters of C2, C4, C8, and C10. The optimum pH and temperature for enzyme activity were pH 9.0 and 30°C, respectively. Relative activity of 55% remained at up to 5°C with an activation energy of 5.84 kcal/mol, which indicates that the enzyme is cold-adapted. Enzyme activity was inhibited by Cd(2+), Cu(2+), and Hg(2+) ions. As expected for a serine esterase, activity was inhibited by phenylmethylsulfonyl fluoride. The enzyme was remarkably active and stable in the presence of commercial detergents and organic solvents. This cold-adapted esterase has potential as a biocatalyst and detergent additive for use at low temperatures.