Clinical Assessment of Thermotherapy Applications during Hepatectomy and Laparotomy in Sturgeon (Acipenser ruthenus): Impact on Bioparameter Variations Based on Liver Condition

Surgical techniques are gaining attention for treating physical diseases in aquaculture and aquarium fish. Sturgeon is a suitable species for surgical experiments due to its industrial significance. Maintaining homeostasis is crucial during surgical procedures, and the liver plays a major role in immune regulation. High temperature is suggested to improve physiological activity and wound healing. This study investigated differences in hepatectomy sturgeons' tolerance and histopathological responses of internal organs. Moreover, this study investigated the effects of high temperatures on wound healing and hematopoietic recovery in fish undergoing surgical procedures. The liver condition was found to play a pivotal role in the analysis, and cortisol levels were affected by anesthesia. The results showed that high temperature facilitated hematopoietic recovery and wound healing, but excessive induction of physiological activity caused damage. Managing high temperatures and liver conditions induced a remarkable improvement in wound healing. However, anesthesia itself can be a significant stressor for fish, and wound healing requires a greater amount of energy. Further research is needed to understand the stress factors caused by surgical procedures and anesthesia and to promote animal welfare in fishery products.

Physical Properties of Poly(ether-thiourea)-Based Elastomer Formed by Zigzag Hydrogen Bonding and Slidable Cross-Linking

In this study, the effects of zigzag hydrogen bonding and slidable cross-linking on the design of stretchable elastomers were explored. Poly(ether-thiourea) (TU), capable of generating strong zigzag hydrogen bonds without crystallization, was introduced as the main chain in the non-cross-linked region of the developed elastomer. Consequently, the toughness of the TU-based elastomer was 14 times higher than that of elastomers formed using linear poly(ethylene glycol), despite the relatively low molecular weight of TU (∼3k). When a slidable polyrotaxane cross-linker was introduced into the TU-based elastomer, its flexibility became twice as high as that of the rigid polymer cross-linker. Moreover, the mechanical properties of the elastomer were prevented from deterioration against repeated deformation under the limited strain condition of 150%.

Identification of Potential Hazards Associated with South Korean Prawns and Monitoring Results Targeting Fishing Bait

This study detected two potential pathogens, Vibro parahaemolyticus, which causes acute hepatopancreatic necrosis disease (AHPND), and white spot syndrome virus (WSSV), in fishing bait in South Korea. However, their infectious nature was not confirmed, possibly due to the degradation caused by freezing/thawing or prolonged storage under frozen conditions. While infectivity was not confirmed in this study, there is still a significant risk of exposure to these aquatic products. Furthermore, fishing bait and feed should be handled with caution as they are directly exposed to water, increasing the risk of disease transmission. In Australia, cases of WSSV infection caused by imported shrimp intended for human consumption have occurred, highlighting the need for preventive measures. While freezing/thawing is a method for inactivating pathogens, there are still regulatory and realistic issues to be addressed.

Meat Quality Changes in Aged Pork Loin using Jeju Volcanic Scoria Earthenware

This study aimed to investigate changes in the quality of meat aged using Jeju scoria earthenware. Water-holding properties, pH, color, tenderization, fatty acid composition, and free amino acid characteristics of aged pork loin were evaluated to determine the effects of wet and dry (normal and Jeju Scoria) aging methods and aging time (0, 10, 20, 30, and 40 days) on meat quality. The aging methods altered pH and CIE L* after 10 days of aging. However, the aging method did not alter the pH and CIE L* of the aged pork loin after 10 days of aging. The shear force was significantly lower in the Scoria aging method than in the wet aging method after 10 and 20 days of aging. Both the normal and Scoria aging methods increased aging loss compared to the wet aging method, which could be attributed to longer air exposure times of the two non-packaged aging methods than in the packaged aging method. The scoria aging method had significantly higher contents and ratios of saturated (SFA) to mono-unsaturated fatty acids but lower ratios of poly-unsaturated fatty acids to SFA than the wet aging method. The content of most free amino acids significantly increased with aging time, especially those related to the sweet, and umami categories. In summary, this study suggests that the Scoria aging method provides positive aspects of eating quality, such as improvement of meat tenderness and taste, including umami, with minimum changes in the overall meat quality.

Manufacture of antibacterial carbon fiber-reinforced plastics (CFRP) using imine-based epoxy vitrimer for medical application

An antibacterial carbon fiber-reinforced plastics (CFRP) was manufactured based on a vitrimer containing imine groups. A liquid curing agent was prepared to include an imine group in the matrix, and was synthesized without a simple mixing reaction and any purification process. The vitrimer used as the matrix for CFRP was prepared by reacting a commercial epoxy with a synthesized curing agent. The structural and thermal properties of the vitrimer were determined by Fourier transform-infrared spectroscopy (FT-IR), differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). In addition, the temperature-dependent behavior of the vitrimer was characterized by stress relaxation, reshaping, and shape memory experiments. The mechanical properties of composites fabricated using vitrimer were fully analyzed by tensile, flexural, short-beam strength, and Izod impact tests and had mechanical properties similar to reference material. Moreover, both the vitrimer and the vitrimer composites showed excellent antibacterial activity against Staphylococcus aureus and Escherichia coil due to the imine group inside the vitrimer. Therefore, vitrimer composites have potential for applications requiring antimicrobial properties, such as medical devices.

Enhancement of Thermomechanical Properties of Sulfur-rich Polymers by Post-Thermal Treatment

Recently, sulfur-rich polymers have been applied in various fields including energy storage, mercury absorption, and infrared (IR) optics. However, sulfur-rich polymers typically exhibit insufficient thermomechanical properties for practical applications. Herein,...

Enterovibrio paralichthyis sp. nov., isolated from the gut of an olive flounder Paralichthys olivaceus

A Gram-stain-negative, facultatively anaerobic, flagellated and coccoid, ovoid or rod-shaped bacterial strain, NIFS-20-8^T, was isolated from the intestine of an olive flounder (Paralichthys olivaceus) from the East Sea, Republic of Korea. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain NIFS-20-8^T fell within the clade comprising the type strains of Enterovibrio species. Strain NIFS-20-8^T exhibited 16S rRNA gene sequence similarities of 97.2 and 97.1 % to the type strains of Enterovibrio nigricans and Enterovibrio norvegicus, respectively, and of 96.6-97.0 % to the type strains of the other Enterovibrio species. The average nucleotide identity and digital DNA-DNA hybridization values between the genomic sequence of strain NIFS-20-8^T and those of the type strains of four Enterovibrio species were 73.8-75.0 and 19.8-21.1 %, respectively. The DNA G+C content of strain NIFS-20-8^T from genomic sequence data was 50.55 mol%. Strain NIFS-20-8^T contained Q-8 as the predominant ubiquinone and summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c), C_16 : 0 and C_18 : 1  ω7c as the major fatty acids. The major polar lipids detected in stain NIFS-20-8^T were phosphatidylethanolamine and phosphatidylglycerol. Distinguishing phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain NIFS-20-8^T is separated from recognized Enterovibrio species. On the basis of the data presented here, strain NIFS-20-8^T is considered to represent a novel species of the genus Enterovibrio, for which the name Enterovibrio paralichthyis sp. nov. is proposed. The type strain is NIFS-20-8^T (= KCTC 82873^T=NBRC 115237^T).

Characterization of TRIM16, a member of the fish-specific finTRIM family, in olive flounder Paralichthys olivaceus

Tripartite motif-containing (TRIM) proteins are conserved throughout the metazoan kingdom, and the TRIM subset finTRIM is highly diversified in fish. We isolated TRIM16 cDNA, a member of the finTRIM family, from the olive flounder Paralichthys olivaceus (PoTRIM16). PoTRIM16 contained a 1,725-bp coding sequence encoding a 574-amino acid polypeptide, which in turn contained a really interesting new gene (RING) finger domain, B-box-type zinc finger (B-BOX), nuclease SbcCD subunit C (SbcC), structural maintenance of chromosome (SMC prok B), and stonustoxin (SNTX) subunit alpha (SPRY-PRY-SNTX). Multiple alignment of related sequences revealed that PoTRIM16 showed 86.63-97.40% identity with fish orthologues, and a phylogenetic tree was constructed of vertebrates. PoTRIM16 mRNA was detected in all tissues examined; levels were highest in the eye and ovary. PoTRIM16 mRNA expression was investigated during early development. Under VHSV infection, PoTRIM16 mRNA was downregulated in the liver of P. olivaceus. This is the first study to characterize fish-specific finTRIM in P. olivaceus, which may play a role in the immune response against virus infection.

Regional Control of Multistimuli-Responsive Structural Color-Switching Surfaces by a Micropatterned DNA-Hydrogel Assembly

Structural colors have advantages compared with chemical pigments or dyes, such as iridescence, tunability, and unfading. Many studies have focused on developing the ability to switch ON/OFF the structural color; however, they often suffer from a simple and single stimulus, remaining structural colors, and target selectivity. Herein, we present regionally controlled multistimuli-responsive structural color switching surfaces. The key part is the utilization of a micropatterned DNA-hydrogel assembly on a single substrate. Each hydrogel network contains a unique type of stimuli-responsive DNA motifs as an additional cross-linker to exhibit swelling/deswelling via stimuli-responsive DNA interactions. The approach enables overcoming the existing limitations and selectively programming the DNA-hydrogel to a decrypted state (ON) and an encrypted state (OFF) in response to multiple stimuli. Furthermore, the transitions are reversible, providing cyclability. We envision the potential of our method for diverse applications, such as sensors or anticounterfeiting, requiring multistimuli-responsive structural color switching surfaces.

The complete mitochondrial genome of Pseudopleuronectes herzensteini

Pseudopleuronectes herzensteini belonging to Pleuronectiformes (family Pleuronectidae) is important in the fishery industry. However, the molecular biology of this valuable fish has hardly been reported. Thus, here we report the complete mitochondrial genome of P. herzensteini. The mitochondrial DNA (mtDNA) of P. herzensteini is 16,719 bp long and contains 13 mitochondrial protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a putative control region between tRNA-P and tRNA-F distinguished by a single short noncoding region. Phylogenetic analysis using PCGs confirmed that this mtDNA sequence belongs to the family Pleuronectidae. This is the first study reporting the complete mitochondrial genome sequence of P. herzensteini.

A Low-Power Analog Processor-in-Memory-Based Convolutional Neural Network for Biosensor Applications

This paper presents an on-chip implementation of an analog processor-in-memory (PIM)-based convolutional neural network (CNN) in a biosensor. The operator was designed with low power to implement CNN as an on-chip device on the biosensor, which consists of plates of 32 × 32 material. In this paper, 10T SRAM-based analog PIM, which performs multiple and average (MAV) operations with multiplication and accumulation (MAC), is used as a filter to implement CNN at low power. PIM proceeds with MAV operations, with feature extraction as a filter, using an analog method. To prepare the input feature, an input matrix is formed by scanning a 32 × 32 biosensor based on a digital controller operating at 32 MHz frequency. Memory reuse techniques were applied to the analog SRAM filter, which is the core of low power implementation, and in order to accurately grasp the MAC operational efficiency and classification, we modeled and trained numerous input features based on biosignal data, confirming the classification. When the learned weight data was input, 19 mW of power was consumed during analog-based MAC operation. The implementation showed an energy efficiency of 5.38 TOPS/W and was differentiated through the implementation of 8 bits of high resolution in the 180 nm CMOS process.

Printable Self-Activated Liquid Metal Stretchable Conductors from Polyvinylpyrrolidone-Functionalized Eutectic Gallium Indium Composites

Stretchable electronic circuits are critical in a variety of next-generation electronics applications, including soft robots, wearable technologies, and biomedical applications. To date, printable composite conductors comprising various types of conductive fillers have been suggested to achieve high electrical conductance and excellent stretchability. Among them, liquid metal particles have been considered as a viable candidate filler that can meet the necessary prerequisites. However, a mechanical activation process is needed to generate interconnected liquid channels inside elastomeric polymers. In this study, we have developed a chemical strategy of surface-functionalizing liquid metal particles to eliminate the necessity of additional mechanical activation processes. We found that the characteristic conformations of the polyvinylpyrrolidone surrounding eutectic gallium indium particles are highly dependent on the molecular weight of polyvinylpyrrolidone. By virtue of the specific chemical roles of polyvinylpyrrolidone, the as-printed composite layers are highly conductive and stretchable, exhibiting an electrical conductivity approaching 8372 S/cm at 100% strain and an invariant resistance change of 0.92 even at 75% strain after a 60,000 cycle test. The results demonstrate that the self-activated liquid metal-based composite conductors are applicable to traditional stretchable electronics, healable stretchable electronics, and shape-morphable applications.

Nocardioides humilatus sp. nov., isolated from farmland soil in the Republic of Korea

A Gram-stain positive, aerobic, irregularly rod-shaped, non-spore-forming bacterium, designated as BN130099T, was isolated from farmland soil sampled in Goesan-gun, Chungbuk, Republic of Korea. Phylogenetic analysis of its 16S rRNA gene sequence showed that the strain is closely related to Nocardioides pelophilus KACC 19192T with 98.11 % similarity. The DNA G+C content of strain BN130099T was 68.84 mol% (draft genome sequence). The genome sequence of BN130099T displayed key enzymes involved in bioremediation of organic pollutants and biosynthetic clusters of saquayamycin. The strain contained ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan and MK-8(H4) as the major respiratory quinone. The predominant fatty acid was iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol. The results of physiological and biochemical characterization allowed the phenotypic differentiation of strain BN130099T from N. pelophilus KACC 19192T. The strain represents a novel species of the genus Nocardioides , for which we propose the name Nocardioides humilatus sp. nov. The type strain is BN130099T (=KCTC 49079T=CCTCC AB 2018135T).

Paenihalocynthiibacter styelae gen. nov., sp. nov., isolated from stalked sea squirt Styela clava

A Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterial strain, MYP1-1^T, was isolated from the intestine of a stalked sea squirt (Styela clava) of the South Sea in the Republic of Korea. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain MYP1-1^T clustered with the type strains of Halocynthiibacter species and Pseudohalocynthiibacter aestuariivivens. Strain MYP1-1^T exhibited 16S rRNA gene sequence similarity values of 97.0-97.6 % to the type strains of Halocynthiibacter namhaensis, Halocynthiibacter arcticus and P. aestuariivivens. The phylogenetic tree based on genomic sequences showed that strain MYP1-1^T formed a distinct branch separating it from the type strains of two Halocynthiibacter species and P. aestuariivivens and other taxa. The DNA G+C content of strain MYP1-1^T from its genomic sequence was 55.0 mol%. Strain MYP1-1^T contained Q-10 as the predominant ubiquinone and C_18 : 1  ω7c as the major fatty acid. The major polar lipids of strain MYP1-1^T were phosphatidylcholine, phosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. The differences in fatty acid and polar lipid profiles and other differential phenotypic properties made it reasonable to distinguish strain MYP1-1^T from the genera Halocynthiibacter and Pseudohalocynthiibacter. On the basis of the polyphasic taxonomic investigations, we conclude that strain MYP1-1^T constitutes a new genus and species within the class Alphaproteobacteria, for which the name Paenihalocynthiibacter styelae gen. nov., sp. nov. is proposed. The type strain is MYP1-1^T (=KCTC 82143^T=NBRC 114355^T).

Structural basis for SdgB- and SdgA-mediated glycosylation of staphylococcal adhesive proteins

The initiation of infection of host tissues by Staphylococcus aureus requires a family of staphylococcal adhesive proteins containing serine-aspartate repeat (SDR) domains, such as ClfA. The O-linked glycosylation of the long-chain SDR domain mediated by SdgB and SdgA is a key virulence factor that protects the adhesive SDR proteins against host proteolytic attack in order to promote successful tissue colonization, and has also been implicated in staphylococcal agglutination, which leads to sepsis and an immunodominant epitope for a strong antibody response. Despite the biological significance of these two glycosyltransferases involved in pathogenicity and avoidance of the host innate immune response, their structures and the molecular basis of their activity have not been investigated. This study reports the crystal structures of SdgB and SdgA from S. aureus as well as multiple structures of SdgB in complex with its substrates (for example UDP, N-acetylglucosamine or SDR peptides), products (glycosylated SDR peptides) or phosphate ions. Together with biophysical and biochemical analyses, this structural work uncovered the novel mechanism by which SdgB and SdgA carry out the glycosyl-transfer process to the long SDR region in SDR proteins. SdgB undergoes dynamic changes in its structure such as a transition from an open to a closed conformation upon ligand binding and takes diverse forms, both as a homodimer and as a heterodimer with SdgA. Overall, these findings not only elucidate the putative role of the three domains of SdgB in recognizing donor and acceptor substrates, but also provide new mechanistic insights into glycosylation of the SDR domain, which can serve as a starting point for the development of antibacterial drugs against staphylococcal infections.

Antimicrobial Activity and Action Mechanisms of Arg-Rich Short Analog Peptides Designed from the C-Terminal Loop Region of American Oyster Defensin (AOD)

American oyster defensin (AOD) was previously purified from acidified gill extract of the American oyster, Crassostrea virginica. AOD is composed of 38 amino acids with three disulfide bonds and exhibits strong antimicrobial activity against Gram-positive bacteria as well as significant activity against Gram-negative bacteria. Here, to develop promising peptides into antibiotic candidates, we designed five arginine-rich analogs (A0, A1, A2, A3, and A4), predicted their loop and extended strand/random structures-including nine amino acids and a disulfide bond derived from the C-terminus of AOD-and described their antimicrobial and cytotoxic effects, as well as their modes of action. In our experimental results, the A3 and A4 analogs exhibited potent antimicrobial activity against all test organisms-including four Gram-positive bacteria, six Gram-negative bacteria, and Candida albicans-without cell toxicity. A sequence of experiments, including a membrane permeabilization assay, DNA binding study, and DNA polymerization inhibition test, indicated that the two analogs (A3 and A4) possibly did not act directly on the bacterial membrane but instead interacted with intracellular components such as DNA or DNA amplification reactions. AOD analogs also showed strong bacterial inhibition activity in the plasma environment. In addition, analog-treated microbial cells clearly exhibited membrane disruption, damage, and leakage of cytoplasmic contents. Collectively, our results suggest that two analogs, A3 and A4, have potent antimicrobial activity via DNA interaction and have the potential for development into novel antimicrobial agents.

Crystal structures of human NSDHL and development of its novel inhibitor with the potential to suppress EGFR activity

NAD(P)-dependent steroid dehydrogenase-like (NSDHL), an essential enzyme in human cholesterol synthesis and a regulator of epidermal growth factor receptor (EGFR) trafficking pathways, has attracted interest as a therapeutic target due to its crucial relevance to cholesterol-related diseases and carcinomas. However, the development of pharmacological agents for targeting NSDHL has been hindered by the absence of the atomic details of NSDHL. In this study, we reported two X-ray crystal structures of human NSDHL, which revealed a detailed description of the coenzyme-binding site and the unique conformational change upon the binding of a coenzyme. A structure-based virtual screening and biochemical evaluation were performed and identified a novel inhibitor for NSDHL harboring suppressive activity towards EGFR. In EGFR-driven human cancer cells, treatment with the potent NSDHL inhibitor enhanced the antitumor effect of an EGFR kinase inhibitor. Overall, these findings could serve as good platforms for the development of therapeutic agents against NSDHL-related diseases.

Structural and functional study of SaAcP, an acylphosphatase from Staphylococcus aureus

Acylphosphatase is the smallest enzyme that is widely distributed in many diverse organisms ranging from archaebacteria to higher-eukaryotes including the humans. The enzyme hydrolyzes the carboxyl-phosphate bonds of the acyl phosphates which are important intermediates in glycolysis, membrane pumps, tricarboxylic acid cycle, and urea biosynthesis. Despite its biological importance in critical cellular functions, very limited structural investigations have been conducted on bacterial acylphosphatases. Here, we first unveiled the crystal structure of SaAcP, an acylphosphatase from gram-positive S. aureus at the atomic level. Structural insights on the active site together with mutation study provided greater understanding of the catalytic mechanism of SaAcP as a bacterial acylphosphatase and as a putative apyrase. Furthermore, through NMR titration experiment of SaAcP in its solution state, the dynamics and the alterations of residues affected by the phosphate ion were validated. Our findings elucidate the structure-function relationship of acylphosphatases in gram-positive bacteria and will provide a valuable basis for researchers in the field related to bacterial acylphosphatases.

Establishment of Conditions for Long-Term Maintenance of Primary Embryonic Cell Cultures from Olive Flounder Paralichthys olivaceus

Primary cell culture is a sufficient method frequently used to study the cellular properties and mechanisms of isolated cells in a controlled environment. In this study, an embryonic cell line (FGBC8) derived from the blastula stages of embryos of olive flounder Paralichthys olivaceus was developed. Furthermore, conditions for optimal long-term maintenance of this primary embryonic cell culture were investigated. Morphologically, FGBC8 cells were composed primarily of epithelial-like cells. FGBC8 cells were subcultured for >160 passages over ~830 days. The doubling time of FGBC8 cells was 73.8 h, and the modal diploid chromosome number was 48. FGBC8 cells transfected with green fluorescence protein (GFP)-expression plasmid exhibited a strong signal 48 h after transfection. Consequently, we demonstrated that fish serum is a crucial supplement for the long-term survival and maintenance of comparable morphology in these primary embryonic cells. Our results can be used as a guide for primary embryonic cell cultures for other fish species and may be useful for cell biotechnological applications.

Crystal structure of the YoeBSa1-YefMSa1 complex from Staphylococcus aureus

Toxin-antitoxin (TA) systems are ubiquitously found in bacteria and are related to cell maintenance and survival under environmental stresses such as heat shock, nutrient starvation, and antibiotic treatment. Here, we report for the first time the crystal structure of the Staphylococcus aureus TA complex YoeB_Sa1-YefM_Sa1 at a resolution of 1.7 Å. This structure reveals a heterotetramer with a 2:2 stoichiometry between YoeB_Sa1 and YefM_Sa1. The N-terminal regions of the YefM_Sa1 antitoxin form a homodimer characteristic of a hydrophobic core, and the C-terminal extended region of each YefM_Sa1 protomer makes contact with each YoeB_Sa1 monomer. The binding stoichiometry of YoeB_Sa1 and YefM_Sa1 is different from that of YoeB and YefM of E. coli (YoeB_Ec and YefM_Ec), which is the only structural homologue among YoeB-YefM families; however, the structures of individual YoeB_Sa1 and YefM_Sa1 subunits in the complex are highly similar to the corresponding structures in E. coli. In addition, docking simulation with a minimal RNA substrate provides structural insight into the guanosine specificity of YoeB_Sa1 for cleavage in the active site, which is distinct from the specificity of YoeB_Ec for adenosine rather than guanosine. Given the previous finding that YoeB_Sa1 exhibits fatal toxicity without inducing persister cells, the structure of the YoeB_Sa1-YefM_Sa1 complex will contribute to the design of a new category of anti-staphylococcal agents that disrupt the YoeB_Sa1-YefM_Sa1 complex and increase YoeB_Sa1 toxicity.

First report of cathepsin E in a teleost (Korean rose bitterling, Rhodeus uyekii): Molecular characterisation and tissue distribution

We isolated and characterised a cDNA encoding the aspartic protease cathepsin E (CTSE) in Korean rose bitterling, Rhodeus uyekii. The full-length Rhodeus uyekii CTSE (RuCTSE) cDNA (1396 bp) contains an open reading frame of 1218 bp, encoding 405 amino acids. Alignment of multiple CTSE protein sequences revealed that two of the aspartyl protease active site residues and a disulphide bond were well-conserved among the other CTSE sequences. Phylogenetic analysis revealed that RuCTSE is most closely related to freshwater fish cathepsin E. RuCTSE is widely expressed in the liver, spleen, ovary, testis, brain, eye, intestine, muscle, fin, stomach, and kidney. This first report of teleost CTSE will provide important information related to the identification of other cathepsin E genes in various fish species and will serve as a useful molecular tool to help clarify biological activities in other teleosts.

A structural study of TatD from Staphylococcus aureus elucidates a putative DNA-binding mode of a Mg2+-dependent nuclease

TatD has been thoroughly investigated as a DNA-repair enzyme and an apoptotic nuclease, and still-unknown TatD-related DNases are considered to play crucial cellular roles. However, studies of TatD from Gram-positive bacteria have been hindered by an absence of atomic detail and the resulting inability to determine function from structure. In this study, an X-ray crystal structure of SAV0491, which is the TatD enzyme from the Gram-positive bacterium Staphylococcus aureus (SaTatD), is reported at a high resolution of 1.85 Å with a detailed atomic description. Although SaTatD has the common TIM-barrel fold shared by most TatD-related homologs, and PDB entry 2gzx shares 100% sequence identity with SAV0491, the crystal structure of SaTatD revealed a unique binding mode of two phosphates interacting with two Ni2+ ions. Through a functional study, it was verified that SaTatD has Mg2+-dependent nuclease activity as a DNase and an RNase. In addition, structural comparison with TatD homologs and the identification of key residues contributing to the binding mode of Ni2+ ions and phosphates allowed mutational studies to be performed that revealed the catalytic mechanism of SaTatD. Among the key residues composing the active site, the acidic residues Glu92 and Glu202 had a critical impact on catalysis by SaTatD. Furthermore, based on the binding mode of the two phosphates and structural insights, a putative DNA-binding mode of SaTatD was proposed using in silico docking. Overall, these findings may serve as a good basis for understanding the relationship between the structure and function of TatD proteins from Gram-positive bacteria and may provide critical insights into the DNA-binding mode of SaTatD.

Myticusin-beta, antimicrobial peptide from the marine bivalve, Mytilus coruscus

We isolated and purified an antimicrobial peptide (AMP) from the mantle of the hard-shelled mussel, Mytilus coruscus. The peptide was purified through C₁₈ reversed-phase high-performance liquid chromatography, and displayed antibacterial activity. Total molecular mass of 11,182 Da was determined using matrix-assisted laser desorption ionization time-of-flight mass spectrophotometry. The N-terminal 23-amino acid sequence of its purified peak was obtained through Edman degradation, revealing 82% identity with myticusin-1 of M. coruscus. Complete sequence of the target peptide was determined through cDNA cloning and rapid amplification of cDNA ends. The complete sequence comprised 574 bp with a 387-bp open reading frame (ORF) encoding 24 amino acids of a signal peptide and 104 amino acids of a mature peptide, which was named myticusin-beta. Furthermore, we discovered two novel isoforms of myticusin-beta. We constructed and expressed recombinant myticusin-beta, which displayed antimicrobial activity against gram-positive (Bacillus cereus, Bacillus subtilis, Clostridium perfringens, Staphylococcus aureus, Streptococcus iniae, Streptococcus mutans) and gram-negative bacteria (Escherichia coli, Pseudomonas aeruginosa, Vibrio alginolyticus, Klebsiella pneumoniae). Purified recombinant myticusin-beta also showed anti-parasitic activity at various concentrations. A short AMP analog was designed and synthesized based on the sequence of myticusin-beta, with markedly improved antimicrobial activity. Expression of myticusin-beta was detected in the mantle at the highest level, followed by hemocytes. The results obtained in this work suggest that myticusin-beta is an immune-related AMP of M. coruscus and an effective alternative to antibiotics.

Dentoalveolar Defects in the Hyp Mouse Model of X-linked Hypophosphatemia

Mutations in PHEX cause X-linked hypophosphatemia (XLH), a form of hypophosphatemic rickets. Hyp (Phex mutant) mice recapitulate the XLH phenotype. Dental disorders are prevalent in individuals with XLH; however, underlying dentoalveolar defects remain incompletely understood. We analyzed Hyp mouse dentoalveolar defects at 42 and 90 d postnatal to comparatively define effects of XLH on dental formation and function. Phex mRNA was expressed by odontoblasts (dentin), osteocytes (bone), and cementocytes (cellular cementum) in wild-type (WT) mice. Enamel density was unaffected, though enamel volume was significantly reduced in Hyp mice. Dentin defects in Hyp molars were indicated histologically by wide predentin, thin dentin, and extensive interglobular dentin, confirming micro-computed tomography (micro-CT) findings of reduced dentin volume and density. Acellular cementum was thin and showed periodontal ligament detachment. Mechanical testing indicated dramatically altered periodontal mechanical properties in Hyp versus WT mice. Hyp mandibles demonstrated expanded alveolar bone with accumulation of osteoid, and micro-CT confirmed decreased bone volume fraction and alveolar bone density. Cellular cementum area was significantly increased in Hyp versus WT molars owing to accumulation of hypomineralized cementoid. Histology, scanning electron microscopy, and nanoindentation revealed hypomineralized "halos" surrounding Hyp cementocyte and osteocyte lacunae. Three-dimensional micro-CT analyses confirmed larger cementocyte/osteocyte lacunae and significantly reduced perilacunar mineral density. While long bone and alveolar bone osteocytes in Hyp mice overexpressed fibroblast growth factor 23 (Fgf23), its expression in molars was much lower, with cementocyte Fgf23 expression particularly low. Expression and distribution of other selected markers were disturbed in Hyp versus WT long bone, alveolar bone, and cementum, including osteocyte/cementocyte marker dentin matrix protein 1 (Dmp1). This study reports for the first time a quantitative analysis of the Hyp mouse dentoalveolar phenotype, including all mineralized tissues. Novel insights into cellular cementum provide evidence for a role for cementocytes in perilacunar mineralization and cementum biology.

Effectiveness of Perioperative Immunologic Markers Monitoring for Predicting Early Acute Cellular Rejection After Living Donor Liver Transplantation

BACKGROUND

The objective of this study was to determine whether perioperative immunologic markers monitoring could predict early acute cellular rejection (ACR) after living donor liver transplantation (LDLT).

MATERIALS AND METHODS

From September 2010 to June 2013, a total of 172 patients underwent LDLT at our transplant center. Of them, 26 patients were excluded because of infection. We retrospectively reviewed the remaining 146 patients. CD4 lymphocyte activity, T cell subsets test, and serum cytokine panel were checked on the day before transplantation and at 20 days after transplantation. These patients were divided into 3 groups: 1. normal liver function test (LFT) group; 2. increased LFT without rejection group; and 3. early ACR group. We excluded the increased LFT without rejection group in order to rule out multiple factors influencing immunologic factors.

RESULTS

CD4 lymphocyte activity (P = .004) was significantly increased while CD4+/CD25+/FOXP3+ cells (P < .001) and interleukin (IL)-17 (P = .002) levels were significantly decreased during the perioperative period. Pretransplant IL-6 (P = .014) and IL-17 (P = .029) levels in the early ACR group were significantly lower than those in the normal LFT group. The proportion of patients with increased IL-6 during perioperative period in the early ACR group was higher than that in the normal LFT group, although the difference was not statistically significant (P = .065).

CONCLUSION

Our results suggest that IL-6 and IL-17 levels are associated with early ACR in LDLT patients. However, whether monitoring perioperative immunologic markers could predict early ACR remains unclear. Further prospective studies are needed to reach a definite conclusion.

[Non-gonococcal urethritis in men]

This literature review is dedicated to urethritis which is one of the most common disorders of urogenital tract in men. The current views in its etiology as well as problems in diagnosis with the main being the frequent inability to isolate etiological factor of inflammation it the urethra are described. The analysis of literature suggests a possible role of bacteria, which are associated with bacterial vaginosis in women, in the development of the urethritis in men. However, the frequency of such urethritis and causative role of specific pathogens has not been studied yet. Meanwhile, the exact determination of the causes of inflammation has direct influence on the choice of appropriate etiologic treatment and can increase its efficiency.

Synthesis of Poly(phenylene polysulfide) Networks from Elemental Sulfur and p-Diiodobenzene for Stretchable, Healable, and Reprocessable Infrared Optical Applications

The synthesis and characterization of poly(phenylene polysulfide) networks (PSNs) with controlled average sulfur ranks, from elemental sulfur (ES) and p-diiodobenzene (DIB), are investigated. The PSN films, prepared via simple hot pressing, are found to possess large extensibility up to around 300% and complete recovery of shape and mechanical properties after deformation, which are attributed to the loosely cross-linked network structures mainly consisting of linear poly(phenylene polysulfide) chains. The covalent polysulfide linkages in the PSNs also exhibit dynamic behaviors under ultraviolet (UV) or thermal treatment, thus, enabling self-healing and reprocessing of the films when scratched and broken, respectively. Combined with the unique mechanical properties of the PSNs, their high refractive index and excellent infrared (IR) transparency contribute to the preparation of stretchable, healable, and reprocessable IR transmitting materials for potential deformable and stretchable optical applications.

Aliishimia ponticola gen. nov., sp. nov., isolated from seawater

A Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated MYP11^T, was isolated from seawater around Jeju island, Republic of Korea and identified by polyphasic taxonomic study. A neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain MYP11^T joined the cluster comprising the type strains of Shimiaabyssi, Shimiaaestuarii and Shimiaaquaeponti, showing 16S rRNA gene sequence similarities of 96.3-96.8 %. Strain MYP11^T exhibited 16S rRNA gene sequence similarity values of 94.2-94.9 % to the type strains of other Shimia species. In the upgma dendrogram based on the average nucleotide identity values of genomic sequences, strain MYP11^T formed an evolutionary lineage independent of those of Shimia species and other taxa. Strain MYP11^T contained Q-10 as the predominant ubiquinone and C_18 : 1  ω7c and cyclo C_19 : 0  ω8c as the major fatty acids. The major polar lipids of strain MYP11^T were phosphatidylcholine, phosphatidylglycerol, two unidentified lipids and one unidentified aminolipid. The DNA G+C content of strain MYP11^T was 63.1 or 61.5 mol%. The differences in the fatty acid and polar lipid profiles and DNA G+C contents made it reasonable to distinguish strain MYP11^T from the type strains of S. abyssi, S. aestuarii and S. aquaeponti and those of other Shimia species. On the basis of the polyphasic data presented here, strain MYP11^T is considered to constitute a new genus and species within the class Alphaproteobacteria, for which the name Aliishimia ponticola gen. nov., sp. nov. is proposed. The type strain is MYP11^T (=KCTC 62899^T=NBRC 113544^T).

Empedobacter tilapiae sp. nov., isolated from an intestine of Nile tilapia (Oreochromis niloticus)

A Gram-stain-negative, aerobic, non-motile and ovoid or rod-shaped bacterial strain, MRS2^T, was isolated from an intestine of Nile tilapia (Oreochromisniloticus) collected from the Republic of Korea. Strain MRS2^T grew optimally at 30 °C and in the presence of 0-2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain MRS2^T clustered with the type strains of Empedobacter species. It exhibited the highest 16S rRNA gene sequence similarity (98.5 %) to the type strain of Empedobacter falsenii and sequence similarities of 97.4-97.6 % to the type strains of two other Empedobacter species. Strain MRS2^T contained MK-6 as the predominant ubiquinone and summed feature 3 (C_16 : 1ω7c and/or C_16 : 1ω6c), iso-C_17 : 0 3-OH and iso-C_15 : 0 as the major fatty acids. The major polar lipids of strain MRS2^T were phosphatidylethanolamine, one unidentified lipid and one unidentified aminolipid. The DNA G+C contents of strain MRS2^T were 32.2 mol% or 30.65 mol%. Strain MRS2^T exhibited DNA-DNA relatedness values of 12-20 % to the type strains of Empedobacter falsenii, Empedobacter brevis and Empedobacter stercoris. The average nucleotide identity values between strain MRS2^T and five strains of E. falsenii and E. brevis were 84.8-91.0 %. The phylogenetic, genetic and differential phenotypic properties indicated that strain MRS2^T is separated from Empedobacter species. On the basis of the data presented here, strain MRS2^T is considered to represent a novel species of the genus Empedobacter, for which the name Empedobactertilapiae sp. nov. is proposed. The type strain is MRS2^T (=KCTC 62904^T=NBRC 113550^T).

FCC to BCC transformation-induced plasticity based on thermodynamic phase stability in novel V10Cr10Fe45CoxNi35-x medium-entropy alloys

We introduce a novel transformation-induced plasticity mechanism, i.e., a martensitic transformation from fcc phase to bcc phase, in medium-entropy alloys (MEAs). A VCrFeCoNi MEA system is designed by thermodynamic calculations in consideration of phase stability between bcc and fcc phases. The resultantly formed bcc martensite favorably contributes to the transformation-induced plasticity, thereby leading to a significant enhancement in both strength and ductility as well as strain hardening. We reveal the microstructural evolutions according to the Co-Ni balance and their contributions to a mechanical response. The Co-Ni balance plays a leading role in phase stability and consequently tunes the cryogenic-temperature strength-ductility balance. The main difference from recently-reported metastable high-entropy dual-phase alloys is the formation of bcc martensite as a daughter phase, which shows significant effects on strain hardening. The hcp phase in the present MEA mostly acts as a nucleation site for the bcc martensite. Our findings demonstrate that the fcc to bcc transformation can be an attractive route to a new MEA design strategy for improving cryogenic strength-ductility.

Development of novel antimicrobial peptides derived from anti-lipopolysaccharide factor of the swimming crab, Portunus trituberculatus

Anti-lipopolysaccharide factors (ALFs) are a representative host defense protein in crustaceans. In this study, we successfully developed two novel antimicrobial peptides (AMPs), named crab-ALF2A and crab-ALF6A, which contain changes to the amino acid sequences of the lipopolysaccharide binding domain and signal peptide, respectively, of the ALF of the swimming crab Portunus trituberculatus. The crab-ALF2A peptide showed potent antimicrobial activity against the Gram-positive bacteria Bacillus cereus, Staphylococcus aureus, and Streptococcus iniae (minimal effective concentration [MEC] 1.51-1.93 μg/mL) and the Gram-negative bacteria Pseudomonas aeruginosa and Escherichia coli (MEC 1.87-1.98 μg/mL), with maximal bactericidal activity at a peptide concentration of 5 μg/mL. The crab-ALF6A peptide also showed potent antimicrobial activity against B. cereus, S. aureus, and S. iniae (MEC 1.49-2.3 μg/mL) and P. aeruginosa and E. coli (MEC 1.72-1.19 μg/mL) at a peptide concentration of 5 μg/mL. Notably, the crab-ALF2A and crab-ALF6A peptides exhibited strong activity against Candida albicans (MECs of 2.11 and 1.95 μg/mL, respectively). These activities were stable following heat treatment. Moreover, the effect of crab-ALF2A and crab-ALF6A peptide treatment on microbe cell morphology was confirmed by scanning electron microscopy. Membrane disruption and damage, and the leakage of cytoplasmic content were clearly observed. A downsizing peptide approach illustrated that the hexapeptide ALF6A8 (RVLLRL) was the shortest peptide showing significant antimicrobial activity. Our approach allows for the generation of novel antimicrobial peptides in a cost effective manner as potential next-generation antibiotics.

Tailoring biomimetic polymer networks towards an unprecedented combination of versatile mechanical characteristics

Biomimetic polymeric materials, adopting the basic molecular design principles of biological materials, have been extensively studied in recent years but it is still challenging to combine assorted mechanical characteristics in a single material. Here, we present a simple and effective strategy to prepare mechanically robust yet resilient biomimetic polymer networks by utilizing dual noncovalent and covalent cross-linkings. Tailoring the dual cross-links consisting of thiourea noncovalent interactions and epoxy–amine covalent linkages in the biomimetic polymer networks enables a rare combination of excellent elastic modulus (1.1 GPa), yield stress (39 MPa), extensibility (320%), as well as complete strain and performance recovery after deformation at room temperature. The biomimetic polymer networks also exhibit highly adaptive mechanical properties in response to multiple-stimuli including strain rate, temperature, light, and solvent.

A simple and effective strategy to prepare biomimetic polymer networks with stiff, strong, tough, resilient, and adaptive mechanical properties, through controlling thiourea noncovalent and epoxy–amine covalent cross-linkings, is presented.

3D hierarchical scaffolds enabled by a post-patternable, reconfigurable, and biocompatible 2D vitrimer film for tissue engineering applications

A mechanically tissue-like, biocompatible vitrimer yields 3D hierarchical tissue engineering scaffolds via hot embossing patterning and additional reconfiguration processes.

Purification and characterization of an antimicrobial peptide mytichitin-chitin binding domain from the hard-shelled mussel, Mytilus coruscus

An antimicrobial peptide with 55 amino acid residues was purified by C₁₈ reversed-phase high-performance liquid chromatography (HPLC) from foot extract of the hard-shelled mussel, Mytilus coruscus. This peptide showed strong antimicrobial activity against Gram-positive and Gram-negative bacteria, as well as fungi. The purified peptide was determined to have a molecular mass of 6202 Da by matrix-assisted laser desorption/ionization time-of-flight mass spectrophotometry (MALDI-TOF/MS). The identified 20-amino acid sequence of the purified peak by Edman degradation shared 100% identity with the N-terminal regions of mytichitin-1, mytichitin-2, mytichitin-3, mytichitin-4, mytichitin-5, and chitinase-like protein-1, and so was named mytichitin-CBD. The cDNA of mytichitin-CBD was cloned and sequenced by rapid amplification of cDNA ends (RACE). The mRNA transcripts were mainly detected in foot tissue, and they were up-regulated and peaked at 4 h after bacterial infection. We constructed and expressed recombinant mytichitin-CBD protein which displayed antimicrobial activity against Gram-negative bacteria Gram-positive bacteria and the fungus as well as anti-parasitic activity against scuticociliates. The results of this study demonstrate that the peptide isolated from M. coruscus is related to the innate immune system of this marine invertebrate and is a possible alternative to antibiotics.

Anisotropy-Driven High Thermal Conductivity in Stretchable Poly(vinyl alcohol)/Hexagonal Boron Nitride Nanohybrid Films

Controlling the anisotropy of two-dimensional materials with orientation-dependent heat transfer characteristics is a possible solution to resolve severe thermal issues in future electronic devices. We demonstrate a dramatic enhancement in the in-plane thermal conductivity of stretchable poly(vinyl alcohol) (PVA) nanohybrid films containing small amounts (below 10 wt %) of hexagonal boron nitride ( h-BN) nanoplatelets. The h-BN nanoplatelets were homogeneously dispersed in the PVA polymer solution by ultrasonication without additional surface modification. The mixture was used to prepare thermally conductive nanocomposite films. The in-plane thermal conductivity of the resulting PVA/ h-BN nanocomposite films increased to 6.4 W/mK when the strain was increased from 0 to 100% in the horizontal direction. More specifically, the thermal conductivity of a PVA/ h-BN composite film with 10 wt % filler loading can be improved by up to 32 times as compared to pristine PVA. This outstanding thermal conductivity value is significantly larger than that of materials currently used in in-plane thermal management systems. This result is attributed to the anisotropic alignment of h-BN particles in the PVA chain matrix during stretching, enhancing phonon conductive paths and hence improving the thermal conductivity and thermal properties of PVA/ h-BN nanocomposite films. These polymer nanocomposites have low cost as the amount of expensive conductive fillers is reduced and can be potentially used as high-performance materials for thermal management systems such as heat sink and thermal interface materials, for future electronic and electrical devices.

Purification and cDNA cloning of the antimicrobial peptide apMolluscidin from the pen shell, Atrina pectinata

A 5.6 kDa antimicrobial peptide (AMP) was purified from acidified gill extract of the pen shell, Atrina pectinata, by cation exchange and C₁₈ reversed-phase high performance liquid chromatography. Comparison of the amino acid sequences and molecular weight of this peptide with those of other known AMPs revealed that it had high sequence homology with that of cgMolluscidin or hdMolluscidin; it was designated apMolluscidin. apMolluscidin comprises 59 amino acid residues containing several dibasic residue repeats and sequence repeats such as Lys-Lys and Lys-Gly. apMolluscidin exhibited potent antimicrobial activity against both Gram-positive bacteria including Bacillus subtilis (minimal effective concentration [MEC], 2.1 μg/mL), and Gram-negative bacteria including E. coli D31 (MEC, 0.5 μg/mL), without hemolytic activity. However, it did not show any activity against fungi such as Candida albicans. Secondary structure prediction suggested that it might form two helical regions and have an amphipathic structure. Full-length apMolluscidin cDNA contained 812 base pairs (bp), including a 5'-untranslated region (UTR) of 82 bp, a 3'-UTR of 547 bp, and a coding sequence of 183 bp encoding 60 amino acids (containing Met). Furthermore, qPCR analyses revealed that the mature peptide translated from apMolluscidin mRNA is expressed in a tissue-specific manner in locations such as the gill and siphon. These results indicate that apMolluscidin might be related to the innate immune defense system of abalone and may not act directly on the bacterial membrane. This is the first report of an AMP from the pen shell with a fully identified amino acid sequence.

Solution-Processable, Thin, and High-κ Dielectric Polyurea Gate Insulator with Strong Hydrogen Bonding for Low-Voltage Organic Thin-Film Transistors

We developed a solution-processable, thin, and high-dielectric polyurea-based organic gate insulator for low-voltage operation and high performance of organic thin-film transistors (OTFTs). A 60 nm-thick polyurea thin film exhibited a high dielectric constant of 5.82 and excellent electrical insulating properties owing to strong hydrogen bonding. The hydrogen bonding of the synthesized polyurea was confirmed using infrared spectroscopy and was quantitatively evaluated by measuring the interactive force using atomic force microscopy. Moreover, the effect of hydrogen bonding of polyurea on the insulating properties was systematically investigated through the combination of various monomers and control of the thickness of the polyurea film. The dinaphtho[2,3- b:2',3'- f]thieno[3,2- b]thiophene-based OTFTs with the polyurea gate insulator showed excellent thin-film transistor (TFT) performance with a field-effect mobility of 1.390 cm²/V·s and an on/off ratio of ∼10⁵ at a low operation voltage below 2 V. In addition, it is possible to fabricate flexible polymer organic semiconductor (OSC)-based TFT devices using a solution process, owing to excellent solvent stability in various organic solvents. We believe that the solution-processable polyurea gate insulator with a high dielectric constant and good insulation properties is a promising candidate for low-voltage-operated OTFTs using various OSCs.

Development and Characterization of a New Cell Line from Olive Flounder Paralichthys olivaceus

A new embryonic cell line (OFEC-17FEN) derived from olive flounder Paralichthys olivaceus was developed. OFEC-17FEN cells were subcultured for <30 passages over ~200 days. OFEC-17FEN cells had a doubling time of 114.34 h and modal diploid chromosome number was 48. The pluripotency genes POU5f1 and NANOG were expressed in OFEC-17FEN cells. However, the lack of several pluripotency-related genes expression indicates that OFEC-17FEN cells are not stem cells. OFEC-17FEN cells transfected with plasmid pEGFP-c1 exhibited a strong green fluorescent signal at 48 h after transfection. Accordingly, OFEC-17FEN cells may be useful for both basic research and biotechnological application.

Molecular characterization of Rhodeus uyekii tripartite motif protein 1 (TRIM1) involved in IFN-γ/LPS-induced NF-κB signaling

The tripartite motif-containing (TRIM) proteins are involved in a wide range of cellular processes, and the role of TRIM1 in immunity has been explored. However, fundamental studies on fish TRIM1 are lacking. In this study, we cloned and characterized TRIM1 cDNA from the Korean rose bitterling, Rhodeus uyekii (RuTRIM1). Two RuTRIM1 isoforms (RuTRIM1-X1 and RuTRIM1-X2) were identified. The coding sequence (CDS) of RuTRIM1-X1 comprised 2157 bp encoding a 718-aa protein, and the CDS of RuTRIM1-X2 comprised 1929 bp encoding a 642-aa protein. Both RuTRIM1 isoforms contained a RING finger domain, B-box 1, B-box 2, coiled-coil domain, COS box, FN3 motif, and PRY/SPRY domain. The deduced RuTRIM1-X1 and RuTRIM1-X2 proteins had high amino acid identity (76.27-98.89%) with orthologs from various other species, and a phylogenetic tree was constructed. RuTRIM1-X1 and RuTRIM1-X2 mRNA were expressed in all tissues examined, with the highest expression levels detected in the hepatopancreas. During early development, RuTRIM1-X1 and RuTRIM1-X2 mRNA levels changed differently from the gastrula period to the first feeding stage. An in vivo ubiquitination assay showed that RuTRIM1 exhibited RING-dependent E3 ubiquitin ligase activity, mainly by comparing RuTRIM1-X2 to RuTRIM1-X1. The subcellular localization of the two RuTRIM1 protein isoforms was characterized, revealing that they formed aggregates in cytoplasmic bodies in Raw264.7 cells. Interferon-γ/lipopolysaccharide-induced nuclear factor-κB signaling was negatively regulated by RuTRIM1-X1 and RuTRIM1-X2, and the negative effect was reversed in RING deletion mutants. To our knowledge, this is the first study to characterize fish TRIM1, which may play a role in the inflammatory response.

Regulatory mechanisms of thiol-based redox sensors: lessons learned from structural studies on prokaryotic redox sensors

Oxidative stresses, such as reactive oxygen species, reactive electrophilic species, reactive nitrogen species, and reactive chlorine species, can damage cellular components, leading to cellular malfunction and death. In response to oxidative stress, bacteria have evolved redox-responsive sensors that enable them to simultaneously monitor and eradicate potential oxidative stress. Specifically, redox-sensing transcription regulators react to oxidative stress by means of modifying the thiol groups of cysteine residues, functioning as part of an efficient survival mechanism for many bacteria. In general, oxidative molecules can induce changes in the three-dimensional structures of redox sensors, which, in turn, affects the transcription of specific genes in detoxification pathways and defense mechanisms. Moreover, pathogenic bacteria utilize these redox sensors for adaptation and to evade subsequent oxidative attacks from host immune defense. For this reason, the redox sensors of pathogenic bacteria are potential antibiotic targets. Understanding the regulatory mechanisms of thiol-based redox sensors in bacteria will provide insight and knowledge into the discovery of new antibiotics.

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.