Characterization of the complete mitochondrial genome of Miamiensis avidus causing flatfish scuticociliatosis.

Miamiensis avidus is a parasitic pathogen that causes the disease scuticociliatosis in teleost fish species. It is a ciliate and a free-living marine protozoan belonging to the order Philasterida, subclass Scuticociliatida, class Oligohymenophorea, and phylum Ciliophora. The complete mt-genome of M. avidus was linear and 38,695 bp in length with 47 genes, including 40 protein-coding genes, two ribosomal RNA (rRNA) genes, and five transfer RNA (tRNA) genes. Of these, 20 genes typically belong to the clusters of orthologous groups, playing roles in energy production and conversion, translation, ribosomal structure and biogenesis, and defense mechanisms. This is the first report of sequencing and characterization of the mt-genome of M. avidus, which was observed to be linear and possessing the typical ciliate mitochondrial genome organization and phylogenetic relationships. Remarkable differences were observed between M. avidus and other ciliates in the mitochondrially encoded rRNAs, extensive gene loss in ribosomal genes and tRNAs, terminal repeat sequences, and stop codon usage. A comparative and phylogenetic analysis of M. avidus and Uronema marinum of the order Hymenostomatida, which is most closely related to the order Philasterida, signified the promise of the mitogenome data of M. avidus as a valuable genetic marker in species detection and taxonomic research. The present study has potential applications in epidemiological studies and host-parasite interaction investigations facilitating disease control.

Thermodynamic patterns duringin-situheating of InAs nanowires encapsulated in Al2O3shells.

Understanding the dynamic thermal behavior of nanomaterials based on their unique physical and chemical properties is critical for their applications. In this study, the thermal behavior of single-crystalline InAs nanowires in an amorphous Al2O3shell was investigated by conductingin situheating experiments in a transmission electron microscope. Two different thermodynamic patterns were observed during thein situheating experiments: (1) continuous vaporization and condensation simultaneously at temperatures lower than 838.15 K, and (2) pure evaporation at temperatures higher than 878.15 K. During the simultaneous condensation and vaporization in closer areas in a single InAs nanowire, the front edge of the vaporization was flat, while that of the condensation actively changed with time and temperature. Pure vaporization was conducted via layer-by-layer evaporation followed by three-dimensional vaporization at the final stage. The thermal behaviors of the InAs nanowires were demonstrated from a thermodynamic point of view.

Accelerated decomposition of Bi2S3 nanorods in water under an electron beam: a liquid phase transmission electron microscopy study.

Evaluating the stability of semiconductor photocatalysts is critical in the development of efficient catalysts. The morphological and microstructural behaviors of nanorod-shaped Bi2S3 semiconductors in aqueous solution were studied using a liquid cell transmission electron microscopy (TEM) technique. The rapid decomposition of Bi2S3 in water was observed under electron beam irradiation during TEM. Rounded bright spots due to a reduction in thickness were observed on the Bi2S3 nanorods at the initial stage of the decomposition, and rounded dark particles appeared outside of the nanorods in the solution, continuing the decomposition. This was confirmed by analyzing the atomic structure of the newly formed small particles, which consisted of an orthorhombic Bi2S3 phase. The stability-related decomposition of the Bi2S3 nanorods was demonstrated by considering the reduction and oxidation potentials of Bi2S3 in an aqueous solution. The effect of water radiolysis by the incident electron during TEM observations on the decomposition process was also determined by considering the time-dependent concentration behavior of the chemical species. Our study therefore reflects a novel route to evaluate the stabilities of semiconductor photocatalysts, which could ultimately solve a range of energy and environmental pollution problems.

Microstructural evolution in self-catalyzed GaAs nanowires during in-situ TEM study.

The microstructural evolutions in self-catalyzed GaAs nanowires (NWs) were investigated by using in situ heating transmission electron microscopy (TEM). The morphological changes of the self-catalyst metal gallium (Ga) droplet, the GaAs NWs, and the atomic behavior at the interface between the self-catalyst metal gallium and GaAs NWs were carefully studied by analysis of high-resolution TEM images. The microstructural change of the Ga-droplet/GaAs-NWs started at a low temperature of ∼200 °C. Formation and destruction of atomic layers were observed at the Ga/GaAs interface and slow depletion of the Ga droplet was detected in the temperature range investigated. Above 300 °C, the evolution process dramatically changed with time: The Ga droplet depleted rapidly and fast growth of zinc-blende (ZB) GaAs structures were observed in the droplet. The Ga droplet was completely removed with time and temperature. When the temperature reached ∼600 °C, the decomposition of GaAs was detected. This process began in the wurtzite (WZ) structure and propagated to the ZB structure. The morphological and atomistic behaviors in self-catalyzed GaAs NWs were demonstrated based on thermodynamic considerations, in addition to the effect of the incident electron beam in TEM. Finally, GaAs decomposition was demonstrated in terms of congruent vaporization.

Whole-genome next-generation sequencing and phylogenetic characterization of viral haemorrhagic septicaemia virus in Korea.

Whole-genome next-generation sequencing was used to investigate the local evolution of viral haemorrhagic septicaemia virus, a serious pathogen affecting economically important fish such as rainbow trout and turbot in Europe and olive flounder in Asia. Sequence analysis showed that all isolates were genotype IVa, but could be classified further into four subgroups (K1-K4). In addition, genomic regions encompassing the nucleoprotein, phosphoprotein, matrix protein and non-virion protein genes, as well as the seven non-coding regions, were relatively conserved, whereas glycoprotein and RNA-dependent RNA polymerase genes were variable in the coding region. Taken together, the data demonstrate that whole-genome next-generation sequencing may be useful for future surveillance, prevention and control strategies against viral haemorrhagic septicaemia.

Abnormal elastic modulus behavior in a crystalline-amorphous core-shell nanowire system.

We investigated the elastic modulus behavior of crystalline InAs/amorphous Al2O3 core-shell heterostructured nanowires with shell thicknesses varying between 10 and 90 nm by conducting in situ tensile tests inside a transmission electron microscope (TEM). Counterintuitively, the elastic modulus behaviors of InAs/Al2O3 core-shell nanowires differ greatly from those of bulk-scale composite materials, free from size effects. According to our results, the elastic modulus of InAs/Al2O3 core-shell nanowires increases, peaking at a shell thickness of 40 nm, and then decreases in the range of 50-90 nm. This abnormal behavior is attributed to the continuous decrease in the elastic modulus of the Al2O3 shell as the thickness increases, which is caused by changes in the atomic/electronic structure during the atomic layer deposition process and the relaxation of residual stress/strain in the shell transferred from the interfacial mismatch between the core and shell materials. A novel method for estimating the elastic modulus of the shell in a heterostructured core-shell system was suggested by considering these two effects, and the predictions from the suggested method coincided well with the experimental results. We also found that the former and latter effects account for 89% and 11% of the change in the elastic modulus of the shell. This study provides new insight by showing that the size dependency, which is caused by the inhomogeneity of the atomic/electronic structure and the residual stress/strain, must be considered to evaluate the mechanical properties of heterostructured nanowires.

Interferon-induced protein 56 (IFI56) is induced by VHSV infection but not by bacterial infection in olive flounder (Paralichthys olivaceus).

Interferon-inducible protein 56 (IFI56, also known as ISG56/IFIT1, interferon-induced protein with tetratricopeptide repeats 1) is strongly induced in response to interferon and a potent inhibitor of viral replication and translational initiation. Here, we describe the identification of IFI56 (OfIFI56) in olive flounder, its characteristic features, and expression levels in various tissues before and after viral hemorrhagic septicemia virus (VHSV) infection. The full-length OfIFI56 sequence was identified from rapid amplification of cDNA ends PCR. The complete coding sequence of OfIFI56 is 1971 bp in length and encodes 431 amino acids. The putative OfIFI56 protein has multiple tetratricopeptide (TPR) motifs, which regulate diverse biological processes, such as organelle targeting, protein import, and vesicle fusion. Based on sequence analysis, the Larimichthys crocea IFI56 protein (61%) had the highest sequence homology to OfIFI56. In healthy olive flounder, OfIFI56 mRNA expression was detected in many tissues such as intestine, gill, head kidney, heart, spleen, and trunk kidney tissues. After VHSV challenge, OfIFI56 mRNA was significantly up-regulated in these tissues. Additionally, OfIFI56 expression was induced by poly I:C but not by Streptococcus parauberis and S. iniae infection or lipopolysaccharide injection in kidney and spleen tissues of olive flounder. These results demonstrate that piscine OfIFI56 expression is not induced by bacterial infection but is selectively induced by viral infection, especially VHSV, and that OfIFI56 may play an important role in the host response against VHSV infection.

Electromechanical Properties and Spontaneous Response of the Current in InAsP Nanowires.

The electromechanical properties of ternary InAsP nanowires (NWs) were investigated by applying a uniaxial tensile strain in a transmission electron microscope (TEM). The electromechanical properties in our examined InAsP NWs were governed by the piezoresistive effect. We found that the electronic transport of the InAsP NWs is dominated by space-charge-limited transport, with a I ∞ V2 relation. Upon increasing the tensile strain, the electrical current in the NWs increases linearly, and the piezoresistance gradually decreases nonlinearly. By analyzing the space-charge-limited I-V curves, we show that the electromechanical response is due to a mobility that increases with strain. Finally, we use dynamical measurements to establish an upper limit on the time scale for the electromechanical response.

Cholinergic left-right asymmetry in the habenulo-interpeduncular pathway.

The habenulo-interpeduncular pathway, a highly conserved cholinergic system, has emerged as a valuable model to study left-right asymmetry in the brain. In larval zebrafish, the bilaterally paired dorsal habenular nuclei (dHb) exhibit prominent left-right differences in their organization, gene expression, and connectivity, but their cholinergic nature was unclear. Through the discovery of a duplicated cholinergic gene locus, we now show that choline acetyltransferase and vesicular acetylcholine transporter homologs are preferentially expressed in the right dHb of larval zebrafish. Genes encoding the nicotinic acetylcholine receptor subunits α2 and ß4 are transcribed in the target interpeduncular nucleus (IPN), suggesting that the asymmetrical cholinergic pathway is functional. To confirm this, we activated channelrhodopsin-2 specifically in the larval dHb and performed whole-cell patch-clamp recording of IPN neurons. The response to optogenetic or electrical stimulation of the right dHb consisted of an initial fast glutamatergic excitatory postsynaptic current followed by a slow-rising cholinergic current. In adult zebrafish, the dHb are divided into discrete cholinergic and peptidergic subnuclei that differ in size between the left and right sides of the brain. After exposing adults to nicotine, fos expression was activated in subregions of the IPN enriched for specific nicotinic acetylcholine receptor subunits. Our studies of the newly identified cholinergic gene locus resolve the neurotransmitter identity of the zebrafish habenular nuclei and reveal functional asymmetry in a major cholinergic neuromodulatory pathway of the vertebrate brain.

Electrochemical DNA hybridization sensors based on conducting polymers.

Conducting polymers (CPs) are a group of polymeric materials that have attracted considerable attention because of their unique electronic, chemical, and biochemical properties. This is reflected in their use in a wide range of potential applications, including light-emitting diodes, anti-static coating, electrochromic materials, solar cells, chemical sensors, biosensors, and drug-release systems. Electrochemical DNA sensors based on CPs can be used in numerous areas related to human health. This review summarizes the recent progress made in the development and use of CP-based electrochemical DNA hybridization sensors. We discuss the distinct properties of CPs with respect to their use in the immobilization of probe DNA on electrode surfaces, and we describe the immobilization techniques used for developing DNA hybridization sensors together with the various transduction methods employed. In the concluding part of this review, we present some of the challenges faced in the use of CP-based DNA hybridization sensors, as well as a future perspective.

Highly stable colorimetric aptamer sensors for detection of ochratoxin A through optimizing the sequence with the covalent conjugation of hemin.

Optimization of hairpin DNA is introduced to detect ochratoxin A (OTA) by chemically conjugating its cofactor, hemin, toward the 5'-end. The newly designed OTA aptasensor showed enhanced stability and sensitivity, thereby lowering the detection limit to an ~1 nM level. Furthermore, an optimal spacer for hemin conjugation was investigated for stable responses toward very diluted OTA solutions.

Role of GO and Photoinitiator Concentration on Curing Behavior of PEG-Based Polymer for DLP 3D Printing.

Photocuring kinetics in photopolymerization-based three-dimensional (3D) printing processes have gained significant attention because they determine the final dimension accuracy of the printed structures. In this study, the curing kinetics of liquid-light-curable resins, including water-dispersed graphene oxide (GO) and ultraviolet (UV)-cured acrylic resins, were investigated during digital light processing (DLP) 3D printing. Various stable composites of water-dispersed GO and UV-cured acrylic resin were prepared to fabricate 3D structures for cure-depth measurements. Several factors, including the UV-exposure conditions, photoinitiator concentration, and composition of the photopolymer resin, were found to significantly affect the cure-depth characteristics of the printed structures. The photocuring depth of the polymeric resin system was investigated as a function of the photoinitiator concentration. In addition, the study showed that the introduction of GO played a significant role in controlling the performance of the highly cross-linked network and the thickness of the cured layer. The curing characteristics of functional photocurable polymer-based DLP 3D printing contribute to process development and improvement of the quality of printed microstructures for industrial applications.

Cloning, heterologous expression, and enzymatic characterization of cathepsin L from starfish (Asterina pectinifera).

To determine the role of cathepsin L in Echinoderms, starfish (Asterina pectinifera) cathepsin L (ApCtL) was cloned. The results of RT-PCR analysis indicated that the expression of ApCtL in all of the tissues. The pro-mature enzyme of ApCtL, proApCtL, was expressed in Escherichia coli, and cathepsin activity was detected by cleaving of synthetic fluorogenic peptide substrates and gelatin zymography.

Intrinsic DNA curvature of double-crossover tiles.

A theoretical model which takes into account the structural distortion of double-crossover DNA tiles has been studied to investigate its effect on lattice formation sizes. It has been found that a single vector appropriately describes the curvature of the tiles, of which a higher magnitude hinders lattice growth. In conjunction with these calculations, normal mode analysis reveals that tiles with relative higher frequencies have an analogous effect. All the theoretical results are shown to be in good agreement with experimental data.

A comprehensive review of glucose biosensors based on nanostructured metal-oxides.

Nanotechnology has opened new and exhilarating opportunities for exploring glucose biosensing applications of the newly prepared nanostructured materials. Nanostructured metal-oxides have been extensively explored to develop biosensors with high sensitivity, fast response times, and stability for the determination of glucose by electrochemical oxidation. This article concentrates mainly on the development of different nanostructured metal-oxide [such as ZnO, Cu(I)/(II) oxides, MnO(2), TiO(2), CeO(2), SiO(2), ZrO(2,) and other metal-oxides] based glucose biosensors. Additionally, we devote our attention to the operating principles (i.e., potentiometric, amperometric, impedimetric and conductometric) of these nanostructured metal-oxide based glucose sensors. Finally, this review concludes with a personal prospective and some challenges of these nanoscaled sensors.

Formation of arsenic clusters in InAs nanowires with an Al2O3 shell.

An in-depth understanding of thermal behavior and phase evolution is required to apply heterostructured nanowires (NWs) in real devices. The intermediate status during the vaporization process of InAs NWs in an Al2O3 shell was studied by conducting quenching during in situ heating experiments, using a transmission electron microscope. The formation of As clusters in the amorphous Al2O3 shell was confirmed by analyzing the high-angle annular dark field images and energy-dispersive X-ray spectra. The As clusters existed independently in the shell and were also observed at the end of the InAs pieces obtained after quenching. The formation process of the As clusters was demonstrated from a theoretical perspective. Moreover, an ab initio molecular dynamics simulation (AIMD) was conducted to study the atomic and molecular behaviors.

Molecular cloning, expression analysis and enzymatic characterization of cathepsin K from olive flounder (Paralichthys olivaceus).

We assessed the putative physiological roles of cathepsin K from a flatfish, olive flounder. We cloned a cDNA encoding for cathepsin K (PoCtK), a cysteine protease of the papain family from olive flounder, Paralichthys olivaceus. The tissue-specific expression pattern of PoCtK, determined via real-time PCR analysis, revealed ubiquitous expression in normal tissues with high levels of expression in the spleen and bone marrow. However, PoCtK expression was significantly increased in the muscle and gill at 3-24 h post-injection with bacterial lipopolysaccharide (LPS). The cDNA encoding for the mature enzyme of PoCtK was expressed in Escherichia coli using the pGEX-4T-1 expression vector system. Its activity was quantified via the cleavage of the synthetic peptide Z-Gly-Pro-Arg-MCA, zymography, and the collagen degradation assay. The optimum pH for the protease activity was 8, and the recombinant PoCtK enzyme degraded collagen types I, II, III, IV, and VI and acid-soluble collagen from olive flounder muscle in the presence of chondroitin 4-sulphate (C-4S). Therefore, our data indicate that cathepsin K may play a role in the immune system of fish skin and muscle, in addition to its principal bone-specific function as a collagenolytic enzyme.

Duplication of phospholipase C-delta gene family in fish genomes.

Fishes possess more genes than other vertebrates, possibly because of a genome duplication event during the evolution of the teleost (ray-finned) fish lineage. To further explore this idea, we cloned five genes encoding phosphoinositide-specific phospholipase C-delta (PLC-delta), designated respectively PoPLC-deltas, from olive flounder (Paralichthys olivaceus), and we performed phylogenetic analysis and sequence comparison to compare our putative gene products (PoPLC-deltas) with the sequences of known human PLC isoforms. The deduced amino acid sequences shared high sequence identity with human PLC-delta1, -delta3, and -delta4 isozymes and exhibited similar primary structures. In phylogenetic analysis of PoPLC-deltas with PLC-deltas of five teleost fishes (zebrafish, stickleback, medaka, Tetraodon, and Takifugu), three tetrapods (human, chicken, and frog), and two tunicates (sea squirt and pacific sea squirt), whose putative sequences of PLC-delta are available in Ensembl genome browser, the result also indicated that the two paralogous genes corresponding to each PLC-delta isoform originated from fish-specific genome duplication prior to the divergence of teleost fish. Our analyses suggest that an ancestral PLC-delta gene underwent three rounds of genome duplication during the evolution of vertebrates, leading to the six genes of three PLC-delta isoforms in teleost fish.

Anisotropic atomistic evolution during the sublimation of polar InAs nanowires.

Sublimation is an interesting phenomenon that is frequently observed in nature. The thermal behavior of InAs NWs with As-face polarity and the [1[combining macron]1[combining macron]1[combining macron]] growth direction of the zinc blende structure were studied by using in situ transmission electron microscopy (TEM). In this study, the anisotropic morphological and atomistic evolution of InAs nanowires (NWs) was observed during decomposition. Two specific phenomena were observed during the continuous heating of the NWs as observed using the TEM: the decomposition of the InAs NWs around 380 °C, much lower than the melting temperature, and the formation of particular crystallographic facets during decomposition. The low decomposition temperature is related to vaporization under the vacuum conditions of the TEM. The anisotropic decomposition of the InAs NWs during heating can be explained based on the polarity and the surface energy difference of the zinc blende structure of InAs. For example, the decomposition along the [111] direction (that is, the indium-atom-terminated plane) was continuous, resulting in a few high-index planes, for example, (022), (3[combining macron]1[combining macron]1[combining macron]), and (200), whereas that in the opposite direction (the [1[combining macron]1[combining macron]1[combining macron]] direction) occurred abruptly with the formation of ledges and steps on the (1[combining macron]1[combining macron]1[combining macron]) planes, accompanied by the generation of small grooves on the surface of the NWs. Finally, density functional theory calculations were conducted to understand the sublimation of the InAs NWs from a theoretical point of view. This study is meaningful that it provides an insight into the microstructural evolution of polar nanomaterials during heating by theoretical and experimental approaches.

MMTS, a new subfamily of Tc1-like transposons.

A novel Tc1-like transposable element has been identified as a new DNA transposon in the mud loach, Misgurnus mizolepis. The M. mizolepis Tc1-like transposon (MMTS) is comprised of inverted terminal repeats and a single gene that codes Tc1-like transposase. The deduced amino acid sequence of the transposase-encoding region of MMTS transposon contains motifs including DDE motif, which was previously recognized in other Tc1-like transposons. However, putative MMTS transposase has only 34-37% identity with well-known Tc1, PPTN, and S elements at the amino acid level. In dot-hybridization analysis used to measure the copy numbers of the MMTS transposon in genomes of the mud loach, it was shown that the MMTS transposon is present at about 3.36 x 104 copies per 2 x 109 bp, and accounts for approximately 0.027% of the mud loach genome. Here, we also describe novel MMTS-like transposons from the genomes of carp-like fishes, flatfish species, and cichlid fishes, which bear conserved inverted repeats flanking an apparently intact transposase gene. Additionally, BLAST searches and phylogenetic analysis indicated that MMTS-like transposons evolved uniquely in fishes, and comprise a new subfamily of Tc1-like transposons, with only modest similarity to Drosophila melanogaster (foldback element FB4, HB2, HB1), Xenopus laevis, Xenopus tropicalis, and Anopheles gambiae (Frisky).