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Background Lentinula edodes is one of the most popular edible mushroom species in the world and contains useful medicinal components, such as lentinan. The light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process for ensuring the quantity and quality of this edible mushroom. To understand the molecular mechanisms underlying this critical developmental process in L. edodes, we characterized the morphological phenotypic changes in a strain, Chamaram, associated with abnormal brown film formation and compared its genome-wide transcriptional features. Results In the present study, we performed genome-wide transcriptome analyses of different vegetative mycelium growth phenotypes, namely, early white, normal brown, and defective dark yellow partial brown films phenotypes which were exposed to different light conditions. The analysis revealed the identification of clusters of genes specific to the light-induced brown film phenotypes. These genes were significantly associated with light sensing via photoreceptors such as FMN- and FAD-bindings, signal transduction by kinases and GPCRs, melanogenesis via activation of tyrosinases, and cell wall degradation by glucanases, chitinases, and laccases, which suggests these processes are involved in the formation of mycelial browning in L. edodes. Interestingly, hydrophobin genes such as SC1 and SC3 exhibited divergent expression levels in the normal and abnormal brown mycelial films, indicating the ability of these genes to act in fruiting body initiation and formation of dikaryotic mycelia. Furthermore, we identified the up-regulation of glycoside hydrolase domain-containing genes in the normal brown film but not in the abnormal film phenotype, suggesting that cell wall degradation in the normal brown film phenotype is crucial in the developmental processes related to the initiation and formation of fruiting bodies. Conclusions This study systematically analysed the expression patterns of light-induced browning-related genes in L. edodes. Our findings provide information for further investigations of browning formation mechanisms in L. edodes and a foundation for future L. edodes breeding. Electronic supplementary material The online version of this article (10.1186/s12864-019-5509-4) contains supplementary material, which is available to authorized users.

MicroRNA (miRNA) are found in numerous biofluids including blood and are considered a new class of biomarkers. The data presented here are related to the research article entitled “Profiling and identification of pregnancy-associated circulating microRNAs in dairy cattle” (Markkandan et al. 2018). In the cited article, we sequenced the circulating microRNAs of the three healthy dairy cows of normal and 30 days of pregnancy (DOP) using Illumina RNA-Seq. Differentially expressed genes (DEG) analysis between normal and pregnant samples showed perturbations in miRNA expression. Herein, we made a comparison of DEGs at normal and 60 DOP libraries. The analysis results showed that 147 known miRNAs were differently expressed at 60 DOP groups when compared to the normal group. In addition, stage specific miRNAs were also predicted. Keywords: Circulating microRNA, Holstein, MiRNA-sequencing, Exosome, Pregnancy

The tight regulation of local auxin homeostasis and signalling maxima in xylem precursor cells specifies the organising activity of the vascular cambium and consequently promotes xylem differentiation and wood formation. However, the molecular mechanisms underlying the local auxin signalling maxima in the vascular cambium are largely unknown. Here, we reveal that brassinosteroid (BR)-activated WALLS ARE THIN1 (WAT1) facilitates wood formation by enhancing local auxin signalling in the vascular cambium in Solanum lycopersicum. Growth defects and low auxin signalling readouts in the BR-deficient tomato cultivar, Micro-Tom, were associated with a novel recessive allele, Slwat1-copi, created by the insertion of a retrotransposon in the last exon of the SlWAT1 locus. Molecular and genetic studies by generating the gain-of-function and loss-of-function tomato mutants revealed that SlWAT1 is a critical regulator for fine tuning local auxin homeostasis and signalling outputs in vascular cambium to facilitate secondary growth. Finally, we discovered that BR-regulated SlBZR1/2 directly activated downstream auxin responses by SlWAT1 upregulation in xylem precursor cells to facilitate xylem differentiation and subsequent wood formation. Our data suggest that the BR-SlBZR1/2-WAT1 signalling network contributes to the high level of auxin signalling in the vascular cambium for secondary growth.

Lentinula edodes is a globally important edible mushroom species that is appreciated for its medicinal properties as well as its nutritional value. During commercial cultivation, a mycelial brown film forms on the surface of the sawdust growth medium at the late vegetative stage. Mycelial film formation is a critical developmental process that contributes to the quantity and quality of the mushroom yield. However, little is known regarding the genetic underpinnings of brown film formation on the surface of mycelial tissue. A novel causal gene associated with the formation of the mycelial brown film, named ABL (Abnormal browning related to light), was identified in this study. The comparative genetic analysis by dihybrid crosses between normal and abnormal browning film cultivars demonstrated that a single dominant allele was responsible for the abnormal mycelium browning phenotype. Whole-genome sequencing analysis of hybrid isolates revealed five missense single-nucleotide polymorphisms (SNPs) in the ABL locus of individuals forming abnormal partial brown films. Additional whole-genome resequencing of a further 16 cultivars showed that three of the five missense SNPs were strongly associated with the abnormal browning phenotype. Overexpression of the dominant abl-D allele in a wild-type background conferred the abnormal mycelial browning phenotype upon transformants, with slender hyphae observed as a general defective mycelial growth phenotype. Our methodology will aid the future discovery of candidate genes associated with favorable traits in edible mushrooms. The discovery of a novel gene, ABL, associated with mycelial film formation will facilitate marker-associated breeding in L. edodes.

Triterpenoid saponins (TSs) are common plant defense phytochemicals with potential pharmaceutical properties. Platycodon grandiflorus (Campanulaceae) has been traditionally used to treat bronchitis and asthma in East Asia. The oleanane-type TSs, platycosides, are a major component of the P. grandiflorus root extract. Recent studies show that platycosides exhibit anti-inflammatory, antiobesity, anticancer, antiviral, and antiallergy properties. However, the evolutionary history of platycoside biosynthesis genes remains unknown. In this study, we sequenced the genome of P. grandiflorus and investigated the genes involved in platycoside biosynthesis. The draft genome of P. grandiflorus is 680.1 Mb long and contains 40,017 protein-coding genes. Genomic analysis revealed that the CYP716 family genes play a major role in platycoside oxidation. The CYP716 gene family of P. grandiflorus was much larger than that of other Asterid species. Orthologous gene annotation also revealed the expansion of β-amyrin synthases (bASs) in P. grandiflorus, which was confirmed by tissue-specific gene expression. In these expanded gene families, we identified key genes showing preferential expression in roots and association with platycoside biosynthesis. In addition, whole-genome bisulfite sequencing showed that CYP716 and bAS genes are hypomethylated in P. grandiflorus, suggesting that epigenetic modification of these two gene families affects platycoside biosynthesis. Thus whole-genome, transcriptome, and methylome data of P. grandiflorus provide novel insights into the regulation of platycoside biosynthesis by CYP716 and bAS gene families.

Triterpenoid saponins (TSs) are common plant defense phytochemicals with potential pharmaceutical properties. Platycodon grandiflorus (Campanulaceae) has been traditionally used to treat bronchitis and asthma in East Asia. The oleanane-type TSs, platycosides, are a major component of the P. grandiflorus root extract. Recent studies show that platycosides exhibit anti-inflammatory, antiobesity, anticancer, antiviral, and antiallergy properties. However, the evolutionary history of platycoside biosynthesis genes remains unknown. In this study, we sequenced the genome of P. grandiflorus and investigated the genes involved in platycoside biosynthesis. The draft genome of P. grandiflorus is 680.1 Mb long and contains 40,017 protein-coding genes. Genomic analysis revealed that the CYP716 family genes play a major role in platycoside oxidation. The CYP716 gene family of P. grandiflorus was much larger than that of other Asterid species. Orthologous gene annotation also revealed the expansion of β-amyrin synthases (bASs) in P. grandiflorus, which was confirmed by tissue-specific gene expression. In these expanded gene families, we identified key genes showing preferential expression in roots and association with platycoside biosynthesis. In addition, whole-genome bisulfite sequencing showed that CYP716 and bAS genes are hypomethylated in P. grandiflorus, suggesting that epigenetic modification of these two gene families affects platycoside biosynthesis. Thus whole-genome, transcriptome, and methylome data of P. grandiflorus provide novel insights into the regulation of platycoside biosynthesis by CYP716 and bAS gene families.

Olive flounder (Paralichthys olivaceus) is one of the most valuable marine aquatic species in South Korea and faces tremendous exposure to the viral hemorrhagic septicemia virus (VHSV). Given the growing importance of flounder, it is therefore essential to understand the host defense of P. olivaceus against VHSV infection, but studies on its immune mechanism are hindered by the lack of genomic resources. In this study, the P. olivaceus was infected with disease-causing VHSV isolates, ADC-VHS2012-11 and ADC-VHS2014-5 which showed moderate virulent (20% mortality) and high virulent (65% mortality), in order to investigate the effect of difference in pathogenicity in head kidney during 1, 3, 7 days of post-infection using Illumina sequencing. After removing low-quality sequences, we obtained 144,933,160 high quality reads from thirty-six libraries which were further assembled into 53,384 unigenes with an average length of 563 bp with a range of 200 to 9605 bp. Transcriptome annotation revealed that 30,475 unigenes with a cut-off e-value of 10−5 were functionally annotated. In total, 10,046 unigenes were clustered into 26 functional categories by searching against the eggNOG database, and 22,233 unigenes to 52 GO terms. In addition, 12,985 unigenes were grouped into 387 KEGG pathways. Among the 13,270 differently expressed genes, 6578 and 6692 were differentially expressed only in moderate and high virulent, respectively. Based on our sequence analysis, many candidate genes with fundamental roles in innate immune system including, pattern recognition receptors (TLRs & RLRs), Mx, complement proteins, lectins, and cytokines (chemokines, IFN, IRF, IL, TRF) were differentially expressed. Furthermore, GO enrichment analysis for these genes revealed gene response to defense response to virus, apoptotic process and transcription factor activity. In summary, this study identifies several putative immune pathways and candidate genes deserving further investigation in the context of novel gene discovery, gene expression and regulation studies and lays the foundation for fish immunology especially in P. olivaceus against VHSV.

Lentinula edodes is one of the most popular edible mushrooms in the world and contains useful medicinal components such as lentinan. The whole-genome sequence of L. edodes has been determined with the objective of discovering candidate genes associated with agronomic traits, but experimental verification of gene models with correction of gene prediction errors is lacking. To improve the accuracy of gene prediction, we produced 12.6 Gb of long-read transcriptome data of variable lengths using PacBio single-molecule real-time (SMRT) sequencing and generated 36,946 transcript clusters with an average length of 2.2 kb. Evidence-driven gene prediction on the basis of long- and short-read RNA sequencing data was performed; a total of 16,610 protein-coding genes were predicted with error correction. Of the predicted genes, 42.2% were verified to be covered by full-length transcript clusters. The raw reads have been deposited in the NCBI SRA database under accession number PRJNA396788. Keywords: Gene model, Gene prediction, Lentinula edodes, PacBio Single-molecule real-time (SMRT) transcriptome sequencing

Olive flounder (Paralichthys olivaceus) is one of the most economically important aquaculture fish. However, its production is often affected by various diseases, especially viral hemorrhagic septicemia virus (VHSV) that cause serious economic losses. In this study, we sequenced the whole transcriptome of the P. olivaceus using Illumina RNA-sEq. De novo assembly of control and virus-infected cDNA libraries of head kidney at 13 and 20 °C was accomplished with 2,007,532,438 raw reads, resulting in 244,578 unigenes with an average length of 533 bp and found 65,535 candidate coding unigenes with homology to other species by BLAST analysis. DEG analysis among control and virus-infected head kidney samples of 13 and 20 °C revealed that 1290 up-regulated and 162 down-regulated genes (p ≤ 0.01), linked to metabolism, virulence factors, adhesion and immune-response. We constructed an expressed gene catalog for the P. olivaceus to serve as a resource for marine environmental genomic and immuno-genetic/genomic studies focused on uncovering the molecular mechanisms underlying the responses of P. olivaceus to VHSV under different temperature.

Gibberellins (GAs) are an important group of phytohormones associated with diverse growth and developmental processes, including cell elongation, seed germination, and secondary growth. Recent genomic and genetic analyses have advanced our knowledge of GA signaling pathways and related genes in model plant species. However, functional genomics analyses of GA signaling pathways in Panax ginseng, a perennial herb, have rarely been carried out, despite its well-known economical and medicinal importance. Here, we conducted functional characterization of GA receptors and investigated their physiological roles in the secondary growth of P. ginseng storage roots. We found that the physiological and genetic functions of P. ginseng gibberellin-insensitive dwarf1s (PgGID1s) have been evolutionarily conserved. Additionally, the essential domains and residues in the primary protein structure for interaction with active GAs and DELLA proteins are well-conserved. Overexpression of PgGID1s in Arabidopsis completely restored the GA deficient phenotype of the Arabidopsis gid1a gid1c (atgid1a/c) double mutant. Exogenous GA treatment greatly enhanced the secondary growth of tap roots, however, paclobutrazol (PCZ), a GA biosynthetic inhibitor, reduced root growth in P. ginseng. Transcriptome profiling of P. ginseng roots revealed that GA-induced root secondary growth is closely associated with cell wall biogenesis, the cell cycle, the jasmonic acid (JA) response, and nitrate assimilation, suggesting that a transcriptional network regulate root secondary growth in P. ginseng. These results provide novel insights into the mechanism controlling secondary root growth in P. ginseng.

Antimicrobial peptides/proteins (AMPs) are present in all types of organisms, from microbes and plants to vertebrates and invertebrates such as insects. The grasshopper Oxya chinensis sinuosa is an insect species that is widely consumed around the world for its broad medicinal value. However, the lack of available genetic information for this species is an obstacle to understanding the full potential of its AMPs. Analysis of the O. chinensis sinuosa transcriptome and expression profile is essential for extending the available genetic information resources. In this study, we determined the whole-body transcriptome of O. chinensis sinuosa and analyzed the potential AMPs induced by bacterial immunization. A high-throughput RNA-Seq approach generated 94,348 contigs and 66,555 unigenes. Of these unigenes, 36,032 (54.14%) matched known proteins in the NCBI database in a BLAST search. Functional analysis demonstrated that 38,219 unigenes were clustered into 5,499 gene ontology terms. In addition, 26 cDNAs encoding novel AMPs were identified by an in silico approach using public databases. Our transcriptome dataset and AMP profile greatly improve our understanding of O. chinensis sinuosa genetics and provide a huge number of gene sequences for further study, including genes of known importance and genes of unknown function.

We used various emissive layer (EML) structures with ultrathin red EMLs to enhance the charge carrier balance and carrier recombination rate in blue PHOLED devices. These EML materials have different energy gaps between highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels. The ultrathin red EMLs, which were inserted in between the blue EMLs, effectively confined the charge carriers in EML, and increased the carrier recombination rate. The thickness of the individual EML was optimized, under 30 nm of the total thickness of EML. The blue PHOLEDs with ultrathin red EMLs achieved a luminous efficiency of 19.24 cd/A, which was 28.7% higher than those without ultrathin red EMLs, and the maximum external quantum efficiency was 11.81% at 500 cd/m2.

The electroluminescent characteristics of blue organic light-emitting diodes (BOLEDs) fabricated with doped charge carrier transport layers are analyzed. The fluorescent blue dopant BCzVBi is doped in an emissive layer, hole transport layer (HTL) and electron transport layer (ETL), respectively, to optimize the probability of exciton generation in the BOLEDs. The luminance and luminous efficiency of BOLEDs made with BCzVBi-doped HTL and ETL increase by 22% and 17% from 11,683 cd/m2 at 8.5 V and 6.08 cd/A at 4.0 V to 14,264 cd/m2 at 8.5 V and 7.13 cd/A at 4.0 V while CIE coordinates of (0.15, 0.15) of both types of BOLEDs remained unchanged. The electron mobility of BCzVBi is estimated to be 1.02×10−5 cm2/Vs by TOF.

The accurate prediction and annotation of gene structures from the genome sequence of an organism enable genome-wide functional analyses to obtain insight into the biological properties of an organism. We recently developed a highly accurate filamentous fungal gene prediction pipeline and web platform called TaF. TaF is a homology-based gene predictor employing large-scale taxonomic profiling to search for close relatives in genome queries. TaF pipeline consists of four processing steps; (1) taxonomic profiling to search for close relatives to query, (2) generation of hints for determining exon–intron boundaries from orthologous protein sequence data of the profiled species, (3) gene prediction by combination of ab inito and evidence-based prediction methods, and (4) homology search for gene models. TaF generates extrinsic evidence that suggests possible exon–intron boundaries based on orthologous protein sequence data, thus reducing false-positive predictions of gene structure based on distantly related orthologs data. In particular, the gene prediction method using taxonomic profiling shows very high accuracy, including high sensitivity and specificity for gene models, suggesting a new approach for homology-based gene prediction from newly sequenced or uncharacterized fungal genomes, with the potential to improve the quality of gene prediction. TaF will be a useful tool for fungal genome-wide analyses, including the identification of targeted genes associated with a trait, transcriptome profiling, comparative genomics, and evolutionary analysis.

This study reports the results of blue phosphorescent organic light emitting diodes (PHOLEDs) employing an electron confinement layer (ECL), tris-(phenylpyrazole)iridium (Ir(ppz) 3 ) and a hole confinement layer (HCl), 1,3,5-tris(N-phenylbenzimiazole-2-yl)benzene (TPBi). The electrical and optical characteristics of PHOLEDs with different emissive layers, including current density, luminance, and luminous efficiency, were analyzed. The thickness of the individual emissive layer was optimized, however, and the total thickness of the emitting region was kept constant at 300 A. This work reveals that the effective electron confinement, due to a large energy level offset between the electron confinement and emitting layers, helps to improve hole–electron current balance in the emitting region. The maximum external quantum efficiency of 23.40% at 1500 cd/m 2 was achieved for PHOLEDs with an ECL, which is 60% higher than the structural identical control device without ECL.

The body louse (Pediculus humanus humanus) is known to have diverged from the head louse (P. humanus capitis) but genomic differences between these two subspecies still remain unexplored. To compare genomic profiles between head and body lice, whole genome sequences of head lice were determined by next generation sequencing methods based on both Illumina Genome analyzer and Roche GS FLX pyrosequencing and compared with the reference genome sequences of the body louse. Total consensuses generated by mapping to the body louse genome in conjunction with de novo assembly of head louse genome sequences revealed a head louse genome size of 110 Mbp with a 96% coverage of the body louse genome sequences. A total of 12,651 genes were predicted from the head louse genome sequences although more precise assembly and functional annotation of the genome is required for a more accurate gene count. Among the 873 genes that were putatively specific to the head louse, 15 genes were confirmed to be transcribed in both head and body lice, suggesting the previously estimated gene number of the body louse was likely underestimated. The single nucleotide polymorphism analysis showed that the nucleotide diversity of genome between head and body lice was 2.2%, which was larger than that of the transcriptome between head and body lice. An endosymbiont genome analysis showed that the composition of endosymbionts in head lice was similar to that of body lice and Candidatus Riesia pediculicola was the primary endosymbiont in both head and body lice.

Blue phosphorescent organic light-emitting diodes (PHOLEDs) were fabricated using double dopants FIrpic and FIr6 in emissive layer (EML) with structure of ITO/NPB (700 A)/mCP:FIrpic-8%:FIr6- x % (300 A)/TPBi (300 A)/Liq (20 A)/Al (1200 A). We optimized concentration of the second dopant FIr6 in the presence of a fixed FIrpic to observe its effect on electrical performance of PHOLED device. 24.8 cd/A of luminous efficiency was achieved by the device with dopant ratio of 8%FIrpic:4%FIr6 in EML. Efficiency roll-off was also improved 20% compared to the PHOLED device singly dopped with FIrpic or FIr6 only. Second doping proved its effect in stabilizing charge balance in EML and enhancing energy transfer of triplet excitons between two dopants.

The performance of three color single emissive layer white phosphorescent organic light-emitting diodes (PHOLEDs), with different hole transporting materials of N,N′-diphenyl-N,N′-bis(l-naphthyl-phenyl)-(l,l′-biphenyl)-4,4′-diamine (NPB), 4,4_,4_-tris_N-carbazolyl_tri-Phenylamine (TCTA) and 1,1-bis[(di-4-tolylamino)phenyl]cyclohexane (TAPC), was analyzed. It is found that the luminous efficiency of white PHOLEDs is closely related to the triplet exciton energy level in the hole transporting layer (HTL). White PHOLEDs with a TAPC as HTL, having the highest triplet exciton energy level amongst the three different hole transporting materials, yielded external quantum efficiency of 25.5% at 4.5 V and a high luminous efficiency of 51 cd/A at 4.5 V with CIE color coordinates of (0.34, 0.39) at 10 V. The results reveal that the effective confinement of triplet excitons in white PHOLEDs with a high triplet exciton energy level HTL (TAPC) allows improving the luminous efficiency, as compared to the devices made with NPB and TCTA. Additionally, we demonstrated possibility for the loss of intensity in EL spectra of the white PHOLED devices with NPB and TCTA as HTL compared to that of the device with TAPC as HTL.

Blue phosphorescent organic light-emitting diodes (OLED) using mixed electron transport layer (ETL) were fabricated with the device structure of ITO/NPB/mCP:Firpic-8%/TPBi:BCP or TPBi:3TPYMB/Liq/Al to observe mixed ETL’s influence on their electrical and optical characteristics. OLED device with mixed ETL of TPBi with BCP or 3TPYMB significantly improved its current efficiency to 30.4 and 34.2 cd/A comparing to 19.8 cd/A of single ETL with BCP only. We examined mixed ETL’s capability of electron transport and triplet exciton confinement enhancing phosphorescent OLED’s luminance and luminous efficiency.

Lentinula edodes is one of the most popular edible mushrooms in the world and contains useful medicinal components such as lentinan. The whole-genome sequence of L. edodes has been determined with the objective of discovering candidate genes associated with agronomic traits, but experimental verification of gene models with correction of gene prediction errors is lacking. To improve the accuracy of gene prediction, we produced 12.6 Gb of long-read transcriptome data of variable lengths using PacBio single-molecule real-time (SMRT) sequencing and generated 36,946 transcript clusters with an average length of 2.2 kb. Evidence-driven gene prediction on the basis of long- and short-read RNA sequencing data was performed; a total of 16,610 protein-coding genes were predicted with error correction. Of the predicted genes, 42.2% were verified to be covered by full-length transcript clusters. The raw reads have been deposited in the NCBI SRA database under accession number PRJNA396788.

The improved external quantum efficiency (EQE) and reduced roll-off properties of blue phosphorescent organic light-emitting diodes (PHOLEDs), were fabricated with structure, ITO/NPB (400 A)/TCTA (200 A)/mCP:FIrpic (7%)(300 A)/TPBi (300 A)/Liq (20 A)/Al (800 A) by incorporating an 4,4′,4′′-tris(carbazol-9-yl)-triphenylamine (TCTA) interlayer. We compared the properties of 2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline (BCP) and 1,3,5-tris(N-phenylbenzimidazole-2-yl)benzene (TPBi) as the electron transport layer (ETL) with a typical structure of hole transport layer (HTL)/emissive layer (EML)/ETL in OLEDs and utilized inter-layer in the optimized structure to enhance EQE to 52% at 5.5 V, also stabilize the roll-off of 23%. The use of inter-layer in blue PHOLEDs exhibits a current efficiency of 10.04 cd/A, an EQE of 6.20% at 5.5 V and the highest luminance of 10310 cd/m2 at 9.5 V. We have identified the properties of electroluminescence through the inter-layer in blue PHOLEDs which can be divided into singlet excitons and triplet excitons which emit fluorescence of N,N′-bis(1-naphthalenyl)-N,N′-bis-phenyl-(1,1′-biphenyl)-4,4′-diamine (NPB) at 420 nm and phosphorescence of Iridium (III) bis[(4,6-difluorophenyl)-pyridinato-N,C2′] picolinate (FIrpic) at 470 nm, 494 nm, respectively.

Blue phosphorescence organic light-emitting diodes (PHOLEDs) with interfacial mixed layer (IML) were fabricated to observe their electrical characteristics. The IML was composed of mCP as host material in the emissive layer (EML) and 3TPYMB as material for the electron transport layer (ETL) with the blue phosphorescent dopant FIrpic. PHOLEDs with IML were improved by 41% of current density and 35% of luminous efficiency compared to PHOLEDs without IML. The electron and energy transition mechanisms between EML and ETL in the presence of IML were confirmed through I–V–L characteristics and blue color coordinates.

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.

Hanwoo, a Korean native cattle (Bos taurus coreana), has great economic value due to high meat quality. Also, the breed has genetic variations that are associated with production traits such as health, disease resistance, reproduction, growth as well as carcass quality. In this study, next generation sequencing technologies and the availability of an appropriate reference genome were applied to discover a large amount of single nucleotide polymorphisms (SNPs) in ten Hanwoo bulls. Analysis of whole-genome resequencing generated a total of 26.5 Gb data, of which 594,716,859 and 592,990,750 reads covered 98.73% and 93.79% of the bovine reference genomes of UMD 3.1 and Btau 4.6.1, respectively. In total, 2,473,884 and 2,402,997 putative SNPs were discovered, of which 1,095,922 (44.3%) and 982,674 (40.9%) novel SNPs were discovered against UMD3.1 and Btau 4.6.1, respectively. Among the SNPs, the 46,301 (UMD 3.1) and 28,613 SNPs (Btau 4.6.1) that were identified as Hanwoo-specific SNPs were included in the functional genes that may be involved in the mechanisms of milk production, tenderness, juiciness, marbling of Hanwoo beef and yellow hair. Most of the Hanwoo-specific SNPs were identified in the promoter region, suggesting that the SNPs influence differential expression of the regulated genes relative to the relevant traits. In particular, the non-synonymous (ns) SNPs found in CORIN, which is a negative regulator of Agouti, might be a causal variant to determine yellow hair of Hanwoo. Our results will provide abundant genetic sources of variation to characterize Hanwoo genetics and for subsequent breeding.

Blue PHOLEDs with interfacial mixed layer (IML) were fabricated to observe their electrical characteristics. IML was composed of mCP as host material in EML and 3TPYMB as electron transport material with phosphorescent blue dopant of FIrpic. PHOLED with IML were improved 41% of current density and 35% of luminous efficiency comparing to PHOLED without IML.

Background: As the elderly population increases, elderly patients visiting emergency departments (ED) with acute abdominal pain will also likely increase. The underlying causative diseases in these older patients are different from younger patients, usually more serious. Thus, correct diagnosis is very important, but difficult. There needs to be a better understanding of the characteristics of the elderly patient with acute abdominal pain seen in the ED. Methods: We retrospectively reviewed the medical records of 98 elderly patients (≥65 years) and 109 adult controls (

Photophysical properties of tetraphenylporphyrin (H2TPP), tetra(p-hydroxyphenyl)porphyrin ((p-OH)4TPPH2), germanium(IV) tetraphenylporphyrin dichloride (GeTPPCl2), and germanium(IV) tetra(p-hydroxyphenyl)porphyrin dichloride (Ge(p-OH)4TPPCl2) have been investigated to elucidate the effects of para OH substituents on the free-base and the metal-incorporated porphyrin π systems by steady-state and time-resolved spectroscopic methods. The observed photophysical properties were correlated with various molecular aspects, such as extended π-conjugation, nonplanar structural distortion, and central heavy atoms. Changes to steady-state absorption and fluorescence spectral characteristics of the OH-substituted porphyrin derivatives were attributed to the enhanced π-conjugation between phenyl ring and porphyrin π-electron system in the ground and the excited states. Such π-conjugation effects of the OH-substituted derivatives are greater when Ge(IV) is introduced into the core. The enhanced π-electron interaction of the OH-substituted derivatives in the excited state shortened the fluorescence lifetimes but increased the fluorescence quantum yields since the radiative rate was enhanced more than the fluorescence decay rate increased. The radiative decay rate of the OH-substituted Ge(IV) porphyrin is even greater due to more intensive π-conjugation of the metalloporphyrin in the excited state. The metal incorporation into the core also enhanced the nonradiative decay rates due to increased spin–orbit coupling and, consequently, reduced the fluorescence lifetimes and quantum yields. However, the spin–orbit coupling effect is not as large as expected. On the other hand, the OH group substitution enhanced only the nonradiative decay rate of the Ge(IV) metalloporphyrin and did not increase that of the free base porphyrin. This is ascribed to much more intensive π-conjugation of the Ge(IV) metalloporphyrin in the excited state which may induce excited state charge transfer and structural distortion.

Background: Leptotrombidium pallidum and Leptotrombidium scutellare are the major vector mites for Orientia tsutsugamushi, the causative agent of scrub typhus. Before these organisms can be subjected to whole-genome sequencing, it is necessary to estimate their genome sizes to obtain basic information for establishing the strategies that should be used for genome sequencing and assembly. Method: The genome sizes of L. pallidum and L. scutellare were estimated by a method based on quantitative real-time PCR. In addition, a k-mer analysis of the whole-genome sequences obtained through Illumina sequencing was conducted to verify the mutual compatibility and reliability of the results. Results: The genome sizes estimated using qPCR were 191 ± 7 Mb for L. pallidum and 262 ± 13 Mb for L. scutellare. The k-mer analysis-based genome lengths were estimated to be 175 Mb for L. pallidum and 286 Mb for L. scutellare. The estimates from these two independent methods were mutually complementary and within a similar range to those of other Acariform mites. Conclusions: The estimation method based on qPCR appears to be a useful alternative when the standard methods, such as flow cytometry, are impractical. The relatively small estimated genome sizes should facilitate whole-genome analysis, which could contribute to our understanding of Arachnida genome evolution and provide key information for scrub typhus prevention and mite vector competence.

In this study, the properties of blue organic light-emitting diodes (OLEDs), employing quantum well-like structure (QWS) that includes four different blue emissive materials of 4,4′-bis(2,2′-diphenylyinyl)-1,1′-biphenyl (DPVBi), 9,10-di(naphth-2-yl)anthracene (ADN), 2-(N,N-diphenyl-amino)-6-[4-(N,N-diphenyl amine)styryl]naphthalene (DPASN), and bis(2-methyl-8-quinolinolate)-4-(phenyl phenolato) aluminum (BAlq), were investigated. Conventional QWS blue OLEDs composed of multiple emissive layers and charge blocking layer with lower highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) energy level, and devices with triple emissive layers for more significant hole-electron recombination and a wider region for exciton generation were designed. The properties of triple emissive layered blue OLEDs with the structure of indium tin oxide (ITO) /N,N′-diphenyl-N,N′-bis(1-naphthyl-phenyl)-(1,1′-biphenyl)-4,4′-diamine (NPB) (700 Ǻ)/X (100 Ǻ)/BAlq (100 Ǻ)/X (100 Ǻ)/4,7-diphenyl-1,10-phenanthroline (Bphen) (300 Ǻ)/lithium quinolate (Liq) (20 Ǻ)/aluminum (Al) (1,200 Ǻ) (X = DPVBi, ADN, DPASN) were examined. HOMO-LUMO energy levels of DPVBi, ADN, DPASN, and BAlq are 2.8 to 5.9, 2.6 to 5.6, 2.3 to 5.2, and 2.9 to 5.9 eV, respectively. The OLEDs with DPASN/BAlq/DPASN QWS with maximum luminous efficiency of 5.32 cd/A was achieved at 3.5 V.

In this study, we fabricated blue OLEDs with quantum well structure (QWS) using four different blue emissive materials such as DPVBi, ADN and DPASN, and BAlq as QWS material. Conventional QWS blue OLEDs used to be composed of emissive layer and charge blocking layer with lower HOMO-LUMO energy level, but we designed triple emitting layer for more significant hole-electron recombination in EML and a wider region of exciton generation as forming QWS spontaneously. The structure of triple emitting layered blue OLED is ITO / NPB(700 Å) / X(100 Å) / BAlq(100 Å) /X (100 Å) / Bphen(300 Å) / Liq(20 Å) / Al(1200 Å) (X= DPVBi, ADN, DPASN). HOMO-LUMO energy levels of DPVBi, ADN, DPASN and BAlq were 2.8-5.9, 2.6-5.6, 2.3-5.2 and 2.9-5.9 eV, respectively. The maximum luminous efficiency was 5.32 cd/A at 3.5 V in a blue OLED with DPASN / BAlq / DPASN QWS.

We analyzed the performance of multi-emissive white phosphorescent organic light-emitting diodes (PHOLEDs) in relation to various red emitting sites of hole and electron transport layers (HTL and ETL). The shift of the recombination zone producing stable white emission in PHOLEDs was utilized as luminance was increased with red emission in its electron transport layer. Multi-emissive white PHOLEDs including the red light emitting electron transport layer yielded maximum external quantum efficiency of 17.4% with CIE color coordinates (−0.030, +0.001) shifting only from 1000 to 10 000 cd/m2. Additionally, we observed a reduction of energy loss in the white PHOLED via Ir(piq)3 as phosphorescent red dopant in electron transport layer.

Rice field art is a large-scale art form in which people design rice fields using various kinds of ornamental rice plants with different leaf colors. Leaf color-related genes play an important role in the study of chlorophyll biosynthesis, chloroplast structure and function, and anthocyanin biosynthesis. Despite the role of different metabolites in the traditional relationship between leaf and color, comprehensive color-specific metabolite studies of ornamental rice have been limited. We performed whole-genome resequencing and transcriptomic analysis of regulatory patterns and genetic diversity among different rice cultivars to discover new genetic mechanisms that promote enhanced levels of various leaf colors. We resequenced the genomes of 10 rice leaf-color accessions to an average of 40× reads depth and >95% coverage and performed 30 RNA-seq experiments using the 10 rice accessions sampled at three developmental stages. The sequencing results yielded a total of 1,814 × 106 reads and identified an average of 713,114 SNPs per rice accession. Based on our analysis of the DNA variation and gene expression, we selected 47 candidate genes. We used an integrated analysis of the whole-genome resequencing data and the RNA-seq data to divide the candidate genes into two groups: genes related to macronutrient (i.e., magnesium and sulfur) transport and genes related to flavonoid pathways, including anthocyanidin biosynthesis. We verified the candidate genes with quantitative real-time PCR using transgenic T-DNA insertion mutants. Our study demonstrates the potential of integrated screening methods combined with genetic-variation and transcriptomic data to isolate genes involved in complex biosynthetic networks and pathways.

In this Letter, blue phosphorescence organic light-emitting diodes (PHOLEDs) employ structures for electron and/or hole confinement; 1,3,5-tris(N-phenylbenzimiazole-2-yl)benzene is used as a hole confinement layer and tris-(phenylpyrazole)iridium [Ir(ppz)3] is utilized for an electron confinement layer (ECL). The electrical and optical properties of the fabricated blue PHOLEDs with various carrier-confinement structures are analyzed. Structures with a large energy offset between the carrier confinement and emitting layers enhance the charge-carrier balance in the emitting region, resulting from the effective carrier confinement. The maximum external quantum efficiency of the blue PHOLEDs with the double-ECLs is 24.02% at 1500 cd/m2 and its luminous efficiency is 43.76 cd/A, which is 70.47% improved compared to the device without a carrier-confinement layer.

We fabricate white phosphorescent organic light-emitting diodes (PHOLEDs) with three dopants and double emissive layer (EML) to achieve color stability. The white PHOLEDs use FIrpic dopant for blue EML (B-EML), and Ir(ppy)3:Ir(piq)3 dopants for green:red EML (GR-EML) with N,N.'-dicarbazolyl-3, 5-benzene (mCP) as host material. Thicknesses of B-EML and GR-EML are adjusted to form a narrow recombination zone at two EML's interface and charge trapping happens in EML according to wide highest occupied molecular orbital and/or lowest unoccupied molecular orbital energy band gap of mCP and smaller energy band gap of dopants. The total thickness of both EMLs is fixed at 30 nm in the device structure of ITO (150 nm)/MoO3 (2 nm)/N,N'-diphenyl-N,N'-bis(l-naphthyl-phenyl)-(l,l'-biphenyl)-4, 4'-diamine (70 nm)/mCP:Firpic-8.0% (12 nm)/mCP:Ir(ppy)3-3.0%:Ir(piq)3-1.5% (18 nm)/2',2',2''-(1,3,5-benzinetriyl)-tris(1-phenyl-1-H-benzimidazole) (30 nm)/8-hydroxyquinolinolato-lithium (2 nm)/Al (120 nm). White PHOLED shows 18.25 cd/A of luminous efficiency and white color coordinates of (0.358 and 0.378) at 5000 cd/m2 and color stability with slight CIEXY change of (0.028 and 0.002) as increasing luminance from 1000 to 5000 cd/m2.