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Abstract Nicotiana benthamiana is a fundamental model organism in plant research. Recent advancements in genomic sequencing have revealed significant intraspecific genetic variations. This study addresses the pressing need for a precise genome sequence specific to its geographic origin by presenting a comprehensive genome assembly of the N. benthamiana LAB strain from the Republic of Korea (NbKLAB). We compare this assembly with the widely used NbLAB360 strain, shedding light on essential genomic differences between them. The outcome is a high-quality, chromosome-level genome assembly comprising 19 chromosomes, spanning 2,762 Mb, with an N50 of 142.6 Mb. Comparative analyses revealed notable variations, including 46,215 protein-coding genes, with an impressive 99.5% BUSCO completeness score. Furthermore, the NbKLAB assembly substantially improved the QV from 33% for NbLAB360 to 49%. This refined chromosomal genome assembly for N. benthamiana, in conjunction with comparative insights, provides a valuable resource for genomics research and molecular biology. This accomplishment forms a strong foundation for in-depth exploration into the intricacies of plant genetics and genomics, improved precision, and a comparative framework.

Objective Pig breeders cannot obtain phenotypic information at the time of selection for sow lifetime productivity (SLP). They would benefit from obtaining genetic information of candidate sows. Genomic data interpreted using deep learning (DL) techniques could contribute to the genetic improvement of SLP to maximize farm profitability because DL models capture nonlinear genetic effects such as dominance and epistasis more efficiently than conventional genomic prediction methods based on linear models. This study aimed to investigate the usefulness of DL for the genomic prediction of two SLP-related traits; lifetime number of litters (LNL) and lifetime pig production (LPP). Methods Two bivariate DL models, convolutional neural network (CNN) and local convolutional neural network (LCNN), were compared with conventional bivariate linear models (i.e., genomic best linear unbiased prediction, Bayesian ridge regression, Bayes A, and Bayes B). Phenotype and pedigree data were collected from 40,011 sows that had husbandry records. Among these, 3,652 pigs were genotyped using the PorcineSNP60K BeadChip. Results The best predictive correlation for LNL was obtained with CNN (0.28), followed by LCNN (0.26) and conventional linear models (approximately 0.21). For LPP, the best predictive correlation was also obtained with CNN (0.29), followed by LCNN (0.27) and conventional linear models (approximately 0.25). A similar trend was observed with the mean squared error of prediction for the SLP traits. Conclusion This study provides an example of a CNN that can outperform against the linear model-based genomic prediction approaches when the nonlinear interaction components are important because LNL and LPP exhibited strong epistatic interaction components. Additionally, our results suggest that applying bivariate DL models could also contribute to the prediction accuracy by utilizing the genetic correlation between LNL and LPP.

Climate change is an imminent threat, particularly affecting agricultural productivity, which relies heavily on weather conditions. Understanding the specific impacts of climate change on key crops is crucial for developing effective adaptation strategies to ensure food security. The growth patterns of onions and garlic were observed at over ten different locations in South Korea, and the yield data from the past 40 years were analyzed. The yield was significantly correlated with temperature and strongly affected by the frequent and unexpected patterns of precipitation. The increase in mean temperature during winter and the spatial and temporal concentration of precipitation are expected to be the most influential factors for Allium crop production in the future. In addition, the yields of onions and garlic can serve as good indicators for predicting the impacts of weather on agricultural productivity, given their extended cultivation periods and significant correlations with temperature and precipitation. As climate change scenarios become available, the results of this study can serve as a basis for predicting changes in agricultural production in the future and identifying opportunities to adapt cultivation systems for food security.

Abstract Hibiscus syriacus L. is a renowned ornamental plant. We constructed 95 chloroplast genomes of H. syriacus L. cultivars using a short-read sequencing platform (Illumina) and a long-read sequencing platform (Oxford Nanopore Technology). The following genome assembly, we delineate quadripartite structures encompassing large single-copy, small single-copy, and inverted repeat (IRa and IRb) regions, from 160,231 bp to 161,041 bp. Our comprehensive analyses confirmed the presence of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes in the pan-chloroplast genome, consistent with prior research on the H. syriacus chloroplast genome. Subsequent pangenome analysis unveiled widespread genome sequence conservation alongside unique cultivar-specific variant patterns consisting of 193 single-nucleotide polymorphisms and 61 insertions or deletions. The region containing intra-species variant patterns, as identified in this study, has the potential to develop accession-specific molecular markers, enhancing precision in cultivar classification. These findings are anticipated to drive advancements in breeding strategies, augment biodiversity, and unlock the agricultural potential inherent in H. syriacus.

Abstract Keratinocytes exposed to UVB induce the production of cytokines, which activate fibroblasts and increase the expression of matrix metalloproteinases (MMPs). The increased expression of MMPs leads to connective tissue damage and wrinkle formation, resulting in skin aging. In this study, we used human dermal fibroblasts cultured in UVB-irradiated keratinocyte-conditioned medium (UV CM) to investigate the potential anti-aging effects of the ginsenoside Rg2 on skin. The inhibitory effect of Rg2 on the MMP-1 gene and protein was determined by real-time PCR and ELISA. We also examined the expression levels of proteins in the mitogen-activated protein kinase (MAPK) signaling pathway using western blotting, to elucidate the underlying mechanism of the inhibitory effect of Rg2. Rg2 inhibited MMP-1 mRNA and protein expression in a concentration-dependent manner. We found that Rg2 inhibited the phosphorylation of extracellular signal-regulated kinase (ERK) and c-Jun N-terminal kinase (JNK) but not that of p38. Therefore, our results suggest that Rg2 is a potential material for the prevention and treatment of photoaging.

Abstract Improvements in long read DNA sequencing and related techniques facilitated the generation of complex eukaryotic genomes. Despite these advances, the quality of constructed plant reference genomes remains relatively poor due to the large size of genomes, high content of repetitive sequences, and wide variety of ploidy. Here, we developed the de novo sequencing and assembly of high polyploid plant genome, Hibiscus syriacus, a flowering plant species of the Malvaceae family, using the Oxford Nanopore Technologies and Pacific Biosciences Sequel sequencing platforms. We investigated an efficient combination of high-quality and high-molecular-weight DNA isolation procedure and suitable assembler to achieve optimal results using long read sequencing data. We found that abundant ultra-long reads allow for large and complex polyploid plant genome assemblies with great recovery of repetitive sequences and error correction even at relatively low depth Nanopore sequencing data and polishing compared to previous studies. Collectively, our combination provides cost effective methods to improve genome continuity and quality compared to the previously reported reference genome by accessing highly repetitive regions. The application of this combination may enable genetic research and breeding of polyploid crops, thus leading to improvements in crop production.

Abstract Background Under conditions of hypoxia, cancer cells with hypoxia inducible factor-1α (HIF-1α) from heterogeneous tumor cells show greater aggression and progression in an effort to compensate for harsh environmental conditions. Extensive study on the stability of HIF-1α under conditions of acute hypoxia in cancer progression has been conducted, however, understanding of its involvement during the chronic phase is limited. Methods In this study, we investigated the effect of SIRT1 on HIF1 stability in a typical chronic hypoxic conditon that maintains cells for 24 h under hypoxia using Western blotting, co-IP, measurement of intracellular NAD + and NADH levels, semi-quantitative RT-PCR analysis, invasion assay, gene knockdown. Results Here we demonstrated that the high concentration of pyruvate in the medium, which can be easily overlooked, has an effect on the stability of HIF-1α. We also demonstrated that NADH functions as a signal for conveyance of HIF-1α degradation via the SIRT1 and VHL signaling pathway under conditions of chronic hypoxia, which in turn leads to attenuation of hypoxically strengthened invasion and angiogenic activities. A steep increase in the level of NADH occurs during chronic hypoxia, leading to upregulation of acetylation and degradation of HIF-1α via inactivation of SIRT1. Of particular interest, p300-mediated acetylation at lysine 709 of HIF-1α is recogonized by VHL, which leads to degradation of HIF-1α via ubiquitin/proteasome machinary under conditions of chronic hypoxia. In addition, we demonstrated that NADH-elevation-induced acetylation and subsequent degradation of HIF-1α was independent of proline hydroxylation. Conclusions Our findings suggest a critical role of SIRT1 as a metabolic sensor in coordination of hypoxic status via regulation of HIF-1α stability. These results also demonstrate the involvement of VHL in degradation of HIF-1α through recognition of PHD-mediated hydroxylation in normoxia and p300-mediated HIF-1α acetylation in hypoxia.

Abstract Accurately detecting disease occurrences of crops in early stage is essential for quality and yield of crops through the decision of an appropriate treatments. However, detection of disease needs specialized knowledge and long-term experiences in plant pathology. Thus, an automated system for disease detecting in crops will play an important role in agriculture by constructing early detection system of disease. To develop this system, construction of a stepwise disease detection model using images of diseased-healthy plant pairs and a CNN algorithm consisting of five pre-trained models. The disease detection model consists of three step classification models, crop classification, disease detection, and disease classification. The ‘unknown’ is added into categories to generalize the model for wide application. In the validation test, the disease detection model classified crops and disease types with high accuracy (97.09%). The low accuracy of non-model crops was improved by adding these crops to the training dataset implicating expendability of the model. Our model has the potential to apply to smart farming of Solanaceae crops and will be widely used by adding more various crops as training dataset.

Many studies have been conducted to improve technology for semen cryopreservation in pigs. However, computer-assisted analysis of sperm motility and morphology is insufficient to predict the molecular function of frozen-thawed semen. More accurate expression patterns of boar sperm proteins may be derived using the isobaric tags for relative and absolute quantification (iTRAQ) technique. In this study, the iTRAQ-labeling system was coupled with liquid chromatography tandem-mass spectrometry (LC-MS/MS) analysis to identify differentially expressed CM10-fractionated proteins between fresh and frozen-thawed boar semen. A total of 76 protein types were identified to be differentially expressed, among which 9 and 67 proteins showed higher and lower expression in frozen-thawed than in fresh sperm samples, respectively. The classified functions of these proteins included oxidative phosphorylation, mitochondrial inner membrane and matrix, and pyruvate metabolic processes, which are involved in adenosine triphosphate (ATP) synthesis; and sperm flagellum and motile cilium, which are involved in sperm tail structure. These results suggest a possible network of biomarkers associated with survival after the cryopreservation of Duroc boar semen.

Introduction: The strut iliac bone graft has been widely used to achieve fusion in various anterior cervical spinal surgeries but some complications often remain, such as pain and gross deformity. Considering these, we designed a new technique to restore the iliac ridge, using the outmost part of the iliac crest. We aim to assess the efficacy of our new restoration technique of the iliac ridge after harvesting strut bone graft for anterior cervical fusion. The clinical and radiological outcomes of our hinged roof method were evaluated. Technical Note: A retrospective review was conducted of 29 patients who underwent hinged roof reconstruction of the iliac ridge after harvesting a bicortical strut bone graft for anterior cervical fusion using a cervical plate system. The clinical outcome for pain and gross appearance and radiological results were evaluated. Three months after the surgery, pain at the donor site became minimal or absent in all cases. At 1 year follow-up, no patient had reported pain and palpable discomfort, such as step-off on the donor site. Final X-ray and follow-up computed tomography revealed a bony union of the reconstructed iliac ridge to both margins. Conclusions: By showing good clinical and radiological outcomes, the authors' hinged roof reconstruction of the iliac crest after harvesting strut bone graft seemed to be a simple and effective technique that can reduce complications, such as pain and deformity on the donor iliac crest.

Fusarium spp. are commonly associated with the root rot complex of soybean (Glycine max). Previous surveys identified six common Fusarium species from Manitoba, including F. oxysporum, F. redolens, F. graminearum, F. solani, F. avenaceum, and F. acuminatum. This study aimed to determine their pathogenicity, assess host resistance, and evaluate the genetic diversity of Fusarium spp. isolated from Canada. The pathogenicity of these species was tested on two soybean cultivars, ‘Akras’ (moderately resistant) and ‘B150Y1′ (susceptible), under greenhouse conditions. The aggressiveness of the fungal isolates varied, with root rot severities ranging from 1.5 to 3.3 on a 0–4 scale. Subsequently, the six species were used to screen a panel of 20 Canadian soybean cultivars for resistance in a greenhouse. Cluster and principal component analyses were conducted based on the same traits used in the pathogenicity study. Two cultivars, ‘P15T46R2′ and ‘B150Y1′, were consistently found to be tolerant to F. oxysporum, F. redolens, F. graminearum, and F. solani. To investigate the incidence and prevalence of Fusarium spp. in Canada, fungi were isolated from 106 soybean fields surveyed across Manitoba, Saskatchewan, Ontario, and Quebec. Eighty-three Fusarium isolates were evaluated based on morphology and with multiple PCR primers, and phylogenetic analyses indicated their diversity across the major soybean production regions of Canada. Overall, this study contributes valuable insights into host resistance and the pathogenicity and genetic diversity of Fusarium spp. in Canadian soybean fields.

Abstract Background Most crop seeds are F1 hybrids. Seed providers and plant breeders must be confident that the seed supplied to growers is of known, and uniform, genetic makeup. This requires maintenance of pure genotypes of the parental lines and testing to ensure the genetic purity of the F1 seed. Traditionally, seed purity has been assessed with a grow-out test (GOT) in the field, a time consuming and costly venture. Early in the last decade, seed testing with molecular markers was introduced as a replacement for GOT, and Kompetitive allele specific PCR (KASP) markers were recognized as promising tools for genetic testing of seeds. However, the markers available at that time could be inaccurate and applicable to only a small number of accessions or varieties due to the limited genetic information and reference genomes available. Results We identified 4,925,742 SNPs in 50 accessions of the Brasscia rapa core collection. From these, we identified 2,925 SNPs as accession-specific, considering properties of flanking region harboring accession-specific SNPs and genic region conservation among accessions by the Next Generation Sequencing (NGS) analysis. In total, 100 accession-specific markers were developed as accession-specific KASP markers. Based on the results of our validation experiments, the accession-specific markers successfully distinguised individuals from the mixed population including 50 target accessions from B. rapa core collection and the outgroup. Additionally, the marker set we developed here discriminated F1 hybrids and their parental lines with distinct clusters. Conclusions This study provides efficient methods for developing KASP markers to distinguish individuals from the mixture comprised of breeding lines and germplasms from the resequencing data of Chinese cabbage (Brassica rapa spp. pekinensis).

Hibiscus syriacus, a member of the tribe Hibisceae, is considered an important ornamental and medicinal plant in east Asian countries. Here, we sequenced and assembled the complete chloroplast genome of H. syriacus var. Baekdansim using the PacBio long-read sequencing platform. A quadripartite structure with 161,026 base pairs was obtained, consisting of a pair of inverted repeats (IRA and IRB) with 25,745 base pairs, separated by a large single-copy region of 89,705 base pairs and a short single-copy region of 19,831 base pairs. This chloroplast genome had 79 protein-coding genes, 30 transfer RNA genes, 4 ribosomal RNA genes, and 109 simple sequence repeat regions. Among them, ndhD and rpoC1, containing traces of RNA-editing events associated with adaptive evolution, were identified by analysis of putative RNA-editing sites. Codon usage analysis revealed a preference for A/U-terminated codons. Furthermore, the codon usage pattern had a clustering tendency similar to that of the phylogenetic analysis of the tribe Hibisceae. This study provides clues for understanding the relationships and refining the taxonomy of the tribe Hibisceae.

Abstract Objectives Phytohormones are small signaling molecules with crucial roles in plant growth, development, and environmental adaptation to biotic and abiotic stress responses. Despite several previously published molecular studies focused on plant hormones, our understanding of the transcriptome induced by phytohormones remains unclear, especially in major crops. Here, we aimed to provide transcriptome dataset using RNA sequencing for phytohormone-induced signaling in plant. Data description We used high-throughput RNA sequencing profiling to investigate the pepper plant response to treatment with four major phytohormones (salicylic acid, jasmonic acid, ethylene, and abscisic acid). This dataset yielded 78 samples containing three biological replicates per six different time points for each treatment and the control, constituting 187.8 Gb of transcriptome data (2.4 Gb of each sample). This comprehensive parallel transcriptome data provides valuable information for understanding the relationships and molecular networks that regulate the expression of phytohormone-related genes involved in plant developments and environmental stress adaptation.

A Korean synthetic pig breed, Woori-Heukdon (WRH; F3), was developed by crossing parental breeds (Korean native pig [KNP] and Korean Duroc [DUC]) with their crossbred populations (F1 and F2). This study in genome-wide assessed a total of 2,074 pigs which include the crossbred and the parental populations using the Illumina PorcineSNP60 BeadChip. After quality control of the initial datasets, we performed population structure, genetic diversity, and runs of homozygosity (ROH) analyses. Population structure analyses showed that crossbred populations were genetically influenced by the parental breeds according to their generation stage in the crossbreeding scheme. Moreover, principal component analysis showed the dispersed cluster of WRH, which might reflect introducing a new breeding group into the previous one. Expected heterozygosity values, which were used to assess genetic diversity, were .365, .349, .336, .330, and .211 for WRH, F2, F1, DUC, and KNP, respectively. The inbreeding coefficient based on ROH was the highest in KNP (.409), followed by WRH (.186), DUC (.178), F2 (.107), and F1 (.035). Moreover, the frequency of short ROH decreased according to the crossing stage (from F1 to WRH). Alternatively, the frequency of medium and long ROH increased, which indicated recent inbreeding in F2 and WRH. Furthermore, gene annotation of the ROH islands in WRH that might be inherited from their parental breeds revealed several interesting candidate genes that may be associated with adaptation, meat quality, production, and reproduction traits in pigs.

Magnetized water is defined as the amount of water that has passed through a magnet. The magnetic field weakens the hydrogen bonds between the water molecules, leading to the magnetized liquid acquiring special characteristics such as easy supercooling and forming smaller ice crystals. We researched the influences of a magnetized freezing extender on cell membrane damage and in vitro fertilization of boar sperm during cryopreservation. The freezing extenders were passed through 0, 2000, 4000, and 6000 gausses (G) of magnetic devices using a liquid cycling pump system and then used for the sperm freezing process. The damage to plasma, acrosomal, and mitochondrial membranes in frozen-thawed spermatozoa was investigated by flow cytometry, and motility was assessed using the CASA system. The fertility of frozen-thawed sperm was estimated using in vitro fertilization. The damage to the membranes was significantly decreased in the magnetized freezing extender by the 6000 G magnetic field compared to that of the control in frozen-thawed sperm, and motility was increased in the 6000 G group. Although there were no significant differences in the cleavage rates of in vitro fertilized oocytes among the treatment groups, the ratio of blastocyst formation increased in the magnetized freezing extender groups compared with that in the control group. The number of blastocysts was significantly higher in the 4000 G group than in the 0 G group. In conclusion, these results suggest that a magnetized freezing extender could improve the freezability of sperm and the development of oocytes fertilized in vitro with frozen-thawed sperm.

In this study, genome-wide CNVs were identified using a total of 469 horses from four horse populations (Jeju horses, Thoroughbreds, Jeju riding horses, and Hanla horses). We detected a total of 843 CNVRs throughout all autosomes: 281, 30, 301, and 310 CNVRs for Jeju horses, Thoroughbreds, Jeju riding horses, and Hanla horses, respectively. Of the total CNVRs, copy number losses were found to be the most abundant (48.99%), while gains and mixed CNVRs accounted for 41.04% and 9.96% of the total CNVRs, respectively. The length of the CNVRs ranged from 0.39 kb to 2.8 Mb, while approximately 7.2% of the reference horse genome assembly was covered by the total CNVRs. By comparing the CNVRs among the populations, we found a significant portion of the CNVRs (30.13%) overlapped; the highest number of shared CNVRs was between Hanla horses and Jeju riding horses. When compared with the horse CNVRs of previous studies, 26.8% of CNVRs were found to be uniquely detected in this study. The CNVRs were not randomly distributed throughout the genome; in particular, the Equus caballus autosome (ECA) 7 comprised the largest proportion of its genome (16.3%), while ECA 24 comprised the smallest (0.7%). Furthermore, functional analysis was applied to CNVRs that overlapped with genes (genic-CNVRs); these overlapping areas may be potentially associated with the olfactory pathway and nervous system. A racing performance QTL was detected in a CNVR of Thoroughbreds, Jeju riding horses, and Hanla horses, and the CNVR value was mixed for three breeds.

Efficient and accurate methods of analysis are needed for the huge amount of biological data that have accumulated in various research fields, including genomics, phenomics, and genetics. Artificial intelligence (AI)-based analysis is one promising method to manipulate biological data. To this end, various algorithms have been developed and applied in fields such as disease diagnosis, species classification, and object prediction. In the field of phenomics, classification of accessions and variants is important for basic science and industrial applications. To construct AI-based classification models, three types of phenotypic image data were generated from 156 Brassica rapa core collections, and classification analyses were carried out using four different convolutional neural network architectures. The results of lateral view data showed higher accuracy compared with top view data. Furthermore, the relatively low accuracy of ResNet50 architecture suggested that definition and estimation of similarity index of phenotypic data were required before the selection of deep learning architectures.

In polyploids, whole genome duplication (WGD) played a significant role in genome expansion, evolution and diversification. Many gene families are expanded following polyploidization, with the duplicated genes functionally diversified by neofunctionalization or subfunctionalization. These mechanisms may support adaptation and have likely contributed plant survival during evolution. Flowering time is an important trait in plants, which affects critical features, such as crop yields. The flowering-time gene family is one of the largest expanded gene families in plants, with its members playing various roles in plant development. Here, we performed genome-wide identification and comparative analysis of flowering-time genes in three palnt families i.e., Malvaceae, Brassicaceae, and Solanaceae, which indicate these genes were expanded following the event/s of polyploidization. Duplicated genes have been retained during evolution, although genome reorganization occurred in their flanking regions. Further investigation of sequence conservation and similarity network analyses provide evidence for functional diversification of duplicated genes during evolution. These functionally diversified genes play important roles in plant development and provide advantages to plants for adaptation and survival in response to environmental changes encountered during evolution. Collectively, we show that flowering-time genes were expanded following polyploidization and retained as large gene family by providing advantages from functional diversification during evolution.

Objective We aimed to characterize linkage disequilibrium (LD) and effective population size (Ne) in a Korean Yorkshire population using genomic data from thousands of individuals. Methods We genotyped 2,470 Yorkshire individuals from four major Grand-Grand-Parent farms in Korea using the Illumina PorcineSNP60 version2 BeadChip, which covers >61,565 single nucleotide polymorphisms (SNPs) located across all chromosomes and mitochondria. We estimated the expected LD and inferred current Ne as well as ancestral Ne. Results We identified 61,565 SNP from autosomes, mitochondria, and sex chromosomes and characterized the LD of the Yorkshire population, which was relatively high between closely linked markers (>0.55 at 50 kb) and declined with increasing genetic distance. The current Ne of this Korean Yorkshire population was 122.87 (106.90; 138.84), while the historical Ne of Yorkshire pigs suggests that the ancestor Ne has decreased by 99.6% over the last 10,000 generations. Conclusion To maintain genetic diversity of a domesticated animal population, we must carefully consider appropriate breed management methods to avoid inbreeding. Although attenuated selection can affect short-term genetic gain, it is essential for maintaining the long-term genetic variability of the Korean Yorkshire population. Continuous and long-term monitoring would also be needed to maintain the pig population to avoid an unintended reduction of Ne. The best way to preserve a sustainable population is to maintain a sufficient Ne.

Functional analyses of genes are crucial for unveiling biological responses, genetic engineering, and developing new medicines. However, functional analyses have largely been restricted to model organisms, representing a major hurdle for functional studies and industrial applications. To resolve this, comparative genome analyses can be used to provide clues to gene functions as well as their evolutionary history. To this end, we present Prometheus, a web-based omics portal that contains more than 17,215 sequences from prokaryotic and eukaryotic genomes. This portal supports interkingdom comparative analyses via a domain architecture-based gene identification system and Gene Search, and users can easily and rapidly identify single or entire gene sets in specific pathways. Bioinformatics tools for further analyses are provided in Prometheus or through Bio-Express, a cloud-based bioinformatics analysis platform. Prometheus is a new paradigm for comparative analyses of large amounts of genomic information.

BackgroundTranslationally controlled tumor protein (TCTP) is a conserved, multifunctional protein involved in numerous cellular processes in eukaryotes. Although the functions of TCTP have been investigated sporadically in animals, invertebrates, and plants, few lineage-specific activities of this molecule, have been reported. An exception is in Arabidopsis thaliana, in which TCTP (AtTCTP1) functions in stomatal closuer by regulating microtubule stability. Further, although the development of next-generation sequencing technologies has facilitated the analysis of many eukaryotic genomes in public databases, inter-kingdom comparative analyses using available genome information are comparatively scarce.MethodologyTo carry out inter-kingdom comparative analysis of TCTP, TCTP genes were identified from 377 species. Then phylogenetic analysis, prediction of protein structure, molecular docking simulation and molecular dynamics analysis were performed to investigate the evolution of TCTP genes and their binding proteins.ResultsA total of 533 TCTP genes were identified from 377 eukaryotic species, including protozoa, fungi, invertebrates, vertebrates, and plants. Phylogenetic and secondary structure analyses reveal lineage-specific evolution of TCTP, and inter-kingdom comparisons highlight the lineage-specific emergence of, or changes in, secondary structure elements in TCTP proteins from different kingdoms. Furthermore, secondary structure comparisons between TCTP proteins within each kingdom, combined with measurements of the degree of sequence conservation, suggest that TCTP genes have evolved to conserve protein secondary structures in a lineage-specific manner. Additional tertiary structure analysis of TCTP-binding proteins and their interacting partners and docking simulations between these proteins further imply that TCTP gene variation may influence the tertiary structures of TCTP-binding proteins in a lineage-specific manner.ConclusionsOur analysis suggests that TCTP has undergone lineage-specific evolution and that structural changes in TCTP proteins may correlate with the tertiary structure of TCTP-binding proteins and their binding partners in a lineage-specific manner.

This study was designed to investigate the effects of dietary fenugreek seed extract (FSE) supplementation on egg production, egg quality, blood profiles, cecal microflora, and excreta noxious gas emission in laying hens. A total of 384 laying hens (26-weeks old, Hyline-brown) were fed three different levels of FSE (0, 0.05, and 0.1%) in a cornsoybean diet for 6 weeks. The inclusion of FSE in the laying hen diet did not affect egg production, feed intake, or feed conversion among treatments; however, egg weight, eggshell breaking strength, eggshell thickness, and yolk color increased in FSE-fed groups (linear, P

A 2-year-old female Maltese dog was presented with a history of anemia and vaginal hemorrhagic discharge. Physical examination revealed severe vaginal hemorrhagic discharge, abdominal pain, pale mucous membranes, low blood pressure and dehydration. Results of serum biochemistry, hematology, venous blood gas, and electrolyte canine C-reactive protein (CRP) test revealed severe normocytic normochromic anemia, severe neutropenia, a high level of CRP, hypoglycemia, and imbalanced electrolytes. Abdominal ultrasound examination showed focal hypoechoic defect with loss of layering in uterine horn wall. A laparotomy revealed a clear reddish fluid in the abdomen, the fistula of left and right uterine horn, the purulent discharge from fistula, and symptoms of septic peritonitis near by the fistula site. The bitch underwent ovariohysterectomy and recovered without complication. Histopathological diagnosis of the uterine fistula site was adenocarcinoma.

Abstract Background Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants. Results We report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific. Conclusions Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants.

Sixty broilers (initially 1.6 kg and 35 d-old) were used to determine the effect of Bacillus subtilis C14 and RX7 strains on growth performance, blood parameter, and intestinal microbiota in response to experimental challenge with Salmonell gallinarum. Broilers were distributed to 4 treatment groups include: C1 (control group; no challenge, no B. subtilis), C2 (Salmonella-challenged group; S. gallinarum 108 cfu/bird), T1 (C2+supplemented with of B. subtilis C14 (1.0×109 cfu/g) at 0.1% in diet) and T2 (C2+supplemented with of B. subtilis RX7 (1.0×109 cfu/g) at 0.1% in diet). Results indicated that inclusion of B. subtilis (T1, T2) in the diet increased (P

Background and Objectives: The purpose of the present study was to investigate the anti-bacterial efficacy of passive ultrasonic irrigation (PUI) and a 980-nm-gallium-aluminum-arsenide (GaAlAs) laser using a real-time DNA-based quantitative polymerase chain reaction (qPCR) assay and scanning electron microscopy (SEM). Materials and Methods: Eighty-six extracted single- and double-rooted human teeth were used in the experiment. The following four experimental groups were evaluated, as well as a control group: group 1: single root + PUI (n = 20); group 2: single root + laser application (n = 20); group 3: double roots + PUI (n = 20); group 4: double roots + laser application (n =20); control group (n = 6): 3 single roots, 3 double roots. The qPCR assay was performed in three stages to evaluate the efficacy of the adjunctive method against Enterococcus faecalis. SEM analysis was also used to examine the microstructure of root canal surfaces. The data were statistically analyzed using the Friedman test and the Kruskal–Wallis test with Bonferroni adjustment. Results: The decrease in the DNA levels from S1 (before preparation) to S2 (just after preparation) was highly significant in all groups, and decreases in DNA levels from S2 to S3 (after incubation for 1 week) were found in all experimental groups except group 1. An inter-group analysis showed that PUI was significantly more effective in terms of antibacterial efficacy than GaAlAs laser irradiation in single root (p < 0.05). However, in double roots, experimental groups did not show significantly lower DNA levels than the control group (p > 0.05). SEM images showed that cleaning of the root canal surface and reduction of dentin debris were achieved only in single-rooted teeth when using PUI application. Conclusions: Two adjunctive methods were effective in reducing E. faecalis in single rooted tooth.

Acoustic emission (AE) has garnered significant interest as a promising way to detect the early-stage development of internal cracks and damage in underground and geotechnical structures, associated with natural disasters. Meanwhile, AE source localization techniques that can identify the damage location in a piled-raft foundation (PRF) are premature because of its complex geometry, although the PRF is a widely used deep foundation type for high-rise buildings. In this study, we propose an integrated approach to localize AE sources in the PRF by using the modified Akaike information criterion (AIC) method and examine its accuracy to mark with pile zones. We performed a series of experiments on a scaled PRF model at a ratio of 1:50, composed of one raft and 25 piles. The results demonstrate that the combined approach with the modified AIC method and the Simplex method can localize the AE source zones with good accuracy, greater than 95% on average. The suggested two-stage AIC picker shows accurate onset time determination, and hence, it significantly improves the accuracy, particularly effective for the signals with low signal-to-noise ratios. The approach exploiting the two-stage AIC picker can be readily used for automated real-time AE monitoring to detect crack generation and its location in buried foundations that cannot be inspected visually.

The aim of this study is to examine current status of swine AI and boar stud in South Korea using survey and data analysis. This survey included 48 boar studs registered as ‘semen processing business’. The survey data were collected by direct visitation, FAX and/or telephone conversation for 7 months from June through December in 2013. 48 boar studs owned a total of 3,537 boars and the Duroc breed accounted for the highest rate (75.3%) of all boar breeds. In case of ownership, agricultural management corporations was the highest (50.0%) and followed by individual ownership (33.3%). Large-scale boar studs in terms of own over 151 boar were surveyed as 4.2% and most boar studs owned less than 100 boars (77.1%). The amount of liquid semen provided by 48 boar studs were 1,889,000 doses and each boar stud provided average of 39,000 does, which is represented for 90% consumption by sows in South Korea.

Cryopreservation of boar semen is continually researched in reproductive technologies and genetic resource banking in breed conservation. For evaluating the boar semen quality, sperm motility (MOT) is an important parameter because the movement of spermatozoa indicates active metabolism, membrane integrity and fertilizing capacity. Various researches have been trying to improve the quality of semen post-thawed in boar. Recently, polymorphism (g.358A>T) of cluster-of-differentiation antigen 9 (CD9) gene reported to be significant association with MOT. Also, CD9 gene was expressed in the male germ line stem cells is crucial for sperm-egg fusion, and was therefore selected as candidate gene for boar semen. This study was conducted to evaluate the pig SNP (g.358A>T) of CD9 gene as a positional controlling for semen parameters of post-thawed boar semen. To results, the g.358A>T SNP of the CD9 gene was significantly associated with the traits such as MOT, curve linear velocity, straight line velocity, average path velocity and amplitude of lateral head displacement. Particularly, the g.358A>T SNP significantly has the highest association with MOT and animals with AA genotype (pT in the intron 6 region of the porcine CD9 may be used as a molecular marker for Duroc boar Post-thawed semen quality, although its functional effect was not defined yet.

ObjectivesChronic rhinosinusitis (CRS) with eosinophilic mucin is relatively rare in Korea. We categorized CRS patients with characteristic eosinophilic mucin into several groups and compared the groups based on their clinicopathological features.MethodsIn total, 52 CRS patients with eosinophilic mucin were enrolled. Based on the presence or absence of an allergy (A) to a fungus or fungal element (F) in the mucin, the patients were divided into four groups: allergic fungal rhinosinusitis (AFRS, A+F+), AFRS-like sinusitis (A+F-), eosinophilic fungal rhinosinusitis (EFRS, A-F+), and eosinophilic mucin rhinosinusitis (EMRS, A-F-). Clinical and immunological variables were compared between the groups.ResultsThere were 13 patients in the AFRS group, 13 in the EFRS group, and 26 in the EMRS group. No patient was assigned to the AFRS-like sinusitis group. The AFRS group showed a significantly higher association with allergic rhinitis than did the EFRS and EMRS groups. The mean total serum IgE level in the AFRS patients was significantly higher than in the EFRS and EMRS patients. While 7.7% of the patients with AFRS and EFRS were asthmatic, 65.4% of the patients with EMRS had bronchial asthma. In the AFRS and EFRS groups, 31% had bilateral disease, in contrast to 100% of EMRS patients with bilateral disease. The prevalence of high attenuation areas by computed tomography was significantly higher in the AFRS group than in the EMRS group, and the mean Hounsfield unit values of the areas of high attenuation in the AFRS patients were significantly greater than those in the EMRS patients.ConclusionAFRS is believed to be an allergic response to colonizing fungi in atopic individuals. In EFRS, local allergies to fungi may play a role in the pathogenesis of the disease. EMRS is thought to be unconnected with fungal allergies.

Background The oriental melon (Cucumis melo L. var. makuwa) is one of the most important cultivated cucurbits grown widely in Korea, Japan, and northern China. It is cultivated because its fruit has a sweet aromatic flavor and is rich in soluble sugars, organic acids, minerals, and vitamins. In order to elucidate the genetic and molecular basis of the developmental changes that determine size, color, and sugar contents of the fruit, we performed de novo transcriptome sequencing to analyze the genes expressed during fruit development. Results We identified a total of 47,666 of representative loci from 100,875 transcripts and functionally annotated 33,963 of the loci based on orthologs in Arabidopsis thaliana. Among those loci, we identified 5,173 differentially expressed genes, which were classified into 14 clusters base on the modulation of their expression patterns. The expression patterns suggested that the differentially expressed genes were related to fruit development and maturation through diverse metabolic pathways. Analyses based on gene set enrichment and the pathways described in the Kyoto Encyclopedia of Genes and Genomes suggested that the expression of genes involved in starch and sucrose metabolism and carotenoid biosynthesis were regulated dynamically during fruit development and subsequent maturation. Conclusion Our results provide the gene expression patterns related to different stages of fruit development and maturation in the oriental melon. The expression patterns give clues about important regulatory mechanisms, especially those involving starch, sugar, and carotenoid biosynthesis, in the development of the oriental melon fruit.

Interleukin (IL)-25 has been shown to play an important role in the pathogenesis of chronic rhinosinusitis with nasal polyps. Nasal polyps are associated with chronic inflammation of the mucous membranes in the paranasal sinuses and are involved in extracellular matrix (ECM) accumulation. The aim of this study is to evaluate the effects of IL-25 on myofibroblast differentiation, ECM production and the expression of matrix metalloproteinases in nasal polyp derived fibroblasts (NPDFs) and to determine the molecular mechanism underlying these processes.A total of 40 patients were enrolled in this study for Immunofluorescence studies. Expression of IL17 receptor B was evaluated by real time reverse transcription polymerase chain reaction (PCR) in NPDFs. NPDFs were stimulated with IL-25 for 48 h in the presence or absence of mitogen-activated protein kinase (MAPK) and NF-κB inhibitors or small interfering RNAs (siRNA). The protein levels of fibrosis active mediators were examined using western blotting. Fibroblast migration was evaluated with a scratch assay. The total collagen amount was analyzed with the Sircol collagen assay.IL-25 induced α-SMA, fibronectin, and MMP-1 and -13, which were dependent on IL-17RB. IL-25 also induced activation of NF-κB and mitogen-activated protein kinase (MAPKs). By using the specific inhibitor of ERK, p38, JNK and NF-κB (U, SB, SP and Bay), we found that IL-25-induced expressions of α-SMA, fibronectin, and MMPs was regulated by the signaling pathways of MAPKs and NF-κB. IL-25 also induces α-SMA, fibronectin, and MMPs expression through IL-17RB-dependent pathways in NPDFs. The increased migration ability induced by IL-25 was suppressed by the specific inhibitors of MAPKs and NF-κB.Our data indicate that IL-25 induced myofibroblast differentiation, fibronectin production, and MMP-1 and -13 expressions through the signaling pathways of MAPKs and NF-κB. in NPDFs and increased expression of IL-25 were also involved in the pathogenesis of nasal polyposis by affecting nasal fibroblasts in chronic rhinosinusitis with nasal polyps.

The purpose of this study was to compare the cytotoxic effects and mineralization activity of three calcium silicate-based root canal sealers to those of a conventional resin-based sealer. Experiments were performed using human dental pulp stem cells grown in a monolayer culture. The root canal sealers tested in this study were EndoSequence BC Sealer (Brasseler), BioRoot RCS (Septodont), Endoseal MTA (Maruchi), and AH Plus (Dentsply DeTrey). Experimental disks 6 mm in diameter and 3 mm in height were made and stored in a 100% humidity chamber at 37 °C for 72 h to achieve setting. The cytotoxicity of various root canal sealers was evaluated using a methyl-thiazoldiphenyl-tetrazolium (MTT) assay. To evaluate cell migration ability, a scratch wound healing method was used, and images of the scratch area were taken using a phase-contrast microscope. Cell morphology was evaluated by a scanning electron microscope after direct exposure for 72 h to each sealer disk. In the cell viability assay, there were no significant differences between the EndoSequence BC, BioRoot RCS, Endoseal MTA, and control groups in any experimental period (p > 0.05). In the cell migration assay, there were no significant differences between the EndoSequence BC, Endoseal MTA, and control groups in any experimental period (p > 0.05). BioRoot RCS exhibited slower cell migration relative to EndoSequence BC and Endoseal MTA for up to 72 h (p < 0.05). Conversely, it showed a similar wound healing percentage at 96 h (p > 0.05). In an evaluation of cell morphology, cells in direct contact with EndoSequence BC, BioRoot RCS, and Endoseal MTA disks showed superior spreading compared to those in contact with the AH Plus disk. In an Alizarin red staining assay, EndoSequence BC, BioRoot RCS, and Endoseal MTA showed a significant increase in mineralized nodule formation compared to the AH Plus group (p < 0.05). In conclusion, all calcium silicate-based root canal sealers tested in this study showed good biological properties and mineralization activity compared to conventional resin-based sealer.

The purpose of this study was to compare the penetration ability of calcium silicate root canal sealers and conventional resin-based sealer using confocal laser scanning microscopy (CLSM). A total of 60 recently extracted single-rooted human premolars were used in this study. The root canals were prepared to a size 40/0.06 taper with ProFile rotary instruments and irrigated with NaOCl and EDTA. After drying all canals, the specimens were randomly divided into three experimental groups (n = 20): Group 1, gutta-percha (GP)/AH Plus with continuous wave compaction; group 2, GP/BioRoot RCS with a single-cone technique; and group 3, GP/Endoseal MTA with a single-cone technique. All experimental samples were sectioned perpendicular to their long axis using a low-speed diamond wheel at the apical, middle, and coronal third levels. The penetration abilities of all samples were evaluated using CLSM. A Kruskal⁻Wallis analysis and a series of Mann⁻Whitney U post hoc tests were performed. A higher intensity level was found in the coronal area and a lower intensity level in the apical area in all the experimental groups. The AH Plus group showed higher sum fluorescence intensity in the apical and coronal thirds compared with the BioRoot RCS and Endoseal MTA groups, whereas the BioRoot RCS group showed a higher intensity level in the middle third, similar to the AH Plus group. The maximum sealer penetration depth was low in the apical area and high in the coronal area in the AH Plus and Endoseal MTA groups. In the BioRoot RCS group, maximum sealer penetration was observed in the middle third. In conclusion, there were significant differences in sealer penetration pattern and distance according to the root level and sealer type.

A 10-year-old spayed female Yorkshire Terrier visited for a physical checkup. The bitch had a history of ovariohysterectomy for treatment of pyometra a year ago. On physical examination, the dog was bright and alert. Complete blood counts, serum biochemistry and blood gas analysis results did not show any deviations within normal ranges. Radiographic and ultrasonographic examinations revealed unilateral hydronephrosis and hydroureter of the right kidney and ureter, and obstruction of the distal ureter was observed. On the basis of these results, nephroureterectomy was performed. During the operation, the adhesion of the distal ureter and surrounding tissue cells were observed without the evidence of the ureteral ligation. The distal ureteral obstruction was presumed to be adhesion caused by fibrous tissue formation between ureter and retained broad ligament, or incompletely removed blood clots following ovariohysterectomy. This case report describes the occurrence of hydroureteronephrosis caused by adhesion of the distal ureter following ovariohysterectomy in a bitch.

FGF-2 is involved in cell survival, proliferation, apoptosis, andangiogenesis in a wide variety of cells. FRGRs, PI3K and MAPkinases are well known mediators of FGF signaling. Despite itsknown roles during many developmental processes, includingosteogenesis, there are few known targets of FGF-2. In thepresent study, we identified Bcl2-A1 and Bcl-xL as two prominenttargets involved in promoting cell survival. Pretreatmentof ATDC5 cells with FGF-2 increased cell survival, whilesiRNAs specific for Bcl2-A1 and Bcl-xL compromised the anti-apoptotic effect of FGF-2, sensitized the cells to apoptosistriggered by TNF-α. Chemical inhibition of FGFR, NFkB, andPI3K activity by PD173074, pyrrolidine dithiocarbamate, andLY294002 respectively abrogated the FGF-2-mediated inductionof Bcl2-A1 and Bcl-xL expression. Taken together, our datademonstrate that a subset of Bcl2 family proteins are the targetsof FGF-2 signaling that promotes the survival of ATDC5cells. [BMB reports 2012; 45(5): 287-292]

Components derived from an infected lesion within the bone can spread through various passages in the mandible, particularly via the mental foramen. Radiologically, the spread of infection is typically nonspecific and challenging to characterize; however, multislice computed tomography (MSCT) can effectively detect pathological changes in soft tissues and the bone marrow space. This report describes the case of a 55-year-old woman who experienced mental nerve paresthesia due to a periapical infection of the right mandibular second premolar. MSCT imaging revealed increased attenuation around the periapical lesion extending into the mandibular canal and loss of the juxtamental foraminal fat pad. Following endodontic treatment of the tooth suspected to be the source of the infection, the patient's symptoms resolved, and the previous MSCT imaging findings were no longer present. Increased bone marrow attenuation and obliteration of the fat plane in the buccal aspect of the mental foramen may serve as radiologic indicators of inflammation spreading from the bone marrow space. [ABSTRACT FROM AUTHOR]

Respiratory epithelial adenomatoid hamartoma (REAH) in the head and neck is a rare benign lesion containing glandular tissue covered with ciliated respiratory epithelium. In the head and neck, REAH of the nasal cavity, paranasal sinuses, and nasopharynx have been reported in literature. Due to rareness of REAH and insufficient knowledge of its imaging features, the diagnosis can be challenging when we encounter a non-specific cystic mass at an uncommon site in the head or neck. Here, we report the case of a pathologically confirmed REAH showing a cystic mass centered at the buccal space (retromaxillary fat pad) with CT and MRI findings. [ABSTRACT FROM AUTHOR]