High-Resolution Melting (HRM) analysis of DNA methylation using semiconductor chip-based digital PCR.

BACKGROUND: Digital PCR (dPCR) technology allows absolute quantification and detection of disease-associated rare variants, and thus the use of dPCR technology has been increasing in clinical research and diagnostics. The high-resolution melting curve analysis (HRM) of qPCR is widely used to distinguish true positives from false positives and detect rare variants. In particular, qPCR-HRM is commonly used for methylation assessment in research and diagnostics due to its simplicity and high reproducibility. Most dPCR instruments have limited fluorescence channels available and separate heating and imaging systems. Therefore, it is difficult to perform HRM analysis using dPCR instruments. OBJECTIVE: A new digital real-time PCR instrument (LOAA) has been recently developed to integrate partitioning, thermocycling, and imaging in a single dPCR instrument. In addition, a new technique to perform HRM analysis is utilized in LOAA. The aim of the present study is to evaluate the efficiency and accuracy of LOAA dPCR on HRM analysis for the detection of methylation. METHODS: In this study, comprehensive comparison with Bio-Rad qRT-PCR and droplet-based dPCR equipment was performed to verify the HRM analysis-based methylation detection efficiency of the LOAA digital PCR equipment. Here, sodium bisulfite modification method was applied to detect methylated DNA sequences by each PCR method. RESULTS: Melting curve analysis detected four different Tm values using LOAA and qPCR, and found that LOAA, unlike qPCR, successfully distinguished between different Tm values when the Tm values were very similar. In addition, melting temperatures increased by each methylation were about 0.5℃ for qPCR and about 0.2 ~ 0.6℃ for LOAA. The melting temperature analyses of methylated and unmethylated DNA samples were conducted using LOAA dPCR with TaqMan probes and EvaGreen, and the result found that Tm values of methylated DNA samples are higher than those of unmethylated DNA samples. CONCLUSION: The present study shows that LOAA dPCR could detect different melting temperatures according to methylation status of target sequences, indicating that LOAA dPCR would be useful for diagnostic applications that require the accurate quantification and assessment of DNA methylation.

Multilocus sequence typing and antibiotic resistance of Aeromonas isolated from freshwater fish in Hebei Province.

Aeromonas spp. are the opportunistic pathogens that infect both aquatic and terrestrial homeotherms. They were commonly present in aquatic environments, including effluent, tap water, marine, river, and lake, where they are often isolated from aquatic animals, including fish, molluscs, and crustaceans. The Aeromonas infections can cause sepsis, ulcer, and other symptoms, resulting in the death of massive aquatic animals. Therefore, the prevention and control of Aeromonas is of great significance for the healthy development of aquaculture. In this study, we used modern molecular methods to enhance disease control of Aeromonas isolates from freshwater fish in Hebei Province. A total of 130 Aeromonas spp. isolates were isolated from freshwater fish farms in Hengshui, Handan, and Shijiazhuang and all 130 Aeromonas spp. isolates were sequenced for species identification. Of the 130 Aeromonas spp. isolates, 104 isolates were successfully sequenced, and BLAST analysis showed that Aeromonas veronii was predominant in freshwater fish farms in Hebei Province. In addition, 26 antibiotic resistance profiles were obtained from 102 fully cultured isolates among the 104 Aeromonas spp. isolates whose species was primarily identified, and 44 multidrug-resistant bacteria among the 102 isolates were identified using an antibiotic susceptibility test. Using the Multilocus Sequence Typing (MLST) method, 33 out of 44 multidrug-resistant isolates with 14 non-Aeromonas reference strains were selected for phylogenetic and MLST analysis, and all 33 multidrug-resistant isolates were A. veronii. A total of 30 new Sequence Types (STs) were obtained by comparing concatenated sequences (gyrB-groL-gltA-metG-ppsA-recA) on PubMLST website. Furthermore, recombination event analysis detected using RDP5 and ClonalFrameML software 42 and 49 recombination events, respectively, and 22 recombination events were validated by four or more algorithms. Since mutation and recombination events increase clonal diversity and single housekeeping gene sequence alignments are limited for identifying species, we propose the use of multiple concatenated sequence loci to increase discriminatory power. In addition, we propose that the MLST method is an appropriate technique to study and develop the resistance mechanisms of multidrug-resistant Aeromonas and to identify Aeromonas systematically in complex samples obtained from the environment.

External and internal maximal intensity periods of elite youth male soccer matches.

Understanding the maximal intensity periods (MIP) of soccer matches can optimise training prescription. The aim was to establish differences between positions and other contextual factors (match location, match outcome, playing formation and score line) for both external and internal MIP variables and to investigate the differences in the match start time between MIP variables. Maximal moving averages (1 to 10 min) for average speed, high-speed running (5.5-7 m·s-1), sprinting (>7 m·s-1; all m·min-1), average acceleration/deceleration (m·s-2) and heart rate (bpm, % maximal) were calculated from 24 professional youth players across 31 matches. Linear mixed models determined differences in MIP variables between positions, contextual factors and in the match start time of MIPs. Trivial to large positional differences existed in maximal external intensities while central defenders presented the lowest heart rate. It was unclear whether maximal intensities were influenced by contextual factors. MIPs for average speed, acceleration/deceleration and heart rate tend to occur concurrently (ES = trivial) within the first 30 min, while high-speed running and sprinting are likely to occur concurrently (ES = trivial) throughout a whole match. Practitioners could target maximising average speed and average acceleration/deceleration in technical-tactical based training to maximise heart rate responses.

The inflammatory signature in monocytes of Sjögren's syndrome and systemic lupus erythematosus, revealed by the integrated Reactome and drug target analysis.

BACKGROUND: The innate immune regulation, especially by the type I IFN signature in the CD14+ monocytes, is known to be critical in the pathogenesis of autoimmune Sjögren's syndrome (SjS) and systemic lupus erythematosus (SLE). OBJECTIVE: Since patients with one condition can be overlapped with another, this study is to identify shared differentially expressed genes (DEGs) in SjS and SLE compared to healthy controls (HCs) and refine transcriptomic profiles with the integrated Reactome and gene-drug network analysis for an anti-inflammation therapy. METHODS: CD14+ monocytes were purified from whole blood of SjS and SLE patients (females, ages from 32 to 62) and subject to bulk RNA-sequencing, followed by data analyses for comparison with HC monocytes (females, ages 30 and 33). Functional categorizations, using Gene Ontology (GO) and the Reactome pathway analysis, were performed and DEGs associated with therapeutic drugs were identified from the Drug Repurposing Hub (DHUB) database. RESULTS: The GO analysis revealed that DEGs in the inflammatory response and the cellular response to cytokine were highly enriched in both conditions. A propensity toward M1 macrophage differentiation appears to be prominent in SjS while the Response to Virus was significant in SLE monocytes. Through the Reactome pathway analysis, DEGs in the IFN signaling and the cytokine signaling in immune system were most significantly enriched in both. Upregulation of NGF-induced transcription activity in SjS and the complement cascade activity in SLE were also noted. Multiple anti-inflammatory drugs, such as prostaglandin-endoperoxide synthase and angiotensin-I-converting- enzyme were associated with the DEGs in these conditions. CONCLUSIONS: Taken together, our analysis indicates distinct inflammatory transcriptomic profiles shared in SjS and SLE monocytes. Comprehensive characterizations of the data from these conditions will ultimately allow differential diagnosis of each condition and identification of therapeutic targets.

Identification of Potentially Pathogenic Variants Associated with Recurrence in Medication-Related Osteonecrosis of the Jaw (MRONJ) Patients Using Whole-Exome Sequencing.

Background: Bisphosphonates are antiresorptive and antiangiogenic drugs that prevent and treat bone loss and mineralization in women with postmenopausal osteoporosis and cancer patients. Medication-related osteonecrosis of the jaw (MRONJ) is commonly caused by tooth extraction and dental trauma. Although genetic and pathological studies about MRONJ have been conducted, the pathogenesis of MRONJ still remains unclear. Methods: We aimed to identify genetic variants associated with MRONJ, using whole-exome sequencing (WES). Ten MRONJ patients prescribed bisphosphonates were recruited for WES, and jawbone tissue and blood samples were collected from the patients. Results: The analysis of the WES data found a total of 1866 SNP and 40 InDel variants which are specific to MRONJ. The functional classification assay using Gene Ontology and pathway analysis discovered that genes bearing the MRONJ variants are significantly enriched for keratinization and calcium ion transport. Some of the variants are potential pathogenic variants (24 missense mutations and seven frameshift mutations) with MAF < 0.01. Conclusions: The variants are located in eight different genes (KRT18, MUC5AC, NBPF9, PABPC3, MST1L, ASPN, ATN1, and SLAIN1). Nine deleterious SNPs significantly associated with MRONJ were found in the KRT18 and PABPC3 genes. It suggests that KRT18 and PABPC3 could be MRONJ-related key genes.

Microarray analysis of lipopolysaccharide-induced endotoxemia in the cochlea.

Lipopolysaccharide (LPS)-induced endotoxemia alters intracochlear homeostasis and potentiates aminoglycoside-induced ototoxicity. However, the pathological mechanisms in the cochlea following systemic LPS-induced inflammation are unclear. In this study, three groups of mice received intraperitoneal injections [group A, saline control (n = 10); group B, 1 mg/kg LPS (n = 10); group C, 10 mg/kg LPS (n = 10)]. After 24 h, gene expression in cochlea samples was analyzed using DNA microarrays covering 28,853 genes in a duplicate manner. A total of 505 differentially expressed genes (DEGs) (≥2.0-fold change; p < 0.05) were identified. Interferon- and chemotaxis-related genes, including gbp2, gbp5, cxcl10, and Rnf125, were dose-dependently upregulated by LPS-induced endotoxemia. These results were verified by RT-qPCR. Upregulated DEGs were associated with inflammation, positive regulation of immune responses, and regulation of cell adhesion, while downregulated ones were associated with chemical synaptic transmission and the synaptic vesicle cycle. Protein-protein interaction included four functional clusters associated with interleukin-4, -10, and -13 and G protein-coupled receptor (GPCR) ligand binding; activation of matrix metalloproteinases and collagen degradation; recruitment of amyloid A proteins; and neutrophil degranulation. The findings of this study provide an additional basis on changes in the expression of genes in the cochlea in response to LPS-induced endotoxemia.

Whole-exome sequencing reveals rare genetic variations in ovarian granulosa cell tumor.

Ovarian granulosa cell tumor (OGCT) is a rare ovarian tumor that accounts for about 2-5% of all ovarian tumors. Despite the low grade of ovarian tumors, high and late recurrences are common in OGCT patients. Even though this tumor usually occurs in adult women with high estrogen levels, the cause of OGCT is still unknown. To screen genetic variants associated with OGCT, we collected normal and matched-tumor formalin-fixed paraffin-embedded (FFPE) from 11 OGCT patients and performed whole-exome sequencing (WES) using Illumina NovaSeq 6000. A total of 1,067,219 single nucleotide polymorphisms (SNPs) and 162,155 insertions/deletions (indels) were identified from 11 pairs of samples. Of these, we identified 44 tumor-specific SNPs in 22 genes and four tumor-specific indels in one gene that were common to 11 patients. We used three cancer databases (TCGA, COSMIC, and ICGC) to investigate genes associated with ovarian cancers. Nine genes (SEC22B, FEZ2, ANKRD36B, GYPA, MUC3A, PRSS3, NUTM2A, OR8U1, and KRTAP10-6) associated with ovarian cancers were found in all three databases. In addition, we identified seven rare variants with MAF ≤ 0.05 in two genes (PRSS3 and MUC3A). Of seven rare variants, five variants in MUC3A are potentially pathogenic. Furthermore, we conducted gene enrichment analysis of tumor-specific 417 genes in SNPs and 106 genes in indels using cytoscape and metascape. In GO analysis, these genes were highly enriched in "selective autophagy", and "regulation of anoikis". Taken together, we suggest that MUC3A is implicated in OGCT development, and MUC3A could be used as a potential biomarker for OGCT diagnosis.

A comprehensive analysis of gorilla-specific LINE-1 retrotransposons.

BACKGROUND: Long interspersed element-1 (LINE-1 or L1) is the most abundant retrotransposons in the primate genome. They have approximately 520,000 copies and make up ~ 17% of the primate genome. Full-length L1s can mobilize to a new genomic location using their enzymatic machinery. Gorilla is the second closest species to humans after the chimpanzee, and human-gorilla split 7-12 million years ago. The gorilla genome provides an opportunity to explore primate origins and evolution. OBJECTIVE: L1s have contributed to genome diversity and variations during primate evolution. This study aimed to identify gorilla-specific L1s using a more recent version of the gorilla reference genome (Mar. 2016 GSMRT3/gorGor5). METHODS: We collected gorilla-specific L1 candidates through computational analysis and manual inspection. L1Xplorer was used to identify whether full-length gorilla-specific L1s were intact. In addition, to determine the level of sequence conservation between intact fulllength gorilla-specific L1s, two ORFs of intact L1s were aligned with the L1PA2 consensus sequence. RESULTS: 2002 gorilla-specific L1 candidates were identified through computational analysis. Among them, we manually inspected 1,883 gorilla-specific L1s, among which most of them belong to the L1PA2 subfamily and 12 were intact L1s that could influence genomic variations in the gorilla genome. Interestingly, the 12 intact full-length gorilla-specific L1s have 14 highly conserved nonsynonymous mutations, including 6 mutations and 8 mutations in ORF1 and ORF2, respectively. In comparison to the intact full-length chimpanzee-specific L1s and human-specific hot-L1s, two of these in ORF1 (L256F and E293G) were shown as gorilla-specific nonsynonymous mutations. CONCLUSION: The gorilla-specific L1s may have had significantly affected the gorilla genome to compose a genome different form that of other primates during primate evolution.

Investigation of high correlation with carcass traits of SNPs of the PLCB1, C/EBPα, and TDRKH genes and the combinations of SNPs using the MDR method in the Hanwoo.

BACKGROUND: Recently, many researchers focus on the best way to produce high-quality meat, as the trend in food consumption today is to focus on quality. In general, consumers' preferences in beef differ depending on taste and meatiness. Therefore, researchers are interested in how the marbling score affects the flavors of meat or the various factors that make up the meatiness to captivate the consumers' tastes. OBJECTIVE: This study identifies single nucleotide polymorphisms (SNPs) or gene combinations that affect the carcass traits of Korean cattle (Hanwoo) by using the multifactor dimensionality reduction (MDR) method. METHODS: We collected the candidate SNPs to identify SNPs related to marbling scores from whole-exome sequencing and bovine SNP genotyping data. Using 96 Hanwoo samples, we performed PCR amplification to investigate the polymorphism status. In addition, we investigated genetic relationships between carcass traits and SNPs using 612 Hanwoo samples. Furthermore, each candidate SNP genotype and the combinations of SNP genotypes were verified to improve the accuracy of genetic relationships using MDR method. RESULTS: Twenty-four candidate SNPs associated with carcass trait and marbling scores were identified from SNP genotyping and whole-exome sequencing. Among them, three SNP markers (c.459 T > C of the PLCB1 gene, c.271 A > C of the C/EBPα gene, and g.17257 A > G of the TDRKH gene) were showed statistically significant differences between intramuscular fat and genotypes. Especially, two candidate SNPs, including c.459 T > C located in the PLCB1 gene and c.271 A > C located in the C/EBPα gene, could be highly associated with the intramuscular fat of Hanwoo quality grade. In addition, the combination of SNP genotypes is showed higher significant differences with carcass weight, backfat thickness, and longissimus dorsi muscle area. CONCLUSION: Three SNP genotypes and the combination of SNP genotypes in the PLCB1, C/EBPα, and TDRKH genes may be useful genetic markers for improving beef quality.

The Strength and Delamination of Graphene/Cu Composites with Different Cu Thicknesses.

This study analyzed the mechanical and fracture behavior of graphene/copper (Cu) composites with different Cu thicknesses by using molecular dynamics (MD) and representative volume element (RVE) analysis. Three graphene/Cu composite analytical models were classified as 4.8, 9.8, and 14.3 nm according to Cu thicknesses. Using MD analysis, zigzag-, armchair-, and z (thickness)-direction tensile analyses were performed for each model to analyze the effect of Cu thickness variation on graphene/Cu composite strength and delamination fracture. In the RVE analysis, the mechanical characteristics of the interface between graphene and Cu were evaluated by setting the volume fraction to 1.39, 2.04, and 4.16% of the graphene/Cu composite model, classified according to the Cu thickness. From their obtained results, whether the graphene bond is maintained has the greatest effect on the strength of graphene/Cu composites, regardless of the Cu thickness. Additionally, graphene/Cu composites are more vulnerable to armchair direction tensile forces with fracture strengths of 14.7, 8.9, and 8.2 GPa depending on the Cu thickness. The results of this study will contribute to the development of guidelines and performance evaluation standards for graphene/Cu composites.

A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome.

Advances in next-generation sequencing (NGS) technology have made personal genome sequencing possible, and indeed, many individual human genomes have now been sequenced. Comparisons of these individual genomes have revealed substantial genomic differences between human populations as well as between individuals from closely related ethnic groups. Transposable elements (TEs) are known to be one of the major sources of these variations and act through various mechanisms, including de novo insertion, insertion-mediated deletion, and TE-TE recombination-mediated deletion. In this study, we carried out de novo whole-genome sequencing of one Korean individual (KPGP9) via multiple insert-size libraries. The de novo whole-genome assembly resulted in 31,305 scaffolds with a scaffold N50 size of 13.23 Mb. Furthermore, through computational data analysis and experimental verification, we revealed that 182 TE-associated structural variation (TASV) insertions and 89 TASV deletions contributed 64,232 bp in sequence gain and 82,772 bp in sequence loss, respectively, in the KPGP9 genome relative to the hg19 reference genome. We also verified structural differences associated with TASVs by comparative analysis with TASVs in recent genomes (AK1 and TCGA genomes) and reported their details. Here, we constructed a new Korean de novo whole-genome assembly and provide the first study, to our knowledge, focused on the identification of TASVs in an individual Korean genome. Our findings again highlight the role of TEs as a major driver of structural variations in human individual genomes.

A comprehensive analysis of chimpanzee (Pan Troglodytes)-specific AluYb8 element.

BACKGROUND: Alu elements are most abundant retrotransposons with > 1.2 million copies in the primate genome. AluYb8 subfamily was diverged from AluY lineage, and has accumulated eight diagnostic mutations and 7-bp duplication during primate evolution. A total of 1851 AluYb copies are present in the human genome, and most of them are human-specific. On the other hand, only a few AluYb8 copies were identified in the chimpanzee genome by previous studies on AluYb8. The significantly different number of species-specific AluYb8 elements between human and chimpanzee might result from the incompletion of chimpanzee reference genome sequences at the time of the previous study. OBJECTIVE: AluYb8 elements could generate genomic structural variations in the chimpanzee genome. This study aimed to identify and characterize chimpanzee-specific AluYb elements using the most updated chimpanzee reference genome sequences (Jan. 2018, panTro6). METHODS: To identify chimpanzee-specific AluYb8, we carried out genomic comparison with non-chimpanzee primate genome using the UCSC table browser. In addition, chimpanzee-specific AluYb8 candidates were manually inspected and experimentally verified using PCR and Sanger sequencing. RESULTS: Among a total of 231 chimpanzee-specific AluYb8 candidates, 11 of the candidates are chimpanzee-specific AluYb8, and 29 elements are shared between the chimpanzee and non-chimpanzee primate genomes. Through the sequence analysis of AluYb8 and other Alu subfamilies, we were able to observe various diagnostic mutations and variable length duplications in 7-bp duplication region of AluYb8 element. In addition, we further validated two of the chimpanzee-specific AluYb8 elements (CS8 and CS20) that were not previously discovered by display PCR and Sanger sequencing. Interestingly, we identified a AluYb8 insertion-mediated deletion (CS8 locus) in the chimpanzee genome. CONCLUSION: Our study found that AluYb8 elements are much more abundant in the human genome than chimpanzee genome, and that it could be due to the absence of hyperactive "master" AluYb8 elements in the chimpanzee genome.

Synthetic Approaches for Poly(Phenylene) Block Copolymers via Nickel Coupling Reaction for Fuel Cell Applications.

Several methods to synthesize poly(phenylene) block copolymers through the nickel coupling reaction were attempted to reduce the use of expensive nickel catalysts in polymerization. The model reaction for poly(phenylene) having different types of dichlorobenzene derivative monomers illustrated the potential use of cost-effective catalysts, such as NiBr2 and NiCl2, as alternatives to more expensive catalysts (e.g., bis(1,5-cyclooctadiene)nickel(0) (Ni(COD)2)). By catalyzing the polymerization of multi-block poly(phenylene) with NiBr2 and NiCl2, random copolymers with similar molecular weights could be prepared. However, these catalysts did not result in a high-molecular-weight polymer, limiting their wide scale application. Further, the amount of Ni(COD)2 could be reduced in this study by approximately 50% to synthesize poly(phenylene) multi-block copolymers, representing significant cost savings. Gel permeation chromatography and nuclear magnetic resonance results showed that the degree of polymerization and ion exchange capacity of the copolymers were almost the same as those achieved through conventional polymerization using 2.5 times as much Ni(COD)2. The flexible quaternized membrane showed higher chloride ion conductivity than commercial Fumatech membranes with comparable water uptake and promising chemical stability.

Differential expressions of L1-chimeric transcripts in normal and matched-cancer tissues.

L1s are a cis-regulatory elements and contain bidirectional internal promoters within the 5' untranslated region (UTR). L1s provide bidirectional promoters that generate alternative transcripts and affect differential expressions in the human genome. In particular, L1 antisense promoters (L1ASPs) could produce aberrant transcripts in cancer tissues compared to normal tissues. In this study, we identified the L1-chimeric transcripts derived from L1ASPs and analyzed relative expression of L1-chimeric transcripts between normal and matched-cancer tissues. First, we collected 425 L1-chimeric transcripts by referring to previous studies. Through the manual inspection, we identified 144 L1-chimeric transcripts derived from 44 L1 antisense promoters, suggesting that the antisense promoter acted as an alternative promoter. We analyzed relative gene expression levels of 16 L1-chimeric transcripts between matched cancer-normal tissue pair (lung, liver, gastric, kidney, thyroid, breast, ovary, uterus, and prostate) using real-time quantitative PCR (RT-qPCR) and investigated putative transcription factor binding motifs to determine activity of L1ASPs. Taken together, we propose that L1ASPs could contribute to the differential gene expression between normal and cancer tissues.

The nature of triple-negative breast cancer classification and antitumoral strategies.

Identifying the patterns of gene expression in breast cancers is essential to understanding their pathophysiology and developing anticancer drugs. Breast cancer is a heterogeneous disease with different subtypes determined by distinct biological features. Luminal breast cancer is characterized by a relatively high expression of estrogen receptor (ER) and progesterone receptor (PR) genes, which are expressed in breast luminal cells. In ~25% of invasive breast cancers, human epidermal growth factor receptor 2 (HER2) is overexpressed; these cancers are categorized as the HER2 type. Triple-negative breast cancer (TNBC), in which the cancer cells do not express ER/PR or HER2, shows highly aggressive clinical outcomes. TNBC can be further classified into specific subtypes according to genomic mutations and cancer immunogenicity. Herein, we discuss the brief history of TNBC classification and its implications for promising treatments.

Identification and characterization of saikosaponins as antagonists of transient receptor potential A1 channel.

Neuropathic pain is associated with an increased sensitivity to painful stimuli or abnormal sensitivity to otherwise innocuous stimuli. However, in addition to adverse effects, currently available drugs have shown limited response in patients with neuropathic pain, which provides a rationale to explore new drug classes acting on novel targets and with better efficacy and safety profiles. Here, we found that saikosaponins potently inhibit agonist-induced activation of the transient receptor potential A1 (TRPA1) channel, which has been reported to mediate neuropathic pain by sensing a variety of chemical irritants. Molecular docking and site-directed mutagenesis analyses suggested that saikosaponins bind to the hydrophobic pocket in TRPA1 near the Asn855 residue, which, when mutated to Ser, was previously associated with enhanced pain perception in humans. In support of these findings, saikosaponin D significantly attenuated agonist-induced nociceptive responses and vincristine-induced mechanical hypersensitivity in mice. These results indicate that saikosaponins are TRPA1 antagonists and provide a basis for further elaboration of saikosaponin derivatives for the development of new therapeutics for neuropathic pain.

Transposable element-mediated structural variation analysis in dog breeds using whole-genome sequencing.

Naturally occurring diseases in dogs provide an important animal model for studying human disease including cancer, heart disease, and autoimmune disorders. Transposable elements (TEs) make up ~ 31% of the dog (Canis lupus familiaris) genome and are one of main drivers to cause genomic variations and alter gene expression patterns of the host genes, which could result in genetic diseases. To detect structural variations (SVs), we conducted whole-genome sequencing of three different breeds, including Maltese, Poodle, and Yorkshire Terrier. Genomic SVs were detected and visualized using BreakDancer program. We identified a total of 2328 deletion SV events in the three breeds compared with the dog reference genome of Boxer. The majority of the genetic variants were found to be TE insertion polymorphism (1229) and the others were TE-mediated deletion (489), non-TE-mediated deletion (542), simple repeat-mediated deletion (32), and other indel (36). Among the TE insertion polymorphism, 286 elements were full-length LINE-1s (L1s). In addition, the 49 SV candidates located in the genic regions were experimentally verified and their polymorphic rates within each breed were examined using PCR assay. Polymorphism analysis of the genomic variants revealed that some of the variants exist polymorphic in the three dog breeds, suggesting that their SV events recently occurred in the dog genome. The findings suggest that TEs have contributed to the genomic variations among the three dog breeds of Maltese, Poodle, and Yorkshire Terrier. In addition, the polymorphic events between the dog breeds indicate that TEs were recently retrotransposed in the dog genome.

Comparison of library construction kits for mRNA sequencing in the Illumina platform.

BACKGROUND: The emergence of next-generation sequencing (NGS) technologies has made a tremendous contribution to the deciphering and significance of transcriptome analysis in biological fields. Since the advent of NGS technology in 2007, Illumina, Inc. has provided one of the most widely used sequencing platforms for NGS analysis. OBJECTIVE: Although reagents and protocols provided by Illumina are adequately performed in transcriptome sequencing, recently, alternative reagents and protocols which are relatively cost effective are accessible. However, the kits derived from various manufacturers have advantages and disadvantages when researchers carry out the transcriptome library construction. METHODS: We compared them using a variety of protocols to produce Illumina-compatible libraries based on transcriptome. Three different mRNA sequencing kits were selected for this study: TruSeq® RNA Sample Preparation V2 (Illumina, Inc., USA), Universal Plus mRNA-Seq (NuGEN, Ltd., UK), and NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England BioLabs, Ltd., USA). We compared them focusing on cost, experimental time, and data output. RESULTS: The quality and quantity of sequencing data obtained through the NGS technique were strongly influenced by the type of the sequencing library kits. It suggests that for transcriptome studies, researchers should select a suitable library construction kit according to the goal and resources of experiments. CONCLUSION: The present work will help researchers to choose the right sequencing library construction kit for transcriptome analyses.

A comprehensive analysis of the Baboon-specific full-length LINE-1 retrotransposons.

BACKGROUND: Long interspersed elements-1 (LINE-1s or L1s) and Alu elements are most successful retrotransposons that have generated genetic diversity and genomic fluidity in the primate genome. They account for ~ 27.7% of the primate genome. Interestingly, a previous study has shown that the retrotransposition rate of Alu elements is nine times higher in baboons than in humans. OBJECTIVE: The expansion of Alu copies could be dependent on the activity of L1-encoded proteins. Thus, we aimed to investigate full-length baboon-specific L1s and characterize structurally and functionally intact baboon-specific L1s (ORF1p/ORF2p and ORF2p only) that could induce trans-mobilization of Alu elements in the baboon genome. RESULTS: A total of 673 baboon-specific L1 candidates (> 4 kb) were identified through the comparative genomic analysis. Applying the baboon-specific correction value obtained from the experimental validation, it demonstrated that approximately 446 baboon-specific L1s (> 4 kb) were present in the baboon reference genome (papAnu2). In addition, we observed phylogenetic relationship of the baboon-specific L1s through the neighbor-joining method and they diverged from the L1PA6 consensus sequence. Finally, we identified 36 full-length baboon-specific L1s that were intact both ORF1p and ORF2p. CONCLUSION: The number of baboon-specific full-length L1s is fewer than the number of human-specific full-length L1s. Therefore, there is possibility that the "L1 master gene" or "L1 source gene" is more abundant in the baboon genome, or that in trans retrotransposition activity of baboon-specific L1s is relatively stronger than in the other genomes.

Application of the fragment molecular orbital method to discover novel natural products for prion disease.

Conformational conversion of the normal cellular isoform of the prion protein PrPC into an infectious isoform PrPSc causes pathogenesis in prion diseases. To date, numerous antiprion compounds have been developed to block this conversion and to detect the molecular mechanisms of prion inhibition using several computational studies. Thus far, no suitable drug has been identified for clinical use. For these reasons, more accurate and predictive approaches to identify novel compounds with antiprion effects are required. Here, we have applied an in silico approach that integrates our previously described pharmacophore model and fragment molecular orbital (FMO) calculations, enabling the ab initio calculation of protein-ligand complexes. The FMO-based virtual screening suggested that two natural products with antiprion activity exhibited good binding interactions, with hotspot residues within the PrPC binding site, and effectively reduced PrPSc levels in a standard scrapie cell assay. Overall, the outcome of this study will be used as a promising strategy to discover antiprion compounds. Furthermore, the SAR-by-FMO approach can provide extremely powerful tools in quickly establishing virtual SAR to prioritise compounds for synthesis in further studies.