• 한국가금학회지
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• 제46권4호
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• pp.287-296
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• 2019

Avian sex determination system involves the male ZZ and female ZW chromosomes. However, very few studies are reported the expression, functional role and importance of genes on the W chromosome because of its small and highly heterochromatic genomic regions. Recent studies demonstrated that the W chromosome may have critical roles in physiology, sex determination and subsequent sexual differentiation in chickens. Therefore, gene annotation, including describing the expression and function of genes in the chicken W chromosome, is needed. In this study, we have searched the W chromosome of chickens and selected a total of 36 genes to evaluated their specific expression in the testis and ovary at various developmental stages such as embryonic day 6 (E6), hatch and adult. Interestingly, out of 36 genes in chicken W chromosome, we have found seven female-specific expression at E6.5 day, indicating that they are functionally related to female chicken gonadal differentiation. In addition, we have identified the stage specific gene expression from the sex specific genes. Furthermore, we analyzed the relative location of genes in the chicken W chromosome. Collectively, these results will contribute molecular insights into the sexual determination, differentiation and female development based on the W chromosome.

• Molecular & Cellular Toxicology
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• 제3권3호
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• pp.208-213
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• 2007

With the help of a development and popularization of microarray technology that enable to us to simultaneously investigate the expression pattern of thousands of genes, the toxicogenomics experimenters can interpret the genome-scale interaction between genes exposed in toxicant or toxicant-related environment. The ultimate and primary goal of toxicogenomics identifies functional context among the group of genes that are differentially or similarly coexpressed under the specific toxic substance. On the other side, public reference databases with transcriptom, proteom, and biological pathway information are needed for the analysis of these complex omics data. However, due to the heterogeneous and independent nature of these databases, it is hard to individually analyze a large omics annotations and their pathway information. Fortunately, several web sites of the public database provide information linked to other. Nevertheless it involves not only approriate information but also unnecessary information to users. Therefore, the systematically integrated database that is suitable to a demand of experimenters is needed. For these reasons, we propose SOP (Search of Omics Pathway) database system which is constructed as the integrated biological database converting heterogeneous feature of public databases into combined feature. In addition, SOP offers user-friendly web interfaces which enable users to submit gene queries for biological interpretation of gene lists derived from omics experiments. Outputs of SOP web interface are supported as the omics annotation table and the visualized pathway maps of KEGG PATHWAY database. We believe that SOP will appear as a helpful tool to perform biological interpretation of genes or proteins traced to omics experiments, lead to new discoveries from their pathway analysis, and design new hypothesis for a next toxicogenomics experiments.

• Asian Pacific Journal of Cancer Prevention
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• 제16권13호
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• pp.5445-5451
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• 2015

Fascin-1 (FSCN1) is an actin-bundling protein that induces cell membrane protrusions, increases cell motility, and is overexpressed in various human epithelial cancers, including esophageal squamous cell carcinoma (ESCC). We analyzed various protein-protein interactions (PPI) of differentially-expressed genes (DEGs), in fascin knockdown ESCC cells, to explore the role of fascin overexpression. The node-degree distributions indicated these PPI sub-networks to be characterized as scale-free. Subcellular localization analysis revealed DEGs to interact with other proteins directly or indirectly, distributed in multiple layers of extracellular membrane-cytoskeleton/ cytoplasm-nucleus. The functional annotation map revealed hundreds of significant gene ontology (GO) terms, especially those associated with cytoskeleton organization of FSCN1. The Random Walk with Restart algorithm was applied to identify the prioritizations of these DEGs when considering their relationship with FSCN1. These analyses based on PPI network have greatly expanded our comprehension of the mRNA expression profile following fascin knockdown to future examine the roles and mechanisms of fascin action.

• Asian Pacific Journal of Cancer Prevention
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• 제15권24호
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• pp.10797-10801
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• 2015

Background: To explore the molecular mechanisms of metastatic osteosarcoma (OS) by using the microarray expression profiles of metastatic and non-metastatic OS samples. Materials and Methods: The gene expression profile GSE37552 was downloaded from Gene Expression Omnibus database, including 2 human metastatic OS cell line models and 2 two non-metastatic OS cell line models. The differentially expressed genes (DEGs) were identified by Multtest package in R language. In addition, functional enrichment analysis of the DEGs was performed by WebGestalt, and the protein-protein interaction (PPI) networks were constructed by Hitpredict, then the signal pathways of the genes involved in the networks were performed by Kyoto Encyclopaedia of Genes and Genomes (KEGG) automatic annotation server (KAAS). Results: A total of 237 genes were classified as DEGs in metastatic OS. The most significant up- and down-regulated genes were A2M (alpha-2-macroglobulin) and BCAN (brevican). The DEGs were significantly related to the response to hormone stimulus, and the PPI network of A2M contained IL1B (interleukin), LRP1 (low-density lipoprotein receptor-related protein 1) and PDGF (platelet-derived growth factor). Furthermore, the MAPK signaling pathway and focal adhesion were significantly enriched. Conclusions: A2M and its interactive proteins, such as IL1B, LRP1 and PDGF may be candidate target molecules to monitor, diagnose and treat metastatic OS. The response to hormone stimulus, MAPK signaling pathway and focal adhesion may play important roles in metastatic OS.

• ALGAE
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• 제35권2호
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• pp.177-187
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• 2020

Cyanobacteria have been widely reported to produce a variety of UV-absorbing mycosporine-like amino acids (MAAs). Herein, we reported production of the unusual MAA, mycosporine-glycine-alanine (MGA) in the cyanobacterium Sphaerospermopsis torques-reginae ITEP-024 using a newly developed UHPLC-DAD-MS/HRMS (ultra-high performance liquid chromatography-diode array detection-high resolution tandem mass spectrometry) method. MGA had previously been first identified in a red-algae, but S. torques-reginae strain ITEP-024 is the first cyanobacteria to be reported as an MGA producer. Herein, the chemical structure of MGA is fully elucidated from one-dimensional / two-dimensional nuclear magnetic resonance and HRMS data analyses. MAAs are unusually produced constitutively in S. torques-reginae ITEP-024, and this production was further enhanced following UV-irradiance. It has been proposed that MAA biosynthesis proceeds in cyanobacteria from the pentose phosphate pathway intermediate sedoheptulose 7-phosphate. Annotation of a gene cluster encoded in the genome sequence of S. torques-reginae ITEP-024 supports these gene products could catalyse the biosynthesis of MAAs. However, addition of glyphosate to cultures of S. torques-reginae ITEP-024 abolished constitutive and ultra-violet radiation induced production of MGA, shinorine and porphyra-334. This finding supports involvement of the shikimic acid pathway in the biosynthesis of MAAs by this species.

• The Plant Pathology Journal
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• 제33권4호
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• pp.362-369
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• 2017

White root rot disease, caused by the pathogen Rosellinia necatrix, is one of the world's most devastating plant fungal diseases and affects several commercially important species of fruit trees and crops. Recent global outbreaks of R. necatrix and advances in molecular techniques have both increased interest in this pathogen. However, the lack of information regarding the genomic structure and transcriptome of R. necatrix has been a barrier to the progress of functional genomic research and the control of this harmful pathogen. Here, we identified 10,616 novel full-length transcripts from the filamentous hyphal tissue of R. necatrix (KACC 40445 strain) using PacBio single-molecule sequencing technology. After annotation of the unigene sets, we selected 14 cell cycle-related genes, which are likely either positively or negatively involved in hyphal growth by cell cycle control. The expression of the selected genes was further compared between two strains that displayed different growth rates on nutritional media. Furthermore, we predicted pathogen-related effector genes and cell wall-degrading enzymes from the annotated gene sets. These results provide the most comprehensive transcriptomal resources for R. necatrix, and could facilitate functional genomics and further analyses of this important phytopathogen.

• Journal of Microbiology and Biotechnology
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• 제33권7호
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• pp.875-885
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• 2023

Volatile organic compounds such as benzene, toluene, ethylbenzene, and isomers of xylenes (BTEX) constitute a group of monoaromatic compounds that are found in petroleum and have been classified as priority pollutants. In this study, based on its newly sequenced genome, we reclassified the previously identified BTEX-degrading thermotolerant strain Ralstonia sp. PHS1 as Cupriavidus cauae PHS1. Also presented are the complete genome sequence of C. cauae PHS1, its annotation, species delineation, and a comparative analysis of the BTEX-degrading gene cluster. Moreover, we cloned and characterized the BTEX-degrading pathway genes in C. cauae PHS1, the BTEX-degrading gene cluster of which consists of two monooxygenases and meta-cleavage genes. A genome-wide investigation of the PHS1 coding sequence and the experimentally confirmed regioselectivity of the toluene monooxygenases and catechol 2,3-dioxygenase allowed us to reconstruct the BTEX degradation pathway. The degradation of BTEX begins with aromatic ring hydroxylation, followed by ring cleavage, and eventually enters the core carbon metabolism. The information provided here on the genome and BTEX-degrading pathway of the thermotolerant strain C. cauae PHS1 could be useful in constructing an efficient production host.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.28-28
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• 2022

This paper presents the first genome assemblies of Philippine mangoes that provide valuable reference for varietal improvement and genomic studies on mango and related fruit crops. WE sequenced whole genomes of3 species, Mangifera odorata (Huani), Mangifera altissima (Paho), and Mangifera indica 'Carabao' (Sweet Elena). 'Carabao' is the major export variety of the Philippines; Paho is identified as vulnerable by the IUCN Red List of Threatened Species; Huani has fruit sap acrid which is the primary defense mechanism against insects and birds. We used Falcon, a diploid aware -de novo assembler to assemble SMRT generated long-read sequences. Falcon-unzip was employed to phase the output assembly producing larger contig sets (primary contigs) and shorter contigs corresponding to haplotypes (haplotigs). Assembly statistics were generated by comparing the assembly to a reference genome, Tommy Atkins, using Quality Assessment Tool (QUAST). Moreover, the extent of duplication and completeness of gene content was measured using Benchmarking Universal Single-Copy Orthologs (BUSCO). Draft assemblies with high duplications were processed using Purge Haplotigs and Purge Dups to lessen duplications with minimal impact on genome completeness. De novo assemblies of Huani, Paho and 'Carabao' were then generated with primary contig sizes of 463.64 Mb, 508.95 Mb and 401.51 Mb respectively. These draft assemblies of Huani, Paho and 'Carabao' showed 96.90%, 95.17% and 99.07% complete BUSCOs respectively which is comparable to 'Tommy Atkins' genome (98.6%). Using two mango transcriptome data (pooled RNA-seq from different mango varieties and tissues), 91-96% or 24-30 million reads were successfully mapped back for each generated assembly indicating high degree of completeness. The results obtained demonstrated the highly contiguous, phased, and near complete genome assembly of three Philippine mango species for structural and functional annotation of gene units, especially those with economic importance.

• Journal of Plant Biotechnology
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• 제50권
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• pp.127-136
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• 2023

Water scarcity decreases the rate of photosynthesis and, consequently, the yield of banana plants (Musa spp). In this study, transcriptome analysis was performed to identify photosynthesis-related genes in banana plants and determine their expression profiles under water stress conditions. Banana plantlets were in vitro cultured on Murashige and Skoog agar medium with and without 10% polyethylene glycol and marked as BP10 and BK. Chlorophyll contents in the plant shoots were determined spectrophotometrically. Two cDNA libraries generated from BK and BP10 plantlets, respectively, were used as the reference for transcriptome data. Gene ontology (GO) enrichment analysis was performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) and visualized using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway prediction. Morphological observations indicated that water deficiency caused chlorosis and reduced the shoot chlorophyll content of banana plantlets. GO enrichment identified 52 photosynthesis-related genes that were affected by water stress. KEGG visualization revealed the pathways related to the 52 photosynthesisr-elated genes and their allocations in four GO terms. Four, 12, 15, and 21 genes were related to chlorophyll biosynthesis, the Calvin cycle, the photosynthetic electron transfer chain, and the light-harvesting complex, respectively. Differentially expressed gene (DEG) analysis using DESeq revealed that 45 genes were down-regulated, whereas seven genes were up-regulated. Four of the down-regulated genes were responsible for chlorophyll biosynthesis and appeared to cause the decrease in the banana leaf chlorophyll content. Among the annotated DEGs, MaPNDO, MaPSAL, and MaFEDA were selected and validated using quantitative real-time PCR.

• Journal of Animal Science and Technology
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• 제66권3호
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• pp.567-576
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• 2024

Subclinical ketosis (SCK) is a prevalent metabolic disorder that occurs during the transition to lactation period. It is defined as a high blood concentration of ketone bodies (beta-hydroxybutyric acid f ≥ 1.2 mmol/L) within the first few weeks of lactation, and often presents without clinical signs. SCK is mainly caused by negative energy balance (NEB). The objective of this study is to identify single nucleotide polymorphisms (SNPs) associated with SCK using genome-wide association studies (GWAS), and to predict the biological functions of proximal genes using gene-set enrichment analysis (GSEA). Blood samples were collected from 112 Holstein cows between 5 and 18 days postpartum to determine the incidence of SCK. Genomic DNA extracted from both SCK and healthy cows was examined using the Illumina Bovine SNP50K BeadChip for genotyping. GWAS revealed 194 putative SNPs and 163 genes associated with those SNPs. Additionally, GSEA showed that the genes retrieved by Database for Annotation, Visualization, and Integrated Discovery (DAVID) belonged to calcium signaling, starch and sucrose, immune network, and metabolic pathways. Furthermore, the proximal genes were found to be related to germ cell and early embryo development. In summary, this study proposes several feasible SNPs and genes associated with SCK through GWAS and GSEA. These candidates can be utilized in selective breeding programs to reduce the genetic risk for SCK and subfertility in high-performance dairy cows.