• Parasites, Hosts and Diseases
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• v.52 no.1
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• pp.21-26
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• 2014

Dirofilaria immitis (heartworm) infections affect domestic dogs, cats, and various wild mammals with increasing incidence in temperate and tropical areas. More sensitive antibody detection methodologies are required to diagnose asymptomatic dirofilariasis with low worm burdens. Applying current transcriptomic technologies would be useful to discover potential diagnostic markers for D. immitis infection. A filarial homologue of the mammalian translationally controlled tumor protein (TCTP) was initially identified by screening the assembled transcriptome of D. immitis (DiTCTP). A BLAST analysis suggested that the DiTCTP gene shared the highest similarity with TCTP from Loa loa at protein level (97%). A histidine-tagged recombinant DiTCTP protein (rDiTCTP) of 40 kDa expressed in Escherichia coli BL21 (DE3) showed immunoreactivity with serum from a dog experimentally infected with heartworms. Localization studies illustrated the ubiquitous presence of rDiTCTP protein in the lateral hypodermal chords, dorsal hypodermal chord, muscle, intestine, and uterus in female adult worms. Further studies on D. immitis-derived TCTP are warranted to assess whether this filarial protein could be used for a diagnostic purpose.

• Korean Journal of Poultry Science
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• v.47 no.1
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• pp.9-19
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• 2020

Avian influenza (AI) viruses are highly contagious viruses that infect many bird species and are zoonotic. Ducks are resistant to the deadly and highly pathogenic avian influenza virus (HPAIV) and remain asymptomatic to the low pathogenic avian influenza virus (LPAIV). In this study, we identified common differentially expressed genes (DEGs) after a reanalysis of previous transcriptomic data for the HPAIV and LPAIV infected duck lung cells. Microarray datasets from a previous study were reanalyzed to identify common target genes from DEGs and their biological functions. A total of 731 and 439 DEGs were identified in HPAIV- and LPAIV-infected duck lung cells, respectively. Of these, 227 genes were common to cells infected with both viruses, in which 193 genes were upregulated and 34 genes were downregulated. Functional annotation of common DEGs revealed that translation related gene ontology (GO) terms were enriched, including ribosome, protein metabolism, and gene expression. REACTOME analyses also identified pathways for protein and RNA metabolism as well as for tissue repair, including collagen biosynthesis and modification, suggesting that AIVs may evade the host defense system by suppressing host translation machinery or may be suppressed before being exported to the cytosol for translation. AIV infection also increased collagen synthesis, showing that tissue lesions by virus infection may be mediated by this pathway. Further studies should focus on these genes to clarify their roles in AIV pathogenesis and their possible use in AIV therapeutics.

• Animal Bioscience
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• v.34 no.8
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• pp.1290-1302
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• 2021

Objective: Follicle selection is an important process in chicken egg laying. Among several small yellow (SY) follicles, the one exhibiting the highest expression of follicle stimulation hormone receptor (FSHR) will be selected to become a hierarchal follicle. The role of lncRNA, miRNA and other non-coding RNA in chicken follicle selection is unclear. Methods: In this study, the whole transcriptome sequencing of SY follicles with different expression levels of FSHR in Jining Bairi hens was performed, and the expression of 30 randomly selected mRNAs, lncRNAs and miRNAs was validated by quantitative real-time polymerase chain reaction. Preliminary studies and bioinformatics analysis were performed on the selected mRNA, lncRNA, miRNA and their target genes. The effect of identified gene was examined in the granulosa cells of chicken follicles. Results: Integrated transcriptomic analysis on chicken SY follicles differing in FSHR expression revealed 467 differentially expressed mRNA genes, 134 differentially expressed lncRNA genes and 34 differentially expressed miRNA genes, and sosondowah ankyrin repeat domain family member A (SOWAHA) was the common target gene of three miRNAs and one lncRNA. SOWAHA was mainly expressed in small white (SW) and SY follicles and was affected by follicle stimulation hormone (FSH) treatment in the granulosa cells. Knockdown of SOWAHA inhibited the expression of Wnt family member 4 (Wnt4) and steroidogenic acute regulatory protein (StAR) in the granulosa cells of prehierarchal follicles, while stimulated Wnt4 in hierarchal follicles. Overexpression of SOWAHA increased the expression of Wnt4 in the granulosa cells of prehierarchal follicles, decreased that of StAR and cytochrome P450 family 11 subfamily A member 1 in the granulosa cells of hierarchal follicles and inhibited the proliferation of granulosa cells. Conclusion: Integrated analysis of chicken SY follicle transcriptomes identified SOWAHA as a network gene that is affected by FSH in granulosa cells of ovarian follicles. SOWAHA affected the expression of genes involved in chicken follicle selection and inhibited the proliferation of granulosa cells, suggesting an inhibitory role in chicken follicle selection.

• Journal of Animal Science and Technology
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• v.64 no.4
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• pp.800-811
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• 2022

The integration of metabolomics and transcriptomics may elucidate the correlation between the genotypic and phenotypic patterns in organisms. In equine physiology, various metabolite levels vary during exercise, which may be correlated with a modified gene expression pattern of related genes. Integrated metabolomic and transcriptomic studies in horses have not been conducted to date. The objective of this study was to detect the effect of moderate exercise on the metabolomic and transcriptomic levels in horses. In this study, using nuclear magnetic resonance (NMR) spectroscopy, we analyzed the concentrations of metabolites in muscle and plasma; we also determined the gene expression patterns of branched chain (alpha) keto acid dehydrogenase kinase complex (BCKDK), which encodes the key regulatory enzymes in branched-chain amino acid (BCAA) catabolism, in two breeds of horses, Thoroughbred and Jeju, at different time intervals. The concentrations of metabolites in muscle and plasma were measured by ¹H NMR (nuclear magnetic resonance) spectroscopy, and the relative metabolite levels before and after exercise in the two samples were compared. Subsequently, multivariate data analysis based on the metabolic profiles was performed using orthogonal partial least square discriminant analysis (OPLS-DA), and variable important plots and t-test were used for basic statistical analysis. The stress-induced expression patterns of BCKDK genes in horse muscle-derived cells were examined using quantitative reverse transcription polymerase chain reaction (qPCR) to gain insight into the role of transcript in response to exercise stress. In this study, we found higher concentrations of aspartate, leucine, isoleucine, and lysine in the skeletal muscle of Jeju horses than in Thoroughbred horses. In plasma, compared with Jeju horses, Thoroughbred horses had higher levels of alanine and methionine before exercise; whereas post-exercise, lysine levels were increased. Gene expression analysis revealed a decreased expression level of BCKDK in the post-exercise period in Thoroughbred horses.

• Korean Journal of Environmental Biology
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• v.27 no.4
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• pp.391-396
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• 2009

The biological effects of carcinogenic polycyclic aromatic hydrocarbons (cPAHs) including benzo[a]pyrene (BaP), dibenzo[a,h]anthracene (DBA), benzo[a]anthracene (BaA), benzo[b] fluoranthene (BbF), benzo[k]fluoranthene (BkF), and indeno[1,2,3-c, d]pyrene (InP) on transcriptomic changes were determined in the liver of Oryzias latipes. Differentially expressed genes (DEGs) by binary exposure to cPAHs (BaP+BaA, BaP+BbF, BaP+BkF, BaP+DbA, BaP+InP) were screened by annealing control primers-based polymerase chain reaction followed by sequence analysis and BLAST searching. The results showed that four DEGs were commonly expressed by cPAHs and they were identified as ribosomal protein S4, coagulation factor II, elongation factor 1 beta, and a predicted protein similar to human immunodeficiency virus type I enhancer binding protein 3. This finding suggests that binary exposure to cPAHs interferes protein synthesis required for fundamental liver functions in fish.

• The Plant Pathology Journal
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• v.30 no.4
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• pp.425-431
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• 2014

Leaf scald caused by the infection of Rhynchosporium secalis, is a worldwide crop disease resulting in significant loss of barley yield. In this study, a systematic sequencing of expressed sequence tags (ESTs) was chosen to obtain a global picture of the assembly of genes involved in pathogenesis. To identify a large number of plant ESTs, which are induced at different time points, an amplified fragment length polymorphism (AFLP) display of complementary DNA (cDNA) was utilized. Transcriptional changes of 140 ESTs were observed, of which 19 have no previously described function. Functional annotation of the transcripts revealed a variety of infection-induced host genes encoding classical pathogenesis-related (PR) or genes that play a role in the signal transduction pathway. The expression analyses by a semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) revealed that Rar1 and Rpg4 are defense inducible genes, and were consistent with the cDNA-AFLP data in their expression patterns. Hence, the here presented transcriptomic approach provides novel global catalogue of genes not currently represented in the EST databases.

• Journal of Soil and Groundwater Environment
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• v.21 no.5
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• pp.16-24
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• 2016

A new strain of Pseudomonas sp. was isolated from mercury (Hg)-contaminated sites in Taiwan. This bacterium removed more than 80% of Hg present in the culture medium at 12 h incubation and was chosen for further analysis of the molecular mechanisms of Hg tolerance/removal abilities in this Pseudomonas sp. We used RNA-seq, one of the next-generation sequencing methods, to investigate the transcriptomic responses of the Pseudomonas sp. exposed to 60 mg/L of Hg²⁺. We de novo assembled 4,963 contigs, of which 10,533 up-regulated genes and 5,451 down-regulated genes were found to be regulated by Hg. The 40 genes most altered in expression levels were associated with tolerance to Hg stress and metabolism. Functional analysis showed that some Hg-tolerant genes were related to the mer operon, sulfate uptake and assimilation, the enzymatic antioxidant system, the HSP gene family, chaperones, and metal transporters. The transcriptome were analyzed further with Gene Ontology (GO) and Cluster of Orthologous Groups (COGs) of proteins and showed diverse biological functions and metabolic pathways under Hg stress.

• Journal of the Korean Wood Science and Technology
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• v.46 no.6
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• pp.670-680
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• 2018

Acanthophysium sp. KMF001, a wood rotting fungus, produces a strong crude enzyme complex that efficiently produces simple sugars from wood. The transcriptomic analysis of Acanthophysium sp. KMF001 identified 14 genes for putative glycoside hydrolases. Among them, isotig01043 was expressed heterogeneously in Escherichia coli BL21(DE3), and the expressed protein exhibited an endo-${\beta}$-1,4-xylanase activity which showed the optimum reaction at pH 5.0 and $30^{\circ}C$. The enzyme kinetic values of $K_m$ and $V_{max}$ were 25.92 mg/ml and $0.628{\mu}mole/mg/ml$, respectively. The enzymatic characteristics of the expressed xylanase showed a typical fungal xylanase. However, the bioinformatics analysis suggested that the protein encoded by isotig01043 was a novel xylanase based on a low identity when it was compared with the closest protein in the NCBI database and a similar protein domain with GH16_fungal_Lam16A_glucanase, which had not been earlier suggested as a xylanase.

• Journal of Microbiology and Biotechnology
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• v.21 no.12
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• pp.1228-1235
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• 2011

We compared the gene expression among four clinical and five environmental V. vulnificus isolates, using a cDNA microarray containing 131 genes possibly associated with pathogenicity, transport, signal transduction, and gene regulations in the pathogen. cDNAs from total RNAs of these isolates were hybridized into the cDNA microarray using the cDNA of the wild-type strain MO6-24/O as a reference. We focused on selecting differentially expressed (DE) genes between clinical and environmental isolates using a modified t-statistic. We could detect two statistically significant DE genes between virulent isolates and less-virulent isolates with a marginal statistical significance (p-value of 0.008). These were genes putatively encoding pilin and adenlyate cylase. Real time-PCR confirmed that these two selected genes transcribed in significantly higher levels in virulent isolates than in less-virulent isolates. Mutants with lesions in the gene encoding pilin showed significantly higher $LD_{50}$ values than that of wild type.

• BMB Reports
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• v.53 no.8
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• pp.393-399
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• 2020

Recent advancements in the resolution and throughput of single-cell analyses, including single-cell RNA sequencing (scRNA-seq), have achieved significant progress in biomedical research in the last decade. These techniques have been used to understand cellular heterogeneity by identifying many rare and novel cell types and characterizing subpopulations of cells that make up organs and tissues. Analysis across various datasets can elucidate temporal patterning in gene expression and developmental cues and is also employed to examine the response of cells to acute injury, damage, or disruption. Specifically, scRNA-seq and spatially resolved transcriptomics have been used to describe the identity of novel or rare cell subpopulations and transcriptional variations that are related to normal and pathological conditions in mammalian models and human tissues. These applications have critically contributed to advance basic cardiovascular research in the past decade by identifying novel cell types implicated in development and disease. In this review, we describe current scRNA-seq technologies and how current scRNA-seq and spatial transcriptomic (ST) techniques have advanced our understanding of cardiovascular development and disease.