• Proceedings of the Plant Resources Society of Korea Conference
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• 2019.10a
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• pp.64-64
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• 2019

Screening and identification of genetic resources based on their phytoconstituents and morphological characters potentially provide baseline data for researchers, breeders, and nutraceutical companies who wish to formulate a nutrient-dense diet and health beneficial supplement. Thus, we evaluated the amount of total phenolic content and major phenolic compounds; examined if phenolic compounds could be used as distinguishing factors for perilla genetic resources; and investigated the relation between some quantitative and qualitative morphological characters with the contents of phenolic compounds in 360 accessions obtained from National Agrobiodiversity Center gene bank, Jeonju, Korea. Total phenolic content (TPC) was estimated using Folin-Ciocalteu colorimetric assay. Individual phenolic compounds were determined using an Ultra-High Performance Liquid Chromatography system equipped with Photodiode Array detector. Considerable variations were observed in TPC (7.99 to 117.47 mg GAE/g DE), rosmarinic acid (RA) (ND to 19.19 mg/g DE), caffeic acid (CA) (ND to 0.72 mg/g DE), apigenin-7-O-diglucuronide (ADG) (ND to 1.24 mg luteolin equivalent (LUE)/g DE), scutellarein-7-O-glucuronide (SG) (ND to 4.32 mg LUE/g DE), and apigenin-7-O-glucuronide (AG) (ND to 1.60 mg LUE/g DE). RA was the most dominant phenolic compound in most accessions (95.3%) followed by SG. The adaxial leaf color was light green, green and dark green in 13.8%, 65.0%, and 21.1 % of the accessions, respectively. 78.8% of the accessions had light green color at the abaxial side with the remaining being described as green. Most of the accessions (96.9%) were cordate shape, the remaining being eclipse. Intensities of green pigment at abaxial and adaxial leaf surfaces were correlated with contents of individual phenolic compounds and TPC whereas leaf length and width had no correlation with TPC, CA and RA, and negatively correlated with ADG, AG, and SG. Leaf shape was not related with content of phenolic compounds, color of leaves, or the length or width of leaves. Accessions IT57426, IT157434, IT267710, and IT267712 which contained relatively high contents of TPC and major phenolic compounds (RA and SG) could be used for further research in breeding and bioassay test. Our study result showed the contents of total phenolics and individual phenolic compounds along with the morphological characters could be useful distinguishing factors for perilla genetic resources.

• The Korean Journal of Mycology
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• v.48 no.4
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• pp.475-484
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• 2020

Various indigenous yeasts were isolated and obtained from flowers in the Republic of Korea, and their distribution and species diversity were studied. Seventy-seven flowers were collected from 25 areas in Korea, and 502 yeast strains were isolated from these flowers. A total of 50 species were identified by comparing large subunit rDNA gene sequence homology with the type strains of yeasts. The analysis of yeast distribution showed that the dominant yeast species were Aureobasidium pullulans, A. leucospermi, and Filobasidium magnum in each region and flower samples. Except for the above three yeast species, no species of yeasts showed any meaningful distribution among the habitat regions and sources. In conclusion, 50 species of indigenous yeasts were obtained from flowers that can be used as industrial resources, and the data could be used for further research on yeast diversity and interactions between yeast and its host.

• Plant Breeding and Biotechnology
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• v.5 no.4
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• pp.334-343
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• 2017

Eclipta prostrata and E. alba are annual herbal medicinal plants and have been used as Chinese medicinal tonics. Both species are widely distributed in tropical and subtropical regions as well as in Korea. Both species have similar morphological features but E. alba has smoother leaf blade margins compared with E. prostrata. Although both species are utilized as oriental medicines, E. prostrata is more widely used than E. alba. Morphological semblances have confounded identification of either species. Here, we report the complete chloroplast genomes of both species to provide an authentication system between the two species and understand their diversity. Both chloroplast genomes were 151,733-151,757 bp long and composed of a large single copy (83,285-83,300 bp), a small single copy (18,283-18,346 bp), and a pair of inverted repeats (25,075-25,063 bp). Gene annotation revealed 80 protein coding genes, 30 tRNA genes and four rRNA genes. A phylogenetic analysis revealed that the genus Eclipta is grouped with Heliantheae tribe species in the Asteraceae family. A comparative analysis verified 29 InDels and 58 SNPs between chloroplast genomes of E. prostrata and E. alba. The low chloroplast genome sequence diversity indicates that both species are really close to each other and are not completely diverged yet. We developed six DNA markers that distinguish E. prostrata and E. alba based on the polymorphisms of chloroplast genomes between E. prostrata and E. alba. The chloroplast genome sequences and the molecular markers generated in this study will be useful for further research of Eclipta species and accurate classification of medicinal herbs.

• Biomolecules & Therapeutics
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• v.29 no.2
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• pp.234-247
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• 2021

We used a heterozygous gene deletion library of fission yeasts comprising all essential and non-essential genes for a microarray screening of target genes of the antifungal terbinafine, which inhibits ergosterol synthesis via the Erg1 enzyme. We identified 14 heterozygous strains corresponding to 10 non-essential [7 ribosomal-protein (RP) coding genes, spt7, spt20, and elp2] and 4 essential genes (tif302, rpl2501, rpl31, and erg1). Expectedly, their erg1 mRNA and protein levels had decreased compared to the control strain SP286. When we studied the action mechanism of the non-essential target genes using cognate haploid deletion strains, knockout of SAGA-subunit genes caused a down-regulation in erg1 transcription compared to the control strain ED668. However, knockout of RP genes conferred no susceptibility to ergosterol-targeting antifungals. Surprisingly, the RP genes participated in the erg1 transcription as components of repressor complexes as observed in a comparison analysis of the experimental ratio of erg1 mRNA. To understand the action mechanism of the interaction between the drug and the novel essential target genes, we performed isobologram assays with terbinafine and econazole (or cycloheximide). Terbinafine susceptibility of the tif302 heterozygous strain was attributed to both decreased erg1 mRNA levels and inhibition of translation. Moreover, Tif302 was required for efficacy of both terbinafine and cycloheximide. Based on a molecular modeling analysis, terbinafine could directly bind to Tif302 in yeasts, suggesting Tif302 as a potential off-target of terbinafine. In conclusion, this genome-wide screening system can be harnessed for the identification and characterization of target genes under any condition of interest.

• Mycobiology
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• v.50 no.1
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• pp.66-78
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• 2022

The identification of oleaginous yeast species capable of simultaneously utilizing xylose and glucose as substrates to generate value-added biological products is an area of key economic interest. We have previously demonstrated that the Cutaneotrichosporon dermatis NICC30027 yeast strain is capable of simultaneously assimilating both xylose and glucose, resulting in considerable lipid accumulation. However, as no high-quality genome sequencing data or associated annotations for this strain are available at present, it remains challenging to study the metabolic mechanisms underlying this phenotype. Herein, we report a 39,305,439 bp draft genome assembly for C. dermatis NICC30027 comprised of 37 scaffolds, with 60.15% GC content. Within this genome, we identified 524 tRNAs, 142 sRNAs, 53 miRNAs, 28 snRNAs, and eight rRNA clusters. Moreover, repeat sequences totaling 1,032,129 bp in length were identified (2.63% of the genome), as were 14,238 unigenes that were 1,789.35 bp in length on average (64.82% of the genome). The NCBI non-redundant protein sequences (NR) database was employed to successfully annotate 11,795 of these unigenes, while 3,621 and 11,902 were annotated with the Swiss-Prot and TrEMBL databases, respectively. Unigenes were additionally subjected to pathway enrichment analyses using the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG), Clusters of orthologous groups for eukaryotic complete genomes (KOG), and Non-supervised Orthologous Groups (eggNOG) databases. Together, these results provide a foundation for future studies aimed at clarifying the mechanistic basis for the ability of C. dermatis NICC30027 to simultaneously utilize glucose and xylose to synthesize lipids.

• Journal of Life Science
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• v.31 no.7
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• pp.671-676
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• 2021

A cDNA encoding the protein lethal (2) essential for life [l(2)efl] was cloned from Gryllus bimaculatus and named GBl(2)efl. This protein is composed of 189 amino acids, including an N-glycosylation site and 15 phosphorylation sites. Its predicted molecular mass is 21.19 kDa, with a theoretical isoelectric point of 6.2. The secondary structure of GBl(2)efl was predicted from the identification of random coils (56.08%), alpha helices (22.22%), extended strands (17.99%), and beta turns (3.7%) through sequence analyses. A homology analysis revealed that GBl(2)efl exhibited a high similarity with other species at the amino acid level, ranging from 52% to 69%. While GBl(2)efl mRNA expression was higher in the dorsal longitudinal flight muscle following a three-day starvation and in the Malpighian tubules following a one-day starvation, no changes in expression were detected in other tissues. Furthermore, tunicamycin-induced endoplasmic reticulum (ER) stress resulted in an approximately 1.8-fold higher expression in the fat body compared with the wild type.

• Animal Bioscience
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• v.36 no.1
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• pp.144-155
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• 2023

Objective: Adipocyte differentiation is regulated by a variety of functional genes and noncoding RNAs. However, the role of miRNAs in lipid deposition of goat white adipose tissue is still unclear. Therefore, this study revealed the miRNA expression profile in goat subcutaneous adipocytes by sRNA-seq. Methods: The miRNA expressed in goat subcutaneous preadipocytes and the mature adipocytes were sequenced by sRNA-seq. The differentially expressed miRNAs (DEm) were screened and gene ontology (GO) and Kyoto encyclopedia for genes and genomes (KEGG) analyses were performed. Gain-of-function and loss-of-function combined with oil red O staining, Bodipy staining, and quantitative reverse-transcription polymerase chain reaction (qPCR) were utilized to determine the effect of miR-133a-3p on adipocyte differentiation. Results: A total of 218 DEm were screened out. The target genes of these DEm were significantly enriched in GO items such as biological regulation and in KEGG terms such as FAK signaling pathway and MAPK signaling pathway. qPCR verified that the expression trend of miRNA was consistent with miRNA-seq. The gain-of-function or loss-of-function of miR-133a-3p showed that it promoted or inhibited the accumulation of lipid droplets, and CCAAT enhancer binding protein α (C/EBPα) and C/EBPβ were extremely significantly up-regulated or down-regulated respectively (p<0.01), the loss-of-function also led to a significant down-regulation of peroxisome proliferator activated receptor gamma (PPARγ) (p<0.01). Conclusion: This study successfully identified miRNAs expression patterns in goat subcutaneous adipocytes, and functional identification indicates that miR-133a-3p is a positive regulator of the differentiation process of goat subcutaneous adipocytes. Our results lay the foundation for the molecular mechanism of lipid deposition in meat-source goats from the perspective of miRNA.

• Journal of Veterinary Science
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• v.23 no.6
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• pp.12.01-12.10
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• 2022

Background: Staphylococcus aureus and Streptococcus agalactiae are the main cause of clinical mastitis in dairy cattle in Argentina, whereas coagulase-negative staphylococci (CNS) and environmental streptococci are the main cause of subclinical mastitis. Bacteria isolated from infected animals show increasing antimicrobial resistance. Objectives: This study aims to determine the antimicrobial resistance of staphylococci and streptococci isolated from milk with mastitis, and to genotypically characterize the methicillin-resistant (MR) staphylococci. Methods: Isolation was performed on blood agar and identification was based on biochemical reactions. Antimicrobial susceptibility was according to the Clinical and Laboratory Standards Institute guidelines. The antimicrobial resistance genes, SCCmec type and spa type were detected by the polymerase chain reaction method. Results: We isolated a total of 185 staphylococci and 28 streptococci from 148 milk samples. Among the staphylococcal isolates, 154 were identified as CNS and 31 as S. aureus. Among the 154 CNS, 24.6% (n = 38) were resistant to penicillin, 14.9% (n = 23) to erythromycin, 17.5% (n = 27) to clindamycin, 6.5% (n = 10) to cefoxitin and oxacillin. Among the S. aureus isolates, 16.1% (n = 5) were resistant to penicillin, 3.2% (n = 1) to cefoxitin and oxacillin (MRSA). Six MR isolates (5 CNS and 1 MRSA) were positive to the mecA gene, and presented the SCCmec IVa. The MRSA strain presented the sequence type 83 and the spa type 002. Among the 28 streptococcal isolates, 14.3% (n = 4) were resistant to penicillin, 10.7% (n = 3) to erythromycin and 14.3% (n = 4) to clindamycin. Conclusions: The present findings of this study indicate a development of antimicrobial resistance in main bacteria isolated from cows with mastitis in Argentina.

• Animal Bioscience
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• v.35 no.2
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• pp.281-289
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• 2022

Objective: The aim of this study was to characterize the exopolysaccharides (EPS)-producing lactic acid bacteria from Taiwanese ropy fermented milk (TRFM) for developing a clean label low-fat fermented milk. Methods: Potential isolates from TRFM were selected based on the Gram staining test and observation of turbid suspension in the culture broth. Random amplified polymorphic DNA-polymerase chain reaction, 16S rRNA gene sequencing, and API CHL 50 test were used for strain identification. After evaluation of EPS concentration, target strains were introduced to low-fat milk fermentation for 24 h. Fermentation characters were checked: pH value, acidity, viable count, syneresis, and viscosity. Sensory evaluation of fermented products was carried out by 30 volunteers, while the storage test was performed for 21 days at 4℃. Results: Two EPS-producing strains (APL15 and APL16) were isolated from TRFM and identified as Lactococcus (Lc.) lactis subsp. cremoris. Their EPS concentrations in glucose and lactose media were higher than other published strains of Lc. lactis subsp. cremoris. Low-fat fermented milk separately prepared with APL15 and APL16 reached pH 4.3 and acidity 0.8% with a viable count of 9 log colony-forming units/mL. The physical properties of both products were superior to the control yogurt, showing significant improvements in syneresis and viscosity (p<0.05). Our low-fat products had appropriate sensory scores in appearance and texture according to sensory evaluation. Although decreasing viable cells of strains during the 21-day storage test, low-fat fermented milk made by APL15 exhibited stable physicochemical properties, including pH value, acidity, syneresis and sufficient viable cells throughout the storage period. Conclusion: This study demonstrated that Lc. lactis subsp. cremoris APL15 isolated from TRFM had good fermentation abilities to produce low-fat fermented milk. These data indicate that EPS-producing lactic acid bacteria have great potential to act as natural food stabilizers for low-fat fermented milk.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.67 no.4
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• pp.274-284
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• 2022

To use kenaf (Hibiscus cannabinus L.) as a fiber and livestock feed, a high-yielding variety needs to be identified. For this, accurate phenotyping of plant height is required for this breeding purpose due to the strong relationship between plant height and yield. Plant height can be estimated using RGB images from unmanned aerial vehicles (UAV-RGB) and photogrammetry based on Structure from Motion (SfM) algorithms. In kenaf, accurate measurement of height is limited because kenaf stems have high flexibility and its height is easily affected by wind, growing up to 3 ~ 4 m. Therefore, we aimed to identify a method suitable for the accurate estimation of plant height of kenaf and investigate the feasibility of using the UAV-RGB-derived plant height map. Height estimation derived from UAV-RGB was improved using multi-point calibration against the five different wooden structures with known heights (30, 60, 90, 120, and 150 cm). Using the proposed method, we analyzed the variation in temporal height of 23 kenaf cultivars. Our results demontrated that the actual and estimated heights were reliably comparable with the coefficient of determination (R²) of 0.80 and a slope of 0.94. This method enabled the effective identification of cultivars with significantly different heights at each growth stages.