CD5L as an Extracellular Vesicle-Derived Biomarker for Liquid Biopsy of Lung Cancer

Cancer screening and diagnosis can be achieved by analyzing specific molecules within serum-derived extracellular vesicles (EVs). This study sought to profile EV-derived proteins to identify potential lung cancer biomarkers. EVs were isolated from 80 serum samples from healthy individuals and cancer patients via polyethylene glycol (PEG)-based precipitation and immunoaffinity separation using antibodies against CD9, CD63, CD81, and EpCAM. Proteomic analysis was performed using 2-D gel electrophoresis and matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). The expression of proteins that were differentially upregulated in the EVs or tissue of lung cancer samples was validated by Western blotting. The area under the curve (AUC) was calculated to assess the predictability of each differentially expressed protein (DEP) for lung cancer. A total of 55 upregulated protein spots were selected, seven of which (CD5L, CLEC3B, ITIH4, SERFINF1, SAA4, SERFINC1, and C20ORF3) were found to be expressed at high levels in patient-derived EVs by Western blotting. Meanwhile, only the expression of EV CD5L correlated with that in cancer tissues. CD5L also demonstrated the highest AUC value (0.943) and was found to be the core regulator in a pathway related to cell dysfunction. Cumulatively, these results show that EV-derived CD5L may represent a potential biomarker-detected via a liquid biopsy-for the noninvasive diagnosis of lung cancer. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.1

Efficient production of d-lactate from methane in a lactate-tolerant strain of Methylomonas sp. DH-1 generated by adaptive laboratory evolution

Background Methane, a main component of natural gas and biogas, has gained much attention as an abundant and low-cost carbon source. Methanotrophs, which can use methane as a sole carbon and energy source, are promising hosts to produce value-added chemicals from methane, but their metabolic engineering is still challenging. In previous attempts to produce lactic acid (LA) from methane, LA production levels were limited in part due to LA toxicity. We solved this problem by generating an LA-tolerant strain, which also contributes to understanding novel LA tolerance mechanisms. Results In this study, we engineered a methanotroph strain Methylomonas sp. DH-1 to produce d-lactic acid (d-LA) from methane. LA toxicity is one of the limiting factors for high-level production of LA. Therefore, we first performed adaptive laboratory evolution of Methylomonas sp. DH-1, generating an LA-tolerant strain JHM80. Genome sequencing of JHM80 revealed the causal gene watR, encoding a LysR-type transcription factor, whose overexpression due to a 2-bp (TT) deletion in the promoter region is partly responsible for the LA tolerance of JHM80. Overexpression of the watR gene in wild-type strain also led to an increase in LA tolerance. When d form-specific lactate dehydrogenase gene from Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 was introduced into the genome while deleting the glgA gene encoding glycogen synthase, JHM80 produced about 7.5-fold higher level of d-LA from methane than wild type, suggesting that LA tolerance is a critical limiting factor for LA production in this host. d-LA production was further enhanced by optimization of the medium, resulting in a titer of 1.19 g/L and a yield of 0.245 g/g CH4. Conclusions JHM80, an LA-tolerant strain of Methylomonas sp. DH-1, generated by adaptive laboratory evolution was effective in LA production from methane. Characterization of the mutated genes in JHM80 revealed that overexpression of the watR gene, encoding a LysR-type transcription factor, is responsible for LA tolerance. By introducing a heterologous lactate dehydrogenase gene into the genome of JHM80 strain while deleting the glgA gene, high d-LA production titer and yield were achieved from methane.This work was supported by C1 Gas Refnery Program through the National Research Foundation of Korean (NRF) funded by the Ministry of Science and ICT (2016M3D3A01913245)

Genome wide association studies correcting population stratification in pepper core collection

Genome-wide association study (GWAS) is an effective approach for identifying genetic variants associated to useful agronomic traits. GWAS has emerged as a powerful approach for identifying genes underlying complex diseases or morphological traits at an unprecedented rate. In such studies, it is very important to correct for population stratification, which refers to allele frequency differences between cases and controls due to systematic ancestry differences. Population stratification can cause false positive findings if not adjusted properly. As we are performing GWAS for various agronomic traits in pepper, a genotyping-by-sequencing (GBS) approach was used to provide dense genome-wide marker coverage (>33,000 SNPs) for a 250 pepper core collection. Using GBS platform, high density haplotype map was constructed and various stratification methods, including distance based phylogenetic methods, principal component analysis (PCA), and bayesian phylogenetic methods (STRUCTURE) were performed to show the genetic diversity and population stratification. As a result, MLM using Q values combined with k-medoids clustering estimated from stratification methods were used to identify quantitative trait loci controlling the variation of ten agronomic traits. These results will help to understand associations between phenotype and genotype and also use for validate the candidate genes or quantitative trait loci previously identified in pepper.OAIID:RECH_ACHV_DSTSH_NO:A201625311RECH_ACHV_FG:RR00200003ADJUST_YN:EMP_ID:A076900CITE_RATE:FILENAME:2016 SOL (이혜영,한고은).pdfDEPT_NM:식물생산과학부EMAIL:[email protected]_YN:FILEURL:https://srnd.snu.ac.kr/eXrepEIR/fws/file/9b9d10b7-072b-458d-a603-55c35c7b02d5/linkCONFIRM:

Genome wide association studies (GWAS) in Capsicum core collection

Genome-wide association study (GWAS) is an effective approach for identifying genetic variants associated to useful agronomic traits. As we are performing GWAS for various agronomic traits in pepper, a genotyping-by-sequencing (GBS) approach was used to provide dense genome-wide marker coverage (>33,000 SNPs) for a 350 pepper core collection. Using GBS platform, a high density haplotype map was constructed and various stratification methods, including principal component analysis (PCA), and bayesian phylogenetic methods (STRUCTURE) were performed to show the genetic diversity and population stratification. Based on the STRUCTURE, four subgroups were identified and each of Q values was estimated. Through these results, MLM using Q values combined with kinship matrix were performed to identify quantitative trait loci controlling the variation of 12 agronomic traits. A set of 37 SNP locus distributed over 12 Capsicum chromosomes was identified for associations. For a validation, the associations were compared with the location of known QTLs which were surveyed from bi-parental population. It showed that, at least two QTLs were matched well with previous study. These results will help to understand associations between phenotype and genotype and also will give more power to validate the candidate genes or quantitative trait loci.OAIID:RECH_ACHV_DSTSH_NO:A201701391RECH_ACHV_FG:RR00200003ADJUST_YN:EMP_ID:A076900CITE_RATE:FILENAME:2017 PAG (이혜영).pdfDEPT_NM:식물생산과학부EMAIL:[email protected]_YN:FILEURL:https://srnd.snu.ac.kr/eXrepEIR/fws/file/24ec6505-0bd3-4519-a8be-2410a4ff901a/linkCONFIRM:

First Report on Pink Rot of Sunflower (Helianthus annuus) Caused by Trichothecium roseum in Korea

Pink rot appeared in greenhouse-grown sunflower (Helianthus annuus L.) in Jeonju, Korea. The symptoms appeared as brown discoloration of sunflower head and progressed into stem in advanced stage. In order to investigate the causal organism of this disease, we isolated a fungus from the infected seeds and maintained the isolated fungal culture on potato dextrose agar medium. Conidiophores were simple or branched, 62.5 to 123.1 μm long. Conidia were produced in basipetal chains, ellipsoidal to pyriform with oblique and prominent truncate basal scars, two-celled, hyaline and measured 10.2–21.4×7.5–12.6 μm. The fungus was inoculated to a new sunflower plant and showed the typical blight on the leaves. Study of morphological characters, pathogenicity tests and sequence analysis revealed that the isolated fungus is confirmed to be Trichothecium roseum. To our knowledge, this is the first report of pink rot on sunflower caused by T. roseum in Korea

Evaluation of Resistance to Ralstonia solanacearum in Tomato Genetic Resources at Seedling Stage

Bacterial wilt of tomatoes caused by Ralstonia solanacearum is a devastating disease that limits the production of tomato in Korea. The best way to control this disease is using genetically resistant tomato plant. The resistance degree to R. solanacearum was evaluated for 285 tomato accessions conserved in the National Agrobiodiversity Center of Rural Development Administration. These accessions of tomato were originated from 23 countries. Disease severity of tomato accessions was investigated from 7 days to 14 days at an interval of 7 days after inoculation of R. solanacearum under greenhouse conditions. A total of 279 accessions of tomato germplasm were susceptible to R. solanacearum, resulting in wilt and death in 70 to 90% of these plants. Two tomato accessions were moderately resistant to R. solanacearum. Only four accessions showed high resistance against R. solanacearum. No distinct symptom of bacterial wilt appeared on the resistant tomato germplasms for up to 14 days after inoculation of R. solanacearum. Microscopy of resistant tomato stems infected with R. solanacearum revealed limited bacterial spread with thickening of pit membrane and gum production. Therefore, these four resistant tomato germplasms could be used in tomato breeding program against bacterial wilt

Glucosinolate Content in Brassica Genetic Resources and Their Distribution Pattern within and between Inner, Middle, and Outer Leaves

Glucosinolates (GSLs) are sulfur-containing secondary metabolites naturally occurring in Brassica species. The purpose of this study was to identify the GSLs, determine their content, and study their accumulation patterns within and between leaves of kimchi cabbage (Brassica rapa L.) cultivars. GSLs were analyzed using UPLC-MS/MS in negative electron-spray ionization (ESI−) and multiple reaction monitoring (MRM) mode. The total GSL content determined in this study ranged from 621.15 to 42434.21 μmolkg−1 DW. Aliphatic GSLs predominated, representing from 4.44% to 96.20% of the total GSL content among the entire samples. Glucobrassicanapin (GBN) contributed the greatest proportion while other GSLs such as glucoerucin (ERU) and glucotropaeolin (TRO) were found in relatively low concentrations. Principal component analysis (PCA) yielded three principal components (PCs) with eigenvalues ≥ 1, altogether representing 74.83% of the total variation across the entire dataset. Three kimchi cabbage (S/No. 20, 4, and 2), one leaf mustard (S/No. 26), and one turnip (S/No. 8) genetic resources were well distinguished from other samples. The GSL content varied significantly among the different positions (outer, middle, and inner) of the leaves and sections (top, middle, bottom, green/red, and white) within the leaves. In most of the samples, higher GSL content was observed in the proximal half and white sections and the middle layers of the leaves. GSLs are regarded as allelochemicals; hence, the data related to the patterns of GSLs within the leaf and between leaves at a different position could be useful to understand the defense mechanism of Brassica plants. The observed variability could be useful for breeders to develop Brassica cultivars with high GSL content or specific profiles of GSLs