Massively parallel sequencing technologies have identified a broad spectrum of human genome diversity. Here we deep sequenced and correlated 18 genomes and 17 transcriptomes of unrelated Korean ...individuals. This has allowed us to construct a genome-wide map of common and rare variants and also identify variants formed during DNA-RNA transcription. We identified 9.56 million genomic variants, 23.2% of which appear to be previously unidentified. From transcriptome sequencing, we discovered 4,414 transcripts not previously annotated. Finally, we revealed 1,809 sites of transcriptional base modification, where the transcriptional landscape is different from the corresponding genomic sequences, and 580 sites of allele-specific expression. Our findings suggest that a considerable number of unexplored genomic variants still remain to be identified in the human genome, and that the integrated analysis of genome and transcriptome sequencing is powerful for understanding the diversity and functional aspects of human genomic variants.
Fusarium root rot, caused by
Fusarium solani
, is a major post-harvest disease in sweet potatoes (
Ipomoea batatas
(L.) Lam.). An effective strategy for controlling this disease is the development of ...resistant varieties. In this study, a genome-wide association study (GWAS) was conducted on 96 sweet potato genotypes to identify novel candidate loci and dissect the genetic basis of Fusarium root rot resistance. Genotyping was performed using genotyping-by-sequencing (GBS), and 44,255 SNPs were identified after filtering. The genotypes (n = 96) were evaluated through resistance tests in 2021 and 2022, separately and combined. The GWAS identified two significant SNP markers (LG3_22903756 and LG4_2449919) on chromosomes 3 and 4 associated with Fusarium root rot resistance, respectively. Lesion length showed significant differences between homozygous A and G alleles of LG3_22903756, which can potentially be used to develop molecular markers for selecting accessions resistant to Fusarium root rot. Expression analysis of 11 putative genes flanking the significant SNPs revealed the alteration in the expression of nine genes, indicating their possible involvement in Fusarium root rot resistance. The results of this study will aid in the marker-assisted selection and functional analysis of candidate genes for Fusarium root rot resistance in sweet potatoes.
Sweetpotatoes require a storage period for year-round use and improved sweetness by starch degradation. However, long-term storage can cause root rot, and a large amount of sweetpotatoes can be ...discarded. Root rot is typically caused by pathogenic soil-borne
spp., and the development of root rot induced by the characteristics of cultivating soil in stored sweetpotato has not yet been identified. In this study, the effect of
spp. and microbial community in the cultivated soil on the root rot of sweetpotatoes was to be elucidated. Wounded sweetpotato were treated in soil cultures inoculated with
or
for 2 days, and showed symptoms of root rot after 2 months of storage. The three study fields (Naju, Yeongam A, and B) were subjected to the same curing and storage treatments after harvest, and the incidence of root rot was 1.7- to 1.8-fold different after 3 months of storage. Across the three fields, concentrations of
spp. and of microbial communities differed according to the cultivation soil and period. In particular, Naju, which had the lowest incidence of root rot, had the lowest concentration of
spp. before harvest, and the smallest change in diversity of the microbial community during the cultivation period. However, tuberous roots harvested from the fields showed no significant differences in antioxidant activity or lesion size with the treatment of 10
conidia/ml
By solidifying the importance of cultivating soil and related microorganisms in the advancement of root rot of sweetpotato, our results may aid in preventing the decrease in the yield of cultivated sweetpotatoes through root rot control.
This study examines the complicated interlink between the Korean state's neoliberal identity politics and working- and lower middle-class Korean students' study abroad as a form of voluntarily exile. ...Drawing on a critical discourse analysis and a 14-month ethnographic study, this study discusses how these students' decisions to study abroad are inextricably intertwined with the authoritarian Korean state's neoliberal political-economic strategies of pushing out seemingly less-profitable citizens (namely, students and graduates of low-ranking 4-year institutions). This study also examines students' strategies for simultaneously resisting and conforming to this neoliberal ethos. For working-class and lower middle-class Korean community college students, study abroad means a deviation from the normal educational and life trajectories in Korea while, at the same time, their education in the USA opens a pathway for reentering the Korean neoliberal system as more profitable citizens. Their being recognized as members of a profitable workforce indicates their achievement of neoliberal normalcy.
For environmental reason, buildings increasingly install smart windows, which can dim incoming daylight based on active electrochromic devices (ECDs). In this work, multi-layered graphene (MLG) was ...investigated as an ECD window electrode, to minimize carbon dioxide (CO
) emissions by decreasing the electricity consumption for building space cooling and heating and as an alternative to the transparent conductor tin-doped indium oxide (ITO) in order to decrease dependence on it. Various MLG electrodes with different numbers of graphene layers were prepared with environmentally friendly poly(3,4-ethylenedioxythiophene):poly(styrene-sulfonate) (PEDOT:PSS) to produce ECD cells. Tests demonstrated the reproducibility and uniformity in optical performance, as well as the flexibility of the ECD fabrication. With the optimized MLG electrode, the ECD cells exhibited a very fast switching response for optical changes from transparent to dark states of a few hundred msec.
Cu–Ti–P oxide catalysts, with Cu (1.0mol%) and P (1.0, 2.0, and 4.0mol%) incorporated into the framework of Ti(1.0mol%)O2, were synthesized using a solvothermal method and their potential ...compatibilities in methanol steam reforming (MSR) were investigated. The scanning electron microscopy (SEM) image of Cu(1)–Ti(1)–P(2) oxide revealed a uniform sheet type, whereas the other two catalysts, Cu(1)–Ti(1)–P(1) and Cu(1)–Ti(1)–P(4), were irregular and non-uniform. Comparative experiments in oxidative MSR were also conducted over a γ-Al2O3 support. The Cu–Ti–P/γ-Al2O3 catalysts provided significantly higher MSR reactivity compared to that without P component, and the tendency was similar in the presence of the γ-Al2O3 support. The main products from steam reforming over the Cu–Ti–P/γ-Al2O3 catalysts were H2, CO, and CO2. The Cu–Ti–P/γ-Al2O3 catalysts also reduced the degree of carbon deposition and improved the H2 product selectivity by facilitating complete oxidation around 600°C. Herein, we suggest a mechanism in which the P component plays the important role of encouraging the Brønsted acid sites, leading to strong partial oxidation and thermal cracking of methanol to acetaldehyde and CO2, and finally to an increased hydrogen yield and suppressed CO generation.
We studied solid electrolyte interphase (SEI) on metallic sodium (Na) electrodes. Among sodium hexafluorophosphate (NaPF6), sodium triflate (NaOTf), and sodium bis(trifluoromethanesulfonyl)imide ...(NaTFSI) electrolytes, sodium fluoride (NaF)‐rich and compact SEI was only formed by chemical reduction of NaPF6. Excellent rigidity and insolubility of NaF‐rich SEI layer enhanced electrochemical cycling performances for both Na/Na symmetric cells and sodium–oxygen (Na–O2) cells. By contrast, the Na electrodes using NaOTf and NaTFSI formed porous and carbonaceous SEI layers rather than NaF. Soluble carbonaceous species were detached from the Na electrode, which led to the undesired decomposition of electrolyte solution. It resulted in the substantial formation of the dead Na and dendritic Na and caused cycling failure of Na–O2 cells within 10 cycles, demonstrated by NaOTf.
Studies of solid electrolyte interface of Na metals and their effects for Na/Na nad Na–O2 cell performances.
FX: an RNA-Seq analysis tool on the cloud DONGWAN HONG; RHIE, Arang; CHONG, Hyonyong ...
Bioinformatics (Oxford, England),
03/2012, Volume:
28, Issue:
5
Journal Article
Peer reviewed
Open access
FX is an RNA-Seq analysis tool, which runs in parallel on cloud computing infrastructure, for the estimation of gene expression levels and genomic variant calling. In the mapping of short RNA-Seq ...reads, FX uses a transcriptome-based reference primarily, generated from ~160 000 mRNA sequences from RefSeq, UCSC and Ensembl databases. This approach reduces the misalignment of reads originating from splicing junctions. Unmapped reads not aligned on known transcripts are then mapped on the human genome reference. FX allows analysis of RNA-Seq data on cloud computing infrastructures, supporting access through a user-friendly web interface.
FX is freely available on the web at (http://fx.gmi.ac.kr), and can be installed on local Hadoop clusters. Guidance for the installation and operation of FX can be found under the 'Documentation' menu on the website.
Supplementary data are available at Bioinformatics online.
Biological synthesis of metal nanoparticles has a significant impact in developing sustainable technologies for human, animal, and environmental safety. In this study, we synthesized gold and silver ...nanoparticles (NPs) using
(SP) extract and characterized them using UV-visible spectrophotometry, FESEM-EDX, HR-TEM, XRD, and FT-IR spectroscopy. Furthermore, antimicrobial and antioxidant activities and cytotoxicity of the synthesized NPs were evaluated. UV-visible absorption spectra showed λ
at 531 and 410 nm, corresponding to the presence of SP gold NPs (SP-AuNPs) and SP silver NPs (SP-AgNPs). Most NPs were spherical and a few were triangular rods, measuring 5-30 and 10-40 nm, respectively. EDX elemental composition analysis revealed that SP-AuNPs and SP-AgNPs accounted for >60% and 30% of NPs, respectively. Additionally, some organic moieties were present, likely derived from various metabolites in the natural plant extract, which acted as stabilizing and reducing agents. Next, the antimicrobial activity of the NPs against pathogenic microbes was tested. SP-AgNPs showed potent antibacterial activity against
and
. Moreover, at moderate and low concentrations, both NPs exhibited weak cytotoxicity in chicken fibroblasts (DF-1) and macrophages (HD11) as well as human intestinal cancer cells (HT-29). Meanwhile, at high concentrations, the NPs exhibited strong cytotoxicity in both chicken and human cell lines. Therefore, the synthesized SP-AuNPs and SP-AgNPs may act as promising materials to treat poultry diseases.
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