Biology subjects

Seo, C.

Publications and source records attributed to Seo, C..

3 recordsLinked to original sources

bioRxiv2018

Endogenous BioID elucidates TCF7L1 interactome modulation upon GSK-3 inhibition in mouse ESCs

Modulation of Wnt target gene expression via the TCF/LEFs remains poorly understood. We employ proximity-based biotin labeling (BioID) to examine GSK-3 inhibitor effects on the TCF7L1 interactome in mouse ESCs. We generated ESC lines with biotin ligase BirA* fused to TCF7L1 by knocking it into the endogenous TCF7L1 locus or by inserting a doxinducible BirA*-TCF7L1 transgene into the Rosa26 locus. Induction yielded BirA*-TCF7L1 levels 3-fold higher than in the endogenous system, but substantial overlap in biotinylated proteins with high peptide counts were detected by each method. Known TCF7L1 interactors TLE3/4 and {beta}-catenin, and numerous proteins not previously associated with TCF7L1, were identified in both systems. Despite reduced BirA*-TCF7L1 levels, the number of hits identified with both BioID approaches increased after GSK-3 inhibition. We elucidate the network of TCF7L1 proximal proteins regulated by GSK-3 inhibition, validate the utility of endogenous BioID, and provide mechanistic insights into TCF7L1 target gene regulation.\n\nHighlightsO_LIBirA*-TCF7L1 at single-copy physiological levels generates robust BioID data\nC_LIO_LICHIR99021 reduces TCF7L1 levels but increases detectable TCF7L1-proximal proteins\nC_LIO_LIThe TCF7L1 interactome of largely epigenetic/transcription factors fluctuates with GSK-3 inhibition\nC_LIO_LIJMJD1C, SALL4 and BRG1/SMARCA4 are validated as TCF7L-interacting proteins\nC_LI

cell biology↗

bioRxiv2018

Altitudinal range-size distribution of breeding birds and environmental factors for the determination of species richness: An empirical test of altitudinal Rapoports rule and rescue effect on a local scale

Range-size distributions are important for understanding species richness patterns and led to the development of the controversial Rapoports rule and Rapoport-rescue effect. This study aimed to understand the relationship between species richness and range-size distribution in relation to environmental factors. The present study tested the following: (1) altitudinal Rapoports rule, (2) climatic and ambient energy hypotheses, (3) non-directional rescue effect, and (4) effect of environmental factors on range-size group. Altitudinal species range-size distribution increased with increasing altitude and showed a negative relationship with climatic variables and habitat heterogeneity, and a positive relationship with primary productivity. These results support the altitudinal Rapoports rule and climatic hypothesis; however, they do not fully support the ambient energy hypothesis. Results from testing the non-directional rescue effect showed that the inflow intensity of species from both directions (high and low elevations) affected species richness. And we found that the 2nd and 3rd quartile species distribution were the main cause of a mid-peak of species richness and the non-directional rescue effect. Additionally, the 2nd quartile species richness was highly related to minimum temperature and possessed thermal specialist species features, and the 3rd quartile species richness was highly related to habitat heterogeneity and primary productivity. Although altitudinal range-size distribution results were similar to the altitudinal Rapoports rule, the mid-peak pattern of species richness could not be explained by the Rapoports-rescue effect; however, the non-directional rescue effect could explain a mid-peak pattern of species richness.

ecology↗

bioRxiv2018

Effective soil extraction method for cultivating previously uncultured soil bacteria

Here, a new medium named as intensive soil extract medium (ISEM) based on new soil extract (NSE) using 80% ethanol was used to efficiently isolate previously uncultured bacteria and new taxonomic candidates, which accounted for 49% and 55% of the total isolates examined (n=258), respectively. The new isolates were affiliating with seven phyla such as Proteobacteria, Acidobacteria, Firmicutes, Actinobacteria, Verrucomicrobia, Planctomycetes, and Bacteroidetes. The result of chemical analysis showed that NSE included more diverse components of low-molecular-weight organic substances than two conventional soil extracts using distilled water. Cultivation of previously uncultured bacteria is expected to extend knowledge through the discovery of new phenotypic, physiological and functional properties, and even roles of unknown genes.\n\nIMPORTANCEEither metagenomics or single-cell sequencing can detect unknown genes from uncultured microbial strains in environments and may find their significant potential metabolites and roles. However, such gene/genome-based techniques still have a critical problem making impossible for further applications through cultivation. To solve this problem, various approaches for cultivation of uncultured bacteria have been developed, but they still have lack of skill to grow them on solid media for isolation and subculture.

microbiology↗