Biology subjects

Baek, J.

Publications and source records attributed to Baek, J..

23 records · Page 2Linked to original sources

bioRxiv2021

Genome assembly of the popular Korean soybean cultivar Hwangkeum

Massive resequencing efforts have been undertaken to catalog allelic variants in major crop species including soybean, but the scope of the information for genetic variation often depends on short sequence reads mapped to the extant reference genome. Additional de novo assembled genome sequences provide a unique opportunity to explore a dispensable genome fraction in the pan-genome of a species. Here, we report the de novo assembly and annotation of Hwangkeum, a popular soybean cultivar in Korea. The assembly was constructed using PromethION nanopore sequencing data and two genetic maps, and was then error-corrected using Illumina short-reads and PacBio SMRT reads. The 933.12 Mb assembly was annotated 79,870 transcripts for 58,550 genes using RNA-Seq data and the public soybean annotation set. Comparison of the Hwangkeum assembly with the Williams 82 soybean reference genome sequence revealed 1.8 million single-nucleotide polymorphisms, 0.5 million indels, and 25 thousand putative structural variants. However, there was no natural megabase-scale chromosomal rearrangement. Incidentally, by adding two novel groups, we found that soybean contains four clearly separated groups of centromeric satellite repeats. Analyses of satellite repeats and gene content suggested that the Hwangkeum assembly is a high-quality assembly. This was further supported by comparison of the marker arrangement of anthocyanin biosynthesis genes and of gene arrangement at the Rsv3 locus. Therefore, the results indicate that the de novo assembly of Hwangkeum is a valuable additional reference genome resource for characterizing traits for the improvement of this important crop species.

genomics↗

bioRxiv2020

Precise, high-throughput production of multicellular spheroids with a bespoke 3D bioprinter

3D in vitro cancer models are important therapeutic and biological discovery tools, yet formation of multicellular spheroids in a throughput and highly controlled manner to achieve robust and statistically relevant data, remains challenging. Here, we developed an enabling technology consisting of a bespoke drop-on-demand 3D bioprinter capable of high-throughput printing of 96-well plates of spheroids. 3D-multicellular spheroids are embedded inside a tissue-like matrix with precise control over size and cell number. Application of 3D bioprinting for high-throughput drug screening was demonstrated with doxorubicin. Measurements showed that IC50 values were sensitive to spheroid size, embedding and how spheroids conform to the embedding, revealing parameters shaping biological responses in these models. Our study demonstrates the potential of 3D bioprinting as a robust high-throughput platform to screen biological and therapeutic parameters. Significance StatementIn vitro 3D cell cultures serve as more realistic models, compared to 2D cell culture, for understanding diverse biology and for drug discovery. Preparing 3D cell cultures with defined parameters is challenging, with significant failure rates when embedding 3D multicellular spheroids into extracellular mimics. Here, we report a new 3D bioprinter we developed in conjunction with bioinks to allow 3D-multicellular spheroids to be produced in a high-throughput manner. High-throughput production of embedded multicellular spheroids allowed entire drug-dose responses to be performed in 96-well plate format with statistically relevant numbers of data points. We have deconvoluted important parameters in drug responses including the impact of spheroid size and embedding in an extracellular matrix mimic on IC50 values.

bioengineering↗

bioRxiv2019

A metal artifact reduction method for small field of view CT imaging.

To reduce metal artifacts, several sinogram inpainting-based metal artifact reduction (MAR) methods have been proposed where projection data within the metal trace region of the sinogram are treated as missing and subsequently estimated. However, these methods generally assume data truncation does not occur and all metal objects reside inside the field-of-view (FOV). For small FOV imaging, these assumptions are violated, and thus existing inpainting-based MAR methods would not be effective. In this paper, we propose a new MAR method to reduce metal artifacts effectively in the presence of data truncation. The main idea behind the proposed method is the synthesis of a sinogram, which is treated as the originally measured sinogram. First, an initial reconstruction step is performed to remove truncation artifacts. The next step consists of a forward projection of the small FOV image, replacing the original sinogram with the synthesized sinogram. The final step is the application of sinogram inpainting based MAR methods using the synthesized sinogram. Verification of the proposed method was performed for three situations: extended cardiac-torso (XCAT) simulation, clinical data, and experimental data. The proposed method was applied with linear MAR (LMAR) and normalized MAR (NMAR), and the performance of the proposed method was compared with that of the previous method. For quantitative evaluation, normalized mean squared error (NMSE) and structure similarity (SSIM) were used. The results show the effectiveness of the proposed method to reduce residual metal artifacts, which are present in the results obtained with the previous method. The evaluation results using NMSE and SSIM also indicate that the proposed method is more effective than the previous method.

bioengineering↗

bioRxiv2019

Ultra-widefield fluorescein angiography findings in patients with multiple retinal holes.

PurposeTo evaluate the ultra-widefield fluorescein angiography (UWFA) findings in patients with multiple retinal holes.\n\nMethodsSeventy-five eyes, each with more than two retinal holes, underwent a comprehensive ophthalmologic examination, including UWFA, along with 77 age-matched control eyes with no retinal holes. The UWFA was scored according to a system suggested by the Angiography Scoring for Uveitis Working Group (ASUWG). UWFA findings from the patients with retinal holes were compared with those of the control group without retinal holes. Factors associated with a high ASUWG score were also evaluated.\n\nResultsPatients with multiple retinal holes showed a significantly higher prevalence of retinal vascular staining/leakage, capillary leakage at the posterior pole, and capillary leakage at the periphery when compared to the control group (p<0.001, for each of them). Univariate analysis revealed that logMAR BCVA (r=0.271, p=0.027), spherical equivalent (r= -0.275, p=0.021), and number of retinal holes (r=0.271, p=0.027) were associated with a higher ASUWG score. After adjustments for age, gender, and logMAR BCVA, multivariate regression analysis revealed that the spherical equivalent was independently associated with a higher ASUWG score (r2=0.161, p=0.001).\n\nConclusionsPatients with multiple retinal holes showed profound peripheral vascular leakages on UWFA findings, suggesting the presence of chronic retinal traction induced by equatorial scleral elongation.

neuroscience↗

bioRxiv2018

A novel photoactivatable tool for intermediate filament disruption indicates a role for keratin filaments in early embryogenesis

The significance of cytoplasmic intermediate filament proteins has previously been examined largely through various genetic approaches, including knockdown, knockout and transgenic overexpression. Few studies to date have attempted to examine the role of specifically the filamentous intermediate filament network in orchestrating various cell functions. To directly assess the role of the filamentous keratin intermediate filament network in regulation of cellular behavior, we created a PhotoActivatable disruptor of keratin Intermediate Filaments (PA-dIF). This genetically encoded construct consists of a peptide derived from the 2B2 region of Keratin 8 fused to the photosensitive LOV2 domain from Avena sativa phototropin-1. Upon 458 nm photoirradiation, PA-dIF disrupts keratin intermediate filaments in multiple species and cell types. Marked remodeling of the keratin intermediate filament network accompanies collective cellular morphogenetic movements that occur during gastrulation and neurulation in the Xenopus laevis frog embryo. Light-based activation of PA-dIF was able to disrupt keratin intermediate filaments in Xenopus cells and lead to tissue-specific disruption of morphogenetic processes. Altogether our data show a fundamental requirement for keratin intermediate filaments in orchestrating morphogenetic movements during early embryonic development that have yet to be revealed in other model systems. Moreover, our data validate the utility of a new genetically encoded photoactivatable tool for the disruption and examination of intermediate filaments.

cell biology↗