Accurate quantification of transcriptome from RNA-Seq data by effective length normalization

Lee, Soohyun,Seo, Chae Hwa,Lim, Byungho,Yang, Jin Ok,Oh, Jeongsu,Kim, Minjin,Lee, Sooncheol,Lee, Byungwook,Kang, Changwon,Lee, Sanghyuk Oxford University Press 2011 Nucleic acids research Vol.39 No.2

<P>We propose a novel, efficient and intuitive approach of estimating mRNA abundances from the whole transcriptome shotgun sequencing (RNA-Seq) data. Our method, NEUMA (Normalization by Expected Uniquely Mappable Area), is based on effective length normalization using uniquely mappable areas of gene and mRNA isoform models. Using the known transcriptome sequence model such as RefSeq, NEUMA pre-computes the numbers of all possible gene-wise and isoform-wise informative reads: the former being sequences mapped to all mRNA isoforms of a single gene exclusively and the latter uniquely mapped to a single mRNA isoform. The results are used to estimate the effective length of genes and transcripts, taking experimental distributions of fragment size into consideration. Quantitative RT–PCR based on 27 randomly selected genes in two human cell lines and computer simulation experiments demonstrated superior accuracy of NEUMA over other recently developed methods. NEUMA covers a large proportion of genes and mRNA isoforms and offers a measure of consistency (‘consistency coefficient’) for each gene between an independently measured gene-wise level and the sum of the isoform levels. NEUMA is applicable to both paired-end and single-end RNA-Seq data. We propose that NEUMA could make a standard method in quantifying gene transcript levels from RNA-Seq data.</P>

ANKRD9 is associated with tumor suppression as a substrate receptor subunit of ubiquitin ligase

Lee, Yejin,Lim, Byungho,Lee, Seon Woo,Lee, Woo Rin,Kim, Yong-In,Kim, Minhyeok,Ju, Hyoungseok,Kim, Mi Young,Kang, Suk-Jo,Song, Ji-Joon,Lee, J. Eugene,Kang, Changwon Elsevier 2018 Biochimica et biophysica acta. Molecular basis of Vol.1864 No.10

<P><B>Abstract</B></P> <P><B>Background</B></P> <P>Human <I>ANKRD9</I> (ankyrin repeat domain 9) expression is altered in some cancers.</P> <P><B>Methods</B></P> <P>We tested genetic association of ANKRD9 with gastric cancer susceptibility and examined functional association of ANKRD9 with altered proliferation of MKN45 gastric cancer cells. We then identified ANKRD9-binding partners in HEK 293 embryonic kidney cells using quantitative proteomics, western blotting and complex reconstitution assays. We finally demonstrated ANKRD9's role of recognizing substrates for ubiquitination using in vitro ubiquitylation assay.</P> <P><B>Results</B></P> <P> <I>ANKRD9</I> is associated with cancer susceptibility in a comparison of single-nucleotide polymorphisms between 1092 gastric cancer patients and 1206 healthy controls. ANKRD9 depletion accelerates tumor progression by increasing cellular proliferation, piling up, and anchorage-independent growth of MKN45 cells. We discovered that ANKRD9 is a ubiquitin ligase substrate receptor subunit and has an anti-proliferative activity. ANKRD9 associates with CUL5 (not CUL2), ELOB, ELOC, and presumably RNF7 subunits, which together assemble into a cullin-RING superfamily E3 ligase complex. ANKRD9 belongs to the ASB family of proteins, which are characterized by the presence of ankyrin repeats and a SOCS box. In addition to its interactions with the other E3 ligase subunits, ANKRD9 interacts with two isoforms of inosine monophosphate dehydrogenase (IMPDH). These IMPDH isoforms are cognate substrates of the ANKRD9-containing E3 enzyme, which ubiquitinates them for proteasomal degradation. Their ubiquitination and turnover require the presence of ANKRD9.</P> <P><B>Conclusion</B></P> <P>ANKRD9, a previously unidentified E3 substrate receptor subunit, functions in tumor suppression by recognizing the oncoprotein IMPDH isoforms for E3 ubiquitination and proteasomal degradation.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Human <I>ANKRD9</I> is genetically associated with gastric cancer susceptibility. </LI> <LI> ANKRD9 protein activity is functionally associated with tumor suppression. </LI> <LI> ANKRD9 is a substrate receptor subunit of CUL5-based ubiquitin ligase E3 complex. </LI> <LI> E3 with ANKRD9 ubiquitinates substrate proteins for proteasomal degradation. </LI> <LI> Two isoforms of oncoprotein IMP dehydrogenase are cognate substrates of ANKRD9. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>

Imaging Characteristics of Perosomus elumbis in a Puppy

Sooyoung Choi,Byungho Lee,Byungdon Lee,Jiwon Seo,Hyunyoung Park,Kyunghun Kwon,Youngwon Lee,Hojung Choi 한국수정란이식학회 2015 한국동물생명공학회지 Vol.30 No.4

A 4-day-old, male Poodle dog was presented with dull, depressed and exhausted activity after the birth. On physical examination, the puppy showed arthrogryposis, muscular atrophy and no movement of hindlimbs. Palpation on dorsum revealed an absence of lumbar and sacral vertebrae. On prenatal and postnatal radiography, lumbar vertebrae, sacrum and coccygeal vertebrae were not visualized. On ultrasonography, bilateral kidney and urinary bladder were observed. On computed tomography, there were no apparent abnormalities in the forelimbs, cervical vertebrae or head, while lumbar vertebrae, sacrum and coccygeal vertebrae were not observed. At necropsy examination, the liver, stomach, intestine, kidney and urinary bladder were normal. This congenital anomaly was consistent with Perosomus elumbis. Perosomus elumbis in dogs is a rare condition of unknown etiology. In this report, Perosomus elumbis was evaluated with radiography, ultrasound and computed tomography.

Effects of Motivational Activation on Processing Positive and Negative Content in Internet Advertisements

Lee, Seungjo,Park, Byungho Korean Society for Emotion and Sensibility 2012 감성과학 Vol.15 No.4

This study investigated the impact of individual differences in motivational reactivity on cognitive effort, memory strength (sensitivity) and decision making (criterion bias) in response to Internet ads with positive and negative content. Individual variation in trait motivational activation was measured using the Motivational Activation Measurement developed by A. Lang and her colleagues (A. Lang, Bradley, Sparks, & Lee, 2007). MAM indexes an individual's tendency to approach pleasant stimuli (ASA, Appetitive System Activation) and avoid unpleasant stimuli (DSA, Defensive System Activation). Results showed that individuals higher in ASA exert more cognitive effort during positive ads than individuals lower in ASA. Individuals higher in DSA exert more cognitive effort during negative ads compared to individuals lower in DSA. ASA did not predict recognition memory. However, individuals higher in DSA recognized ads better than those lower in DSA. The criterion bias data revealed participants higher in ASA had more conservative decision criterion, compared to participants lower in ASA. Individuals higher in DSA also showed more conservative decision criterion compared to individuals lower in DSA. The theoretical and practical implications are discussed.

Evaluating the Optoelectronic Quality of Hybrid Perovskites by Conductive Atomic Force Microscopy with Noise Spectroscopy

Lee, Byungho,Lee, Sangheon,Cho, Duckhyung,Kim, Jinhyun,Hwang, Taehyun,Kim, Kyung Hwan,Hong, Seunghun,Moon, Taeho,Park, Byungwoo American Chemical Society 2016 ACS APPLIED MATERIALS & INTERFACES Vol.8 No.45

<P>Organic-inorganic hybrid perovskite solar cells have emerged as promising candidates for next-generation solar cells. To attain high photovoltaic efficiency, reducing the defects in perovskites is crucial along with a uniform coating of the films. Also, evaluating the quality of synthesized perovskites via facile and adequate methods is important as well. Herein, CH3NH3PbI3 perovskites were synthesized by applying second solvent dripping to nonstoichiometric precursors containing excess CH3NH3I. The resulting perovskite films exhibited a larger average grain size with a better crystallinity compared to that from stoichiometric precursors. As a result, the performance of planar perovskite solar cells was significantly improved, achieving an efficiency of 14.3%. Furthermore, perovskite films were effectively analyzed using a conductive AFM and noise spectroscopy, which have been uncommon in the field of perovskite solar cells. Comparing the topography and photocurrent maps, the variation of photocurrents in nanoscale was systematically investigated, and a linear relationship between the grain size and photocurrent was revealed. Also, noise analyses with a conductive probe enabled examination of the defect density of perovskites at specific grain interiors by excluding the grain-boundary effect, and reduced defects were clearly observed for the perovskites using CH3NH3I-rich precursors.</P>

Changing pattern of postoperative body weight and its association with recurrence and survival after curative resection for gastric cancer.

Lee, Sang Eok,Lee, Jun Ho,Ryu, Keun Won,Nam, Byungho,Kim, Chan Gyoo,Park, Sook Ryun,Kook, Myeong-Cherl,Kim, Young-Woo G. Thieme 2012 Hepato-gastroenterology Vol.59 No.114

<P>The aim of this study was to assess the pattern of body weight change after gastrectomy for gastric cancer and its association with prognosis.</P>

Uniform Cs2SnI6 Thin Films for Lead‑Free and Stable Perovskite Optoelectronics via Hybrid Deposition Approaches

Byungho Lee,신병하,Byungwoo Park 대한금속·재료학회 2019 ELECTRONIC MATERIALS LETTERS Vol.15 No.2

Herein, we synthesized uniform Cs 2 SnI 6 fi lms by two kinds of hybrid deposition methods by considering volume expansioninvolved during phase transformations. First, oblique thermal evaporation for CsI followed by SnI 4 spin-coating resultedin uniform Cs 2 SnI 6 fi lms free of impurity phases. The rapid expansion (within 10 s of spin-coating) from CsI to Cs 2 SnI 6( ΔV = 106%) was accommodated by porous CsI fi lms inhibiting crack formation. Excess S nI4 on the C s 2S nI6 after spincoatingwas eff ectively removed by toluene washing without any damages to Cs 2 SnI 6 , and optimum deposition parameterswere suggested in terms of carrier mobility. Second, annealing CsI with SnI 4 vapor at 250 °C and post-annealing in the SnI 4and I 2 vapor at 300 °C produced Cs 2 SnI 6 fi lm with complete coverage. The slow reaction (70 min for a complete conversion)provided suffi cient time for complete diff usion of SnI 4 into CsI without crack formation even with compact CsI. Thenonradiative recombination path in Cs 2 SnI 6 was suppressed by post-annealing in the SnI 4 - and I 2 -atmosphere, as confi rmedfrom the enhanced photoluminescence.

Route to Improving Photovoltaics Based on CdSe/CdSe_<i>x</i>Te_1–<i>x</i> Type-II Heterojunction Nanorods: The Effect of Morphology and Cosensitization on Carrier Recombination and Transport

Lee, Sangheon,Flanagan, Joseph C.,Lee, Byungho,Hwang, Taehyun,Kim, Jaewook,Gil, Bumjin,Shim, Moonsub,Park, Byungwoo American Chemical Society 2017 ACS APPLIED MATERIALS & INTERFACES Vol.9 No.37

<P>One-dimensionally elongated nanoparticles with type-II staggered band offset are of potential use as light-harvesting materials for photovoltaics, but only a limited attention has been given to elucidate the factors governing the cell performance obtainable from such materials. Herein, we describe a combined strategy to enhance charge collection from CdSe/CdSexTe1-x type-II heterojunction nanorods (HNRs) utilized as light harvesters for sensitized solar cells. By integrating morphology- and composition-tuned type-II HNRs into solar cells, factors that yield interfaces favorable both for the electron injection into TiO2 and hole transfer to electrolyte are examined. Furthermore, it is shown that a more efficient photovoltaic system results from cosensitization with CdS quantum dots (QDs) predeposited on a TiO2 scaffold, which improves charge collection from HNRs. Electrochemical impedance spectroscopy (EIS) analysis suggests that such a synergistically enhanced system benefits from the decreased recombination within HNRs and facilitated charge transport through the cosensitized TiO2 electrode, even with the activation of a recombination path presumably related to the photogenerated holes in CdS QDs.</P>

Efficient Type-II Heterojunction Nanorod Sensitized Solar Cells Realized by Controlled Synthesis of Core/Patchy-Shell Structure and CdS Cosensitization

Lee, Sangheon,Flanagan, Joseph C.,Kim, Jaewook,Yun, Alan Jiwan,Lee, Byungho,Shim, Moonsub,Park, Byungwoo American Chemical Society 2019 ACS APPLIED MATERIALS & INTERFACES Vol.11 No.21

<P>Here, we report the successful application of core/patchy-shell CdSe/CdSe<SUB><I>x</I></SUB>Te<SUB>1-<I>x</I></SUB> type-II heterojunction nanorods (HNRs) to realize efficient sensitized solar cells. The core/patchy-shell structure designed to have a large type-II heterointerface without completely shielding the CdSe core significantly improves photovoltaic performance compared to other HNRs with minimal or full-coverage shells. In addition, cosensitization with CdS grown by successive ionic layer adsorption and reaction further improves the power conversion efficiency. One-diode model analysis reveals that the HNRs having exposed CdSe cores and suitably grown CdS result in significant reduction of series resistance. Investigation of the intercorrelation between diode quality parameters, diode saturation current density (<I>J</I><SUB>0</SUB>) and recombination order (β = (ideality factor)<SUP>−1</SUP>) reveals that HNRs with open CdSe cores exhibit reduced recombination. These results confirm that the superior performance of core/patchy-shell HNRs results from their fine-tuned structure: photocurrent is increased by the large type-II heterointerface and recombination is effectively suppressed due to the open CdSe core enabling facile electron extraction. An optimized power conversion efficiency of 5.47% (5.89% with modified electrode configuration) is reported, which is unmatched among photovoltaics utilizing anisotropic colloidal heterostructures as light-harvesting materials.</P> [FIG OMISSION]</BR>

실리카졸 약액의 환경영향성 검토 및 내구증진방안

이병호(Lee Byungho),김영훈(Kim Younghun),천병식(Chun Byungsik) 한국지반환경공학회 2010 한국지반환경공학회논문집 Vol.11 No.12

본 연구는 최근 개발된 실리카졸 그라우팅재의 환경영향성 및 내구성을 규명한 것으로써 연구에 사용된 그라우트재는 3차원 겔 형성재인 실리카졸 그라우팅제와 규산나트륨 그라우팅제에 대한 공학적 특성을 비교하기 위하여 전자현미경 촬영, 내화학성시험, 용탈시험, 투수시험 등을 통해 친환경성과 내구성을 규명하고자 하였다. 전자현미경 촬영 결과 실리카졸 그라우팅제의 표면 및 내부조직이 규산나트륨보다 치밀함을 확인할 수 있었다. 용탈시험 결과 용탈되는 원소의 총량도 극히 작아 친환경적인 재료임을 입증되어 지반주입재로써 적용성을 확인하였다. 투수시험 결과 실리카졸이 차수성면에서 현장에 적용하는데 무리가 없다고 판단되어 차수성을 요구하는 현장에 적용이 가능하다고 판단된다. This study was made on the fact that the environmental impact and durability of the recently developed alkali silicasol chemical grout material. The grout material used for this study was designed to understand its environmental impact and durability through the SEM, chemical resistance test, leaching test, permeability test. In order to compare with the engineering characteristics regarding alkali silicasol grout material and sodium silicate grout material. As a result of SEM, the surface and internal tissues of alkali silicasol grout material could be identified to be denser than those of sodium silicate. As a result of leaching test the adaptability was identified as grout material as it had proved to be an ecological material owing to the total amount of the element to be leached being extremely little. As a result of permeability test it is judged that it is possible to apply the silicasol to the site in the place requiring the water cut-off as the silicasol.