A Genetically Encoded Biosensor for the Detection of Levulinic Acid

Kim Tae Hyun,Woo Seung-Gyun,Kim Seong Keun,Yoo Byeong Hyeon,Shin Jonghyeok,Rha Eugene,Kim Soo Jung,Kwon Kil Koang,Lee Hyewon,Kim Haseong,Kim Hee-Taek,Sung Bong-Hyun,Lee Seung-Goo,Lee Dae-Hee 한국미생물·생명공학회 2023 Journal of microbiology and biotechnology Vol.33 No.4

Levulinic acid (LA) is a valuable chemical used in fuel additives, fragrances, and polymers. In this study, we proposed possible biosynthetic pathways for LA production from lignin and poly(ethylene terephthalate). We also created a genetically encoded biosensor responsive to LA, which can be used for screening and evolving the LA biosynthesis pathway genes, by employing an LvaR transcriptional regulator of Pseudomonas putida KT2440 to express a fluorescent reporter gene. The LvaR regulator senses LA as a cognate ligand. The LA biosensor was first examined in an Escherichia coli strain and was found to be non-functional. When the host of the LA biosensor was switched from E. coli to P. putida KT2440, the LA biosensor showed a linear correlation between fluorescence intensity and LA concentration in the range of 0.156–10 mM LA. In addition, we determined that 0.156 mM LA was the limit of LA detection in P. putida KT2440 harboring an LA-responsive biosensor. The maximal fluorescence increase was 12.3-fold in the presence of 10 mM LA compared to that in the absence of LA. The individual cell responses to LA concentrations reflected the population-averaged responses, which enabled high-throughput screening of enzymes and metabolic pathways involved in LA biosynthesis and sustainable production of LA in engineered microbes.

Genetic Enzyme Screening System

Haseong KIM,Dae-Hee LEE,Seung-Goo LEE 한국생물공학회 2015 한국생물공학회 학술대회 Vol.2015 No.10

S-188 Incidental pulmonary thromboembolism in malignancy: Clinical characteristics and outcome

( Haseong Chang ),( Eun Kyung Kim ),( Duk-kyung Kim ) 대한내과학회 2016 대한내과학회 추계학술발표논문집 Vol.2016 No.1

Background:?Incidental pulmonary thromboembolism (PTE) is defined as PTE diagnosed on routine computed tomography (CT) without clinical suspicion of PTE. It is a relatively frequent finding occurring 2 to 4% in cancer patients undergoing CT scans for staging work up or treatment response evaluation. Nevertheless, the optimal management of the incidental PTE remains unknown and current treatment choices largely depend on individual clinician’s preference rather than established guidelines. We aim to evaluate clinical characteristics of incidental PTE and its impact on overall survival with or without treatment. Patients and Methods:?We performed a retrospective review of electronic medical records in a single cancer center to identify cancer patients with PTE. We used Cox’s proportional hazard model to assess effect of anticoagulation treatment on incidental PTE. Subgroup analysis was performed to determine whether the effect of treatment was consistent across patients with different embolic burden. Results:?Among 704 cancer patients diagnosed with pulmonary thromboembolism, incidental PTE was identified in 474(67.3%) patients. Compared to symptomatic patients, they tend to have less embolic burden represented by lower rate of both lung involvement and RV dysfunction on echocardiography. Only 52.5% of patients with incidental PTE were treated with anticoagulation for differing duration. While symptomatic PTE showed improved survival with anticoagulation treatment (median survival 6.0 vs 17.3 months, p=0.003), anticoagulation did not result in significant survival benefit in incidental PTE (median survival 15.1 vs 22.1, p=0.205). However, in subgroup analysis, significant survival improvement by anticoagulation was found in proximal incidental PTE (median survival 12.2 vs 23.4 months, p=0.020), but not in distal incidental PTE (15.1 vs 21.2, p=0.906).?Conclusions:?Benefits of anticoagulation treatment differs according to embolic burden in cancer patients with incidental PTE. Proximal incidental PTE warrants anticoagulation treatment while distal incidental PTE may not. Prospective study is needed to confirm this finding.

CRISPRi-Guided Metabolic Engineering of Escherichia coli

Kim SEONG KEUN,Kim HASEONG,Seong WONJAE,Woo SEUNG-GYUN,Lee SEUNG-GOO,Lee DAE-HEE 한국생물공학회 2018 한국생물공학회 학술대회 Vol.2018 No.4

Queuing Networks for Genetic Networks

Haseong KIM,Seung-Goo LEE 한국생물공학회 2014 한국생물공학회 학술대회 Vol.2014 No.4

Effective detection of hazardous compounds with biosensor mixture and 3D printed remote monitoring device

Haseong KIM,Eugene RHA,Soo-Jin KIM,Wonjae SEONG,Hyewon LEE,Seung-goo LEE 한국생물공학회 2019 한국생물공학회 학술대회 Vol.2019 No.10

Distributed CRC scheme for low-complexity successive cancellation flip decoding of polar codes

Haseong Kim,Hyunjee Lee,박호성 한국통신학회 2022 ICT Express Vol.8 No.3

In this paper, we propose a novel successive cancellation flip (SCF) decoding to reduce the computational complexity compared to the conventional SCF decoding by using distributed CRC bits. The proposed decoding reduces the number of estimations for information bits by early termination of decodings for failed frames of the first SC decoding, while trying to minimize the additional sorting operations. Simulation results show that the proposed SCF decoding reduces the computational complexity of repeated SC decoding at least 27% compared to the conventional SCF decoding.

High-throughput part characterization tools with a long-read sequencing technique

Haseong KIM 한국생물공학회 2021 한국생물공학회 학술대회 Vol.2021 No.10

It is known that the optimal performance of a metabolic pathway is achieved by the appropriate expression balance among genes. However, investigating each DNA part that controls the expression of the genes requires time-consuming cloning experiments along with high-cost equipment measuring single-cell fluoresce. This study presents a high-throughput part characterizing technique that increases cloning throughput by combinatorial DNA part assembly approach and quantifies the part characteristics with High-reproducibility plate based image analysis. The PCR based long-read sequencing technique allows us fast identification of part combinations and their genotypes regardless relatively low base-calling accuracy of the long-read sequencing technique. We confirmed the ratios of the part combinations were constantly remained in each assembly step and the fluorescent intensities of the colonies on plates were comparable to the single-cell level fluorescence from a high-end flowcytometry device. Quantitative values of twenty DNA parts (23 promoters and 23 RBSs) were successfully obtained in 1 week without any automated and expensive devices. We anticipate that this high-throughput and easy-to-use part characterization technique will contribute to increase the available parts in the synthetic biology community.

CRISPR interference-guided balancing of a biosynthetic mevalonate pathway increases terpenoid production

Kim, Seong Keun,Han, Gui Hwan,Seong, Wonjae,Kim, Haseong,Kim, Seon-Won,Lee, Dae-Hee,Lee, Seung-Goo Elsevier 2016 Metabolic engineering Vol.38 No.-

<P><B>Abstract</B></P> <P>Methods for simple and efficient regulation of metabolic pathway genes are essential for maximizing product titers and conversion yields, and for minimizing the metabolic burden caused by heterologous expression of multiple genes often in the operon context. Clustered regularly interspaced short palindromic repeats (CRISPR) interference (CRISPRi) is emerging as a promising tool for transcriptional modulation. In this study, we developed a regulatable CRISPRi system for fine-tuning biosynthetic pathways and thus directing carbon flux toward target product synthesis. By exploiting engineered <I>Escherichia coli</I> harboring a biosynthetic mevalonate (MVA) pathway and plant-derived terpenoid synthases, the CRISPRi system successfully modulated the expression of all the MVA pathway genes in the context of operon and blocked the transcription of the acetoacetyl-CoA thiolase enzyme that catalyzes the first step in the MVA pathway. This CRISPRi-guided balancing of expression of MVA pathway genes led to enhanced production of (-)-α-bisabolol (C15) and lycopene (C40) and alleviation of cell growth inhibition that may be caused by expression of multiple enzymes or production of toxic intermediate metabolites in the MVA pathway. Coupling CRISPRi to cell growth by regulating an endogenous essential gene (<I>ispA</I>) increased isoprene (C5) production. The regulatable CRISPRi system proved to be a robust platform for systematic modulation of biosynthetic and endogenous gene expression, and can be used to tune biosynthetic metabolic pathways. Its application can enable the development of microbial ‘smart cell’ factories that can produce other industrially valuable products in the future.</P> <P><B>Highlights</B></P> <P> <UL> <LI> A regulatable CRISPR interference (CRISPRi) system was developed. </LI> <LI> Developed CRISPRi system was successfully applied to terpenoid production. </LI> <LI> CRISPRi-guided balancing of MVA pathway greatly enhanced terpenoid production. </LI> <LI> Regulatable CRISPRi system can be a powerful tool for metabolic engineering. </LI> </UL> </P>

Partitioning of functional gene expression data using principal points

Kim, Jaehee,Kim, Haseong BioMed Central 2017 BMC bioinformatics Vol.18 No.1

<P><B>Background</B></P><P>DNA microarrays offer motivation and hope for the simultaneous study of variations in multiple genes. Gene expression is a temporal process that allows variations in expression levels with a characterized gene function over a period of time. Temporal gene expression curves can be treated as functional data since they are considered as independent realizations of a stochastic process. This process requires appropriate models to identify patterns of gene functions. The partitioning of the functional data can find homogeneous subgroups of entities for the massive genes within the inherent biological networks. Therefor it can be a useful technique for the analysis of time-course gene expression data. We propose a new self-consistent partitioning method of functional coefficients for individual expression profiles based on the orthonormal basis system.</P><P><B>Results</B></P><P>A principal points based functional partitioning method is proposed for time-course gene expression data. The method explores the relationship between genes using Legendre coefficients as principal points to extract the features of gene functions. Our proposed method provides high connectivity in connectedness after clustering for simulated data and finds a significant subsets of genes with the increased connectivity. Our approach has comparative advantages that fewer coefficients are used from the functional data and self-consistency of principal points for partitioning. As real data applications, we are able to find partitioned genes through the gene expressions found in budding yeast data and <I>Escherichia coli</I> data.</P><P><B>Conclusions</B></P><P>The proposed method benefitted from the use of principal points, dimension reduction, and choice of orthogonal basis system as well as provides appropriately connected genes in the resulting subsets. We illustrate our method by applying with each set of cell-cycle-regulated time-course yeast genes and <I>E. coli</I> genes. The proposed method is able to identify highly connected genes and to explore the complex dynamics of biological systems in functional genomics.</P>