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Discovering peptides and computational investigations of a multiepitope vaccine target Mycobacterium tuberculosis

Synthetic and Systems biotechnology 2024年第3期9卷 391-405页

作者： Truc Ly Nguyen Heebal Kim Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences Seoul National UniversitySeoul08826Republic of Korea Interdisciplinary Program in Bioinformatics Seoul National UniversitySeoul08826Republic of Korea eGnome Inc.Seoul05836Republic of Korea

Mycobacterium tuberculosis(MTB)is the causative agent of tuberculosis(TB),a prevalent airborne infectious *** the availability of the Bacille Calmette-Guerin vaccine,its global efficacy remains modest,and tuberculosis persists as a significant global public health *** this challenge and advancing towards the End MTB Strategy,we developed a multiepitope vaccine(MEV)based on immunoinformatics and compu-tational *** screening of MBT protein identified immune-dominant epitopes based on Major Histocompatibility Complex(MHC)allele binding,immunogenicity,antigenicity,allergenicity,toxicity,and cytokine *** epitopes were integrated into an MEV construct with adjuvant and linkers,forming a fully immunogenic vaccine *** analyses encompassed the evaluation of immunological and physicochemical properties,determination of tertiary structure,molecular docking with Toll-Like Receptors(TLR),molecular dynamics(MD)simulations for all atoms,and immune *** MEV comprises 534 amino acids,featuring 6 cytotoxic T lymphocyte,8 helper T lymphocyte,and 7 linear B lymphocyte epitopes,demonstrating high antigenicity and ***,molecular docking studies and triplicate MD simulations revealed enhanced interactions and stability of MEV with the TLR4 complex compared to *** addition,the immune simulation indicated the capacity to effectively induce elevated levels of an-tibodies and cytokines,emphasizing the vaccine’s robust immunogenic *** study presents a promising MEV against TB,exhibiting favorable immunological and physicochemical *** findings provide theoretical support for TB vaccine *** study aligns with the global initiative of the End MTB Strategy,emphasizing its potential impact on addressing persistent challenges in TB control.

关键词： Mycobacterium tuberculosis Tuberculosis Multiepitope vaccine Docking molecular Molecular dynamics simulation Immune simulation

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Development of virus-induced genome editing methods in Solanaceous crops

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园艺研究（英文） 2024年第1期11卷 13-26页

作者： Seo-Young Lee Bomi Kang Jelli Venkatesh Joung-Ho Lee Seyoung Lee Jung-Min Kim Seungki Back Jin-Kyung Kwon Byoung-Cheorl Kang Department of Agriculture Forestry and BioresourcesResearch Institute of Agriculture and Life SciencesPlant Genomics Breeding InstituteCollege of Agriculture and Life SciencesSeoul National UniversitySeoul 08826Republic of Korea Interdisciplinary Program in Agricultural Biotechnology College of Agriculture and Life SciencesSeoul National UniversitySeoul 08826Republic of Korea Department of Agriculture Forestry and BioresourcesResearch Institute of Agriculture and Life SciencesPlant Genomics Breeding InstituteCollege of Agriculture and Life SciencesSeoul National UniversitySeoul 08826Republic of Korea Interdisciplinary Program in Agricultural Biotechnology College of Agriculture and Life SciencesSeoul National UniversitySeoul 08826Republic of Korea

Genome editing(GE)using CRISPR/Cas systems has revolutionized plant ***,conventional transgene-mediated GE methods have limitations due to the time-consuming generation of stable transgenic lines expressing the Cas9/single guide RNA(sgRNA)module through tissue ***-induced genome editing(VIGE)systems have been successfully employed in model plants,such as Arabidopsis thaliana and Nicotiana *** this study,we developed two VIGE methods for Solanaceous ***,we used the tobacco rattle virus(TRV)vector to deliver sgRNAs into a transgenic tomato(Solanum lycopersicum)line of cultivar Micro-Tom expressing ***,we devised a transgene-free GE method based on a potato virus X(PVX)vector to deliver Cas9 and *** designed and cloned sgRNAs targeting Phytoene desaturase in the VIGE vectors and determined optimal conditions for *** evaluated VIGE efficiency through deep sequencing of the target gene after viral vector inoculation,detecting 40.3％and 36.5％mutation rates for TRV-and PVX-mediated GE,*** improve editing efficiency,we applied a 37℃ heat treatment,which increased the editing efficiency by 33％to 46％and 56％to 76％for TRV-and PVX-mediated VIGE,*** obtain edited plants,we subjected inoculated cotyledons to tissue culture,yielding successful editing *** also demonstrated that PVX-mediated GE can be applied to other Solanaceous crops,such as potato(Solanum tuberosum)and eggplant(Solanum melongena).These simple and highly efficient VIGE methods have great potential for generating genome-edited plants in Solanaceous crops.

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Integrating immunoinformatics and computational epitope prediction for a vaccine candidate against respiratory syncytial virus

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Infectious Disease Modelling 2024年第3期9卷 763-774页

Respiratory syncytial virus(RSV)poses a significant global health threat,especially affecting infants and the *** this,the present study proposes an innovative approach to vaccine design,utilizing immunoinformatics and computational *** analyzed RSV's structural proteins across both subtypes A and B,identifying potential helper T lymphocyte,cytotoxic T lymphocyte,and linear B lymphocyte *** such as antigenicity,allergenicity,toxicity,and cytokine-inducing potential were rigorously ***,we evaluated the conservancy of these epitopes and their population coverage across various RSV *** comprehensive analysis identified six major histocompatibility complex class I(MHC-I)binding,five MHC-II binding,and three B-cell *** were integrated with suitable linkers and adjuvants to form the ***,molecular docking and molecular dynamics simulations demonstrated stable interactions between the vaccine candidate and human Toll-like receptors(TLR4 and TLR5),with a notable preference for *** simulation analysis underscored the vaccine's potential to elicit a strong immune *** study presents a promising RSV vaccine candidate and offers theoretical support,marking a significant advancement in vaccine development ***,the promising in silico findings need to be further validated through additional in vivo studies.

关键词： Respiratory syncytial virus Multiepitope vaccine Immunoinformatics Docking molecular Molecular dynamics simulation Immune simulation

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ESR2–HDA6 complex negatively regulates auxin biosynthesis to delay callus initiation in Arabidopsis leaf explants during tissue culture

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Plant Communications 2024年第7期5卷 200-214页

作者： Kyounghee Lee Hobin Yoon Ok-Sun Park Jongbu Lim Sang-Gyu Kim Pil Joon Seo Department of Chemistry Seoul National UniversitySeoul 08826Korea Research Institute of Basic Sciences Seoul National UniversitySeoul 08826Korea Interdisciplinary Program in Agricultural Biotechnology Seoul National UniversitySeoul 08826Korea Plant Genomics and Breeding Institute Seoul National UniversitySeoul 08826Korea Department of Biological Sciences KAISTDaejeon 34141Korea

Plants exhibit an astonishing ability to regulate organ regeneration upon *** of leaf explants promotes the biosynthesis of indole-3-acetic acid(IAA),which is polar-transported to excised regions,where cell fate transition leads to root founder cell specification to induce de novo root *** regeneration capacity of plants has been utilized to develop in vitro tissue culture ***,we report that IAA accumulation near the wounded site of leaf explants is essential for callus formation on 2,4-dichlorophenoxyacetic acid(2,4-D)-rich callus-inducing medium(CIM).Notably,a high concentration of 2,4-D does not compensate for the action of IAA because of its limited efflux;rather,it lowers IAA biosynthesis via a negative feedback mechanism at an early stage of in vitro tissue culture,delaying callus *** auxin negative feedback loop in CIM-cultured leaf explants is mediated by an auxin-inducible APETALA2 transcription factor,ENHANCER OF SHOOT REGENERATION 2(ESR2),along with its interacting partner HISTONE DEACETYLASE 6(HDA6).The ESR2–HDA6 complex binds directly to,and removes the H3ac mark from,the YUCCA1(YUC1),YUC7,and YUC9 loci,consequently repressing auxin biosynthesis and inhibiting cell fate transition on 2,4-D-rich *** findings indicate that negative feedback regulation of auxin biosynthesis by ESR2 and HDA6 interferes with proper cell fate transition and callus initiation.

关键词： auxin biosynthesis negative feedback loop ESR2 HDA6 YUCCA chromatin modification

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HYBRID QUANTUM NEURAL NETWORKS WITH VARIATIONAL QUANTUM REGRESSOR FOR ENHANCING QSPR MODELING OF CO2-CAPTURING AMINE

arXiv

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arXiv 2025年

作者： Cho, Hyein Kim, Jeonghoon Lim, Hocheol The Interdisciplinary Graduate Program in Integrative Biotechnology & Translational Medicine Yonsei University Incheon Korea Republic of Incheon Korea Republic of

Accurate amine property prediction is essential for optimizing CO2 capture efficiency in postcombustion processes. Quantum machine learning (QML) can enhance predictive modeling by leveraging superposition, entanglement, and interference to capture complex correlations. In this study, we developed hybrid quantum neural networks (HQNN) to improve quantitative structure-property relationship modeling for CO2-capturing amines. By integrating variational quantum regressors with classical multi-layer perceptrons and graph neural networks, quantum advantages were explored in physicochemical property prediction under noiseless conditions and robustness was evaluated against quantum hardware noise using IBM quantum systems. Our results showed that HQNNs improve predictive accuracy for key solvent properties, including basicity, viscosity, boiling point, melting point, and vapor pressure. The fine-tuned and frozen pre-trained HQNN models with 9 qubits consistently achieved the highest rankings, highlighting the benefits of integrating quantum layers with pretrained classical models. Furthermore, simulations under hardware noise confirmed the robustness of HQNNs, maintaining predictive performance. Overall, these findings emphasize the potential of hybrid quantum-classical architectures in molecular modeling. As quantum hardware and QML algorithms continue to advance, practical quantum benefits in QSPR modeling and materials discovery are expected to become increasingly attainable, driven by improvements in quantum circuit design, noise mitigation, and scalable architectures. © 2025, CC BY-NC-ND.

关键词： Quantum entanglement

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The processed C-terminus of AvrRps4 effector suppresses plant immunity via targeting multiple WRKYs

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Journal of Integrative Plant Biology 2024年第8期66卷 1769-1787页

作者： Quang-Minh Nguyen Arya Bagus Boedi Iswanto Hobin Kang Jiyun Moon Kieu Anh Thi Phan Geon Hui Son Mi Chung Suh Eui-Hwan Chung Walter Gassmann Sang Hee Kim Division of Applied Life Science(BK21 Four Program) Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 52828Korea Department of Life Science Sogang UniversitySeoul 04107Korea Department of Plant Biotechnology Korea UniversitySeoul 02841Korea Division of Plant Science and Technology Christopher S.Bond Life Sciences Center and Interdisciplinary Plant GroupUniversity of MissouriColumbiaMissouri 65211USA Division of Life Science and Research Institute of Molecular Alchemy Gyeongsang National UniversityJinju 52828Korea

Pathogens generate and secrete effector proteins to the host plant cells during pathogenesis to promote virulence and *** the plant carries resistance(R)proteins that recognize pathogen effectors,effector-triggered immunity(ETI)is activated,resulting in a robust immune response and hypersensitive response(HR).The bipartite effector AvrRps4 from Pseudomonas syringae *** has been well studied in terms of avirulence *** planta,AvrRps4 is processed into two *** Cterminal fragment of AvrRps4(AvrRps4^(C))induces HR in turnip and is recognized by the paired resistance proteins AtRRS1/AtRPS4 in ***,we show that AvrRps4^(C)targets a group of Arabidopsis WRKY,including WRKY46,WRKY53,WRKY54,and WRKY70,to induce its virulence ***,AvrRps4^(C)suppresses the general binding and transcriptional activities of immune-positive regulator WRKY54 and WRKY54-mediated ***4^(C)interferes with WRKY54's binding activity to target gene SARD1 in vitro,suggesting WRKY54 is sequestered from the SARD1 promoter by AvrRps4^(C).Through the interaction of Avr Rps4^(C)with four WRKYs,AvrRps4 enhances the formation of homo-/heterotypic complexes of four WRKYs and sequesters them in the cytoplasm,thus inhibiting their function in plant ***,our results provide a detailed virulence mechanism of AvrRps4 through its C-terminus.

关键词： AvrRps4 bacterial effector effector-triggered immunity immune response suppression transcription factor WRKY

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SAGE-Amine: Generative Amine Design with Multi-Property Optimization for Efficient CO2 Capture

arXiv

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arXiv 2025年

作者： Lim, Hocheol Cho, Hyein Kim, Jeonghoon Incheon21983 Korea Republic of The Interdisciplinary Graduate Program in Integrative Biotechnology & Translational Medicine Yonsei University Incheon21983 Korea Republic of

Efficient CO2 capture is vital for mitigating climate change, with amine-based solvents being widely used due to their strong reactivity with CO2. However, optimizing key properties such as basicity, viscosity, and absorption capacity remains challenging, as traditional methods rely on labor-intensive experimentation and predefined chemical databases, limiting the exploration of novel solutions. Here, SAGE-Amine was introduced, a generative modeling approach that integrates Scoring-Assisted Generative Exploration (SAGE) with quantitative structure-property relationship models to design new amines tailored for CO2 capture. Unlike conventional virtual screening restricted to existing compounds, SAGE-Amine generates novel amines by leveraging autoregressive natural language processing models trained on amine datasets. SAGE-Amine identified known amines for CO2 capture from scratch and successfully performed single-property optimization, increasing basicity or reducing viscosity or vapor pressure. Furthermore, it facilitated multi-property optimization, simultaneously achieving high basicity with low viscosity and vapor pressure. The 10 top-ranked amines were suggested using SAGE-Amine and their thermodynamic properties were further assessed using COSMO-RS simulations, confirming their potential for CO2 capture. These results highlight the potential of generative modeling in accelerating the discovery of amine solvents and expanding the possibilities for industrial CO2 capture applications. © 2025, CC BY-NC-ND.

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Guardian of the rice:Unveiling OsSSP1 for broad-spectrum disease resistance

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Molecular Plant 2024年第7期17卷 996-998页

作者： You-Jin Lim Yong-Hwan Lee Research Institute of Agriculture and Life Sciences Seoul National UniversitySeoul08826Republic of Korea Department of Agricultural Biotechnology Seoul National UniversitySeoul 08826Republic of Korea interdisciplinary Program in Agricultural Genomics Center for Fungal Genetic ResourcesPlant Immunity Research Centerand Center for Plant Microbiome ResearchSeoul National UniversitySeoul 08826Republic of Korea

Plants are continuously exposed to numerous biotic stresses throughout their *** arms race-driven coevolution with pathogens,plants have developed sophisticated immune systems,including pathogen-associated molecular pattern(PAMP)-triggered immunity(PTI)and effector-triggered immunity(ETI).PTI is initiated by the binding of danger signals to extracellular membrane-localized receptors calledpattern recognition receptors(PRRs).PTI triggers responses,including reactive oxygen species(ROS)bursts and the expression of defenseassociated ***,pathogens adapted to PTl secrete virulence proteins,effectors,to aid colonization,and ETl is then triggered by the recognition of these effectors by resistance proteins with a nucleotide-binding domain leucinerich repeat receptor(NLR).To circumvent this immune response,pathogens secrete various effectors into the host intracellular region and induce effector-triggered susceptibility(Zhou and Zhang.,2020).Currently,research on plant immunity has been primarily focused on plasma membrane and cytoplasmlocalized proteins,including oligomeric NLRs,resistosomes,and the secretion mechanisms of cytoplasmic effectors.

关键词： immunity resistance Guard

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Evaluating Crosslinking Efficiency and Cytocompatibility of Three Commonly Used Photoinitiators Across Different Cell-Compatible Hydrogel Platforms

SSRN

引用

SSRN 2025年

作者： Gavish Moscovitz, Aya Simaan Yameen, Haneen Bar-Am, Orit Seliktar, Dror The Faculty of Biomedical Engineering Technion-Israel Institute of Technology Haifa Israel The Interdisciplinary Program in Biotechnology Technion–Israel Institute of Technology Haifa Israel

Biomedical hydrogels that undergo a rapid liquid-to-solid phase transition often use a photopolymerization strategy to crosslink the polymer network. In applications such as 3D bioprinting or tissue engineering that involve cell-laden hydrogels, or where in-vivo polymerization is desired (i.e., in-situ), cytotoxicity of the hydrogel crosslinking reaction becomes an important issue. There are only a few cytocompatible photoinitiators (PIs) that are commonly used for crosslinking biomedical hydrogels, including Irgacure2959 (I2959), lithium phenyl-2,4,6-trimethylbenzoylphosphinate (LAP) and EosinY (EY). These PIs are illuminated at 365nm, 405nm and 525nm, respectively. The photopolymerization conditions, including PI concentration and illumination intensity may affect both the cytotoxicity of the reaction and the crosslinking of the hydrogel. Herein we tested these three PIs to optimize the maximum crosslinking efficiency while minimizing cell death associated with the photochemical reaction. Testing was performed on three different types of cell-compatible hydrogels used for cell encapsulation and 3D cell growth, including a synthetic material (poly(ethylene glycol)-diacrylate, PEG-DA), a semi-synthetic material (PEG-fibrinogen, PF) and a modified biological material (methacrylated fibrinogen, FibMA). Strain-rate controlled rheology was used to characterize the crosslinking reaction efficiency, both in terms of maximum shear storage modulus, G’, and crosslinking kinetics. Viability was examined on human dermal fibroblasts in 3D culture within photopolymerized PF hydrogels crosslinked using each of the PIs. The results showed that PI concentration and the illumination intensity had significant impact on the crosslinking efficiency, with each material system demonstrating different responses to the PI parameters. Optimal photo-crosslinking conditions, considering both crosslinking efficiency and cell viability were not the same for the modified protein hydrogels, as co

关键词： Cell death

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Genome-wide identification and characterization of ACBP gene family in Populus reveal salinity alkali-responsive profiles

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Journal of Forestry Research 2023年第2期34卷 481-496页

作者： Yu Chang Xinru Xu Hongxia Zheng Hao Xie Bo Li Sixue Chen Ying Li Shaojun Dai Key Laboratory of Saline-Alkali Vegetation Ecology Restoration(Northeast Forestry University) Ministry of EducationCollege of Life SciencesNortheast Forestry UniversityHarbin 150040People’s Republic of China Development Center of Plant Germplasm Resources College of Life SciencesShanghai Normal UniversityShanghai 200234People’s Republic of China Department of Biology Genetics InstitutePlant Molecular and Cellular Biology ProgramInterdisciplinary Center for Biotechnology ResearchUniversity of FloridaGainesvilleFloridaUSA

Acyl-CoA-binding proteins(ACBPs)are important for the transport of acyl groups for macro molecular biosynthesis involved in plant growth,development,and diverse stress(e.g.,cold,drought,salinity,and heavy metals)***,we report the phylogeny and characteristics of the ACBP family in the woody plant Populus *** genes encoding ACBP proteins were identified,and they are distributed on eight chromosomes in *** PtACBP genes were divided into four subgroups according to gene structure,conserved motifs and phylogenetic *** analysis revealed that cis-elements were related to stress response,phytohormone response,and physical and reproductive growth *** levels of PtACBP genes varied among different organs,with the highest expression in leaves and the lowest in *** real-time PCR(qRT-PCR)analysis showed that under salinity-alkali stresses(i.e.,200 mM NaCl,75 mM Na2CO3,and 100 mM NaHCO3),four(PtACBP1,PtACBP3,PtACBP4 and PtACBP8)of eight PtACBP genes were significantly induced in roots and *** data provide a comprehensive analysis of the ACBPs family in ***,which could be useful for gene function analyses.

关键词： Acyl-CoA-binding proteins(ACBPs) Gene structure Expression pattern Stress response Populus trichocarpa

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