Category Archives: 研究發表

林志生教授研究團隊發表研究成果於Biosensors & Bioelectronics
連結網址： https://pubmed.ncbi.nlm.nih.gov/39102773/

Abstract
Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is
facilitated by its trimeric surface spike protein, which binds to the human angiotensin-
converting enzyme 2 (hACE2) receptor. This critical interaction facilitates viral entry
and is a primary target for therapeutic intervention against COVID-19. However, it is
difficult to fully optimize viral infection using existing protein-protein interaction
methods. Herein, we introduce a nano-luciferase binary technology (NanoBiT)-based
pseudoviral sensor designed to stimulate the dynamics of viral infection in both living
cells and animals. Infection progression can be dynamically visualized via a rapid
increase in luminescence within 3 h using an in vivo imaging system (IVIS).
Inhibition of viral infection by baicalein and baicalin was evaluated using a NanoBiT-
based pseudoviral sensor. These results indicate that the inhibitory efficacy of
baicalein was strengthened by targeting the spike protein, whereas baicalin targeted
the hACE2 protein. Additionally, under optimized conditions, baicalein and baicalin
provided a synergistic combination to inhibit pseudoviral infection. Live
bioluminescence imaging was used to evaluate the in vivo effects of baicalein and
baicalin treatment on LgBiT-hACE2 mice infected with the BA.2-SmBiT spike
pseudovirus. This innovative bioluminescent system functions as a sensitive and
early-stage quantitative viral transduction in vitro and in vivo. This platform provides
novel opportunities for studying the molecular biology of animal models.

林志生教授研究團隊發表研究成果於J Hazard Mater.

連結網址：https://pubmed.ncbi.nlm.nih.gov/39700942/

Abstract

Particulate matter 2.5 (PM2.5) pollution and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic are the greatest environmental health issues worldwide. Several statistics revealed the significant positive correlation between the morbidity of coronavirus disease-19 (COVID-19) and the levels of air pollution. Nevertheless, there is no direct experimental evidence to indicate the effect of PM2.5 exposure on SARS-CoV-2 infection. The objective of this study was to evaluate whether the infection of SARS-CoV-2 affected by PM2.5 through angiotensin-converting enzyme II (ACE2) expression enhances and investigate the function of ACE2 in lung injury induced by PM2.5. An animal model of PM2.5-induced lung injury was established using wild-type (WT, C57BL/6), human ACE2 transgenic (K18-hACE2 TG), and murine ACE2 gene knockout (mACE2 KO) mice. The results indicate that PM2.5 exposure facilitates SARS-CoV-2 infection through inducing ACE2 expression in vitro (10 μg/mL) and in vivo (6.25 mg/kg/day in 50 μL saline). The levels of ACE, inflammatory cytokines, and mitogen-activated protein kinase (MAPK) proteins in WT, K18-hACE TG and mACE2 KO mice were significantly increased after PM2.5 instillation. The severest PM2.5-induced lung damage was observed in mACE2 KO mice. In summary, ACE2 plays a double-edged sword role in lung injury, PM2.5 exposure contributed to SARS-CoV-2 infection through inducing ACE2 expression, but ACE2 also protected pulmonary inflammation from PM2.5 challenge. Keywords: Air pollution; Angiotensin converting enzyme II; Inflammation; Particulate matter 2.5; Severe acute respiratory syndrome coronavirus 2.

林志生教授研究團隊發表研究成果於Biosensors & Bioelectronics

連結網址：https://pubmed.ncbi.nlm.nih.gov/39102773/

Abstract

Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is facilitated by its trimeric surface spike protein, which binds to the human angiotensin-converting enzyme 2 (hACE2) receptor. This critical interaction facilitates viral entry and is a primary target for therapeutic intervention against COVID-19. However, it is difficult to fully optimize viral infection using existing protein-protein interaction methods. Herein, we introduce a nano-luciferase binary technology (NanoBiT)-based pseudoviral sensor designed to stimulate the dynamics of viral infection in both living cells and animals. Infection progression can be dynamically visualized via a rapid increase in luminescence within 3 h using an in vivo imaging system (IVIS). Inhibition of viral infection by baicalein and baicalin was evaluated using a NanoBiT-based pseudoviral sensor. These results indicate that the inhibitory efficacy of baicalein was strengthened by targeting the spike protein, whereas baicalin targeted the hACE2 protein. Additionally, under optimized conditions, baicalein and baicalin provided a synergistic combination to inhibit pseudoviral infection. Live bioluminescence imaging was used to evaluate the in vivo effects of baicalein and baicalin treatment on LgBiT-hACE2 mice infected with the BA.2-SmBiT spike pseudovirus. This innovative bioluminescent system functions as a sensitive and early-stage quantitative viral transduction in vitro and in vivo. This platform provides novel opportunities for studying the molecular biology of animal models.

李明家副教授研究團隊發表研究成果於ACS Macro Lett.

連結網址：https://pubs.acs.org/doi/full/10.1021/acsmacrolett.4c00122

Abstract We report the preparation of chiral silica using a linear polysiloxane main chain with a preferred-handed helical structure as the template. Poly(methylvinyl siloxane) (PMVS) with a cysteine derivative side chain designated as PMVS-Cys was prepared using anionic polymerization and an ene-thiol reaction. PMVS-Cys forms a helical conformation in both solution and film via hydrogen bonding between amide groups at side chains. The helical structure remains during the calcination process, resulting in silica with helical structure. The silica with a helical structure shows optical activity.

林志生教授研究團隊發表研究成果於Bioresour Technol.
連結網址：https://pubmed.ncbi.nlm.nih.gov/38641299/

Abstract This study established and investigated continuous macular pigment (MP) production with a lutein (L):zeaxanthin (Z) ratio of 4-5:1 by an MP-rich Chlorella sp. CN6 mutant strain in a continuous microalgal culture module. Chlorella sp. CN6 was cultured in a four-stage module for 10 days. The microalgal culture volume increased to 200 L in the first stage (6 days). Biomass productivity increased to 0.931 g/L/day with continuous indoor white light irradiation during the second stage (3 days). MP content effectively increased to 8.29 mg/g upon continuous, indoor white light and blue light-emitting diode irradiation in the third stage (1 day), and the microalgal biomass and MP concentrations were 8.88 g/L and 73.6 mg/L in the fourth stage, respectively. Using a two-step MP extraction process, 80 % of the MP was recovered with a high purity of 93 %, and its L:Z ratio was 4-5:1.

林峻宇副教授研究團隊發表研究成果於Nucleic Acids Res

連結網址：https://pubmed.ncbi.nlm.nih.gov/38096046/

Abstract

Pathway analysis, including nontopology-based (non-TB) and topology-based (TB) methods, is widely used to interpret the biological phenomena underlying differences in expression data between two phenotypes. By considering dependencies and interactions between genes, TB methods usually perform better than non-TB methods in identifying pathways that include closely relevant or directly causative genes for a given phenotype. However, most TB methods may be limited by incomplete pathway data used as the reference network or by difficulties in selecting appropriate reference networks for different research topics. Here, we propose a gene set correlation enrichment analysis method, Gscore, based on an expression dataset-derived coexpression network to examine whether a differentially expressed gene (DEG) list (or each of its DEGs) is associated with a known gene set. Gscore is better able to identify target pathways in 89 human disease expression datasets than eight other state-of-the-art methods and offers insight into how disease-wide and pathway-wide associations reflect clinical outcomes. When applied to RNA-seq data from COVID-19-related cells and patient samples, Gscore provided a means for studying how DEGs are implicated in COVID-19-related pathways. In summary, Gscore offers a powerful analytical approach for annotating individual DEGs, DEG lists, and genome-wide expression profiles based on existing biological knowledge.

朱智瑋教授研究團隊發表研究成果於Nature Chemistry

連結網址：https://www.nature.com/articles/s41557-023-01361-4

Abstract

Many peptide-derived natural products are produced by non-ribosomal peptide synthetases (NRPSs) in an assembly-line fashion. Each amino acid is coupled to a designated peptidyl carrier protein (PCP) through two distinct reactions catalysed sequentially by the single active site of the adenylation domain (A-domain). Accumulating evidence suggests that large-amplitude structural changes occur in different NRPS states; yet how these molecular machines orchestrate such biochemical sequences has remained elusive. Here, using single-molecule Förster resonance energy transfer, we show that the A-domain of gramicidin S synthetase I adopts structurally extended and functionally obligatory conformations for alternating between adenylation and thioester-formation structures during enzymatic cycles. Complementary biochemical, computational and small-angle X-ray scattering studies reveal interconversion among these three conformations as intrinsic and hierarchical where intra-A-domain organizations propagate to remodel inter-A–PCP didomain configurations during catalysis. The tight kinetic coupling between structural transitions and enzymatic transformations is quantified, and how the gramicidin S synthetase I A-domain utilizes its inherent conformational dynamics to drive directional biosynthesis with a flexibly linked PCP domain is revealed.

王雲銘教授研究團隊發表研究成果於 Cancer Cell International

連結網址：https://pubmed.ncbi.nlm.nih.gov/38001420/

Abstract

Background: Despite intensive developments of adoptive T cell and NK cell therapies, the efficacy against solid tumors remains elusive. Our study demonstrates that macrophage-based cell therapy could be a potent therapeutic option against solid tumors.

Methods: To this end, we determine the effect of a natural triterpene glycoside, cucumarioside A₂-2 (CA₂-2), on the polarization of mouse macrophages into the M1 phenotype, and explore the antitumor activity of the polarized macrophage. The polarization of CA₂-2-pretreated macrophages was analyzed by flow cytometry and confocal imaging. The anti-cancer activity of CA₂-2 macrophages was evaluated against 4T1 breast cancer cells and EAC cells in vitro and syngeneic mouse model in vivo.

Results: Incubation of murine macrophages with CA₂-2 led to polarization into the M1 phenotype, and the CA₂-2-pretreated macrophages could selectively target and kill various types of cancer in vitro. Notably, loading near-infrared (NIR) fluorochrome-labeled nanoparticles, MnMEIO-mPEG-CyTE777, into macrophages substantiated that M1 macrophages can target and penetrate tumor tissues in vivo efficiently.

Conclusion: In this study, CA₂-2-polarized M1 macrophages significantly attenuated tumor growth and prolonged mice survival in the syngeneic mouse models. Therefore, ex vivo CA₂-2 activation of mouse macrophages can serve as a useful model for subsequent antitumor cellular immunotherapy developments.

Keywords: Anticancer; Cucumarioside A2-2; Holothurian triterpene glycoside; Immunotherapy; M1 macrophage.

蕭育源教授及朱智瑋教授研究團隊發表研究成果於Nucleic Acids Res

連結網址：https://pubmed.ncbi.nlm.nih.gov/37870446/

Abstract

In various autoimmune diseases, dysfunctional TREX1 (Three prime Repair Exonuclease 1) leads to accumulation of endogenous single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and DNA/RNA hybrids in the cytoplasm and triggers immune activation through the cGAS-STING pathway. Although inhibition of TREX1 could be a useful strategy for cancer immunotherapy, profiling cellular functions in terms of its potential substrates is a key step. Particularly important is the functionality of processing DNA/RNA hybrids and RNA substrates. The exonuclease activity measurements conducted here establish that TREX1 can digest both ssRNA and DNA/RNA hybrids but not dsRNA. The newly solved structures of TREX1-RNA product and TREX1-nucleotide complexes show that 2′-OH does not impose steric hindrance or specific interactions for the recognition of RNA. Through all-atom molecular dynamics simulations, we illustrate that the 2′-OH-mediated intra-chain hydrogen bonding in RNA would affect the binding with TREX1 and thereby reduce the exonuclease activity. This notion of higher conformational rigidity in RNA leading TREX1 to exhibit weaker catalytic cleavage is further validated by the binding affinity measurements with various synthetic DNA-RNA junctions. The results of this work thus provide new insights into the mechanism by which TREX1 processes RNA and DNA/RNA hybrids and contribute to the molecular-level understanding of the complex cellular functions of TREX1 as an exonuclease.