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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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Cancer Prediction using Clinical and Genomic Data Fusion: A Systematic Review 6

Cancer Prediction using Clinical and Genomic Data Fusion: A ...

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6th International Conference on Cybernetics and Intelligent System, ICORIS 2024

作者： Julian, Kelvin Nugroho, Kuncahyo Setyo Nirwantono, Rudi Pardamean, Bens Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Biotechnology Department Faculty of Engineering Bina Nusantara University Jakarta Indonesia

ISBN: (纸本)9798331539603

This systematic review provides a comprehensive overview of the methods used to integrate genomic and clinical data in cancer prediction. The review includes 19 studies across various cancers, including breast, colorectal, melanoma, lung, pancreatic, and thyroid. The studies employed different methods to combine genomic and clinical data, including weighted polygenic risk scores, genetic and non-genetic risk scores, and different machine learning algorithms. The results show significant improvements in model prediction performance accuracy across multiple studies. The review highlights the potential benefits of integrating genetic and phenotypic information to improve disease risk prediction models and inform personalized healthcare strategies. © 2024 IEEE.

关键词： Lung cancer

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Distinctly localized lipid phosphate phosphatases mediate endoplasmic reticulum glycerolipid metabolism in Arabidopsis

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Plant Cell 2023年第5期35卷 1548-1571页

作者： Nguyen, Van C. Nakamura, Yuki RIKEN Center for Sustainable Resource Science (CSRS) Yokohama 230-0045 Japan Institute of Plant and Microbial Biology Academia Sinica 128 Sec. 2 Academia Rd. Nankang Taipei 11529 Taiwan Molecular and Biological Agricultural Sciences Program Taiwan International Graduate Program Academia Sinica and National Chung Hsing University Taipei 11529 Taiwan Graduate Institute of Biotechnology National Chung Hsing University Taichung 40227 Taiwan Biotechnology Center National Chung Hsing University Taichung 40227 Taiwan Graduate School of Science The University of Tokyo Tokyo 113-8654 Japan

Inter-organelle communication is an integral subcellular process in cellular homeostasis. In plants, cellular membrane lipids are synthesized in the plastids and endoplasmic reticulum (ER). However, the crosstalk between these organelles in lipid biosynthesis remains largely unknown. Here, we show that a pair of lipid phosphate phosphatases (LPPs) with differential subcellular localizations is required for ER glycerolipid metabolism in Arabidopsis (Arabidopsis thaliana). LPPα2 and LPPϵ1, which function as phosphatidic acid phosphatases and thus catalyze the core reaction in glycerolipid metabolism, were differentially localized at ER and chloroplast outer envelopes despite their similar tissue expression pattern. No mutant phenotype was observed in single knockout mutants;however, genetic suppression of these LPPs affected pollen growth and ER phospholipid biosynthesis in mature siliques and seeds with compromised triacylglycerol biosynthesis. Although chloroplast-localized, LPPϵ1 was localized close to the ER and ER-localized LPPα2. This proximal localization is functionally relevant, because overexpression of chloroplastic LPPϵ1 enhanced ER phospholipid and triacylglycerol biosynthesis similar to the effect of LPPα2 overexpression in mature siliques and seeds. Thus, ER glycerolipid metabolism requires a chloroplast-localized enzyme in Arabidopsis, representing the importance of inter-organelle communication in membrane lipid homeostasis. © 2023 American Society of Plant Biologists.

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Fucoxanthin induces human melanoma cytotoxicity by thwarting the JAK2/STAT3/BCL-xL signaling axis

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Environmental Toxicology 2024年第6期39卷 3356-3366页

作者： Kuo, Min-Yung Dai, Wen-Chyi Chang, Jie-Li Chang, Jo-Shu Lee, Tse-Min Chang, Chia-Che Pediatric Surgery Division Department of Surgery Tungs' Taichung MetroHarbor Hospital Taichung Taiwan Doctoral Program in Biotechnology Industrial Innovation and Management National Chung Hsing University Taichung Taiwan Taichung Municipal Taichung First Senior High School Taichung Taiwan Department of Chemical and Materials Engineering Research Center for Smart Sustainable Circular Economy Tunghai University Taichung Taiwan Department of Life Sciences National Chung Hsing University Taichung Taiwan Department of Marine Biotechnology and Resources National Sun Yat-sen University Kaohsiung Taiwan Graduate Institute of Biomedical Sciences Master Program in Precision Health Doctoral Program in Translational Medicine Rong Hsing Research Center for Translational Medicine The iEGG and Animal Biotechnology Research Center National Chung Hsing University Taichung Taiwan Department of Medical Laboratory Science and Biotechnology Asia University Taichung Taiwan Department of Medical Research China Medical University Hospital Taichung Taiwan Traditional Herbal Medicine Research Center Taipei Medical University Hospital Taipei Taiwan

Melanoma is the most lethal skin malignancy. Fucoxanthin is a marine carotenoid with significant anticancer activities. Intriguingly, Fucoxanthin's impact on human melanoma remains elusive. Signal Transducer and Activator of Transcription 3 (STAT3) represents a promising target in cancer therapy due to its persistent activation in various cancers, including melanoma. Herein, we revealed that Fucoxanthin is cytotoxic to human melanoma cell lines A2758 and A375 while showing limited cytotoxicity to normal human melanocytes. Apoptosis is a primary reason for Fucoxanthin's melanoma cytotoxicity, as the pan-caspase inhibitor z-VAD-fmk drastically abrogated Fucoxanthin-elicited clonogenicity blockage. Besides, Fucoxanthin downregulated tyrosine 705-phosphorylated STAT3 (p-STAT3 (Y705)), either inherently present in melanoma cells or inducible by interleukin 6 (IL-6) stimulation. Notably, ectopic expression of STAT3-C, a dominant-active STAT3 mutant, abolished Fucoxanthin-elicited melanoma cell apoptosis and clonogenicity inhibition, supporting the pivotal role of STAT3 blockage in Fucoxanthin's melanoma cytotoxicity. Moreover, Fucoxanthin lowered BCL-xL levels by blocking STAT3 activation, while ectopic BCL-xL expression rescued melanoma cells from Fucoxanthin-induced killing. Lastly, Fucoxanthin was found to diminish the levels of JAK2 with dual phosphorylation at tyrosine residues 1007 and 1008 in melanoma cells, suggesting that Fucoxanthin impairs STAT3 signaling by blocking JAK2 activation. Collectively, we present the first evidence that Fucoxanthin is cytotoxic selectively against human melanoma cells while sparing normal melanocytes. Mechanistically, Fucoxanthin targets the JAK2/STAT3/BCL-xL antiapoptotic axis to provoke melanoma cell death. This discovery implicates the potential application of Fucoxanthin as a chemopreventive or therapeutic strategy for melanoma management. © 2024 Wiley Periodicals LLC.

关键词： Carotenoids

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Muntingia calabura fruits as sources of bioactive compounds and fermentative ethanol production

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Biomass Conversion and Biorefinery 2024年第4期14卷 4703-4714页

作者： Nasution, Fitriana Theanhom, Araya Arjcharoen Unpaprom, Yuwalee Ramaraj, Rameshprabu Manmai, Numchok Chumpookam, Jenjira Graduate School Kasetsart University Bangkok10900 Thailand Department of Horticulture Faculty of Agriculture Kasetsart University Bangkok10900 Thailand Program in Biotechnology Faculty of Science Maejo University Chiang Mai50290 Thailand School of Renewable Energy Maejo University Chiang Mai50290 Thailand Department of Forestry National Chung Hsing University Taichung402 Taiwan

Muntingia calabura is a neotropical tree. It is a reforestation tree that grows quickly. It has been neglected as a forest tree for a variety of reasons. However, M. calabura may be a viable alternative food and bioenergy source due to its ability to grow in hard conditions and, the fruit is nutritious. The fruit maturity stage is indicated by color change. There were three stages of maturity: the unripe stage with dull green color, mid ripe stage with green-yellow color, and ripe stage with red color: the total sugars and bioactive components were investigated. Total sugar increased in every maturity stage. The fruits are high in phenolic compounds, which are known for their antioxidant properties. In every stage of fruit ripeness, fructose was the most abundant sugar. M. calabura fruits were combined with the robust yeast Saccharomyces cerevisiae used for bioethanol production. The maximum ethanol productivity (30.531 g/L) was achieved after 48 h of fermentation. Overall, this study suggested that M. calabura fruits extract can be utilized for healthy bioactive compounds consumption as well as production of bioethanol in order to meet the energy demands. © 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.

关键词： Fruits

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Evaluating mechanism of banana pseudo-stem retting using seawater:A cost-effective surface pre-treatment approach

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Journal of Bioresources and Bioproducts 2024年第3期9卷 322-335页

作者： Prince Hotor Ahmed H.Hassanin Osbert Akatwijuka Mohamed A.H.Gepreel Mitsuo Yamamoto Yukie Saito Ahmed Abdel-Mawgood Egypt-Japan University of Science and Technology Biotechnology ProgramAlexandria GovernorateNew Borg Al Arab 21934Egypt Alexandria University Department of Textile EngineeringAlexandria GovernorateBab Sharqi 5424041Egypt Egypt-Japan University of Science and Technology Material Science and EngineeringAlexandria GovernorateNew Borg Al Arab 21934Egypt Graduate School of Agricultural and Life Sciences The University of TokyoBunkyo-KuTokyo 113-8657Japan

Retting has been employed to extract natural fibers from agricultural wastes as a biological and cost-effective approach for *** its global abundance,banana pseudo-stem is a promising agro-waste for lignocellulosic fiber *** this study,fibers were extracted from the pseudo-stems after being pre-treated under four conditions using seawater at room temperature for up to 35 d Bacterial isolation from the fresh seawater sample and screening for ligninolytic ability were *** load as well as laccase and manganese peroxidase enzyme activity profile assay during the retting duration were *** transform infrared(FT-IR)and X-day diffraction(XRD)analyses were also examined for both pre-treated and untreated extracted *** results shows that six out of the eight bacterial isolates had the ability to degrade *** treatments(Raw stem+Raw seawater)and(Autoclaved stem+Raw seawater)recorded the highest viable bacterial load of 9.24×102 and 4.46×102 CFU,respectively,on the 14th day of the retting ***,the highest laccase and manganese peroxidase enzymes activity was recorded for(Raw stem+Raw seawater)and(Autoclaved stem+Raw seawater)treatments in the second to the third *** FT-IR spectra of the pre-treated fibers revealed relative reductions in peaks attributed to polysaccharides and other amorphous substances for all retting *** XRD diffractogram revealed that the crystallinity index(CI)of pre-treated fibers increased in all seawater retting treatment ***,the CI for fibers pre-treated under enzymatic conditions were enhanced even after five *** analysis for selected bacterial isolates showed homology to sequences of Bacillus velezensis,Shewanella sp.L8–5,and Citrobacter amalonaticus and Bacillus subtilis j8 *** these findings,it was suggested that physical,biological,and chemical actions were collectively involved in the seawater retting process of banana ps

关键词： Seawater retting Banana pseudo-stem Natural fiber Enzyme activity Colony forming unit

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Virulence and Ecology of Agrobacteria in the Context of Evolutionary Genomics

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Annual Review of Phytopathology 2023年第1期61卷 1-23页

作者： Weisberg, Alexandra J. Wu, Yu Chang, Jeff H. Lai, Erh-Min Kuo, Chih-Horng Department of Botany and Plant Pathology Oregon State University Corvallis Oregon USA email: weisbeal@oregonstate.edu Institute of Plant and Microbial Biology Academia Sinica Taipei Taiwan email: chk@gate.sinica.edu.tw Molecular and Biological Agricultural Sciences Program Taiwan International Graduate Program National Chung Hsing University and Academia Sinica Taipei Taiwan Graduate Institute of Biotechnology National Chung Hsing University Taichung Taiwan Biotechnology Center National Chung Hsing University Taichung Taiwan

Among plant-associated bacteria, agrobacteria occupy a special place. These bacteria are feared in the field as agricultural pathogens. They cause abnormal growth deformations and significant economic damage to a broad range of plant species. However, these bacteria are revered in the laboratory as models and tools. They are studied to discover and understand basic biological phenomena and used in fundamental plant research and biotechnology. Agrobacterial pathogenicity and capability for transformation are one and the same and rely on functions encoded largely on their oncogenic plasmids. Here, we synthesize a substantial body of elegant work that elucidated agrobacterial virulence mechanisms and described their ecology. We review findings in the context of the natural diversity that has been recently unveiled for agrobacteria and emphasize their genomics and plasmids. We also identify areas of research that can capitalize on recent findings to further transform our understanding of agrobacterial virulence and ecology. © 2023 Annual Reviews Inc.. All rights reserved.

关键词： Agrobacterium evolution genomics phytopathogens plasmids virulence

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High-throughput molecular gut content analysis of aphids identifies plants relevant for potato virus Y epidemioiogy

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Insect Science 2024年第5期31卷 1489-1502页

作者： William Jacob Pitt William Rodney Cooper Derek Pouchnik Heather Headrick Punya Nachappa Department of Agricultural Biology Colorado State UniversityFort CollinsColoradoUSA Graduate Degree Program in Ecology Colorado State UniversityFort CollinsColoradoUSA USDA-ARS Temperate Tree Fruit and Vegetable Research Unit WapatoWashingtonUSA Laboratory for Biotechnology and BioanalysisWashington State University PullmanWashingtonUSA Tree Fruit Research and Extension Center Washington State UniversityWenatcheeWashingtonUSA

Aphids are phloem-feeding insects that reduce crop productivity due to feeding and transmission of plant *** aphids disperse across the landscape to colonize new host plants,they will often probe on a wide variety of nonhost plants before settling on a host suitable for feeding and *** is limited understanding of the diversity of plants that aphids probe on within a landscape,and characterizing this diversity can help us better understand host use patterns of ***,we used gut content analysis(GCA)to identify plant genera that were probed by aphid vectors of potato virus Y(PVY).Aphids were trapped weekly near potato fields during the growing seasons of 2020 and 2021 in San Luis Valley in ***-throughput sequencing of plant barcoding genes,trnF and ITS2,from 200 individual alate(i.e.,winged)aphids representing nine vector species of PVY was performed using the PacBio sequencing platform,and sequences were identi-fied to genus using NCBI *** found that 34.7%of aphids probed upon presumed PVY host plants and that two of the most frequently detected plant genera,Solanum and Brassica,represent important crops and weeds within the study *** found that 75%of aphids frequently probed upon PVY nonhosts including many species that are outside of their reported host ***,19%of aphids probed upon more than one plant *** study provides the first evidence from high-throughput molecular GCA of aphids and reveals host use patterns that are relevant for PVY epidemiology.

关键词： aphids epidemiology gut content analysis insect ecology plant-insect in-teractions plant disease

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Relationship of Resistance-Related Enzyme Activity and Salicylic Acid Content in Phalaenopsis Species with Different Levels of Resistance to Dickeya dadantii

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Journal of Horticultural Research 2021年第2期29卷 31-44页

作者： Sanjaya, I Putu Wahyu Sukma, Dewi Sudarsono, Sudarsono Chan, Ming-Tsair Plant Breeding and Biotechnology Study Program Graduate School IPB University Indonesia Department of Agronomy and Horticulture Faculty of Agriculture IPB University Indonesia Academia Sinica Biotechnology Center in Southern Taiwan Taiwan

Orchids (Phalaenopsis) are ornamental plants that are cultivated commercially and in great demand in the market. Soft-rot disease (SRD) caused by the necrotrophic pathogen Dickeya dadantii is a cause of considerable economic loss to cultivators of many orchid species. Our previous experiment identified a limited number of species that were resistant to D. dadantii. This study aimed to validate the resistance level of four Phalaenopsis species in a detached leaf inoculation protocol to identify the resistance mechanism(s) involved. Soft-rot symptom diameter was measured from 6 to 18 hours post-inoculation (HPI) with D. dadantii. Disease assessment confirmed that P. amboinensis is a resistant species, P. pantherina is a susceptible species, and P. amabilis and P. schilleriana are very susceptible species. There was no difference in the lignin content between the resistant and very susceptible species. Detailed observation of resistant and very susceptible species, P. amboinensis vs. P. amabilis, revealed higher phenylalanine ammonia-lyase (PAL) and peroxidase (POD) in P. amabilis than in P. amboinensis. In contrast, there was higher salicylic acid (SA) content in P. amboinensis than in P. amabilis. These results suggest that POD and PAL activities may not be effective in defense against soft-rot disease, while SA plays an important role in the resistance of P. amboinensis to D. dadantii. Low PAL activity in P. amboinensis implies that the SA contents from the isochorismate pathway may be involved in the mechanism of P. amboinensis resistance to D. dadantii. Therefore, endogenous SA content may be a good indicator for screening resistant species in Phalaenopsis. © 2021 I Putu Wahyu Sanjaya et al., published by Sciendo.

关键词： Salicylic acid

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How does the brown mussel Perna perna respond to environmental pollution?A review on pollution biomarkers

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Journal of Environmental Sciences 2022年第1期34卷 412-428页

作者： Fernanda Silva dos Santos Raquel A.F.Neves Mirian Araújo Carlos Crapez Valéria Laneuville Teixeira Natascha Krepsky Fluminense Federal University(UFF) Institute of BiologyGraduate Program in Science and BiotechnologyMario Santos Braga Streets/n.CentroNiteróiRJ CEP 24.020-141Brazil Federal University of the State of Rio de Janeiro(UNIRIO) Institute of Biosciences(IBIO)Graduate Program in Neotropical Biodiversity(PPGBIO)Pasteur Avenue458.UrcaRio de JaneiroRJ CEP 22.290-255Brazil Fluminense Federal University(UFF) Institute of BiologyGraduate Program in Marine Biology and Coastal EnvironmentsMario Santos Braga Streets/n.CentroNiteróiRJ CEP 24.020-141Brazil Federal University of the State of Rio de Janeiro(UNIRIO) Institute of Biosciences(IBIO)Graduate Program in Ecotourism and ConservationPasteur Avenue458.UrcaRio de JaneiroRJ CEP 22.290-255Brazil

The brown mussel Perna perna(Linnaeus,1758)is a valuable resource for aquaculture in tropical and subtropical coastal *** presents desirable characteristics for biomonitoring,including being sessile,widely distributed and abundant,and is a filter-feeder able to accumulate several classes of pollutants(e.g.,metals,hydrocarbons,among others).Mussels’biological responses to pollution exposure can be measured as biomarkers,which include alterations ranging from molecular to physiological levels,to estimate the degree of environmental contamination and its effects on *** full review compiles two decades(2000–2020)of literature concerning biological effects on *** mussel caused by environmental pollutants(i.e.,metals,hydrocarbons,and emerging pollutants),considering environmental and farm-based *** markers related to mussels’oxidative status were efficient for the biomonitoring of metals(i.e.,antioxidant enzymes associated with oxidative damage in biomolecules).Genotoxicity and cytotoxicity indicators(i.e.,comet,micronucleus,and neutral red assays)provided a depiction of hydrocarbon *** neutral red assay gave a time-concentration cytotoxic response to a wide range of pollutants,including emerging pollutants(e.g.,pharmaceuticals and biocides)and *** perna hemocyte parameters provided a useful approach for biocide *** paper summarizes useful biomarkers from molecular to physiological levels in this mussel species used to identify and quantify the degree of coastal *** integrated biomarker analysis may provide a way to overcome possible biomarker variations and assess multi-polluted ***,it is necessary to investigate biomarker variations according to natural factors(e.g.,season and gonad maturation stage)to standardize them for trustworthy biomonitoring.

关键词： Biological indexes Biomonitoring Emerging pollutants Hydrocarbons Metals Sentinel species

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