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Selecting optimal algal strains for robust photosynthetic upgrading of biogas under temperate oceanic climates

Biotechnology Advances 2025年 82卷 108581页

作者： Haider, Muhammad Nabeel O'Higgins, Linda O'Shea, Richard Archer, Lorraine Wall, David M. Verma, Nikita Rodero, María del Rosario Mehmood, Muhammad Aamer Murphy, Jerry D. Bose, Archishman MaREI Centre for energy climate and marine Environmental Research Institute University College Cork CorkT23 XE10 Ireland School of Engineering and Architecture University College Cork Ireland Department of Plant Sciences University of Cambridge Downing Street CambridgeCB2 3EA United Kingdom Institute of Sustainable Processes University of Valladolid Dr. Mergelina s/n. Valladolid47011 Spain Bioenergy Research Center Department of Bioinformatics and Biotechnology Government College University Faisalabad Faisalabad38000 Pakistan

Biogas generated from anaerobic digestion can be upgraded to biomethane by photosynthetic biogas upgrading, using CO2 as a bioresource for algal (cyanobacteria and microalgae) cultivation. This allows the upgrading technology to offer economic and environmental benefits to conventional physiochemical upgrading techniques (which can be energy-intensive and costly) by co-generating biomethane with high-value biomass. However, a critical challenge in implementing this technology in temperate oceanic climatic conditions (as found in Japan, and the northwest coasts of Europe and of North America, with average temperatures ranging between 5 and 20 °C) is the selection of algal strains that must be capable of sustained growth under lower ambient temperatures. Accordingly, this paper investigated the selection of algae that met seven key criteria: optimal growth at high pH (9–11);at alkalinity of 1.5–2.5 g inorganic carbon per litre;operation at low temperature (5–20 °C);tolerance to high CO2 concentrations (above 20 %);capability for mixotrophic cultivation;ability to accumulate high-value metabolites such as photosynthetic pigments and bioactive fatty acids;and ease of harvesting. Of the twenty-six algal species assessed and ranked using a Pugh Matrix, Anabaena sp. and Phormidium sp. were assessed as the most favourable species, followed by Oscillatoria sp., Spirulina subsalsa, and Leptolyngbya sp. Adaptive laboratory evolution together with manipulation of abiotic factors could be effectively utilised to increase the efficiency and economic feasibility of the use of the selected strain in a photosynthetic biogas upgrading system, through improvement of growth and yield of high-value compounds. © 2024

关键词： Microalgae

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Label-free electrochemical biosensor in highly conductive carbon nanotube and gold nanocomplexes

Label-free electrochemical biosensor in highly conductive ca...

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13th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2009

作者： Park, Tae Jung Kong, Byung-Seon Jung, Hee-Tae Lee, Sang Yup BioProcess Engineering Research Center Center for Systems and Synthetic Biotechnology Institute for the BioCentury KAIST Korea Republic of KAIST Korea Republic of Department of Brain and Bioengineering Bioinformatics Research Center KAIST Korea Republic of

ISBN: (纸本)9780979806421

Transparent conducting carbon nanotube (CNT) films controlled by the single-walled CNT (SWNT) density in the film were fabricated on the glass, which have the electrical conductivity and the optical transparency. Furthermore, the SWNT film was investigated with gold-hybridization by simple and cheap process. The gold (Au)-fabricated CNT film was also utilized for the efficient immobilization of the Au binding polypeptide. We developed a strategy for fabricating a highly electric conductive device and detecting the biomolecular sensing. © 2009 CBMS.

关键词： Biosensors

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Quantification of Oxygen Tension Variation in an in Vitro Tumor Microenvironment Model Based on Co-Culture of Tumor Spheroid and Endothelial Cells in a Microfluidic Device

SSRN

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SSRN 2025年

作者： Chiang, Kuang-Hsing Chang, Wei-Jen Lin, Chih-Ting Wu, Hsiao-Mei Tung, Yi-Chung Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei10617 Taiwan Division of Cardiology Cardiovascular Research Center Department of Internal Medicine Taipei Medical University Hospital Taipei11031 Taiwan Taipei Heart Institute Taipei Medical University Taipei11031 Taiwan Division of Cardiology Department of Internal Medicine School of Medicine College of Medicine Taipei Medical University Taipei11031 Taiwan Research Center for Applied Sciences Academia Sinica Taipei11529 Taiwan Institute of Biophotonics National Yang Ming Chiao Tung University Taipei11221 Taiwan Department of Biomechatronics Engineering National Taiwan University Taipei10617 Taiwan

In this study, we developed an innovative in vitro tumor microenvironment model that integrates a tumor spheroid and a monolayer of endothelial cells within a microfluidic device, aiming to replicate the complex conditions of an avascular solid tumor with limited oxygen supply. The tumor spheroid is cultured in a gas-impermeable plastic chamber, which effectively simulates the hypoxic environment characteristic of solid tumors, thereby providing a realistic platform for studying tumor behavior and interactions with surrounding cells. To characterize the three-dimensional spatial oxygen tension profiles, we utilized oxygen-sensitive microbeads with widefield frequency-domain fluorescence lifetime imaging microscopy (FD-FLIM). This approach allowed us to obtain detailed insights into the oxygen levels within the tumor microenvironment, which are critical for tumor growth and survival. Our findings highlight the significant interactions between the tumor spheroid and endothelial cells, emphasizing the crucial role of the endothelium in regulating oxygen microenvironments and influencing angiogenesis. Furthermore, the model provides a valuable tool for exploring the dynamics of tumor biology, enabling researchers to modulate environmental factors and create specific conditions for various research topics. This capability is particularly beneficial for drug development and clinical verification, as it allows for the observation of interactions among different cell types and the assessment of spatial stress or environmental factors. This work establishes a versatile platform for advancing our understanding of tumor biology and optimizing therapeutic strategies, paving the way for future researches in cancer treatment and drug discovery. © 2025, The Authors. All rights reserved.

关键词： Endothelial cells

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Label-free optical biosensors based on LSPR properties by using gold-capped nanostructure materials

Label-free optical biosensors based on LSPR properties by us...

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13th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2009

作者： Kim, Do-Kyun Park, Tae Jung Tamiya, Eiichi Lee, Sang Yup BioProcess Engineering Research Center Center for Systems and Synthetic Biotechnology Institute for the BioCentury Korea Republic of Department of Applied Physics Graduate School of Engineering Osaka University Japan Bioinformatics Research Center KAIST Korea Republic of

ISBN: (纸本)9780979806421

In this work, we reported two kinds of gold (Au)-capped nanostructure array chips: nanoparticle array chip and porous anodic alumina (PAA) array chip. The silica nanoparticles array formed by chemical reaction and the PAA array fabricated by two-step anodizing process could be used as the bases in Au-capped nanostructure array chips. After deposition Au on the surface, nanostructures of nanoparticle and PAA are obviously expressed the optical absorbance of localized surface plasmon resonance (LSPR) and/or interferometry spectra. We demonstrated that all two types of nanostructure array chips have high potential to develop the extra-sensitive protein sensor with the biomolecular interaction functionalizations.

关键词： Interferometry

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Production of docosahexaenoic acid from corncob residue wastes through integrated whole-cell lignocellulosic saccharification and lipid fermentation by Aurantiochytrium

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Bioresource Technology 2025年 431卷 132606页

作者： Song, Xiaojin Wan, Weijian Zhang, Yuedong Yu, Guang Li, Bin Cui, Qiu Liu, Ya-Jun Feng, Yingang CAS Key Laboratory of Biofuels Shandong Provincial Key Laboratory of Energy Genetics Shandong Engineering Research Center of Single Cell Oil Qingdao Engineering Laboratory of Single Cell Oil Qingdao Institute of Bioenergy and Bioprocess Technology Chinese Academy of Sciences Shandong Qingdao266101 China Academy of Plateau Science and Sustainability Qinghai Normal University Qinghai Xining810016 China Shandong Energy Institute Shandong Qingdao266101 China Qingdao New Energy Shandong Laboratory Shandong Qingdao266101 China University of Chinese Academy of Sciences Beijing100049 China

To convert lignocellulose waste into high-value-added products, we successfully produced docosahexaenoic acid (DHA) oil by Aurantiochytrium sp. SD116 using hydrolysates obtained through a consolidated bio-saccharification (CBS) process with corncob residue (CCR) as the substrate. We conducted fed-batch fermentations using CBS hydrolysates supplemented with sea salt and ammonia, requiring no additional nutrients, and achieved the lipid and DHA titer of 45.10 g L−1 and 16.87 g L−1, respectively. Consequently, 12.6 % (w/w) of the initial CCR was converted to DHA oil. We also assessed the viability of achieving nutrient balance and wastewater recycling in the processes for a substantial reduction of cost. © 2025 Elsevier Ltd

关键词： Clostridium

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Recent Advances in Biobutanol Production

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Industrial Biotechnology 2015年第6期11卷 316-321页

作者： Jang, Yu-Sin Lee, Sang Yup BioProcess Engineering Research Center Center for Systems and Synthetic Biotechnology Institute for the BioCentury KAIST 291 Daehak-ro Yuseong-gu Daejeon34141 Korea Republic of

Butanol has been used as an important solvent in various industries, and is considered a good liquid fuel substitute for gasoline for use in internal combustion engines. Biobased production of butanol has a long history and was one of the first industrial-scale fermentation processes in which Clostridium strains were employed. Recent work on metabolic engineering of Clostridium strains has resulted in considerably improved production of butanol. In addition, several non-clostridial microorganisms have also been developed for butanol production. Here we review the advances in butanol production that have employed Clostridium strains and other microorganisms. © Copyright 2015, Mary Ann Liebert, Inc. 2015.

关键词： Clostridium

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OXidative Stress PREDictor: A Supervised Learning Approach for Annotating Cellular Oxidative Stress States in Inflammatory Cells

Advanced Intelligent Systems

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Advanced Intelligent Systems 2025年第3期7卷

作者： Chen, Po-Yuan Ko, Tai-Ming Institute of Bioinformatics and Systems Biology College of Engineering Bioscience National Yang Ming Chiao Tung University Hsinchu300 Taiwan Bioinformatics Program Institute of Statistical Science Taiwan International Graduate Program Academia Sinica Taipei115 Taiwan Institute of Biomedical Sciences Academia Sinica Taipei115 Taiwan Institute of Statistical Science Academia Sinica Taipei115 Taiwan Department of Biological Science and Technology College of Engineering Bioscience National Yang Ming Chiao Tung University Hsinchu300 Taiwan National Yang Ming Chiao Tung University Hsinchu300 Taiwan School of Pharmacy College of Pharmacy Drug Development and Value Creation Research Center Kaohsiung Medical University Kaohsiung807 Taiwan

Oxidative stress, characterized by an imbalance between reactive oxygen species (ROS) and antioxidants, plays a pivotal role in inflammatory responses associated with both chronic diseases and acute injuries. In this study, OXidative Stress PREDictor (OxSpred), a supervised learning model tailored to accurately annotate the oxidative stress state of innate immune cells at the single-cell level, is introduced. Compared to the traditional gene-set-variation-analysis-based enrichment method, OxSpred demonstrates superior accuracy with an area under the receiver operating characteristic curve of 0.89 and offers interpretable embeddings with significant biological relevance. Using the predicted ROS states, precise elucidation and interpretation of the roles of novel innate immune cell subtypes can be achieved. Overall, OxSpred enhances the utility of single-cell transcriptomic datasets by providing a robust in silico method for determining intracellular oxidative stress states, thereby enriching the understanding of innate immune cell functions during inflammation. © 2024 The Author(s). Advanced Intelligent Systems published by Wiley-VCH GmbH.

关键词： Cells

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Removal of endotoxin during purification of poly(3-hydroxybutyrate) from gram-negative bacteria

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Applied and Environmental Microbiology 1999年第6期65卷 2762-2764页

作者： Lee, Sang Yup Choi, Jong-Il Han, Kyuboem Song, Ji Yong Department of Chemical Engineering and BioProcess Engineering Research Center Korea Advanced Institute of Science and Technology Yusong-gu Taejon 305-701 Korea

Poly(3-hydroxybutyrate) (PHB) was produced by cultivating several gram-negative bacteria, including Ralstonia eutropha, Alcaligenes latus, and recombinant Escherichia coli. PHB was recovered from these bacteria by two different methods, and the endotoxin levels were determined. When PHB was recovered by the chloroform extraction method, the endotoxin level was less than 10 endotoxin units (EU) per g of PHB irrespective of the bacterial strains employed and the PHB content in the cell. The NaOH digestion method, which was particularly effective for the recovery of PHB from recombinant E. coli, was also examined for endotoxin removal. The endotoxin level present in PHB recovered by 0.2 N NaOH digestion for 1 h at 30 °C was higher than 104 EU/g of PHB. Increasing the digestion time or NaOH concentration reduced the endotoxin level to less than 1 EU/g of PHB. It was concluded that PHB with a low endotoxin level, which can be used for various biomedical applications, could be produced by chloroform extraction. Furthermore, PHB with a much lower endotoxin level could be produced from recombinant E. coli by simple NaOH digestion.

关键词： .Removal Endotoxin

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Metabolomics approach using HR-MAS NMR spectroscopy for the assessment of metabolic profiles of uterine fibroids

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Analytical Biochemistry 2025年 704卷 115885页

作者： Düz, Senem Arda Mumcu, Akın Doğan, Berat Sarıdoğan, Erdinç Tuncay, Görkem Onat, Taylan Karaer, Abdullah Reproductive Sciences & Advanced Bioinformatics Application & Research Center Inonu University Malatya Turkey Department of Obstetrics and Gynecology Inonu University School of Medicine Malatya Turkey Laboratory of NMR Scientific and Technological Research Center Inonu University Malatya Turkey Department of Biomedical Engineering Faculty of Engineering Inonu University Malatya Turkey

The aim of this study is to determine dysregulated metabolites and metabolic pathways in uterine fibroids and in the myometrial tissue from which uterine fibroids are derived. Fifteen (15) patients underwent hysterectomy because of uterine fibroids and 14 controls were included in this study. 1H HR-MAS NMR spectroscopy data were obtained from uterine fibroid tissue, the adjacent healthy myometrial tissue from cases, and myometrial tissue from controls. PCA and PLS-DA score plots from multivariate statistical analysis of pre-processed spectral data demonstrated a distinction between cases and control groups. The levels of lactate, alanine, glutamate, glutamine, methionine, acetone, isocitrate, choline, glycerophosphocholine, phosphocholine, o-phosphoethanolamine, taurine, myo-inositol, p-methylhistidine, phenylacetate, ascorbate, glucose, and methylhistidine were significantly higher in uterine fibroid tissue compared to the neighboring healthy myometrial tissue. Additionally, when adjacent healthy myometrial tissue was compared to control myometrial tissue, significantly lower levels of valine, leucine, isoleucine, ethanol, arginine, N-acetyl tyrosine, acetone, p-methylhistidine, glucose, phenylacetate, myo-inositol, and alpha-glucose were observed. The study provides a foundational framework by revealing the metabolomic heterogeneity of uterine fibroids. Strategies should be developed to target the metabolic alterations that contribute to the growth of these common tumors. © 2025 Elsevier Inc.

关键词： Nuclear magnetic resonance spectroscopy

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The Anticancer and Apoptotic Activity of the Endophytic Fungus Phomopsis Sp. Isolated from Soursop Leaves in Mcf-7 Breast Cancer Cells: In Vitro and Computational in Silico Studies

SSRN

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SSRN 2025年

作者： Dwicesaria, Maheswari Alfira Priosoeryanto, Bambang Pontjo Hasan, Akhmad Endang Zainal Irsal, Riyan Alifbi Putera Gholam, Gusnia Meilin Mahendra, Fachrur Rizal Suminto, Syaefudin Indonesia Department of Biochemistry Faculty of Mathematics and Natural Sciences IPB University Dramaga Campus Bogor16680 Indonesia School of Veterinary Medicine and Biomedicine IPB University Bogor16680 Indonesia Faculty of Engineering Kyushu University Nishi-ku Fukuoka819-0395 Japan Tropical Biopharmaca Research Center IPB University Bogor16128 Indonesia Bioinformatics Study Program Faculty of Mathematics and Natural Sciences IPB University Bogor16680 Indonesia

This study investigated the anticancer potential of the endophytic fungus Phomopsis sp., extracted from soursop leaves. The metabolite profile of Phomopsis sp. was analyzed and its anticancer and apoptotic activities were assessed in both human breast cancer cell (MCF-7) and normal Vero cell lines. Phomopsis sp. were cultivated in yeast malt broth, extracted with ethyl acetate, and separated using column chromatography. The brine shrimp lethality test gave ten fractions (F1–F10), with F1 demonstrating the highest cytotoxicity (LC50 = 2.33 µg/mL). The obtained fractions were evaluated for antiproliferative effects, revealing an IC50 of 5.65 µg/mL for MCF-7 cells and 5.21 µg/mL for Vero cells, indicating effective anti-proliferation through apoptosis, as confirmed by acridine orange-ethidium bromide staining. Liquid Chromatography-tandem Mass Spectrometry identified 38 active compounds in F1, including known anticancer agents such as cytosporone C, kynurenic acid, maraniol, (-)-caryophyllene oxide, and chalcone. Computational in silico analyses utilizing PASS online, molecular docking, ADMET/pharmacokinetic studies, density functional theory (DFT) analysis, and molecular dynamics (MD) simulations further validated chalcone as a promising anticancer candidate. Chalcone exhibited favorable ADMET/pharmacokinetic properties and achieved the highest docking score -8.392 kcal/mol among the compounds tested. MD simulations over 300 ns demonstrated that chalcone outperformed tamoxifen, with binding energy calculations revealing a value of -227.069 kJ/mol compared to -45.598 kJ/mol for tamoxifen. These findings highlight the therapeutic potential of Phomopsis sp. and its bioactive compounds, particularly chalcones, as candidates for effective anti-breast cancer therapies. © 2025, The Authors. All rights reserved.

关键词： Column chromatography

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