Article
Biochemistry & Molecular Biology
Heesoo Jeong, Yan Yu, Henrik J. Johansson, Frank C. Schroeder, Janne Lehtio, Nathaniel M. Vacanti
Summary: Stable-isotope tracing is a method used to measure intracellular metabolic pathway utilization by feeding a cell system a stable-isotope-labeled tracer nutrient. An algorithm and tool, PolyMID-Correct, have been developed to computationally remove the influence of naturally occurring heavy isotopes, making the method more accurate and reliable. This algorithm is applicable to data collected on both low- and high-mass resolution mass spectrometers, and PolyMID-Correct is open source under an MIT license.
Article
Biochemistry & Molecular Biology
Mukundan Ragavan, Mengchen Li, Anthony G. Giacalone, Charles E. Wood, Maureen Keller-Wood, Matthew E. Merritt
Summary: Ovine models have been widely used for studying maternal-fetal interactions and congenital heart diseases. This study demonstrates a comprehensive assessment of heart function and metabolism in a perinatal model, with the use of [U-C-13]glucose as a tracer to study central energy metabolism. The methodology presented can be applied to investigate acute and chronic effects of hormonal signaling in future studies.
Article
Biochemistry & Molecular Biology
Jennifer Langenhan, Carsten Jaeger, Katharina Baum, Mareike Simon, Jan Lisec
Summary: Investigation of metabolic fluxes and metabolite distributions within cells using tracer molecules is a valuable tool for understanding complex biological systems. However, there are effects in mass spectrometry analysis that need to be corrected to ensure accurate enrichment calculation. This article presents and evaluates a novel software tool that can automatically perform these corrections, and demonstrates its application on experimental datasets.
Review
Chemistry, Multidisciplinary
Bruna de Falco, Francesco Giannino, Fabrizio Carteni, Stefano Mazzoleni, Dong-Hyun Kim
Summary: This review outlines the experimental procedures used in C-13-MFA, including cell culture preparation, labelled tracer preparation, metabolite extraction and analysis. The limitations and advantages of nuclear magnetic resonance and mass spectrometry techniques in carbon labelled experiments are discussed. Additionally, successful computational modelling approaches in flux analysis and the main application areas in metabolic engineering are summarized.
Article
Biochemical Research Methods
Qiming Tang, Qingfeng Song, Xiaoxiang Ni, Zai Shi, Genyun Chen, Xinguang Zhu
Summary: The development of ILSA supports photosynthetic research on metabolism and metabolic flux analysis, and provides a new tool for the study of leaf physiology.
Article
Cell Biology
Karatatiwant Singh Sidhu, Eyal Amiel, Ralph C. Budd, Dwight E. Matthews
Summary: This study introduces a novel method to measure cell volume in metabolomics experiments using mass spectrometry. The method seamlessly incorporates cell volume determination within the metabolomics workflow, ensuring accuracy in metabolite concentration measurements. By implementing stable isotopically labeled internal standards, this approach provides a reliable way to account for changes in cell size and accurately quantify metabolites in cultured cells.
AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY
(2021)
Article
Biochemical Research Methods
Maria Alcoriza-Balaguer, Juan C. Garcia-Canaveras, Marta Benet, Oscar Juan-Vidal, Agustin Lahoz
Summary: FAMetA is an R package and web-based application that uses C-13 mass isotopologue profiles to estimate fatty acid metabolism. It provides comprehensive characterization of FA biosynthesis and easy-to-interpret graphical representations, allowing for insights into how cells reprogram their FA metabolism and identification of new FAs through metabolic reconstruction.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Alexey Orlov, Savva Semenov, Gleb Rukhovich, Anastasia Sarycheva, Oxana Kovaleva, Alexander Semenov, Elena Ermakova, Ekaterina Gubareva, Anna E. Bugrova, Alexey Kononikhin, Elena I. Fedoros, Evgeny Nikolaev, Alexander Zherebker
Summary: Chronic liver diseases are a major public health issue worldwide, with nonalcoholic fatty liver disease (NAFLD) being the leading cause of mortality and no approved therapeutics available. The use of natural compound mixtures shows promise for NAFLD therapy, but understanding their mechanism of action is crucial for rational application.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Medical Laboratory Technology
Carl Jenkinson, Reena Desai, Andrzej T. Slominski, Robert C. Tuckey, Martin Hewison, David J. Handelsman
Summary: The study developed an LC-MS/MS method to measure 13 vitamin D metabolites simultaneously, providing new insights into the circulating vitamin D metabolite pathways.
CLINICAL CHEMISTRY AND LABORATORY MEDICINE
(2021)
Article
Biochemical Research Methods
Allyson L. Mellinger, Kenneth P. Garrard, Sitora Khodjaniyazova, Zahid N. Rabbani, Michael P. Gamcsik, David C. Muddiman
Summary: This study presents a method using multiple infusion start time protocol, stable isotope labeling technology, and high-resolution accurate mass-mass spectrometry imaging to study spatial changes in glutathione kinetics in sectioned mouse liver tissues. The results provide insights into the heterogeneity of glutathione flux in diseased and healthy tissues.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Chemistry, Analytical
Konomi Suda, Sachiko Sakamoto, Akira Iguchi, Hideyuki Tamaki
Summary: Anaerobic microbial acetogenesis is widely present on Earth and has a significant impact on the global carbon cycle. A new, simple method has been developed to investigate carbon flow in acetogen metabolic reactions by accurately determining the relative abundance of individual isotopomers. By using gas chromatography-mass spectrometry (GC-MS) combined with direct aqueous sample injection, the validity of this method was demonstrated and applied to study the carbon fixation mechanism of Acetobacterium woodii. The results showed that methanol was not the sole carbon precursor of acetate methyl group, and a certain percentage of the methyl group was formed from CO2.
Article
Oncology
Khoa Pham, Allison R. Hanaford, Brad A. Poore, Micah J. Maxwell, Heather Sweeney, Akhila Parthasarathy, Jesse Alt, Rana Rais, Barbara S. Slusher, Charles G. Eberhart, Eric H. Raabe
Summary: The oncogene MYC alters cellular metabolism and its amplification in medulloblastoma leads to distinct metabolic characteristics. Comprehensive metabolic profiling of MYC-amplified medulloblastoma revealed an increased reliance on targetable metabolic pathways. However, metabolism of MYC-amplified cell lines differed from in vivo tumor models, indicating the importance of in vivo metabolic analyses. Understanding the metabolic vulnerabilities of MYC-amplified medulloblastoma may inform the development of targeted therapies.
Article
Chemistry, Analytical
Jie Zheng, Junjie Yang, Xu Liang, Mingliang Fang, Yulan Wang
Summary: In this study, a dual strategy was proposed for accurate detection of metabolites in central carbon and energy metabolism pathways. The method combines derivatization with N-Methylphenylethylamine (MPEA) and direct analysis by liquid chromatography tandem mass spectrometry (LC-MRM-MS) for high sensitivity. Isotope analysis was also performed to assess the mass isotopomer distributions (MIDs) of intracellular C-13-labeled metabolites. The dual method shows reproducibility and potential for studying clinical isotope labeled samples.
Article
Hematology
Mohamad Dandan, Julia Han, Sabrina Mann, Rachael Kim, Hussein Mohammed, Edna Nyangau, Marc Hellerstein
Summary: The study measured the turnover rates of LDLR and PCSK9 in mice and found that under high cholesterol diets, both LDLR and PCSK9 synthesis and secretion in the liver were significantly reduced. This indicates a balancing mechanism in tissue cholesterol homeostasis.
ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY
(2021)
Article
Biochemical Research Methods
Lea Wagmann, Tanja M. Gampfer, Markus R. Meyer
Summary: The increasing number of new psychoactive substances poses challenges for clinical and forensic toxicologists as well as doping control. Limited data on the toxicokinetics and safety properties of these substances highlights the importance of detection methods.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Biotechnology & Applied Microbiology
Fabia Weiland, Michael Kohlstedt, Christoph Wittmann
Summary: Lignin, an important structural component of plants, is considered as an under-utilized and promising feedstock due to its abundance and richness in aromatics. Microbes have evolved enzymes and pathways to break down lignin and metabolize its aromatic components. Systems metabolic engineering offers a sustainable approach to upgrade lignin into a variety of valuable products.
METABOLIC ENGINEERING
(2022)
Correction
Biotechnology & Applied Microbiology
Dominik Weixler, Max Berghoff, Kirill V. Ovchinnikov, Sebastian Reich, Oliver Goldbeck, Gerd M. Seibold, Christoph Wittmann, Nadav S. Bar, Bernhard J. Eikmanns, Dzung B. Diep, Christian U. Riedel
MICROBIAL CELL FACTORIES
(2022)
Article
Biotechnology & Applied Microbiology
Dominik Weixler, Max Berghoff, Kirill Ovchinnikov, Sebastian Reich, Oliver Goldbeck, Gerd M. Seibold, Christoph Wittmann, Nadav S. Bar, Bernhard J. Eikmanns, Dzung B. Diep, Christian U. Riedel
Summary: We have successfully established a two-step process for recombinant production of active nisin with C. glutamicum. This allows for the production of a bacteriocin with complex posttranslational modifications using C. glutamicum, expanding the range of bioactive compounds that can be produced. Our results provide a foundation for further research to optimize product yields, transfer production to sustainable substrates, and purify pharmaceutical grade nisin.
MICROBIAL CELL FACTORIES
(2022)
Article
Biochemistry & Molecular Biology
Thibaut Molinie, Elodie Cougouilles, Claudine David, Edern Cahoreau, Jean-Charles Portais, Arnaud Mourier
Summary: The mitochondrial respiratory chain plays a crucial role in metabolic processes by regenerating NAD+ and ATP. Recent studies have shown that complex I can form functional entities called respirasomes, which facilitate NADH oxidation. However, findings demonstrate that complex II is preferred for electron transfer in heart and liver mitochondria. This unexpected result suggests a new regulatory mechanism for mitochondrial respiration in response to NADH/NAD+ redox stress.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2022)
Article
Biotechnology & Applied Microbiology
Muzi Tangyu, Michel Fritz, Lijuan Ye, Rosa Aragao Boerner, Delphine Morin-Rivron, Esther Campos-Gimenez, Christoph J. Bolten, Biljana Bogicevic, Christoph Wittmann
Summary: This study evaluated the potential of microbes to enhance the nutritional value and flavor of sunflower seed milk. By co-fermenting the milk with two food-grade microbes, vitamin B-12 and other beneficial components were significantly increased, resulting in an attractive and clean-label product.
MICROBIAL CELL FACTORIES
(2022)
Article
Biotechnology & Applied Microbiology
Dennis Schulze, Michael Kohlstedt, Judith Becker, Edern Cahoreau, Lindsay Peyriga, Alexander Makowka, Sarah Hildebrandt, Kirstin Gutekunst, Jean-Charles Portais, Christoph Wittmann
MICROBIAL CELL FACTORIES
(2022)
Article
Oncology
Charlotte Dahlem, Shilpee Chanda, Jan Hemmer, Hanna S. Schymik, Michael Kohlstedt, Christoph Wittmann, Alexandra K. Kiemer
Summary: This study investigates the anti-cancer activities of the purple compound violacein and highlights its inhibitory effect on tumor cell proliferation and migration. The study also demonstrates the association between violacein-induced tumor cell death and inflammatory activation of macrophages. The results suggest that violacein may induce immunogenic cell death.
FRONTIERS IN ONCOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Michael Kohlstedt, Anna Weimer, Fabia Weiland, Jessica Stolzenberger, Mirjam Selzer, Miguel Sanz, Laurenz Kramps, Christoph Wittmann
Summary: In this study, a cascaded value chain for the production of green PET from lignin was demonstrated. By fermenting lignin-based aromatics, PET monomers were synthesized, providing a sustainable alternative to fossil-based PET production.
METABOLIC ENGINEERING
(2022)
Article
Biotechnology & Applied Microbiology
Fabia Weiland, Nadja Barton, Michael Kohlstedt, Judith Becker, Christoph Wittmann
Summary: Lignin, a renewable resource, is mostly burned in lignocellulosic processing facilities due to a lack of value-added alternatives. In this study, C. glutamicum was metabolically engineered to produce cis, cis-muconate (MA) from key aromatics, such as vanillin and vanillate. Through the implementation of synthetic pathway modules and the identification of efficient enzymes, the final strain MA-9 was able to produce bio-based MA with high selectivity.
METABOLIC ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Pierre Millard, Thomas Gosselin-Monplaisir, Sandrine Uttenweiler-Joseph, Brice Enjalbert
Summary: Acetate, previously considered a toxic waste compound, has been found to be a co-substrate of glycolytic nutrients and a global regulator of E. coli metabolism. Decreasing glycolytic flux enhances co-utilization of acetate with glucose, enabling acetate metabolism to compensate for the reduction in glycolytic flux and promote E. coli growth.
Article
Biotechnology & Applied Microbiology
Sarah Pauli, Michael Kohlstedt, Jessica Lamber, Fabia Weiland, Judith Becker, Christoph Wittmann
Summary: The nonproteinogenic cyclic metabolite L-pipecolic acid is a chiral precursor for various commercial drugs. It has multiple uses in the pharmaceutical, medical, cosmetic, and agrochemical markets. The production of L-pipecolic acid from glucose using Corynebacterium glutamicum has been improved through systems metabolic engineering. The advanced mutant strain achieved a high titer of 93 g L-1, approaching the level of biotransformation from L-lysine.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Jens Christmann, Peng Cao, Judith Becker, Christian K. K. Desiderato, Oliver Goldbeck, Christian U. U. Riedel, Michael Kohlstedt, Christoph Wittmann
Summary: This study optimized the production process of pediocin PA-1 and found that an acidic pH of 5.7, microaerobic conditions, and the addition of high levels of CaCl2 significantly increased its production. By applying the optimized conditions, the IPTG-inducible producer C. glutamicum CR099 pXMJ19 P-tac pedACD(Cg) achieved a pediocin titer of 66 mg L-1, while the novel constitutive strain P-tuf pedACD(Cg) successfully produced pediocin without the need for IPTG.
MICROBIAL CELL FACTORIES
(2023)
Article
Biotechnology & Applied Microbiology
Sofija Jovanovic Gasovic, Demian Dietrich, Lars Glaeser, Peng Cao, Michael Kohlstedt, Christoph Wittmann
Summary: This study reveals the cellular dynamics of DHA production in the oleaginous yeast Y. lipolytica Af4 by using transcriptomics, metabolomics, and 13C-based metabolic pathway profiling. It is found that supplementation with ketogenic amino acids such as L-lysine can increase DHA production.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Laura Pause, Anna Weimer, Nicolas T. Wirth, Anh Vu Nguyen, Claudius Lenz, Michael Kohlstedt, Christoph Wittmann, Pablo I. Nikel, Bin Lai, Jens O. Kroemer
Summary: In a bio-electrochemical system, the obligate aerobe Pseudomonas putida is able to survive anaerobically and produce chemicals via oxidative pathways. The utilization of carbon in the cytoplasm is not limited by the stoichiometry of the sugar uptake routes, but could be affected by energy constraints or an oxygen-dependent regulatory mechanism.
MICROBIAL BIOTECHNOLOGY
(2023)
Article
Endocrinology & Metabolism
Noemie Butin, Cecilia Berges, Jean-Charles Portais, Floriant Bellvert
Summary: This study aimed to develop and validate a method to optimize automated data processing for untargeted MS-based isotopic tracing investigations of metabolism. The method utilizes a suitable reference material to rationally perform parameter optimization throughout the complete data processing workflow. It was applied in the context of C-13-labelling experiments and with two different software, geoRge and X13CMS. The study of an E. coli mutant impaired for central metabolism was used as an example to illustrate the method.
Article
Biochemical Research Methods
Saranya Krishnan, Shina Sasi, Preshobha Kodakkattumannil, Salima Al Senaani, Geetha Lekshmi, Martin Kottackal, Khaled M. A. Amiri
Summary: This study aimed to develop an efficient DNA extraction protocol suitable for diverse plant species and tissues. A reliable and consistent protocol was described for the extraction of high-quality DNA from difficult-to-extract plant species. The optimized protocol was successful in extracting high-quality DNA from various plant species and tissues, making it useful for genomic studies of recalcitrant plants.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Eisaku Hokazono, Saori Fukumoto, Takeshi Uchiumi, Susumu Osawa
Summary: This study proposes a method for detecting nucleic acid amplification using pyrophosphate, which requires only two reagents and an automated analyzer. The technique has high sensitivity and reproducibility, and can detect pyrophosphate within 10 minutes. Therefore, this method has the potential to be a new, rapid, and simple detection technique for amplified nucleic acids.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Drew S. Sowersby, L. Kevin Lewis
Summary: SURE electrophoresis is a new method for concentrating samples in gels, which allows efficient detection of highly dilute DNA samples. This approach generates single bands with enhanced signal intensities and minimal band broadening.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Hongyi Liang, Guoliang Yin, Guangxi Shi, Zhiyong Liu, Xiaofei Liu, Jingwei Li
Summary: The mechanism of Echinacoside (ECH) in treating breast cancer (BC) was explored through network pharmacology and experimental validation. It was found that ECH plays an important role in anti-BC by regulating the PI3K/AKT/HIF-1 alpha/VEGF signaling pathway, and it exhibits multi-target and multi-pathway effects.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Daniel S. Kantner, Emily Megill, Anna Bostwick, Vicky Yang, Carmen Bekeova, Alexandria Van Scoyk, Erin L. Seifert, Michael W. Deininger, Nathaniel W. Snyder
Summary: This study compared the results of different methods for measuring the amount of acetyl-Coenzyme A. The colorimetric ELISA kit did not produce interpretable results, while the fluorometric enzymatic kit showed comparable results to the LC-MS-based methods depending on the matrix and extraction conditions. LC-MS/MS and LC-HRMS methods produced well-aligned results, especially when using stable isotope-labeled internal standards.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Jingyan Xu, Hanying Tan, Xionghui Ma, Linjing Su, Zhi Zhang, Yuhao Xiong
Summary: This study investigates the co-catalytic capabilities of MoO3 nanosheets in enhancing the enzyme-like catalytic activity of a two-dimensional ultrathin Fe(III)-modified covalent triazine framework (Fe-CTF) under neutral pH conditions. The Fe-CTF/MoO3 co-catalytic system exhibits enzyme-mimicking activity and enables the development of a colorimetric method for glucose detection. Furthermore, a straightforward one-pot colorimetric method is established for screening XOD inhibitors.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Lichao Zhang, Kang Xiao, Xueting Wang, Liang Kong
Summary: A novel fusion technology was designed to identify FAD-binding sites, achieving the best results on two independent test datasets and outperforming existing methods significantly. The high performance and certainty of the method were demonstrated through statistical tests and cross-entropy loss analysis.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Abdulkadir Kilic, Mehmet Aslan, Abdulkadir Levent
Summary: This study developed a simple, rapid, sensitive, and selective voltammetric technique for the electrochemical characterization and detection of the highly risky drug Edoxaban. The optimized voltammetric method showed good analytical working range and was successfully applied to urine and tablet samples.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Su Hyun Kim, Nara Shin, Jong-Min Jeon, Jeong-Jun Yoon, Jeong Chan Joo, Hee Taek Kim, Shashi Kant Bhatia, Yung-Hun Yang
Summary: To address environmental issues caused by traditional plastics, bioplastics have gained attention as alternatives. Although bioplastics have better degradability, their degradation still takes longer than anticipated. This study proposes a novel screening method to identify bioplastic degraders faster, saving time and providing more quantitative data.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Irem Okman Kocoglu, Pinar Esra Erden, Esma Kilic
Summary: In this study, an electrochemical biosensor based on carbon nanofibers and ionic liquid modification was constructed for tyramine detection. The biosensor showed linear response, low detection limit, high sensitivity, and exhibited good reproducibility, stability, and anti-interference ability.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Liana U. Akhmetzianova, Timur M. Davletkulov, Assol R. Sakhabutdinova, Alexey Chemeris, Irek M. Gubaydullin, Ravil R. Garafutdinov
Summary: A new program called LAMPrimers iQ has been developed for high-quality LAMP primer design, and its advantages in providing higher specificity and reliable detection of viral RNA were validated using SARS-CoV-2 coronavirus RNA as a model target.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Tommaso Pileri, Alberto Sinibaldi, Agostino Occhicone, Norbert Danz, Elena Giordani, Matteo Allegretti, Frank Sonntag, Peter Munzert, Patrizio Giacomini, Francesco Michelotti
Summary: This study developed a biosensing device based on one-dimensional photonic crystal to detect HER2 in breast cancer. The device combines label-free and fluorescence operation modes, allowing for real-time and accurate detection in less than 20 minutes. It offers a promising technique for combined label-free and fluorescence detection in disease diagnosis and therapeutic monitoring.
ANALYTICAL BIOCHEMISTRY
(2024)