Review
Biochemical Research Methods
Jonas Carneiro Cruz, Israel Donizeti de Souza, Fernando Mauro Lancas, Maria Eugenia Costa Queiroz
Summary: Miniaturized liquid chromatography (LC) is recognized as an important analytical method in various research fields, offering higher resolution and lower consumption. However, limitations such as tubing clogging and small sample volumes hinder high throughput and sensitive analyses. Online coupling of sample preparation techniques can overcome these limitations and improve analytical efficiency.
JOURNAL OF CHROMATOGRAPHY A
(2022)
Article
Biochemical Research Methods
Yuanyuan Lu, Zhitong Mai, Hongxia Zhou, Wenda Guan, Shiguan Wu, Heyan Zou, Maoting Shen, Yangqing Zhan, Feng Ye, Minshan Qiu, Lihan Shen, Beibei Zhao, Zifeng Yang
Summary: This study developed a reliable and sensitive method for quantifying eicosanoids in human serum. The method showed good linearity, high recovery rates, and low limits of quantification. In clinical application, different characteristic metabolite profiles were found in patients with severe pneumonia.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Byeong Gwan Cho, Peilin Jiang, Mona Goli, Sakshi Gautam, Yehia Mechref
Summary: This study investigated the viability of a newly commercialized micro array pillar nanoLC columns (mu PAC) for the analysis of permethylated glycans, demonstrating its efficient separation of different types of glycans and multiple advantages.
Article
Biochemical Research Methods
Gabriel Onn Kit Loh, Emily Yii Ling Wong, Yvonne Tze Fung Tan, Loke Meng Ong, Ru Shing Ng, Hong Chin Wee, Kok Khiang Peh
Summary: A simple, fast, and sensitive LC-MS/MS method was developed for quantifying terazosin in human plasma, with prazosin used as an internal standard. The method showed high precision and accuracy, with a linear calibration curve from 1.0 to 100.0 ng/mL. The recovery of analyte and internal standard was also found to be high, demonstrating the stability of terazosin in various storage conditions. The method was successfully applied in a bioequivalence study measuring 935 samples.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2021)
Article
Chemistry, Applied
Yan Zhang, Xiu Qin Li, Zhen Guo, Xia Zhou, Shuang Qing Li, Xiao Min Li, Hui Jiao, Qing He Zhang
Summary: An analytical method based on ID-LC-MS/MS was developed for determining sulfonamides in honey. The impact of hydrolysis on bound SA residues was investigated, along with optimization of sample pretreatment procedures to minimize matrix effects, resulting in efficient hydrolysis, extraction, recovery, and low limit of quantification.
Article
Biochemistry & Molecular Biology
Marina A. Dikunets, Grigory A. Dudko, Edward D. Virus
Summary: The association between adrenocortical steroidogenesis and high intensity exercise in elite athletes is understudied due to the wide range of steroid concentrations in serum and limitations in sampling professional athletes. To overcome this challenge, a novel approach using LC-MS/MS and dual-polarity electrospray ionization was developed and validated for targeted serum metabolic profiling. This method allows for the quantitative determination of 14 stress resistance biomarkers within 8.5 minutes using a small amount of specimen.
Article
Biochemical Research Methods
Xiaoping Qian, Qi Chen, Yunhui Chen, Shiliang Ji, Ying Wang, Ye Sun, Huixin Qi, Kan Zhong, Jinfang Jiang, Xin Chen, Lifeng Huang, Yong Yang
Summary: A simple and fast liquid chromatography-tandem mass spectrometry method was established and validated for the simultaneous determination of tenofovir alafenamide (TAF) and tenofovir (TNF) in human plasma, with acceptable accuracy and precision in the concentration ranges tested.
BIOMEDICAL CHROMATOGRAPHY
(2022)
Article
Biochemical Research Methods
Jia Zhan, Rong-rong Zhang, Xi-zhi Shi, Zhiqiang Huang, Guo-zhou Cao, Xian-feng Chen, Ling Hu
Summary: A rapid, simple, and versatile analytical method was developed for the simultaneous determination of 140 undesirable low-weight pesticides and mycotoxins in black tea. The method involved a combination of dual D-SPE with C-18 sorbent and anhydrous magnesium sulfate to eliminate interferences in the extract, maintaining the chromatographic column under ideal conditions for long-term satisfactory recoveries. Matrix-matched calibration curves were obtained for most target compounds with linear regression coefficients above 0.9900, and the limits of quantification (LOQs) ranged within 0.5-10.0 μg/kg.
JOURNAL OF CHROMATOGRAPHY A
(2021)
Article
Chemistry, Analytical
Zehu Xie, Yinghua Yan, Keqi Tang, Chuan-Fan Ding
Summary: This study successfully prepared a novel COF material with high sensitivity and selectivity through post-synthesis modification, which showed significant enrichment effect on glycopeptides and is expected to be applied in glycoproteomics research.
Article
Agriculture, Multidisciplinary
Myriam Bustamante-Rangel, Maria Milagros Delgado-Zamarreno, Encarnacion Rodriguez-Gonzalo
Summary: A simple and sensitive method has been developed for the analysis of anthelmintic drugs in milk, involving extraction using QuEChERS method and separation and determination by LC-MS/MS. This method provides high sensitivity for the determination of anthelmintics in milk samples and can be successfully used for routine analysis.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2022)
Article
Biochemical Research Methods
Xuan Guo, Lei Zhang, Zihan Lei, Zhe Hou, Hui Li, Xiaodong Li, Jing Dong, Ling Song, Dingding Chen, Dongyang Liu
Summary: The objective of this study was to develop a LC-MS/MS method for quantitation of seven cytochrome P450 (CYP450) enzymes. The method was validated for selectivity, linearity, stability, accuracy, and precision. The abundance of the enzymes in human liver microsomes and CYP3A4 in placenta was accurately determined using this method.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2023)
Article
Chemistry, Analytical
Soon Uk Chae, Ji Seon Kim, Chae Bin Lee, Seong Jun Jo, Kyung Lok Min, Min Jung Chang, Soo Kyung Bae
Summary: A sensitive and fast LC-MS/MS method was developed to quantify remifentanil in human plasma, and prevent its degradation during analysis. The method involved a simple sample preparation process and a short run time. The method was validated and found to be reliable for quantification of remifentanil in plasma. It was successfully applied to measure plasma levels of remifentanil in intensive-care-unit patients.
Article
Biochemical Research Methods
Yifan Xu, Haonan Li, Yiqun Han, Teng Wang, Yanwen Wang, Jicheng Gong, Ke Gao, Wu Chen, Weiju Li, Hongyin Zhang, Junxia Wang, Xinghua Qiu, Tong Zhu
Summary: Sphingolipids are a class of lipids with diverse structures and biological functions, and have been proposed as potential biomarkers for cardiometabolic diseases. The current methods for quantifying sphingolipids have limitations in terms of sample pretreatment and volume. In this study, a simple and rapid method using methanol for plasma sphingolipid extraction was developed, and 37 sphingolipids from 8 classes were successfully quantified using liquid chromatography coupled with tandem mass spectrometry. This method showed good performance and was applied successfully in an epidemiological study.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Zhou Xin, Li Ruo-Qi, Wang Cong, Ma Xiao-Xia, Sun Ying, Song Wen-Xuan, Wei Xue-Bing, Li Dong-Hua, Ma Xiao, Wang Ren-Qi
Summary: CKs are important plant hormones, and a new chemical isotope labelling LC-MS analytical method has been developed to enhance sensitivity and monitor the impact of fertilizers on endogenous CKs metabolism.
JOURNAL OF CHROMATOGRAPHY A
(2021)
Article
Chemistry, Analytical
Karel Stejskal, Op de Beeck Jeff, Manuel Matzinger, Gerhard Durnberger, Alexander Boychenko, Paul Jacobs, Karl Mechtler
Summary: In the field of LC-MS-based proteomics, advances in mass spectrometer technology have increased the depth and coverage of sampling, but the selection of nanoLC separation columns also plays a crucial role in generating comprehensive and high-quality data.
ANALYTICAL CHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Steffen Schmidt, Sandra F. Gallego, Iris Daphne Zelnik, Sergey Kovalchuk, Nanna Albaek, Richard R. Sprenger, Charlotte Overup, Yael Pewzner-Jung, Anthony H. Futerman, Marie W. Lindholm, Ole N. Jensen, Christer S. Ejsing
Summary: Emerging clinical data show that three ceramide molecules, Cer d18:1/16:0, Cer d18:1/24:1, and Cer d18:1/24:0, are biomarkers of a fatal outcome in patients with cardiovascular disease. This study developed a potent N-acetylgalactosamine-conjugated antisense oligonucleotide that specifically targets ceramide synthase 2 in hepatocytes. Results demonstrate that this compound effectively reduces ceramide synthase 2 mRNA level, leading to lower protein expression and activity as well as ceramide levels in the liver. Interestingly, the hepatocyte-specific antisense oligonucleotide also modulates blood plasma ceramides, suggesting that these biomarkers are regulated by ceramide biosynthesis in hepatocytes.
Article
Biochemistry & Molecular Biology
Dawei Huo, Zhaowei Yu, Rui Li, Meihan Gong, Simone Sidoli, Xukun Lu, Yuying Hou, Zhongye Dai, Yu Kong, Guifen Liu, Ole N. Jensen, Wei Xie, Kristian Helin, Chaoyang Xiong, Guohong Li, Yong Zhang, Xudong Wu
Summary: This study reveals the dynamic chromatin configuration of CGIs during exit from naive pluripotency and provides a conceptual framework for the spatiotemporal establishment of PcG functions.
Article
Biochemistry & Molecular Biology
Philipp Michl-Holzinger, Simon Obermeyer, Hanna Markusch, Alexander Pfab, Andreas Ettner, Astrid Bruckmann, Sabrina Babl, Gernot Laengst, Uwe Schwartz, Andrey Tvardovskiy, Ole N. Jensen, Akihisa Osakabe, Frederic Berger, Klaus D. Grasser
Summary: The heterodimeric histone chaperone FACT, composed of SSRP1 and SPT16, is involved in dynamic nucleosome rearrangements during DNA-dependent processes. In this study, post-translational modifications of SSRP1 and SPT16 were investigated in Arabidopsis cells. Acetylation of lysine residues in SSRP1's C-terminal region and phosphorylation of serine/threonine residues in SPT16's acidic C-terminal region were identified. Mutational analysis showed that acetylation of SSRP1 had minimal effects, but phosphorylation of SPT16 by protein kinase CK2 was crucial for histone interactions. Plants expressing a non-phosphorylatable version of SPT16 had reduced histone binding and exhibited growth and developmental defects. These findings suggest that phosphorylation of SPT16 is required for proper nucleosome occupancy at the transcriptional start sites of active genes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Giorgio Oliviero, Sergey Kovalchuk, Adelina Rogowska-Wrzesinska, Veit Schwammle, Ole N. Jensen
Summary: In this study, the chromatin proteomes of various mouse organs were analyzed using quantitative proteomics. The results showed distinct and organ-specific temporal protein expression profiles and regulation at the post-translational level. The spleen exhibited a static chromatin proteome, reflecting its important role in physiological defense and immunity. These findings support the hypothesis that chromatin-associated proteins are involved in distinct and specific physiological functions in ageing organs.
Article
Cell Biology
Helle Sedighi Frandsen, Joel Mario Vej-Nielsen, Lauren Elizabeth Smith, Lang Sun, Karoline Lindgaard Mikkelsen, Annemette Praestegaard Thulesen, Christina Erika Hagensen, Fuquan Yang, Adelina Rogowska-Wrzesinska
Summary: Non-alcoholic fatty liver disease affects a significant portion of the global population, but its underlying mechanisms are still poorly understood. By using a cell-based model and analyzing proteomics and lipidomics data, researchers were able to mimic important clinical features of NAFLD and identify potential molecular changes in the disease.
Article
Biochemistry & Molecular Biology
Marta Ignasiak-Kciuk, Karolina Nowicka-Bauer, Marta Grzechowiak, Tina Ravnsborg, Kamil Frackowiak, Ole N. Jensen, Mariusz Jaskolski, Bronislaw Marciniak
Summary: This study investigates the sensitized photo-oxidation reaction using carboxybenzophenone (CB) as a sensitizer and a PR-10 protein (MtN13) as a quencher. It reveals the specific binding of CB in the protein's hydrophobic cavity and the amino acid residues creating adducts with the sensitizer. The study also elucidates the mechanisms of CB quenching and the influence of neighboring groups on the oxidation process.
FREE RADICAL BIOLOGY AND MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Kseniia A. Palkina, Anastasia V. Balakireva, Olga A. Belozerova, Tatiana V. Chepurnykh, Nadezhda M. Markina, Sergey I. Kovalchuk, Aleksandra S. Tsarkova, Alexander S. Mishin, Ilia V. Yampolsky, Karen S. Sarkisyan
Summary: Hispidin is a polyketide found in plants and fungi, which functions as a precursor of luciferin in bioluminescent fungi. The absence of two domains with predicted ketoreductase and dehydratase activities in hispidin synthases distinguishes them from non-bioluminescent fungi. Our investigation suggests that the loss of these domains in evolution led to the emergence of bioluminescence and the production of hispidin.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Mette Louise Trempenau, Mikkel Bruhn Schuster, Sachin Pundhir, Mafalda Araujo Pereira, Adrija Kalvisa, Marta Tapia, Jinyu Su, Ying Ge, Bauke de Boer, Alexander Balhuizen, Frederik Otzen Bagger, Pavel Shliaha, Patrycja Sroczynska, Julian Walfridsson, Kirsten Gronbaek, Kim Theilgaard-Moench, Ole N. N. Jensen, Kristian Helin, Bo T. T. Porse
Summary: This study identifies the Histone 3 Lysine 4 (H3K4) demethylase KDM5C as a tumor suppressor in acute myeloid leukemia (AML). Decreased KDM5C expression leads to increased cell growth in AML cell lines and mouse models. Mechanistically, KDM5C acts as a transcriptional repressor through its demethylase activity, resulting in upregulation of immature genes marked by H3K4me3. The association of KDM5C levels with long-term disease-free survival in female AML patients highlights the clinical relevance of this finding.
Meeting Abstract
Biochemistry & Molecular Biology
Karolina Nowicka-Bauer, Marta Ignasiak-Kciuk, Marta Grzechowiak, Tina Ravensborg, Kamil Frackowiak, Ole N. Jensen, Mariusz Jaskolski, Bronislaw Marciniak
FREE RADICAL BIOLOGY AND MEDICINE
(2023)
Article
Chemistry, Analytical
Francis Berthias, Dale A. Cooper-Shepherd, Frederik H. V. Holck, James I. Langridge, Ole N. Jensen
Summary: The combination of cyclic ion mobility spectrometry (cIM) and electron capture dissociation (ECD) allows for the complete separation and sequencing of large isomeric peptides, providing a new method for identifying biologically important proteoforms in complex mixtures.
ANALYTICAL CHEMISTRY
(2023)
Article
Medicine, Research & Experimental
Vignesh Ramesh, Paradesi Naidu Gollavilli, Luisa Pinna, Mohammad Aarif Siddiqui, Adriana Martinez Turtos, Francesca Napoli, Yasmin Antonelli, Aldo Leal-Egana, Jesper Foged Havelund, Simon Toftholm Jakobsen, Elisa Le Boiteux, Marco Volante, Nils Joakim Faergeman, Ole N. Jensen, Rasmus Siersbaek, Kumar Somyajit, Paolo Ceppi
Summary: This study found an inverse association between short-chain fatty acids and EMT in non-small cell lung cancer patients. In vitro experiments showed that propionate treatment enhanced the epithelial transcriptional program and reduced the EMT phenotype in lung cancer cell lines. Animal experiments also confirmed that propionate can reduce lung cancer metastasis and lymph node spread. Further mechanistic investigation revealed that propionate treatment caused chromatin remodeling through p300-mediated histone acetylation.
EMBO MOLECULAR MEDICINE
(2023)
Article
Cell Biology
Vincent Gaggioli, Calvin S. Y. Lo, Nazaret Reveron-Gomez, Zuzana Jasencakova, Heura Domenech, Hong Nguyen, Simone Sidoli, Andrey Tvardovskiy, Sidrit Uruci, Johan A. Slotman, Yi Chai, Joao G. S. C. Souto Goncalves, Eleni Maria Manolika, Ole N. Jensen, David Wheeler, Sriram Sridharan, Sanjiban Chakrabarty, Jeroen Demmers, Roland Kanaar, Anja Groth, Nitika Taneja
Summary: Chromatin signalling cascade, regulated by a checkpoint, activates the histone methyltransferase EHMT2/G9a to assemble heterochromatin at stressed replication forks. G9a, together with SUV39h1, induces chromatin compaction through accumulating repressive modifications, H3K9me1/me2/me3, at stressed replication forks. Untimely heterochromatin disassembly by demethylase KDM3A exposes forks to PRIMPOL-mediated genome instability, leading to chemotherapeutic drug sensitivity.
NATURE CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Egor A. Turovsky, Victoria V. Golovicheva, Elena G. Varlamova, Tatyana I. Danilina, Kirill Goryunov, Yulia A. Shevtsova, Irina B. Pevzner, Ljubava D. Zorova, Valentina A. Babenko, Ekaterina A. Evtushenko, Anastasia A. Zharikova, Anastasia A. Khutornenko, Sergey I. Kovalchuk, Egor Y. Plotnikov, Dmitry B. Zorov, Gennady T. Sukhikh, Denis N. Silachev
Summary: Mesenchymal stromal cells extracellular vesicles (MSC-EV) have potential effects in neuroprotective therapy, reducing brain damage and promoting recovery of sensorimotor functions. In vitro experiments have shown that MSC-EV enhance neuroplasticity and growth of neurites. The intercellular positive crosstalk between neural cells mediated by MSC-EV protects against ischemic damage and involves the phosphatidylinositol 3-Kinase/AKT signaling pathway.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Margarita N. Baranova, Arsen M. Kudzhaev, Yuliana A. Mokrushina, Vladislav V. Babenko, Maria A. Kornienko, Maja V. Malakhova, Victor G. Yudin, Maria P. Rubtsova, Arthur Zalevsky, Olga A. Belozerova, Sergey Kovalchuk, Yuriy N. Zhuravlev, Elena N. Ilina, Alexander G. Gabibov, Ivan V. Smirnov, Stanislav S. Terekhov
Summary: The biodiversity of microorganisms is maintained by interactions between species, and the functionality of human microbiomes is influenced by aseptic conditions and antibiotic use. Wild animal microbiomes have a protective shield against pathogen invasion. Using ultrahigh-throughput microfluidic technologies, the researchers identified Bacillus pumilus strains in the microbiomes of wild animals that produce antibacterial metabolites, including amicoumacin A, which can inhibit the growth of both Gram-positive and Gram-negative bacteria. The discovery of these strains opens up new opportunities for pathogen control and microbiome remodeling in various industries.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
