Article
Biochemistry & Molecular Biology
Qi Guo, Lei Liu, Won C. Yim, John C. Cushman, Bronwyn J. Barkla
Summary: The study utilized Free Flow Electrophoresis for high-resolution membrane fractionation of plant leaf tissue, combined with mass spectrometry-based proteomics, allowing simultaneous profiling of multiple cellular membranes. Comparison of protein profiles of fractionated membranes with known cellular compartment markers revealed protein functions and provided new evidence for multiple subcellular localizations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Himadri Biswas, Shu-Jun Zhao, Yetunde Makinwa, James S. Bassett, Phillip R. Musich, Jing-Yuan Liu, Yue Zou
Summary: ATR is a PI3K-like kinase protein that plays different roles in the nucleus and mitochondria through isomerization-induced structural changes. This structural alteration defines the subcellular location and compartment-specific functions of ATR, and is essential for promoting cell survival and DNA damage responses.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Environmental Sciences
Xupeng Wang, Bing Gong, Erkai He, Willie J. G. M. Peijnenburg, Hao Qiu
Summary: The toxicokinetics of Cd, As, and Zn in earthworms at both whole body and subcellular levels were assessed. The study found concentration-dependent increases in Cd and As in earthworms and subcellular compartments, while Zn maintained a steady-state concentration. These subcellular differences in toxicokinetics supported the observed variations in bioaccumulation patterns and revealed the strategies used by earthworms to handle non-essential and essential elements.
Article
Biochemistry & Molecular Biology
Vladimir Skalicky, Tereza Vojtkova, Ales Pencik, Jan Vrana, Katarzyna Juzon, Veronika Kolackova, Michaela Sedlarova, Martin F. Kubes, Ondrej Novak
Summary: This study tested various nuclear isolation protocols and combined with mass spectrometry analysis to obtain information on the auxinome from isolated nuclei of Arabidopsis and tobacco cell cultures, revealing dynamic changes in auxin homeostasis within the nucleus. The methodological procedure combining flow cytometry and mass spectrometry offers new horizons for the study of auxin homeostasis at the subcellular level.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Neurosciences
Hui Liu, Hong-Gang Wang, Geoffrey Pitt, Zhe Liu
Summary: This study investigates the subcellular localization and dynamics of voltage-gated sodium channels Na(v)1.2 and Na(v)1.6 using genome editing, super-resolution, and live-cell single-molecule imaging. The researchers discovered a previously uncharacterized trafficking pathway for Na(v)1.2 and revealed the developmental regulation of Na(v)1.2 and Na(v)1.6 in different subcellular compartments.
JOURNAL OF NEUROSCIENCE
(2022)
Review
Medicine, Research & Experimental
Yanting Shen, Jing Yue, Weiqing Xu, Shuping Xu
Summary: Organelles play crucial roles in cell activities and are closely associated with apoptosis, neurodegenerative diseases, cardiovascular diseases, and cancers. Understanding subcellular structures and their abnormal conditions can lead to insights on pathological mechanisms for early diagnosis and effective therapy. Surface-enhanced Raman spectroscopy (SERS) has been shown to be a powerful tool in studying subcellular compartments with molecular specificity and high sensitivity, meeting the demands of cellular investigations.
Article
Computer Science, Interdisciplinary Applications
Anjan Kumar Payra, Banani Saha, Anupam Ghosh
Summary: This paper proposes a method for predicting essential proteins using a modified Jaccard's coefficient, and it is demonstrated to have excellent accuracy through extensive experiments. Compared to other existing models, this method performs better in predicting essential proteins.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2023)
Article
Multidisciplinary Sciences
Ibrahim E. Elsemman, Angelica Rodriguez Prado, Pranas Grigaitis, Manuel Garcia Albornoz, Victoria Harman, Stephen W. Holman, Johan van Heerden, Frank J. Bruggeman, Mark M. M. Bisschops, Nikolaus Sonnenschein, Simon Hubbard, Rob Beynon, Pascale Daran-Lapujade, Jens Nielsen, Bas Teusink
Summary: The study developed a metabolic model of yeast cells to predict proteome constraints governing metabolic strategies. Under specific conditions, unicellular organisms rewire their metabolism to adapt to growth and maintenance needs.
NATURE COMMUNICATIONS
(2022)
Article
Immunology
Nicholas A. Scott, Melissa A. E. Lawson, Ryan James Hodgetts, Gwenaelle Le Gall, Lindsay J. Hall, Elizabeth R. Mann
Summary: Intestinal macrophage metabolism is influenced by microbial metabolites. Disruption of the intestinal microbiota by antibiotics significantly alters the metabolic environment and functions of intestinal macrophages. The microbiota has compartment-specific effects on gut macrophage metabolism, which have important implications for monocyte recruitment and macrophage differentiation.
Article
Chemistry, Multidisciplinary
Shuchang Lai, Ying Chen, Fan Yang, Weidi Xiao, Yuan Liu, Chu Wang
Summary: Protein lipoylation is an important post-translational modification related to various human diseases. However, a comprehensive strategy for quantifying lipoylation sites is still lacking. In this study, we developed a novel approach to quantify lipoylation sites in complex biological samples and investigated their functional connection with the synthetic pathway. This research will contribute to the understanding of the molecular mechanisms underlying lipoylation-related diseases.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Public, Environmental & Occupational Health
Chao Zuo, Zeyang Meng, Fenping Zhu, Yuzhi Zheng, Yuting Ling
Summary: Vaccines are crucial in preventing and controlling COVID-19, and designing effective vaccination strategies is essential in reducing infections and deaths. Vaccinating older age groups has shown to decrease mortality, while prioritizing the 0-20 age group as the first strategy is the most effective in reducing confirmed cases. Partial vaccination in low-income countries has resulted in fewer infections and deaths compared to full vaccination. Optimizing vaccine allocation requires considering the sensitivity of testing volume and infection rate, as well as the vaccine proportion for the target age group.
FRONTIERS IN PUBLIC HEALTH
(2022)
Article
Multidisciplinary Sciences
Thomas Hu, Mayar Allam, Shuangyi Cai, Walter Henderson, Brian Yueh, Aybuke Garipcan, Anton V. Ievlev, Maryam Afkarian, Semir Beyaz, Ahmet F. Coskun
Summary: The authors developed a framework for joint protein-metabolite profiling at the single-cell level in human tissue combining targeted multiplexed protein imaging and untargeted spatial metabolomics in a single pipeline.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Thomas Wieloch, Thomas David Sharkey
Summary: The oxidative pentose phosphate pathway provides cytosolic NADPH but reduces carbon and energy use efficiency. Repressing this pathway and introducing cytosolic NADPH-dependent malate dehydrogenase may increase crop yields by approximately 5%.
Article
Engineering, Environmental
Yu Miao, Monica B. Heintz, Caitlin H. Bell, Nicholas W. Johnson, Alexandra LaPat Polasko, David Favero, Shaily Mahendra
Summary: The study found that enhancing the degradation of 1,4-dioxane by adding nutrients resulted in increased expression of specific genes, leading to the degradation of organic pollutants and affecting the structure and function of microbial communities. Although the bioaugmented microbes decreased due to insufficient growth substrates and microbial competition, they continued to degrade 1,4-dioxane through indigenous propanotrophic and heterotrophic bacteria. Functional redundancy acted as a buffer capacity to ensure a stable microbiome and drove the restoration of microbial functions to original levels.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Chemistry, Applied
Hanna Barchanska, Ji Tang, Xiangyu Fang, Magdalena Danek, Joanna Plonka, Marcin Sajdak
Summary: In this study, Raphanus sativus var. longipinnatus was exposed to various herbicides and LC-MS/MS-FL analysis was used to identify markers of plant response to herbicide stress, emphasizing the importance of detecting both parent compounds and by-products for reliable information. Differences in content of certain substances were observed in plant tissues exposed to herbicides, indicating their potential as markers for herbicide exposure, while non-target analysis proved useful in recognizing herbicide types used during cultivation.
Article
Multidisciplinary Sciences
Susanne Krause, Sabrina Gfrerer, Andriko von Kuegelgen, Carsten Reuse, Nina Dombrowski, Laura Villanueva, Boyke Bunk, Cathrin Sproeer, Thomas R. Neu, Ute Kuhlicke, Kerstin Schmidt-Hohagen, Karsten Hiller, Tanmay A. M. Bharat, Reinhard Rachel, Anja Spang, Johannes Gescher
Summary: This study reports a stable co-culture of a member of the Micrarchaeota and its host, and sheds light on this symbiosis through multi-omic and physiological analyses.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Davide G. Franchina, Henry Kurniawan, Melanie Grusdat, Carole Binsfeld, Luana Guerra, Lynn Bonetti, Leticia Soriano-Baguet, Anouk Ewen, Takumi Kobayashi, Sophie Farinelle, Anna Rita Minafra, Niels Vandamme, Anais Carpentier, Felix K. Borgmann, Christian Jager, Ying Chen, Markus Kleinewietfeld, Vasilis Vasiliou, Michel Mittelbronn, Karsten Hiller, Philipp A. Lang, Dirk Brenner
Summary: This study reveals that deficiency of glutamate cysteine ligase (Gclc), the enzyme for glutathione synthesis, has differential impacts on the homeostasis of follicular and marginal zone B cells (FoB and MZB), specifically impairing FoB activation and downstream antiviral immunity.
NATURE COMMUNICATIONS
(2022)
Article
Nutrition & Dietetics
Lisa Schlicker, Gang Zhao, Christian-Alexander Dudek, Hanny M. Boers, Michael Meyer-Hermann, Doris M. Jacobs, Karsten Hiller
Summary: The study found that different carbohydrate sources adjust the direction of lactate dehydrogenase and alanine amino transferase fluxes differently to ensure sufficient availability and prevent overflow of the metabolite pools. The systemic lactate pool acts as a metabolic buffer, playing a key role in systemic metabolic homeostasis by being replenished in the early postprandial phase and depleted in the late postprandial phase.
FRONTIERS IN NUTRITION
(2022)
Article
Multidisciplinary Sciences
Fotios Karagiannis, Konrad Peukert, Laura Surace, Marcel Michla, Fabian Nikolka, Mario Fox, Patricia Weiss, Caroline Feuerborn, Paul Maier, Susanne Schulz, Burcu Al, Benjamin Seeliger, Tobias Welte, Sascha David, Inge Grondman, Aline H. de Nooijer, Peter Pickkers, Jan Lukas Kleiner, Marc Moritz Berger, Thorsten Brenner, Christian Putensen, Hiroki Kato, Natalio Garbi, Mihai G. Netea, Karsten Hiller, Katarzyna Placek, Christian Bode, Christoph Wilhelm
Summary: This study found that impaired production of beta-hydroxybutyrate (BHB) is associated with severe COVID-19 respiratory distress syndrome. BHB promotes the survival and interferon-gamma production of CD4(+) T cells. BHB acts as an alternative carbon source, fueling oxidative phosphorylation and maintaining the redox balance.
Article
Nutrition & Dietetics
Jarlei Fiamoncini, Carlos M. Donado-Pestana, Graziela Biude Silva Duarte, Milena Rundle, Elizabeth Louise Thomas, Yoana Kiselova-Kaneva, Thomas E. Gundersen, Diana Bunzel, Jean-Pierre Trezzi, Sabine E. Kulling, Karsten Hiller, Denise Sonntag, Diana Ivanova, Lorraine Brennan, Suzan Wopereis, Ben van Ommen, Gary Frost, Jimmy Bell, Christian A. Drevon, Hannelore Daniel
Summary: This study identified markers associated with differential responses to an OGTT in a population of healthy adults. It found that individuals with distinct postprandial glucose profiles displayed higher postprandial glucose levels and increased fasting plasma concentrations of known biomarkers of insulin resistance. The study suggests that analysis of the corresponding metabolite profile in a fasting blood sample may allow for early identification of individuals at risk for insulin resistance.
FRONTIERS IN NUTRITION
(2022)
Article
Cell Biology
Liliana Francois, Pavle Boskovic, Julian Knerr, Wei He, Gianluca Sigismondo, Carsten Schwan, Tushar H. More, Magdalena Schlotter, Jeroen Krijgsveld, Karsten Hiller, Robert Grosse, Peter Lichter, Bernhard Radlwimmer
Summary: In this study, researchers identified BCAT1 as a metabolic enzyme involved in cell proliferation in aggressive cancers. They found that BCAT1 also has a non-metabolic function as a mitotic regulator, playing a crucial role in chromosome segregation and tumor growth.
Article
Biology
Niklas Lonnemann, Shirin Hosseini, Melanie Ohm, Robert Geffers, Karsten Hiller, Charles A. Dinarello, Martin Korte
Summary: IL-37 has immunomodulatory effects in the central nervous system, protecting neuronal structure and function, inhibiting microglial activation, enhancing long-term potentiation, and exerting anti-inflammatory effects in chronic neuroinflammatory conditions like Alzheimer's disease.
Article
Biochemistry & Molecular Biology
Tushar H. More, Bahareh Mozafari, Andre Maertens, Christian Herr, Philipp M. Lepper, Guy Danziger, Thomas Volk, Sabrina Hoersch, Marcin Krawczyk, Katharina Guenther, Karsten Hiller, Robert Bals
Summary: This study aims to compare the blood metabolome of COVID-19 pneumonia and non-COVID-19 pneumonia, revealing specific metabolic changes in the two pneumonia groups. The results indicate significant differences in blood metabolism between COVID-19 pneumonia and non-COVID-19 pneumonia.
Article
Nutrition & Dietetics
Semira R. Ortiz, Alexander Heinz, Karsten Hiller, Martha S. Field
Summary: Erythritol synthesis in human lung carcinoma cells is proportional to flux through the pentose phosphate pathway (PPP) and regulated by non-oxidative PPP enzymes.
FRONTIERS IN NUTRITION
(2022)
Article
Biochemistry & Molecular Biology
Alexander Heinz, Yannic Nonnenmacher, Antonia Henne, Michelle-Amirah Khalil, Ketlin Bejkollari, Catherine Dostert, Shirin Hosseini, Oliver Goldmann, Wei He, Roberta Palorini, Charlene Verschueren, Martin Korte, Ferdinando Chiaradonna, Eva Medina, Dirk Brenner, Karsten Hiller
Summary: Macrophages undergo extensive metabolic reprogramming during classical pro-inflammatory polarization (M1-like). In this study, the specific functions of itaconate in fractionated mitochondria were examined. It was found that M1 macrophages produce itaconate de novo via aconitase decarboxylase 1 (ACOD1) inside mitochondria. Itaconate was shown to attenuate reductive carboxylation at IDH2, restricting its own production and the accumulation of other immunomodulatory metabolites.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2022)
Article
Clinical Neurology
Max Borsche, Andre Maertens, Philipp Hoermann, Theresa Brueckmann, Katja Lohmann, Sinem Tunc, Christine Klein, Karsten Hiller, Alexander Balck
Summary: This study investigates the differences in glucose metabolism between Parkinson's disease (PD) patients and healthy controls using advanced biochemical methods. The results show that glucose production pathways differ between idiopathic and PRKN mutation carriers, and are associated with diabetes. This study provides the first in vivo evidence for alterations in glucose metabolism in idiopathic PD.
MOVEMENT DISORDERS
(2023)
Article
Biochemistry & Molecular Biology
Matthew S. J. Mangan, Friederike Gorki, Karoline Krause, Alexander Heinz, Anne Pankow, Thomas Ebert, Dieter Jahn, Karsten Hiller, Veit Hornung, Marcus Maurer, Florian Schmidt, Ralf Gerhard, Eicke Latz
Summary: This study reveals that human monocyte-derived macrophages (hMDM) have a different regulation of Pyrin activation compared to monocytes and murine macrophages. Unlike the latter, hMDM fail to activate Pyrin in response to known Pyrin activators and require prolonged priming and increased Pyrin expression for Pyrin inflammasome response. However, FMF mutations lift the requirement for prolonged priming, enabling Pyrin activation without additional inflammatory signals. Additionally, the study unexpectedly finds that TcdB can activate the NLRP3 inflammasome in hMDM even without a Pyrin response.
Article
Biochemistry & Molecular Biology
Antonia Henne, Anna Vigh, Andre Maertens, Yannic Nonnenmacher, Melanie Ohm, Shirin Hosseini, Tushar H. More, Mario A. Lauterbach, Hendrikus Garritsen, Martin Korte, Wei He, Karsten Hiller
Summary: The SiMeEx method is a simplified metabolite extraction method that allows for efficient and rapid extraction of metabolites from adherent mammalian cells without the need for cell scraping. It has advantages in both time and resource efficiency, as well as applicability in high-throughput studies.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Endocrinology & Metabolism
Wei He, Antonia Henne, Mario Lauterbach, Eike Geissmar, Fabian Nikolka, Celia Kho, Alexander Heinz, Catherine Dostert, Melanie Grusdat, Thekla Cordes, Janika Haerm, Oliver Goldmann, Anouk Ewen, Charlene Verschueren, Julia Blay-Cadanet, Robert Geffers, Hendrikus Garritsen, Manfred Kneiling, Christian K. Holm, Christian M. Metallo, Eva Medina, Zeinab Abdullah, Eicke Latz, Dirk Brenner, Karsten Hiller
Summary: This study reveals that mesaconate is synthesized in inflammatory macrophages from itaconate. Both non-derivatized itaconate and mesaconate dampen glycolytic activity to a similar extent, but only itaconate represses tricarboxylic acid cycle activity and cellular respiration. However, both metabolites exert similar immunomodulatory effects in pro-inflammatory macrophages.
