Article
Horticulture
Rongli Mo, Na Zhang, Jinxin Li, Qiang Jin, Zhixian Zhu, Zhaoxia Dong, Yong Li, Cheng Zhang, Cui Yu
Summary: This study identified differentially expressed genes associated with anthocyanin accumulation in mulberries through transcriptome analysis, and found that ethylene enhances anthocyanin accumulation in mulberry fruits.
Article
Biochemistry & Molecular Biology
Zexiu Qi, Jie Lin, Ruichang Gao, Weize Wu, Yan Zhang, Xinyuan Wei, Xiang Xiao, Huili Wang, Ye Peng, John M. Clark, Yeonhwa Park, Quancai Sun
Summary: This study investigates the molecular mechanisms of deltamethrin induced fat accumulation in murine adipocytes. The results show that deltamethrin promotes adipogenesis and involves multiple key functional groups regulating adipogenesis.
PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY
(2022)
Article
Food Science & Technology
Mengyang Niu, Xuan Chen, Wen Zhou, Youyou Guo, Xingxing Yuan, Jin Cui, Zhenguo Shen, Nana Su
Summary: This study investigates the molecular mechanism of increased lysine content during quinoa germination through multi-omics analysis. Proteome analysis identifies lysine-rich proteins and endogenous phytohormones as key factors contributing to lysine accumulation. Additionally, key genes involved in lysine biosynthesis are identified, and their relation to amino acid metabolism and starch and sucrose metabolism is explored. These findings provide a foundation for breeding lysine-rich quinoa sprouts and valuable multi-omics resources for studying nutrient characteristics during quinoa germination.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Biology
Kimleng Chuon, Jin-Gon Shim, Kun-Wook Kang, Shin-Gyu Cho, Chenda Hour, Seanghun Meas, Ji-Hyun Kim, Ahreum Choi, Kwang-Hwan Jung
Summary: The position of carotenoid in xanthorhodopsin has been elucidated, but the challenging expression of this opsin and the complex biosynthesis of carotenoid in the laboratory have hindered the insightful study of this rhodopsin. This study demonstrated co-expression of Gloeobacter rhodopsin (GR) with a biosynthesized keto-carotenoid targeting the carotenoid binding site, and revealed three crucial features of carotenoid-rhodopsin interaction. The study highlights the critical position of the carotenoid binding site, which allows another protein engineering approach in the microbial rhodopsin family.
COMMUNICATIONS BIOLOGY
(2022)
Article
Virology
Shruti S. Patil, Helen N. Catanese, Kelly A. Brayton, Eric T. Lofgren, Assefaw H. Gebremedhin
Summary: This study focuses on the temporal and geographical distribution of mutant S proteins of SARS-CoV-2 across the US over a period of 19 months in 2020 and 2021. The S protein sequences are analyzed using multiple methods, including sequence alignment and similarity networks. The study also utilizes visualizations on geographical maps to track variants and shows that DiWANN networks are superior in analyzing transmission profiles compared to BLAST networks.
Article
Biology
Kahlan E. Newman, Sarah N. Tindall, Sophie L. Mader, Syma Khalid, Gavin H. Thomas, Marjan W. van der Woude
Summary: In this study, a computational model of a bacterial O-antigen modifying acetyltransferase, OafB, was built using evolutionary co-variance analysis. The model revealed a novel fold for the AT3 domain, which was shown to be stable in the membrane through molecular dynamics simulations. The study also proposed a model for the function of the AT3 domain, suggesting how the acyl-coA donor spans the membrane and how OafB presents the acetyl group close to the catalytic residues on the extracytoplasmic surface. The findings provide insights into the structure and mechanism of AT3 proteins and offer a framework for developing inhibitors against bacterial pathogens.
Article
Chemistry, Multidisciplinary
Lizhen Chen, Lars Klemeyer, Mingbo Ruan, Xin Liu, Stefan Werner, Weilin Xu, Andrea Koeppen, Robert Buecker, Marta Gallego Gonzalez, Dorota Koziej, Wolfgang J. Parak, Indranath Chakraborty
Summary: Nanozymes, with biocatalytic properties, are used as artificial enzymes to overcome the limitations of natural enzymes. Ligand-free PtAg nanoclusters are synthesized and applied as nanozymes, exhibiting good catalytic activity for various enzyme-mimicking reactions. Comparison between PtAg nanoclusters and PtAg nanoparticles reveals a converse dependency of Ag-loading on their activity. This study contributes to the field of nanozymes and presents a potential option for ligand-free bimetal biocatalysts.
Article
Chemistry, Multidisciplinary
Cheng Zhang, Mei Ding, Yonggang Ren, Along Ma, Zhengmao Yin, Xiaoshuang Ma, Shuxin Wang
Summary: Atomically precise metal nanoclusters with precise structures and free valence electrons provide great opportunities to understand the relationship between structure and properties. The synthesis and structure of Au4(PPh3)4I2 nanoclusters with two free electrons are reported. The Au4 nanocluster exhibits high selectivity for CO electrocatalytic reduction at positive potentials and hydrogen evolution reaction at negative potentials. Structural and electronic analysis reveals the instability of Au4 tetrahedron at negative potentials, leading to the decay in catalytic performance.
NANOSCALE ADVANCES
(2023)
Article
Plant Sciences
Liyun Yang, Jing Gao, Mengze Gao, Lingyan Jiang, Lijuan Luo
Summary: Plant plasma membranes (PM) play a crucial role in maintaining intracellular stability and exchanging information with the external environment. This study developed a simplified method to enrich PM proteins in Stylosanthes plants, which can be used to study the dynamics of PM proteome in response to various stresses.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Polymer Science
Miroslav Janata, Sachin Gupta, Eva Cadova, Pavla Angelisova, Bankala Krishnarjuna, Ayyalusamy Ramamoorthy, Vaclav Horejsi, Vladimir Raus
Summary: Amphiphilic polymers are widely used in the isolation and functional studies of membrane proteins. This study addressed the limitations of carboxylate groups in these polymers by replacing them with more acidic sulfonate groups. The newly synthesized copolymers solubilized membranes and liposomes, and remained soluble at low pH and in the presence of Mg2+ ions.
EUROPEAN POLYMER JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Qingsong Gao, Lei Liu, Haiying Zhou, Xi Liu, Wei Li, Yu Min, Yurong Yan, Jianhui Ji, Hao Zhang, Xiangxiang Zhao
Summary: OsFWL7 gene in rice is preferentially expressed in roots and is involved in reducing Cd uptake and root-to-shoot translocation, affecting Cd and micronutrient metal accumulation. Additionally, osfwl7 mutation also impacts the expression of some heavy metal transporter genes, further influencing the accumulation of micronutrient metals.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Diana B. Peckys, Daniel Gaa, Dalia Alansary, Barbara A. Niemeyer, Niels de Jonge
Summary: The study found that ORAI1 channels can form supra-molecular clusters, and different structures can be formed during SOCE activation, rather than simply being trapped near active STIM.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Lisa M. Butler, Emma Evergren
Summary: Membrane trafficking and organelle contact sites play important roles in regulating cell metabolism and survival, which are often deregulated in cancer. Prostate cancer is a leading cause of cancer-related death in men, and there is a need to identify prognostic biomarkers and therapeutic targets. This study explored the morphology of organelles and membrane contact sites in prostate cancer tissue and found that there are adaptations in membrane contact sites between mitochondria and the ER during prostate cancer progression. These adaptations are androgen-dependent and may support pro-proliferative signaling and metabolic changes in prostate cancer cells.
FRONTIERS IN ONCOLOGY
(2023)
Article
Clinical Neurology
Lyduine E. Collij, Gemma Salvado, Viktor Wottschel, Sophie E. Mastenbroek, Pierre Schoenmakers, Fiona Heeman, Leon Aksman, Alle Meije Wink, Bart N. M. Berckel, Wiesje M. van de Flier, Philip Scheltens, Pieter Jelle Visser, Frederik Barkhof, Sven Haller, Juan Domingo Gispert, Isadora Lopes Alves
Summary: This study applied the SuStaIn model to analyze Aβ-PET data and identified 3 optimal Aβ accumulation subtypes, referred to as frontal, parietal, and occipital. These subtypes showed distinct associations with APOE epsilon 4 carriers, participants with dementia, and age. Most participants maintained baseline subtype assignment at follow-up.
Article
Biochemical Research Methods
Christopher W. Koo, Jasmine M. Hershewe, Michael C. Jewett, Amy C. Rosenzweig
Summary: The study developed a cell-free protein synthesis system based on Escherichia coli lysate, which can be used to express particulate methane monooxygenase (pMMO) in vitro in the presence of nanodiscs. The findings demonstrate that the pMMO complex can form without the need for exogenous translocon machinery or chaperones.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Cecilia P. Sanchez, Pintu Patra, Shih-Ying Scott Chang, Christos Karathanasis, Lukas Hanebutte, Nicole Kilian, Marek Cyrklaff, Mike Heilemann, Ulrich S. Schwarz, Mikhail Kudryashev, Michael Lanzer
Summary: KAHRP plays a key role in Plasmodium falciparum malaria by forming membrane protrusions in infected erythrocytes, anchoring parasite-encoded adhesins to the membrane skeleton. Through super-resolution microscopy, it was found that KAHRP initially associates with various skeletal components before eventually colocalizing with remnant actin junctions under the spiral scaffold forming knobs. Additionally, a dynamic model of KAHRP organization and its function in attaching other factors to the spiral scaffold was proposed based on the findings.
MOLECULAR MICROBIOLOGY
(2022)
Article
Cell Biology
Sebastian Malkusch, Johanna Rahm, Marina S. Dietz, Mike Heilemann, Jean-Baptiste Sibarita, Jorn Lotsch
Summary: This study proposes a method that analyzes the differences in receptor mobility between internalin B-treated and -untreated cells. By using hidden Markov modeling and explainable artificial intelligence, the key differences in MET under different treatment conditions are learned from single-particle tracking data, allowing for inference of cellular information.
MOLECULAR BIOLOGY OF THE CELL
(2022)
Article
Multidisciplinary Sciences
Shivam Yadav, Martin Centola, Mathilda Glaesmann, Denys Pogoryelov, Roman Ladig, Mike Heilemann, L. C. Rai, Ozkan Yildiz, Enrico Schleiff
Summary: This study reveals the role of a cyanobacterial cyclophilin in stress responses and assembly of photosynthetic complexes, and presents its unique structural features.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Nicole Koller, Philipp Hoellthaler, Martina Barends, Marius Doering, Christoph Spahn, Veronica Duran, Bibiana Costa, Jennifer Becker, Mike Heilemann, Ulrich Kalinke, Robert Tampe
Summary: Dendritic cells (DCs) translate innate immune responses into adaptive immunity, but the spatial organization of underlying processes is not well understood. By studying human monocyte-derived DCs, we discovered a nanoscale organization of antigen-loading machinery and observed an increase in density during DC maturation.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biology
Christoph Spahn, Estibaliz Gomez-de-Mariscal, Romain F. Laine, Pedro M. Pereira, Lucas von Chamier, Mia Conduit, Mariana G. Pinho, Guillaume Jacquemet, Seamus Holden, Mike Heilemann, Ricardo Henriques
Summary: This work demonstrates the use of state-of-the-art artificial neural networks in analyzing bacterial microscopy images. It provides strategies for data acquisition, curation, and model training, and showcases the capabilities of deep learning in tasks such as image segmentation, growth stage classification, phenotypic profiling, and image denoising. The creation of a purposefully-built database aids novice users in quickly exploring data analysis through deep learning.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Marius Glogger, Dongni Wang, Julian Kompa, Ashwin Balakrishnan, Julien Hiblot, Hans-Dieter Barth, Kai Johnsson, Mike Heilemann
Summary: Combining label exchange and the synergy of different types of exchangeable labels can increase the multiplexing capabilities in fluorescence microscopy and the information content of microscopy images.
Article
Chemistry, Multidisciplinary
Julian Kompa, Jorick Bruins, Marius Glogger, Jonas Wilhelm, Michelle S. Frei, Miroslaw Tarnawski, Elisa D'Este, Mike Heilemann, Julien Hiblot, Kai Johnsson
Summary: The specific and covalent labeling of the protein HaloTag with fluorescent probes in living cells makes it a powerful tool for bioimaging. However, the irreversible attachment of the probe to HaloTag precludes imaging applications that require transient binding of the probe and comes with the risk of irreversible photobleaching. Here, we introduce exchangeable ligands for fluorescence labeling of HaloTag (xHTLs) that reversibly bind to HaloTag and that can be coupled to rhodamines of different colors.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Review
Chemistry, Multidisciplinary
Lorenzo Albertazzi, Mike Heilemann
Summary: The exploitation of low-affinity molecular interactions in protein labeling is an emerging topic in optical microscopy, which allows for a constant renewal of fluorescence signals at target sites. It has versatile use across microscopy methods and has shown potential in 3D, live, and many-target applications. Although some progress has been made in developing low-affinity labels, this research field still has a lot of untapped potential.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Claudia Catapano, Johanna V. Rahm, Marjan Omer, Laura Teodori, Jorgen Kjems, Marina S. Dietz, Mike Heilemann
Summary: HER2 belongs to the ErbB sub-family of receptor tyrosine kinases and is activated through heterodimerization with other ErbB receptors. This study found that HER2 is strongly activated by EGFR-targeting ligands EGF and TGFa, with a distinguishable temporal fingerprint. HER4-targeting ligands EREG and NRG beta 1 showed weaker activation of HER2, with a preference for EREG and a delayed response to NRG beta 1.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Neurosciences
Isa Jauch, Jan Kamm, Luca Benn, Lukas Rettig, Hans-Christoph Friederich, Jonas Tesarz, Thomas Kuner, Sebastian Wieland
Summary: Post-traumatic stress disorder and other mental disorders can be treated with Eye Movement Desensitization and Reprocessing (EMDR), a psychotherapy that involves traumatic memory confrontation and bilateral stimuli. The effects of bilateral stimuli on the brain and their potential use in different patients or mental disorders are unknown. A new device called 2MDR was developed to stimulate rodents with multimodal visual stimuli and analyze their behavior. Using 2MDR, it was confirmed that EMDR-like bilateral stimuli improved fear extinction in mice and these effects were dependent on physical stimulus properties. This study demonstrates the potential of noninvasive brain stimulation using visual stimuli to alter emotional processing in mice.
Article
Chemistry, Multidisciplinary
Laurell F. F. Kessler, Ashwin Balakrishnan, Nina S. S. Deussner-Helfmann, Yunqing Li, Maximilian Mantel, Marius Glogger, Hans-Dieter Barth, Marina S. S. Dietz, Mike Heilemann
Summary: Super-resolution techniques such as SMLM and STED microscopy are enhanced by using weak affinity-based transient labelling systems, such as DNA-based hybrid systems. However, these techniques suffer from high background fluorescence signal caused by unbound fluorophore-labelled oligonucleotides. This study introduces short-distance self-quenching in fluorophore dimers as an efficient mechanism to reduce background fluorescence signal and increase photon budget in the bound state.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemical Research Methods
Alon Saguy, Onit Alalouf, Nadav Opatovski, Soohyen Jang, Mike Heilemann, Yoav Shechtman
Summary: Single-molecule localization microscopy (SMLM) has significantly improved spatial resolution in biological imaging, but has limitations in observing dynamics at high temporal resolution. In this study, we introduce DBlink, a deep-learning-based method that reconstructs super spatiotemporal resolution videos from SMLM data. DBlink utilizes a convolutional neural network combined with a bidirectional long short-term memory network to capture long-term dependencies between different frames. Experimental results demonstrate the effectiveness of DBlink in various scenarios, including simulated structures and live-cell dynamic SMLM. This advancement in super-resolution imaging of dynamic processes in living cells is crucial.
Review
Biology
Deepti Mittal, Rebecca Mease, Thomas Kuner, Herta Flor, Rohini Kuner, Jamila Andoh
Summary: The importance of effective research data management (RDM) strategies grows with advancements in data acquisition techniques and research methods, especially in neuroscience. However, large-scale neuroscience research consortia face challenges in implementing a coherent RDM plan due to the diverse research strategies and requirements they encompass. This article presents a concrete RDM strategy implemented for the Heidelberg Collaborative Research Consortium, focusing on sustainable solutions that incentivize incremental RDM while respecting research-specific requirements.
Article
Biophysics
Soohyen Jang, Kaarjel K. Narayanasamy, Johanna V. Rahm, Alon Saguy, Julian Kompa, Marina S. Dietz, Kai Johnsson, Yoav Shechtman, Mike Heilemann
Summary: Single-molecule localization microscopy achieves nanometer spatial resolution but faces challenges of long acquisition time and photobleaching. This study combines a neural network and a protein labeling method to improve acquisition speed and temporal resolution, enabling capturing of cellular structure dynamics in live cells.
BIOPHYSICAL REPORTS
(2023)
Proceedings Paper
Cell Biology
Johanna Rahm, Sebastian Malkusch, Ulrike Endesfelder, Marina S. Dietz, Mike Heilemann
Summary: This study presents a pipeline for the analysis of single-particle tracking data, allowing for the determination of biomolecule mobility and diffusion state transitions. The application of this pipeline to receptor trajectories revealed that activated receptors move slower and more confined, with more transitions from free to confined diffusion states. The analysis also identified three diffusion states, with increased transition probabilities towards the less mobile and immobile states upon ligand activation.
SINGLE MOLECULE SPECTROSCOP AND SUPERRESOLUTION IMAGING XV
(2022)
