Article
Multidisciplinary Sciences
Wanze Chen, Orane Guillaume-Gentil, Pernille Yde Rainer, Christoph G. Gaebelein, Wouter Saelens, Vincent Gardeux, Amanda Klaeger, Riccardo Dainese, Magda Zachara, Tomaso Zambelli, Julia A. Vorholt, Bart Deplancke
Summary: Live-seq is a novel single-cell transcriptomic profiling approach that preserves cell viability during RNA extraction, allowing for the correlation analysis between a cell's ground-state transcriptome and its downstream molecular or phenotypic behavior. It accurately stratifies diverse cell types and states without major cellular perturbations, and can be used to map a cell's trajectory and evaluate gene effects on cell phenotypes.
Article
Chemistry, Analytical
Robert Knitsch, Mohammad AlWahsh, Hannes Raschke, Joerg Lambert, Roland Hergenroeder
Summary: Three-dimensional cell cultures are becoming increasingly important in biochemical research, requiring adaptations of established analytical techniques for more accurate representation of tissue features. This study presents an NMR-based approach to obtain dynamically radial metabolite profiles for cell spheroids, one of the most frequently used 3D models, using spatially selective NMR pulse sequences and a commercially available cryogenic NMR probe.
ANALYTICAL CHEMISTRY
(2021)
Article
Optics
Yi-Chun Hung, Ta-Hsuan Chao, Pojen Yu, Shang-Hua Yang
Summary: This paper proposes a supervised THz deep learning computed tomography (THz DL-CT) framework based on time-domain information, which can restore superior THz tomographic images by extracting features from spatio-temporal THz signals. Compared with conventional methods, THz DL-CT delivers significantly better performance in terms of error and similarity index, and can be applied to reconstructing multi-material systems.
Article
Chemistry, Analytical
Dan Xie, Yanrong Wen, Jingran Chen, Zhanchen Guo, Pengfei Li, Zhen Liu
Summary: In this study, a molecularly imprinted polymer (MIP)-based plasmonic immunosandwich assay (PISA) was developed for the specific recognition of 4PPTylation and detection of ALDH1L1 in single cells. The MIP-based PISA showed excellent binding properties and enabled the specific and sensitive detection of 4PPTylated ALDH1L1 in single living cells. The study also demonstrated possible crosstalk between different pathways in folate metabolism.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Wesley B. Asher, Peter Geggier, Michael D. Holsey, Grant T. Gilmore, Avik K. Pati, Jozsef Meszaros, Daniel S. Terry, Signe Mathiasen, Megan J. Kaliszewski, Mitchell D. McCauley, Alekhya Govindaraju, Zhou Zhou, Kaleeckal G. Harikumar, Khuloud Jaqaman, Laurence J. Miller, Adam W. Smith, Scott C. Blanchard, Jonathan A. Javitch
Summary: This study presents a generally applicable method for using single-molecule fluorescence resonance energy transfer (smFRET) to detect and track transmembrane proteins diffusing within the plasma membrane of mammalian cells. The in-cell smFRET approach reveals agonist-induced structural dynamics within individual metabotropic glutamate receptor dimers. Evidence for receptor monomers, density-dependent dimers, and constitutive dimers in representative class A, B, and C receptors were observed using these methods.
Article
Mechanics
Deyou Li, Zhipeng Ren, Liang Yu, Qi Yang, Hongjie Wang
Summary: This study investigated the generation and transformation of cavitation vortex ropes in a swirling flow. Four types of stable cavitation vortex ropes were observed, and pressure fluctuation characteristics were presented under different operating conditions. The study also revealed the regional distribution of vortex ropes under different Reynolds and cavitation numbers. Dominant characteristic frequencies and unstable transitions during the conversion process were identified, providing valuable insights for improving hydraulic instabilities induced by cavitation vortex ropes in hydraulic machinery.
Article
Chemistry, Analytical
Xintong Lu, Luoyu Ding, Haohan Song, Wenxin Yu, Chaoqing Dong, Jicun Ren
Summary: A novel in situ single molecule spectroscopy method based on fluorescent correlation spectroscopy (FCS) technique was proposed for measuring MMP-9 activity in single living cells. The method utilizes a fluorescent specific peptide and a reference dye as dual probes, and ratiometric translational diffusion time as the measurement parameter.
Article
Green & Sustainable Science & Technology
Yan Zhang, Bak Koon Teoh, Limao Zhang, Jiayu Chen
Summary: Conventional building energy analysis methods often overlook the spatial and temporal heterogeneity of energy consumption. This study proposes a geographically and temporally weighted regression (GTWR) model to improve the accuracy and reliability of building energy modeling. The results show that the GTWR model outperforms other models in terms of goodness-of-fit and average absolute error. The number of floors and energy stars are identified as the most significant factors in evaluating site energy use intensity (EUI).
JOURNAL OF CLEANER PRODUCTION
(2022)
Article
Multidisciplinary Sciences
Olivier Cartapanis, Lukas Jonkers, Paola Moffa-Sanchez, Samuel L. Jaccard, Anne de Vernal
Summary: Analysis of a large database of Holocene temperature time series challenges the concept of a globally synchronous Holocene Thermal Maximum. The discrepancies between climate reconstructions and model simulations highlight the need for reevaluation of climate models and proxy temperature records. The heterogeneous response to climate forcing indicates the lack of globally synchronous HTM.
NATURE COMMUNICATIONS
(2022)
Article
Mathematics
Hongxia Wang, Zihan Zhao, Hongxia Hao, Chao Huang
Summary: This paper considers spatio-temporal correlation and heterogeneity to build a model, and proposes an estimation method by improving the single-index model and incorporating the variance function. The efficacy of the proposed methodologies is evaluated through simulation studies and a case study.
Article
Multidisciplinary Sciences
Mi Ke, Xiao Yuan, An He, Peiyuan Yu, Wendong Chen, Yu Shi, Tony Hunter, Peng Zou, Ruijun Tian
Summary: By developing more selective proximity labeling probes and combining them with label-free quantitative proteomics, the study enables exploration of cytosolic protein assemblies, such as phosphotyrosine-mediated protein complexes formed in response to minute-scale EGF stimulation. The authors demonstrate the application of this method in profiling the spatiotemporal interactome of the EGFR signaling component STS1.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Shiori Iida, Soya Shinkai, Yuji Itoh, Sachiko Tamura, Masato T. Kanemaki, Shuichi Onami, Kazuhiro Maeshima
Summary: The study revealed that local chromatin motion remains steady in live human cells throughout the phases of G1, S, and G2, driven mainly by thermal fluctuations, with an increase in motion following a DNA damage response. These findings support the viscoelastic properties of chromatin and suggest that steady-state chromatin motion enables cells to perform housekeeping functions during interphase.
Article
Robotics
Yubo Cui, Zhiheng Li, Zheng Fang
Summary: In this letter, a method for 3D single object tracking with point clouds is proposed. Compared to previous methods, this method inputs multi-frame point clouds to encode the spatio-temporal information of the target and uses sparse attention mechanism to encode patch-level similarity, achieving efficient tracking.
IEEE ROBOTICS AND AUTOMATION LETTERS
(2023)
Article
Multidisciplinary Sciences
Zhongwen Chen, Yuhong Cao, Chun-Wei Lin, Steven Alvarez, Dongmyung Oh, Peidong Yang, Jay T. Groves
Summary: This study presents a practical method for intracellular multicolor single-molecule tracking using nanopore-electroporation (NanoEP) technique, which can be easily applied to commercial microscopes. By utilizing this method, successful three-color single-molecule tracking of EGFR signaling pathways in living cells was demonstrated, providing detailed spatial localization and dynamics information of Grb2 and SOS.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Oncology
Dieuwke L. Marvin, Li You, Laura Bornes, Maarten van Dinther, Niek Peters, Hao Dang, Sarah K. Hakuno, Marten Hornsveld, Onno Kranenburg, Jacco van Rheenen, Jos H. T. Rohling, Miao-Ping Chien, Peter ten Dijke, Laila Ritsma
Summary: This study developed a dynamic TGF-beta/SMAD3 transcriptional fluorescent reporter to monitor the kinetics of TGF-beta/SMAD3 signaling. The reporter showed specificity and sensitivity in both in vitro and in vivo systems, and observed heterogeneity in cellular response to TGF-beta challenge.
Article
Biochemistry & Molecular Biology
Nicola J. Smyllie, Violetta Pilorz, James Boyd, Qing-Jun Meng, Ben Saer, Johanna E. Chesham, Elizabeth S. Maywood, Toke P. Krogager, David G. Spiller, Raymond Boot-Handford, Michael R. H. White, Michael H. Hastings, Andrew S. I. Loudon
Article
Multidisciplinary Sciences
Antony Adamson, Christopher Boddington, Polly Downton, William Rowe, James Bagnall, Connie Lam, Apolinar Maya-Mendoza, Lorraine Schmidt, Claire V. Harper, David G. Spiller, David A. Rand, Dean A. Jackson, Michael R. H. White, Pawel Paszek
NATURE COMMUNICATIONS
(2016)
Article
Biology
John M. Ankers, Raheela Awais, Nicholas A. Jones, James Boyd, Sheila Ryan, Antony D. Adamson, Claire V. Harper, Lloyd Bridge, David G. Spiller, Dean A. Jackson, Pawel Paszek, Violaine See, Michael R. H. White
Article
Biochemistry & Molecular Biology
Lee S. S. Dunham, Hiroshi Momiji, Claire V. Harper, Polly J. Downton, Kirsty Hey, Anne McNamara, Karen Featherstone, David G. Spiller, David A. Rand, Barbel Finkenstadt, Michael R. H. White, Julian R. E. Davis
Article
Multidisciplinary Sciences
C. V. Harper, D. J. Woodcock, C. Lam, M. Garcia-Albornoz, A. Adamson, L. Ashall, W. Rowe, P. Downton, L. Schmidt, S. West, D. G. Spiller, D. A. Rand, M. R. H. White
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Biochemical Research Methods
Giorgos Minas, Dan J. Woodcock, Louise Ashall, Claire Harper, Michael R. H. White, David A. Rand
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Cell Biology
Katie Lloyd, Stamatia Papoutsopoulou, Emily Smith, Philip Stegmaier, Francois Bergey, Lorna Morris, Madeleine Kittner, Hazel England, Dave Spiller, Mike H. R. White, Carrie A. Duckworth, Barry J. Campbell, Vladimir Poroikov, Vitor A. P. Martins dos Santos, Alexander Kel, Werner Muller, D. Mark Pritchard, Chris Probert, Michael D. Burkitt
DISEASE MODELS & MECHANISMS
(2020)
Article
Endocrinology & Metabolism
Claire Harper, Anne McNamara, David G. Spiller, Jayne C. Charnock, Michael R. H. White, Julian R. E. Davis
Summary: Pituitary cells display heterogeneity in calcium activity and prolactin transcription, with a significant correlation between spontaneous calcium spikes and bursts in prolactin expression. There may be two subsets of cells within the population based on their basal calcium activity, with different transcriptional responses to stimulation. Maintaining a bimodal population phenotype may be driven by calcium activation and histone acetylation.
JOURNAL OF MOLECULAR ENDOCRINOLOGY
(2021)
Article
Cell Biology
Daniel Friedman, Poppy Simmonds, Alexander Hale, Leoma Bere, Nigel W. Hodson, Michael R. H. White, Daniel M. Davis
Summary: NK cells are more effectively stimulated to secrete various antibodies when encountering stiff targets compared to soft targets, which may impact NK cell recognition and response. Varying target stiffness can alter the mechanosensitivity of immune synapses, highlighting soft targets as a blind spot in NK cell recognition.
JOURNAL OF CELL SCIENCE
(2021)
Article
Multidisciplinary Sciences
Polly Downton, Fabio Sanna, Robert Maidstone, Toryn M. Poolman, Edward A. Hayter, Suzanna H. Dickson, Nick A. Ciccone, James O. Early, Antony Adamson, David G. Spiller, Devin A. Simpkins, Matthew Baxter, Roman Fischer, Magnus Rattray, Andrew S. I. Loudon, Julie E. Gibbs, David A. Bechtold, David W. Ray
Summary: Chronic inflammation is associated with metabolic dysfunction, with a temporal crosstalk between inflammatory and metabolic processes. Research has shown that arthritis drives changes in lipid metabolism and mitochondrial function, leading to the accumulation of bioactive lipid species.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Alex A. Koch, James S. Bagnall, Nicola J. Smyllie, Nicola Begley, Antony D. Adamson, Jennifer L. Fribourgh, David G. Spiller, Qing-Jun Meng, Carrie L. Partch, Korbinian Strimmer, Thomas A. House, Michael H. Hastings, Andrew S. Loudon
Summary: This study develops a quantitative model to explain how a finite pool of BMAL1 protein regulates gene expression at thousands of target sites over daily time scales. By tracking dynamic changes in endogenous labeled proteins in tissues, the researchers determine the contribution of multiple rhythmic processes in coordinating BMAL1 DNA binding. The results also reveal the role of nuclear BMAL1 concentration in determining CLOCK and the mechanism of repression of CLOCK:BMAL1 through interactions with PER2:CRY1 and BMAL1:CRY1.
Article
Developmental Biology
Elis Torrezan-Nitao, Sean G. Brown, Linda Lefievre, Jennifer Morris, Joao Correia, Claire Harper, Stephen Publicover
Summary: Exposure of human sperm to progesterone activates CatSper channels, leading to an increase in intracellular calcium concentration and oscillations. The inhibitor SKF96365 can enhance these oscillations. The presence of bovine serum albumin affects the ability of SKF to induce oscillations.
MOLECULAR HUMAN REPRODUCTION
(2023)
Article
Cell Biology
Samantha J. McDonnell, David G. Spiller, Michael R. H. White, Ian A. Prior, Luminita Paraoan
CELL DEATH DISCOVERY
(2019)
Review
Biochemical Research Methods
Pei-Ru Chen, Peng-Fei Xia
Summary: Carbon dioxide plays a crucial role in mitigating global climate change and supporting life on Earth. Synthetic biology and metabolic engineering offer a promising approach to enhance CO2 fixation by combining the advantages of autotrophic and heterotrophic organisms. This article reviews the current progress in constructing synthetic CO2 fixation pathways, discusses the underlying design principles and challenges, and provides insights into the future of carbon recycling through engineered synthetic carbon fixation pathways.
CURRENT OPINION IN BIOTECHNOLOGY
(2024)