Article
Biochemical Research Methods
Johannes Dornhof, Jochen Kieninger, Harshini Muralidharan, Jochen Maurer, Gerald A. Urban, Andreas Weltin
Summary: The study introduced a microfluidic organ-on-chip platform for matrix-based, heterogeneous 3D cell cultures with integrated electrochemical sensors for metabolites. The system allowed precise control of culture conditions and real-time multi-analyte metabolite monitoring, demonstrating potential applications in personalized medicine and cancer research.
Article
Multidisciplinary Sciences
Gi Bae Kim, Ye Gao, Bernhard O. Palsson, Sang Yup Lee
Summary: Transcription factors are proteins that regulate gene expression by binding to specific DNA sequences, traditionally predicted through sequence homology analysis. However, the development of the deep learning-based tool DeepTFactor has shown high performance in predicting transcription factors efficiently and accurately, even for those with no homology to reported ones.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Siqian Feng, Richard S. Mann
Summary: Chromatin immunoprecipitation (ChIP) is a crucial technique for studying protein-DNA interactions, but lacks cell type-specificity in complex tissues. SpyChIP overcomes this limitation by utilizing a specific isopeptide bond to identify cell type-specific transcription factor (TF) binding sites, offering insights into TF mechanisms in different cell types.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Analytical
Korakot Boonyaphon, Zhenglin Li, Sung-Jin Kim
Summary: In this study, a microfluidic recirculation system driven by water-head pressures was developed, which enables media recirculation in parallel channels with pulsatile and constant flows. The system allows control of flow rates and shear stress, and can be used for systematic and parallel analysis of cell response to fluidic shearing patterns.
ANALYTICA CHIMICA ACTA
(2022)
Article
Immunology
Manon Henry, Anais Burgain, Faiza Tebbji, Adnane Sellam
Summary: This research identified the transcription factors Ahr1 and Tye7 as central regulators of filamentous growth in Candida albicans under hypoxic conditions. These transcription factors directly modulate a set of genes and biological processes to negatively regulate hypoxic filamentation. Additionally, the study found that Ahr1 and Tye7 repress filamentation through different signaling pathways.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Chemistry, Analytical
Shan He, Huiting Lian, Xuegong Cao, Bin Liu, Xiaofeng Wei
Summary: A light-driven photocatalytic-photothermal synergetic system integrated with a microfluidic distance-based analytical device (PCPT-mu DAD) was developed for visual, portable, sensitive, and quantitative detection of targets. This system effectively translates target concentration into a visual distance signal readout by utilizing the photosensitization and photothermal effect.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Timo Rey, Luis Carlos Tabara, Julien Prudent, Michal Minczuk
Summary: This article introduces a single-cell image analysis tool called mtFociCounter for reproducible quantification of mitochondrial nucleoids and other foci. Analysis of 2165 single fibroblasts shows substantial cell-to-cell heterogeneity in nucleoid numbers. mtFociCounter can quantify mitochondrial content and reveals a good correlation between nucleoid number and mitochondrial area.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Analytical
Tomoya Ide, Yong-Joon Choi, Yasuyuki Kimura, Takeshi Hizawa, Kazuhiro Takahashi, Hiromu Ishii, Toshihiko Noda, Kazuaki Sawada
Summary: This study reports a compact microfluidic measurement system that can selectively identify wavelengths without using an optical component, based on a filter-free multiple-wavelength sensor. The system successfully identified two types of fluorescent beads and detected both wavelength and intensity of light using a potential peak formed by the photogate voltage.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Agronomy
Feng Luo, Guo-Bao Niu, Qian Zhou, Li-Jie Wang, Li-Juan Bai, Wen-Zheng Gao
Summary: This study identified six anthocyanin-related metabolites in postharvest Pr mutants of purple cauliflower using metabolomic analyses. The main component responsible for the pungent flavor of the Pr mutant was found to be 6-gingerol, which is involved in several biosynthesis pathways. The expression level of caffeoyl coenzyme A O-methyltransferase (CCoAOMT) was correlated with the pungent flavor, and the transcription factor (TF) BoMYB2 was found to negatively regulate BoCCoAOMT transcription and promote 6-gingerol accumulation.
POSTHARVEST BIOLOGY AND TECHNOLOGY
(2023)
Article
Biochemical Research Methods
Maria Osmala, Gokcen Eraslan, Harri Lahdesmaki
Summary: ChromDMM is a mixture model based on multiple chromatin features, which accurately clusters genomic regions and discovers distinctive patterns of epigenetic signals at regulatory elements. Validated with simulated data and ENCODE data, ChromDMM demonstrates higher accuracy and robustness.
Article
Optics
Ying Huang, Hengsong Yue, Wei Ma, Yiyuan Zhang, Yao Xiao, Yong Tang, He Tang, Tao Chu
Summary: We propose and demonstrate a highly parallel photonic acceleration processor based on a wavelength division multiplexing (WDM) system and a non-coherent Mach-Zehnder interferometer (MZI) array. The use of WDM devices enables dimensional expansion and, combined with the broadband characteristics of an MZI, allows for matrix-matrix multiplication. Through experiments, we achieve an inference accuracy of 90.5% in a classification task using a reconfigurable 8x8 MZI array structure for a 2x2 non-negative valued matrix. This research provides a new effective solution for large-scale integrated optical computing systems based on convolution acceleration processors.
Article
Engineering, Biomedical
Sanaullah, Muhammad Arshad Javid, Saeed Ahmad Buzdar
Summary: Cancer diagnosis is a challenging task in medical image processing. A novel method using MRI and MRS images to locate tumors and sub-regions was explored in this study. An automated CAD system was developed to classify and segment brain cancer tissues, achieving high diagnostic accuracy for high- and low-grade tumors.
BIOMEDICAL SIGNAL PROCESSING AND CONTROL
(2021)
Article
Chemistry, Physical
Chengming Jiang, Dongchen Tan, Nan Sun, Jijie Huang, Ruonan Ji, Qikun Li, Sheng Bi, Qinglei Guo, Xiaohu Wang, Jinhui Song
Summary: The HPPMS is a high-resolution pressure piezo-memory system with a 60 nm pixel size, featuring non-volatile force resistive conversion and force-tunable synaptic functions. It enables nanoscale force image sensing and memory actions, along with enhanced processing efficiencies and recognition rates for neuromorphic tactile preprocessing.
Article
Immunology
Chenshen Huang, Na Zhang, Hao Xiong, Ning Wang, Zhizhong Chen, Zhizhan Ni, Xiaohong Liu, Boxu Lin, Bujun Ge, Bing Du, Qi Huang
Summary: This study aims to explore a novel method for transcriptional regulation and proposes a new pipeline for analyzing the role of GPRC5B in COAD. By using RNA-seq, ATAC-seq, and ChIP-seq, researchers found the correlation between GPRC5B and macrophages and identified TF GATA4 as a key upstream factor.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Optics
Guannan Shi, Randy Shurtz, Gary Pickrell, Anbo Wang, Yizheng Zhu
Summary: In this study, the point-by-point inscription of sapphire parallel fiber Bragg gratings (sapphire pFBGs) in a fully multi-mode system is investigated. The critical role of parallel FBGs in enabling detectable and reliable high-order grating signals is demonstrated. The impacts of modal volume, spatial coherence, and grating location on reflectivity are examined. Three cascaded seventh-order pFBGs are fabricated in one sapphire fiber for wavelength multiplexed temperature sensing, and reliable measurement up to 1500 degrees C is demonstrated using a low-cost, fully multimode 850-nm interrogator.
Article
Multidisciplinary Sciences
Chao Su, Marta Rodriguez-Franco, Beatrice Lace, Nils Nebel, Casandra Hernandez-Reyes, Pengbo Liang, Eija Schulze, Evgeny V. Mymrikov, Nikolas M. Gross, Julian Knerr, Hong Wang, Lina Siukstaite, Jean Keller, Cyril Libourel, Alexandra A. M. Fischer, Katharina E. Gabor, Eric Mark, Claudia Popp, Carola Hunte, Wilfried Weber, Petra Wendler, Thomas Stanislas, Pierre-Marc Delaux, Oliver Einsle, Robert Grosse, Winfried Roemer, Thomas Ott
Summary: The organization of membranes in plants is mainly controlled by the cell wall and cytoskeleton, with some proteins, such as remorins, playing a role in protein and lipid organization. Symbiosis-specific SYMREM1 gene mutations disrupt membrane organization in root nodules. AlphaFold modeling and biochemical analyses reveal that SYMREM1 forms oligomers and may contribute to higher-order membrane scaffolding.
NATURE COMMUNICATIONS
(2023)
Review
Plant Sciences
Kai R. Konrad, Shiqiang Gao, Matias D. Zurbriggen, Georg Nagel
Summary: Optogenetics is a technique that uses light-sensitive receptors in transgenic organisms to manipulate biological activities. It allows for fine-tuning of cellular processes using light in a noninvasive and spatiotemporally resolved manner. Despite its success in various model organisms, optogenetic tools have been rarely applied in plants. Recent progress has overcome the challenges of plant dependency on light and the absence of the rhodopsin chromophore, allowing for the establishment of plant optogenetics.
ANNUAL REVIEW OF PLANT BIOLOGY
(2023)
Editorial Material
Biochemistry & Molecular Biology
Wilfried Weber, Martin Fussenegger
CURRENT OPINION IN CHEMICAL BIOLOGY
(2023)
Article
Plant Sciences
Rhonda C. Meyer, Kathleen Weigelt-Fischer, Henning Tschiersch, Georgia Topali, Lothar Altschmied, Marc C. Heuermann, Dominic Knoch, Markus Kuhlmann, Yusheng Zhao, Thomas Altmann
Summary: Plant growth is influenced by numerous genetic and environmental factors. In this study, the genetic factors affecting plant performance under different light regimes were identified using high-throughput phenotyping and genome-wide association studies. The results showed that the identified quantitative trait loci (QTL) for leaf area, growth rate, and PSII efficiency were specific to different light conditions and displayed distinct temporal activity patterns. Several candidate genes were identified at consistently found QTL regions under both light regimes. These findings highlight the importance of considering environmental and temporal patterns of gene actions in understanding plant growth.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemical Research Methods
Jaewan Jang, Kun Tang, Jeffrey Youn, Sherin McDonald, Hannes M. Beyer, Matias D. Zurbriggen, Maruti Uppalapati, G. Andrew Woolley
Summary: By engineering synthetic light-dependent interactors, we developed bidirectional, cyanobacteriochrome-based light-inducible dimers (BICYCL) for optogenetic control of protein-protein interactions with green and red light. This systematic approach enables the future engineering of a broad chromatic palette of CBCRs for optogenetics use.
Article
Biochemistry & Molecular Biology
Celine Bournonville, Kentaro Mori, Paul Deslous, Guillaume Decros, Tim Blomeier, Jean-Philippe Mauxion, Joana Jorly, Stephanie Gadin, Cedric Cassan, Mickael Maucourt, Daniel Just, Cecile Bres, Christophe Rothan, Carine Ferrand, Lucie Fernandez-Lochu, Laure Bataille, Kenji Miura, Laure Beven, Matias D. Zurbriggen, Pierre Petriacq, Yves Gibon, Pierre Baldet
Summary: Mutation in the PAS/LOV protein gene in tomato plants leads to ascorbate-enriched fruits, indicating the light-dependent regulation of ascorbate metabolism. Blue light modulates the interaction between PLP and GGP, resulting in increased synthesis of ascorbate.
Article
Multidisciplinary Sciences
Pamela E. Molinari, Adriana R. Krapp, Andrea Weiner, Hannes M. Beyer, Arun Kumar Kondadi, Tim Blomeier, Melina Lopez, Pilar Bustos-Sanmamed, Evelyn Tevere, Wilfried Weber, Andreas S. Reichert, Nora B. Calcaterra, Mathias Beller, Nestor Carrillo, Matias D. Zurbriggen
Summary: NADP(H) is a central metabolic hub that provides reducing equivalents to various pathways in living organisms. The genetically-encoded biosensor NERNST is able to interact with NADP(H) and estimate its redox state, allowing for the monitoring of NADP(H) dynamics in different organisms and potential applications in biochemical, biotechnological, and biomedical research.
NATURE COMMUNICATIONS
(2023)
Article
Oncology
Katrin Raute, Juliane Strietz, Maria Alejandra Parigiani, Geoffroy Andrieux, Oliver S. Thomas, Klaus M. Kistner, Marina Zintchenko, Peter Aichele, Maike Hofmann, Houjiang Zhou, Wilfried Weber, Melanie Boerries, Mahima Swamy, Jochen Maurer, Susana Minguet
Summary: There is currently no targeted therapy for patients with triple-negative breast cancer (TNBC). TNBC is enriched in breast cancer stem cells (BCSC), which play a key role in metastasis, chemoresistance, relapse, and mortality. y8 T cells hold great potential in immuno-therapy against cancer and might provide an approach to therapeutically target TNBC.
CANCER IMMUNOLOGY RESEARCH
(2023)
Article
Materials Science, Multidisciplinary
Maximilian Hoerner, Jan Becker, Rebecca Bohnert, Miguel Banos, Carolina Jerez-Longres, Vanessa Muehlhaeuser, Daniel Haerrer, Tin Wang Wong, Matthias Meier, Wilfried Weber
Summary: Hydrogels with adjustable mechanical properties have been developed to manipulate cell fate and function by converting optical signals into reversible changes in hydrogel mechanics. However, the limited dynamic range of addressable stiffness hampers their broader implementation. In this study, a photoreceptor-based hydrogel with reversibly adjustable stiffness is developed, enabling a wide range of stiffness from approximately 800 Pa to the sol state. The hydrogel's light-responsive mechanical properties are characterized and it is applied for the spatiotemporally controlled deposition of mammalian cells, which holds promise in overcoming spatial restrictions.
ADVANCED MATERIALS TECHNOLOGIES
(2023)
Article
Biochemistry & Molecular Biology
Marissa Russ, Anna K. Ehret, Maximilian Hoerner, Daniel Peschkov, Rebecca Bohnert, Vincent Idstein, Susana Minguet, Wilfried Weber, Bjoern F. Lillemeier, O. Sascha Yousefi, Wolfgang W. Schamel
Summary: The kinetics of ligand-receptor interaction can be experimentally and reversibly changed using optogenetics. Researchers have developed a method to control the interaction between a modified receptor and an engineered ligand using light. By expressing the SpyCatcher fused to a transmembrane domain, they successfully displayed PhyB as a membrane-bound protein and coupled it with ligands expressed on other cells. These cells, called opto-antigen presenting cells (opto-APCs), allow two-dimensional ligand-receptor interactions to be controlled by light stimulation.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Materials Science, Biomaterials
Carolina Jerez-Longres, Marieta Gomez-Matos, Jan Becker, Maximilian Hoerner, Franz-Georg Wieland, Jens Timmer, Wilfried Weber
Summary: Encapsulated cell-based therapies involve genetically-modified cells embedded in a material to produce therapeutic agents at specific locations in the body. While promising, safety concerns such as cell escape and uncontrolled production of therapeutic agents still exist. This study develops a material-genetic interface as a safety switch for engineered mammalian cells, improving the safety and translation of cell therapies.
BIOMATERIALS ADVANCES
(2023)
Review
Biochemistry & Molecular Biology
Pamela E. Molinari, Adriana R. Krapp, Matias D. Zurbriggen, Nestor Carrillo
Summary: Oxygenic photosynthesis involves light and dark phases. In the light phase, photosynthetic electron transport provides reducing power and energy to support the carbon assimilation process. Genetically encoded indicators based on fluorescent proteins provide new opportunities to understand and engineer plant metabolism.
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES
(2023)
Article
Multidisciplinary Sciences
Marc C. Heuermann, Dominic Knoch, Astrid Junker, Thomas Altmann
Summary: The study presents a plant cultivation infrastructure, PhenoSphere, that can simulate field-like environments. By comparing it with a standard glasshouse and field trials, the authors find that simulating weather conditions of a single maize growing season in PhenoSphere is more effective in triggering plant growth similar to field observations. The PhenoSphere enables detailed analysis of performance-related trait expression and biological mechanisms in plant populations exposed to current and future climate scenarios.
NATURE COMMUNICATIONS
(2023)
Editorial Material
Oncology
Pierre V. M. Trehin, Geisler Munoz-Guamuro, Wilfried Weber
MOLECULAR THERAPY-ONCOLYTICS
(2023)
Article
Plant Sciences
Dominic Knoch, Rhonda C. Meyer, Marc C. Heuermann, David Riewe, Fritz F. Peleke, Jedrzej Szymanski, Amine Abbadi, Rod J. Snowdon, Thomas Altmann
Summary: This study utilized multi-omics technologies to analyze a canola population, resulting in the discovery of prime candidate genes associated with metabolic and vegetative growth variation. The study revealed a large number of quantitative trait loci and clustered hotspots, as well as unequal effects of the Brassica A and C subgenomes on early biomass production.