Article
Biochemistry & Molecular Biology
Karolina Kucharska, Marta Pilz, Krzysztof Bielec, Tomasz Kalwarczyk, Patrycja Kuzma, Robert Holyst
Summary: The oxazole yellow dye YOYO-1 has two binding modes with DNA: mono-intercalation and bis-intercalation. Bis-intercalation involves two consecutive steps of mono-intercalation with distinct equilibrium constants. Mono-intercalation is dominant at high concentrations while bis-intercalation occurs at low concentrations.
Article
Chemistry, Multidisciplinary
Yoonjung Cho, Hyeong Jeon An, Taehoon Kim, Chulbom Lee, Nam Ki Lee
Summary: The article reports the mechanism of photoconversion of cyanine dyes under photoexcitation, indicating that the process can be achieved mainly through an intermolecular pathway involving bond cleavage and reconstitution. Additionally, the study shows that ketone products generated from singlet oxygen-mediated photooxidation undergo a series of carbon-carbon bond-breaking and -forming events, resulting in dye-to-dye transformation.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Engineering, Environmental
Hanane Chakhtouna, Nadia Zari, Rachid Bouhfid, Abou el kacem Qaiss, Hanane Benzeid
Summary: The study focused on utilizing date palm fibers and TiO2 nanoparticles to create a green photocatalyst for dye degradation. The resulting composite showed impressive adsorption capacity, high photocatalytic efficiency, and easy regeneration, making it a promising option for environmental applications.
JOURNAL OF WATER PROCESS ENGINEERING
(2021)
Editorial Material
Medicine, Research & Experimental
Hugh Rosen, Michael B. A. Oldstone
Summary: In this study, the researchers explored the association between S1P serum levels and the severity of COVID-19, proposing a new prognostic indicator.
EMBO MOLECULAR MEDICINE
(2021)
Article
Chemistry, Multidisciplinary
Bowen Wang, Michael Xiong, Josephine Susanto, Xue Li, Wai-Yee Leung, Ke Xu
Summary: We propose a strategy to optimize the photoswitching behavior of rhodamines for (d)STORM super-resolution microscopy. By replacing the benzene ring with a permanently charged 1,3-disubstituted imidazolium, the resulting dyes show enhanced photoswitching capability and exhibit excellent performance in (d)STORM with fast on-off switching, long-lasting blinking, and bright single-molecule emission. Our method achieves high-quality (d)STORM images under green excitation that are comparable to those obtained using ideal red-excited dyes, even for challenging structures like the mammalian actin cytoskeleton. We also demonstrate high-quality two-color three-dimensional (d)-STORM.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Engineering, Electrical & Electronic
S. Sivapriya, R. Subramaniyan Raja, A. Arun Kumar, K. Balasubramanian, T. Joselin Beaula, G. Padmasree
Summary: Pyridin-1-ium-2-carboxylate Benzimidazole hydrate (PCBH) crystals were synthesized and grown as single crystals using the conventional evaporation growth method. The crystal structure and functional groups of PCBH compound were determined using X-Ray Diffraction and FTIR spectra. The optical, mechanical, dielectric, and antibacterial properties of the crystals were analyzed. The molecular docking study and pharmacokinetic prediction suggest that PCBH compound has potential for bacterial illness prevention.
JOURNAL OF MATERIALS SCIENCE-MATERIALS IN ELECTRONICS
(2023)
Article
Biotechnology & Applied Microbiology
Xianmei Cao, Ruibai Zhao, Hongxing Wang, Huaiwen Zhang, Xue Zhao, Latif Ullah Khan, Xi Huang
Summary: Twenty new and complete APV1 genomes were identified in Hainan, with the majority belonging to phylogroup A. Mixed infections with different genotypes may lead to genomic recombination of APV1.
Article
Chemistry, Analytical
Karima Azoulay, Imane Bencheikh, Jamal Mabrouki, Nora Samghouli, Ahmed Moufti, Abdelmalek Dahchour, Souad El Hajjaji
Summary: This study aimed to understand the adsorption mechanism of dyes in a binary system onto different raw palm wastes and highlighted its high efficiency for the removal of methylene blue and methyl orange in competition in aqueous solution. The specific surface characteristics and morphology of the raw palm wastes were studied, and the effects of different factors on the adsorption process were evaluated using central composite design. The results showed that the adsorption of the mixture of methylene blue and methyl orange followed a pseudo-first-order kinetic model and could be described by the Langmuir isotherm model.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Organic
Ilya V. Nechaev, Georgij V. Cherkaev
Summary: The reaction of cyclopropenones with pyridines having an attached integer-charged electron-withdrawing group was found to produce high yields of novel indolizin-1-ol derivatives without the need for chromatographic purification. While stable as solids, these derivatives have limited lifetime in solution due to an oxidative pathway. Further exploration led to the discovery of a reaction that produces rare pseudo-cross-conjugated mesomeric betaines. The reaction involves the sequential introduction of nucleophiles, with various types of amines and phenols being suitable.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Engineering, Chemical
Basma G. Alhogbi, Shoruq Altayeb, Effat. A. Bahaidarah, Mahmoud F. Zawrah
Summary: This study focuses on the green preparation of activated carbon from palm tree fiber waste for the removal of anionic and cationic dyes from wastewater. The synthesized activated carbon showed high adsorption capacity for both dyes, with favorable isotherm and kinetic studies. Additionally, the activated carbon demonstrated reusability for five cycles, indicating its environmental friendliness and effectiveness in dye removal.
Article
Chemistry, Organic
Jiaxing Bai, Nengni Xu, Hui Wang, Xinjun Luan
Summary: A palladium-catalyzed [2+2+1] annulation of alkynes and hydroxylamines has been developed for the rapid construction of fully substituted pyrroles. This strategy enabled alteration of the photophysical properties of pyrrole products by varying the aryl substituents, leading to the development of N-functionalized tetraarylpyrroles as new fluorophores.
Article
Plant Sciences
Huaiwen Zhang, Xue Zhao, Xianmei Cao, Latif Ullah Khan, Ruibai Zhao, Hongxing Wang, Xi Huang
Summary: This study demonstrates that APV1 is the causal agent of YLD in betel palm and is transmitted by Ferrisia virgata and Pseudococcus cryptus mealybugs. APV1 was detected in various parts of the mealybug vectors. However, it was not transmitted from female F. virgata to their offspring. This research fills important knowledge gaps in velarivirus transmission and has implications for YLD management.
Article
Chemistry, Physical
Khalil Ahmad, Habib-Ur-Rehman Shah, Sajidah Parveen, Tariq Aziz, Hafiza Ammara Naseem, Muhammad Ashfaq, Abdul Rauf
Summary: A cobalt MOF with morpholine as the base named KIUB-MOF-1 was successfully synthesized and found to have a highly porous structure suitable for adsorptive elimination of contaminants. The removal of dyes followed a chemisorption mechanism, with electrostatic and hydrogen bonding responsible for dye elimination and high adsorption capacities. This study is the first to demonstrate the removal of organic dyes from brackish water using a morpholine-based MOF.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Plant Sciences
Latif Ullah Khan, Xianmei Cao, Ruibai Zhao, Hang Tan, Zengyu Xing, Xi Huang
Summary: Yellow leaf disease (YLD) is a major limiting factor in the betel palm plantations in Hainan, China, and is closely associated with the areca palm velarivirus 1 (APV1). This study found that the severity of YLD symptoms is related to temperature, with the most severe symptoms at low temperature and milder symptoms at high temperature.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Amina Aichour, Hassina Zaghouane-Boudiaf, Hakim Djafer Khodja
Summary: The study showed that biochar derived from date palm petioles via thermal treatment exhibited high stability in methyl orange adsorption, with adsorption process dependent on initial dye concentration and equilibrium time, and exothermic and spontaneous nature. The maximum adsorption capacity of the biochar was found to be 461 mg.g^-1, and it could be reused for three cycles with a slight decrease in adsorption capacity.
ARABIAN JOURNAL OF CHEMISTRY
(2022)
Article
Cell Biology
Konstanty Cieslinski, Wu Yu-Le, Lisa Nechyporenko, Sarah Janice Hoerner, Duccio Conti, Michal Skruzny, Jonas Ries
Summary: In this study, the authors used single-molecule localization microscopy to visualize individual kinetochore complexes in budding yeast, and proposed a quantitative model of the budding yeast kinetochore based on their comprehensive dataset.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Cell Biology
Markus Mund, Aline Tschanz, Yu-Le Wu, Felix Frey, Johanna L. Mehl, Marko Kaksonen, Ori Avinoam, Ulrich S. Schwarz, Jonas Ries
Summary: The study reveals the three-dimensional shapes of clathrin coats during endocytosis and introduces a novel Cooperative Curvature Model that accurately describes the changes in shapes and dynamics. The findings provide insights into the mechanism of clathrin coat remodeling during endocytosis and offer a potential general model for clathrin coat remodeling on the plasma membrane.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Charlotte M. Fonta, Thomas Loustau, Chengbei Li, Suchithra Poilil Surendran, Uwe Hansen, Devadarssen Murdamoothoo, Mario C. Benn, Ines Velazquez-Quesada, Raphael Carapito, Gertraud Orend, Viola Vogel
Summary: Immunostainings of mouse breast tumors reveal that tumor matrix tracks, with immunosuppressive functions, are surrounded by an endothelial-like basement membrane and contain collagen and fibronectin fibers. These tracks form in early-stage tumors and mature over time, and their maturation depends on host-derived tenascin-C (TNC). Tumor infiltrating leukocytes, mainly M2 macrophages and CD8+ T cells, are retained in early-stage tumor tracks but reduce in number after track maturation.
Article
Biochemical Research Methods
Yu-Le Wu, Philipp Hoess, Aline Tschanz, Ulf Matti, Markus Mund, Jonas Ries
Summary: Quantitative data analysis is crucial for extracting biological insights from the coordinates of single fluorophores in a single-molecule localization microscopy (SMLM) workflow. LocMoFit, an open-source framework, is introduced to fit an arbitrary model to localization coordinates, extract meaningful parameters, and select suitable models. It enables the analysis of complex, heterogeneous, and dynamic structures, and has been demonstrated in assembling multi-protein distribution maps, calculating single-particle averages, and performing time-resolved reconstruction of dynamic processes from static snapshots. Extensive simulation and visualization routines validate the robustness of LocMoFit, and tutorials are provided to enhance users' extraction of information from SMLM data.
Letter
Biochemical Research Methods
Klaus C. Gwosch, Francisco Balzarotti, Jasmin K. Pape, Philipp Hoess, Jan Ellenberg, Jonas Ries, Ulf Matti, Roman Schmidt, Steffen J. Sahl, Stefan W. Hell
Article
Optics
Jan Becker, Takahiro Deguchi, Alexander Juegler, Ronny Foerster, Uwe Huebner, Jonas Ries, Rainer Heintzmann
Summary: This paper proposes a method to improve the signal-to-noise ratio (SNR) of an imaging system by splitting the pupil and simultaneously acquiring and recombining two sub-images. This method achieves better SNR for transmitting high spatial frequency information without capturing more photons.
Article
Chemistry, Multidisciplinary
Ria Thielhorn, Isabelle Heing-Becker, Nadja Huempfer, Jakob Rentsch, Rainer Haag, Kai Licha, Helge Ewers
Summary: Expansion microscopy (ExM) is a technique that enlarges a hydrogel-embedded facsimile of a biological sample to improve resolution below the diffraction limit. However, gel formation and digestion cause a loss in label. In this study, a small molecule agent combining targeting, fluorescent labeling, and gel linkage was developed to overcome this issue, resulting in improved fluorescence signal retention and the resolution of nuclear pores. Mechanistic insight into dye retention in ExM was also provided.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Editorial Material
Cell Biology
Serge Mostowy, Aurelie Bertin, Helge Ewers
Article
Biochemical Research Methods
Shuang Fu, Wei Shi, Tingdan Luo, Yingchuan He, Lulu Zhou, Jie Yang, Zhichao Yang, Jiadong Liu, Xiaotian Liu, Zhiyong Guo, Chengyu Yang, Chao Liu, Zhen-li Huang, Jonas Ries, Mingjie Zhang, Peng Xi, Dayong Jin, Yiming Li
Summary: We propose a deep-learning method for precise localization of spatially variant point emitters, covering the full chip of a modern sCMOS camera. By using a graphic processing unit-based vectorial point spread function fitter, we accurately model the spatially variant PSF of a high numerical aperture objective in the entire field of view. Combined with deformable mirror-based optimal PSF engineering, we demonstrate high-accuracy three-dimensional single-molecule localization microscopy over a large volume, enabling imaging of mitochondria and nuclear pore complexes in entire cells without hardware scanning, with a 100-fold increase in throughput compared to existing techniques.
Article
Multidisciplinary Sciences
Michael C. A. Dyhr, Mohsen Sadeghi, Ralitsa Moynova, Carolin Knappe, Burcu Kepsutlu Cakmak, Stephan Werner, Gerd Schneider, James McNally, Frank Noe, Helge Ewers
Summary: Cryo-soft X-ray tomography (cryo-SXT) is a powerful method for investigating cell ultrastructure, offering high resolution and contrast without the need for labeling. A new automated 3D segmentation pipeline based on semi-supervised deep learning enables high-throughput analysis of tomographic data with limited manual annotations and variations in conditions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Takahiro Deguchi, Malina K. Iwanski, Eva-Maria Schentarra, Christopher Heidebrecht, Lisa Schmidt, Jennifer Heck, Tobias Weihs, Sebastian Schnorrenberg, Philipp Hoess, Sheng Liu, Veronika Chevyreva, Kyung-Min Noh, Lukas C. Kapitein, Jonas Ries
Summary: We developed a live-cell tracking method with nanometer spatial and millisecond temporal resolution using MINFLUX super-resolution technique. This method allowed us to resolve the precise stepping motion of motor protein kinesin-1 on microtubules in living cells. Tracking of motors on fixed cell microtubules also revealed the architecture of the microtubule cytoskeleton with protofilament resolution.
Article
Polymer Science
Joanna Ward, Eimear Dunne, Ingmar Schoen, Adrian R. Boyd, Dermot Kenny, Brian J. Meenan
Summary: Platelet function testing is crucial for diagnosing patients with bleeding disorders. A whole blood assay that can analyze platelet behavior in contact with patient-specific autologous von Willebrand factor (vWF) under physiologically relevant conditions is needed. This study demonstrates that spin coating polystyrene/poly (methyl methacrylate) (PS/PMMA) solutions onto glass substrates can create topographical features capable of entrapping vWF and facilitating platelet adhesion.
Article
Engineering, Electrical & Electronic
Joran Deschamps, Christian Kieser, Philipp Hoess, Takahiro Deguchi, Jonas Ries
Summary: Modern microscopy increasingly relies on microscope automation for improved throughput, reproducibility, and observation of rare events. Arduino microcontrollers are widely used for automation due to their low cost and accessibility, while field programmable gate arrays (FPGA) are capable of high-speed and parallel signal processing. However, configuring FPGA remains complex. In this work, an affordable FPGA called MicroFPGA with an open-source and user-friendly programming language is used to create a versatile microscope control platform.
Article
Biochemical Research Methods
Yu-Le Wu, Philipp Hoess, Aline Tschanz, Ulf Matti, Markus Mund, Jonas Ries
Summary: This paper presents an open-source framework called LocMoFit for fitting arbitrary models to localization coordinates. The framework has significant potential for analyzing complex, heterogeneous, and dynamic structures, and can be used for assembling protein distribution maps, calculating single-particle averages, and performing time-resolved analysis of highly dynamic processes.
Correction
Multidisciplinary Sciences
Morteza Aramesh, Diana Stoycheva, Ioana Sandu, Stephan J. Ihle, Tamara Zuend, Jau-Ye Shiu, Csaba Forro, Mohammad Asghari, Margherita Bernero, Sebastian Lickert, Mateusz Kotowski, Simon J. Davis, Annette Oxenius, Viola Vogel, Enrico Klotzsch
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)