Article
Chemistry, Applied
Qingxia Yuan, Hong Li, Qian Wang, Shujing Sun, Ziyu Fang, Hao Tang, Xiaohuo Shi, Jing Wen, Lianghua Huang, Meng Bai, Shengping Zhong, Yonghong Liu, Chenghai Gao, Longyan Zhao
Summary: The tropical sea cucumber Stichopus monotuberculatus exhibits strong anticoagulant activity by selectively inhibiting intrinsic tenase complex. The anticoagulant activity decreases with the decrease of molecular weight, while the unusual branch and novel reducing end may enhance anticoagulant activity.
CARBOHYDRATE POLYMERS
(2022)
Article
Hematology
Caroline Kardeby, Alice Evans, Joana Campos, Afraa Moosa Al-Wahaibi, Christopher W. Smith, Alexandre Slater, Eleyna M. Martin, Sonia Severin, Alexander Brill, Gunnar Pejler, Yi Sun, Steve P. Watson
Summary: English Summary: The study identified PEAR1 as a receptor for heparin and HPGM, and PI3K(3 as a key signaling molecule downstream of PEAR1 in platelets. These findings may provide important insights into the role of PEAR1 in cardiovascular disease.
JOURNAL OF THROMBOSIS AND HAEMOSTASIS
(2023)
Article
Multidisciplinary Sciences
Ke Xia, James T. Hagan, Li Fu, Brian S. Sheetz, Somdatta Bhattacharya, Fuming Zhang, Jason R. Dwyer, Robert J. Linhardt
Summary: The application of solid-state nanopore devices for analyzing synthetic heparan sulfate GAG chains is feasible, with clear differences between signals generated by different GAGs detected through machine learning and data analysis. These findings suggest that ultrasensitive GAG analysis could be achieved using SS nanopore detection and well-characterized molecular training sets.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Juan Zhou, Qing Lan, Wang Li, Li-Na Ji, Kang Wang, Xing-Hua Xia
Summary: Obtaining sequential and conformational information on proteins is important for understanding their functions. This study combines surface enhanced Raman scattering (SERS) with a nanopore to observe the unfolding and multistep sequential translocation of single molecule (SM) cytochrome c (cyt c). The high bias voltage unfolds the SM protein, slowing down the translocation and allowing specific SERS traces of different SM cyt c segments to be recorded. This research provides insight into protein segments and accelerates the development of nanopore-based SM protein sequencing.
Review
Chemistry, Multidisciplinary
Siavash Iravani, Rajender S. Varma
Summary: This review highlights the recent advancements in using natural oligo- and polysaccharides for antiviral applications against SARS-CoV-2, showing their potential in preventing and inhibiting COVID-19 infections, including their use as vaccine adjuvants and drug delivery platforms.
APPLIED SCIENCES-BASEL
(2021)
Article
Food Science & Technology
Amalie Younes, Salwa Karboune
Summary: Cell wall polysaccharides from cocoa bean shell consist mainly of pectic polysaccharides and hemicelluloses. Enzymatic hydrolysis can produce oligosaccharides and feruloylated polysaccharides with high yield and antioxidant activity, which have the potential to promote the growth of probiotic bacteria.
Article
Chemistry, Multidisciplinary
Jinze Dou, Martin Kogler, Kavindra Kumar Kesari, Leena Pitkanen, Tapani Vuorinen
Summary: This study examines the seasonal dynamics of chemical characteristics in Scandinavian willow bark. It finds that starch is more linked with hemicellulose and pectin in non-winter seasons, while protein is more prominent in winter-harvested bark. The study also reveals significant differences in the structural characteristics of pectin between winter and non-winter harvested bark.
Article
Food Science & Technology
Erin J. Davis, Eugenio Spadoni Andreani, Salwa Karboune
Summary: This study focused on the microwave-assisted production of extracts from cranberry pomace and their structural characterization. Different extraction methods and microwave power settings were compared, with sequential extraction showing the highest yield of highly branched pectic polysaccharides. Response surface methodology was used to optimize the extraction conditions, resulting in improved yield and recovery rates.
FOOD AND BIOPROCESS TECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Lahari Uppuluri, Yilin Wang, Eleanor Young, Jessica S. Wong, Heba Z. Abid, Ming Xiao
Summary: Identification of structural variants (SVs) breakpoints is crucial for studying mutations, mutagenic causes, and functional impacts. This study proposes a strategy combining optical mapping and Cas9-assisted targeted nanopore sequencing to analyze SVs. The approach successfully resolved breakpoints of multiple types of SVs in a single experiment.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Physical
Max Linhorst, Jasper Wattjes, Bruno M. Moerschbacher
Summary: Chitosans, derived from chitin, are versatile biopolymers with unique properties that can be further improved through biocatalytic N-acylation. Using recombinant chitin deacetylase for N-acylation can yield highly substituted chitosan polymers, which can be further functionalized using copper-catalyzed reactions. This chemoenzymatic approach offers a pathway to a wide variety of functionalized chitosans with nonrandom substitution patterns.
Article
Chemistry, Physical
Tarsis Ferreira Gesteira, Tainah Dorina Marforio, Jonathan Wolf Mueller, Matteo Calvaresi, Vivien Jane Coulson-Thomas
Summary: The study identified the substrate specificity and catalytic mechanism of two HS sulfotransferases, HS2ST and HS6ST, shedding light on how these enzymes recognize different substrates and catalyze sugar sulfation. This information could be valuable for the development of enzymes that can create specific heparin epitopes.
Article
Food Science & Technology
Ziwen Ding, Fan Jiang, Kun Liu, Fangshuo Gong, Yuanfa Liu, Zhaojun Zheng, Yong-Jiang Xu
Summary: Glycosylation coupling with pullulan polysaccharide can enhance the structural and functional properties of hemp protein isolate, expanding its potential implementation in food systems.
Article
Chemistry, Multidisciplinary
Xialin Zhang, Nicole Stephanie Galenkamp, Nieck Jordy van der Heide, Giovanni Maglia, Jorgen Kjems, Julian Moreno
Summary: Nanopores functionalized with different nanobodies show great potential for stochastic sensing of proteins. They can detect Spike protein, HER2 receptor, and muPA protein through reversible blockade events or larger blockage signals, enabling the clinical detection of protein biomarkers.
Review
Biochemical Research Methods
Asif Shajahan, Lauren E. Pepi, Daniel S. Rouhani, Christian Heiss, Parastoo Azadi
Summary: The COVID-19 pandemic is caused by the SARS-CoV-2 virus, which contains glycosylated proteins that interact with host receptors like hACE2 to facilitate infection. Studies show that these glycosylated proteins play important roles in viral infection and immune evasion, understanding which can aid in developing suitable prevention and therapy strategies.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Cell Biology
Lili Zhang, Weiqi Rong, Jie Ma, Hexin Li, Xiaokun Tang, Siyuan Xu, Luyao Wang, Li Wan, Qing Zhu, Boyue Jiang, Fei Su, Hongyuan Cui
Summary: DNA methylation is a widespread epigenetic signal in the human genome. This study used Nanopore technology to analyze methylation modifications in hepatocellular carcinoma samples, identifying genes with both 5mC and 6mA modifications and uncovering potential tumor suppressor genes. The findings provide a new approach for studying epigenetic regulation and therapy in hepatocellular carcinoma.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Mazdak Afshar Bakshloo, John J. Kasianowicz, Manuela Pastoriza-Gallego, Jerome Mathe, Regis Daniel, Fabien Piguet, Abdelghani Oukhaled
Summary: This study demonstrates a method for protein detection and classification using a nanometer-scale pore formed by the protein aerolysin, achieving detection at the single-molecule level. Different water-soluble proteins treated with the same protease produce different polypeptide fragments, which can be distinguished based on their impact on the nanopore's ionic current, consistent with predicted fragments.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemical Research Methods
Salome Poyer, Laurent Laboureur, Teo Hebra, Nicolas Elie, Guillaume Van der Rest, Jean-Yves Salpin, Pierre Champy, David Touboul
Summary: This study developed analytical strategies for the complete chemical characterization of annonaceous acetogenins, natural products that are responsible for atypical Parkinsonism. By using tandem mass spectrometry and copper adducts, the researchers were able to identify the position of ketones, oxygen rings, and hydroxyl substituents, providing valuable structural information.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biochemical Research Methods
Parisa Bayat, David Gatineau, Denis Lesage, Alexandre Martinez, Richard B. Cole
Summary: The synthesis of host molecules with defined characteristics for molecular recognition of guest molecules is a key goal of synthetic host-guest chemistry. Evaluating host selectivity and guest affinities through measuring binding energies is crucial, and mass spectrometry offers a unique opportunity to measure gas-phase binding energies. The presented HCD approach for determining critical energies of dissociation of H-G complexes is a relatively straightforward method that requires prior knowledge of the complexes to obtain their critical energies of dissociation.
JOURNAL OF MASS SPECTROMETRY
(2022)
Article
Chemistry, Physical
Delphine Dessaux, Jerome Mathe, Rosa Ramirez, Nathalie Basdevant
Summary: In order to understand the physical processes of nanopore experiments at the molecular level, we performed coarse-grained molecular dynamics simulations of ionic transport through the alpha-hemolysin protein nanopore. By simulating different charged amino acids under different electric fields, we observed current asymmetry and anion selectivity, and identified the responsible amino acids for these features.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
Mazdak Afshar Bakshloo, Safia Yahiaoui, Fabien Piguet, Manuela Pastoriza-Gallego, Regis Daniel, Jerome Mathe, John J. Kasianowicz, Abdelghani Oukhaled
Summary: This study investigates a method for protein identification using nanopores. The capture rate and dwell time of polypeptide fragments in the pore are found to depend on the ionic strength and magnitude of the applied voltage. The method is capable of accurately identifying proteins, but further research is needed to optimize the analysis.
Article
Chemistry, Physical
Aurica Farcas, Hadjer Ouldali, Comeliu Cojocaru, Manuela Pastoriza-Gallego, Ana -Maria Resmerital, Abdelghani Oukhaled
Summary: A multi-technique approach was used to prepare poly(3,4-ethylenedioxythiophene/cucurbit[7]uril) pseudorotaxanes (PEDOT.CB7-PPs), and their complexation ability with 3,4-ethylenedioxythiophene (EDOT) was confirmed. The synthesized PEDOT-CB7-PPs showed stable water dispersion as evidenced by dynamic light scattering measurements. The interaction between PEDOT-CB7-PPs and aerolysin nanopore was studied using nanopore resistive pulse sensing and computational modeling techniques, revealing strong interactions. This study provides new insights into supramolecular complexes based on CB7 for future applications in nanobiotechnology.
Article
Chemistry, Multidisciplinary
Pauline J. Kolbeck, Dihia Benaoudia, Leia Chazot-Franguiadakis, Gwendoline Delecourt, Jeirome Mathei, Sha Li, Romeo Bonnet, Pascal Martin, Jan Lipfert, Anna Salvetti, Mordjane Boukhet, Veironique Bennevault, Jean-Christophe Lacroix, Philippe Guegan, Fabien Montel
Summary: Researchers have developed a selective and switchable nanopore by grafting polymers within artificial nanopores to control the transport of biomolecules. Using fluorescence microscopy with a zero-mode waveguide set up, they measured transport at the scale of individual biomolecules. They demonstrated tight control over DNA and viral capsid transport with a sharp transition based on temperature, and proposed a simple physical model to predict key features of this transition. This approach offers the potential for controllable and responsive nanopores in various applications.
Article
Biochemistry & Molecular Biology
Mazdak Afshar Bakshloo, Safia Yahiaoui, Matthieu Bourderioux, Regis Daniel, Manuela Pastoriza-Gallego, John J. Kasianowicz, Abdelghani Oukhaled
Summary: Alpha-synuclein plays a crucial role in regulating nerve activity. Mutations in this protein can lead to its aggregation and fibril formation, which is associated with neurodegenerative diseases like Parkinson's. Our study demonstrates that a nanometer-scale pore can effectively distinguish between different forms of alpha-synuclein, including wild-type, mutated, and post-translationally modified variants.
ACS CHEMICAL NEUROSCIENCE
(2023)
Article
Chemistry, Physical
Aurica Farcas, Hadjer Ouldali, Comeliu Cojocaru, Manuela Pastoriza-Gallego, Ana -Maria Resmerital, Abdelghani Oukhaled
Summary: A multi-technique approach was used to prepare and characterize poly(3,4-ethylenedioxythiophene/cucurbit[7]uril) pseudorotaxanes (PEDOT.CB7-PPs). By combining computational modeling and experimental validation, strong interactions between PEDOT-CB7-PPs and the aerolysin nanopore were identified. This study provides valuable insights into the interactions between CB7-based supramolecular complexes and biological entities.
Article
Biochemistry & Molecular Biology
Lewis Rolband, Damian Beasock, Yang Wang, Yao-Gen Shu, Jonathan D. Dinman, Tamar Schlick, Yaoqi Zhou, Jeffrey S. Kieft, Shi-Jie Chen, Giovanni Bussi, Abdelghani Oukhaled, Xingfa Gao, Petr Sulc, Daniel Binzel, Abhjeet S. Bhullar, Chenxi Liang, Peixuan Guo, Kirill A. Afonin
Summary: The International Society of RNA Nanotechnology and Nanomedicine (ISRNN) aims to advance the development of functional nucleic acids and related nanotechnology platforms. This article summarizes recent advancements in viral biology, structure-function relationships of genomic viral RNA, and various applications in drug delivery and nanotechnology.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)