Article
Multidisciplinary Sciences
Marialetizia Palomba, Pietro Libro, Jessica Di Martino, Xavier Roca-Gerones, Armando Macali, Tiziana Castrignano, Daniele Canestrelli, Simonetta Mattiucci
Summary: This study generated a de novo transcriptome of the Antarctic anisakid Contracaecum osculatum sp. D for the first time, providing a valuable resource for future research on the genomic architecture of thermal tolerance and metabolic pathways related to temperature stress.
Article
Chemistry, Analytical
Alexandar L. Hansen, Erriks Kupce, Da-Wei Li, Lei Bruschweiler-Li, Cheng Wang, Rafael Brueschweiler
Summary: This study presents sensitivity-improved versions of two-dimensional NMR experiments optimized for small biological molecules encountered in metabolomics, allowing for rapid acquisition techniques and incorporation into supersequences for compact acquisition of multiple 2D NMR data sets. These new pulse sequences offer an attractive approach for efficient measurement of multiple 2D NMR spectra in a single experiment, enhancing identification and quantitation of metabolites in metabolomics samples. The advantages of 2D NMR have been extended to metabolomics studies with larger sample cohorts.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Huan Du, Xiu Gu, Jialuo Chen, Caihong Bai, Xiaohui Duan, Kaifeng Hu
Summary: The 2D 1H-13C HSQC method is widely used in metabolomics studies, but its preprocessing methods are lagging behind those of the 1D 1H NMR method. Therefore, we propose a new algorithm called Global Intensity-Guided Peak Matching and Alignment (GIPMA) for peak matching and alignment in 2D 1H-13C HSQC-based metabolomics. This algorithm dynamically searches for and intelligently selects the optimal chemical shift tolerance to improve the accuracy of the results.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Michael J. Jaroszewicz, Mengxiao Liu, Jihyun Kim, Guannan Zhang, Yaewon Kim, Christian Hilty, Lucio Frydman
Summary: Nuclear magnetic resonance (NMR) spectroscopy provides detailed information about dynamic processes through line-shape changes under equilibrium conditions. However, studying chemical reactions under off-equilibrium conditions and monitoring the reactants and products in real time can provide additional valuable information. In this study, the authors propose and demonstrate a time-resolved kinetic NMR experiment that combines rapid mixing techniques, continuous flow, and single-scan spectroscopic imaging methods, leading to a 2D spectrotemporal NMR correlation that provides high-quality kinetic information of off-equilibrium chemical reactions.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Philippe Berdague, Boris Gouilleux, Markus Noll, Stefan Immel, Michael Reggelin, Philippe Lesot
Summary: This study focuses on the molecular factors involved in the orientation/discrimination phenomena of analytes in polymer-based chiral liquid crystals. The researchers propose a method to quantify and compare the enantiodiscrimination power of different polymer-based liquid crystals. The results show that the l-MSP phase exhibits promising enantiodiscrimination capacities.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Review
Chemistry, Analytical
Prabhakar S. Achanta, Birgit U. Jaki, James B. McAlpine, J. Brent Friesen, Matthias Niemitz, Shao-Nong Chen, Guido F. Pauli
Summary: Issues related to pharmaceutical quality are on the rise, with an increase in reports of harmful impurities in marketed drug formulations. Current detection techniques may not be able to identify unknown impurities, highlighting the need for more advanced methods in pharmaceutical quality control.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2021)
Article
Chemistry, Multidisciplinary
Hongxian Zheng, Wenbin Li, Yurong Chen, Baichuan Jiang, Yu Che, Cailing Ou, Jun Li, Xiao Han, Chuanhui Liu, Lei Zhang
Summary: Polymeric semiconductors are important for next-generation electronic devices, and researchers have developed versatile P3HT nanofibers and achieved high-resolution lateral heterojunctions. By constructing planar photovoltaic devices, the impact of channel length on photovoltaic efficiency has been observed.
Article
Chemistry, Analytical
Haolin Zhan, Chengda Huang, Cunyuan Gao, Enping Lin, Yuqing Huang, Zhong Chen
Summary: A general NMR method has been proposed for collecting high-resolution 2D J-edited NMR spectra, facilitating J coupling partner assignments and measurements, and allowing simultaneous determination of multiple coupling networks for highly efficient multiplet analyses. Another variant for high resolution applications under adverse magnetic field conditions has also been suggested.
ANALYTICA CHIMICA ACTA
(2021)
Article
Chemistry, Analytical
Mengnan Ma, Xiong-Fei Pan, An Pan, Limiao Jiang
Summary: This study systematically investigated the effect of urine dilution on 1H NMR metabolic profiles and found that mild dilution can preserve high-abundance metabolites, reduce chemical shift variations, and increase signal separations. These findings are important for NMR-based metabolomics research and large-scale epidemiological studies with limited samples.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Mengnan Ma, Xiong-Fei Pan, An Pan, Limiao Jiang
Summary: This study systematically investigated the effect of urine dilution on 1H NMR metabolic profiles. It found that mild dilution (e.g. 40%) of human urine can preserve high-abundance metabolites, reduce intersample chemical shift variations, and increase separations of overlapped signals. This improvement is applicable for NMR-based metabolomics studies with limited urine volumes, including large-scale epidemiological studies.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
K. Fiederling, S. Kupfer, S. Graefe
Summary: Experimental evidence indicates that tip-enhanced Raman spectroscopy (TERS) has an extremely high spatial resolution, possibly even at a sub-molecular level. While the underlying mechanism is still under discussion, researchers have identified the electromagnetic effect and the chemical effect as the main contributions to the observed phenomena. The impact of static charges on the tip's frontmost atom on the TERS signal and lateral resolution was evaluated through quantum chemical simulations, showing significant enhancements under non-resonant and resonant conditions.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Ivan Hung, Eric G. Keeler, Wenping Mao, Peter L. Gor'kov, Robert G. Griffin, Zhehong Gan
Summary: This study addresses the challenges of low sensitivity, low resolution, and large quadrupolar couplings in the NMR study of oxygen by employing efficient isotopic labeling, high magnetic fields, fast sample spinning, and H-1 detection. Oxygen sites specific to each amino acid residue are observed through multidimensional experiments. The use of cross-polarization at high sample spinning frequencies enables efficient C-13<->O-17 polarization transfer. Results show that using O-17 for initial polarization provides better sensitivity per unit time compared to H-1.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Yun-Seo Kil, Joo-Won Nam
Summary: This study successfully achieved a full assignment of the 1H NMR spectrum of choline sulfate using quantum-mechanical driven methods, revealing complex peak patterns and investigating heteronuclear and non-first-order coupling, which will provide important precise spectral interpretation for future research.
Article
Materials Science, Characterization & Testing
Kirill Alferov, Shuanjin Wang, Dongmei Han, Shanyue Guan, Min Xiao, Yuezhong Meng
Summary: This article introduces a new metal-free synthesis method for carbon dioxide/propylene oxide co-oligomers, and analyzes them in detail using NMR spectroscopy methods, finding signals of different chain ends and specific units.
Article
Chemistry, Multidisciplinary
Rohit Roy, Ainan Geng, Honglue Shi, Dawn K. Merriman, Elizabeth A. Dethoff, Loic Salmon, Hashim M. Al-Hashimi
Summary: Understanding the 3D structures and kinetic rates of interconversion of RNA conformations is crucial for studying RNA folding and function. This study developed an approach that combines computational modeling with experimental data to determine the 3D structures, relative abundance, and interconversion rates of RNA subensembles. The approach was applied to HIV-1 TAR and revealed the atomic-level details of sparsely populated RNA excited conformational states. This work provides important insights into the dynamics and structures of RNA conformational substates.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Maximilian J. Helf, Bennett W. Fox, Alexander B. Artyukhin, Ying K. Zhang, Frank C. Schroeder
Summary: In this study, untargeted metabolomics using high-resolution mass spectrometry and Metaboseek software was applied to uncover the biosynthetic functions of a fat metabolism pathway in C. elegans. Over 200 previously uncharacterized metabolites related to the alpha-oxidation pathway were identified, highlighting the importance of alpha-oxidation in fatty acid and lipid metabolism.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Sarah M. Cohen, Chester J. J. Wrobel, Sharan J. Prakash, Frank C. Schroeder, Paul W. Sternberg
Summary: This study investigates the biosynthetic pathways and functions of ascaroside signaling molecules in the nematode Caenorhabditis briggsae. It shows that ascarosides in C. briggsae are synthesized in the same manner as C. elegans and induce the alternative developmental pathway that generates the stress-resistant dauer lifestage.
G3-GENES GENOMES GENETICS
(2022)
Article
Genetics & Heredity
Deepshikha Dogra, Warakorn Kulalert, Frank C. Schroeder, Dennis H. Kim
Summary: Under stressful growth conditions, young larvae of the nematode Caenorhabditis elegans can enter a developmentally arrested stage called dauer, which involves a conserved c-Jun N-terminal Kinase-like mitogen-activated protein kinase pathway. Genetic analysis suggests that this pathway acts in the sensory neurons, independent of diminished food levels or elevated temperatures.
Article
Biochemistry & Molecular Biology
Antonia Piazzesi, Yiru Wang, Joshua Jackson, Lena Wischhof, Viktoria Zeisler-Diehl, Enzo Scifo, Ina Oganezova, Thorben Hoffmann, Pablo Gomez Martin, Fabio Bertan, Chester J. J. Wrobel, Frank C. Schroeder, Dan Ehninger, Kristian Haendler, Joachim L. Schultze, Lukas Schreiber, Gerhild Van Echten-Deckert, Pierluigi Nicotera, Daniele Bano
Summary: Mitochondrial dysfunction can be influenced by enhanced metabolic flexibility, which can extend the lifespan of mitochondrial mutants. CEST-2.2, a carboxylesterase mainly localized in the intestine, has been found to stimulate the survival of mitochondrial deficient animals. Through transcriptome and lipidome analysis, it has been shown that CEST-2.2 promotes lipid metabolism and fatty acid beta-oxidation, enhancing the respiratory capacity of mitochondria and extending the lifespan of mutant nematodes.
Article
Multidisciplinary Sciences
Kenta Shinoda, Andrea Choe, Kiyoshi Hirahara, Masahiro Kiuchi, Kota Kokubo, Tomomi Ichikawa, Jason S. Hoki, Akane S. Suzuki, Neelanjan Bose, Judith A. Appleton, Raffi Aroian, Frank C. Schroeder, Paul W. Sternberg, Toshinori Nakayama
Summary: Mounting evidence suggests that nematode infection may help protect against immune disorders. Nanogram quantities of a family of nematode pheromones called ascarosides, when administered, were found to modulate the pulmonary immune response and reduce asthma severity in mice. Ascr#7, one of the ascarosides, suppressed the production of IL-33 and reduced the number of pathogenic Th2 cells and ILC2s in the lung, indicating its potential as a treatment strategy for allergic diseases.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Bennett W. Fox, Olga Ponomarova, Yong-Uk Lee, Gaotian Zhang, Gabrielle E. Giese, Melissa Walker, Nicole M. Roberto, Huimin Na, Pedro R. Rodrigues, Brian J. Curtis, Aiden R. Kolodziej, Timothy A. Crombie, Stefan Zdraljevic, L. Safak Yilmaz, Erik C. Andersen, Frank C. Schroeder, Albertha J. M. Walhout
Summary: Individuals can exhibit differences in metabolism caused by genetic background, nutritional input, microbiota and other environmental factors. This study used the nematode Caenorhabditis elegans to explore inter-individual variation in metabolism and discovered differences in the abundances of known and unknown metabolites, including conjugates between 3-hydroxypropionate (3HP) and amino acids. The accumulation of these conjugates was found to be caused by genetic variation in the HPHD-1 gene.
Article
Multidisciplinary Sciences
Tae Hyung Won, Jin Woo Bok, Nischala Nadig, Nandhitha Venkatesh, Grant Nickles, Claudio Greco, Fang Yun Lim, Jennifer B. Gonzalez, B. Gillian Turgeon, Nancy P. Keller, Frank C. Schroeder
Summary: The genomes of filamentous fungi include many biosynthetic gene clusters of unknown function. In this study, the authors show that copper starvation induces expression of an enzyme (CrmA) that generates a valine-derived isocyanide participating in two different pathways for biosynthesis of acylated sugar alcohols and modified ergot alkaloids.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
David S. Wishart, Leo L. Cheng, Valerie Copie, Arthur S. Edison, Hamid R. Eghbalnia, Jeffrey C. Hoch, Goncalo J. Gouveia, Wimal Pathmasiri, Robert Powers, Tracey B. Schock, Lloyd W. Sumner, Mario Uchimiya
Summary: Metabolomics investigates the global metabolic alterations associated with various processes, and NMR-based methods have considerable benefits and advantages. The growing number of publications on NMR-based metabolomics suggests its continuous development and contributions to the scientific community.
Article
Multidisciplinary Sciences
Mohammad Arifuzzaman, Tae Hyung Won, Ting-Ting Li, Hiroshi Yano, Sreehaas Digumarthi, Andrea F. Heras, Wen Zhang, Christopher N. Parkhurst, Sanchita Kashyap, Wen-Bing Jin, Gregory Garbes Putzel, Amy M. Tsou, Coco Chu, Qianru Wei, Alex Grier, Stefan Worgall, Chun-Jun Guo, Frank C. Schroeder, David Artis
Summary: Dietary fibre, particularly inulin, alters the composition of the microbiota and levels of microbiota-derived metabolites, such as bile acids, leading to type 2 inflammation in the intestine and lungs. This study provides insights into the pathophysiology of allergic inflammation, tissue protection, and host defense.
Article
Biochemistry & Molecular Biology
Jingfang Yu, Merly C. Vogt, Bennett W. Fox, Chester J. J. Wrobel, Diana Fajardo Palomino, Brian J. Curtis, Bingsen Zhang, Henry H. Le, Arnaud Tauffenberger, Oliver Hobert, Frank C. Schroeder
Summary: Untargeted comparative metabolomics revealed the biosynthesis and metabolism pathways of serotonin in nonneuronal tissues, suggesting its important roles in serotonin-dependent phenotypes in C. elegans. Serotonin is abundantly produced in nonneuronal tissues via phenylalanine hydroxylase, in addition to its canonical biosynthesis in neurons via tryptophan hydroxylase. Most serotonin in C. elegans is incorporated into N-acetylserotonin-derived glucosides and further modified via the carboxylesterase CEST-4. Bacterial indole production interacts with serotonin metabolism via CEST-4. These findings indicate the significance of nonneuronal serotonin biosynthesis and metabolism in contributing to serotonin-dependent phenotypes.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Russell N. Burkhardt, Alexander B. Artyukhin, Erin Z. Aprison, Brian J. Curtis, Bennett W. Fox, Andreas H. Ludewig, Diana Fajardo Palomino, Jintao Luo, Amaresh Chaturbedi, Oishika Panda, Chester J. J. Wrobel, Victor Baumann, Douglas S. Portman, Siu Sylvia Lee, Ilya Ruvinsky, Frank C. Schroeder
Summary: Recent studies have shown that there are pervasive metabolomic differences between hermaphrodites and males of the C. elegans nematode. Numerous new metabolites that incorporate building blocks from various metabolic pathways have been identified, some of which are specifically associated with the male germline or soma. One male germline-dependent metabolite, a dipeptide incorporating N,N-dimethyltryptophan, has been found to affect food consumption, lifespan, and larval development in hermaphrodites. These findings provide a foundation for understanding how the genetic sex influences the metabolome and offer insights into sex-dependent metabolites in other animals.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Brian J. Curtis, Tyler J. Schwertfeger, Russell N. Burkhardt, Bennett W. Fox, Jude Andrzejewski, Chester J. J. Wrobel, Jingfang Yu, Pedro R. Rodrigues, Arnaud Tauffenberger, Frank C. Schroeder
Summary: Glucose-based nucleosides with diverse modifications were discovered in C. elegans and related nematodes. These gluconucleosides exist in phosphorylated and non-phosphorylated forms, and can be further modified with acyl moieties from amino acid catabolism. Stable-isotope labeling experiments indicated that these gluconucleosides incorporate modified nucleobases derived from RNA and possibly DNA breakdown.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Chester J. J. Wrobel, Frank C. Schroeder
Summary: Recent studies have found that nematodes, including Caenorhabditis elegans, use products from biochemical degradation pathways to assemble complex modular structures for various signaling functions. These structures, called ascarosides and glucosides, are made up of building blocks from neurotransmitter, amino acid, nucleoside, and fatty acid metabolism. Carboxylesterases are key enzymes that mediate the assembly of these modular structures, which are derived from conserved detoxification mechanisms. These modular metabolites represent a distinct biosynthetic strategy for generating diversity in nematodes and complement the microbial natural products derived from polyketide synthase and nonribosomal peptide synthetase. They also serve as a target for compound discovery using metabolomics and genomic approaches.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Daehan Lee, Bennett W. Fox, Diana Fajardo Palomino, Oishika Panda, Francisco J. Tenjo, Emily J. Koury, Kathryn S. Evans, Lewis Stevens, Pedro R. Rodrigues, Aiden R. Kolodziej, Frank C. Schroeder, Erik C. Andersen
Summary: From bacterial quorum sensing to human language, communication is essential for social interactions. Nematodes produce and sense pheromones to communicate among individuals and respond to environmental changes. The genetic basis and molecular mechanisms underlying the variation in the nematode pheromone language remain largely unknown, but our study provides valuable insights into the genetic mechanisms underlying the evolution of chemical communication.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Olga B. Ponomarova, Hefei W. Zhang, Xuhang N. Li, Shivani E. Nanda, Thomas C. Leland, Bennett Fox, Alyxandra Starbard, Gabrielle Giese, Frank Schroeder, L. Safak Yilmaz, Albertha J. M. Walhout
Summary: In humans, mutations in D-2-hydroxyglutarate (D-2HG) dehydrogenase (D2HGDH) lead to the accumulation of D-2HG, causing delayed development, seizures, and ataxia. Using Caenorhabditis elegans as a model organism, researchers found that D-2HG is produced in the propionate shunt pathway when the vitamin B12-dependent propionate breakdown pathway is disrupted. Loss of the D2HGDH ortholog, dhgd-1, leads to embryonic lethality and mitochondrial defects, but can be rescued by RNAi of hphd-1 or supplementation of vitamin B12 or ketone bodies. This study reveals the role of ketone bodies in energy production when vitamin B12 levels are low and highlights the importance of dhgd-1 in ketone body production.
