Article
Biochemistry & Molecular Biology
Lubaba Migdadi, Joerg Lambert, Ahmad Telfah, Roland Hergenroeder, Christian Woehler
Summary: Metabolomics is widely used in medical diagnostics for disease diagnosis and molecular mechanism insights. This study introduced an automated metabolite identification and assignment method using 2D NMR techniques, improving the NMR metabolic profiling approach.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Margherita Bazzoni, Rituraj Mishra, Jean-Nicolas Dumez
Summary: Selective NMR experiments are essential for analyzing large molecules and complex mixtures. A novel type of single-scan ultraselective experiments described in this study can significantly improve the sensitivity and broaden the applicability of this powerful class of experiments.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Lubaba Migdadi, Ahmad Telfah, Roland Hergenroeder, Christian Woehler
Summary: Most metabolic profiling approaches focus on identifying pre-known metabolites, while there is a lack of automated detection for new metabolites that may appear during dynamic cell evolution. In this study, a novelty detection system was proposed to detect novel metabolites in the 2D NMR TOCSY spectrum of breast cancer tissue samples. Different classifiers were used to build one- and multi-class recognition systems, and training models based on different sizes of training data were employed for the novelty detection procedure. The performance of the novelty detection methods was evaluated using multiple measures.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Food Science & Technology
Raju Doddipalla, Deviprasad Rendedula, Sireesha Ganneru, Muralidharan Kaliyaperumal, Mohana Krishna Reddy Mudiam
Summary: The study investigated the metabolic changes in palm wine during storage using NMR and LC-HRMS, identifying sugars and organic acids as significantly altered metabolites. MetPA analysis revealed changes in multiple metabolic pathways. The study highlights the potential of NMR and LC-HRMS in identifying metabolites and understanding the fermentation process of palm wine.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Microbiology
Flavia Silva-Sousa, Ticiana Fernandes, Fabio Pereira, Diana Rodrigues, Teresa Rito, Carole Camarasa, Ricardo Franco-Duarte, Maria Joao Sousa
Summary: Torulaspora delbrueckii is gaining importance in the wine industry for its beneficial effects on wine characteristics such as low volatile acidity production, increased release of aromatic compounds, and enhanced color intensity. Research on 40 different strains of T. delbrueckii showed that factors like high temperature, ethanol concentrations, and SO2 levels significantly affect the yeast's fermentative performance and growth.
Article
Endocrinology & Metabolism
Christoffer A. Hagemann, Chen Zhang, Henrik H. Hansen, Tina Jorsal, Kristoffer T. G. Rigbolt, Martin R. Madsen, Natasha C. Bergmann, Sebastian M. N. Heimbuerger, Mechthilde Falkenhahn, Stefan Theis, Kristin Breitschopf, Stephanie Holm, Morten A. Hedegaard, Mikkel B. Christensen, Tina Vilsboll, Birgitte Holst, Niels Vrang, Jacob Jelsing, Filip K. Knop
Summary: The study aimed to identify gut-derived peptides with therapeutic potential in obesity and diabetes by profiling molecular changes in enteroendocrine cells following RYGB-induced weight loss. Results showed that RYGB increased expression levels of LEAP2 in the small intestine, with the LEAP2(38-47) fragment demonstrating insulinotropic properties in vitro but no glucoregulatory effects in healthy human subjects.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2021)
Article
Food Science & Technology
Zhao Jin, Guolin Cai, Chun Wu, Zhiming Hu, Xibiao Xu, Guangfa Xie, Dianhui Wu, Jian Lu
Summary: The study quantitatively profiled 83 low-molecular-weight metabolites in Chinese rice wine brewing process, demonstrating active metabolisms during primary fermentation but slower metabolisms in secondary fermentation. The end of brewing process showed higher levels of amino acids, organic acids, and reducing sugars in the wine.
FOOD RESEARCH INTERNATIONAL
(2021)
Article
Plant Sciences
Ji-Eun Sim, Sung-Dug Oh, Kiyoon Kang, Yu-Mi Shin, Doh-Won Yun, So-Hyeon Baek, Yong-Eui Choi, Sang-Un Park, Jae-Kwang Kim
Summary: Using GC-MS-based metabolomics, we found that genetically modified rice had different metabolic profiles compared to non-genetically modified rice, potentially due to competition for the same precursor molecules. Additionally, metabolic composition in rice leaves was found to vary by growth stage rather than genetic modifications. These results demonstrate the potential of metabolomics for identifying metabolic alterations in response to genetic modifications.
Article
Food Science & Technology
Jeongmin Cha, Seong-Eun Park, Eun-Ju Kim, Seung-Ho Seo, Kwang-Moon Cho, Sun Jae Kwon, Mee-Hyun Lee, Hong-Seok Son
Summary: A saccharification agent is crucial for brewing rice wine, as it provides the necessary sugars for yeast fermentation. Nuruk, a traditional Korean saccharification agent, contains saccharification enzymes and various microorganisms. By analyzing makgeolli (Korean rice wine) brewed with different saccharification agents, this study found that nuruk resulted in a higher proportion of lactic acid bacteria (LAB) in the microbial profile compared to koji. The dominant microorganisms and metabolites in makgeolli were determined by the saccharification agents used, leading to distinct microbial and metabolic profiles in different types of makgeolli.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Biochemical Research Methods
Alexandra Bourdin-Pintueles, Laurent Galineau, Lydie Nadal-Desbarats, Camille Dupuy, Sylvie Bodard, Julie Busson, Antoine Lefevre, Patrick Emond, Sylvie Mavel
Summary: Studying the metabolome of specific gestational compartments is increasingly important in the context of developmental disorders in fetuses. A validation of fingerprinting methodology was presented in this study, showing that methanol and acetonitrile had equivalent extraction capabilities for the amniotic fluid, while MTBE extraction was more informative for the placental lipidome.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Agriculture, Multidisciplinary
Mengjie Zhou, Tingting Bu, Jiexia Zheng, Ling Liu, Songfeng Yu, Shanshan Li, Jianping Wu
Summary: This review discusses the structural and functional characteristics of peptides in traditional low-alcoholic beverages like grape wine, Chinese rice wine, and Japanese sake, as well as their formation mechanisms and health-promoting activities. The formation of peptides in these beverages imparts sensorial, technological, and biological attributes. Prospects for future research focus on peptide characterization, formation mechanism, physiological activity, and molecular mechanisms of action.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Review
Food Science & Technology
Marko Viskic, Luna Maslov Bandic, Ana-Marija Jagatic Korenika, Ana Jeromel
Summary: NMR is a fast and reproducible technique for analyzing the components and origin of wine, tracing the geographical origin and detecting chaptalization. However, the current sample preparation process is still time-consuming and expensive, requiring further improvements.
Article
Chemistry, Analytical
Krzysztof Ossolinski, Tomasz Ruman, Valerie Copie, Brian P. Tripet, Artur Kolodziej, Aneta Plaza-Altamer, Anna Ossolinska, Tadeusz Ossolinski, Anna Nieczaj, Joanna Niziol
Summary: This study investigated polar metabolite profiles in urine samples from BC patients and normal controls using NMR and LDI-MS and identified potential markers for bladder cancer. The metabolites were able to distinguish urine samples from BC and NCs individuals, and correlate with tumor stages and grades. The findings suggest that these metabolite markers may be useful for non-invasive detection and monitoring of bladder cancer.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2023)
Article
Biochemistry & Molecular Biology
Simone Vink, Kalyana Bharati Akondi, Jean Jin, Kim Poth, Allan M. Torres, Philip W. Kuchel, Sandra L. Burke, Geoffrey A. Head, Paul F. Alewood
Summary: Cardiovascular diseases, particularly hypertension, are a leading cause of mortality, affecting over 1.3 billion people. Snake venoms contain natriuretic peptides that show potential for treating hypertension and related cardiovascular diseases. A specific natriuretic peptide called TNPc has been found to lower blood pressure and enhance cardiac vagal reflexes without causing tachycardia.
Article
Food Science & Technology
Daehyeon Kim, Seong-Eun Park, Eun-Ju Kim, Hyun-Woo Kim, Seung-Ho Seo, Tae Woong Whon, Seong Woon Roh, Hong-Seok Son
Summary: This study investigated the microbial and metabolic changes during the long-term aging of rice wine with different amounts of sediment and aging temperatures. It was found that rice wine samples with higher amounts of sediment had higher yeast counts and alcohol content, while rice wine aged at 12 degrees C exhibited an increase in the relative abundance of Lactobacillus. Metabolic profiling showed that the production of metabolites during rice wine aging was greatly influenced by sediment and temperature.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Optics
Zhenhua Du, Feifei Wei, Jiaxin He
Summary: This work designs a new type of photonic crystal fiber using tellurite glass as the material. The finite element method is used to study its features, including dispersion, birefringence, and nonlinearity. The simulation results show that the designed photonic crystal fiber has a high birefringence and nonlinear coefficient, and can generate a wide spectrum supercontinuum at a specific pumping wavelength. These features may be utilized in optical fiber sensing and dispersion compensation.
JOURNAL OF OPTICS-INDIA
(2023)
Article
Chemistry, Multidisciplinary
Chao Li, Xin Gao, Hongbin Qi, Wei Zhang, Lei Li, Cancan Wei, Meijing Wei, Xiaoxuan Sun, Shusen Wang, Liyan Wang, Yingbin Ji, Shuhong Mao, Zhangliang Zhu, Masaru Tanokura, Fuping Lu, Hui-Min Qin
Summary: In this study, a genetically encoded biosensor based on a D-allulose-responsive transcriptional regulator was redesigned for real-time monitoring of D-allulose. Furthermore, an ultrahigh-throughput droplet-based microfluidic screening platform was constructed for the directed evolution of ketose 3-epimerases (KEases). Structural analysis revealed a lid conformation in Sinorhizobium fredii D-allulose 3-epimerase (SfDAE) that regulates substrate recognition, and through rational design and directed evolution, a mutant M3-2 with 17-fold enhanced catalytic efficiency was identified. This research provides a paradigm for the design and optimization of biosensor-based microdroplet screening platforms.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Biotechnology & Applied Microbiology
Feifei Wei, Zhiying Yan, Xianming Zhang, Yaoyao Wang, MiaoJing Wang, Yingwei Zhu, Kequn Xu
Summary: This study aimed to investigate the inhibitory effect of LNCNA-NEA1 on pancreatic cancer development and progression via spongiosa miR-146b-5p/TRAF6. The expression level of NEAT1 in cancerous and adjacent non-cancerous tissues was detected using real-time fluorescence quantitative polymerase chain reaction (RTFQ-PCR). Cell counting kit-8 (CCK-8) and transwell assays were conducted to determine the effect of LNCNA-NEA1 on the proliferation and migration of pancreatic cancer cells (Panc-1). The results showed that knockdown of nea 1 could inhibit the proliferation, migration and invasion of pancreatic cancer cells by upregulating the level of miR-146b-5p/TRAF6, suggesting that the expression of lnc RNA-nea 1 could be used as an indicator for preoperative diagnosis and postoperative prognosis of pancreatic cancer patients.
BIOTECHNOLOGY AND GENETIC ENGINEERING REVIEWS
(2023)
Article
Oncology
Hidetomo Himuro, Yoshiro Nakahara, Yuka Igarashi, Taku Kouro, Naoko Higashijima, Norikazu Matsuo, Shuji Murakami, Feifei Wei, Shun Horaguchi, Kayoko Tsuji, Yasunobu Mano, Haruhiro Saito, Koichi Azuma, Tetsuro Sasada
Summary: Checkpoint inhibitors have improved the prognosis of NSCLC, but only a limited number of patients benefit from this therapy and predictive biomarkers remain unclear. The study found that higher levels of sPD-L1 before treatment predicted worse PFS and OS in NSCLC patients treated with ICI monotherapy. After treatment, higher levels of sPD-1 were associated with better OS, while higher levels of sPD-L1 were associated with worse PFS and OS.
CANCER IMMUNOLOGY IMMUNOTHERAPY
(2023)
Article
Biochemistry & Molecular Biology
Zhangmei Hu, Dandan Peng, Feiyue Xing, Xiang Wen, Kun Xie, Xuemei Xu, Hui Zhang, Feifei Wei, Xiaoke Zheng, Meikun Fan
Summary: A highly sensitive liquid freestanding membrane SERS method was developed for quantitative detection of insecticide deltamethrin residues. It showed good accuracy and high sensitivity, and could be applied in household pesticide residues analysis.
Article
Multidisciplinary Sciences
Satoshi Kidokoro, Izumi Konoura, Fumiyuki Soma, Kazuo Shinozaki, Takamasa Suzuki, Masaru Tanokura, Takuya Miyakawa, Takato Imaizumi, Kazuko Yamaguchi-Shinozaki
Summary: Plants respond to severe temperature changes by inducing the expression of numerous genes whose products enhance stress tolerance and responses. DREB1 genes are rapidly and strongly induced by cold stress and their molecular mechanisms are vital for recognizing the initial responses to cold stress in plants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Cell Biology
Jiaqi Liu, Linna Kong, Wenqing Bian, Xiaona Lin, Feifei Wei, Jun Chu
Summary: circ_0001006 is upregulated in triple-negative breast cancer (TNBC) and is closely associated with patients' histological grade, Ki67 level, and TNM stage. Upregulated circ_0001006 predicts a worse prognosis and high risk in TNBC patients. Silencing circ_0001006 suppresses cell proliferation, migration, and invasion by negatively regulating miR-424-5p.
Article
Immunology
Yimei Wang, Tomohiro Takano, Yingyu Zhou, Rong Wang, Takayuki Toshimitsu, Toshihiro Sashihara, Masaru Tanokura, Takuya Miyakawa, Haruyo Nakajima-Adachi, Satoshi Hachimura
Summary: This study investigated the effects of Lactiplantibacillus plantarum OLL2712 on obesity-induced inflammation. It was found that the LAB strain regulated gut microbiota, suppressed intestinal inflammation, and improved gut barrier function, thereby reducing obesity-related inflammation.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biology
Akira Nozawa, Ryoko Miyazaki, Yoshinao Aoki, Reina Hirose, Ryosuke Hori, Chihiro Muramatsu, Yukinori Shigematsu, Keiichirou Nemoto, Yoshinori Hasegawa, Keiko Fujita, Takuya Miyakawa, Masaru Tanokura, Shunji Suzuki, Tatsuya Sawasaki
Summary: A new gibberellin receptor agonist, diphegaractin, has been identified in this study, which shows gibberellin-like activity in the growth and maturation of grapes, lettuce, Arabidopsis, and citrus fruit. This is the first successful identification of a GA receptor agonist with GA-like activity in agricultural plants using an in vitro molecular-targeted drug screening system.
COMMUNICATIONS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Satoshi Yamanaka, Hirotake Furihata, Yuta Yanagihara, Akihito Taya, Takato Nagasaka, Mai Usui, Koya Nagaoka, Yuki Shoya, Kohei Nishino, Shuhei Yoshida, Hidetaka Kosako, Masaru Tanokura, Takuya Miyakawa, Yuuki Imai, Norio Shibata, Tatsuya Sawasaki
Summary: Lenalidomide is an effective drug for treating hematological cancers, but has teratogenic effects on fetuses. This study identifies modifications that enhance the selectivity and effectiveness of lenalidomide as a standalone molecular glue or integrated in PROTACs.
NATURE COMMUNICATIONS
(2023)
Article
Oncology
Feifei Wei, Koichi Azuma, Yoshiro Nakahara, Haruhiro Saito, Norikazu Matsuo, Tomoyuki Tagami, Taku Kouro, Yuka Igarashi, Takaaki Tokito, Terufumi Kato, Tetsuro Kondo, Shuji Murakami, Ryo Usui, Hidetomo Himuro, Shun Horaguchi, Kayoko Tsuji, Kenta Murotani, Tatsuma Ban, Tomohiko Tamura, Yohei Miyagi, Tetsuro Sasada
Summary: A machine learning-based platform, CIRI, was developed to predict the ICI response of patients with NSCLC based on peripheral blood cytokine profiles. The CIRI model accurately determines the patients who would benefit from anti-PD-1/PD-L1 therapy with prolonged overall survival, aiding in clinical decision-making.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2023)
Article
Plant Sciences
Takafumi Hashimoto, Kenji Hashimoto, Hiroki Shindo, Shoko Tsuboyama, Takuya Miyakawa, Masaru Tanokura, Kazuyuki Kuchitsu
Summary: This study reveals a mechanism of Ca2+ and phosphorylation regulating the activity of MpRBOHB, highlighting the importance of Ca2+ binding in this process. This mechanism is likely to be conserved among land plant RBOHs.
PHYSIOLOGIA PLANTARUM
(2023)
