Article
Plant Sciences
Ayesha Ramzan, Mohibullah Shah, Najeeb Ullah, Sheheryar, Jose R. S. Nascimento, Francisco A. P. Campos, Gilberto B. Domont, Fabio C. S. Nogueira, Magda H. Abdellattif
Summary: This study conducted a proteomic analysis of the embryo of Jatropha curcas seeds, identifying a large number of proteins and revealing their roles in seed germination and defense functions.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Food Science & Technology
Qiong He, Yihua Xue, Yaxiu Wang, Ninan Zhang, Lugang Zhang
Summary: This study identified 102 flavonoids in purple heading Chinese cabbages with different purple colors, including anthocyanins, flavanols, flavanones, flavones, flavonols, isoflavones, and proanthocyanidins. The main flavonoids were gallocatechin-gallocatechin, hesperetin C-hexosyl-O-hexosyl-O-hexoside, and tricin O-sac-charic acid, while the main anthocyanins were cyanidin 3,5-O-diglucoside, delphinidin 3-O-glucoside, cyanidin 3-O-glucoside, and pelargonidin 3-O-beta-D-glucoside. The difference in color occurred in the middle leaf-head, and 323 flavonoid biosynthesis genes were identified. The BrMYB2 gene played a crucial role in anthocyanin production in these cabbages.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Green & Sustainable Science & Technology
Mengmeng Hao, Yushu Qian, Xiaolan Xie, Shuai Chen, Fangyu Ding, Tian Ma
Summary: Given the limited reserves of conventional fossil fuels and their negative impact on global climate, governments are seeking alternatives to polluting energy. Bioenergy from energy plants is considered a promising option. This study proposes a method to identify marginal lands using a machine learning algorithm, natural occurrence records of energy plants, and multiple influencing factors. Using Jatropha curcas L. as an example, the global marginal land distribution is simulated, resulting in 1588.46 million hectares of marginal land resources, with 49.34% in Africa.
JOURNAL OF CLEANER PRODUCTION
(2022)
Article
Plant Sciences
Yushen Huang, Wen Luo, Siyun Chen, Hongmei Su, Wuchang Zhu, Yuanyuan Wei, Yue Qiu, Yan Long, Yanxia Shi, Jinbin Wei
Summary: This study is the first to propose a protective effect of Ivitexin (IVT) against hepatic fibrosis. The mechanism of IVT against hepatic fibrosis is based on the regulation of miR-21, targeting PTEN-Akt signaling and the GSH metabolic pathway, which is also a novel discovery.
Article
Oncology
Ming-zhe Xin, Ying-ying Shi, Chun-shen Li, Li-hua Zuo, Na Li, Li-wei Liu, He-xin Ma, Qiu-zheng Du, Peng Xue, Zhi Sun, Hong-yu Zhao
Summary: A total of 19 and 25 differential metabolites were identified in the EOLP group and the ROLP group compared with the HC group, respectively. 14 different metabolites were identified between EOLP and ROLP, and two diagnostic models were constructed based on these differential metabolites. A total of 14 differential metabolites were shared by EOLP and ROLP. Enrichment analysis suggested that alanine, aspartate and glutamate metabolism were closely associated with the pathogenesis of OLP. The study also provided potential gene perturbation of OLP and supported further exploration of its pathogenic mechanism.
FRONTIERS IN ONCOLOGY
(2021)
Article
Plant Sciences
Huiying Lu, Ziqi Wang, Chenyang Xu, Luhao Li, Chunwu Yang
Summary: Sunflower exhibits strong alkali tolerance. Alkali stress alters the lipid components of sunflower seeds, potentially affecting the quality of sunflower seed oils. Alkali stress promotes the accumulation of various substances in sunflower roots. Interaction of multiple phytohormones and bioactive molecules play a role in mediating alkali tolerance in sunflower.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Lu Ma, Hongshun Wang, Jun Yao, Qinjun Wei, Xin Cao
Summary: The lipid transporter protein apolipoprotein E (APOE) plays an important role in various organ functions. Recent studies have focused on the association of APOE with hearing loss. This study investigated the effects of APOE knockout on HEI-OC1 cells and found that glutamate deficiency caused by reduced expression of glutamine transporter proteins is a key factor in hearing loss.
Article
Biochemical Research Methods
Zhuoru He, Zhongqiu Liu, Lingzhi Gong
Summary: This study revealed the pathogenesis of rheumatoid arthritis through metabolomics, constructed a biomarker panel for accurate prediction, and identified dysregulated metabolic pathways associated with RA.
Article
Plant Sciences
Marcelo F. Pompelli, Pedro P. B. Ferreira, Agnaldo R. M. Chaves, Regina C. Q. Q. Figueiredo, Auxiliadora O. Martins, Alfredo Jarma-Orozco, Arvind Bhatt, Willian Batista-Silva, Lauricio Endres, Wagner L. Araujo
Summary: This study investigated the impact of salinity on Jatropha curcas and the salt responses of different genotypes. The results showed distinct stomatal development and metabolic reprogramming characteristics under salt stress among different genotypes. These findings provide valuable insights for screening salt tolerance in J. curcas breeding programs.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Plant Sciences
Eduardo Muniz Santana Bastos, Alessandra Bispo Silva, Paulo Lucas Cerqueira Coelho, Julita Maria Pereira Borges, Victor Diogenes Amaral Silva, Vitor Hugo Moreau Cunha, Silvia Lima Costa
Summary: This study demonstrates that the methanolic extract from the leaves of Jatropha curcas L. has anti-inflammatory activity on glial cells in response to inflammatory stimuli, showing potential as a therapeutic strategy for neuroinflammation-related diseases.
JOURNAL OF ETHNOPHARMACOLOGY
(2021)
Article
Plant Sciences
Xue Li, Ming-sheng Zhang, Liang-qing Zhao, Qian-qian Ling-hu, Gang Xu
Summary: In this study, JcGASA6, a member of the GASA family in Jatropha curcas, was cloned and found to play a crucial role in growth regulation and floral development, especially in male flowers. Additionally, JcGASA6 is involved in the signal transduction of plant hormones such as ABA, ET, GA, BR, and SA, and has potential antimicrobial properties based on its three-dimensional structure.
Article
Cell Biology
Xiao Yu, Hui Sun, Xingyu Gao, Chang Zhang, Yanan Sun, Huan Wang, Haiying Zhang, Yingai Shi, Xu He
Summary: This study investigates the molecular mechanisms of rat bone marrow mesenchymal stem cell (BMSC) aging using metabolomics and transcriptomics technologies. The analysis reveals differential metabolites and differentially expressed genes related to lipid metabolism, indicating their significant association with BMSC senescence.
Article
Cardiac & Cardiovascular Systems
Kyle L. Fulghum, Juliette B. Smith, Julia Chariker, Lauren F. Garrett, Kenneth R. Brittian, Pawel K. Lorkiewicz, Lindsey A. McNally, Shizuka Uchida, Steven P. Jones, Bradford G. Hill, Helen E. Collins
Summary: The goal of this study was to develop an atlas of the metabolic, transcriptional, and proteomic changes in the maternal heart during and after pregnancy. The results showed significant increases in heart size, cardiac hypertrophy, and myocyte cross-sectional area during pregnancy and post-birth, accompanied by changes in metabolites, gene expression, and protein levels. These findings provide important insights into the coordinated molecular changes that occur in the maternal heart during and after pregnancy.
AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Suzanne Paley, Richard Billington, James Herson, Markus Krummenacker, Peter D. Karp
Summary: Metabolomics, synthetic biology, and microbiome research require information on organism-scale metabolic networks. Software tools have been developed to generate and analyze comprehensive metabolic-network diagrams, aiding researchers in understanding, analyzing, and exploiting metabolic reconstructions. These tools also enable comparisons of metabolic networks and interpretation of high-throughput datasets.
Article
Plant Sciences
Hui Li, Shangling Han, Yiqiong Huo, Guifang Ma, Zhaoxia Sun, Hongying Li, Siyu Hou, Yuanhuai Han
Summary: This study identified and analyzed genes related to carotenoid metabolism in foxtail millet, revealing their correlation with carotenoid content and constructing a gene coexpression network. The findings provide insights into the regulatory network of carotenoid metabolism in foxtail millet, laying the foundation for genetic modification to enhance carotenoid content in the future.
Article
Plant Sciences
Haruka Shinkawa, Masataka Kajikawa, Tomoyuki Furuya, Ryuichi Nishihama, Hirokazu Tsukaya, Takayuki Kohchi, Hideya Fukuzawa
Summary: This study discovered the important role of DYRKs protein kinases, specifically the MpYAK1 subfamily, in regulating plant growth and development in the liverwort Marchantia polymorpha. MpYAK1 was found to be involved in maintaining plant responses to light conditions and nutrient signaling.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Microbiology
Nobuaki Shono, Mana Ito, Akio Umezawa, Kenji Sakata, Ailong Li, Jun Kikuchi, Katsutoshi Ito, Ryuhei Nakamura
Summary: This study investigates the redox homeostasis of a benthic ecosystem in aquaculture fields by monitoring the real-time redox potential. The researchers found that a cooperative relationship between oligochaetes and sediment microorganisms reinforces redox homeostasis and promotes the decomposition of organic compounds. This study suggests that the electrochemical monitoring and physiologic regulation of marine oligochaetes can contribute to sustainable aquaculture practices.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Plant Sciences
Kanade Tatsumi, Takuji Ichino, Natsumi Isaka, Akifumi Sugiyama, Eiko Moriyoshi, Yozo Okazaki, Yasuhiro Higashi, Masataka Kajikawa, Yoshinori Tsuji, Hideya Fukuzawa, Kiminori Toyooka, Mayuko Sato, Ikuyo Ichi, Koichiro Shimomura, Hiroyuki Ohta, Kazuki Saito, Kazufumi Yazaki
Summary: Plants produce a variety of lipophilic metabolites, some of which are secreted by cells. Triacylglycerol acts as a matrix lipid to facilitate the secretion of these lipophilic compounds.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Environmental Sciences
Hirokuni Miyamoto, Nobuhiro Kawachi, Atsushi Kurotani, Shigeharu Moriya, Wataru Suda, Kenta Suzuki, Makiko Matsuura, Naoko Tsuji, Teruno Nakaguma, Chitose Ishii, Arisa Tsuboi, Chie Shindo, Tamotsu Kato, Motoaki Udagawa, Takashi Satoh, Satoshi Wada, Hiroshi Masuya, Hisashi Miyamoto, Hiroshi Ohno, Jun Kikuchi
Summary: Coastal aquaculture significantly impacts the distribution of seagrass and seaweed. A study found an exceptional area near the onshore aquaculture facility where seagrass thrives. The sediment in this area is suitable for seagrass growth and harbors beneficial bacterial populations. These findings have important implications for the conservation of coastal ecosystems and blue carbon.
ENVIRONMENTAL RESEARCH
(2023)
Article
Computer Science, Interdisciplinary Applications
He Liu, Chuanjun Dai, Hengguo Yu, Qing Guo, Jianbing Li, Aimin Hao, Jun Kikuchi, Min Zhao
Summary: This paper presents an analytical and numerical investigation of a stochastic non-autonomous phytoplankton-zooplankton system with toxin-producing phytoplankton (TPP) and impulsive perturbations. The study examines the impact of white noise, impulsive perturbations, and TPP on the system dynamics. Mathematical derivations are used to analyze threshold conditions for the existence of global positive solution, population extinction, and persistence in the mean. The results demonstrate the effects of white noise, impulsive control parameter, and toxin liberation rate on population extinction and persistence in the mean. The findings contribute to a better understanding of the dynamics of aquatic ecosystems in fluctuating environments.
MATHEMATICS AND COMPUTERS IN SIMULATION
(2023)
Article
Biochemistry & Molecular Biology
Hirokuni Miyamoto, Jun Kikuchi
Summary: The natural world is undergoing constant changes, with planetary boundaries warning about biodiversity and the cycles of carbon, nitrogen, and phosphorus. Furthermore, social issues like global warming and food shortages are spreading across different fields. These seemingly unrelated problems are closely interconnected, but a comprehensive understanding is still a work in progress. However, advancements in analytical technologies, such as next-generation sequencers (NGS) and mass spectrometry, have made it possible to obtain various forms of molecular information. Additionally, the development of environmental analytical instruments and measurement facilities have increased the availability of data for different environmental factors. Computational science plays a vital role in integrating and understanding these disparate data sets through techniques like machine learning and statistical causal inference.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Chemistry, Analytical
Tharatorn Rungreungthanapol, Chishu Homma, Ken-ichi Akagi, Masayoshi Tanaka, Jun Kikuchi, Hideyuki Tomizawa, Yoshiaki Sugizaki, Atsunobu Isobayashi, Yuhei Hayamizu, Mina Okochi
Summary: Researchers designed an olfactory receptor mimetic peptide-modified graphene field-effect transistor (gFET) to address the low specificity challenge of graphene-based sensors for volatile organic compound (VOC) sensing. Peptides mimicking a fruit fly olfactory receptor were designed using a high-throughput analysis method and successfully achieved sensitive and selective detection of limonene. The peptide probe was bifunctionalized and facilitated facile sensor functionalization. This study demonstrates the advancement of a precise VOC detection system using a target-specific peptide selection and functionalization strategy for gFET sensors.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Shunji Yamada, Yuuri Tsuboi, Daiki Yokoyama, Jun Kikuchi
Summary: As the focus on global environmental sustainability grows, the development of ecofriendly materials, including addressing the issue of marine plastics, is flourishing. The vast parameter space of materials poses a challenge for efficient search. Time-domain nuclear magnetic resonance offers a way to gather information about material properties through complex T2 relaxation curves. In this research, we used a pulse sequence to assess water affinity in polymers and evaluated their relaxation properties using various techniques. By separating the relaxation curves and utilizing polymer properties, we developed a method to optimize polymer composition for desired water affinity and rigidity.
JOURNAL OF MAGNETIC RESONANCE
(2023)
Article
Multidisciplinary Sciences
Shunnosuke Okada, Yudai Inabu, Hirokuni Miyamoto, Kenta Suzuki, Tamotsu Kato, Atsushi Kurotani, Yutaka Taguchi, Ryoichi Fujino, Yuji Shiotsuka, Tetsuji Etoh, Naoko Tsuji, Makiko Matsuura, Arisa Tsuboi, Akira Saito, Hiroshi Masuya, Jun Kikuchi, Yuya Nagasawa, Aya Hirose, Tomohito Hayashi, Hiroshi Ohno, Hideyuki Takahashi
Summary: Reducing antibiotic usage among livestock animals to prevent antimicrobial resistance has become an urgent issue worldwide. This study evaluated the effects of administering chlortetracycline (CTC), a versatile antibacterial agent, on the performance, blood components, fecal microbiota, and organic acid concentrations of calves. The results showed that CTC administration had an impact on the correlation between fecal organic acids and bacterial genera, and also affected the populations of various types of fecal bacteria.
SCIENTIFIC REPORTS
(2023)
Article
Chemistry, Multidisciplinary
Hideaki Shima, Kenji Sakata, Jun Kikuchi
Summary: Aquaculture is being acknowledged as a solution to the global food problem. This study focuses on the impact of fish and their environment on the stability and quality of fish meat. Nuclear magnetic resonance is used to non-destructively acquire metabolite information, while machine learning and artificial neural network analysis provide comprehensive analysis. It was found that the antioxidant anserine is reduced in fish muscles at low water temperature, affecting other metabolites. The relationship between water temperature and fish intestinal microbiota was also established.
APPLIED SCIENCES-BASEL
(2023)
Article
Environmental Sciences
Daiki Yokoyama, Jun Kikuchi
Summary: In this study, the assembly processes of particle-associated and free-living surface water microbiomes in an urban river in Japan were analyzed. The variation in microbiomes was successfully explained by environmental factors, such as organic matter, nitrogen metabolism, and salinity. The study also revealed the dominance of stochastic processes over deterministic processes in community assembly, and the potential enhanced contribution of heterogeneous selection to community assembly in areas with salinity gradient.
ENVIRONMENTAL RESEARCH
(2023)
Article
Environmental Sciences
Hiroshi Kudo, Ning Han, Daiki Yokoyama, Tomoko Matsumoto, Mei-Fang Chien, Jun Kikuchi, Chihiro Inoue
Summary: Phytoextraction is a cost-effective and eco-friendly method for removing pollutants from contaminated soil. Bayesian network analysis revealed that the microbial strain Pseudomonas sp. m307 and MND1 order microbes positively contribute to arsenic accumulation in P. vittata.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Ecology
Hirokuni Miyamoto, Katsumi Shigeta, Wataru Suda, Yasunori Ichihashi, Naoto Nihei, Makiko Matsuura, Arisa Tsuboi, Naoki Tominaga, Masahiko Aono, Muneo Sato, Shunya Taguchi, Teruno Nakaguma, Naoko Tsuji, Chitose Ishii, Teruo Matsushita, Chie Shindo, Toshiaki Ito, Tamotsu Kato, Atsushi Kurotani, Hideaki Shima, Shigeharu Moriya, Satoshi Wada, Sankichi Horiuchi, Takashi Satoh, Kenichi Mori, Takumi Nishiuchi, Hisashi Miyamoto, Hiroaki Kodama, Masahira Hattori, Hiroshi Ohno, Jun Kikuchi, Masami Yokota Hirai
Summary: The study investigated the effects of compost on the growth and quality of carrots and the soil bacterial composition. The results showed that exposure to compost significantly improved carrot productivity, antioxidant activity, color, and taste. It also altered the soil bacterial composition and influenced the levels of characteristic metabolites. Structural equation modeling revealed the optimal linkages between amino acids, antioxidant activity, flavonoids and/or carotenoids in plants, and the involvement of Paenibacillus genus and nitrogen compounds in the soil during exposure to compost. These findings suggest the presence of a complex cascade of plant growth-promoting effects and modulation of the nitrogen cycle by compost.
ISME COMMUNICATIONS
(2023)
Article
Ecology
Daiki Yokoyama, Ayari Takamura, Yuuri Tsuboi, Jun Kikuchi
Summary: In this study, the authors compared the microbiomes and degradation processes of different biodegradable polymers using prompt evaluation systems. They found differences in the microbial community compositions among the polymer materials, with the largest differences observed in one particular polymer material, PHBH. Time-series sampling showed several stages of microbial succession during polymer degradation. Metagenome prediction revealed functional changes, including the adhesion of free-swimming microbes onto the polymer and the formation of a biofilm by certain microbes.
ISME COMMUNICATIONS
(2023)
Correction
Plant Sciences
Ryosuke Mega, Fumitaka Abe, June-Sik Kim, Yuuri Tsuboi, Keisuke Tanaka, Hisato Kobayashi, Yoichi Sakata, Kousuke Hanada, Hisashi Tsujimoto, Jun Kikuchi, Sean R. Cutler, Masanori Okamoto