Article
Environmental Sciences
Tae Hee Park, Chung Il Lee, Tae-Hoon Kim, Dongyoung Kim, Hyun Je Park
Summary: In order to evaluate the impact of rainfall on the basal resources supporting food webs, we compared stable isotope ratios (813C and 815N) of fish consumers and organic matter sources between up- and down-sites in an estuary across different seasons and years. Our study found seasonal differences in the isotopic values of basal resources and fish consumers in both years. Changes in rainfall period resulted in significant differences in the isotopic values of fish consumers at the up-site, indicating a shift in food availability. However, the isotopic values of fishes remained consistent at the down-site, suggesting a negligible impact of rainfall on fish resources.
MARINE POLLUTION BULLETIN
(2023)
Article
Marine & Freshwater Biology
P. Nodo, A. -R. Childs, P. Pattrick, N. C. James
Summary: Estuaries and shallow marine nearshore areas are important nursery habitats for fish. However, there is a lack of research on fish community patterns in these areas, particularly in southern Africa. This study aimed to assess the role of estuaries and marine nearshore areas in Algoa Bay as settlement and nursery habitats for demersal fishes.
ESTUARINE COASTAL AND SHELF SCIENCE
(2023)
Article
Marine & Freshwater Biology
R. W. Schloesser, K. M. Leber, N. P. Brennan, P. Caldentey
Summary: The study presents a novel approach to assess short-term apparent survival of hatchery-reared fish stocked into open estuarine systems. By using PIT tags and multistate mark-recapture models, the researchers found weekly apparent survival rates of released snook varied in the short term and were influenced by residency behaviors. The highest survival was observed for individuals released in lower reaches of tidal creek systems in the spring.
BULLETIN OF MARINE SCIENCE
(2021)
Article
Chemistry, Applied
Aatif Rashid, Villayat Ali, Manu Khajuria, Sheenam Faiz, Sumeet Gairola, Dhiraj Vyas
Summary: This study conducted an untargeted metabolomic study on cannabis seeds, finding that the Himalayan accession exhibited superior accumulation of nutrients and higher antioxidant and nutraceutical potential compared to the subtropical accession. The exclusive presence of linoleic acid and a-linolenic acid in the seed oil of the Himalayan accession was noted. The environmental impact on the antioxidant and nutraceutical value in seeds was also discussed.
Article
Biochemistry & Molecular Biology
Pingli Yuan, Nan He, Muhammad Jawad Umer, Shengjie Zhao, Weinan Diao, Hongju Zhu, Junling Dou, Mohamed Omar Kaseb, Hanhui Kuang, Xuqiang Lu, Wenge Liu
Summary: The study found significant metabolic differences between wild and cultivated watermelons, mainly in different metabolites. Additionally, different flesh-colored cultivated watermelons also showed variations in key metabolites. Correlation analysis highlighted that flavonoids were clustered tightly in terms of metabolites. A total of 431 differentially accumulated metabolites were identified through pairwise comparative analyses.
Article
Chemistry, Medicinal
Tao Xue, Yujie Xiong, Jiang Shi, Qiujie Chao, Yanfang Zhu, Yongbo Duan, Wei Sheng, Jingtong Teng, Jianping Xue
Summary: Pinellia ternata, a native herb in China, has been found to have increased tuber production with shading treatment. Metabolomic analysis revealed that organic acids enriched in shaded environments may contribute to tuber quality improvement.
JOURNAL OF NATURAL MEDICINES
(2021)
Article
Chemistry, Applied
Tengfei Xia, Zijun Xiong, Xiuxiu Sun, Jiali Chen, Chunmei Wang, Yeguang Chen, Daojun Zheng
Summary: UPLC-MS/MS- and HS-SPME/GC-MS-based metabolomic analyses and network pharmacology approaches were used to study Camellia drupifera mature-seeds samples (CMSSs) from Hainan and Liangguang. A total of 1057 metabolites were identified, with 76 and 99 metabolites annotated as key active ingredients in Traditional Chinese Medicines and active pharmaceutical ingredients for human disease resistance, respectively. Comparative analysis showed different metabolomic profiles between CMSSs from Hainan and Liangguang. Secondary metabolic pathways, especially flavone and flavonol biosynthesis, played important roles. Additionally, 22 metabolites exclusively detected in CMSSs from either Hainan or Liangguang were explored as potential indicators to differentiate CMS from Hainan and Liangguang. This study provides valuable information for the healthy development of the oil-tea Camellia industry in Hainan.
Article
Biochemistry & Molecular Biology
Izabela Burzynska-Pedziwiatr, Danuta Dudzik, Anna Sansone, Beata Malachowska, Andrzej Zieleniak, Monika Zurawska-Klis, Carla Ferreri, Chryssostomos Chatgilialoglu, Katarzyna Cypryk, Lucyna A. Wozniak, Michal J. Markuszewski, Malgorzata Bukowiecka-Matusiak
Summary: Gestational diabetes mellitus (GDM) is a disorder related to glucose metabolism during pregnancy. Our study found higher levels of 2-hydroxybutyric and 3-hydroxybutyric acids in the plasma of GDM patients, which are associated with impaired glucose metabolism. We also observed significant changes in the fatty acid composition of cholesteryl esters in GDM patients' plasma. Our findings highlight the importance of hydroxybutyric acid derivatives, cholesteryl ester composition, and the reduction of oleic acid in the pathophysiology of GDM.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Alkisti Manousaki, James Bagnall, David Spiller, Laura Natalia Balarezo-Cisneros, Michael White, Daniela Delneri
Summary: This study successfully quantified low abundant membrane-binding proteins using fluorescence correlation spectroscopy and found that the localization and copy number of Fis1p and Mdv1p proteins in mitochondria are influenced by the environment. In addition, a compensatory mechanism was observed in Fis1p protein upon deletion of one allele.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Yuqin Wang, Yuan Nong, Xing Zhang, Tingyu Mai, Jiansheng Cai, Jiaqi Liu, Keng Po Lai, Zhiyong Zhang
Summary: This study investigates the changes in plasma metabolites as potential biomarkers for assessing cognitive impairment induced by heavy metals. The findings highlight the importance of specific metabolites, such as docosahexaenoic acid and glyco-ursodeoxycholic acid, in brain functions and neurodegenerative diseases. Overall, these plasma metabolites provide novel insights into the evaluation of metal-induced cognitive impairment.
CHEMICO-BIOLOGICAL INTERACTIONS
(2022)
Article
Energy & Fuels
Jing Yu, Xiaopeng Su, Zhaotong Shi, Yan Li, Chaowen Wang, Shukui Zhu, Yamei Wang
Summary: A new analytical platform was used to analyze the chemical compositions of fossil resins from ancient gymnosperms and angiosperms, leading to the identification of chemotaxonomic markers. These findings are significant for understanding paleoenvironment and plant evolution.
INTERNATIONAL JOURNAL OF COAL GEOLOGY
(2023)
Article
Fisheries
James T. Thorson
Summary: Phylogenetic comparative methods (PCM) and phylogenetic structural equation models (PSEM) can replace linear models and improve performance in fisheries meta-analyses, but they are rarely applied in fisheries science.
FISH AND FISHERIES
(2023)
Article
Food Science & Technology
Daniela Eliza Marin, Ionelia Taranu
Summary: In this study, an in silico working model based on online computational programs was used to predict the Phase I and II metabolites of alternariol and provide a detailed ADME/Tox profile. A total of 12 metabolites were identified corresponding to the metabolomic profile of alternariol. The ADME profile indicated moderate or high intestinal absorption probability but low probability to penetrate the blood-brain barrier. The computational model also predicted other toxicological endpoints for the compounds, such as vascular toxicity, haemato-toxicity, diarrhea, and nephrotoxicity.
Article
Environmental Sciences
Pranab Gogoi, C. M. Roshith, Ranjan Kumar Manna, Thangjam Nirupada Chanu, Chayna Jana, Dibakar Bhakta, Satish K. Koushlesh, Sanjoy Kumar Das, Archana Sinha, Srikanta Samanta, Basanta Kumar Das
Summary: This study reports on the ecohydrological interactions and distribution patterns of fish species composition in the Indian Sundarbans estuarine system. The research found significant differences in fish species diversity and abundance across seasons and stations. The study also identified salinity and water temperature as important predictor variables for fish abundance and community composition.
Article
Green & Sustainable Science & Technology
Ruben van Treeck, Johannes Radinger, Nicole Smialek, Joachim Pander, Juergen Geist, Melanie Mueller, Christian Wolter
Summary: Hydropower plants have severe impacts on aquatic habitat and biota, disrupting migration routes and causing high fish mortality rates. The European Fish Hazard Index (EFHI) is useful for assessing and mitigating risks, but current environmental impact assessments tend to underestimate the hazards.
SUSTAINABLE ENERGY TECHNOLOGIES AND ASSESSMENTS
(2022)
Article
Plant Sciences
Yoshimi Nakano, Hitoshi Endo, Lorenz Gerber, Chiaki Hori, Ayumi Ihara, Masayo Sekimoto, Tomoko Matsumoto, Jun Kikuchi, Misato Ohtani, Taku Demura
Summary: Researchers have developed a self-reinforced system to enhance the formation of secondary cell walls (SCW) in poplar xylem. By using transcription factors fused with specific gene promoters, the expression levels of SCW-related genes were increased, resulting in enhanced SCW thickening in transgenic plants. Furthermore, this method was found to affect the properties of cell walls.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Daiki Yokoyama, Sosei Suzuki, Taiga Asakura, Jun Kikuchi
Summary: Efficient membrane filtration requires understanding the membrane foulants and the functional properties of different membrane types. This study used chemical analysis and modeling techniques to investigate membrane foulants and classify the effect of different membrane materials on filtration performance.
Article
Biotechnology & Applied Microbiology
Kayo Ito, Hirokuni Miyamoto, Makiko Matsuura, Chitose Ishii, Arisa Tsuboi, Naoko Tsuji, Teruno Nakaguma, Yumiko Nakanishi, Tamotsu Kato, Wataru Suda, Fuyuko Honda, Toshiyuki Ito, Shigeharu Moriya, Hideaki Shima, Ryounosuke Michibata, Ryouichi Yamada, Yosuke Takahashi, Hirohisa Koga, Hiroaki Kodama, Yuko Watanabe, Jun Kikuchi, Hiroshi Ohno
Summary: This study evaluated the composition of fecal metabolites in broiler chickens continuously administered with W. coagulans SANK70258 and found that this bacterial strain can significantly modulate the gut metabolism of the chickens. The levels of short-chain fatty acids propionate and butyrate in the feces of the chickens were increased, while acetate and lactate levels were reduced. In addition, the levels of carbohydrates that are substrates for SCFA production also increased, and the correlation between metabolites changed. Enrichment pathway analysis revealed the activation of metabolic pathways related to SCFAs, amino acids, and energy.
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2022)
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
