Article
Biochemistry & Molecular Biology
Tuan-Wu Cao, Chun-Lan Xie, Chao-Qun Chen, Zhi-Hui He, Qing-Xiang Yan, Gang Xu, Xian-Wen Yang
Summary: Lotus seed pod (LSP) has been traditionally used in herbal cuisine to modulate immunity. A new aporphine alkaloid and 19 known ones were isolated from the AcOEt-soluble extract of LSP, showing potent in vitro anti-food allergic activity.
CHEMISTRY & BIODIVERSITY
(2021)
Article
Biochemistry & Molecular Biology
Zhanmin Sun, Sanjie Jiang, Dan Wang, Linxia Li, Boxin Liu, Qifan Ran, Lizhen Hu, Junbo Xiong, Yixiong Tang, Xiaofeng Gu, Yanmin Wu, Zhe Liang
Summary: Using single-cell RNA sequencing, we obtained the transcriptome profiles of seven major cell types in the root tips of Lotus japonicus, a legume model species. Our findings revealed regulatory programs associated with phytohormones and nodulation for specific cell types, and identified conserved and diverged features for these cell types.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Biochemical Research Methods
Masataka Nakagawa, Yui Tomioka, Chiaki Sakuma, Yasunori Kurosawa, Takashi Shibata, Tsutomu Arakawa, Teruo Akuta
Summary: A new protocol for conducting two-dimensional (2D) electrophoresis was developed by combining agarose native gel electrophoresis with sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) or flat SDS agarose gel electrophoresis. The technique utilizes His/MES buffer during the first-dimensional agarose native gel electrophoresis to visualize basic and acidic proteins in their native states or complex structures. The gel strip from the first-dimensional agarose gel electrophoresis is soaked in SDS and placed on top of vertical SDS-PAGE gels or flat SDS-MetaPhor high-resolution agarose gels for the second-dimensional separation.
Article
Chemistry, Medicinal
Jingjing Tai, Chaoyin Ye, Xiaoji Cao, Huang Hu, Wanzhen Li, Hong Zhang
Summary: This study used the non-targeted approach of UPLC-QTOF-MS/MS to identify the main chemical components in lotus seed pod extracts, finding a total of 118 compounds, with 25 of them being identified for the first time. Molecular docking technique was then used to screen for compounds with anti-gout activity, and acid precipitation fractions were prepared to further analyze these compounds. The results showed that the acid precipitation could effectively alleviate joint swelling and reduce pathological damage in the treatment of gouty arthritis.
Article
Ecology
Temidayo Ayodeji Adeyemi, Alaba Oluwafunmilayo Jolaosho, Peter Aniwe Dele, Adetomiwa Tolulade Adekoya, Funmilayo Adeola Oloyede, Victoria Olubunmi Aderemi Ojo, Oluwafemi Adeyemi Okukenu, Ahmed Adeyemi Amisu
Summary: The study found that the competitive effects of neighboring plants on the seeds and pod traits of focal plants depend on plant identity and nutrient availability. Passive trait responses were observed to magnify competitive effects on progenies after successful recruitment.
ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY
(2021)
Article
Biochemical Research Methods
Katrina Carbonara, Matthew P. Padula, Jens R. Coorssen
Summary: Integrative top-down proteomics aims to comprehensively analyze the breadth and depth of proteomes. This study disproves long-held beliefs about protein losses during front-end proteome resolution and confirms that standard facedown rehydration method has minimal impact on overall proteome resolution. This research demonstrates the importance of quantitative front-end 2DE/LC/MS/MS in analyzing proteomes by resolving their constituent proteoforms.
Article
Biology
Jorge Cebrian, Victor Martinez, Pablo Hernandez, Dora B. Krimer, Maria-Jose Fernandez-Nestosa, Jorge B. Schvartzman
Summary: The study utilized two-dimensional agarose gel electrophoresis to investigate the efficiency of three type II DNA topoisomerases on partially replicated bacterial plasmids. The results revealed the preferential functions and some redundancy, shedding light on their abilities to resolve supercoiling and pre-catenanes in vitro.
Article
Plant Sciences
Francesco Venice, Matteo Chialva, Guido Domingo, Mara Novero, Andrea Carpentieri, Alessandra Salvioli di Fossalunga, Stefano Ghignone, Angela Amoresano, Candida Vannini, Luisa Lanfranco, Paola Bonfante
Summary: By analyzing Lotus japonicus roots colonized by the fungal line with bacteria (B+) and by the cured line (B-) through deep dual-mRNA sequencing and proteomics, it was found that L. japonicus activates its symbiotic pathways regardless of the presence of endobacteria, but perceives the two fungal lines as different physiological entities. Significant differences were observed in respiratory pathways and lipid biosynthesis between the mycorrhizal plants colonized by the B+ and B- lines, indicating a reduced capacity in antioxidant metabolism and symbiotic lipid biosynthesis in the cured line.
Article
Biochemistry & Molecular Biology
Dafni-Alexandra Kavvoura, Michalis K. Stefanakis, Dimitris Kletsas, Haralambos E. Katerinopoulos, Harris Pratsinis
Summary: This study aimed to characterize two common Cretan carob tree cultivars by assessing their essential oil, fatty acid, and carbohydrate profiles, as well as evaluate the use of deseeded pod and seed extracts for cosmetic applications. The extracts showed antioxidant, tyrosinase- and collagenase-inhibitory activities, ability to block glucose-induced AGEs, and in some cases, UVB absorbance and photoprotective activities. Seed extracts exhibited higher activity, and 30% aqueous methanol was more efficient for extraction than n-hexane. Serial partitioning yielded fractions with enriched biological activities. These Cretan carob extracts and fractions are promising candidates for use in cosmetics.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Celia Sze-Nga Kwok, Kaze King-Yip Lai, Winnie Lam, Steven Jing-Liang Xu, Sai-Wo Lam, Fred Wang-Fat Lee
Summary: This study investigated the fish-killing mechanisms of Karenia mikimotoi through comparative proteomic analysis, revealing that oxidative stress-mediated muscle damage may explain the symptoms developed during ichthyotoxicity. The findings lay the foundations for more in-depth studies of the mechanisms underlying K. mikimotoi's toxicity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Analytical
Fenglong Jiao, Clinton Yu, Andrew Wheat, Xiaorong Wang, Scott D. Rychnovsky, Lan Huang
Summary: Cross-linking mass spectrometry (XL-MS) is an emerging technology for studying protein-protein interactions and protein complex architectures. However, the current XL-MS technologies have limitations in revealing the scope and depth of cellular networks. Peptide enrichment prior to MS analysis is necessary to enhance cross-link identification for proteome-wide studies.
ANALYTICAL CHEMISTRY
(2022)
Article
Forestry
Mariana Duarte-da-Silva, Danilo Flademir Alves-de-Oliveira, Francival Cardoso Felix, Cibele dos Santos Ferrari, Elizangela Emidio Cunha, Eduardo Luiz Voigt, Mauro Vasconcelos Pacheco
Summary: This study provides an integrative analysis of physiological and biochemical changes during pod and seed development in Acacia mangium. Early pod growth is characterized by water uptake, low levels of soluble sugars and proteins, and high activity of acid proteases. Late pod growth is marked by reserve deposition, with an accumulation of non-structural carbohydrates and soluble proteins. Seed physiological maturity is achieved before the end of dry weight accumulation.
Article
Engineering, Aerospace
Riccardo Rubini, Davide Lasagna, Andrea Da Ronch
Summary: This paper discusses a physics-informed methodology for reconstructing efficiently the fluid state of a system using sparsity-promoting statistical learning techniques. The approach leverages on l(1) regularised regression to generate accurate reduced order models of two-dimensional unsteady flows. The methodology shows promising results in maintaining original accuracy level while reducing the number of active coefficients, leading to improved predictive performance and temporal stability of the models.
CHINESE JOURNAL OF AERONAUTICS
(2021)
Article
Plant Sciences
Vivek Ambastha, Sudhir K. Sopory, Baishnab C. Tripathy, Budhi Sagar Tiwari
Summary: Soil salinity can lead challenged plants to death or survival with compromised productivity, with plants often surviving moderate salinity through programmed cell death by sacrificing some cells. The mechanistic details of this process in plants are still unclear, while the differential expression of chloroplastic proteins may involve some novel candidates. Phosphorylation patterns of chloroplastic proteins were observed to be highest at an early time point (12 h) of salt exposure.
FUNCTIONAL PLANT BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Akari Harada, Nanami Tsuji, Nozomi Fujimoto, Mia Matsuo, Miha Saito, Nobuyuki Kanzawa
Summary: The flowering locus T (FT) gene plays a crucial role in the flowering process and other physiological phenomena. This study demonstrates that heterologous expression of AtFT promotes flowering in Lotus japonicus without affecting stomatal movement or leaf motion.
PLANT BIOTECHNOLOGY
(2022)
Article
Plant Sciences
Arina Shrestha, Sihui Zhong, Jasmine Therrien, Terry Huebert, Shusei Sato, Terry Mun, Stig U. Andersen, Jens Stougaard, Agnes Lepage, Andreas Niebel, Loretta Ross, Krzysztof Szczyglowski
Summary: Legume root nodule organogenesis is initiated by the stimulation of root cells and involves the regulation of specific gene families to promote cellular differentiation and auxin signaling. The emergence of nodules is dependent on a regulatory cascade involving NF-YA1, STY genes, and downstream targets YUCCA1 and YUCCA11. These genes are important regulators of auxin signaling during the specific stage of nodule emergence in Lotus japonicus and Medicago truncatula.
Article
Horticulture
Tomoki Matsuyama, Manabu Watanabe, Yuri Murota, Nanako Nakata, Hisashi Kitamura, Takashi Shimokawa, Toshikazu Ebisuzaki, Satoshi Wada, Shusei Sato, Satoshi Tabata
SCIENTIA HORTICULTURAE
(2020)
Article
Plant Sciences
Bogumil J. Karas, Loretta Ross, Mara Novero, Lisa Amyot, Arina Shrestha, Sayaka Inada, Michiharu Nakano, Tatsuya Sakai, Dario Bonetta, Sushei Sato, Jeremy D. Murray, Paola Bonfante, Krzysztof Szczyglowski
Summary: Root hair cells are crucial for nutrient uptake and defense in plants, with the gene CSLD1 playing a role in root hair development in the legume species Lotus japonicus. Multiple mutant alleles of Ljcsld1 result in varying root hair phenotypes, with certain mutations affecting root nodule symbiosis. Intragenic complementation is observed between alleles with mutations in different CSLD1 domains, suggesting modular function of CSLD1 during root hair development.
Article
Biochemistry & Molecular Biology
Natalya Kudryavtseva, Aleksey Ermolaev, Gennady Karlov, Ilya Kirov, Masayoshi Shigyo, Shusei Sato, Ludmila Khrustaleva
Summary: The study aimed to improve the reliability of genome assembly at the chromosome level and develop a simpler and more reliable method for in situ mapping of short unique DNA sequences on plant chromosomes. By adjusting key steps, the short DNA sequence was successfully detected and a new dual-color Tyr-FISH visualization protocol was developed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Ecology
Haruka Arashida, Haruka Odake, Masayuki Sugawara, Ryota Noda, Kaori Kakizaki, Satoshi Ohkubo, Hisayuki Mitsui, Shusei Sato, Kiwamu Minamisawa
Summary: Symbiosis between organisms influences evolution through adaptive changes in genome architectures. Interactions between soybeans and Bradyrhizobium involve IS-mediated duplications and deletions on symbiosis islands, with host plants selecting mutualistic variants from the pool of rhizobial populations. Homologous recombination between direct IS copies provides a natural mechanism for generating deletions and duplications in symbiosis islands.
Article
Genetics & Heredity
Richard Finkers, Martijn van Kaauwen, Kai Ament, Karin Burger-Meijer, Raymond Egging, Henk Huits, Linda Kodde, Laurens Kroon, Masayoshi Shigyo, Shusei Sato, Ben Vosman, Wilbert van Workum, Olga Scholten
Summary: This study presents the de novo assembly and annotation of the onion genome, resulting in a high-quality sequence for future research on onion genetics. The genome assembly revealed insights into the repetitive sequences and gene distribution, as well as the synteny with garlic, showing both collinearity and major rearrangements between the two species.
G3-GENES GENOMES GENETICS
(2021)
Article
Oncology
Rikke L. Nielsen, Benjamin O. Wolthers, Marianne Helenius, Birgitte K. Albertsen, Line Clemmensen, Kasper Nielsen, Jukka Kanerva, Riitta Niinimaki, Thomas L. Frandsen, Andishe Attarbaschi, Shlomit Barzilai, Antonella Colombini, Gabriele Escherich, Derya Aytan-Aktug, Hsi-Che Liu, Anja Moricke, Sujith Samarasinghe, Inge M. van der Sluis, Martin Stanulla, Morten Tulstrup, Rachita Yadav, Ester Zapotocka, Kjeld Schmiegelow, Ramneek Gupta
Summary: This study explores machine learning strategies for predicting individual risk of asparaginase-associated pancreatitis (AAP) in children with acute lymphoblastic leukemia (ALL). The results show that adding age, sex, and specific gene polymorphisms can improve predictive accuracy. These machine learning models can assist in individual-level risk assessment of AAP and support the re-exposure to asparaginase when the risk is predicted to be low.
JOURNAL OF PEDIATRIC HEMATOLOGY ONCOLOGY
(2022)
Article
Multidisciplinary Sciences
Jieshun Lin, Yuda Purwana Roswanjaya, Wouter Kohlen, Jens Stougaard, Dugald Reid
Summary: Legumes balance nitrate signaling and symbiotic nitrogen fixation through cytokinin biosynthesis, with low nitrate conditions promoting cytokinin induction and high nitrate inhibiting it. This differential response is further seen in mutants, which show hypersensitivity to nitrate inhibition but can be rescued by cytokinin application. Nitrate's inhibitory effect on symbiosis occurs in a Nlp1 and Nlp4 dependent manner, contrasting with its positive influence on non-legumes.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Shintaro Hara, Naohisa Wada, Sliver Sung-Yun Hsiao, Meng Zhang, Zhihua Bao, Yoshiyuki Iizuka, Der-Chuen Lee, Shusei Sato, Sen-Lin Tang, Kiwamu Minamisawa
Summary: This study demonstrates that type II methanotrophs in the root tissues of paddy rice perform methane oxidation and nitrogen fixation simultaneously at the single-cell level. The findings provide direct evidence of the activities of methanotrophs in root tissues, suggesting that they may provide fixed nitrogen to root systems or depend on different microenvironmental niches.
Article
Multidisciplinary Sciences
Soren Knudsen, Toni Wendt, Christoph Dockter, Hanne Cecilie Thomsen, Magnus Rasmussen, Morten Egevang Jorgensen, Qiongxian Lu, Cynthia Voss, Emiko Murozuka, Jeppe Thulin Osterberg, Jesper Harholt, Ilka Braumann, Jose A. Cuesta-Seijo, Sandip M. Kale, Sabrina Bodevin, Lise Tang Petersen, Massimiliano Carciofi, Pai Rosager Pedas, Jeppe Opstrup Husum, Martin Toft Simmelsgaard Nielsen, Kasper Nielsen, Mikkel K. Jensen, Lillian Ambus Moller, Zoran Gojkovic, Alexander Striebeck, Klaus Lengeler, Ross T. Fennessy, Michael Katz, Rosa Garcia Sanchez, Natalia Solodovnikova, Jochen Forster, Ole Olsen, Birger Lindberg Moller, Geoffrey B. Fincher, Birgitte Skadhauge
Summary: To meet future global food demands and counteract climate change, it is crucial to enhance agricultural and industrial production organisms. The FIND-IT resource allows for rapid identification and isolation of targeted genetic variants, enabling functional gene analysis and accelerating germplasm evolution.
Article
Plant Sciences
Yusdar Mustamin, Turgut Yigit Akyol, Max Gordon, Andi Madihah Manggabarani, Yoshiko Isomura, Yasuko Kawamura, Masaru Bamba, Cranos Williams, Stig Uggerhj Andersen, Shusei Sato
Summary: This research found that winter survival was the direct target of selection during colonization of Japan by Lotus japonicus. Two candidate genes, FERONIA-receptor like kinase (LjFER) and a S-receptor-like kinase gene (LjLecRK), were identified to be required for non-acclimated freezing tolerance and exhibited haplotype-dependent cold-responsive expression. The study suggests that incorporating a conserved growth regulator gene, FER, and a receptor-like kinase gene, LecRK, into the cold-responsive genes contributed to freezing tolerance and local climate adaptation in L. japonicus, providing insights into the genetic mechanisms of perennial herb evolution.
Article
Plant Sciences
Jesus Montiel, Ivette Garcia-Soto, Euan K. James, Dugald Reid, Luis Cardenas, Selene Napsucialy-Mendivil, Shaun Ferguson, Joseph G. Dubrovsky, Jens Stougaard
Summary: This study demonstrates the crucial role of the regulation of aromatic amino acid biosynthesis in sustaining root hair growth and establishing symbiotic relationships in the legume Lotus japonicus. The enzyme DAHPS1 is found to be critical for root hair development and for the symbioses with both rhizobial and mycorrhizal microbes. Mutants lacking DAHPS1 show altered root hair morphology, reduced symbiotic interactions, and downregulation of cell wall-related genes.
Article
Genetics & Heredity
Daisuke Sekine, Satoshi Oku, Tsukasa Nunome, Hideki Hirakawa, Mai Tsujimura, Toru Terachi, Atsushi Toyoda, Masayoshi Shigyo, Shusei Sato, Hikaru Tsukazaki
Summary: This study presents a genome-wide marker design workflow for onions, which is applied in a high-throughput genotyping method using target amplicon sequencing. The efficiency of the method is evaluated by genotyping F-2 populations. The results show that our marker design workflow and target amplicon sequencing are useful for genome-wide genotyping of onions. However, there are missing or sparse marker regions in the resulting genetic linkage map, which need further improvement.
Article
Plant Sciences
Jesus Montiel, Dugald Reid, Thomas H. Gronbaek, Caroline M. Benfeldt, Euan K. James, Thomas Ott, Franck A. Ditengou, Marcin Nadzieja, Simon Kelly, Jens Stougaard
Summary: This study reports intercellular infection of the model legume Lotus japonicus by the IRBG74 strain and reveals the genetic requirements and differences in the pathways governing this process compared to intracellular infection. The results indicate a differential requirement for cytokinin signaling during intercellular rhizobial entry, highlighting distinct modalities of inter- and intracellular infection mechanisms in L. japonicus.