Article
Plant Sciences
Jun Liu, Chuanbo Sun, Siqi Guo, Xiaohong Yin, Yuling Yuan, Bing Fan, Qingxue Lv, Xinru Cai, Yi Zhong, Yuanfeng Xia, Xiaomei Dong, Zhifu Guo, Guangshu Song, Wei Huang
Summary: This study constructed a maize brittle stalk mutant (bk5) and identified differential genes and pathways related to cellulose and lignin synthesis, shedding light on the molecular mechanisms regulating the brittle stalk phenotype in maize.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Horticulture
Hui Li, Yibo Bai, Yaxin Yang, Huan Zheng, Xianbin Xu, Haoran Li, Wu Wang, Jianmin Tao
Summary: Teinturier grapevine cultivars, characterized by red pulp berries, showed inhibited anthocyanin accumulation under bagging treatment, while rapid accumulation of malvidin, cyanidin, and delphinidin derivatives was observed after exposure to light. Transcriptomic analysis revealed that genes associated with light-responsive factors, transcription factors, and structural genes were significantly up-regulated under bag removal treatment. These findings provide insights into the molecular mechanism of light-induced anthocyanin biosynthesis in teinturier grapes.
SCIENTIA HORTICULTURAE
(2023)
Article
Biochemistry & Molecular Biology
Shaymaviswanathan Karnaneedi, Roger Huerlimann, Elecia B. Johnston, Roni Nugraha, Thimo Ruethers, Aya C. Taki, Sandip D. Kamath, Nicholas M. Wade, Dean R. Jerry, Andreas L. Lopata
Summary: This study successfully identified seven known crustacean allergens and up to 39 unreported allergens in different shrimp species through mining complete transcriptomes. Multiple sequence alignment revealed high homology of these shrimp allergens with allergens from other invertebrates such as mites and cockroaches. This first transcriptomic analyses of allergens in a major food source provides a valuable resource for investigating shellfish allergens, comparing invertebrate allergens and future development of improved diagnostics for food allergy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Andrea Termine, Carlo Fabrizio, Juliette Gimenez, Anna Panuccio, Francesca Balsamo, Noemi Passarello, Silvia Caioli, Luana Saba, Marco De Bardi, Francesco Della Valle, Valerio Orlando, Laura Petrosini, Daniela Laricchiuta
Summary: The study analyzed the interaction between the gene expression of the endocannabinoid system (ECS) and the immune system (IS) in relation to individual differences. It found that this interaction is associated with approach and avoidance behavioral tendencies and may modulate synaptic plasticity and neuronal metabolism.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Ying Huang, Huijun Ma, Yuanzhi Yue, Tianchang Zhou, Zhenyu Zhu, Chao Wang
Summary: In this study, the transcriptomic response of P. davidiana x P. bollena to Alternaria alternata infection was analyzed using RNA-Seq. Differentially expressed genes (DEGs) related to resistance were identified, and the lipoxygenase gene PdbLOX2 was found to play a key role in JA biosynthesis and resistance. These findings provide insights into the molecular mechanisms of poplar resistance to A. alternata and offer candidate genes for breeding resistant cultivars.
Article
Biochemistry & Molecular Biology
Abrahan Hernandez-Hernandez, Tayde Lopez-Santaella, Aranxa Torres-Caballero, Amarantha Serrato, Ulises Torres-Flores, Diego Montesinos-Valencia, Fernando Chico-Ponce De Leon, Vicente Gonzalez-Carranza, Samuel Torres-Garcia, Rosa Rebollar-Vega, Inti Alberto De la Rosa-Velazquez, Rosario Ortiz, Monserrat Perez-Ramirez, Normand Garcia-Hernandez, Antonio Garcia-Mendez, Francisco Arenas-Huertero
Summary: Central nervous system tumors are common in childhood and contribute to cancer-related mortality. This study explored the transcriptomic landscape of pediatric astrocytoma, focusing on the genetic alterations associated with tumorigenesis. The findings provide insights into the biological functions and pathways involved in astrocytoma, and establish a transcriptional signature for identifying different grades of the tumor.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Xupeng Zang, Ting Gu, Qun Hu, Zhiqian Xu, Yanshe Xie, Chen Zhou, Enqin Zheng, Sixiu Huang, Zheng Xu, Fanming Meng, Gengyuan Cai, Zhenfang Wu, Linjun Hong
Summary: This study utilized RNA-Seq and real-time PCR to analyze gene expression changes during the implantation period of pig conceptus. Various genes were identified to play essential roles in conceptus development and implantation, and PAG-2 was found to inhibit trophoblast cell proliferation and migration. The analysis provides valuable insights into the mechanisms of conceptus development and implantation in pigs.
FRONTIERS IN GENETICS
(2021)
Article
Plant Sciences
Harold Suarez-Baron, Juan F. Alzate, Barbara A. Ambrose, Soraya Pelaz, Favio Gonzalez, Natalia Pabon-Mora
Summary: This study aims to explore the genetic regulatory network underlying multicellular trichome development in Aristolochia. By comparing two different morphological species of Aristolochia, we found significant modifications in gene composition, expression, and function compared to model plants. We propose the first hypothetical genetic regulatory network for floral multicellular trichome development in Aristolochia and identify key factors responsible for the presence and specialization of floral trichomes in different species.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Biochemistry & Molecular Biology
Luigi Chiricosta, Santino Blando, Simone D'Angiolini, Agnese Gugliandolo, Emanuela Mazzon
Summary: Multiple Sclerosis (MS) is an incurable disease of the nervous system characterized by demyelination. Genetic mutations cannot explain all diagnosed cases, suggesting a role of altered gene expression. This review explores the role of the transcriptomic profile in MS, highlighting specific molecular signatures in different stages and the involvement of non-coding RNAs. RNA-seq methods, replacing microarrays, provide valuable insights into new mechanisms and pathways, such as neddylation and inflammation linked to neuron degeneration.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Xueling Ye, Qiang Li, Changying Liu, Qi Wu, Yan Wan, Xiaoyong Wu, Gang Zhao, Liang Zou, Dabing Xiang
Summary: This study investigated the responses and regulatory pathways of Tartary buckwheat to cadmium (Cd) stress by assessing its phenotypic, cytological, physiological, and transcriptomic characteristics under different concentrations of Cd treatments. The results showed that Tartary buckwheat could tolerate high Cd concentrations and accumulated Cd primarily in the roots. Cd stress also led to the formation of Casparian strips in roots and damage to the cytoderm and organelles. Additionally, several core genes were found to be involved in the response to Cd stress.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Horticulture
Yuying Ma, Zhen Gao, Wensheng Du, Fei Xie, Guikuan Ren, Meiling Tang, Qiuling Zheng, Hui Kang, Yuanpeng Du
Summary: 'Ruidu kemei' (Kemei) is a new variety of rose-scented grape that was selected from among the hybrid offspring of 'Italy' x 'Muscat Louis'. Bagging was found to increase the total soluble solid (TSS) content and sugar-acid ratio in Kemei grapes, but had no significant effect on titratable acid (TA) levels. Metabolomic and RNA sequencing analysis revealed differentially accumulated metabolites and expressed genes between bagged and natural-light samples, indicating the involvement of starch and sucrose metabolic pathways, glycolysis, and the tricarboxylic acid (TCA) cycle in bagging-induced changes. These findings contribute to a comprehensive understanding of the molecular and metabolic mechanisms underlying the effects of fruit bagging on Kemei grape quality formation.
SCIENTIA HORTICULTURAE
(2023)
Article
Biochemistry & Molecular Biology
Ruizhen Zhao, Wei Cheng, Juan Shen, Weiming Liang, Zhao Zhang, Yifei Sheng, Tailiang Chai, Xueting Chen, Yin Zhang, Xiang Huang, Huanjie Yang, Chunqing Song, Li Pang, Cuoji Nan, Yangrui Zhang, Rouxi Chen, Junpu Mei, Hong Wei, Xiaodong Fang
Summary: The gut-liver axis is a bidirectional communication pathway between the intestine and the liver that affects liver function. This study used single-cell and spatial transcriptomic analysis to investigate the effects of microorganisms on the liver. The results showed alterations in immune cells, changes in gene expression, and metabolic differences in germ-free mice compared to specific-pathogen-free mice.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Forestry
Haiyue Wang, Lin Guo, Ruofei Zha, Zhipeng Gao, Fen Yu, Qiang Wei
Summary: The Moso bamboo leaf has evolved special histological structures, metabolic pathways and a cold stress-tolerant transcriptome to adapt to the cold weather. These adaptations include more trichomes, fewer fusiform cells, lower stomata density and higher levels of stress-resistant metabolites. The cold stress response network involves trehalose, glutathione, flavonoid metabolism, DNA repair, reactive oxygen species degradation, stress-associated genes and abiotic stress-related plant hormones.
Article
Biochemistry & Molecular Biology
Tao Zhang, Kaile Sun, Xiaoke Chang, Zhaopeng Ouyang, Geng Meng, Yanan Han, Shunshan Shen, Qiuju Yao, Fengzhi Piao, Yong Wang
Summary: As a glycophyte plant, pepper is susceptible to salinity damage, especially at the seedling stage. This study compared the physiological and transcriptional differences between two different pepper genotypes under salt stress. The more salt-tolerant genotype, P300, exhibited higher K+ contents, antioxidase activities, compatible solutes, and lower Na+ contents in both its roots and leaves compared to the less salt-tolerant genotype, 323F3. RNA-seq analysis revealed more up-regulated genes and fewer down-regulated genes in salt-treated P300 seedlings compared to the controls, and many ROS-scavenging genes and SOS pathway genes were significantly induced by salt stress. The biosynthesis of unsaturated fatty acids and protein processing in the endoplasmic reticulum pathways were also involved in P300's response to salt stress. Additionally, differences in hormone synthesis and signaling pathway genes were observed in both genotypes under salt stress. Overall, this study provides valuable insights into the physiological and molecular mechanisms underlying salt tolerance in pepper seedlings and identifies candidate genes for improving salt tolerance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Yuxiang Zhang, Jianping Wei, Hong Guo, Chen Niu, Yahong Yuan, Tianli Yue
Summary: This study revealed the antibacterial mechanism of cinnamic acid (CA) against food-derived Pseudomonas fragi 38-8. CA exerted its antibacterial effect mainly by disrupting cell membrane homeostasis, leading to depolarization of the cell membrane, intracellular pH reduction, and decrease in intracellular ATPase activity, ultimately inhibiting bacterial growth.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Oncology
Biaoyang Lin, Hwahyung Lee, Jae-Geun Yoon, Anup Madan, Elizabeth Wayner, Sanja Tonning, Parvinder Hothi, Brett Schroeder, Ilya Ulasov, Gregory Foltz, Leroy Hood, Charles Cobbs
Article
Oncology
Jan Roger Olsen, Waqas Azeem, Margrete Reime Hellem, Kristo Marvyin, Yaping Hua, Yi Qu, Lisha Li, Biaoyang Lin, Xi-Song Ke, Anne Margrete Oyan, Karl-Henning Kalland
Meeting Abstract
Oncology
Jan Roger Olsen, Waqas Azeem, Margrete R. Hellem, Kristo Marvyin, Yaping Hua, Yi Qu, Lisha Li, Biaoyang Lin, XiSong Ke, Anne Margrete Oyan, Karl-Henning Kalland
Meeting Abstract
Oncology
Waqas Azeem, Margrete R. Hellem, Jan R. Olsen, Yaping Hua, Kristo Marvyin, Lisha Li, Yi Qu, Biaoyang Lin, Xisong Ke, Anne M. Oyan, Karl-Henning Kalland
Letter
Biotechnology & Applied Microbiology
Eyup Ilker Saygili, Alaa H. Abou-Zeid, Salih Murat Akkin, Eleni Aklillu, Ibrahim Omer Barlas, Alexander Borda-Rodriguez, Filiz Aydogan Boschele, Zafer Cetin, Enes Coskun, Yavuz Coskun, Guner Dagli, Turkan Ugur Dai, Collet Dandara, Turkay Dereli, Levent Elbeyli, Laszlo Endrenyi, Can Polat Eyigun, Alexandros Georgakilas, Bircan Gunbulut, Kivanc Gungor, Asim Guzelbey, Can Hekim, Farah Huzair, Sabit Kimyon, Umit Karakas, Biaoyang Lin, Adrian LLerena, Collen Masimirembwa, Ruth McNally, Alper Mete, Pesvin Sancar, Sanjeeva Srivastava, Lotte M. Steuten, Oylum Tanriover, David Tyfield, Volkan Ihsan Tore, Deniz Vuruskan, Wei Wang, Louise Warnich, Ambroise Wonkam, Yusuf Ziya Yildirim, Ismet Yilmaz, Ahmet Sinav, Nezih Hekim
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2016)
Article
Multidisciplinary Sciences
Yi Qu, Naouel Gharbi, Xing Yuan, Jan Roger Olsen, Pernille Blicher, Bjorn Dalhus, Karl A. Brokstad, Biaoyang Lin, Anne Margrete Oyan, Weidong Zhang, Karl-Henning Kalland, Xisong Ke
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Multidisciplinary Sciences
Waqas Azeem, Margrete Reime Hellem, Jan Roger Olsen, Yaping Hua, Kristo Marvyin, Yi Qu, Biaoyang Lin, Xisong Ke, Anne Margrete Oyan, Karl-Henning Kalland
Article
Oncology
Ruifang Mao, Jie Liu, Guanfeng Liu, Shanshan Jin, Qingzhong Xue, Liang Ma, Yan Fu, Na Zhao, Jinliang Xing, Lanjuan Li, Yunqing Qiu, Biaoyang Lin
Article
Biophysics
Liang Ma, Bin Zhang, Changchun Zhou, Yuting Li, Binjie Li, Mengfei Yu, Yichen Luo, Lei Gao, Duo Zhang, Qian Xue, Qingchong Qiu, Biaoyang Lin, Jun Zou, Huayong Yang
COLLOIDS AND SURFACES B-BIOINTERFACES
(2018)
Article
Multidisciplinary Sciences
Qing-Chong Qiu, Lin Wang, Shan-Shan Jin, Guan-Feng Liu, Jie Liu, Liang Ma, Rui-Fang Mao, Ying-Ying Ma, Na Zhao, Ming Chen, Biao-Yang Lin
SCIENTIFIC REPORTS
(2018)
Review
Biotechnology & Applied Microbiology
Biaoyang Lin, Yingying Ma, ShengJun Wu
Summary: Chronic liver disease (CLD) is a global health burden, and there is a need for improved biomarkers, diagnostic methods, and the integration of multi-omics data with the help of artificial intelligence. This review summarizes the emerging frontiers and challenges in multi-omics data integration in liver pathology research, as well as the impact of digital transformation in this field.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Biaoyang Lin, Shengjun Wu
Summary: Digital transformation is revolutionizing personalized medicine and systems science by enabling real-time patient feedback and in-depth phenotypic analysis with advanced technologies like artificial intelligence and the Internet of Medical Things.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Biaoyang Lin, Yingying Ma, Shengjun Wu, Yunhua Liu, Longgen Liu, Lihua Wu
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2019)
Article
Biotechnology & Applied Microbiology
Jie Liu, Ruifang Mao, Guoping Ren, Xiaoyan Liu, Yanling Zhang, Jili Wang, Yan Wang, Meiling Li, Qingchong Qiu, Lin Wang, Guanfeng Liu, Shanshan Jin, Liang Ma, Yingying Ma, Na Zhao, Jiajun Yan, Hongwei Zhang, Biaoyang Lin
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2019)
Letter
Biotechnology & Applied Microbiology
Biaoyang Lin
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2019)