Article
Biochemical Research Methods
Feifei Zhu, Han Chen, Jinying Han, Weiwei Zhou, Qi Tang, Qian Yu, Shangshang Ma, Xiaoyong Liu, Shuhao Huo, Keping Chen
Summary: The study reports the development of a neurotoxin-induced silkworm model for Parkinson's disease and explores possible molecular mechanisms using proteomic and targeted metabolomic approaches. Results show that 6-OHDA treatment can induce PD-like symptoms in silkworms, indicating the potential of silkworm models in understanding the molecular and cellular mechanisms underlying PD.
JOURNAL OF PROTEOME RESEARCH
(2022)
Review
Chemistry, Analytical
Sara Ramirez-Acosta, Ana Arias-Borrego, Francisco Navarro-Roldan, Marta Selma-Royo, Marta Calatayud, Maria Carmen Collado, Paula V. Huertas-Abril, Nieves Abril, Tamara Garcia Barrera
Summary: Omic methodologies are crucial analytical tools in various research fields, particularly in understanding microbial functionality. The impact of metals and metalloids on gut microbiota and gut-brain axis is still being explored.
ANALYTICA CHIMICA ACTA
(2021)
Article
Behavioral Sciences
Megan E. Huibregtse, Jeffrey J. Bazarian, Sandy R. Shultz, Keisuke Kawata
Summary: Blood biomarkers can provide objective measures in traumatic brain injury (TBI) assessment and predict recovery duration. Proteomic markers, often examined in research, have short half-lives due to degradation, while emerging biomarkers like microRNA and extracellular vesicles can better reflect the genetic and metabolic alterations following TBI.
NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS
(2021)
Article
Multidisciplinary Sciences
Rotimi Fasimoye, Wentao Dong, Raja S. Nirujogi, Eshaan S. Rawat, Miharu Iguchi, Kwamina Nyame, Toan K. Phung, Enrico Bagnoli, Alan R. Prescott, Dario R. Alessi, Monther Abu-Remaileh
Summary: The Golgi is a crucial organelle involved in protein and lipid biosynthesis, as well as sorting and secretion. Dysfunctional Golgi is associated with various diseases. This study presents a Golgi immunoprecipitation technique to isolate intact Golgi mini-stacks for analysis. The analysis pipeline reveals the molecular features of the human Golgi, including proteome, metabolome, and lipidome profiles. This comprehensive molecular map provides a powerful method to study the Golgi in health and disease.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemical Research Methods
Benjamin C. Orsburn
Summary: Mutations in the KRAS gene are common drivers of cancer in humans. This study discovered a promising compound, MRTX1133, that inhibits the activity of KRAS(G12D) mutant proteins in pancreatic cancer cells. Through proteomics and metabolomics analysis, it was found that after 48 hours of treatment, the compound showed different levels of effectiveness in reducing the abundance of KRAS protein in different cell populations.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Clinical Neurology
Dominique F. Leitner, Yik Siu, Aryeh Korman, Ziyan Lin, Evgeny Kanshin, Daniel Friedman, Sasha Devore, Beatrix Ueberheide, Aristotelis Tsirigos, Drew R. Jones, Thomas Wisniewski, Orrin Devinsky
Summary: High-fat and low-carbohydrate diets, such as the modified Atkins diet (MAD), can reduce seizure frequency in treatment-resistant epilepsy patients. These diets mimic fasting and induce high levels of ketone bodies, potentially shifting brain energy production and impacting neuronal and astrocyte metabolism.
Article
Engineering, Environmental
Ye Zhu, Yukang Zhang, Yanbo Li, Caixia Guo, Zhuying Fan, Yang Li, Man Yang, Xianqing Zhou, Zhiwei Sun, Ji Wang
Summary: This study investigated the effects of silica nanoparticles (SiNPs) on the metabolic spectrum in hepatocytes, revealing the metabolic mechanisms underlying SiNP-induced hepatotoxicity. Integrative omics analyses proved to be a powerful approach for toxicity evaluations and risk assessments of nanoparticles.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Multidisciplinary Sciences
Lei Li, Lin Huang, Chenyang Huang, Jia Xu, Yukai Huang, Haihua Luo, Xinya Lu, Shuyue He, Gang Yuan, Li Chen, Xue Han, Xusong Cao, Aolin Jiang, Cuiting Liu, Junmin Shi, Hong Yang, Yong Jiang
Summary: This study focused on the molecular dynamics profiles of exosomes in serum during the development of sepsis. High-performance liquid chromatography-tandem mass spectrometry and RNA-seq were used to detect the dynamic profiles of exosome proteins and RNAs. Integrative multiomics analyses revealed the association of exosome components with various biological processes and molecular pathways. Importantly, exosomes derived from septic serum showed potential therapeutic effects in septic mice.
JOURNAL OF ADVANCED RESEARCH
(2022)
Article
Environmental Sciences
Saurabh Gangola, Pankaj Bhatt, Alagarasan Jagadeesh Kumar, Geeta Bhandari, Samiksha Joshi, Arjita Punetha, Kalpana Bhatt, Eldon R. Rene
Summary: Pesticides have negative effects on the environment and human health, but biological approaches have proven to be effective in removing pesticide contamination. There is a lack of understanding on the factors affecting microbial degradation ability, and the use of advanced tools and omics technology can help fill this knowledge gap.
Review
Plant Sciences
Xiangyu Xu, Cassio Flavio Fonseca de Lima, Lam Dai Vu, Ive De Smet
Summary: Changes in weather patterns, drought risks, and rising global temperature negatively impact crop growth and productivity. Plants are exposed to multiple stresses simultaneously, but most studies focus on individual stress conditions. This mini-review focuses on the combination of drought and heat, summarizing current research results, identifying knowledge gaps, and suggesting potential future focus areas.
FRONTIERS IN PLANT SCIENCE
(2023)
Review
Endocrinology & Metabolism
Giuseppe Grande, Luca De Toni, Andrea Garolla, Domenico Milardi, Alberto Ferlin
Summary: Metabolomics is used to investigate the molecular mechanisms of specific diseases by analyzing low-molecular-weight metabolites in biological samples. This mini-review focuses on metabolomics studies using ultra-high-performance liquid chromatography-high-resolution mass spectrometry (HRMS) to examine metabolic pathways involved in male hypogonadism and testosterone replacement therapy. It reveals that glycolysis, amino acid degradation, and gluconeogenesis are affected in functional hypogonadism, whereas beta-oxidation of fatty acids is not an energy source. After testosterone replacement therapy, only some metabolites are completely restored, and high levels of ketone bodies are produced in functionally hypogonadal patients, possibly leading to symptoms similar to keto flu.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Plant Sciences
Xiajing Xu, Yong Ding, Meihan Liu, Xuanmeng Zhang, Dongmei Wang, Yingni Pan, Shumeng Ren, Xiaoqiu Liu
Summary: Walnut powder has nourishing, antioxidant, and neuroprotective effects, but its effectiveness in treating Alzheimer's disease is unclear. This study aims to investigate the potential mechanism of walnut powder in treating Alzheimer's disease.
JOURNAL OF ETHNOPHARMACOLOGY
(2024)
Article
Biochemistry & Molecular Biology
Xiaochen Lyu, Chunyan Sun, Jin Zhang, Chang Wang, Shuhong Zhao, Chunmei Ma, Sha Li, Hongyu Li, Zhenping Gong, Chao Yan
Summary: The specific mechanisms by which nitrogen affects nodulation and nitrogen fixation in leguminous crops are still unclear. This study investigates the effects of exogenous nitrogen on proteins and metabolites in soybean root nodules. The findings reveal that exogenous nitrogen regulates multiple metabolic pathways, promotes the synthesis of signaling molecules, and inhibits energy supply for nitrogen fixation, leading to reduced root nodule growth and nitrogen fixation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biology
Jiahao Shao, Ting Pan, Jie Wang, Tao Tang, Yanhong Li, Xianbo Jia, Songjia Lai
Summary: Obesity and related diseases are increasing rapidly globally. Many people, especially women, are trying to lose weight. A study on obese rabbits showed significant molecular changes in perirenal adipose tissue due to dieting, with altered proteins and metabolites related to amino acid and lipid metabolism. Inflammation-related molecules may play key roles in fighting inflammation induced by a high-fat diet.
Article
Entomology
Yi Li, Xin Wang, Haonan Dong, Qingyou Xia, Ping Zhao
Summary: A comprehensive transcriptome analysis on silkworms was conducted to investigate the influence of starvation on animal brains. Significant changes were found in pathways related to tissue structure, hormone metabolism, longevity, nucleic acid metabolism, immune response, and disease in the silkworm brain after a period of starvation. Starvation imposes significant stress on animal survival and development, resulting in organ damage within the organism. The brain, as one of the most vital organs in animals, plays a crucial role in coordinating the physiological functions of other organs.
Article
Engineering, Biomedical
Xin Wang, Xiaoqian Xie, Kang Xie, Qingsong Liu, Yi Li, Xiaoyin Tan, Haonan Dong, Xinning Li, Zhaoming Dong, Qingyou Xia, Ping Zhao
Summary: Chitin plays an important role in the spinning duct of silkworm, where it co-locates with cuticle proteins to form a multilayer structure in the cuticular layer. Knocking down the expression of cuticle proteins leads to disruption of the fine structure of the cuticular layer and negative impacts on the mechanical properties of silk.
ACTA BIOMATERIALIA
(2022)
Article
Biochemistry & Molecular Biology
Lixia Qin, Jing Li, Kaiyu Guo, Mengyao Lu, Yan Zhang, Xiaolu Zhang, Yanqiong Zeng, Xin Wang, Qingyou Xia, Ping Zhao, Ai-bing Zhang, Zhaoming Dong
Summary: Animals use minerals and organic components to construct biomaterials. The cocoon of the oriental moth contains mineral crystals, silk fibers, and other organic matter. It is mainly composed of calcium oxalates and Asx/Ser/Gly-rich cocoon proteins. The findings provide important references for understanding the formation mechanism and mechanical properties of the oriental moth cocoon.
INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yi Li, Xin Wang, Xiaoqian Xie, Qingsong Liu, Haonan Dong, Yong Hou, Qingyou Xia, Ping Zhao
Summary: Animal behavior regulation is a complex process influenced by various factors, with the nervous system being a key factor. Pathogens can alter host behavior by affecting the host's nervous system. In this study, the researchers analyzed the transcriptome of silkworm brains infected with the nucleopolyhedrosis virus and found that genes related to behavior regulation changed after infection. The tyrosine hydroxylase gene was identified as a potential candidate gene, and its inhibition successfully blocked the enhanced locomotor behavior caused by the virus.
INSECT MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Tong Zhang, Weiqing Xing, Aoming Wang, Na Zhang, Ling Jia, Sanyuan Ma, Qingyou Xia
Summary: High-quality genome sequencing and assembly uncover the genetic foundation of pest occurrence and provide guidance for pest control measures. This study used high-coverage datasets and new assembly methods to test genome sequencing and assembly, and achieved high-quality genomic information. Choosing the appropriate assembly tool can lead to better and more accurate results, as demonstrated by the evaluation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Xiaoqian Xie, Xin Wang, Qingsong Liu, Yi Li, Zhaoming Dong, Lingyan Wang, Qingyou Xia, Ping Zhao
Summary: This study investigated the transcriptional regulation mechanism of the ASSCP2 gene and identified the -357 to -257 sequence as the key region responsible for its regulation. The study also discovered the ASG-specific transcription factor Sox-2, which binds to the -357 to -257 sequence and regulates the tissue-specific expression of ASSCP2.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Qingsong Liu, Xin Wang, Yifan Zhou, Xiaoyin Tan, Xiaoqian Xie, Yi Li, Haonan Dong, Zhangchen Tang, Ping Zhao, Qingyou Xia
Summary: This study found various metal elements in the silk glands of silkworms, with higher levels in the anterior silk glands. The content of metal elements in the silk glands changed significantly before and after spinning, similar to the content in different cocoon layers, indicating that the anterior silk glands maintain a certain metal ion environment for silk protein transport and conformational transformation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Riyuan Wang, Yuancheng Wang, Jianxin Song, Huanhuan Tan, Chi Tian, Dongchao Zhao, Sheng Xu, Ping Zhao, Qingyou Xia
Summary: In this study, a novel method of screening targeted therapeutic peptides in natural proteins was established, with details provided for library construction, transcription assays, receptor selection, therapeutic peptide screening, and biological activity analysis. This method successfully screened the therapeutic peptides TS263 and TS1000, which have the ability to specifically promote the synthesis of the extracellular matrix. We believe that this method provides a reference for screening other drugs in natural resources, including proteins, peptides, fats, nucleic acids, and small molecules.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Yu-Jun Wang, Qing-Song Liu, Li-Ping Liu, Yi-Chuan Zhang, Shuang Qiu, Wen-Guang Zhang, Jin-Hang Lin, Yu-Ting Qin, Xin Wang, Yue-Ying Wu, Ping Zhao, Qing-You Xia, Ling Ding, Dong-Ying Rong, Hong Wang, Zhao-Ming Dong
Summary: Studies have found that the fibroin heavy chain of caddisworm silk contains phosphorylation for stable secondary structure. Recent studies also identified new silk proteins within caddisworm silk. By using LC-MS/MS, researchers identified a large number of proteins in the silk gland and determined some as secreted silk proteins. This study provides valuable information for understanding the secretion and adhesion of caddisworm silk.
INSECT MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Guanwang Shen, Die Liu, Haoran Xu, Jinxin Wu, Luyu Hou, Chunyan Yang, Qingyou Xia, Ping Lin
Summary: This study demonstrates that accelerating energy metabolism promotes embryonic development and enhances motility in hatched silkworms. It provides a novel perspective on the relationship between energy metabolism and embryonic development in other insects.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Entomology
Yi Li, Xin Wang, Haonan Dong, Qingyou Xia, Ping Zhao
Summary: A comprehensive transcriptome analysis on silkworms was conducted to investigate the influence of starvation on animal brains. Significant changes were found in pathways related to tissue structure, hormone metabolism, longevity, nucleic acid metabolism, immune response, and disease in the silkworm brain after a period of starvation. Starvation imposes significant stress on animal survival and development, resulting in organ damage within the organism. The brain, as one of the most vital organs in animals, plays a crucial role in coordinating the physiological functions of other organs.
Article
Biochemistry & Molecular Biology
Dong Cheng, Zhaoming Dong, Ping Lin, Guanwang Shen, Qingyou Xia
Summary: This study reveals the crucial role of acetylation modification and chromatin accessibility in the transcriptional activation of ecdysone-responsive genes during insect development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)