Article
Oncology
Magdalena Surman, Urszula Jankowska, Magdalena Wilczak, Malgorzata Przybylo
Summary: This study used shotgun nanoLC-MS/MS to obtain protein profiles of melanoma cells and exosomes. The results provide a deeper understanding of the role of exosomes in melanoma progression and suggest potential biomarkers for circulating melanoma.
Article
Biotechnology & Applied Microbiology
Xue Yao, Baixue Liao, Feng Chen, Lueye Liu, Kaiwen Wu, Yaying Hao, Yanping Li, Yuebin Wang, Ruiling Fan, Jun Yin, Lei Liu, Yuanbiao Guo
Summary: By comparing three different methods for isolating extracellular vesicles from pleural effusion (lung cancer patients), it was found that the combination of ultracentrifugation and size exclusion chromatography (UC-SEC) yielded the highest purity of vesicles. CD11C, HLA DPA1, and HLA DRB1 were identified as potential protein markers for pleural effusion-derived vesicles (pEVs), providing important information for studying diseases complicated with pleural effusion.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Immunology
Haoran Guo, Qi Wang, Tao Li, Jingwen Chen, Chao Zhang, Ying Xu, Qing Chang, Hangyi Li, Weiqiang Sun, Ruidi Han, Chi Wang, Chengbin Wang
Summary: This study discovered that ascending to high altitude can lead to physiological and molecular changes, resulting in some individuals being unable to acclimatize. Predicting acute mountain sickness (AMS) prior to ascent remains a challenge. Proteomic analysis revealed significant differences in inflammatory and immune-related processes between AMS-susceptible and AMS-resistant groups. Potential biomarkers, such as SAP, AAT, LTF, and HSP90-alpha, were identified for the prediction of AMS at low altitudes.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemical Research Methods
Huu-Quang Nguyen, Dabin Lee, Yeoseon Kim, Geul Bang, Kun Cho, Young-Sun Lee, Jong Eun Yeon, David M. Lubman, Jeongkwon Kim
Summary: This study utilized LC-MS/MS to analyze the protein expression profiles of extracellular vesicles from serum samples of patients with various fatty liver diseases, revealing significant differences in protein expression levels of apolipoproteins, immunoglobulins, and other markers. Through principal component analysis, a clear differentiation between ALD and NAFLD was achieved. The up-regulation of alpha-2-macroglobulin in alcoholic hepatitis and apolipoprotein C3 in NAFLD were identified as significant findings.
JOURNAL OF PROTEOMICS
(2021)
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
Chemistry, Multidisciplinary
Xin Zhao, Kun Wang, Guoping Yang, Xiao Wang, Chenguang Qiu, Jian Huang, Yanglin Long, Xiaoxin Yang, Boyuan Yu, Guodong Jia, Feng Yang
Summary: This study reported a method for selectively separating metallic SWCNTs through density gradient ultracentrifugation, resulting in the successful separation of high-purity POM@m-SWCNTs. The results showed that the separation depended not only on the size of the nanotube/cluster, but also on the conductivity of the SWCNTs.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Food Science & Technology
Jing Pu, Bingye Zhao, Xin Liu, Shugang Li, Beibei Wang, Di Wu, Jinqiu Wang, Fang Geng
Summary: This study comprehensively compared the protein profiles and properties of chicken egg white and its three components. The proteomes of thick and thin egg white are similar, but thick egg white has higher abundance of ovomucin subunits and lysozymes. The properties of thick and thin egg white are significantly different. Additionally, the chalaza component has higher abundance of insoluble proteins and lower abundance of soluble proteins, which explains its insolubility. These findings are important for further research and development of egg white, such as thinning of egg white, understanding changes in egg white properties, and differential application of thick and thin egg white.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Food Science & Technology
Wenjuan Chen, Xiaohui Chen, Yun Qian, Xingyun Wang, Yahui Zhou, Xiangyun Yan, Boshi Yu, Shuwen Yao, Zhangbin Yu, Jingai Zhu, Shuping Han
Summary: The study reveals the complexity of lipid expression profiles in exosomes derived from preterm and term human milk. The top 50 lipids identified in the exosomes regulate intestinal epithelial cell function via the ERK/MAPK pathway, providing novel mechanistic insight on how human milk prevents the development of necrotizing enterocolitis (NEC).
MOLECULAR NUTRITION & FOOD RESEARCH
(2021)
Article
Cell Biology
Juan A. Martinez-Greene, Karina Hernandez-Ortega, Ricardo Quiroz-Baez, Osbaldo Resendis-Antonio, Israel Pichardo-Casas, David A. Sinclair, Bogdan Budnik, Alfredo Hidalgo-Miranda, Eileen Uribe-Querol, Maria del Pilar Ramos-Godinez, Eduardo Martinez-Martinez
Summary: The study aimed to improve the yield and purity of EV preparations through a Pre-SEC isolation workflow, analyzing EV subsets based on markers such as CD9, CD63, and CD81, revealing differences in protein composition and function among EV subtypes.
JOURNAL OF EXTRACELLULAR VESICLES
(2021)
Article
Chemistry, Analytical
Dilip Kumar Singh, Abdul Basit, Allan E. Rettie, Nathan Alade, Kenneth Thummel, Bhagwat Prasad
Summary: Gamma carboxylation is a crucial post-translational modification involved in maintaining biological stability. This study utilizes liquid chromatography-mass spectrometry with an alkaline mobile phase and polarity switching technique to simultaneously identify and quantify gamma-carboxylated proteins. This method provides insights into the active state of VKDPs.
ANALYTICA CHIMICA ACTA
(2023)
Article
Biochemical Research Methods
Vincent R. Richard, Claudia Gaither, Robert Popp, Daria Chaplygina, Alexander Brzhozovskiy, Alexey Kononikhin, Yassene Mohammed, Rene P. Zahedi, Evgeny N. Nikolaev, Christoph H. Borchers
Summary: This study used multiplexed targeted mass spectrometry assays to determine the concentrations of hundreds of substances in the plasma of hospitalized COVID-19 patients. The researchers found clear distinctions between COVID-19 patients and controls, as well as significant differences between survivors and nonsurvivors. Using a machine learning model, they were able to predict patient survival with high accuracy based on the concentrations of a limited number of substances on the day of hospitalization.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Biochemistry & Molecular Biology
Heba Badr, Ron Blutrich, Kaitlin Chan, Jiefei Tong, Paul Taylor, Wen Zhang, Ran Kafri, Hannes L. Rost, Ming-Sound Tsao, Michael F. Moran
Summary: Proteome analysis revealed co-expressed upregulated metabolism proteins highly conserved between primary NSCLC and patient-derived xenograft tumors. The encoded genes of these proteins are associated with the survival of NSCLC patients, suggesting their role in driving NSCLC through metabolic processes.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Analytical
Francis Berthias, Dale A. Cooper-Shepherd, Frederik H. V. Holck, James I. Langridge, Ole N. Jensen
Summary: The combination of cyclic ion mobility spectrometry (cIM) and electron capture dissociation (ECD) allows for the complete separation and sequencing of large isomeric peptides, providing a new method for identifying biologically important proteoforms in complex mixtures.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Runmin Yang, Jingjing Ma, Shu Zhang, Yu Zheng, Lusheng Wang, Daming Zhu
Summary: This study introduces a new storage format called mzMD for MS datasets and presents an algorithm to query this format for summarizing a given data window. Experimental results demonstrate the high speed and stability of mzMD in retrieving high-quality data window summaries.
Article
Biochemistry & Molecular Biology
Petra Palenikova, Michael E. Harbour, Shujing Ding, Ian M. Fearnley, Lindsey Van Haute, Joanna Rorbach, Rick Scavetta, Michal Minczuk, Pedro Rebelo-Guiomar
Summary: The method described utilizes density separation and mass spectrometric quantitation for quantitative analysis of native protein or ribonucleoprotein complexes, with the ComPrAn software package providing tools for data organization, analysis, and visualization. This technology can be applied to study the assembly and dynamic properties of macromolecular complexes.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2021)
Article
Immunology
Yiqing Tong, Xin Ku, Chunrong Wu, Jianjun Liu, Chunhui Yang, Wenzhi Tang, Wei Yan, Jianguo Tang
SCANDINAVIAN JOURNAL OF IMMUNOLOGY
(2019)
Article
Oncology
Xin Ku, Yan Xu, Chunlin Cai, Yili Yang, Long Cui, Wei Yan
ANALYTICAL CELLULAR PATHOLOGY
(2019)
Article
Oncology
Xin Ku, Qiangling Sun, Lei Zhu, Zhitao Gu, Yuchen Han, Ning Xu, Chen Meng, Xiaohua Yang, Wei Yan, Wentao Fang
MOLECULAR ONCOLOGY
(2020)
Article
Biochemical Research Methods
Minghui Chen, Tingxiang Yan, Liyun Ji, Yu Dong, Simone Sidoli, Zuofei Yuan, Chunlin Cai, Jiwei Chen, Yueli Tang, Qian Shen, Qifang Pan, Xueqing Fu, Xin Ku, Lujian Liao, Benjamin A. Garcia, Wei Yan, Kexuan Tang
Article
Oncology
Xin Ku, Chunlin Cai, Yan Xu, Su Chen, Zhenhua Zhou, Jianru Xiao, Wei Yan
TRANSLATIONAL CANCER RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
Zhijue Xu, Xin Ku, Azusa Tomioka, Wenxian Xie, Tao Liang, Xia Zou, Yalu Cui, Takashi Sato, Hiroyuki Kaji, Hisashi Narimatsu, Wei Yan, Yan Zhang
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2020)
Article
Biochemistry & Molecular Biology
Jingjing Shi, Xin Ku, Xia Zou, Jingli Hou, Wei Yan, Yan Zhang
Summary: This study established a comprehensive O-glycopeptide mass spectrometry analysis strategy for APP O-glycopeptide identification, successfully identifying 14 O-glycosites on APP695 expressed in HEK-293 T cells. The research found at least four O-glycans present at specific residues on APP, providing valuable insights into the O-glycosylation patterns of APP.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2021)
Article
Medicine, General & Internal
Xiaowei Ojanen, Runtan Cheng, Timo Tormakangas, Noa Rappaport, Tomasz Wilmanski, Na Wu, Erik Fung, Rozenn Nedelec, Sylvain Sebert, Dimitris Vlachopoulos, Wei Yan, Nathan D. Price, Sulin Cheng, Petri Wiklund
Summary: This study identified childhood metabolic predictors of adult cardiovascular disease risk in females using machine learning and metabolomics data. The identified biomarkers were associated with increased cardio-metabolic risk in early adulthood and this association was confirmed in validation cohorts. Furthermore, a bidirectional causal relationship between metabolic biomarkers and cardio-metabolic risk score from childhood to early adulthood was suggested.
Article
Biology
Ziyun Zhou, Yu Lu, Zhitao Gu, Qiangling Sun, Wentao Fang, Wei Yan, Xin Ku, Zhongjie Liang, Guang Hu
Summary: In this study, the researchers constructed protein-protein interaction networks to investigate the molecular mechanisms of primary and recurrent thymic epithelial tumors (TETs). They found common molecular mechanisms shared by both types of tumors, as well as a specific pathway related to recurrent TETs. They also identified hnRNPA2B1 as a potential therapeutic target for recurrent TETs. Drug repurposing and molecular dynamics simulations suggested that ergotamine could be a potential repurposing drug for targeting hnRNPA2B1 in recurrent TETs. This study demonstrates the value of integrative network analysis in understanding proteotype robustness and its relationship with genotype, and provides leads for further research on cancer therapeutics.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Chemistry, Medicinal
Fei Zhu, Sijie Yang, Fanwang Meng, Yuxiang Zheng, Xin Ku, Cheng Luo, Guang Hu, Zhongjie Liang
Summary: This research presents two deep learning models, cDL-PAU and cDL-FuncPhos, that incorporate sequence, structure, and dynamics-based features to predict post-translational modifications (PTMs). The models achieve satisfactory prediction scores and provide insights into the molecular basis and functional landscape of PTMs.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemistry & Molecular Biology
Soojung Hahn, Gyuri Kim, Sang-Man Jin, Jae Hyeon Kim
Summary: This study utilized three-dimensional intestinal organoids to investigate the effects of metformin on inflammatory bowel disease (IBD) and found that metformin can enhance intestinal barrier function and reduce levels of inflammatory cytokines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
V. V. Sudarev, M. S. Gette, S. V. Bazhenov, O. M. Tilinova, E. V. Zinovev, I. V. Manukhov, A. I. Kuklin, Yu. L. Ryzhykau, A. V. Vlasov
Summary: This study investigated the self-assembly processes of ferritin-based protein complexes and obtained structurally characterized oligomeric states. These results provide new potential and opportunities for the application of ferritin in various fields.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Yalda Sabaghi, Farnaz Pourfarzad, Leila Zolghadr, Azita Bahrami, Tahereh Shojazadeh, Alireza Farasat, Nematollah Gheibi
Summary: p-Coumaric acid (p-CA) is a plant compound with anti-cancer activities. This study designed a nano-liposomal carrier containing p-CA to enhance its effectiveness against melanoma cells. The findings showed that the liposomal form of p-CA had a greater impact on the cells. Kinetic modeling indicated that the best fitting model was zero-order.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
M. D. Nazmul Hasan, Md Mahfuzur Rahman, Al Asmaul Husna, Nobuhiro Nozaki, Osamu Yamato, Naoki Miura
Summary: This study investigated the expression of ncRNAs other than miRNAs in different histologic subtypes of canine mammary gland tumors (MGT). Three aberrantly expressed ncRNAs were identified as potential biomarkers for differentiating MGT subtypes. YRNA and tRFs expression levels were found to be decreased in metastatic compared to primary MGT cell lines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Seine A. Shintani
Summary: In this study, the researchers used signal analysis to study the instantaneous amplitude and phase of sarcomeric oscillations in skeletal muscle. They identified two types of oscillations, sarcomeric oscillations and sarcosynced oscillations, and visualized their behavior during propagating waves. The researchers discovered the presence of sarcomeric defect holes and sarcomeric collision holes, which are important indicators for understanding the oscillation properties of sarcomeres. This finding has important implications for improving our understanding of muscle function and its regulatory mechanisms.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Shuanglin Zhang, Yuzhong Jia, Guolan Ma, Yanyan Yang, Zhenzhen Cao, Antao Luo, Zefu Zhang, Shihan Li, Jie Wen, Hanfeng Liu, Jihua Ma
Summary: Bupleurum is an antiarrhythmic agent that may exert its effects by inhibiting L-type calcium channels.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Tomotaka Ohkubo, Yasuhiko Matsumoto, Hiroaki Sasaki, Kaoru Kinoshita, Yuki Ogasawara, Takashi Sugita
Summary: This study found that Citrobacter koseri inhibits the growth of Staphylococcus epidermidis, disrupting the balance between S. epidermidis and Staphylococcus aureus, and exacerbating inflammation in atopic dermatitis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Toshifumi Asano, Philipp Sasse, Takao Nakata
Summary: A Cre recombination-based fluorescent reporter system was developed to monitor cell-cell fusion. The system successfully detected the formation of multinuclear myotubes and placental syncytiotrophoblast. This tool could facilitate the study of cell-to-cell fusion.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Ke Shi, Yunlong Shan, Xiao Sun, Kuida Chen, Qiong Luo, Qiang Xu
Summary: This study found that low expression of TP53INP2 is associated with poor survival in colorectal cancer (CRC) patients. As the malignancy of CRC progresses, TP53INP2 expression gradually decreases. Knockdown of TP53INP2 promotes CRC cell proliferation and tumor growth. Mechanistically, TP53INP2 deficiency decreases phosphorylation of beta-catenin, leading to increased accumulation and enhanced nuclear translocation and transcriptional activity. Additionally, TP53INP2 sequesters TIM50, inhibiting its activation of beta-catenin. In conclusion, downregulation of TP53INP2 promotes CRC progression by activating beta-catenin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Martina Rossi, Fabio Tomaselli, Alejandro Hochkoeppler
Summary: Oligomeric enzymes are known for their higher catalytic rates compared to monomeric enzymes, but the extent of additivity in their activity is still not well understood. This study used tetrameric rabbit lactate dehydrogenase as a model to examine the kinetics of its catalytic action. Surprisingly, when the concentration of the limiting reactant exceeded that of a single subunit, there was a significant slowdown in the enzyme's conformational rearrangements.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Amin Sahraei, Mohammad Javad Shamsoddini, Fakhrossadat Mohammadi, Leila Hassani
Summary: This study explored the inhibitory effects of gallium curcumin, indium curcumin, and vanadyl curcumin on the amyloid fibrillation of hen egg white lysozyme, as well as the binding interactions of these metal complexes with the enzyme. The results showed that indium curcumin and vanadyl curcumin exhibited higher binding affinities and stronger inhibitory effects on amyloid fibrillation compared to gallium curcumin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Takahiro Sasaki, Yoshiki Kuse, Shinsuke Nakamura, Masamitsu Shimazawa
Summary: PGRN deficiency plays a significant role in cardiac remodeling and arrhythmias post-myocardial infarction (MI), potentially by promoting metabolic abnormalities in macrophages.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Hongwei Zhao, Yiqiang Li, Yibo Zhang, Chi Zhang
Summary: Electrical brain stimulation technology is commonly used to treat brain neurological disorders, but it can cause side effects. This study investigated the impact of electric fields on nerve fibers and revealed the possible origin of side effects. The findings provide guidance for selecting electrical parameters in clinical stimulation therapy.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Julia S. Scott, Lake-Ee Quek, Andrew J. Hoy, Johannes V. Swinnen, Zeyad D. Nassar, Lisa M. Butler
Summary: The fatty acid elongation enzyme ELOVL5 plays a critical role in promoting metastasis in prostate cancer. Knocking down ELOVL5 leads to the accumulation of malonyl-CoA, which inhibits fatty acid oxidation in mitochondria. This study highlights the importance of fatty acid elongation in regulating cell viability and provides a potential target for prostate cancer treatment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Zan Zhou, Wen-jun Jiang, Li Li, Jun-qiang Si
Summary: This study investigates the effect of noise exposure on cognitive function in mice and explores the underlying molecular mechanisms. The findings suggest that noise exposure leads to increased inflammation, increased phosphorylation of Tau protein, and decreased levels of postsynaptic density protein, resulting in cognitive impairment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)