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JOURNAL ARTICLE
Yue Wang, Dong Wang, Jingxia Du, Yan Wang, Chunxue Shao, Chuwen Cui, Jianwei Xiao, Xinwei Wang
The disruption of the SWL1 gene leads to a significant down regulation of chloroplast and secondary metabolites gene expression in Arabidopsis thaliana. And finally results in a dysfunction of chloroplast and plant growth. Although the development of the chloroplast has been a consistent focus of research, the corresponding regulatory mechanisms remain unidentified. In this study, the CRISPR/Cas9 system was used to mutate the SWL1 gene, resulting in albino cotyledons and variegated true leaf phenotype. Confocal microscopy and western blot of chloroplast protein fractions revealed that SWL1 localized in the chloroplast stroma...
May 5, 2024: Plant Cell Reports
#2
JOURNAL ARTICLE
Hong Hu, Wenhui He, Zhiguang Qu, Xiang Dong, Zhiyong Ren, Mengyuan Qin, Hao Liu, Lu Zheng, Junbin Huang, Xiao-Lin Chen
As a signaling molecule, nitric oxide (NO) regulates the development and stress response in different organisms. The major biological activity of NO is protein S-nitrosylation, whose function in fungi remains largely unclear. Here, it is found in the rice blast fungus Magnaporthe oryzae, de-nitrosylation process is essential for functional appressorium formation during infection. Nitrosative stress caused by excessive accumulation of NO is harmful for fungal infection. While the S-nitrosoglutathione reductase GSNOR-mediated de-nitrosylation removes excess NO toxicity during appressorium formation to promote infection...
May 5, 2024: Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
#3
JOURNAL ARTICLE
Kruti Nataraj, Michael Schonfeld, Adriana Rodriguez, Irina Tikhanovich
BACKGROUND: Alcohol-associated liver disease is a complex disease regulated by genetic and environmental factors such as diet and sex. The combination of high-fat diet and alcohol consumption has synergistic effects on liver disease progression. Female sex hormones are known to protect females from liver disease induced by high-fat diet. In contrast, they promote alcohol-mediated liver injury. We aimed to define the role of female sex hormones on liver disease induced by a combination of high-fat diet and alcohol...
May 1, 2024: Hepatology Communications
#4
JOURNAL ARTICLE
Zhijian Huang, Cuncan Deng, Caiqi Ma, Guirong He, Jian Tao, Lijun Zhang, Xiaoyun Hu, Yanfang Mo, Lumei Qiu, Ningfang Zhang, Chuanghua Luo, Shan Xing, Jinye Xie, Haofan Yin
OBJECTIVES: The absence of non-invasive biomarkers for the early diagnosis of colorectal cancer (CRC) has contributed to poor prognosis. Extracellular vesicles (EVs) have emerged as promising candidates for cancer monitoring using liquid biopsy. However, the complexity of EVs isolation procedures and absence of clear targets for detecting serum-derived EVs have hindered the clinical application of EVs in early CRC diagnosis. METHODS: In the discovery phase, we conducted a comprehensive 4D-DIA proteomic analysis of serum-derived EVs samples from 37 individuals, performing an initial screening of EVs surface proteins...
May 3, 2024: International Journal of Surgery
#5
Tomonori Kaneko, Sally Ezra, Rober Abdo, Courtney Voss, Shanshan Zhong, Xuguang Liu, Owen Hovey, Marat Slessarev, Logan Robert Van Nynatten, Mingliang Ye, Douglas D Fraser, Shawn Shun-Cheng Li
No abstract text is available yet for this article.
May 4, 2024: Clinical Proteomics
#6
JOURNAL ARTICLE
Janet P Raja Xavier, Carmela Rianna, Emily Hellwich, Iliana Nikolou, Aditya Kumar Lankapalli, Sara Y Brucker, Yogesh Singh, Florian Lang, Tilman E Schäffer, Madhuri S Salker
Cell stiffness is regulated by dynamic interaction between ras-related C3 botulinum toxin substrate 1 (Rac1) and p21 protein-activated kinase 1 (PAK1) proteins, besides other biochemical and molecular regulators. In this study, we investigated how the Placental Growth Factor (PlGF) changes endometrial mechanics by modifying the actin cytoskeleton at the maternal interface. We explored the global effects of PlGF in endometrial stromal cells (EnSCs) using the concerted approach of proteomics, atomic force microscopy (AFM), and electrical impedance spectroscopy (EIS)...
May 4, 2024: Communications Biology
#7
JOURNAL ARTICLE
Cecile Jacovetti, Chris Donnelly, Véronique Menoud, Mara Suleiman, Cristina Cosentino, Jonathan Sobel, Kejing Wu, Karim Bouzakri, Piero Marchetti, Claudiane Guay, Bengt Kayser, Romano Regazzi
OBJECTIVE: The contribution of the mitochondrial electron transfer system to insulin secretion involves more than just energy provision. We identified a small RNA fragment (mt-tRF-LeuTAA ) derived from the cleavage of a mitochondrially-encoded tRNA that is conserved between mice and humans. The role of mitochondrially-encoded tRNA-derived fragments remains unknown. This study aimed to characterize the impact of mt-tRF-LeuTAA , on mitochondrial metabolism and pancreatic islet functions...
May 2, 2024: Molecular Metabolism
#8
JOURNAL ARTICLE
Konstantinos Kalogeropoulos, Aleksander Moldt Haack, Elizabeta Madzharova, Antea Di Lorenzo, Rawad Hanna, Erwin M Schoof, Ulrich Auf dem Keller
Positional proteomics methodologies have transformed protease research, and have brought mass spectrometry (MS)-based degradomics studies to the forefront of protease characterization and system-wide interrogation of protease signaling. Considerable advancements in both sensitivity and throughput of liquid chromatography (LC)-MS/MS instrumentation enable the generation of enormous positional proteomics datasets of natural and protein termini and neo-termini of cleaved protease substrates. However, a concomitant progress has not been observed to the same extent in data analysis and post-processing steps, arguably constituting the largest bottleneck in positional proteomics workflows...
May 2, 2024: Molecular & Cellular Proteomics: MCP
#9
JOURNAL ARTICLE
Katri Vaparanta, Johannes A M Merilahti, Veera K Ojala, Klaus Elenius
New tools for cell signaling pathway inference from multi-omics data that are independent of previous knowledge are needed. Here we propose a new de novo method, the de novo multi-omics pathway analysis (DMPA), to model and combine omics data into network modules and pathways. DMPA was validated with published omics data and was found accurate in discovering reported molecular associations in transcriptome, interactome, phosphoproteome, methylome, and metabolomics data and signaling pathways in multi-omics data...
May 2, 2024: Molecular & Cellular Proteomics: MCP
#10
JOURNAL ARTICLE
Zhi Liu, Zhiqiang Han, Lan Xue, Wei Wei, Batudeligen
Daruqi is a Traditional Mongolian medicine with anti-inflammatory, anti-bacterial, and immune-regulatory effects. However, the mechanisms of its activity were unclear. In the present study, we confirmed the anti-inflammation effect of Daruqi on inflammation induced by LPS using animal models. Then, THP-1 cells treated with LPS was used as a positive control to explore the effective component of Daruqi on inflammation. We identified that Oxymatrine was the essential effector of Daruqi. Furthermore, the mechanism of Oxymatrine on inflammation was verified through proteomics analyses and validation assays...
May 2, 2024: Gene
#11
JOURNAL ARTICLE
Dengjing Huang, Xinfang Chen, Fahong Yun, Hua Fang, Chunlei Wang, Weibiao Liao
Cadmium (Cd), as a non-essential and toxic heavy metal in plants, has deleterious effects on plant physiological and biochemical processes. Nitric oxide (NO) is one of the most important signaling molecules for plants to response diverse stresses. Here, we found that Cd-induced programmed cell death (PCD) was accompanied by NO bursts, which exacerbated cell death when NO was removed and vice versa. Proteomic analysis of S-nitrosylated proteins showed that the differential proteins in Cd-induced PCD and in NO-alleviated PCD mainly exist together in carbohydrate metabolism and amino acid metabolism, while some of the differential proteins exist alone in metabolism of cofactors and vitamins and lipid metabolism...
May 2, 2024: Science of the Total Environment
#12
JOURNAL ARTICLE
Isis Botelho Nunes da Silva, Juliano de Moraes Rodrigues, Ramon Cid Gismonti Batista, Vivian Dos Santos Gomes, Clarissa de Souza Chacon, Marcius da Silva Almeida, Talita Stelling de Araujo, Bianca Ortiz da Silva, Terezinha Marta Pereira Pinto Castiñeiras, Orlando da Costa Ferreira, Fabiana Avila Carneiro, Monica Montero-Lomeli
Immunodiagnostic tests for detecting dengue virus infections encounter challenges related to cross-reactivity with other related flaviviruses. Our research focuses on the development of a synthetic multiepitope antigen tailored for dengue immunodiagnostics. Selected dengue epitopes involved structural linearity and dissimilarity from the proteomes of Zika and Yellow fever viruses which served for computationally modeling the three-dimensional protein structure, resulting in the design of two proteins: rDME-C and rDME-BR...
May 1, 2024: Brazilian Journal of Infectious Diseases
#13
JOURNAL ARTICLE
Leenor Alfahel, Thomas Gschwendtberger, Velina Kozareva, Laura Dumas, Rachel Gibbs, Alexander Kertser, Kuti Baruch, Shir Zaccai, Joy Kahn, Nadine Thau-Habermann, Reto Eggenschwiler, Jared Sterneckert, Andreas Hermann, Niveda Sundararaman, Vineet Vaibhav, Jennifer E Van Eyk, Victor F Rafuse, Ernest Fraenkel, Tobias Cantz, Susanne Petri, Adrian Israelson
Mutations in SOD1 cause amyotrophic lateral sclerosis (ALS), a neurodegenerative disease characterized by motor neuron (MN) loss. We previously discovered that macrophage migration inhibitory factor (MIF), whose levels are extremely low in spinal MNs, inhibits mutant SOD1 misfolding and toxicity. In this study, we show that a single peripheral injection of adeno-associated virus (AAV) delivering MIF into adult SOD1G37R mice significantly improves their motor function, delays disease progression, and extends survival...
April 29, 2024: Cell reports medicine
#14
JOURNAL ARTICLE
Ginny Xiaohe Li, Lijun Chen, Yi Hsiao, Rahul Mannan, Yuping Zhang, Jie Luo, Francesca Petralia, Hanbyul Cho, Noshad Hosseini, Felipe da Veiga Leprevost, Anna Calinawan, Yize Li, Shankara Anand, Aniket Dagar, Yifat Geffen, Chandan Kumar-Sinha, Seema Chugh, Anne Le, Sean Ponce, Shenghao Guo, Cissy Zhang, Michael Schnaubelt, Nataly Naser Al Deen, Feng Chen, Wagma Caravan, Andrew Houston, Alex Hopkins, Chelsea J Newton, Xiaoming Wang, Daniel A Polasky, Sarah Haynes, Fengchao Yu, Xiaojun Jing, Siqi Chen, Ana I Robles, Mehdi Mesri, Mathangi Thiagarajan, Eunkyung An, Gad A Getz, W Marston Linehan, Galen Hostetter, Scott D Jewell, Daniel W Chan, Pei Wang, Gilbert S Omenn, Rohit Mehra, Christopher J Ricketts, Li Ding, Arul M Chinnaiyan, Marcin P Cieslik, Saravana M Dhanasekaran, Hui Zhang, Alexey I Nesvizhskii
Non-clear cell renal cell carcinomas (non-ccRCCs) encompass diverse malignant and benign tumors. Refinement of differential diagnosis biomarkers, markers for early prognosis of aggressive disease, and therapeutic targets to complement immunotherapy are current clinical needs. Multi-omics analyses of 48 non-ccRCCs compared with 103 ccRCCs reveal proteogenomic, phosphorylation, glycosylation, and metabolic aberrations in RCC subtypes. RCCs with high genome instability display overexpression of IGF2BP3 and PYCR1...
April 26, 2024: Cell reports medicine
#15
JOURNAL ARTICLE
Venkatesh L Murthy, Jonathan D Mosley, Andrew S Perry, David R Jacobs, Kahraman Tanriverdi, Shilin Zhao, Konrad T Sawicki, Mercedes Carnethon, John T Wilkins, Matthew Nayor, Saumya Das, E Dale Abel, Jane E Freedman, Clary B Clish, Ravi V Shah
While weight gain is associated with a host of chronic illnesses, efforts in obesity have relied on single "snapshots" of body mass index (BMI) to guide genetic and molecular discovery. Here, we study >2,000 young adults with metabolomics and proteomics to identify a metabolic liability to weight gain in early adulthood. Using longitudinal regression and penalized regression, we identify a metabolic signature for weight liability, associated with a 2.6% (2.0%-3.2%, p = 7.5 × 10-19 ) gain in BMI over ≈20 years per SD higher score, after comprehensive adjustment...
April 25, 2024: Cell reports medicine
#16
JOURNAL ARTICLE
Induction of acrosome reaction by 4-Br-A23187 alters the glycoproteomic profile of boar spermatozoa.
David Martín-Hidalgo, Mercedes Izquierdo, Nicolás Garrido, Paloma Bartolomé-García, Beatriz Macías-García, Lauro González-Fernández
Protein glycosylation is a post-translational modification involved in wide range of biological processes. In mammalian spermatozoa this modification has been identified in numerous proteins, and membrane glycoproteins are involved in the fertilization process. The objective of the present study was to identify changes in protein glycosylation after acrosome reaction (AR) induction using the 4-Br-A23187 ionophore. Our results showed that treatment with 10 μM of 4-Br-A23187 for 20 min significantly increased the percentage of live acrosome-reacted spermatozoa compared to the control (69...
April 17, 2024: Theriogenology
#17
JOURNAL ARTICLE
Carole Saintomé, Océane Monfret, Gilles Doisneau, Dominique Guianvarc'h
A variety of proteins interact with DNA and RNA, including polymerases, histones, ribosomes, transcription factors, and repair enzymes. However, the transient non-covalent nature of these interactions poses challenges for analysis. Introducing a covalent bond between proteins and DNA via photochemical activation of a photosensitive functional group introduced onto nucleic acids offers a means to stabilize these often weak interactions without significantly altering the binding interface. Consequently, photoactivatable oligonucleotides are powerful tools for investigating nucleic acid-protein interactions involved in numerous biological and pathological processes...
May 4, 2024: Chembiochem: a European Journal of Chemical Biology
#18
JOURNAL ARTICLE
Yao Fei, Danping Cao, Runyu Dong, Yanna Li, Zhixiong Wang, Peng Gao, Menglin Zhu, Xiaoming Wang, Xueliang Zuo, Juan Cai
BACKGROUND: Cuproptosis, as a unique modality of regulated cell death, requires the involvement of ubiquitin-binding enzyme UBE2D2. However, the prognostic and immunotherapeutic values of UBE2D2 in pan-cancer remain largely unknown. METHODS: Using UCSC Xena, TIMER, Clinical Proteomic Tumor Analysis Consortium (CPTAC), and Human Protein Atlas (HPA) databases, we aimed to explore the differential expression pattern of UBE2D2 across multiple cancer types and to evaluate its association with patient prognosis, clinical features, and genetic variations...
May 4, 2024: Clinical & Translational Oncology
#19
REVIEW
Alba Rodriguez-Muñoz, Hanieh Motahari-Rad, Laura Martin-Chaves, Javier Benitez-Porres, Jorge Rodriguez-Capitan, Andrés Gonzalez-Jimenez, Maria Insenser, Francisco J Tinahones, Mora Murri
PURPOSE OF REVIEW: The present study aims to review the existing literature to identify pathophysiological proteins in obesity by conducting a systematic review of proteomics studies. Proteomics may reveal the mechanisms of obesity development and clarify the links between obesity and related diseases, improving our comprehension of obesity and its clinical implications. RECENT FINDINGS: Most of the molecular events implicated in obesity development remain incomplete...
May 4, 2024: Current Obesity Reports
#20
JOURNAL ARTICLE
Joseph W Galvin, Rachel J Milam, Brendan M Patterson, James V Nepola, Joseph A Buckwalter, Brian R Wolf, Felicity M Say, Katherine E Free, Elizabeth Yohannes
BACKGROUND: The incremental biological changes in the synovial microenvironment of the shoulder in acute and chronic instability that may contribute to joint degeneration are poorly understood. Proteomic analysis of synovial fluid in patients with shoulder instability may improve our understanding of proteins that are shed into shoulder synovial fluid after an injury. HYPOTHESIS: Injury-specific factors such as the direction of instability and the severity of glenoid and humeral bone loss are associated with the proteome of synovial fluid in patients with shoulder instability...
May 4, 2024: American Journal of Sports Medicine
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