Article
Microbiology
Sheng Chen, Yiming Yan, Liguo Gao, Shuang Gao, Keyu Feng, Hongxin Li, Xinheng Zhang, Weiguo Chen, Feng Chen, Qingmei Xie
Summary: In this study, proteomic analysis revealed that 53 cellular proteins are incorporated into mature ALV-J virions, with potential functions in the viral life cycle and tumorigenesis. These findings provide new insights into the interaction between ALV-J and its host, and shed light on the cellular requirements for ALV-J infection.
VETERINARY MICROBIOLOGY
(2023)
Review
Biochemical Research Methods
Zhanhong Hu, Hongcheng Li, Xiaohui Wang, Kifayat Ullah, Guoqiang Xu
Summary: Protein ubiquitylation plays critical roles in regulating various biological processes in eukaryotic cells with dysregulation leading to the onset of diseases; Identifying ubiquitylation sites is crucial for uncovering key ubiquitylation events associated with diseases and specific signaling pathways, and for understanding the biological functions of specific ubiquitylation events.
JOURNAL OF PROTEOMICS
(2021)
Article
Computer Science, Artificial Intelligence
Zhengyi Du, Xiongtao Pang, Haifeng Qian
Summary: This paper proposes a better blockchain storage scheme named PartitionChain that addresses three problems in system scalability, while maintaining the merits of BFT-Store. The scheme reduces storage costs by using aggregate signatures as proof of encoded data and eliminates the need for a trusted third party. It also significantly lowers computational complexity for retrieving data and reduces transmitted data for recovering each block, allowing for dynamic network adaptation and improved efficiency and scalability compared to BFT-Store.
IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Adriana Ferre, Lucia Santiago, Jose Francisco Sanchez-Herrero, Olga Lopez-Rodrigo, Josvany Sanchez-Curbelo, Lauro Sumoy, Lluis Bassas, Sara Larriba
Summary: Small RNA-seq has revealed the presence of miRNA isoforms or isomiRs, but their validation by RT-qPCR is challenging due to their small size and sequence similarity. This study investigated the discriminatory capacity of three poly(A)-based RT-qPCR strategies for closely-related miRNA isoforms and found significant cross-reactivity between them, compromising the reliable quantification of individual isoforms. However, the RT-qPCR results were consistent with the small RNA-seq findings in the biological context. The study suggests careful miRNA selection and prioritization for RT-qPCR validation to avoid confounding results.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Analytical
Hongxian Zhao, Yongle Chen, Hang Li, Yangjun Zhang, Wanjun Zhang, Weijie Qin
Summary: Profiling proteins is crucial for understanding biological systems, and a new angled-shape tip-based strategy has been developed for rapid sample preparation and sensitive proteomic profiling. The angled-shape tip provides a reactor for the entire proteomic sample processing workflow, eliminating sample transfer-induced protein loss. This approach shows great potential for in-depth proteomic profiling of rare cells (<1000 cells) in both biological research and clinical applications.
ANALYTICAL METHODS
(2023)
Article
Biochemistry & Molecular Biology
Claudia Maria do Nascimento Moreira, Cristina D. Kelemen, Samson O. Obado, Farnaz Zahedifard, Ning Zhang, Fabiola B. Holetz, Laura Gauglitz, Bruno Dallagiovanna, Mark C. Field, Susanne Kramer, Martin Zoltner
Summary: The characterization of protein-protein interactions (PPIs) is important for understanding protein function. Two popular strategies, affinity capture and BioID, are used to identify PPIs in the cellular environment. A comparison of these methods using different trypanosome proteins as baits showed that BioID had fewer candidate interacting proteins with more confined bait protein localization, produced more false positives, and was less efficient in identifying low molecular weight proteins. These differences indicate the importance of using multiple methods to identify PPIs and suggest that BioID and affinity capture are complementary approaches.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Urology & Nephrology
Hye Yun Jeong, Hyun-Ju An, Min Ji Sung, Min Heui Ha, Yu Ho Lee, Dong Ho Yang, Tae Young Yang, Dohyun Han, So-Young Lee
Summary: The prevalence of chronic kidney disease (CKD) is increasing and it is a global health burden. This study investigated the change in physical performance after exercise in dialysis-dependent patients with CKD and analyzed differentially expressed proteins before and after the exercise. The results showed that exercise improved physical performance and the significantly expressed proteins were involved in immune response.
Article
Oncology
Andrea Bileck, Patricia Bortel, Michelle Kriz, Lukas Janker, Endre Kiss, Christopher Gerner, Giorgia Del Favero
Summary: Ovarian cancer cells exhibit unpredictable adaptive potential, which may be influenced by the tumor's genetic ancestry and post-translational protein modifications. This study used advanced proteome analysis and morphometric profiling to investigate the adaptive responses of ovarian carcinoma cells to different environmental conditions. The findings suggest that ovarian cancer cells show distinct adaptive responses to hypoxia and fluid shear stress, involving regulation of multiple signaling pathways and protein expression levels.
FRONTIERS IN ONCOLOGY
(2022)
Article
Computer Science, Hardware & Architecture
Debao Wei, Zhelong Piao, Hua Feng, Liyan Qiao, Cong Hu, Xiyuan Peng
Summary: This article proposes a data storage strategy for NAND flash and demonstrates its significant reduction in bit error rate through experimentation, indicating its high reliability.
IEEE TRANSACTIONS ON COMPUTER-AIDED DESIGN OF INTEGRATED CIRCUITS AND SYSTEMS
(2022)
Article
Immunology
Thirupathi Kasthuri, Sivaraj Barath, Muruganandam Nandhakumar, Shunmugiah Karutha Pandian
Summary: This study demonstrates the anti-virulence efficacy of umbelliferone (UMB) against Pseudomonas aeruginosa. UMB inhibits biofilm formation and downregulates major virulence-associated proteins in the bacteria. It also enhances antibiotic susceptibility and shows biocompatibility with human cells.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Cell Biology
Liming Shen, Aochu Yang, Xinqian Chen, Shifeng Xiao, Xukun Liu, Jing Lin, Yuxi Zhao, Kaoyuan Zhang, Cuihua Li, Junyan Ke, Huajie Zhang, Naseer Ullah Khan
Summary: Alzheimer's disease is the most common age-associated dementia with complex pathological hallmarks, and proteomics analysis revealed vulnerable subcellular components and differential protein expression between AD and WT mice; these findings suggest that early events of AD involve decreased energy metabolism, impaired neurotransmitter synthesis, and changes in cytoskeletal proteins.
CELLULAR AND MOLECULAR NEUROBIOLOGY
(2022)
Article
Green & Sustainable Science & Technology
Di Li, Qianbin Di, Hailin Mu, Zenglin Han, Hongye Wang, Ye Duan
Summary: This study constructs a repeated dynamic game model to investigate the response and stability of output adjustment in the steel industry under carbon trading policy and other mixed reduction policies. The results suggest the importance of considering multiple factors to avoid market imbalance.
Article
Astronomy & Astrophysics
Nina Hernitschek, Keivan G. Stassun
Summary: This paper introduces the LSST survey of the Vera C. Rubin Observatory and addresses the question of optimizing the observing strategy. By evaluating metrics for simulated potential survey designs, the study aims to assess the impact of different observing strategies on the reliable detectability and classification of standard candle variable stars, such as RRL.
ASTROPHYSICAL JOURNAL SUPPLEMENT SERIES
(2022)
Article
Dentistry, Oral Surgery & Medicine
Y. Myoken, T. Kawamoto, Y. Fujita, S. Sakurai, S. Toratani, S. Yanamoto
Summary: The study evaluated the clinical outcomes of patients with stage 3 mandibular MRONJ treated using a submental island flap combined with mylohyoid muscle reconstruction after rim mandibulectomy. Medical records of 12 patients were retrospectively analysed. Primary wound healing was achieved in all patients with normal mouth opening and occlusion during the follow-up period. New bone formation was observed in four patients. The overall success rate was 91.7%.
INTERNATIONAL JOURNAL OF ORAL AND MAXILLOFACIAL SURGERY
(2023)
Article
Biochemical Research Methods
Tanja Grossmann, Barbara Darnhofer, Ruth Birner-Gruenberger, Andrijana Kirsch, Markus Gugatschka
Summary: The study compared human buccal and vocal fold mucosa at the proteomic level, identifying 1575 proteins with consistent biological processes, cellular components, and molecular functions. The buccal mucosa is a promising alternative for laryngological research due to its easier accessibility and less invasive harvesting process.
PROTEOMICS CLINICAL APPLICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Karina A. Stadler, Walter Becker, Barbara Darnhofer, Ruth Birner-Gruenberger, Klaus Zangger
Summary: Vibrio natriegens, known as the fastest growing organism, has potential as an alternative to E. coli in recombinant protein production. In this study, the engineered V. natriegens strain was used to incorporate the non-canonical amino acid AzF into recombinant proteins, resulting in efficient suppression of stop codons and high protein yields. The newly introduced azido-group was used as a coupling site for NMR-sensitive F-19 tags, enabling the observation of protein-observed F-19-NMR.
Article
Biochemistry & Molecular Biology
Markus Galhuber, Helene Michenthaler, Christoph Heininger, Isabel Reinisch, Christoph Noessing, Jelena Krstic, Nadja Kupper, Elisabeth Moyschewitz, Martina Auer, Ellen Heitzer, Peter Ulz, Ruth Birner-Gruenberger, Laura Liesinger, Georgia Ngawai Lenihan-Geels, Moritz Oster, Emil Spreitzer, Riccardo Zenezini Chiozzi, Tim J. Schulz, Michael Schupp, Tobias Madl, Albert J. R. Heck, Andreas Prokesch
Summary: This study reveals the mechanisms of p53 signaling during starvation using multiple methods. By utilizing BioID and immunoprecipitation techniques, the interaction network of p53 with metabolic enzymes and kinases was identified. Additionally, transcriptomics analysis identified a starvation-specific transcriptome response. These findings shed new light on our understanding of p53 as a nutrient stress sensor.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Juergen Gindlhuber, Maximilian Schinagl, Laura Liesinger, Barbara Darnhofer, Tamara Tomin, Matthias Schittmayer, Ruth Birner-Gruenberger
Summary: Non-alcoholic fatty liver disease has a high prevalence and is related to the types and concentrations of fatty acids. Saturated fatty acids impair cell growth and lipid droplet formation, potentially leading to cell death, while oleic acid and mixtures containing oleic acid do not have adverse effects on cell growth and promote lipid droplet accumulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Endocrinology & Metabolism
Ivan Bradic, Katharina B. Kuentzel, Sophie Honeder, Gernot F. Grabner, Nemanja Vujic, Robert Zimmermann, Ruth Birner-Gruenberger, Dagmar Kratky
Summary: Our findings demonstrate that Lalistat-1 and Lalistat-2 not only inhibit the action of LAL, but also suppress the activity of cytosolic lipid hydrolases responsible for lysosomal function. This has critical implications for understanding the role of LAL in lysosomal function, signaling pathways, and autophagy.
MOLECULAR METABOLISM
(2022)
Article
Biochemistry & Molecular Biology
Christina Wagner, Bernd Innthaler, Martin Lemmerer, Robert Pletzenauer, Ruth Birner-Gruenberger
Summary: Ion-exchange chromatography coupled to light scattering detectors is a fast and simple analytical method for assessing multiple critical quality attributes in gene therapy products. The method allows for comprehensive characterization of the products, serving as an orthogonal approach to other established analytical techniques.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Iva Klobucar, Julia T. Stadler, Lucija Klobucar, Margarete Lechleitner, Matias Trbusic, Gudrun Pregartner, Andrea Berghold, Hansjoerg Habisch, Tobias Madl, Gunther Marsche, Sasa Frank, Vesna Degoricija
Summary: Metabolic syndrome (MS) affects the association between HDL and endothelial function, as well as between EL and HDL. HDL cholesterol efflux capacity and arylesterase activity, as well as EL serum levels, are not correlated with endothelial function in both healthy volunteers (HV) and MS patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Chemistry, Multidisciplinary
Sophie Elisabeth Honeder, Tamara Tomin, Maximilian Schinagl, Raphael Pfleger, Julia Hoehlschen, Barbara Darnhofer, Matthias Schittmayer, Ruth Birner-Gruenberger
Summary: Activity-based proteomic profiling (ABPP) is a versatile protein profiling technique that allows the functional study of enzymes by using small molecule probes that bind covalently to the active site of an enzyme. This technique enables the targeting and labeling of enzymes in their native state, even in cells and tissues. In the context of lipid hydrolase research, ABPP has been used to discover and characterize lipid hydrolases, as well as to identify commonly used probes and inhibitors through competitive ABPP. However, there are caveats and limitations that need to be considered when using this protein profiling technique.
ISRAEL JOURNAL OF CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Julia T. Stadler, Mireille N. M. van Poppel, Christian Wadsack, Michael Holzer, Anja Pammer, David Simmons, David Hill, Gernot Desoye, Gunther Marsche
Summary: Pregravid obesity is a major risk factor for pregnancy complications and cardiovascular events in children. However, the biological mechanisms underlying these adverse outcomes are not well understood. Impairment of HDL function in obese and GDM-complicated pregnancies may have long-term effects on maternal and offspring health.
Review
Pharmacology & Pharmacy
Alankrita Rani, Gunther Marsche
Summary: High-density lipoproteins (HDL) are complex nanoparticles involved in important metabolic and vascular functions. Dysregulation of HDL can lead to inflammatory remodeling and dysfunction. Monocytes and macrophages play a critical role in vascular inflammation. HDL-based nanotherapeutics show potential in treating vascular diseases by targeting these cells.
Article
Biochemistry & Molecular Biology
Julia T. Stadler, Hubert Scharnagl, Christian Wadsack, Gunther Marsche
Summary: Preeclampsia is associated with increased cardiovascular risk for both mother and child. This study investigated the effects of preeclampsia on lipid metabolism, HDL composition, and function in mothers and neonates. Preeclampsia was linked to dyslipidemia in mothers, including high triglycerides and low HDL-cholesterol levels. Mothers with preeclampsia showed shifts in HDL subclasses and increased levels of HDL-associated apolipoprotein C-II. Neonates born to mothers with preeclampsia had increased total cholesterol levels and reduced HDL cholesterol efflux capacity. These findings suggest that preeclampsia affects both maternal and neonatal lipoprotein metabolism.
Article
Biochemistry & Molecular Biology
Nejra Cosic-Mujkanovic, Paulina Valadez-Cosmes, Kathrin Maitz, Anna Lueger, Zala N. Mihalic, Marah C. Runtsch, Melanie Kienzl, Michael J. Davies, Christine Y. Chuang, Akos Heinemann, Rudolf Schicho, Gunther Marsche, Julia Kargl
Summary: This study shows that myeloperoxidase (MPO), a neutrophil-derived enzyme, promotes the proliferation and inhibits the apoptosis of lung cancer cells. It functions by increasing the phosphorylation of AKT and ERK, and can be found inside the cells and in the nucleus. Blocking MPO uptake or inhibiting its enzymatic activity reduces its effects on cancer cell function. Animal experiments demonstrate that tumor-bearing mice treated with the MPO inhibitor 4-ABAH have reduced tumor burden.
Article
Biochemistry & Molecular Biology
Julia T. Stadler, Hansjoerg Habisch, Florian Prueller, Harald Mangge, Thomas Baernthaler, Julia Kargl, Anja Pammer, Michael Holzer, Sabine Meissl, Alankrita Rani, Tobias Madl, Gunther Marsche
Summary: This study compares the lipoprotein and metabolic profiles of COVID-19-infected patients and non-COVID-19 pneumonia patients, and finds significant differences in HDL-related parameters between the two groups. The cholesterol efflux capacity (CEC) shows the strongest negative association with COVID-19 mortality.
Meeting Abstract
Obstetrics & Gynecology
Natascha Berger, Thomas Baernthaler, Juergen Gindlhuber, Nermeen Girgis, Tom Van der Wel, Birgit Hirschmugl, Ruth Birner-Gruenberger, Mario Van der Stelt, Christian Wadsack
REPRODUCTIVE SCIENCES
(2022)