Article
Microbiology
Christoph H. R. Senges, Jennifer J. Stepanek, Michaela Wenzel, Nadja Raatschen, Uemran Ay, Yvonne Maertens, Pascal Prochnow, Melissa Vazquez Hernandez, Abdulkadir Yayci, Britta Schubert, Niklas B. M. Janzing, Helen L. Warmuth, Martin Kozik, Jens Bongard, John N. Alumasa, Bauke Albada, Maya Penkova, Tadeja Lukezic, Nohemy A. Sorto, Nicole Lorenz, Reece G. Miller, Bingyao Zhu, Martin Benda, Joerg Stuelke, Sina Schaekermann, Lars Leichert, Kathi Scheinpflug, Heike Broetz-Oesterhelt, Christian Hertweck, Jared T. Shaw, Hrvoje Petkovic, Jean M. Brunel, Kenneth C. Keiler, Nils Metzler-Nolte, Julia E. Bandow
Summary: This study introduces a proteomic approach for rapid classification of new antibiotics, aiming to accelerate antibiotic research. Comparison of proteomic responses allows quick identification of antibiotics with dual mechanisms, and helps generate hypotheses on mechanisms of action. Proteomic profiling also reveals the impact of antibiotics on bacterial physiology.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Review
Cell Biology
Paul Dowling, Dieter Swandulla, Kay Ohlendieck
Summary: This review discusses the main bioanalytical methods used in the proteomic characterization of skeletal muscle tissues and the impact of skeletal muscle proteomics on whole-body physiology. Mass spectrometric studies have greatly improved our understanding of protein diversity and muscle tissue, which can be integrated with other omics-type methods to establish a systems biology view of skeletal muscle function.
Review
Cell Biology
Rachel A. Kline, Lena Loesslein, Dominic Kurian, Judit Aguilar Marti, Samantha L. Eaton, Felipe A. Court, Thomas H. Gillingwater, Thomas M. Wishart
Summary: Recent advances in proteomic technologies have enabled unprecedented assessment of molecular composition in various sample types. However, careful consideration is required when applying these technologies, including methodological selection and analysis workflow. The effectiveness of most proteomics screens is hindered by inadequate analyses, rather than technical limitations. Furthermore, studying progressive neurodegenerative conditions presents inherent difficulties that should be addressed.
Article
Respiratory System
Shahram Parvin, Masoud Arabfard, Ali Ghazvini, Mostafa Ghanei, Ali Najafi
Summary: This study compared the serum proteome of chronic gas-exposed patients and healthy controls, revealing significant differences in protein expression associated with inflammatory and cell adhesion signaling pathways. The findings suggest impaired repair cycles of cell degeneration and regeneration in the injured organs of exposed individuals. The study highlights the role of systems biology in enhancing our understanding of pathophysiological mechanisms and identifying potential disease biomarkers.
BMC PULMONARY MEDICINE
(2022)
Article
Dentistry, Oral Surgery & Medicine
Marcela R. Carrilho, Polliana M. C. Scaffa, Aline Dionizio, Talita M. O. Ventura, Marilia A. R. Buzalaf, Cristina M. P. Vidal
Summary: The study aims to analyze the differential proteins in dentin and assess the effects of tissue health state and protein extraction protocol. The findings suggest that the composition and abundance of soluble proteins in dentin depend on the tissue's physiopathological state and the protocol used for protein extraction.
JOURNAL OF DENTISTRY
(2023)
Article
Biochemical Research Methods
Mohammad Arefian, Thottethodi Subrahmanya Keshava Prasad
Summary: This study characterized the early effects of salt stress on the proteome and metabolome of rice tissues. It identified numerous signaling pathways that were rapidly induced or partially induced by salt stress. Through a combined analysis, it revealed the most sensitive components of signaling pathways causing salt-susceptibility in rice and suggested potential targets for crop improvement.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Mohammad Arefian, Thottethodi Subrahmanya Keshava Prasad
Summary: Rice, a staple food crop worldwide, is estimated to have its global production reduced by 50% due to salinity stress. However, limited knowledge exists regarding the initial molecular signaling and proteins associated with sensing salinity in crop plants. In this study, we characterized the early effects of salt on the proteome and metabolome of rice tissues and identified numerous signaling pathways induced by salinity. By combining omics data and physiological changes, we identified the most susceptible proteins and metabolites in each pathway, providing potential targets for improving rice's sensitivity to salinity.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Food Science & Technology
Kristen Clermont, Charles J. J. Graham, Steven W. W. Lloyd, Casey C. C. Grimm, Jennifer J. J. Randall, Christopher P. P. Mattison
Summary: Proteomic analyses were used to study the protein accumulation during pecan kernel development. Proteins were analyzed through gel-free and label-free mass spectrometry and 2-D gel electrophoresis. Specific proteins related to pecan allergens, histones, and different stages of development were identified. These findings provide a foundation for future research on identifying proteins associated with desirable traits in pecans.
Review
Neurosciences
Paola Rampelotto Ziani, Jacson Gabriel Feiten, Jeferson Ferraz Goularte, Rafael Colombo, Barbara Antqueviezc, Luiza Paul Gea, Adriane Ribeiro Rosa
Summary: This study used a proteomic approach to investigate bipolar disorder and identified several biological processes and metabolic pathways associated with the disease. The findings have important implications for improving the diagnosis, prognosis, and pharmacological strategies of bipolar disorder.
CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE
(2022)
Article
Food Science & Technology
Shimo Kang, Chunlei Shi, Jiang Chang, Fanhua Kong, Mohan Li, Boyuan Guan, Zhenghan Zhang, Xinyang Shi, Huiwen Zhao, Yanqi Peng, Yan Zheng, Xiqing Yue
Summary: This study conducted a comparative proteomic analysis of P. fluorescens in response to lactobionic acid (LBA), revealing that LBA induced oxidative stress, cell wall stress signals, DNA damage, and various biological responses. These findings provide a theoretical basis for the application of LBA as a novel bacteriostat in the food and pharmaceutical industries.
Article
Plant Sciences
Zheng-Jun Guan, Min Zheng, Zhi-Xi Tang, Wei Wei, C. Neal Stewart Jr
Summary: In this study, differential expression of total protein in leaves of two transgenic oilseed rape lines and their non-transgenic parent plant was analyzed. Fourteen differential protein spots were identified, including eleven upregulated and three downregulated proteins, involved in photosynthesis, transporter function, metabolism, protein synthesis, and cell growth and differentiation. These changes in protein spots may be attributed to the insertion of foreign transgenes in transgenic oilseed rape, but transgenic manipulation does not necessarily cause significant changes in the proteomes of oilseed rape.
Article
Biochemical Research Methods
Khushman Taunk, Debasish Paul, Raju Dabhi, Chanukuppa Venkatesh, Saikiran Jajula, Venkateshwarlu Naik, Anup Tamhankar, Tufan Naiya, Manas Kumar Santra, Srikanth Rapole
Summary: Proteins play a crucial role in modern biology, and the study of proteomics is important for understanding the protein content in biological samples. This study developed a simple single step method for efficient protein extraction, applicable to a wide range of biological samples.
Article
Materials Science, Biomaterials
Andreia Cerqueira, Francisco Romero-Gavilan, Heike Helmholz, Mikel Azkargorta, Felix Elortza, Marilo Gurruchaga, Isabel Goni, Regine Willumeit-Roemer, Julio Suay
Summary: New methodologies, such as proteomics, are necessary to improve in vitro characterization methods and better model natural tissues by analyzing cell-material interactions. In this study, label-free liquid chromatography tandem mass spectrometry proteomic methods were used to characterize the effects of a bioactive sol-gel coating on co-cultured human mesenchymal stem cells (MSCs) and CD14(+) monocytes. The results showed that the material mainly affected cell adhesion, while both cellular cross-talk and the material impacted inflammation.
ACS BIOMATERIALS SCIENCE & ENGINEERING
(2023)
Article
Biochemical Research Methods
Katherine M. Fomchenko, Elise M. Walsh, Xiaoping Yang, Rohan X. Verma, Brian L. Lin, Tim O. Nieuwenhuis, Arun H. Patil, Karen Fox-Talbot, Matthew N. McCall, David A. Kass, Avi Z. Rosenberg, Marc K. Halushka
Summary: In this study, a visual proteomic approach was used to analyze the protein expression in skeletal muscle myofibers, leading to the identification of a large number of potentially fiber-type-specific novel proteins.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Multidisciplinary Sciences
Elena Dmitrieva, Liudmila Smirnova, Alexander Seregin, Victor Zgoda, Arkadij Semke, Svetlana Ivanova
Summary: This article uses mass spectrometry to analyze the proteins and molecular processes of schizophrenic spectrum disorders. The results show that different types of schizophrenia have distinct protein characteristics, which are closely related to translation, transcription, metabolism, and cell transport processes. These findings contribute to our understanding of the pathogenesis of these disorders.
Article
Geriatrics & Gerontology
Marco Raffaele, Kristina Kovacovicova, Tommaso Biagini, Oriana Lo Re, Jan Frohlich, Sebastiano Giallongo, James D. Nhan, Antonino Giulio Giannone, Daniela Cabibi, Martin Ivanov, Anton B. Tonchev, Martin Mistrik, Matthew Lacey, Petr Dzubak, Sona Gurska, Marian Hajduch, Jiri Bartek, Tommaso Mazza, Vincenzo Micale, Sean P. Curran, Manlio Vinciguerra
Summary: The study identified MCOPB as a NOP ligand with tissue-specific senolytic effects, reducing the senescent cell burden in peripheral tissues but not affecting the central nervous system. Additionally, exposure to MCOPB led to changes in locomotion and lipid storage. Mechanistically, MCOPB treatment activated transcriptional networks involved in immune responses to external stressors, implicating Toll-like receptors (TLRs).
Article
Chemistry, Multidisciplinary
Klaudia Kvakova, Martin Ondra, Jiri Schimer, Milos Petrik, Zbynek Novy, Helena Raabova, Marian Hajduch, Petr Cigler
Summary: This study developed a sensitive approach using fluorescent nanodiamonds for visualizing tumor-draining sentinel lymph nodes. The results showed that the modified nanodiamonds have potential as a tracer for cancer diagnostics and fluorescence-guided surgery.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Review
Biochemistry & Molecular Biology
Natalie Kudlova, Juan Bautista De Sanctis, Marian Hajduch
Summary: Cellular senescence is an irreversible cell cycle arrest associated with age-related pathologies, DNA damage, and tissue repair. However, there is contradictory research concerning its triggering mechanisms and detection. This review summarizes recent findings, presents commonly used senescence models, and briefly describes well-known anti-aging drugs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Pharmacology & Pharmacy
Radu A. Paun, Daciana C. Dumut, Amanda Centorame, Thusanth Thuraisingam, Marian Hajduch, Martin Mistrik, Petr Dzubak, Juan B. De Sanctis, Danuta Radzioch, Maryam Tabrizian
Summary: The study developed a stable and scalable formulation of CuET by encapsulating it in nanoliposomes, addressing the issues of poor solubility in water and low bioavailability. The formulation demonstrated excellent stability and controlled drug release, showing significant anticancer effects on melanoma cells in vivo.
Article
Biochemistry & Molecular Biology
Aneta Vrzalova, Petra Pecinkova, Peter Illes, Sona Gurska, Petr Dzubak, Martin Szotkowski, Marian Hajduch, Sridhar Mani, Zdenek Dvorak
Summary: Aryl hydrocarbon receptor (AHR) plays important roles in intestinal physiology and is activated by microbial metabolites, with synergistic effects observed in combinations of low- or medium-efficacy agonists. High-efficacy agonists may show antagonist effects on AHR activation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Zuleima Blanco, Esteban Fernandez-Moreira, Michael R. Mijares, Carmen Celis, Gricelis Martinez, Juan B. De Sanctis, Sona Gurska, Petr Dzubak, Marian Hajduch, Ali Mijoba, Yael Garcia, Xenon Serrano, Nahum Herrera, Jhonny Correa-Abril, Yonathan Parra, Jorge Angel, Hegira Ramirez, Jaime E. Charris
Summary: This research reports 16 synthetic chalcone derivatives with potential therapeutic activities against parasites and cancer cells.
Article
Chemistry, Medicinal
Joyce E. Gutierrez, Esteban Fernandez-Moreira, Miguel A. Rodriguez, Michael R. Mijares, Juan Bautista De Sanctis, Sona Gurska, Petr Dzubak, Marian Hajduch, Julia Bruno-Colmenarez, Luis Rojas, Denis Deffieux, Laurent Pouysegu, Stephane Quideau, Jaime Charris, Hegira Ramirez
Summary: Some sulfanyl and sulfinyl derivatives exhibited lower cytotoxicity for cancer cell lines compared to sulfonyl N-oxide derivatives. Compound 81 showed pronounced selectivity for human colorectal cancer cells and leukemia cell lines.
Article
Biochemistry & Molecular Biology
Tomas Ozdian, Jan Vodicka, Jiri Dostal, Dusan Holub, Jana Vaclavkova, Michal Jeseta, Barbora Hamernikova, Pavla Kourilova, Ondrej Malchar, Vladimir Dvorak, Pavel Hejtmanek, Katerina Sobkova, Pavel Ventruba, Radovan Pilka, Petr Dzubak, Marian Hajduch
Summary: This study focuses on the proteomic characterization of cervical mucus (CM), examining its potential as a source of non-invasive biomarkers and understanding the molecular physiology of the female genital tract. Proteomic analysis revealed 4370 proteins involved in processes such as neutrophil degranulation, cellular stress response, and hemostasis. The study also identified differences in the proteomic composition of CM during natural ovulatory cycles obtained from intrauterine insemination (IUI) and in vitro fertilization (IVF) cycles.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Virology
Ondrej Bouska, Hana Jaworek, Vladimira Koudelakova, Katerina Kubanova, Petr Dzubak, Rastislav Slavkovsky, Branislav Siska, Petr Pavlis, Jana Vrbkova, Marian Hajduch
Summary: This study investigated the stability of SARS-CoV-2 in a novel medium for gargle-lavage (GL) self-sampling and compared the performance of SARS-CoV-2 detection in paired GL and clinician-obtained nasopharyngeal swab (NPS) samples. The results showed that GL self-sampling offers a suitable alternative for SARS-CoV-2 detection, with similar performance to NPS samples. The study also demonstrated the excellent stability of SARS-CoV-2 in the novel medium for 14 days.
Review
Biochemistry & Molecular Biology
Monika Vidlarova, Alona Rehulkova, Pavel Stejskal, Andrea Prokopova, Hanus Slavik, Marian Hajduch, Josef Srovnal
Summary: Circulating tumor cells (CTCs) are released from primary tumors and have been identified as a negative prognostic factor for survival in many types of cancer. They also provide valuable insights into tumor progression, cell senescence, and cancer dormancy. Various methods with different specificity, utility, costs, and sensitivity have been developed for isolating and characterizing CTCs, with novel techniques being developed to overcome limitations of existing methods. This literature review describes the current and emerging methods for enriching, detecting, isolating, and characterizing CTCs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Obstetrics & Gynecology
J. Vodicka, J. Dostal, D. Holub, R. Pilka, P. Dzubak, M. Hajduch, T. Ozdian
Summary: Cervical mucus is a viscous fluid that acts as a plug for the cervix. It contains products from the endometrial and cervical glands, as well as transudate from the fallopian tubes and proteins from the ovaries, peritoneum and distant tissues.
CESKA GYNEKOLOGIE-CZECH GYNAECOLOGY
(2023)
Article
Oncology
Lubomir Vecera, Petr Prasil, Josef Srovnal, Emil Berta, Monika Vidlarova, Tomas Gabrhelik, Pavla Kourilova, Martin Lovecek, Pavel Skalicky, Jozef Skarda, Zdenek Kala, Pavel Michalek, Marian Hajduch
Summary: Patients with pancreatic cancer who received morphine for postoperative analgesia had longer cancer-specific survival compared to those who received piritramide. Additionally, high expressions of cannabinoid receptor 2 (CB2) and opioid growth factor receptor (OGFR) genes were associated with improved overall survival, while high expression of delta opioid receptor gene shortened survival.
Article
Biology
Martin Ondra, Lukas Lenart, Amanda Centorame, Daciana C. Dumut, Alexander He, Syeda Sadaf Zehra Zaidi, John W. Hanrahan, Juan Bautista De Sanctis, Danuta Radzioch, Marian Hajduch
Summary: This article describes the preparation and validation of a novel in vitro model system using CRISPR/Cas9 genome editing, which can tag the endogenously expressed WT-CFTR and detect CFTR in the plasma membrane of live cells. By inserting the HiBiT tag in WT-CFTR, a reporter luciferase with bright luminescence can be generated. Nine homozygous clones with the HiBiT knock-in were identified from the screened clones, and two clones were genetically and functionally validated. This work lays the foundation for developing unique cellular CF models by CRISPR-mediated insertion of CF-causing mutations.
LIFE SCIENCE ALLIANCE
(2023)
Review
Biochemistry & Molecular Biology
Jenny Valentina Garmendia, Alexis Hipolito Garcia, Claudia Valentina De Sanctis, Marian Hajduch, Juan Bautista De Sanctis
Summary: SARS-CoV-2 causes COVID-19, a complex respiratory illness that can also harm multiple organs and lead to long-lasting effects. While most individuals have mild symptoms or are asymptomatic, around 20% develop severe respiratory illness and organ failure. Compromised immune response, caused by immunodeficiency and autoimmunity, allows the virus to replicate and escape. Autoantibodies against various proteins have been reported, with their type and level depending on age and gender. Screening for immunodeficiency and autoimmunity is important in identifying risk factors for severe or prolonged COVID-19.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2023)
Article
Health Care Sciences & Services
Denis Horgan, Marian Hajduch, Marilena Vrana, Jeannette Soderberg, Nigel Hughes, Muhammad Imran Omar, Jonathan A. Lal, Marta Kozaric, Fidelia Cascini, Verena Thaler, Oriol Sola-Morales, Mario Romao, Frederic Destrebecq, Edith Sky Gross
Summary: The European Commission has proposed a 'European health data space' to harness the benefits of the growing health data in Europe. However, there are clarifications needed to ensure success, including freeing data, gaining trust from patients and citizens, and promoting wide engagement.
Article
Toxicology
Kathryn Page, Walter Westerink, Kristie Sullivan, Thomas McDonald, Clive Roper
Summary: This study developed a new method to assess the skin irritation of antimicrobial cleaning products. The method utilized a more human-like model and demonstrated its effectiveness through comparison with in vivo rabbit skin irritation data.
TOXICOLOGY IN VITRO
(2024)
Article
Toxicology
Arupam Patra, Thirukumaran Kandasamy, Siddhartha Sankar Ghosh, Gurvinder Kaur Saini
Summary: This study successfully produced recombinant anisoplin and demonstrated its significant anti-cancer effect and ability to induce apoptosis in breast cancer cells. The activation of related signaling pathways may be the key to cell death.
TOXICOLOGY IN VITRO
(2024)
Article
Toxicology
Thomas Haller, Alexander Jesacher, Alberto Hidalgo, Christina Schmidt
Summary: This study used live cell imaging to observe the accumulation of amiodarone in primary rat alveolar type II cells, and found that it specifically accumulates in lamellar bodies. The uptake is rapid, while storage is persistent. The main mechanisms for intracellular bioaccumulation of amiodarone are proposed to be passive diffusion, ion-trapping, and lipophilic interactions.
TOXICOLOGY IN VITRO
(2024)
Article
Toxicology
Filiz Bakar-Ates, Erva Ozkan
Summary: This study investigated the ferroptotic effect of CuB in breast cancer cells and evaluated its combination with erastin, a ferroptosis inducer. The results showed that the combination treatment significantly activated the ferroptotic pathways and altered the expression of iron-related proteins in breast cancer cells.
TOXICOLOGY IN VITRO
(2024)
Article
Toxicology
Rachel Z. Bennie, Ian C. Shaw
Summary: Estrogen mimics are synthetic and naturally occurring compounds that can interact with estrogen receptors in animals. In vitro transactivation reporter gene assay and in silico molecular modelling can be used to predict the mimicry of these compounds, reducing reliance on animal studies.
TOXICOLOGY IN VITRO
(2024)
Article
Toxicology
Sevda Isik, Semra Cicek
Summary: This study found that high doses of riboflavin can cause cytotoxicity in rainbow trout gonad cells and affect the transcriptional expressions of antioxidant enzymes and growth and reproductive genes, potentially leading to DNA damage and cell death.
TOXICOLOGY IN VITRO
(2024)
Article
Toxicology
Ying Wang, Jie Wu, Mengqi Wan, Dou Yang, Fasheng Liu, Kehao Li, Manxin Hu, Yuanyuan Tang, Huiqiang Lu, Shouhua Zhang, Yuanzhen Xiong
Summary: m-Cresol is commonly used as an intermediate for pesticides and other industrial applications. This study investigated the hepatotoxicity of m-cresol using zebrafish larvae and explored its molecular mechanisms. The results suggest that m-cresol may induce liver damage in zebrafish larvae through oxidative stress and cell apoptosis pathways.
TOXICOLOGY IN VITRO
(2024)
Article
Toxicology
Vincent J. Manna, Shannon Dwyer, Vanessa Pizutelli, Salvatore J. Caradonna
Summary: The widespread use of electronic cigarettes and the emergence of a new illness have raised concerns about the effects of e-cigarette vapor on respiratory tissues. Researchers have developed a simple device to mimic the response of human airway tissue after long-term exposure to e-cigarette vapor, and have identified differences in the effects of different vapor compositions on airway tissue.
TOXICOLOGY IN VITRO
(2024)