Article
Pharmacology & Pharmacy
Valerie Amann, Ann-Kathrin Kissmann, Markus Kramer, Imke Krebs, Julio A. Perez-Erviti, Anselmo J. Otero-Gonzalez, Fidel Morales-Vicente, Armando Rodriguez, Ludger Standker, Tanja Weil, Frank Rosenau
Summary: Antimicrobial peptides (AMPs) are a potential therapeutic option for infectious diseases due to their broad range of activity against diverse pathogens. However, their unspecific pore formation in biomembranes can cause significant side effects in human cells. AMPs isolated from sea and freshwater molluscs show promising antimicrobial activities, as these organisms primarily rely on innate defense mechanisms to fight pathogens. Pomacea poeyana, a Cuban freshwater snail, is a promising candidate for AMPs isolation, with Pom-1 and Pom-2 peptides showing significant antimicrobial activities.
Review
Biochemistry & Molecular Biology
Gabriela Vieira Silva Zolin, Fauller Henrique da Fonseca, Carolina Reis Zambom, Saulo Santesso Garrido
Summary: Buccal candidiasis, caused by Candida albicans, can lead to systemic infection with resistance to common antifungal drugs. Histatin 5, a natural antimicrobial peptide found in human saliva, shows high antifungal activity against C. albicans. Research aims to explore the promising use of Hst5 metallopeptides in developing effective drugs to overcome antifungal resistance.
Article
Biotechnology & Applied Microbiology
Lan Jiang, Pei Huang, Biao Ren, Zhijun Song, Guoliang Zhu, Wenni He, Jingyu Zhang, Ayokunmi Oyeleye, Huanqin Dai, Lixin Zhang, Xueting Liu
Summary: Marine microbes provide a valuable resource for discovering new bioactive compounds, including polyene macrolides and cyclic peptides. These compounds showed significant activities against various bacteria and fungi, indicating their potential as drug candidates.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Food Science & Technology
Peng-Wei Wei, Chao-Rong Song, Xu Wang, Ming Chen, Yong-Xin Yang, Cong Wang, Zu-Quan Hu, Hong-Mei Liu, Bing Wang
Summary: This study synthesized a housefly larval antimicrobial peptide, Phormicin C-NS, and found that it exhibited anti-C. albicans activity. Transcriptomic analysis revealed the mechanism by which Phormicin C-NS inhibited C. albicans. The peptide was able to inhibit bud-to-hyphal transition and biofilm formation, and reduce C. albicans propagation in pasteurized milk. Therefore, Phormicin C-NS has potential as a new preservative in the milk industry.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Food Science & Technology
Shuai Wang, Yujiao Zhang, Mandlaa, Ziyu Sun, Zhongjun Chen
Summary: This study focused on an antimicrobial peptide (APT) produced by Lactobacillus ALAC-4, isolated from traditional fermented sour porridge in Inner Mongolia. The APT showed significant anti-growth activity against most foodborne microorganisms, especially Candida albicans. The study found that APT damaged the cell walls and decreased the metabolic activity and enzyme activity within Candida albicans.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Robert Zarnowski, Andrea Noll, Marc G. Chevrette, Hiram Sanchez, Ryley Jones, Hanna Anhalt, Jen Fossen, Anna Jaromin, Cameron Currie, Jeniel E. Nett, Aaron Mitchell, David R. Andes
Summary: The fungal pathogen Candida albicans can form biofilms that protect it from drugs and the immune system by releasing extracellular vesicles (EVs) that promote extracellular matrix formation and resistance to antifungal drugs. The study identifies functions for numerous EV cargo proteins in biofilm matrix assembly, drug resistance, fungal cell adhesion, and dissemination. The findings suggest that EVs play a crucial role in coordinating biofilm development in C. albicans.
NATURE COMMUNICATIONS
(2021)
Article
Immunology
Alessandra Fusco, Vittoria Savio, Maria Donniacuo, Brunella Perfetto, Giovanna Donnarumma
Summary: The intestinal mucosa is made up of a single layer of epithelial cells that are highly polarized and connected by tight junctions. Disruption of the mucus layer and tight junctions can increase intestinal permeability, leading to microbial translocation and systemic disorders. Studying the interaction between antimicrobial peptides and microbiota can help us understand how they play a role in host defense against intestinal pathogens.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Food Science & Technology
Pedro Henrique de Oliveira Cardoso, Ana Paula de Araujo Boleti, Patricia Souza E. Silva, Lincoln Takashi Hota Mukoyama, Alexya Sandim Guindo, Luiz Filipe Ramalho Nunes de Moraes, Caio Fernando Ramalho de Oliveira, Maria Ligia Rodrigues Macedo, Cristiano Marcelo Espinola Carvalho, Alinne Pereira de Castro, Ludovico Migliolo
Summary: The importance of neuroinflammation is increasingly recognized in neurological disorders, including both inflammatory diseases like multiple sclerosis and non-inflammatory conditions such as stroke, epilepsy, and cancer. A peptide called Ca-MAP1, inspired by a toxin from C. albicans, has shown promising anti-neuroinflammatory, antibacterial, and cytotoxic activity. In vitro and in silico studies demonstrated its effectiveness at lower concentrations, with low toxicity to normal cells. Ca-MAP1 also exhibited activity against various bacteria and demonstrated anti-neuroinflammatory effects. This peptide holds potential for controlling infections and serving as an alternative therapy for cancer.
Article
Microbiology
Jonggwan Park, Hyeongsun Kim, Hee-Kyoung Kang, Moon-Chang Choi, Yoonkyung Park
Summary: Lycosin-II, an antimicrobial peptide, exhibits antifungal activity against Candida albicans by damaging the fungal membrane and inducing oxidative stress. It also inhibits dual-species biofilm formation of Candida albicans and Staphylococcus aureus.
Article
Biochemistry & Molecular Biology
Yi Gong, Haoyi Li, Fei Wu, Yishuai Li, Shicui Zhang
Summary: Derived from AP-2 complex subunit mu-A, the short peptide AP10W exhibits notable antifungal activities against Candida albicans and Aspergillus fumigatus. It inhibits fungal biofilm formation and reduces pre-established fungal biofilms. AP10W acts through various mechanisms including interaction with fungal cell walls, enhancement of cell wall permeability, membrane depolarization induction, and increase in intracellular ROS generation. It shows low toxicity towards mammalian cells and promotes wound healing in C. albicans-infected skin.
Article
Infectious Diseases
Yasamin Masoudi, Wilma van Rensburg, Bernice Barnard-Jenkins, Marina Rautenbach
Summary: Candida species show high adaptability and increasing drug resistance. Tyrocidines demonstrate synergistic activity with antifungal drugs, but can also exhibit toxicity. Formulating with soluble cellulose can improve stability and activity against Candida spp., with hydroxy-propyl-methyl cellulose showing the most promising results.
Article
Biochemistry & Molecular Biology
Rosa Bellavita, Falanga Annarita, Francesco Merlino, Gabriella D'Auria, Nicola Molfetta, Anella Saviano, Francesco Maione, Umberto Galdiero, Maria Rosaria Catania, Galdiero Stefania, Paolo Grieco, Emanuela Roscetto, Lucia Falcigno, Buommino Elisabetta
Summary: This study investigated the antifungal properties of acylated Temporin L derivatives against Candida albicans, including multidrug-resistant strains. The acylated peptides showed good antifungal activity against both reference and clinical strains, with no cytotoxicity on human keratinocytes. Furthermore, they exhibited a synergistic or additive effect with voriconazole on voriconazole-resistant Candida strains. The mechanism of action was found to involve an initial electrostatic interaction with the fungal membrane, followed by aggregation and insertion into the lipid bilayer, causing membrane perturbation.
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Bianca A. Pauletti, Daniela C. Granato, Carolina M. Carnielli, Guilherme A. Camara, Ana Gabriela C. Normando, Guilherme P. Telles, Adriana F. Paes Leme
Summary: To address the challenge of selecting suitable proteotypic peptides for targeted quantitative proteomics assays, we have developed an open-source program called Typic. Typic is a practical and semiautomated workflow that combines input data with additional data from public repositories to select a list of proteotypic peptides. The program provides relevant information, a colored ranking of peptides, and auxiliary plots to assist users in the selection process. Overall, Typic allows for a more robust and standardized targeted proteomics assay.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Bianca A. Pauletti, Daniela C. Granato, Carolina M. Carnielli, Guilherme A. Camara, Ana Gabriela C. Normando, Guilherme P. Telles, Adriana F. Paes Leme
Summary: In this study, we developed a practical tool called Typic to assist in the selection of a list of proteotypic peptides for targeted quantitation. Typic integrates input data and downloads additional data to generate output files for each protein, which includes relevant information and auxiliary plots for peptide selection.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Xiaohua Li, Qun Hu, Qiong Lin, Jianxiong Luo, Junping Xu, Lifang Chen, Liyu Xu, Xin Lin
Summary: This study confirms the inhibitory effect of Chromogranin A-N12 (CGA-N12) on Candida albicans (C. albicans) and demonstrates significant improvement in histological damage through the microRNA-155/SOCS1 pathway. It provides a novel therapeutic strategy for the treatment and prevention of C. albicans.
Article
Infectious Diseases
Andres Ceballos-Garzon, Lucia Monteoliva, Concha Gil, Carlos Alvarez-Moreno, Nelson E. Vega-Vela, David M. Engelthaler, Jolene Bowers, Patrice Le Pape, Claudia M. Parra-Giraldo
Summary: This study identified the mechanism of caspofungin resistance, evaluated the proteomic response to caspofungin, and found that calmodulin inhibition can restore caspofungin susceptibility, reduce stress response, biofilm formation, and pathogenicity in vivo.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2022)
Article
Oncology
Montserrat Carrascal, Aina Areny-Balaguero, Enrique de-Madaria, Karina Cardenas-Jaen, Guillermo Garcia-Rayado, Robin Rivera, Rosa Maria Martin Mateos, Isabel Pascual-Moreno, Meritxell Gironella, Joaquin Abian, Daniel Closa
Summary: This study found that the inflammatory capacity of exosomes in the early stages of acute pancreatitis strongly correlates with the final severity of the disease. The concentration of different proteins in exosomes also correlates with the clinical classification of pancreatitis. An increase in S100A8 and S100A9 in exosomes of severe pancreatitis suggests that their action is mediated by these proteins on NADPH oxidase, leading to free radical generation and inflammatory responses.
JOURNAL OF PATHOLOGY
(2022)
Article
Microbiology
Norida Velez, Lucia Monteoliva, Zilpa-Adriana Sanchez-Quitian, Ahinara Amador-Garcia, Rocio Garcia-Rodas, Andres Ceballos-Garzon, Concha Gil, Patricia Escandon, Oscar Zaragoza, Claudia-Marcela Parra-Giraldo
Summary: This study found that the combination of iron and copper can enhance the pathogenicity of Cryptococcus neoformans and increase the abundance of proteins related to virulence factors. This suggests that the uptake of metals may affect the pathogenicity of fungi.
Article
Microbiology
Raquel Martinez-Lopez, Maria Luisa Hernaez, Esther Redondo, Guillermo Calvo, Sonja Radau, Mercedes Pardo, Concha Gil, Lucia Monteoliva
Summary: This first analysis of HEVs of C. albicans has revealed distinct differences between them and the YEVs of C. albicans, indicating their importance and potential use in identifying new diagnostic markers and treatment targets for C. albicans infections. The data suggest different mechanisms of YEVs and HEVs biogenesis, as well as different roles in cell biology and host interaction. YEVs play a significant role in cell wall maintenance, while HEVs are more closely associated with virulence, exerting greater effects on human immune cells. Notably, an active 20S proteasome complex is exclusively secreted by HEVs. Further investigation into the functions of proteins exclusively found in HEVs could open up new research avenues in combating C. albicans.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Claudia Saralegui, Carmen Garcia-Duran, Eduardo Romeu, Maria Luisa Hernaez-Sanchez, Ainhize Maruri, Natalia Baston-Paz, Adelaida Lamas, Saioa Vicente, Estela Perez-Ruiz, Isabel Delgado, Carmen Luna-Paredes, Juan de Dios Caballero, Javier Zamora, Lucia Monteoliva, Concepcion Gil, Rosa del Campo
Summary: In recent years, various techniques have been used to study microbial ecosystems, with 16S rRNA gene sequencing being the most common method. Metaproteomics can identify the interaction between microorganisms and human cells, but the available databases are limited and imprecise. This study compares the differences between 16S rRNA amplicon sequencing and metaproteomics in identifying microorganisms and analyzing alpha diversity. Additionally, the study explores the establishment of intestinal ecosystems in newborns with cystic fibrosis, characterized by host inflammation and enrichment of Ruminococcus gnavus.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemical Research Methods
Eric W. Deutsch, Juan Antonio Vizcaino, Andrew R. Jones, Pierre-Alain Binz, Henry Lam, Joshua Klein, Wout Bittremieux, Yasset Perez-Riverol, David L. Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D. Mak, Shin Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy Carver, Benjamin Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C. E. Tosatto, Sandra E. Orchard
Summary: The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been developing guidelines and standards for the proteomics community for 20 years. The organization describes its operation, the current state of existing standards, and the proposals currently being developed. They emphasize the importance of community participation and collaboration with other organizations to promote data sharing and accelerate progress in proteomics.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Tobias G. Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Benjamin A. Neely, Magnus Palmblad, Yasset Perez-Riverol, Tobias Schmidt, Juan Antonio Vizcaino, Eric W. Deutsch
Summary: Data set acquisition and curation are challenging in machine learning, particularly for proteomics-based LC-MS data sets due to data reduction. ProteomicsML is introduced as an online resource for accessing proteomics-based data sets and tutorials. It simplifies data access and provides tutorials for interacting with advanced algorithms. ProteomicsML enables comparison of machine learning algorithms and offers introductory material for newcomers in the field. The platform is freely available at https://www.proteomicsml.org/, and contributions are welcome at https://github.com/ProteomicsML/ProteomicsML.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Eric W. Deutsch, Luis Mendoza, David D. Shteynberg, Michael R. Hoopmann, Zhi Sun, Jimmy K. Eng, Robert L. Moritz
Summary: The Trans-Proteomic Pipeline (TPP) mass spectrometry data analysis suite has undergone continuous development and refinement since the publication of its first tools, PeptideProphet and ProteinProphet, 20 years ago. The latest release offers a wide range of tools for spectrum processing, spectrum searching, search validation, abundance computation, protein inference, and more. These tools incorporate machine-learning modeling to maximize information extraction and establish robust statistical models for accurate information derivation. This article presents an overview of the latest TPP tools, their deployment on different platforms, tutorials for their usage, and synergistic projects leveraging TPP. The article concludes with outlined plans for future TPP development.
JOURNAL OF PROTEOME RESEARCH
(2023)
Editorial Material
Immunology
Priya Uppuluri, Concha Gil, Jose Luis Lopez-Ribot
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Immunology
Marianne Burbage, Ares Rocarn-Arjo, Blandine Baudon, Yago A. Arribas, Antonela Merlotti, Derek C. Rookhuizen, Sandrine Heurtebise-Chretien, Mengliang Ye, Alexandre Houy, Nina Burgdorf, Guadalupe Suarez, Marine Gros, Benjamin Sadacca, Montserrat Carrascal, Andrea Garmilla, Mylene Bohec, Sylvain Baulande, Berangere Lombard, Damarys Loew, Joshua J. Waterfall, Marc-Henri Stern, Christel Goudot, Sebastian Amigorena
Summary: The noncanonical splice junctions between exons and transposable elements (TEs) have been identified as a source of tumor-specific antigens, and immunization with peptides derived from these junctions can delay tumor growth in mice. Inactivation of TE-silencing genes can result in overexpression of immunogenic junctions.
SCIENCE IMMUNOLOGY
(2023)
Article
Immunology
Antonela Merlotti, Benjamin Sadacca, Yago A. Arribas, Mercia Ngoma, Marianne Burbage, Christel Goudot, Alexandre Houy, Ares Rocafiln-Arjo, Ana Lalanne, Agathe Seguin-Givelet, Marine Lefevre, Sandrine Heurtebise-Chretien, Blandine Baudon, Giacomo Oliveira, Damarys Loew, Montserrat Carrascal, Catherine J. Wu, Olivier Lantz, Marc-Henri Stern, Nicolas Girard, Joshua J. Waterfallz, Sebastian Amigorena
Summary: Noncanonical mRNA splicing events can encode recurrent and immunogenic tumor-specific antigens in NSCLC patients.
SCIENCE IMMUNOLOGY
(2023)
Article
Biochemical Research Methods
Benjamin A. Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W. Deutsch, Siegfried Gessulat, Lukas Kaell, Pawel Palczynski, Samuel H. Payne, Tobias Greisager Rehfeldt, Tobias Schmidt, Veit Schwaemmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Summary: In recent years, machine learning has made significant progress in modeling mass spectrometry data for proteomics analysis. A workshop was conducted to evaluate and explore machine learning applications in multidimensional mass spectrometry-based proteomics analysis. The workshop helped identify knowledge gaps, define needs, and discuss the possibilities, challenges, and future opportunities. The summary of the discussions conveys excitement about the potential of machine learning in proteomics and aims to inspire future research.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Klaas J. van Wijk, Tami Leppert, Zhi Sun, Eric W. Deutsch
Summary: A recent paper in Science Advances suggests that intrachloroplast proteins in Arabidopsis can be polyubiquitinated and transferred to the cytosol for degradation, challenging the existing belief that chloroplast organelles lack polyubiquitination mechanisms. However, a reanalysis of the raw mass spectrometry data revealed discrepancies and issues with the results, including extensive artifactual modifications caused by the use of alkylating agent iodoacetamide. As a result, the conclusions regarding intra-chloroplast polyubiquitination cannot be supported by these data. Recommendations for future research are provided to avoid similar pitfalls.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Engineering, Environmental
Montserrat Carrascal, Ester Sanchez-Jimenez, Jie Fang, Carlos Perez-Lopez, Antoni Ginebreda, Damia Barcelo, Joaquin Abian
Summary: A large-scale proteomics approach was used to investigate the protein composition of wastewater from 10 different municipalities in Catalonia. The study revealed that excreta from humans and residues from livestock were the main sources of proteins in wastewater. These findings provide new insights into wastewater proteomics and propose specific bioindicators for wastewater-based environmental monitoring.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Plant Sciences
Klaas J. van Wijk, Stephane Bentolila, Tami Leppert, Qi Sun, Zhi Sun, Luis Mendoza, Margaret Li, Eric W. Deutsch
Summary: This study investigates the impact of RNA editing on the protein accumulation of organelle-encoded proteins in Arabidopsis. It identifies the nonredundant set of protein identifiers and predicted editing sites, and determines the accumulation of edited and unedited proteoforms at the protein level. The results show that major RNA editing sites are required for stable protein accumulation.
Article
Biochemical Research Methods
Tanushree Halder, Elke Stroeher, Hui Liu, Yinglong Chen, Guijun Yan, Kadambot H. M. Siddique
Summary: Improving the root system of wheat is crucial for enhancing grain yield and climate resilience. This study identified proteins associated with root length and root mass in wheat using label-free quantitative proteomics. The findings revealed potential biomarkers that could be used for improving the root system of wheat.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Yinhua Pan, Quanqing Zou, Wu Yin, Zhen Huang, Yingzhu Zhao, Zongming Mo, Lihui Li, Jianrong Yang
Summary: A prognostic model of BC based on LNM-related genes was established in this study, providing guidance for prognosis evaluation and precise treatment of BC. The genes related to lymph node metastasis in BC are largely unknown and need further exploration. Searching for potential lymph node metastasis-related genes of BC will provide meaningful biomarkers for BC treatment. Our model, based on TCGA-BRCA data, effectively predicted patient outcomes and classified BC patients. The identified feature genes might have a predictive function in immunotherapy. The results of this study provide a new reference for the prognosis and treatment of BC patients with lymph node metastasis.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Qiushi Liang, Joon M. Pijnenburg, Erikjan Rijkers, Arnold G. Vulto, Ans T. van der Ploeg, Niek P. van Til, Eva C. Vlaar, Jeroen A. A. Demmers, W. W. M. Pim Pijnappel
Summary: Pompe disease is a lysosomal storage disorder characterized by glycogen accumulation in skeletal muscle, leading to profound pathology. This study showed that lentiviral gene therapy with LV-IGF2.GAAco can nearly completely correct disease-associated proteomic changes, supporting its future clinical development as a new treatment option for Pompe disease.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Chuang Liu, Wenjing Zhang, Qianli Dong, Haipeng Liu
Summary: This study fills the knowledge gap about the matrix proteins involved in the formation of mineralized exoskeletons in decapod crustaceans. By comparing with well-studied molluscan biomineralization proteins, it is proposed that decapod crustaceans evolved novel proteins while sharing some proteins with molluscs. This study provides insights into the evolution and adaptation of crustaceans and molluscs in forming their exoskeletons.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Rania D. Baka, Josipa Kules, Angelo Beletic, Vladimir Farkas, Dina Resetar Maslov, Blanka Beer Ljubic, Ivana Rubic, Vladimir Mrljak, Mark McLaughlin, David Eckersall, Zoe Polizopoulou
Summary: This study analyzed serum samples from dogs with epilepsy and identified potential markers of epilepsy, proteins involved in nerve tissue regeneration, and proteins altered by antiepileptic medication. The findings provide insight into the pathogenesis of epilepsy and the effects of medication on extracellular matrix proteins.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Viviane M. Codognoto, Fabiana F. de Souza, Thais R. Cataldi, Carlos A. Labate, Laiza S. de Camargo, Pedro H. Esteves Trindade, Roberto R. da Rosa Filho, Diego J. B. de Oliveira, Eunice Oba
Summary: This study aimed to compare urine proteomics from non- and pregnant buffaloes to identify potential biomarkers of early pregnancy. A total of 798 proteins were reported in the urine considering all groups, and the differential proteins play essential roles during pregnancy.
JOURNAL OF PROTEOMICS
(2024)