Article
Oncology
Ji'an Yang, Qian Yang
Summary: The study identified differentially expressed genes related to neural cell signal transduction through reanalysis of GBM and LGG datasets, and highlighted the significance of core molecules in ionic signaling pathways. The research further validated the significant relationship between these core genes and patient survival, and identified drugs related to cancer and neuropsychiatric diseases through database analysis. Further exploration of these core genes is needed to understand their potential in diagnosis, prognosis, and targeted therapy for neurological tumors and related diseases.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Sophia A. H. Heyde, Jenny Arnling Baath, Peter Westh, Morten H. H. Norholm, Kenneth Jensen
Summary: PET is the most common polyester plastic in the world, but its accumulation in nature is causing global environmental issues. Current recycling processes deteriorate the mechanical properties of PET, necessitating more efficient and bio-sustainable hydrolysis methods. A recently discovered PETase enzyme has shown potential for biodegrading PET, but engineering more efficient PETases is currently progressing slowly.
MICROBIAL CELL FACTORIES
(2021)
Article
Multidisciplinary Sciences
Daiki Kashima, Masahiro Kawahara
Summary: The KIPPIS system successfully detected 6 peptide aptamer-polypeptide interactions, with sensitivity modulated in a helper ligand-dependent manner and correlated with the activation levels of Src downstream of c-kit-mediated signal transduction. KIPPIS clearly discriminates interacting aptamers from non-interacting ones, proving to be a versatile platform for evaluating the binding properties of peptide aptamers.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Multidisciplinary
Hermann Neitz, Niels Benjamin Paul, Florian R. Hage, Christina Lindner, Roman Graebner, Michael Kovermann, Franziska Thomas
Summary: The study presents a combinatorial approach to identify novel functional mini-proteins based on the WW-domain scaffold. The WW domain fragments were reconstituted through coiled coil association, and the binding properties were fully restored. Using this approach, specific binding domains for ATP and phosphorylcholine were identified.
Article
Gastroenterology & Hepatology
Juan Bayo, Esteban J. Fiore, Luciana Maria Dominguez, Maria Jose Cantero, Matias S. Ciarlantini, Mariana Malvicini, Catalina Atorrasagasti, Mariana Gabriela Garcia, Mario Rossi, Claudio Cavasotto, Elisabeth Martinez, Julieta Comin, Guillermo D. Mazzolini
Summary: The study identified RAC1 as a potential therapeutic target for HCC and demonstrated the potent antitumor effect of the RAC1 inhibitor 1D-142 in highly proliferative HCC. The inhibition of RAC1 by 1D-142 resulted in apoptosis and cell cycle arrest in HCC cells, as well as a decrease in tumor growth and metastasis in HCC mouse models. Additionally, 1D-142 showed an anti-fibrotic effect by decreasing hepatic stellate cell activation in vivo.
Article
Biochemistry & Molecular Biology
Ian Sillitoe, Nicola Bordin, Natalie Dawson, Vaishali P. Waman, Paul Ashford, Harry M. Scholes, Camilla S. M. Pang, Laurel Woodridge, Clemens Rauer, Neeladri Sen, Mahnaz Abbasian, Sean Le Cornu, Su Datt Lam, Karel Berka, Ivana Hutarova Varekova, Radka Svobodova, Jon Lees, Christine A. Orengo
Summary: CATH identifies protein domains in structures and classifies them into evolutionary superfamilies, providing structural and functional annotations. The latest release significantly increases coverage of structural and sequence data, with additional derived data such as predicted sequence domains and functionally coherent sequence subsets. The FunFam generation pipeline has been re-engineered to capture more sequences with increased functional purity and information content.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Cell Biology
Jung Sun Park, Dong-Hyun Kim, Hoon-In Choi, Chang Seong Kim, Eun Hui Bae, Seong Kwon Ma, Soo Wan Kim
Summary: This study investigated the effects of uremic toxins on ferroptosis in the kidney, finding that protein-bound uremic toxins can induce ferroptosis and result in cell death.
CELL DEATH & DISEASE
(2023)
Article
Biochemical Research Methods
Yijun Xia, Juan Xie, Jun Zhao, Yin Lou, Dongsheng Cao
Summary: Bioinformatics analysis identified five central genes related to melanoma, with CCNA2 and TRIM32 potentially serving as novel targets for treatment of the disease. These genes are associated with patient survival outcomes.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jone Amuategi, Rocio Alonso, Helena Ostolaza
Summary: Adenylate Cyclase Toxin (ACT) is an important virulence factor secreted by Bordetella pertussis, and its activities depend on its interaction with membrane cholesterol and the stabilization of transmembrane helices. Our study provides insights into the molecular mechanisms underlying the dependence of ACT activities on cholesterol and the modulation of toxicity in pore-forming toxins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Raghuvir Viswanatha, Enzo Mameli, Jonathan Rodiger, Pierre Merckaert, Fabiana Feitosa-Suntheimer, Tonya M. Colpitts, Stephanie E. Mohr, Yanhui Hu, Norbert Perrimon
Summary: The authors have developed a new method for genetic screening in mosquito cell lines using a bioinformatics portal and optimized genetic exchange systems. This approach aids in identifying essential genes and those influencing host-pathogen interactions.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Shilun Yang, Simeng Li, Junlei Chang
Summary: This study used a virtual screening strategy to identify potential inhibitors of A-FABP in an FDA-approved drug library. Four compounds with the highest scores were identified and further evaluated in cellular assays. Cobimetinib was identified as a novel A-FABP inhibitor with potential for the treatment of metabolic diseases and associated vascular complications.
Article
Cardiac & Cardiovascular Systems
Jiali Yao, Jingyan Liang, Hongliang Li
Summary: By bioinformatics analysis, we identified 2 key genes associated with circadian regulation in atherosclerosis (AS), providing new insights into the relationship between circadian rhythm and AS.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2023)
Article
Oncology
Xiaoqin Zhang, Ziyue Wang, Zixin Zeng, Ningning Shen, Bin Wang, Yaping Zhang, Honghong Shen, Wei Lu, Rong Wei, Wenxia Ma, Chen Wang
Summary: This study identified that FGF1 expression was aberrant lost in ccRCC through bioinformatic analysis, which significantly correlated with patients' overall survival. The clinical features and potential biological functions of the gene were explored, indicating its potential role as a drug target in clinical medical use pending further detailed experiments and clinical trials.
CANCER CELL INTERNATIONAL
(2021)
Article
Biochemical Research Methods
Liam M. Longo, Rachel Kolodny, Shawn E. McGlynn
Summary: This study reveals the origin of the beta-trefoil protein lineage and suggests that it arose from a peptide fragment of the ancient IgG-like beta-sandwich lineage through a process called peptide budding. The findings highlight the interconnectedness of the protein universe and the evolutionary mechanisms by which new proteins emerge.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Plant Sciences
Erik Jacobsson, Steve Peigneur, Hakan S. Andersson, Quentin Laborde, Malin Strand, Jan Tytgat, Ulf Goransson
Summary: This study reports the synthesis and activity of a novel family of peptide toxins called cystine-knotted alpha nemertides. These peptides were found to have potential in ion channel activity and could be optimized for improved selectivity.
JOURNAL OF NATURAL PRODUCTS
(2021)
Article
Plant Sciences
Tanya Welgemoed, Rian Piemeef, Lieven Sterck, Yves Van de Peer, Velushka Swart, Kevin Daniel Scheepers, Dave K. Berger
FRONTIERS IN PLANT SCIENCE
(2020)
Article
Multidisciplinary Sciences
Cristina Maria Osuna-Cruz, Gust Bilcke, Emmelien Vancaester, Sam De Decker, Atle M. Bones, Per Winge, Nicole Poulsen, Petra Bulankova, Bram Verhelst, Sien Audoor, Darja Belisova, Aikaterini Pargana, Monia Russo, Frederike Stock, Emilio Cirri, Tore Brembu, Georg Pohnert, Gwenael Piganeau, Maria Immacolata Ferrante, Thomas Mock, Lieven Sterck, Koen Sabbe, Lieven De Veylder, Wim Vyverman, Klaas Vandepoele
NATURE COMMUNICATIONS
(2020)
Article
Genetics & Heredity
Jaakko S. Tyrmi, Jaana Vuosku, Juan J. Acosta, Zhen Li, Lieven Sterck, Maria T. Cervera, Outi Savolainen, Tanja Pyhajarvi
G3-GENES GENOMES GENETICS
(2020)
Correction
Multidisciplinary Sciences
Cristina Maria Osuna-Cruz, Gust Bilcke, Emmelien Vancaester, Sam De Decker, Atle M. Bones, Per Winge, Nicole Poulsen, Petra Bulankova, Bram Verhelst, Sien Audoor, Darja Belisova, Aikaterini Pargana, Monia Russo, Frederike Stock, Emilio Cirri, Tore Brembu, Georg Pohnert, Gwenael Piganeau, Maria Immacolata Ferrante, Thomas Mock, Lieven Sterck, Koen Sabbe, Lieven De Veylder, Wim Vyverman, Klaas Vandepoele
NATURE COMMUNICATIONS
(2020)
Article
Ecology
Nuria de Maria, Maria Angeles Guevara, Pedro Perdiguero, Maria Dolores Velez, Jose Antonio Cabezas, Miriam Lopez-Hinojosa, Zhen Li, Luis Manuel Diaz, Alberto Pizarro, Jose Antonio Mancha, Lieven Sterck, David Sanchez-Gomez, Celia Miguel, Carmen Collada, Maria Carmen Diaz-Sala, Maria Teresa Cervera
ECOLOGY AND EVOLUTION
(2020)
Article
Plant Sciences
Ines Modesto, Lieven Sterck, Vicent Arbona, Aurelio Gomez-Cadenas, Isabel Carrasquinho, Yves Van de Peer, Celia M. Miguel
Summary: Pine wilt disease caused by Bursaphelenchus xylophilus is a severe problem in Pinus pinaster forests, but some trees show heritable resistance. Resistance mechanisms in P. pinaster include enhanced lignification of cell walls and activation of defense pathways involving jasmonic acid and salicylic acid. Understanding these mechanisms is crucial for developing strategies to reduce the impact of the disease.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Zongcheng Lin, Fei Xie, Marina Trivino, Tao Zhao, Frederik Coppens, Lieven Sterck, Maurice Bosch, Vernonica E. Franklin-Tong, Moritz K. Nowack
Summary: In this study, the researchers identified the key role of glycosylphosphatidylinositol-anchored proteins (GPI-APs) in self-incompatibility (SI) in plants. They discovered the HLD1/AtPGAP1 gene as a critical component required for SI response and demonstrated its function as a GPI-inositol deacylase.
Article
Medicine, Legal
Patricia A. Bauman, Andrew C. Doxey, Ivano Eberini, Emir Islamovic, Florence Jungo, Colton Kessenich, John Kough, Mansi Krishan, Luca Palazzolo, Laura Privalle, Chester E. Rodriguez, Karla J. F. Satchell, Andre Silvanovich, Lucilia Pereira Mouries
Summary: The workshop discussed the safety assessment of novel proteins and protein toxins. It brought together experts from academia, government and non-government organizations, and agricultural biotechnology developers. Key outcomes of the workshop included the complexity of defining a protein toxin for food and feed safety, the need for a case-by-case interpretation of bioinformatic results, and the use of existing databases for toxin detection.
REGULATORY TOXICOLOGY AND PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Qing Lu, Anaxi Houbaert, Qian Ma, Jingjing Huang, Lieven Sterck, Cheng Zhang, Rene Benjamins, Frederik Coppens, Frank Van Breusegem, Eugenia Russinova
Summary: In this study, researchers found that a mutation in the AMPD gene reduces the sensitivity of Arabidopsis seedlings to brassinosteroids by modulating BIN2 oligomerization and activity in a hydrogen peroxide-dependent manner. They also discovered an H2O2 homeostasis-mediated regulation loop between AMPD and BIN2, which fine-tunes the BIN2 kinase activity to control plant growth and development.
Article
Biochemistry & Molecular Biology
Jian Chen, Yangjie Hu, Pengchao Hao, Tashi Tsering, Jian Xia, Yuqin Zhang, Ohad Roth, Maria F. Njo, Lieven Sterck, Yun Hu, Yunde Zhao, Danny Geelen, Markus Geisler, Eilon Shani, Tom Beeckman, Steffen Vanneste
Summary: Based on the research, the positioning of the lateral root (LR) is influenced by an internal spacing mechanism controlled by auxin oscillations known as the root clock. Surprisingly, none of the previously identified PIN and ABCB auxin transporters are involved in this LR prepatterning mechanism. However, the novel auxin-transporting ABCBs, ABCB15-22, were found to contribute to shootward auxin transport in the lateral root cap (LRC) and epidermis, thereby explaining the reduced auxin oscillation that correlates with strongly reduced LR densities. These findings suggest that LRC-derived auxin contributes to the amplitude of the root clock.
Article
Cell & Tissue Engineering
Takeshi Watanabe, Satoshi Yasuda, Connie L. Chen, Louise Delsing, Mick D. Fellows, Gabor Foldes, Shinji Kusakawa, Lucilia Pereira Mouries, Yoji Sato
Summary: The study evaluated the sensitivity and reproducibility of the highly efficient culture (HEC) assay for detecting residual undifferentiated human pluripotent stem cells (hPSCs) in cell therapy products. All facilities were able to detect spiked hiPSCs in hiPSC-derived cardiomyocytes, with repeatability being the main factor affecting reproducibility. The results show that the HEC assay is highly sensitive and can be widely used for tumorigenicity evaluation of hPSC-derived cell therapy products.
REGENERATIVE MEDICINE
(2023)
Article
Allergy
J. H. Akkerdaas, A. Cianferoni, E. Islamovic, J. Kough, G. S. Ladics, S. McClain, L. K. Poulsen, A. Silvanovich, L. Pereira Mouries, R. van Ree
Summary: This study evaluates the impact of experimental and endogenous food matrices on the susceptibility of homologous proteins with different degrees of allergenicity to proteases. The results demonstrate that protein-rich food matrices delay pepsin digestion but do not help in understanding the differences in allergenicity between homologous proteins.
FRONTIERS IN ALLERGY
(2022)
Article
Allergy
Ronald van Ree, Dexter Sapiter Ballerda, M. Cecilia Berin, Laurent Beuf, Alexander Chang, Gabriele Gadermaier, Paul A. Guevera, Karin Hoffmann-Sommergruber, Emir Islamovic, Liisa Koski, John Kough, Gregory S. Ladics, Scott McClain, Kyle A. McKillop, Shermaine Mitchell-Ryan, Clare A. Narrod, Lucilia Pereira Mouries, Syril Pettit, Lars K. Poulsen, Andre Silvanovich, Ping Song, Suzanne S. Teuber, Christal Bowman
Summary: The availability of a transparent and consensus-based scientific approach for identifying allergenic proteins is crucial for safety review of genetically-modified foods and public safety. The COMprehensive Protein Allergen REsource (COMPARE) database was developed by an international collaborative scientific group to provide a publicly accessible allergen sequence data resource with bioinformatics analytical tools following FAO/WHO and CODEX Alimentarius Commission guidelines. The novel process involves automated keyword-based sorting algorithm, manual curation of annotated sequence entries, and continuous improvement documented with each version, with additional yearly literature database searches for new allergen sequences and peer-review panel feedback for transparency in decision-making.
FRONTIERS IN ALLERGY
(2021)
Article
Toxicology
Gregory S. Ladics, Kang-Hyun Han, Min S. Jang, Heejin Park, Valerie Marshall, Yueming Dersjant-Li, Vincent J. Sewalt
TOXICOLOGY REPORTS
(2020)
Article
Biotechnology & Applied Microbiology
Lyam Baudry, Nadege Guiglielmoni, Herve Marie-Nelly, Alexandre Cormier, Martial Marbouty, Komlan Avia, Yann Loe Mie, Olivier Godfroy, Lieven Sterck, J. Mark Cock, Christophe Zimmer, Susana M. Coelhe, Romain Koszul