Article
Astronomy & Astrophysics
S. S. A. Silva, M. Lennard, G. Verth, I. Ballai, E. L. Rempel, J. Warnecke, H. Iijima, H. Hotta, S. -H. Park, A. C. Donea, K. Kusano, V. Fedun
Summary: In this study, the authors simulate the emergence of solar active regions and analyze the dynamics of the photospheric flows. They find that there are repelling and attracting structures in the lower photosphere that act as sources and sinks for magnetic element transport. They also observe changes in the flow organization prior, during, and following the rise of an active region, as well as the influence of strong magnetic field on the flow dynamics in neighboring regions.
ASTROPHYSICAL JOURNAL LETTERS
(2023)
Article
Materials Science, Paper & Wood
Amy Y. Xu, Duncan J. McGillivray, Andrew J. Dingley
Summary: The study investigated the prevention of bacteria colonization on cotton fabrics by immobilizing antimicrobial proteins, showing that the antimicrobial activities varied between different functionalized surfaces. Citric acid immobilized lysozyme exhibited superior activity against Gram-positive bacteria, while APTES immobilized HM-1 had an advantage in inhibiting growth of Gram-negative bacteria. The dual coating of fibers with both antimicrobial proteins demonstrated efficient antimicrobial activities against both bacterial species.
Article
Chemistry, Applied
Seyedeh Fatemeh Mirpoor, Simona Varriale, Raffaele Porta, Daniele Naviglio, Mariachiara Spennato, Lucia Gardossi, C. Valeria L. Giosafatto, Cinzia Pezzella
Summary: Cardoon is a perennial plant that can be used as a biomass source for bioactive compounds and proteins. Naviglio technology efficiently extracts bioactive compounds from cardoon leaves and proteins can create green films with promising properties. The combination of cardoon leaf extract and proteins results in films with improved mechanical and barrier properties.
FOOD HYDROCOLLOIDS
(2022)
Article
Biochemical Research Methods
Vincent Rocher, Matthieu Genais, Elissar Nassereddine, Raphael Mourad
Summary: DNA is a complex molecule that carries instructions for organism development, living, and reproduction, with G4 being an important structure in DNA that plays a key role in cells. DeepG4 is a novel convolutional neural network that accurately predicts cell-type specific active G4 regions, identifying multiple predictive DNA motifs for G4 region activity.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Chemistry, Physical
Zhixiong Deng, Xin You, Zhao Lin, Xuewei Dong, Bing Yuan, Kai Yang
Summary: Using molecular dynamics simulations and theoretical analysis, this study investigated the interactions between membrane-active peptides (MAPs) and realistic cell membrane systems. The simulations revealed that MAPs can attack membranes by generating and sensing positive mean curvature, dependent on lipid composition. Theoretical calculations further demonstrated that this curvature-based mechanism is a result of multiple effects, including peptide-induced membrane wedge and softening effects, lipid shape effect, area-difference elastic effect, and the boundary edge effect of peptide-lipid nanodomains. This study enhances our comprehension of MAP-membrane interactions and highlights the potential for developing membrane-specific MAP-based agents.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Multidisciplinary Sciences
Ester Lilian Acen, David Patrick Kateete, William Worodria, Ronald Olum, Moses L. Joloba, Mudarshiru Bbuye, Irene Andia Biraro
Summary: This study found significantly higher LL-37 levels among active tuberculosis patients compared to those with latent tuberculosis and without tuberculosis. LL-37 showed better discriminatory potential between active TB and no TB, and moderate differentiation between latent TB and no TB. Further assessment is needed to determine the usefulness of LL-37 as a screening tool for excluding tuberculosis.
Article
Chemistry, Multidisciplinary
Ana Margarida Pereira, Diana Gomes, Andre da Costa, Simoni Campos Dias, Margarida Casal, Raul Machado
Summary: The text discusses the use of genetically engineered recombinant protein polymers with antimicrobial peptides for the production of new antimicrobial materials. These polymers demonstrate antimicrobial activity, indicating their potential for the development of advanced antimicrobial materials.
APPLIED SCIENCES-BASEL
(2021)
Article
Engineering, Civil
A. Morabbi, A. Bouziane, O. Seidou, N. Habitou, D. Ouazar, T. B. M. J. Ouarda, C. Charron, M. D. Hasnaoui, M. Benrhanem, K. Sittichok
Summary: Hydrologic regionalization involves regrouping stations and catchments based on a similarity measure, to extract a robust signal for describing the hydrology of a region. However, existing methods often overlook the non-linear and non-stationary nature of hydrometeorological variables. This study introduces a novel similarity measure based on changepoint locations in hydrological time series, applied to the Tensift watershed in Morocco, with coherence of detected regions verified using wavelet coherence.
JOURNAL OF HYDROLOGY
(2022)
Article
Multidisciplinary Sciences
Weimin Feng, Shuai Liu, Qiuting Deng, Sulei Fu, Yunzhi Yang, Xi Dai, Shuai Wang, Yijin Wang, Yang Liu, Xiumei Lin, Xiangyu Pan, Shijie Hao, Yue Yuan, Ying Gu, Xiuqing Zhang, Hanbo Li, Longqi Liu, Chuanyu Liu, Ji-Feng Fei, Xiaoyu Wei
Summary: In this study, we utilized single-cell ATAC sequencing to comprehensively analyze the chromatin accessibility of the axolotl brain, identifying key transcription factors specific to different cell types and comparing cell type functions across brain regions.
Article
Multidisciplinary Sciences
Diego Jerez, Eleanor Stuart, Kylie Schmitt, Debbie Guerrero-Given, Jason M. Christie, Naomi Kamasawa, Michael S. Smirnov
Summary: Gold Digger is a software tool developed to automate the detection and annotation of colloidal gold particles in biological EM images, achieving near-human-level accuracy and capable of handling large images. It includes a user-friendly graphical interface for proof reading outputs by users and manual error correction for continued improvement in annotation accuracy.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Paolo Stincone, Flavio Fonseca Veras, Giuseppe Micalizzi, Danilo Donnarumma, Gaetano Vitale Celano, Daniel Petras, Maria de Angelis, Luigi Mondello, Adriano Brandelli
Summary: This study investigated the effect of antimicrobial peptides on L. monocytogenes using mass spectrometry-based lipidomics and proteomics. The results showed that the treatment with antimicrobial peptides caused changes in lipid and protein profiles, affecting the biofilm formation.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Shao-hua Li, Jiao Xiang, Ying-yue Zeng, Xuan-xian Peng, Hui Li
Summary: This study investigates the tetracycline resistance mechanisms of Edwardsiella tarda using GC-MS based untargeted metabolomics and biochemistry and molecular biology techniques. The results indicate that elevated proton motive force (PMF) contributes to the resistance, and a combination of tetracycline with gentamicin can effectively kill resistant bacteria.
MICROBIAL BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Phasit Charoenkwan, Sakawrat Kanthawong, Nalini Schaduangrat, Pietro Li', Mohammad Ali Moni, Watshara Shoombuatong
Summary: This study presents a computational approach (SCMRSA) for identifying and characterizing anti-MRSA peptides without the use of 3D structural information. SCMRSA accurately identifies anti-MRSA peptides and provides a more in-depth explanation. A user-friendly web server has also been established for easy access.
Article
Plant Sciences
Ying-Yu Liao, Jorge Pereira, Ziyang Huang, Qiurong Fan, Swadeshmukul Santra, Jason C. White, Roberto De la Torre-roche, Susannah Da Silva, Gary E. Vallad, Joshua H. Freeman, Jeffrey B. Jones, Mathews L. Paret
Summary: Bacterial spot of tomato is a significant disease affecting tomato plants. Previous research has shown that non-formulated magnesium oxide nanoparticles can reduce disease severity. However, the aggregation of the nanoparticles makes it difficult to use in field applications. Therefore, novel MgO and MgOH2 nanomaterials were formulated and their characteristics and disease reduction abilities were evaluated. Among the nanomaterials, SgMc showed the highest efficacy in vitro and in greenhouse experiments. However, its effectiveness was inconsistent in field conditions. Further research is needed to determine the specific variables that affect its performance in different environments.
Article
Chemistry, Physical
Sankaran Nampoothiri
Summary: This study systematically investigates the impact of breaking the rotational symmetry of a surface on the positioning of spots in reaction-diffusion systems. Specifically, we analytically and numerically analyze the steady-state positioning of a single spot on a prolate and an oblate ellipsoid. Linear stability analysis is conducted using perturbative techniques, and the steady-state spot positions of non-linear reaction-diffusion equations are numerically obtained on both ellipsoids. Our findings suggest that preferential spot positioning can be observed on non-spherical surfaces, providing insights into the role of cell geometry in symmetry-breaking mechanisms in cellular processes.
Article
Biochemistry & Molecular Biology
Andrea Vandelli, Fernando Cid Samper, Marc Torrent Burgas, Natalia Sanchez De Groot, Gian Gaetano Tartaglia
Summary: Condensation, or liquid-like phase separation, is an important phenomenon for the spatiotemporal regulation of molecules within the cell. Recent studies have shown that components of phase-separated organelles like Stress Granules (SGs) and Processing Bodies (PBs) exhibit high variability and dynamics in their composition and molecular organization. The formation of SGs and PBs is regulated by a dense contact network involving both RNAs and proteins, and the molecular architecture of these organelles is not yet fully understood.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Guillem Prats-Ejarque, Helena Lorente, Clara Villalba, Raul Anguita, Lu Lu, Sergi Vazquez-Monteagudo, Pablo Fernandez-Millan, Ester Boix
Summary: Bacterial resistance to antibiotics has led to the development of a hybrid enzyme with high antimicrobial and catalytic activities. After multiple improvements, the RNase 3/1-v3 chimera was designed, which exhibited enhanced antimicrobial and catalytic activities, as well as low cytotoxicity. Furthermore, the RNase 3/1-v3 chimera was able to effectively eradicate intracellular infection in macrophages and induce autophagy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Jiarui Li, Guillem Prats-Ejarque, Marc Torrent, David Andreu, Klaus Brandenburg, Pablo Fernandez-Millan, Ester Boix
Summary: Antimicrobial peptides are alternative therapeutics to traditional antibiotics against bacterial resistance. This study designed a peptide compound with antimicrobial and endotoxin-neutralization activities, and found that it had good efficacy in treating Acinetobacter baumannii infection in mice.
Article
Biochemistry & Molecular Biology
Lu Lu, Jiarui Li, Ranlei Wei, Irene Guidi, Luca Cozzuto, Julia Ponomarenko, Guillem Prats-Ejarque, Ester Boix
Summary: RNase2, the most abundant member of the RNaseA family in macrophages, has been found to have antiviral effects. In this study, RNase2 was knocked out in THP-1 cells and the response to Respiratory Syncytial Virus (RSV) was analyzed. RSV was found to induce expression of RNase2, which significantly enhanced cell survival. Sequencing analysis revealed that tRNA-derived fragments (tRFs) and second miRNAs were mostly accumulated in WT cells compared to KO cells.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Chemistry, Medicinal
Maria Angeles Abengozar, Maria Fernandez-Reyes, Vivian A. Salazar, Marc Torrent, Beatriz G. de la Torre, David Andreu, Ester Boix, Luis Rivas
Summary: Eosinophil cationic protein (ECP) can enter the cytoplasm of Leishmania parasites, leading to RNA degradation and playing a key role in parasite killing. ECP combines membrane destabilization and enzymatic activities to effect parasite killing.
ACS INFECTIOUS DISEASES
(2022)
Article
Biochemistry & Molecular Biology
Riccardo Delli Ponti, Laura Broglia, Andrea Vandelli, Alexandros Armaos, Marc Torrent Burgas, Natalia Sanchez de Groot, Gian Gaetano Tartaglia
Summary: RNA molecules undergo chemical modifications that can alter their structure and molecular interactions. This study introduces a predictor of A-to-I effects on RNA structure and finds enrichment of double-stranded regions caused by A-to-I in long intergenic noncoding RNAs. Investigation of specific cases suggests that A-to-I editing is linked to the alteration of interaction sites with proteins involved in phase separation.
Article
Pharmacology & Pharmacy
Daniel Sandin, Javier Valle, Jordi Morata, David Andreu, Marc Torrent
Summary: Research has shown that antimicrobial peptides can induce tolerance in bacteria, which may be an important step in the development of antibiotic resistance. The tolerance is dependent on the type of antimicrobial peptide the bacteria are exposed to and can also affect antibiotic treatment.
Article
Biochemistry & Molecular Biology
Pablo Fernandez-Millan, Sergi Vazquez-Monteagudo, Ester Boix, Guillem Prats-Ejarque
Summary: Designing novel antibiotics to fight antimicrobial resistance is a top priority in global health. In this study, a chimeric protein was engineered based on the structure-function knowledge of the RNase A superfamily, combining the catalytic activity and antipathogen properties of two different RNases. The three-dimensional structures of the chimeric proteins were solved, and the key functional regions were identified. The results provide guidance for designing effective anti-infective therapies.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemical Research Methods
Andrea Vandelli, Magdalena Arnal Segura, Michele Monti, Jonathan Fiorentino, Laura Broglia, Alessio Colantoni, Natalia Sanchez de Groot, Marc Torrent Burgas, Alexandros Armaos, Gian Gaetano Tartaglia
Summary: PRALINE is a database that provides information on protein-protein, protein-RNA, and RNA-RNA interactions in stress granules, processing bodies, and other assemblies. It also reports the liquid-liquid and liquid-solid phase separation propensities of proteins and provides predicted secondary structure content of RNAs.
Meeting Abstract
Biochemistry & Molecular Biology
Marc Torrent Burgas
JOURNAL OF PEPTIDE SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Javier Macho Rendon, Rocio Rebollido-Rios, Marc Torrent Burgas
Summary: Protein-protein interactions play important roles in cellular processes. To address the limited knowledge of host-pathogen interactomes, we developed HPIPred, a numerical encoding-based host-pathogen PPI prediction tool. Through screening the entire proteomes of Homo sapiens and Pseudomonas aeruginosa PAO1, we generated a highly connected network topology of host-pathogen interactome using HPIPred.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Jordi Gomez Borrego, Marc Torrent Burgas
Summary: Adhesion and colonization of host cells by pathogenic bacteria rely on protein-protein interactions (PPIs). This study developed a filtering process to obtain a reliable list of domains and motifs participating in PPIs between bacteria and human cells. Structural analysis revealed that human proteins involved in these interactions are rich in alpha helix and disordered regions. The most significant domain-domain interactions were validated, but verifying domain-motif interactions was more challenging. Post-translational modifications, especially phosphorylation, also play a role in these interactions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Medicinal
Maria Angeles Abengozar, Maria Fernandez-Reyes, Vivian A. Salazar, Marc Torrent, Beatriz G. de la Torre, David Andreu, Ester Boix, Luis Rivas
Summary: The research suggests that eosinophils recruitment into Leishmania lesions may contribute to treatment. Eosinophil cationic protein (ECP) shows broad antimicrobial activity and enters the Leishmania cytoplasm leading to parasite killing through mechanisms such as RNA degradation.
ACS INFECTIOUS DISEASES
(2022)