Article
Biochemistry & Molecular Biology
Angelita Rebollo, Eric Savier, Pierre Tuffery
Summary: PEPscan is an effective method for identifying interfering peptides, which can interfere with protein-protein interactions. It is able to rapidly and accurately identify specific interfering peptides, but further validation is needed regarding their location at the protein-protein interface.
Article
Chemistry, Multidisciplinary
Jiajun Wang, Jigneshkumar Dahyabhai Prajapati, Fan Gao, Yi-Lun Ying, Ulrich Kleinekathoefer, Mathias Winterhalter, Yi-Tao Long
Summary: Chirality is important but often overlooked in biological and chemical processes due to technical limitations. Researchers have used an electrostatically asymmetric membrane channel to successfully identify chiral amino acids in single peptides. This study provides a new approach for developing chiral recognition and protein sequencing methods.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemical Research Methods
Chen Wang, Daniel M. Konecki, David C. Marciano, Harikumar Govindarajan, Amanda M. Williams, Brigitta Wastuwidyaningtyas, Thomas Bourquard, Panagiotis Katsonis, Olivier Lichtarge
Summary: The study investigates the evolutionary history of the entire SARS-CoV-2 proteome to identify functionally conserved sites that could inform the search for treatments with broader coverage. The results suggest evolutionarily stable sites that may provide useful drug and vaccine targets, less likely to be compromised by new virus strains. Additionally, the evolutionary information can aid in prioritizing cross reactive antigens for multi-epitope vaccine strategies against the betacoronavirus family.
Article
Chemistry, Medicinal
Christian Borgo, Luca Cesaro, Tsuyoshi Hirota, Keiko Kuwata, Claudio D'Amore, Thomas Ruppert, Renata Blatnik, Mauro Salvi, Lorenzo A. Pinna
Summary: CK2, a protein kinase with pleiotropic functions, is implicated in global human pathologies, particularly cancer. Selective inhibitors like CX4945 and GO289 show promise in controlling the CK2-dependent phosphoproteome.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Plant Sciences
Sho Furumura, Taro Ozaki, Akihiro Sugawara, Yohei Morishita, Kento Tsukada, Tatsuya Ikuta, Asuka Inoue, Teigo Asai
Summary: By mining fungal genomic information, a non-canonical iterative type I PKS with an N-terminal adenylation-thiolation didomain was found to catalyze the formation of naringenin chalcone. Analysis suggested the involvement of a C-terminal thioesterase domain in Claisen-type cyclization. Furthermore, an enzyme responsible for the biosynthesis of (2S)-flavanone in fungal flavonoids was also identified. These findings reveal novel fungal biosynthetic processes leading to plant-like metabolites.
JOURNAL OF NATURAL PRODUCTS
(2023)
Article
Biochemistry & Molecular Biology
J. Manuel Quijano-Barraza, Gerardo Zuniga, Claudia Cano-Ramirez, Maria Fernanda Lopez, Gema L. Ramirez-Salinas, Moises Becerril
Summary: Dendroctonus bark beetles are important ecological agents in coniferous forests, and their cytochrome P450 enzymes exhibit diversification in detoxification of terpenes. The study found that cytochromes in the CYP6DE and CYP6DJ subfamilies can hydroxylate different monoterpenes with varying affinities. The CYP6DE subfamily evolved to enhance detoxification capacity, while the CYP6DJ subfamily retained their original detoxification function.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Immunology
Duncan Kirby, Baljyot Parmar, Sepehr Fathi, Sagar Marwah, Chitra R. Nayak, Vera Cherepanov, Sonya MacParland, Jordan J. Feld, Gregoire Altan-Bonnet, Anton Zilman
Summary: The Type I Interferon family of cytokines act through the same cell surface receptor but have different functions during immune response to infection. A computational model focusing on Interferon-alpha and Interferon-beta, validated with experimental data, identifies key determinants of specificity and functional plasticity in signaling. Factors such as binding affinity, receptor expression levels, receptor internalization, and feedback mechanisms contribute to ligand specificity and differential signal processing downstream of STAT phosphorylation. The negative feedback by protein USP18 enhances differences in signaling between Interferons, contributing to functional plasticity in Interferon-alpha and Interferon-beta signaling.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Computer Science, Interdisciplinary Applications
Joel N. Swerdel, Martijn Schuemie, Gayle Murray, Patrick B. Ryan
Summary: The study shows that the performance characteristics estimates of phenotype algorithms generated by PheValuator 2.0 are closer to the results obtained through traditional validation using chart review. This tool can help researchers improve the reliability and reproducibility of studies using observational data.
JOURNAL OF BIOMEDICAL INFORMATICS
(2022)
Article
Biochemical Research Methods
Christopher T. Boughter, Martin Meier-Schellersheim
Summary: The adaptive immune system relies on a diverse set of receptors to respond to pathogens or molecular aberrations. This article introduces a software package for the integrated analysis of immune repertoire data, highlighting its capabilities and applications.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Yoav Printz, Pritish Patil, Mathias Mahn, Asaf Benjamin, Anna Litvin, Rivka Levy, Max Bringmann, Ofer Yizhar
Summary: This study developed a new method to map the synaptic connectivity of the medial prefrontal cortex (mPFC). The researchers found that mPFC neurons projecting to the basolateral amygdala (BLA) have unique spatial patterns of local-circuit synaptic connectivity. The probability of synaptic connections is mainly determined by the intrinsic properties of the postsynaptic cell and the anatomical positions of both cells.
NATURE COMMUNICATIONS
(2023)
Article
Geosciences, Multidisciplinary
Ludovic Schorpp, Julien Straubhaar, Philippe Renard
Summary: This paper presents a new method for automatically generating realistic geological and parameter models in Quaternary formations when modeling groundwater systems. The approach, utilizing the ArchPy Python module, operates in a hierarchical manner and streamlines the modeling process by automatically simulating stratigraphic unit boundaries, filling lithologies, and simulating petrophysical properties inside lithologies. The automation provides a flexible framework for generating stochastic models end-to-end and allows for uncertainty quantification at any level.
FRONTIERS IN EARTH SCIENCE
(2022)
Review
Biochemistry & Molecular Biology
Anastasiia I. Petushkova, Lyudmila V. Savvateeva, Andrey A. Zamyatnin
Summary: Papain-like cysteine proteases are widely expressed enzymes that regulate protein turnover in lysosomes. Recent discoveries have shown that these proteases also have specific functions in different organelles and extracellular environments. Human cysteine cathepsins are the most studied proteases in this family and are involved in both physiological and pathological processes. The specificity of each protease to its substrates is determined by the structure of the binding cleft and the amino acid motifs in this region.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Automation & Control Systems
Fatima Zahra Lahbiri, Said Hadd
Summary: This paper investigates infinite dimensional stochastic systems with unbounded control and observation operators, addressing the well-posedness of systems and a new variation of constants formula for perturbed abstract stochastic Cauchy problems. It also examines perturbed boundary control systems, general stochastic systems with delays, and admissible observation operators and exact observability for semilinear stochastic systems.
SIAM JOURNAL ON CONTROL AND OPTIMIZATION
(2021)
Article
Plant Sciences
Huai-Na Gao, Han Jiang, Xin-Yu Lian, Jian-Ying Cui, Chun-Xiang You, Yu-Jin Hao, Yuan-Yuan Li
Summary: In this study, 26 potential LTPG genes were identified in apple using bioinformatics methods, and 20 of them were confirmed as MdLTPG family members based on subcellular localization predictions. These MdLTPG genes were induced by growth conditions and one protein was shown to interact with another protein, collectively participating in wax transport during plant growth and development.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Business, Finance
Maria Martinez-Cillero, Martina Lawless, Conor O'Toole
Summary: In this paper, the authors analyze the relationship between investment by Small and Medium Enterprises (SMEs) and their economic characteristics, as well as the presence of financing constraints during the post-2008 crisis recovery period. Using novel survey data for Irish SMEs, they find a clear link between investment and its marginal product, with elasticities of between 0.55 and 0.65. The study also reveals the presence of financing constraints and the impact of liquid assets, indebtedness, and investment satisfaction on SMEs' investment constraints.
INTERNATIONAL REVIEW OF ECONOMICS & FINANCE
(2023)
Article
Biochemical Research Methods
Galya Klink, Olga Kalinina, Georgii Bazykin
Summary: Fitness conferred by the same allele may differ between genotypes and environments, and these differences shape variation and evolution. In this study, a new method is developed to detect individual amino acids that confer different fitness in different groups of species. The method combines sequence and phylogenetic data, and is validated using simulated evolution and applied to HIV-1 and influenza A. The results are consistent with fitness differences observed in experiments.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Marin Matic, Gurdeep Singh, Francesco Carli, Natalia De Oliveira Rosa, Pasquale Miglionico, Lorenzo Magni, J. Silvio Gutkind, Robert B. Russell, Asuka Inoue, Francesco Raimondi
Summary: This study demonstrates that protein language models can encode structural and functional information of GPCR sequences for predicting their signaling and functional repertoire. The researchers developed a machine learning predictor called PRECOGx, which outperforms its predecessor PRECOG in predicting GPCR-transducer couplings and considers all GPCR classes. The study also introduces new functionalities in a webserver, allowing for the projection of input sequences and analysis of sequence and structural determinants responsible for coupling.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Elena Porcellato, Juan Carlos Gonzalez-Sanchez, Constantin Ahlmann-Eltze, Mahmoud Ali Elsakka, Itamar Shapira, Juergen Fritsch, Juan Antonio Navarro, Simon Anders, Robert B. Russell, Felix T. Wieland, Christoph Metzendorf
Summary: Protein S-palmitoylation, a reversible protein modification, plays a crucial role in neuronal diseases and cancer. However, its study in Drosophila melanogaster has been limited. In this study, the palmitoylome of Drosophila S2R+ cells was analyzed, and a method called DHHC-BioID was established to identify client proteins and interaction partners of protein acyl-transferases (PATs). The results showed that S-palmitoylated proteins are conserved between mammals and Drosophila, and DHHC-BioID is a sensitive and specific method for identifying DHHC-PAT client proteins.
Article
Multidisciplinary Sciences
Alexandra M. Ozerova, Mikhail S. Gelfand
Summary: Holometabolous insects show significant changes in gene expression during metamorphosis, resembling the embryonic stage rather than the larval stage. The transition from pupa to imago shows similar gene expression patterns as the transition from embryo to larva. Genes associated with metabolism and development undergo changes in expression levels during the larval stage and revert to an embryonic-like state during metamorphosis.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Torsten Schmenger, Gaurav D. Diwan, Gurdeep Singh, Gordana Apic, Robert B. Russell
Summary: The rapid pace of genetic variant discovery is crucial for understanding their impact on biological systems. By studying genetic variants in healthy individuals, we identified potential disease-causing variants that have an impact on biological function. These findings suggest the presence of many relatively common lethal or disease-causing variants in healthy human populations.
NPJ GENOMIC MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Narcis A. Petriman, Marta Loureiro-Lopez, Michael Taschner, Nevin K. Zacharia, Magdalena M. Georgieva, Niels Boegholm, Jiaolong Wang, Andre Mourao, Robert B. Russell, Jens S. Andersen, Esben Lorentzen
Summary: Cilia are essential organelles for cellular functions such as motility, signaling, and sensory reception. In this study, the researchers used Alphafold to model the structure of the IFT-B complex, which is involved in cilium formation. The results provide insights into the assembly and function of the IFT-B complex.
Article
Multidisciplinary Sciences
Andrea Zanotti, Joao P. L. Coelho, Dinah Kaylani, Gurdeep Singh, Marina Tauber, Manuel Hitzenberger, Donem Avci, Martin Zacharias, Robert B. Russell, Marius K. Lemberg, Matthias J. Feige
Summary: This study reveals a previously unknown function of the human signal peptidase complex (SPC) as a membrane protein quality control factor. The SPC cleaves membrane proteins at hidden cleavage sites when they fail to fold or assemble correctly, contributing to membrane protein homeostasis and cellular fitness.
Article
Cell Biology
Mariam G. Aslanyan, Cenna Doornbos, Gaurav D. Diwan, Zeinab Anvarian, Tina Beyer, Katrin Junger, Sylvia E. C. van Beersum, Robert B. Russell, Marius Ueffing, Alexander Ludwig, Karsten Boldt, Lotte B. Pedersen, Ronald Roepman
Summary: By studying ubiquitination modifications in cells, we have identified the involvement of ESCRT-dependent clathrin-mediated endocytosis vesicles and caveolae components in ciliary function. These findings contribute to a better understanding of the mechanisms underlying cilia biology in health and disease.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Ivan N. Semenkov, Pavel Shelyakin, Daria D. Nikolaeva, Maria N. Tutukina, Anna Sharapova, Sergey A. Lednev, Yuliya Sarana, Mikhail S. Gelfand, Pavel P. Krechetov, Tatiana Koroleva
Summary: This article presents original data on the impact of jet-fuel spillage on topsoil properties. The data set includes information on kerosene concentration over time, as well as physicochemical and biological properties of the soil. Additionally, sequencing data on microbial communities are provided.
Article
Chemistry, Multidisciplinary
Sebastian Adam, Dazhong Zheng, Andreas Klein, Carsten Volz, William Mullen, Sally L. Shirran, Brian O. Smith, Olga V. Kalinina, Rolf Mueller, Jesko Koehnke
Summary: In this study, we identified three proteins (CgnB, CgnC, and CgnE) responsible for the production of the tetracyclic crocagin core. Crystal structures of two homologues (CgnB and CgnE) provided insights into their functions. We also discovered the roles of CgnD and CgnL in the liberation and modification of the crocagin core, respectively, and proposed a biosynthetic scheme. Bioinformatic analyses further revealed potential pathways for the synthesis of structurally diverse peptide-derived pyrroloindoline alkaloids.
Review
Biochemistry & Molecular Biology
Fabiola De Marchi, Toni Franjkic, Paride Schito, Tommaso Russo, Jerneja Nimac, Anna A. Chami, Angelica Mele, Lea Vidatic, Jasna Kriz, Jean-Pierre Julien, Gordana Apic, Robert B. Russell, Boris Rogelj, Jason R. Cannon, Marco Baralle, Federica Agosta, Silva Hecimovic, Letizia Mazzini, Emanuele Buratti, Ivana Munitic
Summary: Proteinopathy and neuroinflammation are two main features of neurodegenerative diseases with high heterogeneity. This review focuses on ALS and FTD spectrum disorder, highlighting neuroinflammation and immune imbalance as novel therapeutic targets. Dysregulation of TDP-43 is a common mechanism in most ALS and 50% of FTD patients, leading to altered cellular events. Experimental attempts targeting TDP-43 aggregates and inflammation will be discussed.
Article
Biochemical Research Methods
Sanjay K. Srikakulam, Sebastian Keller, Fawaz Dabbaghie, Robert Bals, Olga Kalinina
Summary: MetaProFi is a Bloom filter-based tool that allows rapid searches in large sequence datasets. It is the first tool that can build indexes of amino acid sequences and query them with both amino acid and nucleotide sequences, bringing sequence comparison to the biologically relevant protein level.
Article
Cell Biology
Grace Mercedes Freke, Tiago Martins, Rosalind Jane Davies, Tina Beyer, Marian Seda, Emma Peskett, Naila Haq, Avishek Prasai, Georg Otto, Jeshmi Jeyabalan Srikaran, Victor Hernandez, Gaurav D. Diwan, Robert B. Russell, Marius Ueffing, Martina Huranova, Karsten Boldt, Philip L. Beales, Dagan Jenkins
Summary: Bardet-Biedl syndrome is a ciliopathy that affects multiple tissues. Research suggests that BBS1 plays a crucial role in suppressing the transition from epithelial cells to mesenchymal cells, and dysregulation of epithelial-to-mesenchymal transition genes may be a predisposing feature of BBS.
Article
Biology
Alexander Gress, Sanjay K. Srikakulam, Sebastian Keller, Vasily Ramensky, Olga Kalinina
Summary: This study presents a novel computational method called d-StructMAn for structural annotation of local genetic variants. By annotating multiple datasets of human genetic variants, it was found that d-StructMAn can provide structural annotation for a significant portion of the human proteome. This method is instrumental in predicting genotype-to-phenotype relationships.
