Explanipedia

Identification and characterization of botulinum neurotoxin–like two-component toxins in Paeniclostridium ghonii Open

Pyung‐Gang Lee, Linxiang Yin, Xin Wei, Geoffrey Masuyer, Ying Xu , et al. · 2025

Insecticidal bacterial proteins play key roles in insect-bacteria interactions and have been used as biopesticides. Here, we identify two insecticidal proteins in Paeniclostridium ghonii , designated PG-toxin 1 (PG1) and PG-toxin 2 (PG2), …

Peptide abundance correlations in metaproteomics enhance taxonomic and functional analysis of the human gut microbiome Open

Zhongzhi Sun, Zhibin Ning, Qing Wu, Leyuan Li, Andrew C. Doxey , et al. · 2025

Mass spectrometry (MS)-based proteomics is widely used for quantitative protein profiling and protein interaction studies. However, most current research focuses on single-species proteomics, while protein interactions within complex micro…

Pharmacological inhibition of Peroxisome Proliferation-Activated Receptor Delta (PPARδ) imparts selective leukemia cell death Open

Yingying Yang, Ekaterina Parfenova, Nikolina Vrdoljak, Mark D. Minden, Jessica Luc , et al. · 2025

Pharmacological inhibition of PPARδ with 6ME is a novel approach to inducing selective death in AML.

Early innate immune response and evolution of a SARS-CoV-2 furin cleavage site inactive variant in bat cells Open

Kaushal Baid, Sauhard Shrivastava, Jessica G.Y. Luc, Daniel Richard, Jennifer A. Aguiar , et al. · 2025

SARS-CoV-2 has caused the largest known coronavirus pandemic and is believed to have emerged from insectivorous bats. Little is known about the evolution of these viruses in their reservoir bat species. In this study, we investigate the SA…

Bat-specific adaptations in interferon signaling and GBP1 contribute to enhanced antiviral capacity Open

Victoria Gonzalez, Briallen Lobb, Jacob A. Cote, Arkadeb Bhuinya, Adriana G Tubb , et al. · 2025

Bats are reservoirs of emerging zoonotic viruses that may cause severe disease in humans and agricultural animals. However, it is poorly understood how bats can tolerate diverse viral infections. Here, we characterized type I interferon re…

Comparative proteomics of biofilm development in Pseudoalteromonas tunicata discovers a distinct family of Ca 2+ -dependent adhesins Open

Sura Mazin Ali, Andreas Stavropoulos, Benjamin Jenkins, Stephen Graves, Atiyeh Ahmadi , et al. · 2025

The marine bacterium, Pseudoalteromonas tunicata , is a useful model for studying biofilm development due to its ability to colonize and form biofilms on a variety of marine and eukaryotic host-associated surfaces. However, the pathways re…

Widespread occurrence of botulinum and tetanus neurotoxin genes in ancient DNA Open

Shyan Mascarenhas, Harold P. Hodgins, Andrew C. Doxey · 2025

Our work reveals that clostridial neurotoxin genes occur frequently in aDNA samples, including human and animal-associated toxin variants. We conclude that the frequent association of these genes with aDNA likely reflects a strong ecologic…

Metatranscriptomic profiling reveals pathogen and host response signatures of pediatric acute sinusitis and upper respiratory infection Open

Andrew C. Doxey, Nooran Abu Mazen, Max Homm, Vivian H. Chu, Manjot S. Hunjan , et al. · 2025

Background Acute sinusitis (AS) is a frequent cause of antibiotic prescriptions in children. Distinguishing bacterial AS from common viral upper respiratory infections (URIs) is crucial to prevent unnecessary antibiotic use but is challeng…

Widespread occurrence of botulinum and tetanus neurotoxin genes in ancient DNA Open

Shyan Mascarenhas, Harold Hodgins, Andrew C. Doxey · 2025

Background Ancient DNA collected from archaeological specimens not only provides a window into ancient human genetic diversity but also contains a rich mixture of associated microbial DNA including potential pathogens. In recent work, we i…

Identification of a divergent botulinum neurotoxin like gene cluster in Furfurilactobacillus Open

Xin Wei, Pyung‐Gang Lee, Min Dong, Andrew C. Doxey · 2025

Botulinum neurotoxins (BoNTs) are among the most potent biological toxins and are traditionally associated with Clostridium species. However, recent discoveries have identified BoNT-like proteins in diverse bacterial genera, revealing an e…

Cyanobacteriochrome-like GAF folds in phages revealed via AlphaFold proteomic modelling Open

Isaac Meza‐Padilla, Andrew C. Doxey, Jozef I. Nissimov · 2025

AlphaFold 3 proteomic modelling reveals multiple photosystem structural homologs in freshwater cyanophages Open

Isaac Meza‐Padilla, Andrew C. Doxey, Jozef I. Nissimov · 2024

Accurate protein structure prediction followed by structural homology detection enable the functional annotation of large numbers of otherwise obscure viral protein-coding genes. Here we employ AlphaFold 3 modeling and DALI structural homo…

Bat-specific adaptations in interferon signaling and GBP1 contribute to enhanced viral tolerance Open

Arinjay Banerjee, Victoria Gonzalez, Briallen Lobb, Jacob A. Cote, Arkadeb Bhuinya , et al. · 2024

Bats are reservoirs of emerging zoonotic viruses of concern that cause severe disease in humans and agricultural animals. However, it is poorly understood how bats are able to tolerate diverse viral infections, knowledge that could help pa…

A widespread accessory protein family diversifies the effector repertoire of the type VI secretion system spike Open

Jake Colautti, Huagang Tan, Nathan P. Bullen, Stephanie S. Thang, Dirk Hackenberger , et al. · 2024

Comparative proteomics of biofilm development inPseudoalteromonas tunicatadiscovers a distinct family of Ca2+-dependent adhesins Open

Sura Mazin Ali, Andreas Stavropoulos, Benjamin Jenkins, Stephen Graves, Guowei Che , et al. · 2024

The marine bacterium, Pseudoalteromonas tunicata , is a useful model for studying mechanisms of biofilm development due to its ability to colonize and form biofilms on a variety of marine and eukaryotic host-associated surfaces. However, t…

COVID‐19 severity gradient differentially dysregulates clinically relevant drug processing genes in nasopharyngeal swab samples Open

Chukwunonso K. Nwabufo, Jessica G.Y. Luc, Allison McGeer, Jeremy A. Hirota, Samira Mubareka , et al. · 2024

Aim Understanding how COVID‐19 impacts the expression of clinically relevant drug metabolizing enzymes and membrane transporters (DMETs) is vital for addressing potential safety and efficacy concerns related to systemic and peripheral drug…

AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods Open

Xin Wei, Huagang Tan, Briallen Lobb, William Zhen, Zijing Wu , et al. · 2024

The analysis and comparison of gene neighborhoods is a powerful approach for exploring microbial genome structure, function, and evolution. Although numerous tools exist for genome visualization and comparison, genome exploration across la…

Nasopharyngeal metatranscriptomics reveals host-pathogen signatures of pediatric sinusitis Open

Nooran AbuMazen, Vivian H. Chu, Manjot S. Hunjan, Briallen Lobb, Sojin Lee , et al. · 2024

Acute sinusitis (AS) is the fifth leading cause of antibiotic prescriptions in children. Distinguishing bacterial AS from common viral upper respiratory infections in children is crucial to prevent unnecessary antibiotic use but is challen…

Characterization of CXCL10 as a biomarker of respiratory tract infections detectable by open-source lateral flow immunoassay Open

Dayna Mikkelsen, Jennifer A. Aguiar, Benjamin J.-M. Tremblay, Manjot S. Hunjan, Ulrich Eckhard , et al. · 2024

Understanding core mechanisms common to respiratory tract viral pathogenesis and host-responses to infections may provide biomarkers for at-risk patient populations that guide interventions aimed at reducing morbidity, mortality, and econo…

AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods Open

Xin Wei, Huagang Tan, Briallen Lobb, William Zhen, Zijing Wu , et al. · 2024

The analysis and comparison of gene neighborhoods is a powerful approach for exploring microbial genome structure, function, and evolution. Although numerous tools exist for genome visualization and comparison, genome exploration across la…

Evaluation of multiple displacement amplification for metagenomic analysis of low biomass samples Open

Melody Cabrera Ospino, Katja Engel, Santiago Ruiz-Navas, W. Jeffrey Binns, Andrew C. Doxey , et al. · 2024

Combining multiple displacement amplification (MDA) with metagenomics enables the analysis of samples with extremely low DNA concentrations, making them suitable for high-throughput sequencing. Although amplification bias and nonspecific a…

Genomic and transcriptomic characterization of delta SARS-CoV-2 infection in free-ranging white-tailed deer (Odocoileus virginianus) Open

Jonathon D. Kotwa, Briallen Lobb, Ariane Massé, Marianne Gagnier, Patryk Aftanas , et al. · 2023

Genomic classification and antimicrobial resistance profiling of Streptococcus pneumoniae and Haemophilus influenzae isolates associated with paediatric otitis media and upper respiratory infection Open

Briallen Lobb, Matthew C. Lee, Christi L. McElheny, Yohei Doi, Kristin Yahner , et al. · 2023

Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains Open

Harold P. Hodgins, Pengsheng Chen, Briallen Lobb, Xin Wei, Benjamin J.-M. Tremblay , et al. · 2023

The analysis of microbial genomes from human archaeological samples offers a historic snapshot of ancient pathogens and provides insights into the origins of modern infectious diseases. Here, we analyze metagenomic datasets from 38 human a…

Cannabis smoke suppresses antiviral immune responses to influenza A in mice Open

Nadia Milad, Matthew F. Fantauzzi, Joshua J.C. McGrath, Steven P. Cass, Danya Thayaparan , et al. · 2023

Rationale Despite its increasingly widespread use, little is known about the impact of cannabis smoking on the response to viral infections like influenza A virus (IAV). Many assume that cannabis smoking will disrupt antiviral responses in…

Identification of a botulinum neurotoxin-like gene cluster inBacillus toyonensis Open

Xin Wei, Briallen Lobb, Kang Wang, Min Dong, Andrew C. Doxey · 2023

Clostridial neurotoxins, which include botulinum neurotoxins (BoNTs) and tetanus neurotoxin (TeNT) are the most potent toxins known, and are the causative agents of the neuroparalytic diseases, botulism and tetanus. Until recently, the clo…

Phylogenomic Analysis of 155 Helminth Species Reveals Widespread Absence of Oxygen Metabolic Capacity Open

Emma Collington, Briallen Lobb, Nooran Abu Mazen, Andrew C. Doxey, D. Moira Glerum · 2023

The terminal electron acceptor of most aerobic respiratory chains, cytochrome c oxidase (COX), has been highly conserved throughout evolution, from aerobic prokaryotes to complex eukaryotes. Oxygen metabolism in parasitic helminths differs…

A Machine Learning Framework Identifies Plastid-Encoded Proteins Harboring C3 and C4 Distinguishing Sequence Information Open

Nilanth Yogadasan, Andrew C. Doxey, Simon D. X. Chuong · 2023

C4 photosynthesis is known to have at least 61 independent origins across plant lineages making it one of the most notable examples of convergent evolution. Of the >60 independent origins, a predicted 22–24 origins, encompassing greater…

Functional Profiling and Evolutionary Analysis of a Marine Microalgal Virus Pangenome Open

Briallen Lobb, Anson Shapter, Andrew C. Doxey, Jozef I. Nissimov · 2023

Phycodnaviridae are large double-stranded DNA viruses, which facilitate studies of host–virus interactions and co-evolution due to their prominence in algal infection and their role in the life cycle of algal blooms. However, the genomic i…

Data from Glutamine Metabolism Mediates Sensitivity to Respiratory Complex II Inhibition in Acute Myeloid Leukemia Open

Alessia Roma, Matthew Tcheng, Nawaz Ahmed, Sarah Walker, Preethi Jayanth , et al. · 2023

Acute myeloid leukemia (AML) is a hematologic malignancy metabolically dependent on oxidative phosphorylation and mitochondrial electron transport chain (ETC) activity. AML cells are distinct from their normal hematopoietic counterparts by…

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