Article
Immunology
Sutonuka Bhar, Guanqi Zhao, Julia D. Bartel, Heather Sterchele, Alexa Del Mazo, Lisa E. Emerson, Mariola J. Edelmann, Melissa K. Jones
Summary: Human norovirus is a major cause of non-bacterial gastroenteritis worldwide and is the second leading cause of diarrheal deaths in children in developing countries. This study shows that bacterial extracellular vesicles may play a role in controlling murine norovirus infection through modulation of the antiviral immune response.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Engineering, Biomedical
Kanika Suri, Anisha D'Souza, Di Huang, Aashray Bhavsar, Mansoor Amiji
Summary: Cancer therapy is shifting towards immunotherapy that activates the host immune system. Bacterial extracellular vesicles (BEVs) are being studied as a potential tool for controlling immune responses and for drug delivery. However, there are still unanswered questions regarding the use of BEVs, especially for long-term immunotherapies.
BIOACTIVE MATERIALS
(2023)
Article
Cell Biology
Laura Chalupowicz, Gideon Mordukhovich, Nofar Assoline, Leron Katsir, Noa Sela, Ofir Bahar
Summary: Gram-negative bacteria can produce outer membrane vesicles (OMVs) that promote infection and disease by inducing immune responses in both mammals and plants. In this study, OMVs purified from Xanthomonas campestris pv. campestris were used to treat Arabidopsis plants, leading to a significant transcriptional shift towards immune system activation. The upregulation of multiple immune pathways by OMVs facilitated resistance to bacterial infection. Mutations in certain immune receptors did not affect the immune priming effect of OMVs.
JOURNAL OF EXTRACELLULAR VESICLES
(2023)
Review
Microbiology
Jianwei Chen, Hongfang Zhang, Siqi Wang, Yujie Du, Bin Wei, Qiang Wu, Hong Wang
Summary: Bacterial extracellular vesicles (EVs) play a significant role in bacterial infections by influencing the infection process through various mechanisms. With the increasing problem of antibiotic resistance, researching and developing novel therapeutic approaches is of high importance.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Microbiology
Yanzhen Wang, Xinghong Luo, Xiaozhen Xiang, Chunbo Hao, Dandan Ma
Summary: Accumulating evidence suggests that not all bidirectional microbiota-host interactions involve direct cell contact. Bacterial extracellular vesicles (BEVs) mediate microbiota functions by delivering effector molecules that modulate host signaling pathways, potentially driving or inhibiting disease pathogenesis in different systems within the host.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Felix Behrens, Teresa C. Funk-Hilsdorf, Wolfgang M. Kuebler, Szandor Simmons
Summary: Respiratory infection-induced pneumonia is the leading cause of death in global infectious diseases, with antibiotics and vaccines helping to reduce the burden. However, lack or refusal of vaccines and antibiotics in some regions, the rise of multidrug-resistant pathogens, and high fatality rates even in patients treated appropriately pose a global threat. Bacteria's secretome contains extracellular vesicles that can trigger inflammatory responses and serve as promising vaccine candidates.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Jingmei Pan, Xilin Li, Binfen Shao, Funeng Xu, Xuehui Huang, Xing Guo, Shaobing Zhou
Summary: A nanocarrier that achieves self-blockade of PD-L1 in tumor cells and a detection kit to quantitatively measure the binding rate of PD-1/PD-L1 have been developed, improving the efficacy of PD-1/PD-L1 self-blocking therapy.
ADVANCED MATERIALS
(2022)
Review
Pharmacology & Pharmacy
Jin Gao, Yujie Su, Zhenjia Wang
Summary: This review provides an overview of the current research on bacterial membrane vesicles (BMVs), including their production, types, and therapeutic applications. The authors discuss various platforms of BMVs and how they can be engineered using chemical, physical, and genetic methods. The review also examines the methods of drug loading in BMVs and their limitations. Several therapeutic platforms of BMVs for improving the treatment of infectious diseases and cancers are reviewed. The authors emphasize the need for rigorous approaches and methods to develop reproducible and scalable drug delivery systems for translation.
ADVANCED DRUG DELIVERY REVIEWS
(2022)
Article
Immunology
Nina Pennetzdorfer, Medeea C. Popescu, Naomi L. Haddock, Fannie Dupuy, Gernot Kaber, Aviv Hargil, Patrik K. Johansson, Annika Enejder, Paul L. Bollyky
Summary: Pseudomonas aeruginosa, a major human pathogen, can effectively colonize the airways of patients with cystic fibrosis. This study found that the bacteriophage Pf4 produced by P. aeruginosa modifies the innate immune response to P. aeruginosa infections via TLR3 signaling. The phage dampens inflammatory responses to bacterial endotoxin by attaching to bacterial vesicles, potentially reducing inflammation at sites of bacterial colonization or infection.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Biology
Daniel A. Phillips, Lori A. Zacharoff, Cheri M. Hampton, Grace W. Chong, Anthony P. Malanoski, Lauren Ann Metskas, Shuai Xu, Lina J. Bird, Brian J. Eddie, Aleksandr E. Miklos, Grant J. Jensen, Lawrence F. Drummy, Mohamed Y. El-Naggar, Sarah M. Glaven
Summary: BAR domain proteins are a superfamily of coiled-coil proteins that influence membrane curvature in eukaryotes, and a bacterial protein BdpA with BAR domain-like activity has been discovered to impact the formation of membrane vesicles and outer membrane extensions. BdpA is essential for the uniform size distribution of membrane vesicles and the scaffolding of consistent diameter and curvature in OMEs, influencing the morphology of these structures. Overexpression of BdpA can promote the formation of OMEs in bacterial species where it is not typically observed, suggesting a new class of bacterial BAR domain-like proteins.
Article
Chemistry, Multidisciplinary
Jennie L. Cawley, Megan E. Blauch, Shannon M. Collins, Justin B. Nice, Qing Xie, Luke R. Jordan, Angela C. Brown, Nathan J. Wittenberg
Summary: Characterization of small biological particles, such as extracellular vesicles, is complicated due to their extreme heterogeneity. Liftoff nanocontact printing (LNCP) enables high-throughput analysis of individual particles by defining hexagonal antibody and toxin arrays. This approach can generate high density arrays of various small biological particles.
Review
Microbiology
Zhuang Zhu, Fabio Antenucci, Kasper Romer Villumsen, Anders Miki Bojesen
Summary: Gram-negative bacterial vaccines are important tools for preventing bacterial infections and reducing the need for antibiotics. Outer membrane vesicles have great potential as adjuvants, antigens, and delivery platforms in vaccine development. There is a need for the development of novel bacterial vaccines to prevent the advent of a postantibiotic era.
Article
Chemistry, Multidisciplinary
Hao Qin, Hejia Li, Jin Zhu, Yuting Qin, Nan Li, Jian Shi, Guangjun Nie, Ruifang Zhao
Summary: Cancer vaccines need to effectively deliver antigens and trigger immune reactions. This study presents a strategy to assemble tumor antigens into bacterial outer membrane vesicles (OMVs) via electrostatic interaction. The OMV-delivered vaccine (OMVax) stimulates immune responses and inhibits metastasis, but immune response activation decreases with increased positive surface charge. These findings highlight the importance of optimizing vaccine formulations.
Review
Biochemistry & Molecular Biology
Yosuke Tashiro
Summary: Outer membrane vesicles (OMVs) produced by bacteria have versatile functions and potential applications in biotechnology.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2022)
Article
Microbiology
Alfonso Olaya-Abril, Rafael Prados-Rosales, Jose A. Gonzalez-Reyes, Arturo Casadevall, Liise-anne Pirofski, Manuel J. Rodriguez-Ortega
Summary: This study demonstrates that extracellular vesicles produced by different serotypes of Streptococcus pneumoniae can be internalized by macrophages through fusion with host cell membranes, and have the ability to induce an immune response and promote the production of proinflammatory cytokines, with higher levels observed in certain serotypes.
Article
Public, Environmental & Occupational Health
Courtney R. Lane, Norelle L. Sherry, Ashleigh F. Porter, Sebastian Duchene, Kristy Horan, Patiyan Andersson, Mathilda Wilmot, Annabelle Turner, Sally Dougall, Sandra A. Johnson, Michelle Sait, Anders Gonsalves da Silva, Susan A. Ballard, Tuyet Hoang, Timothy P. Stinear, Leon Caly, Vitali Sintchenko, Rikki Graham, Jamie McMahon, David Smith, Lex E. X. Leong, Ella M. Meumann, Louise Cooley, Benjamin Schwessinger, William Rawlinson, Sebastiaan J. van Hal, Nicola Stephens, Mike Catton, Clare Looker, Simon Crouch, Brett Sutton, Charles Alpren, Deborah A. Williamson, Torsten Seemann, Benjamin P. Howden
Summary: This study conducted genomic sequencing of COVID-19 cases in Victoria, Australia, identifying the source of the second wave outbreak and showing the effectiveness of genomic epidemiology in eliminating COVID-19 for a second time. The results indicated that a single incursion from hotel quarantine led to a large outbreak, but strict interventions and decisive public health responses were successful in controlling the spread. Real-time genomic surveillance played a crucial role in shaping public health strategies during the outbreak.
LANCET PUBLIC HEALTH
(2021)
Review
Microbiology
Minh Thuy Vi Hoang, Laszlo Irinyi, Yiheng Hu, Benjamin Schwessinger, Wieland Meyer
Summary: Identification of the causative infectious agent is crucial for the management of infectious diseases. Traditional diagnostic techniques have limitations in terms of time and specificity, while long-read sequencing has the potential to provide accurate identification of pathogens directly from clinical samples and additional clinical information.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Evolutionary Biology
Barsha Poudel, Neeraj Purushotham, Ashley Jones, Jamila Nasim, Dante L. Adorada, Adam H. Sparks, Benjamin Schwessinger, Niloofar Vaghefi
Summary: Charcoal rot is a significant soilborne disease caused by Macrophomina species, but the mechanism and host range of these fungal pathogens are poorly understood. The first high-quality genome assembly and annotation of Macrophomina tecta strain BRIP 70781 associated with charcoal rot symptoms on sorghum was presented in this study. The generated genome will contribute to further comparative and population genomics studies of Macrophomina species.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Benjamin Schwessinger, Ashley Jones, Mustafa Albekaa, Yiheng Hu, Amy Mackenzie, Rita Tam, Ramawatar Nagar, Andrew Milgate, John P. Rathjen, Sambasivam Periyannan
MOLECULAR PLANT-MICROBE INTERACTIONS
(2022)
Article
Microbiology
Yiheng Hu, Laszlo Irinyi, Minh Thuy Vi Hoang, Tavish Eenjes, Abigail Graetz, Eric A. Stone, Wieland Meyer, Benjamin Schwessinger, John P. Rathjen
Summary: Our study compared classification and community composition analysis pipelines using different sequencing technologies for fungal communities. We found that sequence alignment against a fungal-specific database achieved the highest accuracy of species identification. Applying cutoffs to the query coverage of each read or contig significantly improved the classification accuracy and community composition analysis without major data loss. Our study also generated draft genome assemblies for three fungal species that were not present in genome databases. This study provides a practical guide for metagenomics analyses focusing on fungi.
Article
Environmental Sciences
Anna Kristina Witte, Janina Grosch, Beate Conrady, Lena Schomakers, Marcus Grohmann
Summary: This study investigated the usage of free SARS-CoV-2 point-of-care antigen tests during the third wave of the COVID-19 pandemic in a typical medium-sized European city. The results showed that different age groups had different preferences for test center locations and frequency. Offering diverse test opportunities to accommodate individual behavioral patterns is crucial for attracting more people to voluntarily participate in antigen testing.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2022)
Article
Biochemistry & Molecular Biology
Scott Ferguson, Ashley Jones, Kevin Murra, Benjamin Schwessinger, Justin O. Borevitz
Summary: Synteny loss, primarily caused by unequal homologous recombination, is commonly observed when comparing closely related species. In this study, the genomes of three closely related Eucalyptus species were analyzed, revealing that approximately 48% of the genomes remained syntenic while approximately 36% underwent rearrangements. It was found that rearrangements highly fragmented microsynteny and potentially altered the phenotypes of the Eucalyptus species. This study highlights the importance of using an unbiased framework in genomic variation studies and emphasizes the potential impact of rearrangements on species differentiation and adaptation.
Article
Biochemistry & Molecular Biology
Brianne A. Kent, Constance Holman, Emmanuella Amoako, Alberto Antonietti, James M. Azam, Hanne Ballhausen, Yaw Bediako, Anat M. Belasen, Clarissa F. D. Carneiro, Yen-Chung Chen, Ewoud B. Compeer, Chelsea A. C. Connor, Sophia Cruwell, Humberto Debat, Emma Dorris, Hedyeh Ebrahimi, Jeffrey C. Erlich, Florencia Fernandez-Chiappe, Felix Fischer, Malgorzata Anna Gazda, Toivo Glatz, Peter Grabitz, Verena Heise, David G. Kent, Hung Lo, Gary McDowell, Devang Mehta, Wolf-Julian Neumann, Kleber Neves, Mark Patterson, Naomi C. Penfold, Sophie K. Piper, Iratxe Puebla, Peter K. Quashie, Carolina Paz Quezada, Julia L. Riley, Jessica L. Rohmann, Shyam Saladi, Benjamin Schwessinger, Bob Siegerink, Paulina Stehlik, Alexandra Tzilivaki, Kate D. L. Umbers, Aalok Varma, Kaivalya Walavalkar, Charlotte M. de Winde, Cecilia Zaza, Tracey L. Weissgerber
Summary: This study summarizes the outputs of a virtual unconventional conference that gathered experts with experience in ECR initiatives to improve the culture and practice of science. The recommendations highlight the need to incentivize and provide resources for ECRs involved in systemic science improvement, involve ECRs in decision-making processes, and address barriers to participation for marginalized groups.
Article
Biochemical Research Methods
Scott Ferguson, Todd McLay, Rose L. Andrew, Jeremy J. Bruhl, Benjamin Schwessinger, Justin Borevitz, Ashley Jones
Summary: This study utilizes ONT and PacBio sequencing platforms to improve sequencing accuracy by training species-specific basecaller models. The results show that species-specific basecaller models and improved sequencing kits can significantly improve sequencing accuracy.
Article
Multidisciplinary Sciences
Ashley Jones, David Stanley, Scott Ferguson, Benjamin Schwessinger, Justin Borevitz, Norman Warthmann
Summary: This study presents a cost-conscious protocol for generating multiplexed short-read DNA libraries using a bead-linked transposome from Illumina, which reduces costs and labor time compared to conventional methods.
Article
Ecology
Daniel Powell, Benjamin Schwessinger, Celine H. Frere
Summary: Researchers uncover new information on the evolutionary relationship of emerging fungal pathogens through mitochondrial genome sequencing and phylogenetic analysis of seven species. They also develop a species-specific qPCR assay for rapid detection and demonstrate its application in a wild urban population of a dragon lizard.
ECOLOGY AND EVOLUTION
(2023)
Article
Public, Environmental & Occupational Health
Robyn N. Hall, Ashley Jones, Emma Crean, Victoria Marriott, Nevada Pingault, Alexandra Marmor, Timothy Sloan-Gardner, Karina Kennedy, Kerryn Coleman, Vanessa Johnston, Benjamin Schwessinger
Summary: The Australian Capital Territory (ACT) detected an incursion of the SARS-CoV-2 Delta variant. Public health interventions, including a territory-wide lockdown and comprehensive contact tracing, were rapidly implemented. Genomic sequencing revealed at least 13 independent incursions with onward spread in the community, and different incursions affected distinct cohorts.
EPIDEMIOLOGY AND INFECTION
(2023)
Correction
Genetics & Heredity
Peri A. Tobias, Benjamin Schwessinger, Cecilia H. Deng, Chen Wu, Chongmei Dong, Jana Sperschneider, Ashley Jones, Zhenyan Lou, Peng Zhang, Karanjeet Sandhu, Grant R. Smith, Josquin Tibbits, David Chagne, Robert F. Park
G3-GENES GENOMES GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Hongyu Duan, Ashley W. Jones, Tim Hewitt, Amy Mackenzie, Yiheng Hu, Anna Sharp, David Lewis, Rohit Mago, Narayana M. Upadhyaya, John P. Rathjen, Eric A. Stone, Benjamin Schwessinger, Melania Figueroa, Peter N. Dodds, Sambasivam Periyannan, Jana Sperschneider
Summary: This study presents the first chromosome-scale, fully-phased assembly for the dikaryotic leaf rust fungus Puccinia triticina and compares the performance of Nanopore MinION and PacBio HiFi sequencing technologies. The study shows that false-positive Hi-C contacts between haplotypes are mainly caused by phase switches.
Article
Genetics & Heredity
Peri A. Tobias, Benjamin Schwessinger, Cecilia H. Deng, Chen Wu, Chongmei Dong, Jana Sperschneider, Ashley Jones, Zhenyan Lou, Peng Zhang, Karanjeet Sandhu, Grant R. Smith, Josquin Tibbits, David Chagne, Robert F. Park
Summary: Austropuccinia psidii, a globally invasive fungal plant pathogen with a broad host range, negatively impacts Myrtaceae. Assembly of the genome for the pandemic biotype revealed the significant role of transposable elements in shaping the evolutionary trajectory of A. psidii.
G3-GENES GENOMES GENETICS
(2021)