Article
Multidisciplinary Sciences
Joshua R. Elmore, Gara N. Dexter, Henri Baldino, Jay D. Huenemann, Ryan Francis, V. George L. Peabody, Jessica Martinez-Baird, Lauren A. Riley, Tuesday Simmons, Devin Coleman-Derr, Adam M. Guss, Robert G. Egbert
Summary: SAGE is a highly efficient and extensible genome engineering technology that allows selection marker-free, site-specific genome integration of multiple DNA constructs in bacteria. It shows superior efficiency compared to replicating plasmids and overcomes host range limitations. SAGE has the potential to expand high-throughput genetics and synthetic biology in industrial and environmental bacteria.
Article
Biochemistry & Molecular Biology
Maria H. T. Nguyen, Zoe Netter, Angus Angermeyer, Kimberley D. Seed
Summary: Bacteria can acquire mobile genetic elements to combat viral infection. Satellite viruses restrict viral replication for the benefit of their host bacterium. In the arms race against satellite viruses, certain viruses can evade restriction through unknown mechanisms. This study identifies a viral protein that counteracts satellite viruses by exploiting a specific enzyme within the viruses.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Matthew G. Durrant, Alison Fanton, Josh Tycko, Michaela Hinks, Sita S. Chandrasekaran, Nicholas T. Perry, Julia Schaepe, Peter P. Du, Peter Lotfy, Michael C. Bassik, Lacramioara Bintu, Ami S. Bhatt, Patrick D. Hsu
Summary: Large serine recombinases (LSRs) are DNA integrases that facilitate the site-specific integration of mobile genetic elements into bacterial genomes. In this study, a computational approach was developed to identify thousands of LSRs and their DNA attachment sites, expanding known LSR diversity and enabling more efficient DNA integration. This research provides new tools for inserting large sequences into the human genome.
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Adriana Adolfi, Amy Lynd, Gareth J. Lycett, Anthony A. James
Summary: The phi C31 system is a crucial genetic tool for the transgenic manipulation of malaria mosquitoes and other insect vectors, enabling precise modification of the Anopheles genome to achieve genetic control of malaria.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Microbiology
Chengjin Ye, Luis Martinez-Sobrido
Summary: Reporter-expressing recombinant virus is a powerful tool for studying viral infection and therapeutic approaches. To facilitate COVID-19 research, we established a BAC-based reverse genetics system to rapidly generate rSARS-CoV-2 and engineered recombinant viruses with reporter genes. We shared this system and provided detailed technical steps to aid other laboratories in their investigations.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Alejandra Fuentes, Hector Herrera, Trevor C. Charles, Cesar Arriagada
Article
Multidisciplinary Sciences
Tam T. Tran, Trevor C. Charles
Editorial Material
Biochemistry & Molecular Biology
M. J. Ryan, M. Schloter, G. Berg, T. Kostic, L. L. Kinkel, K. Eversole, J. A. Macklin, B. Schelkle, M. Kazou, I. Sarand, B. K. Singh, D. Fischer, E. Maguin, I. Ferrocino, N. Lima, R. S. McClure, T. C. Charles, R. S. C. de Souza, G. S. Kiran, H. L. Krug, J. Taffner, H. Roume, J. Selvin, D. Smith, D. Rybakova, A. Sessitsch
Summary: The microbiome research field is rapidly advancing and requires a well-established biobanking infrastructure for preserving microbiome samples and their functional potential. There is an urgent need for assessing how biobanks can support research in this rapidly evolving field.
TRENDS IN MICROBIOLOGY
(2021)
Correction
Biochemistry & Molecular Biology
M. J. Ryan, M. Schloter, G. Berg, T. Kostic, L. L. Kinkel, K. Eversole, J. A. Macklin, B. Schelkle, M. Kazou, I. Sarand, B. K. Singh, D. Fischer, E. Maguin, I. Ferrocino, N. Lima, R. S. McClure, T. C. Charles, R. S. C. de Souza, G. S. Kiran, H. L. Krug, J. Taffner, H. Roume, J. Selvin, D. Smith, D. Rybakova, A. Sessitsch
TRENDS IN MICROBIOLOGY
(2021)
Article
Environmental Sciences
Gem Thomas-Barry, Chaney C. G. St Martin, Michael D. J. Lynch, Adesh Ramsubhag, Judy Rouse-Miller, Trevor C. Charles
Summary: This study investigated the changes in rhizobacteriome community structure in hyper-seasonal edaphic savannas, showing that soil and season were key determinants influencing the community structure. Plant biomass, root traits, and rhizobacterial community compositions were found to be influenced by seasonal changes and savanna-specific drivers.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Editorial Material
Biotechnology & Applied Microbiology
Stuart J. Smyth, Trevor C. Charles
Summary: Digital sequence information (DSI), defined as nonphysical genetic resources like genetic sequence data, lacks a clear definition and is not consistent among countries. Restricting the free sharing of DSI may conflict with core principles in fields like microbiology and molecular genetics, potentially impacting international research collaborations.
TRENDS IN BIOTECHNOLOGY
(2021)
Article
Genetics & Heredity
Tam T. Tran, Trevor C. Charles
Summary: Promoter engineering can enhance bio-product production, but the activity of a promoter may vary in different gene contexts. Inserted genes can affect promoter activity, leading to changes at the transcriptional level, which influence downstream applications.
Article
Biodiversity Conservation
Javiera Soto, Trevor C. Charles, Michael D. J. Lynch, Giovanni Larama, Hector Herrera, Cesar Arriagada
Summary: A novel strain of Brevundimonas sp. capable of growing under high doses of arsenic was isolated from metal(loid) contaminated soil in central Chile. Real-time PCR analysis revealed down-regulation of the arsB gene involved in arsenic efflux, while arsR, arsH, and ACR3 genes showed no significant differences in expression levels with the addition of arsenic.
Editorial Material
Microbiology
Vanessa A. Varaljay, Trevor C. Charles, Rolf Daniel
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Xueya Zhang, Shuang Liang, Qingnan Wu, Trevor C. Charles, Rui He, Jiakai Wu, Yuhui Zhao, Zhiyi Zhao, Hezhong Wang
Summary: This study investigated the mode of action of nanochitin whisker (NC) against Fusarium pseudograminearum (Fpg), an important pathogenic fungus causing wheat crown rot disease. The results showed that NC significantly reduced hyphal growth and spore germination rate of Fpg. It exerted its effects by disrupting cell wall structure, altering membrane integrity, decreasing enzyme activity related to energy-supply, and reducing mycotoxin production.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Review
Environmental Sciences
Aleksander Cholewinski, Eugenia Dadzie, Cassandra Sherlock, William A. Anderson, Trevor C. Charles, Komal Habib, Steven B. Young, Boxin Zhao
Summary: The resilience and low cost of plastics have led to their widespread use, but also contribute to their abundance and persistence as waste. Plastic pollution is a major concern for global ecosystems and their health. Material flow analysis, previously used in other industries, has been applied to plastics to understand how waste enters the environment. However, research on degradation strategies for microplastics has been limited and material flow analysis lacks data. The variety of plastics, their additives, and contaminants present significant challenges in degrading microplastic particles.
ENVIRONMENTAL POLLUTION
(2022)
Article
Environmental Sciences
Rashmi Chandra, Aranksha Thakor, Tizazu H. Mekonnen, Trevor C. Charles, Hyung-Sool Lee
Summary: The production of polyhydroxyalkanoates (PHAs) with high carboxylate concentration accumulated from solid-state fermentation (SSF) of food waste (FW) was tested using Pseudomonas putida strain KT2440. The mixed-culture SSF of FW supplied in a high carboxylate concentration led to a high PHA production of 0.56 g PHA/g CDM under nutrients control. The dominant PHA building block produced was 3-hydroxybutyrate, followed by 3-hydroxy-2-methylvalerate and 3-hydroxyhexanoate, indicating that acetate, butyrate, and propionate were the main precursors to PHA.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
Article
Microbiology
Meghan Donovan, Calvin S. Mackey, Michael D. J. Lynch, Grayson N. Platt, Amber N. Brown, Brian K. Washburn, Darryl J. Trickey, J. Thomas Curtis, Yan Liu, Trevor C. Charles, Zuoxin Wang, Kathryn M. Jones
Summary: Research on the role of gut microbiota in behavior has advanced significantly. The probiotic L. reuteri can affect social and stress-related behaviors, but the mechanisms behind this are still unclear. Using prairie voles, a socially-monogamous species, the study found that treatment with live L. reuteri led to decreased social affiliation compared to heat-killed L. reuteri in females but not males. There were also differences in neurochemical markers, gut microbiome composition, and behaviors between the sexes and treatments.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Microbiology
Angela Sessitsch, Steve Wakelin, Michael Schloter, Emmanuelle Maguin, Tomislav Cernava, Marie-Christine Champomier-Verges, Trevor C. Charles, Paul D. Cotter, Ilario Ferrocino, Aicha Kriaa, Pedro Lebre, Don Cowan, Lene Lange, Seghal Kiran, Lidia Markiewicz, Annelein Meisner, Marta Olivares, Inga Sarand, Bettina Schelkle, Joseph Selvin, Hauke Smidt, Leo van Overbeek, Gabriele Berg, Luca Cocolin, Yolanda Sanz, Wilson Lemos Fernandes, S. J. Liu, Matthew Ryan, Brajesh Singh, Tanja Kostic
Summary: Microbiomes play crucial roles in ecosystem functioning, supporting planetary health through nutrient cycling, climate regulation, and water filtration. They are closely associated with complex multicellular organisms and contribute to the health of their hosts. However, there is still limited understanding of microbiome transfer and connectivity.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2023)
Review
Biotechnology & Applied Microbiology
Nicole LeBlanc, Trevor C. Charles
Summary: Bacterial cells are commonly used for the production of value-added products. However, their own metabolism, genetic instability, and the toxicity of the product often hinder efficient production. Genome reductions have been performed to create strains that can serve as chassis for downstream applications. Despite improvements in cellular characteristics, the construction of these cells efficiently and rapidly remains a major challenge.
FRONTIERS IN GENOME EDITING
(2022)