Browsing by Author "Dupont, Chris L."

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    Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection
    (2020) Kau, Drishti; Rathnasinghe, Raveen Shevantha; Ferrés, Marcela; Tan, Gene S.; Barrera Vásquez, Aldo Vincent; Pickett, Brett E.; Methe, Barbara A.; Das, Suman; Budnik Ojeda, Isolda Cecilia; Halpin, Rebecca A.; Wentworth, David; Schmolke, Mirco; Mena, Ignacio; Albrecht, Randy A.; Singh, Indresh; Nelson, Karen E.; Garcia Sastre, Adolfo; Dupont, Chris L.; Medina, Rafael
    Infection with influenza can be aggravated by bacterial co-infections, which often results in disease exacerbation. The effects of influenza infection on the upper respiratory tract (URT) microbiome are largely unknown. Here, we report a longitudinal study to assess the temporal dynamics of the URT microbiomes of uninfected and influenza virus-infected humans and ferrets. Uninfected human patients and ferret URT microbiomes have stable healthy ecostate communities both within and between individuals. In contrast, infected patients and ferrets exhibit large changes in bacterial community composition over time and between individuals. The unhealthy ecostates of infected individuals progress towards the healthy ecostate, coinciding with viral clearance and recovery. Pseudomonadales associate statistically with the disturbed microbiomes of infected individuals. The dynamic and resilient microbiome during influenza virus infection in multiple hosts provides a compelling rationale for the maintenance of the microbiome homeostasis as a potential therapeutic target to prevent IAV associated bacterial co-infections. Influenza A virus (IAV) infection can be exacerbated by bacterial co-infections but the effect of IAV on the upper respiratory tract (URT) microbiome remains unclear. Here, the authors compare the dynamics of the UTR microbiome in IAV-infected ferrets and humans, finding similar trends at the ecosystem and individual taxon level in both hosts.
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    Universal loop assembly: open, efficient and cross-kingdom DNA fabrication.
    (2020) Pollak, Bernardo; Matute Torres, Tamara Francisca; Núñez Quijada, Isaac Natán; Cerda Rojas, Ariel; López Sierra, Constanza Andrea; Vargas Torres, Valentina Isabel; Kan, Anton; Bielinski,Vincent; Dassow, Peter von; Dupont, Chris L.; Federici, Fernán
    Standardized type IIS DNA assembly methods are becoming essential for biological engineering and research. These methods are becoming widespread and more accessible due to the proposition of a 'common syntax' that enables higher interoperability between DNA libraries. Currently, Golden Gate (GG)-based assembly systems, originally implemented in hostspecific vectors, are being made compatible with multiple organisms. We have recently developed the GG-based Loop assembly system for plants, which uses a small library and an intuitive strategy for hierarchical fabrication of large DNA constructs (>30 kb). Here, we describe 'universal Loop' (uLoop) assembly, a system based on Loop assembly for use in potentially any organismof choice. This design permits the use of a compact number of plasmids (two sets of four odd and even vectors), which are utilized repeatedly in alternating steps. The elements required for transformation/maintenance in target organisms are also assembled as standardized parts, enabling customization of host-specific plasmids. Decoupling of the Loop assembly logic from the host-specific propagation elements enables universal DNA assembly that retains high efficiency regardless of the final host. As a proof-of-concept, we show the engineering of multigene expression vectors in diatoms, yeast, plants and bacteria. These resources are available through the OpenMTA for unrestricted sharing and open access.