Now showing items 1-10 of 141
Understanding the Principles of Pattern Formation Driven by Notch Signaling by Integrating Experiments and Theoretical Models
Notch signaling is an evolutionary conserved cell-cell communication pathway. Besides regulating cell-fate decisions at an individual cell level, Notch signaling coordinates the emergent spatiotemporal patterning in a tissue through ligand-receptor interactions among transmembrane molecules of neighboring cells, as seen in embryonic development, ...
Functional diversity and redundancy of tropical forest mammals over time
Globally, tropical rain forests comprise some of the most diverse and functionally rich ecosystems but are increasingly degraded by human impacts. Protected areas have been shown to conserve species diversity, but their effectiveness at maintaining functional diversity over time is less well known, despite the fact that functional diversity likely ...
A Simple Nematode Infection Model for Studying Candida albicans Pathogenesis
Candida albicans is an opportunistic fungal pathogen and a model organism to study fungal pathogenesis. It exists as a harmless commensal organism and member of the healthy human microbiome, but can cause life‐threatening mucosal and systemic infections. A model host to study C. albicans infection and pathogenesis is the nematode Caenorhabditis ...
Molecular-replacement phasing using predicted protein structures from AWSEM-Suite
(International Union of Crystallography, 2020)
The phase problem in X-ray crystallography arises from the fact that only the intensities, and not the phases, of the diffracting electromagnetic waves are measured directly. Molecular replacement can often estimate the relative phases of reflections starting with those derived from a template structure, which is usually a previously solved structure ...
Surveying biomolecular frustration at atomic resolution
(Springer Nature, 2020)
To function, biomolecules require sufficient specificity of interaction as well as stability to live in the cell while still being able to move. Thermodynamic stability of only a limited number of specific structures is important so as to prevent promiscuous interactions. The individual interactions in proteins, therefore, have evolved collectively ...
Open questions: how do engineered nanomaterials affect our cells?
(BioMed Central, 2020)
Our cells have evolutionarily conserved mechanisms that battle foreign and toxic materials to maintain cellular homeostasis and viability. How do these cellular machineries respond to engineered nanomaterials?
A suppressor tRNA-mediated feedforward loop eliminates leaky gene expression in bacteria
(Oxford University Press, 2021)
Ligand-inducible genetic systems are the mainstay of synthetic biology, allowing gene expression to be controlled by the presence of a small molecule. However, ‘leaky’ gene expression in the absence of inducer remains a persistent problem. We developed a leak dampener tool that drastically reduces the leak of inducible genetic systems while retaining ...
Translating New Synthetic Biology Advances for Biosensing Into the Earth and Environmental Sciences
The rapid diversification of synthetic biology tools holds promise in making some classically hard-to-solve environmental problems tractable. Here we review longstanding problems in the Earth and environmental sciences that could be addressed using engineered microbes as micron-scale sensors (biosensors). Biosensors can offer new perspectives on open ...
A zero-dimensional view of atmospheric degradation of levoglucosan (LEVCHEM_v1) using numerical chamber simulations
(Copernicus Publications, 2021)
Here, we developed a zero-dimensional (0-D) modeling framework (LEVCHEM_v1) to provide insights into the atmospheric degradation of a key tracer emitted during biomass burning – levoglucosan (LEV), while additionally exploring its effects on the dynamics of secondary organic aerosols (SOA) and other gases. For this, we updated existing chemical ...
Comprehensive genetic analysis of adhesin proteins and their role in virulence of Candida albicans
(Oxford University Press, 2021)
Candida albicans is a microbial fungus that exists as a commensal member of the human microbiome and an opportunistic pathogen. Cell surface-associated adhesin proteins play a crucial role in C. albicans’ ability to undergo cellular morphogenesis, develop robust biofilms, colonize, and cause infection in a host. However, a comprehensive analysis of ...