Browsing by Author "Chen, Ye"

Now showing 1 - 7 of 7
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    Biochar and Microbial Signaling: Production Conditions Determine Effects on Microbial Communication
    (American Chemical Society, 2013) Masiello, Caroline A.; Chen, Ye; Gao, Xiaodong; Liu, Shirley; Cheng, Hsiao-Ying; Bennett, Matthew R.; Rudgers, Jennifer A.; Wagner, Daniel S.; Zygourakis, Kyriacos; Silberg, Jonathan J.; Bioengineering; Biosciences; Chemical and Biomolecular Engineering; Earth, Environmental and Planetary Sciences
    Charcoal has a long soil residence time, which has resulted in its production and use as a carbon sequestration technique (biochar). A range of biological effects can be triggered by soil biochar that can positively and negatively influence carbon storage, such as changing the decomposition rate of organic matter and altering plant biomass production. Sorption of cellular signals has been hypothesized to underlie some of these effects, but it remains unknown whether the binding of biochemical signals occurs, and if so, on time scales relevant to microbial growth and communication. We examined biochar sorption of N-3-oxo-dodecanoyl-L-homoserine lactone, an acyl-homoserine lactone (AHL) intercellular signaling molecule used by many gram-negative soil microbes to regulate gene expression. We show that wood biochars disrupt communication within a growing multicellular system that is made up of sender cells that synthesize AHL and receiver cells that express green fluorescent protein in response to an AHL signal. However, biochar inhibition of AHL-mediated cell–cell communication varied, with the biochar prepared at 700 °C (surface area of 301 m2/g) inhibiting cellular communication 10-fold more than an equivalent mass of biochar prepared at 300 °C (surface area of 3 m2/g). These findings provide the first direct evidence that biochars elicit a range of effects on gene expression dependent on intercellular signaling, implicating the method of biochar preparation as a parameter that could be tuned to regulate microbial-dependent soil processes, like nitrogen fixation and pest attack of root crops.
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    Emergent genetic oscillations in a synthetic microbial consortium
    (American Association for the Advancement of Science, 2015) Chen, Ye; Kim, Jae Kyoung; Hirning, Andrew J.; Josić, Krešimir; Bennett, Matthew R.; Institute of Biosciences and Bioengineering
    A challenge of synthetic biology is the creation of cooperative microbial systems that exhibit population-level behaviors. Such systems use cellular signaling mechanisms to regulate gene expression across multiple cell types. We describe the construction of a synthetic microbial consortium consisting of two distinct cell types—an "activator" strain and a "repressor" strain. These strains produced two orthogonal cell-signaling molecules that regulate gene expression within a synthetic circuit spanning both strains. The two strains generated emergent, population-level oscillations only when cultured together. Certain network topologies of the two-strain circuit were better at maintaining robust oscillations than others. The ability to program population-level dynamics through the genetic engineering of multiple cooperative strains points the way toward engineering complex synthetic tissues and organs with multiple cell types.
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    Engineering genetically controlled microbial consortia
    (2016-06-24) Chen, Ye; Bennett, Matthew; Beckingham, Kathleen
    To date, the majority of synthetic gene circuits have been constructed to operate within single, isogenic cellular populations. Two of the toughest challenges for synthetic biologists to achieve complicated multi-strain systems are the limited choice of inducible signals and tuning regulatory components within a gene circuit to elicit desired outputs. Here, we describe a method that allows one to tune the dynamic range in a motif based construction of promoters with regulatory elements. To do this, we first assembled and then tested a library of promoters using different -10 and -35 sites taken from endogenous promoters within Escherichia coli. By mixing and matching the -10 and -35 sites, we were able to create a large number of ligand-inducible promoters exhibiting a wide variety of dynamic ranges. Using this method, we developed an orthogonal, tightly controlled two-signaling system. Then, we used two genetically distinct populations of Escherichia coli and this signaling system to engineer a bacterial consortium that exhibits robust oscillations in gene transcription. When co-cultured in a microfluidic device, the two strains form coupled positive and negative feedback loops at the population-level. The interacting strains exhibit robust, synchronized oscillations that are absent if either strain is cultured in isolation. We further used a combination of mathematical modeling and targeted genetic perturbations to better understand the roles of circuit topology and regulatory promoter strengths in generating and maintaining these oscillations. We found that the dual-feedback topology was robust to changes in promoter strengths and fluctuations in the population ratio of the two strains. These findings demonstrate that one can program population-level dynamics through the genetic engineering of multiple cooperative strains and point the way towards engineering complex synthetic tissues and organs with multiple cell types.
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    Fully gapped d-wave superconductivity in CeCu2Si2
    (National Academy of Sciences, 2018) Pang, Guiming; Smidman, Michael; Zhang, Jinglei; Jiao, Lin; Weng, Zongfa; Nica, Emilian M.; Chen, Ye; Jiang, Wenbing; Zhang, Yongjun; Xie, Wu; Jeevan, Hirale S.; Lee, Hanoh; Gegenwart, Philipp; Steglich, Frank; Si, Qimiao; Yuan, Huiqiu
    The nature of the pairing symmetry of the first heavy fermion superconductor CeCu2Si2 has recently become the subject of controversy. While CeCu2Si2 was generally believed to be a d-wave superconductor, recent low-temperature specific heat measurements showed evidence for fully gapped superconductivity, contrary to the nodal behavior inferred from earlier results. Here, we report London penetration depth measurements, which also reveal fully gapped behavior at very low temperatures. To explain these seemingly conflicting results, we propose a fully gapped d+d band-mixing pairing state for CeCu2Si2, which yields very good fits to both the superfluid density and specific heat, as well as accounting for a sign change of the superconducting order parameter, as previously concluded from inelastic neutron scattering results.
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    Majority sensing in synthetic microbial consortia
    (Springer Nature, 2020) Alnahhas, Razan N.; Sadeghpour, Mehdi; Chen, Ye; Frey, Alexis A.; Ott, William; Josić, Krešimir; Bennett, Matthew R.; Bioengineering; Biosciences
    As synthetic biocircuits become more complex, distributing computations within multi-strain microbial consortia becomes increasingly beneficial. However, designing distributed circuits that respond predictably to variation in consortium composition remains a challenge. Here we develop a two-strain gene circuit that senses and responds to which strain is in the majority. This involves a co-repressive system in which each strain produces a signaling molecule that signals the other strain to down-regulate production of its own, orthogonal signaling molecule. This co-repressive consortium links gene expression to ratio of the strains rather than population size. Further, we control the cross-over point for majority via external induction. We elucidate the mechanisms driving these dynamics by developing a mathematical model that captures consortia response as strain fractions and external induction are varied. These results show that simple gene circuits can be used within multicellular synthetic systems to sense and respond to the state of the population.
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    Tuning the dynamic range of bacterial promoters regulated by ligand-inducible transcription factors
    (Springer Nature, 2018) Chen, Ye; Ho, Joanne M.L.; Shis, David L.; Gupta, Chinmaya; Long, James; Wagner, Daniel S.; Ott, William; Josić, Krešimir; Bennett, Matthew R.; Bioengineering; Biosciences
    One challenge for synthetic biologists is the predictable tuning of genetic circuit regulatory components to elicit desired outputs. Gene expression driven by ligand-inducible transcription factor systems must exhibit the correct ON and OFF characteristics: appropriate activation and leakiness in the presence and absence of inducer, respectively. However, the dynamic range of a promoter (i.e., absolute difference between ON and OFF states) is difficult to control. We report a method that tunes the dynamic range of ligand-inducible promoters to achieve desired ON and OFF characteristics. We build combinatorial sets of AraC-and LasR-regulated promoters containing -10 and -35 sites from synthetic and Escherichia coli promoters. Four sequence combinations with diverse dynamic ranges were chosen to build multi-input transcriptional logic gates regulated by two and three ligand-inducible transcription factors (LacI, TetR, AraC, XylS, RhlR, LasR, and LuxR). This work enables predictable control over the dynamic range of regulatory components.
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    Tuning the dynamic range of bacterial promoters regulated by ligand-inducible transcription factors
    (Springer Nature, 2018) Chen, Ye; Ho, Joanne M.L.; Shis, David L.; Gupta, Chinmaya; Long, James; Wagner, Daniel S.; Ott, William; Josić, Krešimir; Bennett, Matthew R.; Bioengineering; Biosciences
    One challenge for synthetic biologists is the predictable tuning of genetic circuit regulatory components to elicit desired outputs. Gene expression driven by ligand-inducible transcription factor systems must exhibit the correct ON and OFF characteristics: appropriate activation and leakiness in the presence and absence of inducer, respectively. However, the dynamic range of a promoter (i.e., absolute difference between ON and OFF states) is difficult to control. We report a method that tunes the dynamic range of ligand-inducible promoters to achieve desired ON and OFF characteristics. We build combinatorial sets of AraC-and LasR-regulated promoters containing -10 and -35 sites from synthetic and Escherichia coli promoters. Four sequence combinations with diverse dynamic ranges were chosen to build multi-input transcriptional logic gates regulated by two and three ligand-inducible transcription factors (LacI, TetR, AraC, XylS, RhlR, LasR, and LuxR). This work enables predictable control over the dynamic range of regulatory components.