Eric Sembrat's Test Bonanza

The ribosome translates the genetic information encoded in messenger RNA into protein. Folded structures in the coding region of an mRNA represent
a kinetic barrier that lowers the peptide elongation rate, as the ribosome must disrupt structures it encounters in the mRNA to allow translocation to the next codon. Such structures are exploited by the cell to create diverse strategies for translation regulation. Although strand separation activity is inherent to the ribosome, requiring no exogenous helicases, its mechanism is still unknown. By using a single-molecule optical tweezers assay to follow in real time the codon-by-codon translation of mRNA hairpins, we conducted a quantitative characterization of the effect of the RNA structural stability on the peptide elongation rate, which revealed distinct mechanisms utilized by the ribosome to unwind mRNA structures. Our results establish a quantitative mechanical basis for understanding the mechanism of translational regulation of the elongation rate by structured mRNAs.

One of the fundamental problems in biology is understanding how phenotypic variations arise in individuals. Phenotypic variation is generally attributed to genetic or environmental factors. However, in several important cases, phenotypic variations are observed even among genetically identical cells in homogeneous environments. Recent research indicates that such `non-genetic individuality' can arise due to intrinsic stochasticity in the process of gene expression. Correspondingly there is a need to develop a framework for quantitative modeling of stochastic gene expression and its regulation. Of particular interest is modeling of regulation by non-coding RNAs, which is often a critical component of cellular processes such as development, differentiation and cancer.

In this talk, I will discuss approaches developed by my group that lead to new analytical results for stochastic models of gene expression. In biologically relevant limits, we develop a mapping to queueing theory to derive exact results for general models of stochastic gene expression. Focusing on specific regulatory mechanisms, we propose and analyze a comprehensive model for regulation by non-coding RNAs.  The results obtained provide new insights into the role of non-coding RNAs in fine-tuning the noise in gene expression. I will conclude with a discussion of protocols for inferring gene expression parameters from observations of mRNA and protein distributions.

Riboswitches are RNA elements located in the untranslated regions of mRNAs that regulate gene expression by sensing and binding target cellular metabolites. In bacteria, they bind specific metabolites with a conserved aptamer domain, resulting in a change of the folding patterns of downstream expression platform that controls transcription termination or translation initiation. Purine riboswitches, which are among the simplest, display remarkable ligand selectivity and carry out entirely different functions despite the structural similarity of the aptamers. In this talk I will describe coarse-grained to map the folding landscape of purine riboswitches.  The folding landscapes provide insights into the differences between two purine riboswitches.  The results of the simulations are used as guide to develop a kinetic network model at the system level.

Engineered biological circuits expressed in living cells are becoming increasingly attractive as a technology, with applications ranging from biofuel production to medical treatments.  A major goal in synthetic biology is to facilitate the rational design of biological circuits by discovering design principles.  In this talk, a brief background to synthetic biology will precede a discussion of three topics (synthetic oscillators, queueing systems, and multicellular environments) where such design principles have been explored by us.

In the natural world, complex behaviors such as learning, aggression and sleep are regulated by interconnected networks of genes and their products. Owing to their nontrivial topology and large number of components, most of these networks are poorly understood and consequently, our knowledge of how diverse behaviors arise remains limited. In this talk, I will argue that the fruit fly circadian clock, a genetic circuit that signals to and modulates several key behavioral networks, is an ideal system with which to dissect the fundamental principles that govern organismal behavior. I will discuss recent results from experimental studies at the transcriptional and post-translational levels of the fly clock as well as simple mathematical models aimed at understanding fruit fly locomotion. The talk will end with an outline of future studies using the fly that will provide novel mechanistic insights into how complex behavior emerges from simple molecular events. 

Membrane proteins are critical components of all cells, controlling, e.g., signaling, nutrient exchange, and energy production, and are the target of over half of all drugs currently in production.  At an early stage of their synthesis, nearly all membrane proteins are directed to a protein-conducting channel, the SecY/Sec61 complex, which permits access to the membrane via its lateral gate.  By combining molecular dynamics simulations with cryo-electron microscopy data, we recently resolved the first structure of a membrane-protein-insertion intermediate state of SecY bound to a translating ribosome, with a transmembrane (TM) segment caught at the open gate. Beginning from that state, multi-microsecond simulations of different putative TM segments at the gate have been carried out. The simulations reveal spontaneous motion of the TM segment, either inserting into the membrane or toward the channel interior, depending on its sequence, in agreement with a thermodynamic partitioning proposed previously.  However, attempts to quantify this partitioning led to experiment- and simulation-based scales for the free-energy insertion cost of various amino acids that differ significantly, leaving open the question of the true insertion process.  Now, using novel free-energy calculations and by carefully matching the context of the simulations to experiment, I will demonstrate a significantly improved agreement for multiple membrane-protein-insertion assays.  Thus, it is suggested that the discrimination step between membrane-inserted and secreted states of a nascent protein occurs primarily in the SecY channel.

 Cosmological hydrodynamical simulations are a useful tool for following the formation and evolution of galaxies over long timescales, but we must prescribe accurate models for the physics on small scales, below the resolution limits of our simulations. I investigate several different "subgrid models" at these scales to see what their effects are on a single Milky Way sized galaxy evolved from just after the Big Bang until the present. I grade the success of each model on how well it matches the dynamics of typical disk galaxies, creates a realistic star formation history, and produces a reasonable circumgalactic halo.

Squeezed states allow interferometers to surpass the standard quantum limit of the Heisenberg uncertainty principle.  Here we study spin-nematic squeezing of a spin-1 condensate following a quench through a nematic-ferromagnetic quantum phase transition.  We observe up to -8.3 dB squeezing in the variance of the spin-nematic quadratures.  This squeezing is observed for negligible occupation of the squeezed modes and is analogous to optical two-mode vacuum squeezing [1].

1. C.D. Hamley, C.D. Gerving, T.M. Hoang, E.M. Bookjans, and M.S. Chapman, “Spin-Nematic Squeezed Vacuum in a Quantum Gas,” To appear in Nature Phys.

Trapped attractive atomic Bose-Einstein condensates (BECs) in three spatial dimensions are known to exist for some finite time only. This is because the gas is prone to self-collapse, due to the attractive nature of the interaction. The 'mainstream' way to describe the state of the condensate is a mean-field (MF) theory, that assumes total condensation of the system.  In this talk I will introduce the notion of fragmentation, in contrast to coherence, and show that the states of definite angular momentum of the 3D many-body system cannot be condensed MF states. With this at hand, I examine the impact of the angular momentum to the stability of the attractive gas and show that there is a general stabilizing tendency.