Ned S. Wingreen

The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae

Quorum-sensing bacteria communicate with extracellular signal molecules called autoinducers. This process allows community-wide synchronization of gene expression. A screen for additional components of the Vibrio harveyi and Vibrio cholerae quorum-sensing circuits revealed the protein Hfq. Hfq mediates interactions between small, regulatory RNAs (sRNAs) and specific messenger RNA (mRNA) targets. These interactions typically alter the stability of the target transcripts. We show that Hfq mediates the destabilization of the mRNA encoding the quorum-sensing master regulators LuxR (V. harveyi) and HapR (V. cholerae), implicating an sRNA in the circuit. Using a bioinformatics approach to identify putative sRNAs, we identified four candidate sRNAs in V. cholerae. The simultaneous deletion of all four sRNAs is required to stabilize hapR mRNA. We propose that Hfq, together with these sRNAs, creates an ultrasensitive regulatory switch that controls the critical transition into the high cell density, quorum-sensing mode.

Emergence of Preferred Structures in a Simple Model of Protein Folding

Protein structures in nature often exhibit a high degree of regularity (for example, secondary structure and tertiary symmetries) that is absent from random compact conformations. With the use of a simple lattice model of protein folding, it was demonstrated that structural regularities are related to high “designability” and evolutionary stability. The designability of each compact structure is measured by the number of sequences that can design the structure—that is, sequences that possess the structure as their nondegenerate ground state. Compact structures differ markedly in terms of their designability; highly designable structures emerge with a number of associated sequences much larger than the average. These highly designable structures possess “proteinlike” secondary structure and even tertiary symmetries. In addition, they are thermodynamically more stable than other structures. These results suggest that protein structures are selected in nature because they are readily designed and stable against mutations, and that such a selection simultaneously leads to thermodynamic stability.

Low-temperature transport through a quantum dot: The Anderson model out of equilibrium.

Abstract : The infinite-U Anderson model is applied to non-equilibrium transport through a quantum dot containing two spin levels weakly coupled to two leads. At low temperatures, the Kondo peak in the equilibrium density of states is split upon the application of a voltage bias. The split peaks, one at the chemical potential of each lead, are suppressed by non-equilibrium dissipation. In a magnetic field, the Kondo peaks shift away from the chemical potentials by the Zeeman energy, leading to an observable peak in the differential conductance when the non-equilibrium bias equals the Zeeman energy. Infinite-U Anderson model, Kondo peak, Zeeman energy, Low-temperature transport through a quantum dot, Kondo effect.

Diet-induced extinctions in the gut microbiota compound over generations

The gut is home to trillions of microorganisms that have fundamental roles in many aspects of human biology, including immune function and metabolism. The reduced diversity of the gut microbiota in Western populations compared to that in populations living traditional lifestyles presents the question of which factors have driven microbiota change during modernization. Microbiota-accessible carbohydrates (MACs) found in dietary fibre have a crucial involvement in shaping this microbial ecosystem, and are notably reduced in the Western diet (high in fat and simple carbohydrates, low in fibre) compared with a more traditional diet. Here we show that changes in the microbiota of mice consuming a low-MAC diet and harbouring a human microbiota are largely reversible within a single generation. However, over several generations, a low-MAC diet results in a progressive loss of diversity, which is not recoverable after the reintroduction of dietary MACs. To restore the microbiota to its original state requires the administration of missing taxa in combination with dietary MAC consumption. Our data illustrate that taxa driven to low abundance when dietary MACs are scarce are inefficiently transferred to the next generation, and are at increased risk of becoming extinct within an isolated population. As more diseases are linked to the Western microbiota and the microbiota is targeted therapeutically, microbiota reprogramming may need to involve strategies that incorporate dietary MACs as well as taxa not currently present in the Western gut.

Electron Transport in Quantum Dots

The ongoing miniaturization of solid state devices often leads to the question: “How small can we make resistors, transistors, etc., without changing the way they work?” The question can be asked a different way, however: “How small do we have to make devices in order to get fundamentally new properties?” By “new properties” we particularly mean those that arise from quantum mechanics or the quantization of charge in units of eeffects that are only important in small systems such as atoms. “What kind of small electronic devices do we have in mind?” Any sort of clustering of atoms that can be connected to source and drain contacts and whose properties can be regulated with a gate electrode. Practically, the clustering of atoms may be a molecule, a small grain of metallic atoms, or an electronic device that is made with modern chip fabrication techniques. It turns out that such seemingly different structures have quite similar transport properties and that one can explain their physics within one relatively simple framework. In this paper we investigate the physics of electron transport through such small systems.

Self-Organization of the Escherichia Coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy

Photoactivated localization microscopy analysis of chemotaxis receptors in bacteria suggests that the non-random organization of these proteins results from random self-assembly of clusters without direct cytoskeletal involvement or active transport.

Collective transport in arrays of small metallic dots

Collective charge transport is studied in one- and two-dimensional arrays of small normal-metal dots separated by tunneling barriers. At temperatures well below the charging energy of a dot, disorder leads to a threshold for conduction which grows linearly with the size of the array. For short-ranged interactions, one of the correlation length exponents near threshold is found from a novel argument based on interface growth. The dynamical exponent for the current above threshold is also predicted analytically, and the requirements for its experimental observation are described.

The bacterial actin MreB rotates, and rotation depends on cell-wall assembly

Bacterial cells possess multiple cytoskeletal proteins involved in a wide range of cellular processes. These cytoskeletal proteins are dynamic, but the driving forces and cellular functions of these dynamics remain poorly understood. Eukaryotic cytoskeletal dynamics are often driven by motor proteins, but in bacteria no motors that drive cytoskeletal motion have been identified to date. Here, we quantitatively study the dynamics of the Escherichia coli actin homolog MreB, which is essential for the maintenance of rod-like cell shape in bacteria. We find that MreB rotates around the long axis of the cell in a persistent manner. Whereas previous studies have suggested that MreB dynamics are driven by its own polymerization, we show that MreB rotation does not depend on its own polymerization but rather requires the assembly of the peptidoglycan cell wall. The cell-wall synthesis machinery thus either constitutes a novel type of extracellular motor that exerts force on cytoplasmic MreB, or is indirectly required for an as-yet-unidentified motor. Biophysical simulations suggest that one function of MreB rotation is to ensure a uniform distribution of new peptidoglycan insertion sites, a necessary condition to maintain rod shape during growth. These findings both broaden the view of cytoskeletal motors and deepen our understanding of the physical basis of bacterial morphogenesis.

Vibrio harveyi quorum sensing: a coincidence detector for two autoinducers controls gene expression

In a process called quorum sensing, bacteria communicate with one another by exchanging chemical signals called autoinducers. In the bioluminescent marine bacterium Vibrio harveyi, two different auto inducers (AI‐1 and AI‐2) regulate light emission. Detection of and response to the V.harveyi autoinducers are accomplished through two two‐component sensory relay systems: AI‐1 is detected by the sensor LuxN and AI‐2 by LuxPQ. Here we further define the V.harveyi quorum‐sensing regulon by identifying 10 new quorum‐sensing‐controlled target genes. Our examination of signal processing and integration in the V.harveyi quorum‐sensing circuit suggests that AI‐1 and AI‐2 act synergistically, and that the V.harveyi quorum‐sensing circuit may function exclusively as a ‘coincidence detector’ that discriminates between conditions in which both autoinducers are present and all other conditions.

Responding to chemical gradients: bacterial chemotaxis.

Chemotaxis allows bacteria to follow gradients of nutrients and other environmental stimuli. The bacterium Escherichia coli performs chemotaxis via a run-and-tumble strategy in which sensitive temporal comparisons lead to a biased random walk, with longer runs in the preferred gradient direction. The chemotaxis network of E. coli has developed over the years into one of the most thoroughly studied model systems for signal transduction and behavior, yielding general insights into such properties of cellular networks as signal amplification, signal integration, and robustness. Despite its relative simplicity, the operation of the E. coli chemotaxis network is highly refined and evolutionarily optimized at many levels. For example, recent studies revealed that the network adjusts its signaling properties dependent on the extracellular environment, apparently to optimize chemotaxis under particular conditions. The network can even utilize potentially detrimental stochastic fluctuations in protein levels and reaction rates to maximize the chemotactic performance of the population.