Pseudobulbiferamides: Plasmid-Encoded Ureidopeptide Natural Products with Biosynthetic Gene Clusters Shared Among Marine Bacteria of Different Genera

Ureidopeptidic natural products possess a wide variety of favorable pharmacological properties. In addition, they have been shown to mediate core physiological functions in producer bacteria. Here, we report that similar ureidopeptidic natural products with conserved biosynthetic gene clusters are produced by different bacterial genera that coinhabit marine invertebrate microbiomes. We demonstrate that a Microbulbifer strain isolated from a marine sponge can produce two different classes of ureidopeptide natural products encoded by two different biosynthetic gene clusters that are positioned on the bacterial chromosome and on a plasmid. The plasmid encoded ureidopeptide natural products, which we term the pseudobulbiferamides (5-8), resemble the ureidopeptide natural products produced by Pseudovibrio, a different marine bacterial genus that is likewise present in marine sponge commensal microbiomes. Using imaging mass spectrometry, we find that the two classes of Microbulbifer-derived ureidopeptides occupy different physical spaces relative to the bacterial colony, perhaps implying different roles for these two compound classes in Microbulbifer physiology and environmental interactions.

Discovery and Biosynthesis of Ureidopeptide Natural Products Macrocyclized via Indole N-acylation in Marine Microbulbifer spp. Bacteria

Commensal bacteria associated with marine invertebrates are underappreciated sources of chemically novel natural products. Using mass spectrometry, we had previously detected the presence of peptidic natural products in obligate marine bacteria of the genus Microbulbifer cultured from marine sponges. In this report, the isolation and structural characterization of a panel of ureidohexapeptide natural products, termed the bulbiferamides, from Microbulbifer strains is reported wherein the tryptophan side chain indole participates in a macrocyclizing peptide bond formation. Genome sequencing identifies biosynthetic gene clusters encoding production of the bulbiferamides and implicates the involvement of a thioesterase in the indolic macrocycle formation. The structural diversity and widespread presence of bulbiferamides in commensal microbiomes of marine invertebrates point toward a possible ecological role for these natural products.

Metabolomics Approaches to Dereplicate Natural Products from Coral-Derived Bioactive Bacteria

Stony corals (Scleractinia) are invertebrates that form symbiotic relationships with eukaryotic algal endosymbionts and the prokaryotic microbiome. The microbiome has the potential to produce bioactive natural products providing defense and resilience to the coral host against pathogenic microorganisms, but this potential has not been extensively explored. Bacterial pathogens can pose a significant threat to corals, with some species implicated in primary and opportunistic infections of various corals. In response, probiotics have been proposed as a potential strategy to protect corals in the face of increased incidence of disease outbreaks. In this study, we screened bacterial isolates from healthy and diseased corals for antibacterial activity. The bioactive extracts were analyzed using untargeted metabolomics. Herein, an UpSet plot and hierarchical clustering analyses were performed to identify isolates with the largest number of unique metabolites. These isolates also displayed different antibacterial activities. Through application of in silico and experimental approaches coupled with genome analysis, we dereplicated natural products from these coral-derived bacteria from Florida's coral reef environments. The metabolomics approach highlighted in this study serves as a useful resource to select probiotic candidates and enables insights into natural product-mediated chemical ecology in holobiont symbiosis.

Classical dynamical coarse-grained entropy and comparison with the quantum version

We develop the framework of classical observational entropy, which is a mathematically rigorous and precise framework for nonequilibrium thermodynamics, explicitly defined in terms of a set of observables. Observational entropy can be seen as a generalization of Boltzmann entropy to systems with indeterminate initial conditions, and it describes the knowledge achievable about the system by a macroscopic observer with limited measurement capabilities; it becomes Gibbs entropy in the limit of perfectly fine-grained measurements. This quantity, while previously mentioned in the literature, has been investigated in detail only in the quantum case. We describe this framework reasonably pedagogically, then show that in this framework, certain choices of coarse-graining lead to an entropy that is well-defined out of equilibrium, additive on independent systems, and that grows toward thermodynamic entropy as the system reaches equilibrium, even for systems that are genuinely isolated. Choosing certain macroscopic regions, this dynamical thermodynamic entropy measures how close these regions are to thermal equilibrium. We also show that in the given formalism, the correspondence between classical entropy (defined on classical phase space) and quantum entropy (defined on Hilbert space) becomes surprisingly direct and transparent, while manifesting differences stemming from noncommutativity of coarse-grainings and from nonexistence of a direct classical analog of quantum energy eigenstates.

Online Liquid Chromatography-Sheath-Flow Surface Enhanced Raman Detection of Phosphorylated Carbohydrates

Online detection and quantification of three phosphorylated carbohydrate molecules: glucose 1-phosphate, glucose 6-phosphate, and fructose 6-phosphate was achieved by coupling sheath-flow surface enhanced Raman spectroscopy (SERS) to liquid chromatography. The presence of an alkanethiol (hexanethiol) self-assembled monolayer adsorbed to a silver SERS-active substrate helps retain and concentrate the analytes of interest at the SERS substrate to improve the detection sensitivity significantly. Mixtures of 2 μM of phosphorylated carbohydrates in pure water as well as in cell culture media were successfully separated by HPLC, with identification using the sheath-flow SERS detector. The quantification of each analyte was achieved using partial least-squares (PLS) regression analysis and acetonitrile in the mobile phases as an internal standard. These results illustrate the utility of sheath-flow SERS for molecular specific detection in complex biological samples appropriate for metabolomics and other applications.

Motor function in interpolar microtubules during metaphase

We analyze experimental motility assays of microtubules undergoing small fluctuations about a "balance point" when mixed in solution of two different kinesin motor proteins, KLP61F and Ncd. It has been proposed that the microtubule movement is due to stochastic variations in the densities of the two species of motor proteins. We test this hypothesis here by showing how it maps onto a one-dimensional random walk in a random environment. Our estimate of the amplitude of the fluctuations agrees with experimental observations. We point out that there is an initial transient in the position of the microtubule where it will typically move of order its own length. We compare the physics of this gliding assay to a recent theory of the role of antagonistic motors on restricting interpolar microtubule sliding of a cell's mitotic spindle during prometaphase. It is concluded that randomly positioned antagonistic motors can restrict relative movement of microtubules, however they do so imperfectly. A variation in motor concentrations is also analyzed and shown to lead to greater control of spindle length.

Microscopic origin of thermodynamic entropy in isolated systems

The quantum entropy is usually defined using von Neumann's formula, which measures lack of information and vanishes for pure states. In contrast, we obtain a formula for the entropy of a pure state as it is measured from thermodynamic experiments, solely from the self-entanglement of the wave function, and find strong numerical evidence that the two are in agreement for nonintegrable systems, both for energy eigenstates and for states that are obtained at long times under the evolution of more general initial conditions. This is an extension of Boltzmann's hypothesis for classical systems, relating microscopic motion to thermodynamics.

Ideal linear-chain polymers with fixed angular momentum

The statistical mechanics of a linear noninteracting polymer chain with a large number of monomers is considered with fixed angular momentum. The radius of gyration for a linear polymer is derived exactly by functional integration. This result is then compared to simulations done with a large number of noninteracting rigid links at fixed angular momentum. The simulation agrees with the theory up to finite-size corrections. The simulations are also used to investigate the anisotropic nature of a spinning polymer. We find universal scaling of the polymer size along the direction of the angular momentum, as a function of rescaled angular momentum.

Collision of polymers in a vacuum

In a number of experimental situations, single-polymer molecules can be suspended in a vacuum. Here collisions between such molecules are considered. The limit of high collision velocity is investigated numerically for a variety of conditions. The distribution of contact times, scattering angles, and final velocities are analyzed. In this limit, self-avoiding chains are found to become highly stretched as they collide with each other and have a distribution of scattering times that depends on the scattering angle. The velocity of the molecules after the collisions is similar to predictions of a model assuming thermal equilibration of molecules during the collision. The most important difference is a significant subset of molecules that inelastically scatter but do not substantially change direction.

Density fluctuations of polymers in disordered media

We study self-avoiding random walks in an environment where sites are excluded randomly, in two and three dimensions. For a single polymer chain, we study the statistics of the time averaged monomer density and show that these are well described by multifractal statistics. This is true even far from the percolation transition of the disordered medium. We investigate solutions of chains in a disordered environment and show that the statistics cease to be multifractal beyond the screening length of the solution.

Internal dissipation of a polymer

The dynamics of flexible polymer molecules are often assumed to be governed by hydrodynamics of the solvent. However there is considerable evidence that internal dissipation of a polymer contributes as well. Here we investigate the dynamics of a single chain in the absence of solvent to characterize the nature of this internal friction. We model the chains as freely hinged but with localized bond angles and threefold symmetric dihedral angles. We show that the damping is close but not identical to Kelvin damping, which depends on the first temporal and second spatial derivative of monomer position. With no internal potential between monomers, the magnitude of the damping is small for long wavelengths and weakly damped oscillatory time dependent behavior is seen for a large range of spatial modes. When the size of the internal potential is increased, such oscillations persist, but the damping becomes larger. However underdamped motion is present even with quite strong dihedral barriers for long enough wavelengths.

Induced orientational effects in relaxation of polymer melts

We study stress relaxation in bidisperse entangled polymer solutions. Shorter chains embedded in a majority of longer ones are known to be oriented by coupling to them. We analyze the mechanism for this both by computer simulation and theoretically. We show that the results can be understood in terms of stress fluctuations in a polymer melt and chain screening. Stress fluctuations are frozen on the relaxation time of the longer chains, and these will induce strong orientational couplings in the shorter chains.

Exact solution to ideal chain with fixed angular momentum

The statistical mechanics of a noninteracting polymer chain in the limit of a large number of monomers is considered when the total angular momentum L is fixed. The radius of gyration for a ring polymer in this situation is derived exactly in closed form by functional integration techniques. Even when L=0 the radius of gyration differs from that of a random walk by a prefactor of order unity. The dependence on L is discussed qualitatively and the large- L limit can be understood by physical arguments, which can also be extended to self-avoiding chains.

Polymers in a vacuum

In a variety of situations, isolated polymer molecules are found in a vacuum, and here we examine their properties. Angular momentum conservation is shown to significantly alter the average size of a chain and its conservation is only broken slowly by thermal radiation. For an ideal chain, the time autocorrelation for monomer position oscillates with a period proportional to chain length. The oscillations and damping are analyzed in detail. Short-range repulsive interactions suppress oscillations and speed up relaxation, but stretched chains still show damped oscillatory correlations.

Spin precession and avalanches

In many magnetic materials, spin dynamics at short times are dominated by precessional motion as damping is relatively small. We describe how avalanches evolve under these conditions. The growth front is spread out over a large region and consists of rapidly fluctuating spins often above the ferromagnetic transition temperature. In the limit of no damping the system will transition to an ergodic state if the initial instability is large enough, but otherwise can die out. This dynamic nucleation phenomenon is analyzed theoretically and the implications for real materials are discussed.

Energy dissipation and fluctuation response for particles in fluids

An equality was recently proved relating energy dissipation to the difference of the response and velocity correlation functions for a class of Langevin equations. We generalize this for the physically important case of particles in a fluid, where bath fluctuations are nonlocal in time due to hydrodynamic modes. We also show that the inclusion of a mass term does not alter the result and provide a simple physical interpretation of the original equality.

Scaling of polymers in aligned rods

We study the behavior of self-avoiding polymers in a background of infinitely long vertically aligned rods that are either frozen in random positions or free to move horizontally. We find that in both cases the polymer chains are highly elongated, with vertical and horizontal size exponents that differ by a factor of 3. Though these results are different than previous predictions, our results are confirmed by detailed computer simulations.

Mechanism for nonequilibrium symmetry breaking and pattern formation in magnetic films

Magnetic thin films exhibit a strong variation in properties depending on their degree of disorder. Recent coherent x-ray speckle experiments on magnetic films have measured the loss of correlation between configurations at opposite fields and at the same field, upon repeated field cycling. We perform finite temperature numerical simulations on these systems that provide a comprehensive explanation for the experimental results. The simulations demonstrate, in accordance with experiments, that the memory of configurations increases with film disorder. We find that nontrivial microscopic differences exist between the zero field spin configuration obtained by starting from a large positive field and the zero field configuration starting at a large negative field. This seemingly paradoxical behavior is due to the nature of the vector spin dynamics and is also seen in the experiments. For low disorder, there is an instability which causes the spontaneous growth of linelike domains at a critical field, also in accord with experiments. It is this unstable growth, which is highly sensitive to thermal noise, that is responsible for the small correlation between patterns under repeated cycling. The domain patterns, hysteresis loops, and memory properties of our simulated systems match remarkably well with the real experimental systems.

Hysteresis multicycles in nanomagnet arrays

We predict two physical effects in arrays of single-domain nanomagnets by performing simulations using a realistic model Hamiltonian and physical parameters. First, we find hysteretic multicycles for such nanomagnets. The simulation uses continuous spin dynamics through the Landau-Lifshitz-Gilbert (LLG) equation. In some regions of parameter space, the probability of finding a multicycle is as high as approximately 0.6 . We find that systems with larger and more anisotropic nanomagnets tend to display more multicycles. Our results also demonstrate the importance of disorder and frustration for multicycle behavior. Second, we show that there is a fundamental difference between the more realistic vector LLG equation and scalar models of hysteresis, such as Ising models. In the latter case spin and external field inversion symmetry is obeyed, but in the former it is destroyed by the dynamics, with important experimental implications.

Disorder-induced microscopic magnetic memory

Using coherent x-ray speckle metrology, we have measured the influence of disorder on major loop return point memory (RPM) and complementary point memory (CPM) for a series of perpendicular anisotropy Co/Pt multilayer films. In the low disorder limit, the domain structures show no memory with field cycling--no RPM and no CPM. With increasing disorder, we observe the onset and the saturation of both the RPM and the CPM. These results provide the first direct ensemble-sensitive experimental study of the effects of varying disorder on microscopic magnetic memory and are compared against the predictions of existing theories.

Return to return point memory

We describe a new class of systems exhibiting return point memory (RPM), different from those discussed before in the context of ferromagnets. We show numerically that one-dimensional random Ising antiferromagnets have exact RPM when evolving from a large field, but not when started at finite field, unlike the ferromagnetic case. This implies that the standard approach to understanding ferromagnetic RPM will fail for this case. We also demonstrate RPM with a set of variables that keeps track of spin flips at each site. Conventional RPM for the spins is a projection of this result, suggesting that spin flip variables might be a more fundamental representation of the dynamics. We also present a mapping that embeds the antiferromagnetic chain in a two-dimensional ferromagnet, and prove RPM for spin-exchange dynamics in the interior of the chain with this mapping.

Subharmonics and aperiodicity in hysteresis loops

We show that it is possible to have hysteretic behavior for magnets that does not form simple closed loops in steady state, but cycles multiple times before returning to its initial state. We show this by studying the low temperature dynamics of the 3D Edwards-Anderson spin glass. The specific multiple varies from system to system and is often quite large and increases with system size. The last result suggests that the magnetization could be aperiodic in the large system limit for some realizations of randomness. It should be possible to observe this phenomenon experimentally.

Correlations and scaling in one-dimensional heat conduction

We examine numerically the full spatiotemporal correlation functions for all hydrodynamic quantities for the random collision model introduced recently. The autocorrelation function of the heat current, through the Kubo formula, gives a thermal conductivity exponent of 1/3 in agreement with the analytical prediction and previous numerical work. Remarkably, this result depends crucially on the choice of boundary conditions: for periodic boundary conditions (as opposed to open boundary conditions with heat baths) the exponent is approximately 1/2. All primitive hydrodynamic quantities scale with the dynamic critical exponent predicted analytically.

One-dimensional heat conductivity exponent from a random collision model

We obtain numerically the thermal conductivity of a quasi-one-dimensional classical chain of hard sphere particles as a function of the length of the chain, introducing a fresh model for this problem. The conductivity scales as a power law of the length over two decades, with an exponent very close to the analytical prediction of 1/3.

Evolutionary algorithms for finding optimal gene sets in microarray prediction

MOTIVATION

Microarray data has been shown recently to be efficacious in distinguishing closely related cell types that often appear in different forms of cancer, but is not yet practical clinically. However, the data might be used to construct a minimal set of marker genes that could then be used clinically by making antibody assays to diagnose a specific type of cancer. Here a replication algorithm is used for this purpose. It evolves an ensemble of predictors, all using different combinations of genes to generate a set of optimal predictors.

RESULTS

We apply this method to the leukemia data of the Whitehead/MIT group that attempts to differentially diagnose two kinds of leukemia, and also to data of Khan et al. to distinguish four different kinds of childhood cancers. In the latter case we were able to reduce the number of genes needed from 96 to less than 15, while at the same time being able to classify all of their test data perfectly. We also apply this method to two other cases, Diffuse large B-cell lymphoma data (Shipp et al., 2002), and data of Ramaswamy et al. on multiclass diagnosis of 14 common tumor types.

AVAILABILITY

http://stravinsky.ucsc.edu/josh/gesses/.

How does a virus bud?

How does a virus bud from the plasma membrane of its host? Here we investigate several possible rate-limiting processes, including thermal fluctuations of the plasma membrane, hydrodynamic interactions, and diffusion of the glycoprotein spikes. We find that for bending moduli greater than 3 x 10(-13) ergs, membrane thermal fluctuations are insufficient to wrap the viral capsid, and the mechanical force driving the budding process must arise from some other process. If budding is limited by the rate at which glycoprotein spikes can diffuse to the budding site, we compute that the budding time is 10-20 min, in accord with the experimentally determined upper limit of 20 min. In light of this, we suggest some alternative mechanisms for budding and provide a rationale for the observation that budding frequently occurs in regions of high membrane curvature.

Theoretical studies of DNA during gel electrophoresis

A numerical study of the motion of a long-chain macromolecule in a gel has shown unexpected features. The application of a field appears to induce the chain to contract on itself. This is followed by its "unwinding" into an extended configuration. For long chains, the mobility tends toward a constant, in accord with experiments. For the parameter range used, the observed molecular motion differs strongly from assumptions made in the present theory of electrophoresis.