Dynamical description of vesicle growth and shape change

We systematize and extend the description of vesicle growth and shape change using linear nonequilibrium thermodynamics. By restricting the study to shape changes from spheres to axisymmetric ellipsoids, we are able to give a consistent formulation which includes the lateral tension of the vesicle membrane. This allows us to generalize and correct a previous calculation. Our present calculations suggest that, for small growing vesicles, a prolate ellipsoidal shape should be favored over oblate ellipsoids, whereas for large growing vesicles oblates should be favored over prolates. The validity of this prediction is examined in the light of the various assumptions made in its derivation.Comment: 6 page

Impact of pseudouridylation, substrate fold, and degradosome organization on the endonuclease activity of RNase E.

The conserved endoribonuclease RNase E dominates the dynamic landscape of RNA metabolism and underpins control mediated by small regulatory RNAs in diverse bacterial species. We explored the enzyme's hydrolytic mechanism, allosteric activation, and interplay with partner proteins in the multicomponent RNA degradosome assembly of Escherichia coli. RNase E cleaves single-stranded RNA with preference to attack the phosphate located at the 5' nucleotide preceding uracil, and we corroborate key interactions that select that base. Unexpectedly, RNase E activity is impeded strongly when the recognized uracil is isomerized to 5-ribosyluracil (pseudouridine), from which we infer the detailed geometry of the hydrolytic attack process. Kinetics analyses support models for recognition of secondary structure in substrates by RNase E and for allosteric autoregulation. The catalytic power of the enzyme is boosted when it is assembled into the multienzyme RNA degradosome, most likely as a consequence of substrate capture and presentation. Our results rationalize the origins of substrate preferences of RNase E and illuminate its catalytic mechanism, supporting the roles of allosteric domain closure and cooperation with other components of the RNA degradosome complex

A spatial model of autocatalytic reactions

Biological cells with all of their surface structure and complex interior stripped away are essentially vesicles - membranes composed of lipid bilayers which form closed sacs. Vesicles are thought to be relevant as models of primitive protocells, and they could have provided the ideal environment for pre-biotic reactions to occur. In this paper, we investigate the stochastic dynamics of a set of autocatalytic reactions, within a spatially bounded domain, so as to mimic a primordial cell. The discreteness of the constituents of the autocatalytic reactions gives rise to large sustained oscillations, even when the number of constituents is quite large. These oscillations are spatio-temporal in nature, unlike those found in previous studies, which consisted only of temporal oscillations. We speculate that these oscillations may have a role in seeding membrane instabilities which lead to vesicle division. In this way synchronization could be achieved between protocell growth and the reproduction rate of the constituents (the protogenetic material) in simple protocells.Comment: Submitted to Phys. Rev.

The GBT Diffuse Ionized Gas Survey (GDIGS): Discrete Sources

The Green Bank Telescope (GBT) Diffuse Ionized Gas Survey (GDIGS) traces ionized gas in the Galactic midplane by observing radio recombination line (RRL) emission from 4–8 GHz. The nominal survey zone is 32.3◦ \u3e ℓ \u3e −5◦, | b | \u3c 0.5◦. Here, we analyze GDIGS Hnα ionized gas emission toward discrete sources. Using GDIGS data, we identify the velocity of 35 H II regions that have multiple detected RRL velocity components. We identify and characterize RRL emission from 88 H II regions that previously lacked measured ionized gas velocities. We also identify and characterize RRL emission from eight locations that appear to be previously-unidentified H II regions and 30 locations of RRL emission that do not appear to be H II regions based on their lack of mid-infrared emission. This latter group may be a compact component of the Galactic Diffuse Ionized Gas (DIG). There are an additional 10 discrete sources that have anomalously high RRL velocities for their locations in the Galactic plane. We compare these objects’ RRL data to 13CO, H I and mid-infrared data, and find that these sources do not have the expected 24 µm emission characteristic of H II regions. Based on this comparison we do not think these objects are H II regions, but we are unable to classify them as a known type of object

Synthetic organisms and living machines: Positioning the products of synthetic biology at the borderline between living and non-living matter

The difference between a non-living machine such as a vacuum cleaner and a living organism as a lion seems to be obvious. The two types of entities differ in their material consistence, their origin, their development and their purpose. This apparently clear-cut borderline has previously been challenged by fictitious ideas of “artificial organism” and “living machines” as well as by progress in technology and breeding. The emergence of novel technologies such as artificial life, nanobiotechnology and synthetic biology are definitely blurring the boundary between our understanding of living and non-living matter. This essay discusses where, at the borderline between living and non-living matter, we can position the future products of synthetic biology that belong to the two hybrid entities “synthetic organisms” and “living machines” and how the approaching realization of such hybrid entities affects our understanding of organisms and machines. For this purpose we focus on the description of three different types of synthetic biology products and the aims assigned to their realization: (1) synthetic minimal cells aimed at by protocell synthetic biology, (2) chassis organisms strived for by synthetic genomics and (3) genetically engineered machines produced by bioengineering. We argue that in the case of synthetic biology the purpose is more decisive for the categorization of a product as an organism or a machine than its origin and development. This has certain ethical implications because the definition of an entity as machine seems to allow bypassing the discussion about the assignment and evaluation of instrumental and intrinsic values, which can be raised in the case of organisms

Timing molecular motion and production with a synthetic transcriptional clock

The realization of artificial biochemical reaction networks with unique functionality is one of the main challenges for the development of synthetic biology. Due to the reduced number of components, biochemical circuits constructed in vitro promise to be more amenable to systematic design and quantitative assessment than circuits embedded within living organisms. To make good on that promise, effective methods for composing subsystems into larger systems are needed. Here we used an artificial biochemical oscillator based on in vitro transcription and RNA degradation reactions to drive a variety of “load” processes such as the operation of a DNA-based nanomechanical device (“DNA tweezers”) or the production of a functional RNA molecule (an aptamer for malachite green). We implemented several mechanisms for coupling the load processes to the oscillator circuit and compared them based on how much the load affected the frequency and amplitude of the core oscillator, and how much of the load was effectively driven. Based on heuristic insights and computational modeling, an “insulator circuit” was developed, which strongly reduced the detrimental influence of the load on the oscillator circuit. Understanding how to design effective insulation between biochemical subsystems will be critical for the synthesis of larger and more complex systems

The crystal structure of the outer membrane protein VceC from the bacterial pathogen Vibrio cholerae at 1.8 Å resolution

Multidrug resistance in Gram-negative bacteria arises in part from the activities of tripartite drug efflux pumps. In the pathogen Vibrio cholerae, one such pump comprises the inner membrane proton antiporter VceB, the periplasmic adaptor VceA, and the outer membrane channel VceC. Here, we report the crystal structure of VceC at 1.8 Å resolution. The trimeric VceC is organized in the crystal lattice within laminar arrays that resemble membranes. A well resolved detergent molecule within this array interacts with the transmembrane -barrel domain in a fashion that may mimic proteinlipopolysaccharide contacts. Our analyses of the external surfaces of VceC and other channel proteins suggest that different classes of efflux pumps have distinct architectures. We discuss the implications of these findings for mechanisms of drug and protein export

The GBT Diffuse Ionized Gas Survey (GDIGS): Survey Overview and First Data Release

The Green Bank Telescope (GBT) Diffuse Ionized Gas Survey (GDIGS) traces ionized gas in the Galactic midplane by measuring $4-8$GHz radio recombination line (RRL) emission. The nominal survey zone is $32.3^{\circ}> l >-5^{\circ}$, $|b|<0.5^{\circ}$, but coverage extends above and below the plane in select fields, and additionally includes the areas around W47 ($l \simeq 37.5^{\circ}$) and W49 ($l \simeq 43^{\circ}$). GDIGS simultaneously observes 22 Hn$\alpha$ (15 usable), 25 Hn$\beta$ (18 usable), and 8 Hn$\gamma$ RRLs (all usable), as well as multiple molecular line transitions (including of H$_2^{13}$CO, H$_2$CO, and CH$_3$OH). Here, we describe the GDIGS survey parameters and characterize the RRL data, focusing primarily on the Hn$\alpha$ data. We produce sensitive data cubes by averaging the usable RRLs, after first smoothing to a common spectral resolution of 0.5km/s and a spatial resolution of 2.65' for Hn$\alpha$, 2.62' for Hn$\beta$, and 2.09' for Hn$\gamma$. The average spectral noise per spaxel in the \hna\ data cubes is $\sim\!10$mK ($\sim\!5$mJy/beam). This sensitivity allows GDIGS to detect RRLs from plasma throughout the inner Galaxy. The GDIGS Hn$\alpha$ data are sensitive to emission measures $EM \gtrsim 1100$cm$^{-6}$pc, which corresponds to a mean electron density $\langle n_e \rangle \gtrsim 30$cm$^{-3}$ for a 1pc path length or $\langle n_e \rangle \gtrsim 1$cm$^{-3}$ for a 1kpc path length.Comment: Accepted for publication by ApJS. Data may be downloaded here: http://astro.phys.wvu.edu/gdigs