Lessons from a Minimal Genome: What Are the Essential Organizing Principles of a Cell Built from Scratch?

One of the primary challenges facing synthetic biology is reconstituting a living system from its component parts. A particularly difficult landmark is reconstituting a self‐organizing system that can undergo autonomous chromosome compaction, segregation, and cell division. Here, we discuss how the syn3.0 minimal genome can inform us of the core self‐organizing principles of a living cell and how these self‐organizing processes can be built from the bottom up. The review underscores the importance of fundamental biology in rebuilding life from its molecular constituents.A primary challenge in synthetic biology is reconstituting self‐organizing systems that can undergo autonomous chromosome compaction, segregation, and cell division. Here, we discuss how the syn3.0 minimal genome sheds light on the core self‐organizing principles of living cells and how these self‐organizing processes can be built from the bottom up.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/152011/1/cbic201900249.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152011/2/cbic201900249_am.pd

Infrared Multiphoton Dissociation Enables Top-Down Characterization of Membrane Protein Complexes and G Protein-Coupled Receptors

Membrane proteins are challenging to analyze by native mass spectrometry (MS) as their hydrophobic nature typically requires stabilization in detergent micelles that are removed prior to analysis via collisional activation. There is however a practical limit to the amount of energy which can be applied, which often precludes subsequent characterization by top-down MS. To overcome this barrier, we have applied a modified Orbitrap Eclipse Tribrid mass spectrometer coupled to an infrared laser within a high-pressure linear ion trap. We show how tuning the intensity and time of incident photons enables liberation of membrane proteins from detergent micelles. Specifically, we relate the ease of micelle removal to the infrared absorption of detergents in both condensed and gas phases. Top-down MS via infrared multiphoton dissociation (IRMPD), results in good sequence coverage enabling unambiguous identification of membrane proteins and their complexes. By contrasting and comparing the fragmentation patterns of the ammonia channel with two class A GPCRs, we identify successive cleavage of adjacent amino acids within transmembrane domains. Using gas-phase molecular dynamics simulations, we show that areas prone to fragmentation maintain aspects of protein structure at increasing temperatures. Altogether, we propose a rationale to explain why and where in the protein fragment ions are generated

Searching for Far-Ultraviolet Auroral/Dayglow Emission from HD209458b

We present recent observations from the HST-Cosmic Origins Spectrograph aimed at characterizing the auroral emission from the extrasolar planet HD209458b. We obtained medium-resolution (R~18-20,000) far-ultraviolet (1150-1700A) spectra at both the Phase 0.25 and Phase 0.75 quadrature positions as well as a stellar baseline measurement at secondary eclipse. This analysis includes a catalog of stellar emission lines and a star-subtracted spectrum of the planet. We present an emission model for planetary H2 emission, and compare this model to the planetary spectrum. No unambiguously identifiable atomic or molecular features are detected, and upper limits are presented for auroral/dayglow line strengths. An orbital velocity cross-correlation analysis finds a statistically significant (3.8 sigma) feature at +15 (+/- 20) km/s in the rest frame of the planet, at 1582 A. This feature is consistent with emission from H2 B-X (2-9) P(4) (lambda_{rest} = 1581.11 A), however the physical mechanism required to excite this transition is unclear. We compare limits on relative line strengths seen in the exoplanet spectrum with models of ultraviolet fluorescence to constrain the atmospheric column density of neutral hydrogen between the star and the planetary surface. These results support models of short period extrasolar giant planets with weak magnetic fields and extended atomic atmospheres.Comment: Accepted to ApJ. 12 pages, 5 figures, 4 table

On the calculation of effective electric field in In0.53Ga0.47As surface channel metal-oxide-semiconductor field-effect-transistors

The effective electron mobility of In0.53Ga0.47As metal-oxide-semiconductor field-effect-transistors with HfO2 gate oxide was measured over a wide range of channel doping concentration. The back bias dependence of effective electron mobility was used to correctly calculate the vertical effective electric field. The effective electron mobility at moderate to high vertical effective electric field shows universal behavior independent of substrate impurity concentration. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3588255

The Far-Ultraviolet "Continuum" in Protoplanetary Disk Systems II: CO Fourth Positive Emission and Absorption

We exploit the high sensitivity and moderate spectral resolution of the $HST$-Cosmic Origins Spectrograph to detect far-ultraviolet spectral features of carbon monoxide (CO) present in the inner regions of protoplanetary disks for the first time. We present spectra of the classical T Tauri stars HN Tau, RECX-11, and V4046 Sgr, representative of a range of CO radiative processes. HN Tau shows CO bands in absorption against the accretion continuum. We measure a CO column density and rotational excitation temperature of N(CO) = 2 +/- 1 $\times$ 10$^{17}$ cm$^{-2}$ and T_rot(CO) 500 +/- 200 K for the absorbing gas. We also detect CO A-X band emission in RECX-11 and V4046 Sgr, excited by ultraviolet line photons, predominantly HI LyA. All three objects show emission from CO bands at $\lambda$ $>$ 1560 \AA, which may be excited by a combination of UV photons and collisions with non-thermal electrons. In previous observations these emission processes were not accounted for due to blending with emission from the accretion shock, collisionally excited H$_{2}$, and photo-excited H2; all of which appeared as a "continuum" whose components could not be separated. The CO emission spectrum is strongly dependent upon the shape of the incident stellar LyA emission profile. We find CO parameters in the range: N(CO) 10$^{18-19}$ cm$^{-2}$, T_{rot}(CO) > 300 K for the LyA-pumped emission. We combine these results with recent work on photo- and collisionally-excited H$_{2}$ emission, concluding that the observations of ultraviolet-emitting CO and H2 are consistent with a common spatial origin. We suggest that the CO/H2 ratio in the inner disk is ~1, a transition between the much lower interstellar value and the higher value observed in solar system comets today, a result that will require future observational and theoretical study to confirm.Comment: 12 pages, 7 figures, 3 tables. ApJ - accepte

A Study of Fluid-Membrane Transport Processes and Their Applications: A Molecular Dynamics Approach

Selectively permeable membranes perform important roles in a wide range of systems including naturally occurring lipid membranes in biological systems to engineered polymeric membranes in filtration and energy technologies. In order to design technologies that incorporate such membranes it is crucial to understand the behavior of these systems on the molecular level so that optimal performance and maximum efficiencies can be achieved. One of the main focuses of this thesis is how ionic hydration affects the transport of electrolyte species through porous membranes. Molecular dynamics simulations are used to examine this in detail both for model systems as well as for actual industrial membranes including zeolite materials as potential ion exchange membranes (IEMs) in energy systems such as redox flow batteries. In addition, model selective membranes are used to computationally predict the phase equilibrium behavior of various gas/liquid systems at experimentally difficult conditions. Because of their safety, capacity, and small environmental footprint, redox flow batteries (RFBs) have become an attractive form of energy storage. However, this technology is not yet widely used commercially due to inefficiencies in the ion-exchange membrane. The current technology widely utilizes polymeric membranes that have stability problems in the highly reactive environment of the RFB and tend to break down, shortening the life of the battery. Also, they present less than desirable selectivity for proton transport, which is crucial to the overall efficiency of the battery. It has been proposed that thin zeolite membranes will provide both the stability and the selectivity to improve the performance of RFBs and make their wide-scale application more feasible. A molecular dynamics study of six zeolite framework types and the ions present in the vanadium-RFB has been undertaken to determine their transport behavior and investigate at the molecular level the requirements for suitability in IEM applications. In addition to investigating different zeolite frameworks, the effect of composition was examined by introducing different levels of aluminum substitution into the crystalline structure of one specific framework, namely MFI. By investigating two characteristics, membrane loading and intramembrane diffusion, it is possible to predict the overall ion permeability with the goal of optimizing the amount of substitution for high proton permeability while maintaining selectivity to undesirable ions. Beyond these specific applications, model selective membranes were also used in molecular dynamics simulations to predict phase behavior of various gas/liquid at conditions difficult to achieve in experiments. This research was carried out to fill data gaps that are urgently needed for the design of industrial processes for gas capture/ storage or separation. By validating our models against limited experimental data available, we show that molecular modeling can be a useful predictive tool for industrial applications. Simulations are currently not widely used in industry for data prediction even though they can be carried out at a small fraction of the cost of experimental studies

Of Mice and men : Level 2

46 p. : col. ill. ; 20 cm

The Evolution of Early Literacy: A History of Best Practices in Storytimes”. Children and Libraries: The Journal of the Association for Library Service to Children

The article offers a history of children\u27s library storytimes beginning in the 1940s with particular focus given to best practices. Story selection criteria including rhythm or rhyme and repetition within the text are examined and early values of story hours including playing with others, listening to stories, and looking at picture books are discussed. The role of parents in story hour participation and in emergent literacy is also explored. Early literacy skills and standards promoted in contemporary storytimes are also discussed and include print motivation, phonological awareness, and vocabulary