The spatial biology of transcription and translation in rapidly growing Escherichia coli.

Single-molecule fluorescence provides high resolution spatial distributions of ribosomes and RNA polymerase (RNAP) in live, rapidly growing Escherichia coli. Ribosomes are more strongly segregated from the nucleoids (chromosomal DNA) than previous widefield fluorescence studies suggested. While most transcription may be co-translational, the evidence indicates that most translation occurs on free mRNA copies that have diffused from the nucleoids to a ribosome-rich region. Analysis of time-resolved images of the nucleoid spatial distribution after treatment with the transcription-halting drug rifampicin and the translation-halting drug chloramphenicol shows that both drugs cause nucleoid contraction on the 0-3 min timescale. This is consistent with the transertion hypothesis. We suggest that the longer-term (20-30 min) nucleoid expansion after Rif treatment arises from conversion of 70S-polysomes to 30S and 50S subunits, which readily penetrate the nucleoids. Monte Carlo simulations of a polymer bead model built to mimic the chromosomal DNA and ribosomes (either 70S-polysomes or 30S and 50S subunits) explain spatial segregation or mixing of ribosomes and nucleoids in terms of excluded volume and entropic effects alone. A comprehensive model of the transcription-translation-transertion system incorporates this new information about the spatial organization of the E. coli cytoplasm. We propose that transertion, which radially expands the nucleoids, is essential for recycling of 30S and 50S subunits from ribosome-rich regions back into the nucleoids. There they initiate co-transcriptional translation, which is an important mechanism for maintaining RNAP forward progress and protecting the nascent mRNA chain. Segregation of 70S-polysomes from the nucleoid may facilitate rapid growth by shortening the search time for ribosomes to find free mRNA concentrated outside the nucleoid and the search time for RNAP concentrated within the nucleoid to find transcription initiation sites

Band gap opening by two-dimensional manifestation of Peierls instability in graphene

Using first-principles calculations of graphene having high-symmetry distortion or defects, we investigate band gap opening by chiral symmetry breaking, or intervalley mixing, in graphene and show an intuitive picture of understanding the gap opening in terms of local bonding and antibonding hybridizations. We identify that the gap opening by chiral symmetry breaking in honeycomb lattices is an ideal two-dimensional (2D) extension of the Peierls metal-insulator transition in 1D linear lattices. We show that the spontaneous Kekule distortion, a 2D version of the Peierls distortion, takes place in biaxially strained graphene, leading to structural failure. We also show that the gap opening in graphene antidots and armchair nanoribbons, which has been attributed usually to quantum confinement effects, can be understood with the chiral symmetry breaking

Optimizing Reinforcing Steel in 12-In and 13-In Continuously Reinforced Concrete Pavement (CRCP)

0-7026The performance of continuously reinforced concrete pavement (CRCP) in Texas has been excellent. However, truck traffic in Texas has been increasing, which required thicker slabs. Since TxDOT placed steel at the mid-depth of the slab, the use of thicker slabs increased the distance between top of the slab and longitudinal steel. This increase resulted in larger crack spacing and occasional horizontal cracking. Continued wheel loading applications degrade the top half of the concrete and partial depth distress. Traditionally, punchout has been reported as a major and only structural distress in CRCP. However, it has been observed that different types of cracking and resulting distresses have taken place in CRCP that has had improved design features such as thicker slabs, stabilized bases, and tied concrete shoulders. These cracks, which cannot be explained by traditional theories related to punchout and spalling, are normally associated with horizontal cracking at approximately mid-depth of the slab. This horizontal cracking has been observed in CRCP with thicker slabs, thickness of 12 inches or larger. It was also observed that horizontal cracks occurred at early ages before the pavement was open to traffic. These findings strongly indicate that horizontal cracks are not due to structural deficiencies of CRCP. Rather, concrete material properties, environmental conditions during and right after concrete placement, and most importantly longitudinal steel placement layouts must play a significant role in the development of horizontal cracking. The primary objective of this study is to identify the mechanisms and associated variables of horizontal cracking in CRCP and to develop mitigation methodologies. To this end, theoretical analyses of early-age CRCP behavior were conducted using 3-dimensional CRCP modeling, and field testing was conducted at 4 different CRCP construction projects. The behavior of CRCP at early ages under environmental loading (temperature and moisture variations) obtained from the field testing was compared with numerical analysis results and the model was calibrated. The effect of each variable related to design, material, and construction on the horizontal cracking potential was evaluated through comprehensive numerical analysis with a calibrated model. One of the major findings is that steel depth has significant effects on CRCP behavior and a modest decrease in the distance between slab surface and steel depth reduces horizontal cracking potential substantially. It is expected that the implementation of the findings from this study is expected to improve CRCP performance substantially for thicker CRCP

Graphene-passivated nickel as an oxidation-resistant electrode for spintronics.

We report on graphene-passivated ferromagnetic electrodes (GPFE) for spin devices. GPFE are shown to act as spin-polarized oxidation-resistant electrodes. The direct coating of nickel with few layer graphene through a readily scalable chemical vapor deposition (CVD) process allows the preservation of an unoxidized nickel surface upon air exposure. Fabrication and measurement of complete reference tunneling spin valve structures demonstrate that the GPFE is maintained as a spin polarizer and also that the presence of the graphene coating leads to a specific sign reversal of the magneto-resistance. Hence, this work highlights a novel oxidation-resistant spin source which further unlocks low cost wet chemistry processes for spintronics devices.R.S.W. acknowledges funding from EPSRC (Doctoral training award). S.H. acknowledges funding from ERC Grant InsituNANO (Project Reference 279342). P.S. acknowledges the Institut Universitaire de France for junior fellowship support. This research was partially supported by the EU FP7 work programme under Grant GRAFOL (Project Reference 285275).This is the accepted manuscript. The final version is available from ACS at http://pubs.acs.org/doi/abs/10.1021/nn304424x

The Spatial Relationship between Patterns of Disappeared streams and residential development in Portland, Oregon, USA

Disappeared streams are streams that have been buried, removed, or moved as part of the urbanization process. We identified disappeared streams in the Portland, Oregon metropolitan area using historical topographic maps for four time periods, and related them to the history of urban development. The historical maps were used to identify streams visible in older maps but not shown in a more recent version. From 1852 to 1895, 15% of streams disappeared, but the majority of streams disappeared between 1896 and 1953 (65%). This trend continued mainly in suburban areas after 1954 with 12% of streams being removed from 1954 to 1989 and 8% from 1990 to 2017. Stream disappearance can be linked to residential development and prior conversion of land for agriculture depending on the area and time period. Mapping disappeared streams can help urban spatial planners identify where stream daylighting or restoration could be targeted

Spatial Distribution and Ribosome-Binding Dynamics of EF-P in Live Escherichia coli

In vitro assays find that ribosomes form peptide bonds to proline (Pro) residues more slowly than to other residues. Ribosome profiling shows that stalling at Pro-Pro-X triplets is especially severe but is largely alleviated in Escherichia coli by the action of elongation factor EF-P. EF-P and its eukaryotic/archaeal homolog IF5A enhance the peptidyl transfer step of elongation. Here, a superresolution fluorescence localization and tracking study of EF-P-mEos2 in live E. coli provides the first in vivo information about the spatial distribution and on-off binding kinetics of EF-P. Fast imaging at 2 ms/frame helps to distinguish ribosome-bound (slowly diffusing) EF-P from free (rapidly diffusing) EF-P. Wild-type EF-P exhibits a three-peaked axial spatial distribution similar to that of ribosomes, indicating substantial binding. The mutant EF-P-K34A exhibits a homogeneous distribution, indicating little or no binding. Some 30% of EF-P copies are bound to ribosomes at a given time. Two-state modeling and copy number estimates indicate that EF-P binds to 70S ribosomes during 25 to 100% of translation cycles. The timescale of the typical diffusive search by free EF-P for a ribosome-binding site is tau(free) approximate to 16 ms. The typical residence time of an EF-P on the ribosome is very short, tau(bound) approximate to 7 ms. Evidently, EF-P binds to ribosomes during many or most elongation cycles, much more often than the frequency of Pro-Pro motifs. Emptying of the E site during part of the cycle is consistent with recent in vitro experiments indicating dissociation of the deacylated tRNA upon translocation. IMPORTANCE Ribosomes translate the codon sequence within mRNA into the corresponding sequence of amino acids within the nascent polypeptide chain, which in turn ultimately folds into functional protein. At each codon, bacterial ribosomes are assisted by two well-known elongation factors: EF-Tu, which aids binding of the correct aminoacyl-tRNA to the ribosome, and EF-G, which promotes tRNA translocation after formation of the new peptide bond. A third factor, EF-P, has been shown to alleviate ribosomal pausing at rare Pro-Pro motifs, which are translated very slowly without EF-P. Here, we use superresolution fluorescence imaging to study the spatial distribution and ribosome-binding dynamics of EF-P in live E. coli cells. We were surprised to learn that EF-P binds to and unbinds from translating ribosomes during at least 25% of all elongation events; it may bind during every elongation cycle

Antimicrobial peptides and their MICs for <i>E</i>. <i>coli</i> MG1655 in aerobic growth vs anaerobic fermentation in EZRDM at 30°C.

<p>Antimicrobial peptides and their MICs for <i>E</i>. <i>coli</i> MG1655 in aerobic growth vs anaerobic fermentation in EZRDM at 30°C.</p

Schematic of the branch of the aerobic electron transport chain of <i>E</i>. <i>coli</i> terminating at cytochrome oxidase-<i>bd</i>.

<p>We suggest that LL-37 enters the periplasm, binds to the outer leaflet of the cytoplasmic membrane, and disrupts the proper activity of the terminal cytochrome oxidase-<i>bd</i> complex, releasing the intermediate superoxide (•O₂^–) into the periplasm.</p