ALBERT

Description: Internal cavities are a common feature of many proteins, often having profound effects on the dynamics of their interactions with substrate and binding partners. RB69 DNA polymerase (pol) has a hydrophobic cavity right below the nucleotide binding pocket at the tip of highly conserved L415 side chain. Replacement of this residue with Gly or Met in other B family pols resulted in higher mutation rates. When similar substitutions for L415 were introduced into RB69pol, only L415A and L415G had dramatic effects on pre-steady-state kinetic parameters, reducing base selectivity by several hundred fold. On the other hand, the L415M variant behaved like the wild-type. Using a novel tC o -tC nitro Förster Resonance Energy Transfer (FRET) assay, we were able to show that the partition of the primer terminus between pol and exonuclease (exo) domains was compromised with the L415A and L415G mutants, but not with the L415M variant. These results could be rationalized by changes in their structures as determined by high resolution X-ray crystallography.

Description: Environmental Science & Technology DOI: 10.1021/es103923j

Description: Slow slip events (SSE) in many subduction zones incrementally stress the adjacent locked megathrust, suggesting that they could potentially either trigger or evolve into damaging earthquakes. We explore this with 2D quasi-dynamic simulations with rate-state friction, dilatancy, and coupled 1D pore-fluid and heat transport. Steady-state weakening friction allows transient slip to nucleate, but is inhibited by dilatant strengthening and destabilized by thermal pressurization. SSE spontaneously nucleate in Low Effective-Stress Velocity-Weakening (LESVW) regions. If the dimension of the LESVW is relatively small the SSE are trapped at its updip end, imparting a strong stress concentration in the locked zone. After several centuries SSE penetrate into the region of higher effective stress, where thermal pressurization eventually leads to dynamic rupture. For larger LESVW regions SSE tend to increase in length with time; ultimately higher slip speeds enhance thermal weakening, leading to dynamic instability within the SSE zone. In both cases the onset of the ultimate SSE is essentially indistinguishable from preceding events.

Description: [1]  Deep aseismic roots of faults play a critical role in transferring tectonic loads to shallower, brittle crustal faults that rupture in large earthquakes. Yet, until the recent discovery of deep tremor and creep, direct inference of the physical properties of lower-crustal fault roots has remained elusive. Observations of tremor near Parkfield, CA provide the first evidence for present-day localized slip on the deep extension of the San Andreas fault and triggered transient creep events. We developnumerical simulations of fault slip to show that the spatiotemporal evolution of triggered tremor near Parkfield is consistent with triggered fault creep governed by laboratory-derived friction laws between depths of 20-35 km on the fault. Simulated creep and observed tremor northwest of Parkfield nearly ceased for 20-30 days in response to small coseismic stress changes of order 10 4 Pa from the 2003 M6.5 San Simeon Earthquake. Simulated afterslip and observed tremor following the 2004 M6.0 Parkfield earthquake show a coseismically-induced pulse of rapid creep and tremor lasting for one day followed by a longer 30-day period of sustained accelerated rates due to propagation of shallow afterslip into the lower crust. These creep responses require very low effective normal stress of ∼ 1 MPa on the deep San Andreas Fault and near-neutral-stability frictional properties expected for gabbroic lower-crustal rock.

Description: Environmental Science & Technology DOI: 10.1021/es301540g

Description: Environmental Science & Technology DOI: 10.1021/es2000134

Description: Approaches are needed to better predict spatial variation in riverine Hg concentrations across heterogeneous landscapes that include mountains, wetlands, and open waters. We applied multivariate linear regression to determine the landscape factors and chemical variables that best account for the spatial variation of total Hg (THg) and methyl Hg (MeHg) concentrations in 27 sub-basins across the 493 km2 upper Hudson River basin in the Adirondack Mountains of New York. THg concentrations varied by sixfold, and those of MeHg by 40-fold in synoptic samples collected at low-to-moderate flow, during spring and summer of 2006 and 2008. Bivariate linear regression relations of THg and MeHg concentrations with either percent wetland area or DOC concentrations were significant but could account for only about 1/3 of the variation in these Hg forms in summer. In contrast, multivariate linear regression relations that included metrics of (1) hydrogeomorphology, (2) riparian/wetland area, and (3) open water, explained about 66% to 〉90% of spatial variation in each Hg form in spring and summer samples. These metrics reflect the influence of basin morphometry and riparian soils on Hg source and transport, and the role of open water as a Hg sink. Multivariate models based solely on these landscape metrics generally accounted for as much or more of the variation in Hg concentrations than models based on chemical and physical metrics, and show great promise for identifying waters with expected high Hg concentrations in the Adirondack region and similar glaciated riverine ecosystems.

Description: Episodic Tremor and Slip (ETS), involving transient deformations accompanied by emergent, low-frequency tremor occurs in subduction zones around the world. ETS events increase the shear stress on locked megathrusts and may potentially trigger damaging earthquakes. Despite the clear association of tremor and slip the physical relationship between them is unresolved. Tremor appears to result from slip on small asperities on the plate interface due to either creep on the surrounding fault, or stress increases ahead of the propagating slow-slip front. Previous studies of migrating slow slip events have not had sufficient spatial and temporal resolution to differentiate between these two models. To address this, we invert GPS data from the August 2009 ETS event in central Cascadia for the space-time evolution of fault slip-rate. We find a correlation in both space and time between tremor epicenters and the independently determined position of high fault slip-rate. This supports the first hypothesis that tremor asperities are loaded directly by slow slip, rather than by stress increases ahead of the slip front, and provides new insights into the mechanics of ETS.

Description: Mercury (Hg) is one of the leading water quality concerns in surface waters of the United States. Although watershed-scale Hg cycling research has increased in the past two decades, advances in modeling watershed Hg processes in diverse physiographic regions, spatial scales, and land cover types are needed. The goal of this study was to assess Hg cycling in a Coastal Plain system using concentrations and fluxes estimated by multiple watershed-scale models with distinct mathematical frameworks reflecting different system dynamics. We simulated total mercury (HgT, the sum of filtered and particulate forms) concentrations and fluxes from a Coastal Plain watershed (McTier Creek) using three watershed Hg models and an empirical load model. Model output was compared with observed in-stream HgT. We found that shallow subsurface flow is a potentially important transport mechanism of particulate HgT during periods when connectivity between the uplands and surface waters is maximized. Other processes (e.g., stream bank erosion, sediment re-suspension) may increase particulate HgT in the water column. Simulations and data suggest that variable source area (VSA) flow and lack of rainfall interactions with surface soil horizons result in increased dissolved HgT concentrations unrelated to DOC mobilization following precipitation events. Although flushing of DOC-HgT complexes from surface soils can also occur during this period, DOC-complexed HgT becomes more important during base flow conditions. TOPLOAD simulations highlight saturated subsurface flow as a primary driver of daily HgT loadings, but shallow subsurface flow is important for HgT loads during high-flow events. Results suggest limited seasonal trends in HgT dynamics.

Description: Background: Many synthetic biologists seek to increase the degree of autonomy in the assembly of long DNA (L-DNA) constructs from short synthetic DNA fragments, which are today quite inexpensive because of automated solid-phase synthesis. However, the low information density of DNA built from just four nucleotide “letters”, the presence of strong (G:C) and weak (A:T) nucleobase pairs, the non-canonical folded structures that compete with Watson–Crick pairing, and other features intrinsic to natural DNA, generally prevent the autonomous assembly of short single-stranded oligonucleotides greater than a dozen or so. Results: We describe a new strategy to autonomously assemble L-DNA constructs from fragments of synthetic single-stranded DNA. This strategy uses an artificially expanded genetic information system (AEGIS) that adds nucleotides to the four (G, A, C, and T) found in standard DNA by shuffling hydrogen-bonding units on the nucleobases, all while retaining the overall Watson–Crick base-pairing geometry. The added information density allows larger numbers of synthetic fragments to self-assemble without off-target hybridization, hairpin formation, and non-canonical folding interactions. The AEGIS pairs are then converted into standard pairs to produce a fully natural L-DNA product. Here, we report the autonomous assembly of a gene encoding kanamycin resistance using this strategy. Synthetic fragments were built from a six-letter alphabet having two AEGIS components, 5-methyl-2’-deoxyisocytidine and 2’-deoxyisoguanosine (respectively S and B ), at their overlapping ends. Gaps in the overlapped assembly were then filled in using DNA polymerases, and the nicks were sealed by ligase. The S : B pairs in the ligated construct were then converted to T:A pairs during PCR amplification. When cloned into a plasmid, the product was shown to make Escherichia coli resistant to kanamycin. A parallel study that attempted to assemble similarly sized genes with optimally designed standard nucleotides lacking AEGIS components gave successful assemblies of up to 16 fragments, but generally failed when larger autonomous assemblies were attempted. Conclusion: AEGIS nucleotides, by increasing the information density of DNA, allow larger numbers of DNA fragments to autonomously self-assemble into large DNA constructs. This technology can therefore increase the size of DNA constructs that might be used in synthetic biology. Beilstein J. Org. Chem. 2014, 10, 2348–2360. doi:10.3762/bjoc.10.245