[1] We observed transient stratification and mixing events associated with nearshore internal bores in southern Monterey Bay using an array of instruments with high spatial and temporal resolution. The arrival of the bores is characterized by surging masses of dense (cold) water that tend to stratify the water column. The bore is followed by a gradual drop in the temperature throughout the water column over several hours (defined here as the bore period) until a sharp warm-front relaxation, followed by high frequency temperature fluctuations, returns the column back to nearly its original state (defined here as the mixing period). Mixing periods revealed increased temperature variance at high frequencies (w > N), as well as a greater percentage of events where dynamic instabilities may be present (Ri < 0.25), suggesting active mixing of the stratified water column. Turbulent dissipation rates in the stratified interior during the mixing period, estimated using the technique of isopycnal slope spectra, revealed mean values the same order of magnitude as near-bed bottom-generated turbulence. Observations indicate that local shear-produced turbulent kinetic energy by the warm front relaxations dominates mixing in the stratified interior. The non-canonical nature of these bore and relaxation events is also investigated with a numerical model, and the dynamics are shown to depend on the internal Iribarren number. Our results suggest that nearshore internal bores interacting with local bathymetry dramatically alter local dynamics and mixing in the nearshore with important ecological implications.

This study utilizes field observations in southern Monterey Bay, CA, to examine how regionalscale upwelling and changing offshore (shelf) conditions influence nearshore internal bores. We show that the low-frequency wind forcing (e.g., upwelling/relaxation time scales) modifies the offshore stratification and thermocline depth. This in turn alters the strength and structure of observed internal bores in the nearshore. An internal bore strength index is defined using the high-pass filtered potential energy density anomaly in the nearshore. During weak upwelling favorable conditions and wind relaxations, the offshore thermocline deepens. In this case, both the amplitude of the offshore internal tide and the strength of the nearshore internal bores increase. In contrast, during strong upwelling conditions, the offshore thermocline shoals toward the surface, resulting in a decrease in the offshore internal tide amplitude. As a result, cold water accumulates in the nearshore (nearshore pooling), and the internal bore strength index decreases. Empirical orthogonal functions are utilized to support the claim that the bore events contribute to the majority of the variance in cross-shelf exchange and transport in the nearshore. Observed individual bores can drive shock-like drops in dissolved oxygen (DO) with rapid onset times, while extended upwelling periods with reduced bore activity produce longer duration, low DO events.

High-frequency measurements of stratified turbulence throughout the water column were collected over a 2 week period in the nearshore environment of southern Monterey Bay, CA, using a cabled observatory system and an underwater turbulence flux tower. The tower contained a vertical array of acoustic Doppler velocimeters and fast-response conductivity-temperature sensors, providing a nearly continuous data set of turbulent velocity and density fluctuations and a unique look into the stratified turbulence field. The evolution of various turbulence quantities and direct measurements of the vertical turbulent diffusivity is examined in the presence of nearshore internal bores, both in the near-bed region and in the stratified interior. We show that individual bores can drive substantial changes in local turbulence and mixing dynamics, with considerable differences between the leading and trailing edges of the bores. Using direct observations of the flux Richardson number, our measurements confirm previous observations that show the highest mixing efficiencies (C) occurring in regions of buoyancy-controlled turbulence. Parameterizations of the flux Richardson number as a function of the turbulence activity number are also presented. Finally, we demonstrate that the commonly used assumption of a constant mixing efficiency (C 5 0.2) for calculating turbulent diffusivities leads to significant overestimates compared to diffusivity values calculated using the directly measured mixing efficiency. Implications of the results are discussed.

[1] Measured turbulence power spectra, cospectra, and ogive curves from a shallow tidal flow were scaled using Monin-Obukhov similarity theory to test the applicability to a generic tidal flow of universal curves found from a uniform, neutrally stable atmospheric boundary layer (ABL). While curves from individual 10 min data bursts deviate significantly from similarity theory, averages over large numbers of sufficiently energetic bursts follow the general shape. However, there are several differences: (1) Variance in the measured curves was shifted toward higher frequencies, (2) at low frequencies, velocity spectra were significantly more energetic than theory while cospectra were weaker, and (3) spectral ratios of momentum flux normalized by turbulent kinetic energy (TKE) indicate decreased fluxes and/or elevated TKE levels. Several features of the turbulence structure may explain these differences. First, turbulent dissipation exceeded production, indicating nonequilibrium turbulence, possibly from advection of TKE. Indeed, using the production rate rather than dissipation markedly improves agreement in the inertial subrange. Second, spectral lag of the largest eddies due to inhomogeneous boundary conditions and decaying turbulence could explain spectral deviations from theory at low frequencies. Finally, since the largest eddies dominate momentum transfer, the consequence of the cospectra difference is that calculated ogive curves produced smaller total momentum fluxes compared to theory, partly because of countergradient fluxes. While ABL similarity scaling applied to marine bottom boundary layers (MBBLs) will produce curves with the general shape of the universal curves, care should be taken in determining details of turbulent energy and stress estimates, particularly in shallow and inhomogeneous MBBLs.

We collected high-resolution observations of nonlinear internal waves (NLIWs) at a persistent upwelling front in the shallow coastal environment (~20 m) of northern Monterey Bay, CA. The coastal upwelling front forms between recently upwelled waters and warmer stratified waters that are trapped in the bay (upwelling shadow). The front propagates up and down the coast in the along-shore direction as a buoyant plume front due to modulation by strong diurnal wind forcing. The evolution of the coastal upwelling front, and the subsequent modulation of background environmental conditions, is examined using both individual events and composite day averages. We demonstrate that regional-scale upwelling and local diurnal wind forcing are key components controlling local stratification and the formation of internal wave guides that allow for high-frequency internal wave activity. Finally, we discuss the ability of theoretical models to describe particularly large-amplitude internal waves that exist in the presence of a strong background shear and test a fully nonlinear model (i.e., the Dubreil-Jacotin-Long equation).

Plastic piping made of polyvinyl chloride (PVC), and chlorinated PVC (CPVC), is being increasingly used for drinking water distribution lines. Given the formulation of the material from vinyl chloride (VC), there has been concern that the VC (a confirmed human carcinogen) can leach from the plastic piping into drinking water. PVC/CPVC pipe reactors in the laboratory and tap samples collected from consumers homes (n = 15) revealed vinyl chloride accumulation in the tens of ng/L range after a few days and hundreds of ng/L after two years. While these levels did not exceed the EPA's maximum contaminant level (MCL) of 2 μg/L, many readings that simulated stagnation times in homes (overnight) exceeded the MCL-Goal of 0 μg/L. Considerable differences in VC levels were seen across different manufacturers, while aging and biofilm effects were generally small. Preliminary evidence suggests that VC may accumulate not only via chemical leaching from the plastic piping, but also as a disinfection byproduct (DBP) via a chlorine-dependent reaction. This is supported from studies with CPVC pipe reactors where chlorinated reactors accumulated more VC than dechlorinated reactors, copper pipe reactors that accumulated VC in chlorinated reactors and not in dechlorinated reactors, and field samples where VC levels were the same before and after flushing the lines where PVC/CPVC fittings were contributing. Free chlorine residual tests suggest that VC may be formed as a secondary, rather than primary, DBP. Further research and additional studies need to be conducted in order to elucidate reaction mechanisms and tease apart relative contributions of VC accumulation from PVC/CPVC piping and chlorine-dependent reactions.

The oceanic response to high‐frequency local diurnal wind forcing is examined in a small coastal embayment located along an understudied stretch of the central California coast. We show that local diurnal wind forcing is the dominant control on nearshore temperature variability and circulation patterns. A complex empirical orthogonal function (CEOF) analysis of velocities in San Luis Obispo Bay reveals that the first‐mode CEOF amplitude time series, which accounts for 47.9% of the variance, is significantly coherent with the local wind signal at the diurnal frequency and aligns with periods of weak and strong wind forcing. The diurnal evolution of the hydrographic structure and circulation in the bay is examined using both individual events and composite‐day averages. During the late afternoon, the local wind strengthens and results in a sheared flow with near‐surface warm waters directed out of the bay and a compensating flow of colder waters into the bay over the bottom portion of the water column. This cold water intrusion into the bay causes isotherms to shoal toward the surface and delivers subthermocline waters to shallow reaches of the bay, representing a mechanism for small‐scale upwelling. When the local winds relax, the warm water mass advects back into the bay in the form of a buoyant plume front. Local diurnal winds are expected to play an important role in nearshore dynamics and local upwelling in other small coastal embayments with important implications for various biological and ecological processes.

Fanconi anemia (FA) is a chromosome instability syndrome characterized by increased cancer predisposition. Specifically, the FA pathway functions to protect genome stability during DNA replication. The central FA pathway protein, FANCD2, locates to stalled replication forks and recruits homologous recombination (HR) factors such as CtBP interacting protein (CtIP) to promote replication fork restart while suppressing new origin firing. Here, we identify alpha-thalassemia retardation syndrome X-linked (ATRX) as a novel physical and functional interaction partner of FANCD2. ATRX is a chromatin remodeler that forms a complex with Death domain-associated protein 6 (DAXX) to deposit the histone variant H3.3 into specific genomic regions. Intriguingly, ATRX was recently implicated in replication fork recovery; however, the underlying mechanism(s) remained incompletely understood. Our findings demonstrate that ATRX forms a constitutive protein complex with FANCD2 and protects FANCD2 from proteasomal degradation. ATRX and FANCD2 localize to stalled replication forks where they cooperate to recruit CtIP and promote MRE11 exonuclease-dependent fork restart while suppressing the firing of new replication origins. Remarkably, replication restart requires the concerted histone H3 chaperone activities of ATRX/DAXX and FANCD2, demonstrating that coordinated histone H3 variant deposition is a crucial event during the reinitiation of replicative DNA synthesis. Lastly, ATRX also cooperates with FANCD2 to promote the HR-dependent repair of directly induced DNA double-stranded breaks. We propose that ATRX is a novel functional partner of FANCD2 to promote histone deposition-dependent HR mechanisms in S-phase.