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Ponds are characterized by high biodiversity, intense biogeochemical cycling, and susceptibility to anthropogenic impacts. Yet few studies have quantified the water velocities responsible for vertical mixing or lateral transport in ponds. We used high‐resolution observations of velocity to examine mixing and transport during summer in a 50‐m‐long, 2.7‐m‐deep temperate pond. Many observed transport and mixing processes resembled those found in larger stratified lakes. A surface mixed layer was observed, whose depth ranged between ~ 1 m at night and < 0.3 m during the day. Turbulence was usually sufficient to vertically mix the surface layer in 4–12 min, but no turbulence was observed in the hypolimnion. Persistent (2.5‐h‐averaged) currents usually flowed downwind near the surface and returned upwind near the mixed layer base. Surface currents were proportional to windspeed, with root‐mean‐squared speed of 8×10−3ms−1$$ 8\times {10}^{-3}\ \mathrm{m}\;{\mathrm{s}}^{-1} $$ (persistent hypolimnion currents were much weaker). Superposed on persistent currents were 30‐ to 100‐min‐period fluctuations resulting from internal seiches. These fluctuations were comparable in magnitude to more persistent currents in the mixed layer and dominated in the hypolimnion. Seiches did not advect particles far across the pond, but did contribute to production of mixed layer turbulence. Seiches also contributed to shear dispersion, which was sufficient to mix near‐surface tracers across the pond in 2–4 d. Theory suggests that hypolimnion bottom boundary layers were laminar during the downslope phase of seiche motion, but became turbulent during the upslope phase as near‐bed water flows created unstable stratification. [ABSTRACT FROM AUTHOR]

Lateral intrusions flowing from the boundaries of lakes and oceans might influence basin‐scale distributions of heat, chemical solutes, sediments, and organisms. Here, observations of numerous intrusions from multiple locations in a small lake were used to examine the relation of intrusions to a lakewide internal seiche, and to estimate mean exchange between sloping bottom boundary layers (BBLs) and the lake interior. BBL waters were observed periodically separating from the bed and flowing laterally offshore. Boundary layer separation was initiated where strong downslope flows encountered upslope‐propagating temperature fronts. These separation events propagated upslope, coherent with the vertically propagating internal seiche, resembling previously reported cases of upslope‐propagating internal bores. Following separation, jets flowed offshore immediately above temperature fronts, transporting boundary layer water at least 61 m into the interior. Jet propagation could be traced upwards, from the bed at 9.4 m depth to the base of the surface mixed layer. Mean offshore transport was most intense within the metalimnion (4–7 m depth). Intruding intermediate‐temperature thermocline water was likely supplied both by river inputs and by boundary mixing of cold and warm waters. These findings suggest that periodic jets, resulting from seiche‐induced boundary layer separation, transported significant quantities of water from the boundary layer toward the stratified lake interior, with possible implications for distributions of sediments, solutes, and organisms. [ABSTRACT FROM AUTHOR]

Methane (CH4) produced in anoxic sediments plays a significant role in the carbon economy of many lakes and reservoirs. CH4 released from sediments first crosses the bottom boundary layer (BBL), the layer of water overlying the lakebed where currents are slowed by friction with the sediments below. Physical and biogeochemical conditions in the BBL, which can fluctuate hourly to daily with basin‐wide internal waves (seiches), likely influence CH4 transport from sediments into the hypolimnion. In this study, we estimated CH4 fluxes across the BBL of a eutrophic lake using a novel in situ flux gradient approach adapted from marine applications. For 2–6 h periods throughout the spring and summer, we estimated CH4 fluxes across the BBL using simultaneous measurements of CH4 concentrations, turbulent mixing, and thermal stratification. Sub‐daily variation in CH4 fluxes was high, and CH4 fluxes sometimes changed several‐fold within hours. These rapid shifts in BBL fluxes were likely influenced by fluctuations in seiche‐driven variations in the intensity of BBL turbulent mixing. Fluxes increased from spring to summer, concurrent with the development of lake stratification, and fueled an accumulation of CH4 below the thermocline. Throughout the summer, CH4 flux across the BBL exceeded CH4 accumulation below the thermocline, suggesting significant methanotrophy in the hypolimnion, consistent with incubation‐based oxidation rates. Our results are the first to demonstrate sub‐daily and seasonal variability in the timing and magnitude of CH4 fluxes within a lake BBL, and highlight a need to quantify such variability in other lentic systems. [ABSTRACT FROM AUTHOR]

In a stratified lake, where an internal seiche maintained an oscillating bottom boundary layer (BBL), processes including strain‐induced periodic stratification (SIPS), a downslope mean flow, and upslope‐propagating internal waves controlled fluctuating BBL mixing rates. To investigate these processes, high‐resolution temperature and velocity profiles were measured within 2 m of the sloping bed, through more than 100 cycles of upslope and downslope flows. The associated seiche‐induced velocity reversals coincided with the arrival of upslope‐propagating cold fronts. Although fronts are sometimes associated with internal wave breaking, in this lake the measured frontal slopes were small and breaking did not occur. When fronts were not propagating past instruments, near‐bed stratification was consistent with SIPS, being intensified by downslope flows and reduced by upslope flows. Owing to a downslope near‐bed mean flow, which was previously shown to cancel an upslope internal‐wave Stokes drift, peak downslope velocities regularly exceeded peak upslope velocities. Given these strong downslope velocities, turbulent dissipation rates were most intense during downslope phases. Therefore, during downslope flow, creation of stratification by SIPS coincided with elevated dissipation, creating conditions for effective mixing. Correspondingly, two simple parameterizations for mixing efficiency suggest that most of the total near‐bed buoyancy flux (≥ 82%), and most of the irreversible flux (87%), occurred during the downslope‐flow phase of internal seiche cycles. The observed mechanism for dominant mixing during downslope flow has potential to act in other environments where internal waves propagate up sloping beds. [ABSTRACT FROM AUTHOR]

T‐bet is the lineage‐specifying transcription factor for CD4+ TH1 cells. T‐bet has also been found in other CD4+ T cell subsets, including TH17 cells and Treg, where it modulates their functional characteristics. However, we lack information on when and where T‐bet is expressed during T cell differentiation and how this impacts T cell differentiation and function. To address this, we traced the ontogeny of T‐bet‐expressing cells using a fluorescent fate‐mapping mouse line. We demonstrate that T‐bet is expressed in a subset of CD4+ T cells that have naïve cell surface markers and transcriptional profile and that this novel cell population is phenotypically and functionally distinct from previously described populations of naïve and memory CD4+ T cells. Naïve‐like T‐bet‐experienced cells are polarized to the TH1 lineage, predisposed to produce IFN‐γ upon cell activation, and resist repolarization to other lineages in vitro and in vivo. These results demonstrate that lineage‐specifying factors can polarize T cells in the absence of canonical markers of T cell activation and that this has an impact on the subsequent T‐helper response. [ABSTRACT FROM AUTHOR]

Within a wave‐exposed mangrove forest, novel field observations are presented, comparing millimeter‐scale turbulent water velocity fluctuations with contemporaneous subtidal bed elevation changes. High‐resolution velocity and bed level measurements were collected from the unvegetated mudflat, at the mangrove forest fringe, and within the forest interior over multiple tidal cycles (flood–ebb) during a 2‐week period. Measurements demonstrated that the spatial variability in vegetation density is a control on sediment transport at sub‐meter scales. Scour around single and dense clusters of pneumatophores was predicted by a standard hydraulic engineering equation for wave‐induced scour around regular cylinders, when the cylinder diameter in the equations was replaced with the representative diameter of the dense pneumatophore clusters. Waves were dissipated as they propagated into the forest, but dissipation at infragravity periods (> 30 s) was observed to be less than dissipation at shorter periods (< 30 s), consistent with the predictions of a simple model. Cross‐wavelet analysis revealed that infragravity‐frequency fluctuations in the bed level were occasionally coherent with velocity, possibly indicating scour upstream of dense pneumatophore patches when infragravity waves reinforced tidal currents. Consequently, infragravity waves were a likely driver of sediment transport within the mangrove forest. Near‐bed turbulent kinetic energy, estimated from the turbulent dissipation rate, was also correlated with bed level changes. Specifically, within the mangrove forest and over the unvegetated mudflat, high‐energy events were associated with erosion or near‐zero bed level change, whereas low‐energy events were associated with accretion. In contrast, no single relationship between bed level changes and mean current velocity was applicable across both vegetated and unvegetated regions. These observations support the theory that sediment mobilization scales with turbulent energy, rather than mean velocity, a distinction that becomes important when vegetation controls the development of turbulence. [ABSTRACT FROM AUTHOR]

High‐resolution velocity measurements were collected within and above two dense canopies of mangrove pneumatophore roots in a wave‐exposed mangrove forest. In both canopies, root density decreased steadily with height above bed owing to the variability in root heights and the tapered shape of the roots. Within the canopies, we consider turbulence within three zones: near the bed above the wave boundary layer, around the mean canopy height, and above the canopy. The near‐bed turbulence was particularly intense (up to 6.5 × 10−4 W/kg), likely owing to oscillatory wave‐driven currents flowing past dense vegetation. Near the bed and around the mean canopy height, peaks in horizontal velocity power spectra at frequencies corresponding to Strouhal numbers of ~0.2 may indicate Von Kármán wake shedding in the lee of the pneumatophores. Furthermore, a recirculation zone was observed immediately behind a cluster of pneumatophores at intermediate heights. These coherent flow structures were associated with zones of enhanced Reynolds stresses (up to 5.3 × 10−3 m2/s2) and eddy viscosities (up to 1.9 × 10−3 m2/s). Large near‐bed stresses were associated with near‐bed drag coefficients that are up to an order of magnitude larger than those expected in the absence of vegetation. Observed eddy viscosities are consistent with theoretical expectations, derived from scaling arguments using a standard mixing‐length model. These results suggest that pneumatophore roots can contribute greatly to turbulent mixing (e.g., eddy viscosities were on average O(10−4–10−3 m2/s) and therefore may enhance the sediment transport occurring in mangrove forest fringes. Plain Language Summary: Mangrove forests comprise the dominant plant communities in tropical and subtropical coasts and provide many important physical and biological functions. However, mangrove forests are largely in decline worldwide, and hence, there is interest in rehabilitating or replanting damaged forests. The success rate of these efforts may be improved by understanding the physical forces that shape mangrove ecosystems. In this study, we deployed several high‐resolution velocity sensors within the pneumatophore roots of a coastal mangrove forest in the lower Mekong Delta, Vietnam. From velocity measurements, we assessed the spatial distribution of turbulence that formed in the wake of the roots when they were submerged during the rising or falling tide. We found that enhanced turbulence was associated with denser vegetation, particularly near the bed. This result indicates that pneumatophore roots do not necessarily shelter the bed from erosional forces and instead may enhance sediment transport occurring within the forest. Key Points: Turbulent dissipation, Reynolds stress, and eddy viscosity are enhanced near the bed within clusters of mangrove pneumatophore rootsEddy viscosities up to 1.9 x 10‐3 m2/s were estimated within the vegetationPneumatophore roots may inhibit sediment deposition, which contradicts the expectation that dense vegetation promotes sediment retention [ABSTRACT FROM AUTHOR]

The three-dimensional (across-shore, alongshore, and vertical) structure of hourly mean currents and <0.01 Hz eddies was measured on a natural beach using 12 Acoustic Doppler Profilers. Both eddies and alongshore currents became relatively depth-uniform inside the surfzone. Eddies showed greater depth dependence than alongshore currents. A two-layer model, derived by scaling of the wave-averaged shallow water equations, yielded separate equations for depth-averaged and depth-dependent velocity components. Scaling suggests, and observations confirm, only a small role for lateral advection in most surfzone cases, leading to one-dimensional vertical models for depth dependence. For alongshore currents, depth dependence is generated by opposite forcing on lower and upper layers, respectively by bottom friction (quantified by time scale [ABSTRACT FROM AUTHOR]

Dendritic cells (DCs) play a vital role in innate and adaptive immunities. Inducible depletion of CD11c+ DCs engineered to express a high-affinity diphtheria toxin receptor has been a powerful tool to dissect DC function in vivo. However, despite reports showing that loss of DCs induces transient monocytosis, the monocyte population that emerges and the potential impact of monocytes on studies of DC function have not been investigated. We found that depletion of CD11c+ cells from CD11c.DTR mice induced the expansion of a variant CD64+ Ly6C+ monocyte population in the spleen and blood that was distinct from conventional monocytes. Expansion of CD64+ Ly6C+ monocytes was independent of mobilization from the BM via CCR2 but required the cytokine, G-CSF. Indeed, this population was also expanded upon exposure to exogenous G-CSF in the absence of DC depletion. CD64+ Ly6C+ monocytes were characterized by upregulation of innate signaling apparatus despite the absence of inflammation, and an increased capacity to produce TNF-α following LPS stimulation. Thus, depletion of CD11c+ cells induces expansion of a unique CD64+ Ly6C+ monocyte population poised to synthesize TNF-α. This finding will require consideration in experiments using depletion strategies to test the role of CD11c+ DCs in immunity. [ABSTRACT FROM AUTHOR]

In lakes and reservoirs, the bottom boundary layer (BBL) mediates chemical fluxes between sediments and the overlying water column. At the internal shoreline, where the thermocline contacts the lakebed, the motions of internal waves can create fluctuating redox conditions and dynamic physical forcing that may support ecologically important reactions such as denitrification. We characterized physical and chemical dynamics within the internal shoreline of a eutrophic reservoir during the spring and early summer of 2012 (18 May to 18 July). An internal seiche was found to generate quasi-periodic fluctuations (periods about 12-24 h) in BBL stratification, temperature, and redox conditions. To examine possible implications for chemical mixing and microbial processing, differences between vertically offset, simultaneous BBL measurements of velocity, temperature, N2, and N2O were made over 23 h. Vertical differences in BBL temperature, N2, and N2O formed and collapsed during the wave cycle, with the largest differences occurring following the arrival of an internal bore. Through much of the wave cycle, chemical differences were explained by physical advection and mixing. However, chemical differences measured after bore arrival were not explained by advection, possibly owing to local production of N2 and N2O. These results highlight the dynamic physical environment within the internal shoreline, and the potential of this zone to contribute to system wide denitrification and nitrous oxide production. [ABSTRACT FROM AUTHOR]

Chordoma is a rare malignant tumour of bone, the molecular marker of which is the expression of the transcription factor, brachyury. Having recently demonstrated that silencing brachyury induces growth arrest in a chordoma cell line, we now seek to identify its downstream target genes. Here we use an integrated functional genomics approach involving shRNA-mediated brachyury knockdown, gene expression microarray, ChIP-seq experiments, and bioinformatics analysis to achieve this goal. We confirm that the T-box binding motif of human brachyury is identical to that found in mouse, Xenopus, and zebrafish development, and that brachyury acts primarily as an activator of transcription. Using human chordoma samples for validation purposes, we show that brachyury binds 99 direct targets and indirectly influences the expression of 64 other genes, thereby acting as a master regulator of an elaborate oncogenic transcriptional network encompassing diverse signalling pathways including components of the cell cycle, and extracellular matrix components. Given the wide repertoire of its active binding and the relative specific localization of brachyury to the tumour cells, we propose that an RNA interference-based gene therapy approach is a plausible therapeutic avenue worthy of investigation. Copyright © 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

D cyclins (D1, D2 and D3) and their catalytic subunits (cyclin-dependent kinases cdk4 and cdk6) have a facilitating, but nonessential, role in cell cycle entry. Tissue-specific functions for D-type cyclins and cdks have been reported; however, the biochemical properties of these kinases are indistinguishable. We report that an F box protein, Fbxo7, interacted with cellular and viral D cyclins and distinguished among the cdks that bind D-type cyclins, specifically binding cdk6, in vitro and in vivo. Fbxo7 specifically regulated D cyclin/cdk6 complexes: Fbxo7 knockdown decreased cdk6 association with cyclin and its overexpression increased D cyclin/cdk6 activity and E2F activity. Fbxo7 interacted with p27, but its enhancement of cyclin D/cdk6 activity was p21/p27 independent. Fbxo7 overexpression transformed murine fibroblasts, rendering them tumorigenic in athymic nude mice. Transformed phenotypes were dependent on cdk6, as knockdown of cdk6 reversed them. Fbxo7 was highly expressed in epithelial tumors, but not in normal tissues, suggesting that it may have a proto-oncogenic role in human cancers. [ABSTRACT FROM AUTHOR]