Complete dataset of pore water chemical parameters measured at the Marsh Resource Meadowlands Mitigation Bank, a tidal marsh within the New Jersey Meadowlands, from March 2011 to April 2012. Analytes measured include dissolved methane, sulfate, dissolved organic carbon, temperature, salinity, and pH. Measurements were conducted using porewater dialysis samplers, and water was sampled from the surface to a depth of 60 cm.
The Kelvin-Helmholtz (KH) instability of magnetohydrodynamic surface waves at the low latitude boundary layer is examined using both an eigenfrequency analysis and a time-dependent wave simulation. The analysis includes the effects of sheared flow and Alfven velocity gradient. When the magnetosheath flows are perpendicular to the ambient magnetic field direction, unstable KH waves that propagate obliquely to the sheared flow direction occur at the sheared flow surface when the Alfv\'en Mach number is higher than an instability threshold. Including a shear transition layer between the magnetosphere and magnetosheath leads to secondary KH waves (driven by the sheared flow) that are coupled to the resonant surface Alfven wave. There are remarkable differences between the primary and the secondary KH waves including wave frequency, the growth rate, and the ratio between transverse and the compressional component. The secondary KH wave energy is concentrated near the shear Alfven wave frequency at the magnetosheath with a lower frequency than the primary KH waves. Although the growth rate of the secondary KH waves is lower than the primary KH waves, the threshold condition is lower, so it is expected that these types of waves will dominate at lower Mach number. Because the transverse component of the secondary KH waves is stronger than the primary KH waves, more efficient wave energy transfer from the boundary layer to the inner magnetosphere is also predicted.
Martin, Nicholas R; Blackman, Edith; Bratton, Benjamin P; Chase, Katelyn J; Bartlett, Thomas M; Gitai, Zemer
Abstract:
Bacterial species have diverse cell shapes that enable motility, colonization, and virulence. The cell wall defines bacterial shape and is primarily built by two cytoskeleton-guided synthesis machines, the elongasome and the divisome. However, the mechanisms producing complex shapes, like the curved-rod shape of Vibrio cholerae, are incompletely defined. Previous studies have reported that species-specific regulation of cytoskeleton-guided machines enables formation of complex bacterial shapes such as cell curvature and cellular appendages. In contrast, we report that CrvA and CrvB are sufficient to induce complex cell shape autonomously of the cytoskeleton in V. cholerae. The autonomy of the CrvAB module also enables it to induce curvature in the Gram-negative species Escherichia coli, Pseudomonas aeruginosa, Caulobacter crescentus, and Agrobacterium tumefaciens. Using inducible gene expression, quantitative microscopy, and biochemistry we show that CrvA and CrvB circumvent the need for patterning via cytoskeletal elements by regulating each other to form an asymmetrically-localized, periplasmic structure that directly binds to the cell wall. The assembly and disassembly of this periplasmic structure enables dynamic changes in cell shape. Bioinformatics indicate that CrvA and CrvB may have diverged from a single ancestral hybrid protein. Using fusion experiments in V. cholerae, we find that a synthetic CrvA/B hybrid protein is sufficient to induce curvature on its own, but that expression of two distinct proteins, CrvA and CrvB, promotes more rapid curvature induction. We conclude that morphological complexity can arise independently of cell shape specification by the core cytoskeleton-guided synthesis machines.
Physical and biogeochemical variables from the NOAA-GFDL Earth System Model 2M experiments (pre-processed), previously published observation-based datasets, and code to reproduce figures from these datasets, used for the study 'Hydrological cycle amplification reshapes warming-driven oxygen loss in Atlantic Ocean'.
Microscopy images are part of a paper entitled "Structured foraging of soil predators unveils functional responses to bacterial defenses" by Fernando Rossine, Gabriel Vercelli, Corina Tarnita, and Thomas Gregor. For detailed acquisition methods see the paper. Experiments were performed between 2019 and 2020 at Princeton University. Two types of images are provided, macroscopic and microscopic widefiled Images. Macroscopic images all show Petri dishes covered in fluorescent bacteria being consumed by amoebae. Images are shown for D. discoideum, P. violaceum, and A. castellanii. Images depicting drug treatments (Nystatin and Fluorouracil) were obtained using D. discoideum. Images used for the creation of a profile were all taken within 30 minutes of each other. Within each directory numbered images are independent replicates. The raw video directory contains time series for dishes under drug treatments. Each numbered folder is a sequence of photos (taken 30 minutes apart of each other) of a single dish. Microscopic images all show amoebae consuming bacteria on a petri dish. The 45 minute videos show either edge cells (located at the edge of amoebae colonies), or inner cells (located 2.5 millimeters towards the center of the colony, from the edge). Videos are confocal stacks, with bacteria showing in green and amoebae appearing as black holes within the bacterial lawn. As was for the macroscopic images, images are shown for D. discoideum, P. violaceum, and A. castellanii. Images depicting drug treatments (Nystatin and Fluorouracil) were obtained using D. discoideum.
Bhattacharjee, Tapomoy; Amchin, Daniel; Alert, Ricard; Ott, Jenna; Datta, Sujit
Abstract:
Collective migration -- the directed, coordinated motion of many self-propelled agents -- is a fascinating emergent behavior exhibited by active matter that has key functional implications for biological systems. Extensive studies have elucidated the different ways in which this phenomenon may arise. Nevertheless, how collective migration can persist when a population is confronted with perturbations, which inevitably arise in complex settings, is poorly understood. Here, by combining experiments and simulations, we describe a mechanism by which collectively migrating populations smooth out large-scale perturbations in their overall morphology, enabling their constituents to continue to migrate together. We focus on the canonical example of chemotactic migration of Escherichia coli, in which fronts of cells move via directed motion, or chemotaxis, in response to a self-generated nutrient gradient. We identify two distinct modes in which chemotaxis influences the morphology of the population: cells in different locations along a front migrate at different velocities due to spatial variations in (i) the local nutrient gradient and in (ii) the ability of cells to sense and respond to the local nutrient gradient. While the first mode is destabilizing, the second mode is stabilizing and dominates, ultimately driving smoothing of the overall population and enabling continued collective migration. This process is autonomous, arising without any external intervention; instead, it is a population-scale consequence of the manner in which individual cells transduce external signals. Our findings thus provide insights to predict, and potentially control, the collective migration and morphology of cell populations and diverse other forms of active matter.
Pan, Da; Gelfand, Ilya; Tao, Lei; Abraha, Michael; Sun, Kang; Guo, Xuehui; Chen, Jiquan; Robertson, G. Philip; Zondlo, Mark A.
Abstract:
This dataset contains spectroscopic simulations, experimental results for the 2202 cm-1 N2O absorption line, and N2O flux measurements shown in "A New Open-path Eddy Covariance Method for N2O and Other Trace Gases that Minimizes Temperature Corrections" by Da Pan, Ilya Gelfand, Lei Tao, Michael Abraha, Kang Sun, Xuehui Guo, Jiquan Chen, G. Philip Robertson, and Mark A. Zondlo. The HITRAN Application Programming Interface (HAPI) with HITRAN 2016 was used for spectroscopic simulations. Experiments were conducted to quantify H2O-broadened half-width at half maximum and validate spectroscopic simulations. N2O flux was measured with both eddy covariance and static chamber methods.
Elevated reactive nitrogen (Nr) deposition is a concern for alpine ecosystems, and dry NH3 deposition is a key contributor. Understanding how emission hotspots impact downwind ecosystems through dry NH3 deposition provides opportunities for effective mitigation. However, direct NH3 flux measurements with sufficient temporal resolution to quantify such events are rare. Here, we measured NH3 fluxes at Rocky Mountain National Park (RMNP) during two summers and analyzed transport events from upwind agricultural and urban sources in northeastern Colorado. We deployed open-path NH3 sensors on a mobile laboratory and an eddy covariance tower to measure NH3 concentrations and fluxes. Our spatial sampling illustrated an upslope event that transported NH3 emissions from the hotspot to RMNP. Observed NH3 deposition was significantly higher when backtrajectories passed through only the agricultural region (7.9 ng m-2 s-1) versus only the urban area (1.0 ng m-2 s-1) and both urban and agricultural areas (2.7 ng m-2 s-1). Cumulative NH3 fluxes were calculated using observed, bidirectional modeled, and gap-filled fluxes. More than 40% of the total dry NH3 deposition occurred when air masses were traced back to agricultural source regions. More generally, we identified that 10 (25) more national parks in the U.S. are within 100 (200) km of an NH3 hotspot, and more observations are needed to quantify the impacts of these hotspots on dry NH3 depositions in these regions.
