Ruptures of mixed lipid monolayers under tension and supercooling: implications for nanobubbles in plants.

Mixed phospholipid and glycolipid monolayers likely coat the surfaces of pressurised gas nanobubbles within the hydraulic systems of plants. The lipid coatings bond to water under negative pressure and are thus stretched out of equilibrium. In this work, we have used molecular dynamics simulations to produce trajectories of a biologically relevant mixed monolayer, pulled at mild negative pressures (-1.5 to -4.5 MPa). Pore formation within the monolayer is observed at both 270 and 310 K, and proceeds as an activated process once the lipid tails fully transition from the two dimensional liquid condensed to liquid expanded phase. Pressure:area isotherms showed reduced surface pressure under slight supercooling (T = 270 K) at all observed areas per lipid. Finally, Rayleigh-Plesset simulations were used to predict evolving nanobubble size using the calculated pressure:area isotherms as dynamic surface tensions. We confirm the existence of a second critical radius with respect to runaway growth, above the homogeneous cavitation radius.

Homeotic transformations suggest mechanisms for rapid evolution diversification in Drosophila sex combs.

Evolutionary innovations refer to the emergence of new traits, functions, or behaviors in organisms and lineages over time. Although research has demonstrated that such innovations can arise gradually or through small steps (Chouard 2010), the mechanisms by which rapid morphological diversification takes place remain poorly understood (Bailey et al. 2019). To explore this question, we used the evolution of sex combs, as a system (Ho et al. 2018). We used this male-specific row of leg bristles, comprising sex combs as a system, because it displays spectacular morphological diversification in a short time (Kopp 2011). Homeotic mutations in the fruit fly, Drosophila melanogaster, are those which create modifications in one part of a fly to resemble another region. Here we describe effects of some of these mutations which transform the D. melanogaster fly sex comb morphology to closely resemble sex comb morphology in other species. These findings support previous research indicating that minor alterations to regulatory elements can play a significant role in explaining morphological evolution (Atallah et al. 2004). Thus, our results suggest that rapid diversification may not require starting from scratch, but rather may require minor modifications to the sex comb ground plan, which may account for its rapid morphological evolution (Lee et al. 2011).

Lipid-Coated Nanobubbles in Plants.

One of the more surprising occurrences of bulk nanobubbles is in the sap inside the vascular transport system of flowering plants, the xylem. In plants, nanobubbles are subjected to negative pressure in the water and to large pressure fluctuations, sometimes encompassing pressure changes of several MPa over the course of a single day, as well as wide temperature fluctuations. Here, we review the evidence for nanobubbles in plants and for polar lipids that coat them, allowing nanobubbles to persist in this dynamic environment. The review addresses how the dynamic surface tension of polar lipid monolayers allows nanobubbles to avoid dissolution or unstable expansion under negative liquid pressure. In addition, we discuss theoretical considerations about the formation of lipid-coated nanobubbles in plants from gas-filled spaces in the xylem and the role of mesoporous fibrous pit membranes between xylem conduits in creating the bubbles, driven by the pressure gradient between the gas and liquid phase. We discuss the role of surface charges in preventing nanobubble coalescence, and conclude by addressing a number of open questions about nanobubbles in plants.

Dynamics of changes in apical cell area during sex comb rotation in Drosophila melanogaster.

Epithelia are highly dynamic tissues displaying various types of tissue rearrangements (Weliky and Oster, 1990; Taylor and Adler, 2008; Harris and Tepass, 2010; Lee et al. , 2013; Firmino et al. , 2016; Rupprecht et al. , 2017). Here, we describe the dynamics of changes in apical cell area (ACA) in an epithelial system displaying tissue rearrangement resulting in sex comb rotation on the forelegs of male Drosophila melanogaster . The sex comb is a row of leg bristles which rotates during morphogenesis (Atallah, 2008; Atallah et al. , 2009; Malagon, 2013). We quantified the ACA in the region proximal to the developing sex comb by tracing apical cell boundaries using ImageJ in pupal first leg imaginal discs. We found that cells display intricate irregular oscillations in size as the comb rotates. However, the net changes in ACA within most of the cells studied are subtle, only 0 to +/-15%. Our current working hypothesis suggests these irregular oscillations confer flexibility during tissue rearrangement and can be an important mechanism for tissue homeostasis.

Accurate Prediction of Organic Aerosol Evaporation Using Kinetic Multilayer Modeling and the Stokes-Einstein Equation.

Organic aerosol can adopt a wide range of viscosities, from liquid to glass, depending on the local humidity. In highly viscous droplets, the evaporation rates of organic components are suppressed to varying degrees, yet water evaporation remains fast. Here, we examine the coevaporation of semivolatile organic compounds (SVOCs), along with their solvating water, from aerosol particles levitated in a humidity-controlled environment. To better replicate the composition of secondary aerosol, nonvolatile organics were also present, creating a three-component diffusion problem. Kinetic modeling reproduced the evaporation accurately when the SVOCs were assumed to obey the Stokes-Einstein relation, and water was not. Crucially, our methodology uses previously collected data to constrain the time-dependent viscosity, as well as water diffusion coefficients, allowing it to be predictive rather than postdictive. Throughout the study, evaporation rates were found to decrease as SVOCs deplete from the particle, suggesting path function type behavior.

Dynamic Surface Tension Enhances the Stability of Nanobubbles in Xylem Sap.

Air seeded nanobubbles have recently been observed within tree sap under negative pressure. They are stabilized by an as yet unidentified process, although some embolize their vessels in extreme circumstances. Current literature suggests that a varying surface tension helps bubbles survive, but few direct measurements of this quantity have been made. Here, we present calculations of dynamic surface tension for two biologically relevant lipids using molecular dynamics simulations. We find that glycolipid monolayers resist expansion proportionally to the rate of expansion. Their surface tension increases with the tension applied, in a similar way to the viscosity of a non-Newtonian fluid. In contrast, a prototypical phospholipid was equally resistant to all applied tensions, suggesting that the fate of a given nanobubble is dependent on its surface composition. By incorporating our results into a Classical Nucleation Theory (CNT) framework, we predict nanobubble stability with respect to embolism. We find that the metastable radius of glycolipid coated nanobubbles is approximately 35 nm, and that embolism is in this case unlikely when the external pressure is less negative than -1.5 MPa.

Transient cavity dynamics and divergence from the Stokes-Einstein equation in organic aerosol.

The diffusion of small molecules through viscous matrices formed by large organic molecules is important across a range of domains, including pharmaceutical science, materials chemistry, and atmospheric science, impacting on, for example, the formation of amorphous and crystalline phases. Here we report significant breakdowns in the Stokes-Einstein (SE) equation from measurements of the diffusion of water (spanning 5 decades) and viscosity (spanning 12 decades) in saccharide aerosol droplets. Molecular dynamics simulations show water diffusion is not continuous, but proceeds by discrete hops between transient cavities that arise and dissipate as a result of dynamical fluctuations within the saccharide lattice. The ratio of transient cavity volume to solvent volume increases with size of molecules making up the lattice, increasing divergence from SE predictions. This improved mechanistic understanding of diffusion in viscous matrices explains, for example, why organic compounds equilibrate according to SE predictions and water equilibrates more rapidly in aerosols.

Characterising the evaporation kinetics of water and semi-volatile organic compounds from viscous multicomponent organic aerosol particles.

The physicochemical changes experienced by organic aerosol particles undergoing dehydration into the surrounding gas phase can be drastic, forcing rapid vitrification of the particle and suppressing internal diffusion. Until recently, experimental studies have concentrated on quantifying diffusional mixing of either water or non-volatile components, while relatively little attention has been paid to the role of semivolatile organic component (SVOC) diffusion and volatilisation in maintaining the equilibrium between the gas and particle phases. Here we present methods to simultaneously investigate diffusivities and volatilities in studies of evolving single ternary aerosol particle size and composition. Analysing particles of ternary composition must account for the multiple chemical species that volatilise in response to a step change in gas phase water activity. In addition, treatments of diffusion in multicomponent mixtures are necessary to represent evolving heterogeneities in particle composition. We find that the contributions to observed size behaviour from volatilisation of water and a SVOC can be decoupled and treated separately. Employing Fickian diffusion modelling, we extract the compositional dependence of the diffusion constant of water and compare the results to recently published parametrisations in binary aerosol particles. The treatment of ideality and activity in each case is discussed, with reference to use in multicomponent core shell models. Meanwhile, the evaporation of an SVOC into an unsaturated gas flow may be treated by Maxwell's equation, with slow diffusional transport manifesting as a suppression in the extracted vapour pressure.

Overview: The Design, Adoption, and Analysis of a Visual Document Mining Tool for Investigative Journalists.

For an investigative journalist, a large collection of documents obtained from a Freedom of Information Act request or a leak is both a blessing and a curse: such material may contain multiple newsworthy stories, but it can be difficult and time consuming to find relevant documents. Standard text search is useful, but even if the search target is known it may not be possible to formulate an effective query. In addition, summarization is an important non-search task. We present Overview, an application for the systematic analysis of large document collections based on document clustering, visualization, and tagging. This work contributes to the small set of design studies which evaluate a visualization system "in the wild", and we report on six case studies where Overview was voluntarily used by self-initiated journalists to produce published stories. We find that the frequently-used language of "exploring" a document collection is both too vague and too narrow to capture how journalists actually used our application. Our iterative process, including multiple rounds of deployment and observations of real world usage, led to a much more specific characterization of tasks. We analyze and justify the visual encoding and interaction techniques used in Overview's design with respect to our final task abstractions, and propose generalizable lessons for visualization design methodology.

Glimmer: multilevel MDS on the GPU.

We present Glimmer, a new multilevel algorithm for multidimensional scaling designed to exploit modern graphics processing unit (GPU) hardware. We also present GPU-SF, a parallel, force-based subsystem used by Glimmer. Glimmer organizes input into a hierarchy of levels and recursively applies GPU-SF to combine and refine the levels. The multilevel nature of the algorithm makes local minima less likely while the GPU parallelism improves speed of computation. We propose a robust termination condition for GPU-SF based on a filtered approximation of the normalized stress function. We demonstrate the benefits of Glimmer in terms of speed, normalized stress, and visual quality against several previous algorithms for a range of synthetic and real benchmark datasets. We also show that the performance of Glimmer on GPUs is substantially faster than a CPU implementation of the same algorithm.

Disruption and overexpression of the Schizosaccharomyces pombe aps1 gene, and effects on growth rate, morphology and intracellular diadenosine 5',5"'-P1,P5-pentaphosphate and diphosphoinositol polyphosphate concentrations.

Schizosaccharomyces pombe Aps1 is an enzyme that degrades both diadenosine oligophosphates (Ap(n)A, n =5 or 6) and diphosphoinositol polyphosphates [diphosphoinositol pentakisphosphate (PP-InsP(5)) and bisdiphosphoinositol tetrakisphosphate ([PP](2)-InsP(4))] in vitro. The in vivo substrates of Aps1 are unknown. We report here the identification of Ap(5)A, PP-InsP(5), [PP](2)-InsP(4) and a novel diphosphoinositol polyphosphate ([PP](x)-InsP(x)) in S. pombe using HPLC methods. Ap(5)A was present at 0.06 pmol/mg of protein (approx. 4 nM). PP-InsP(5), [PP](x)-InsP(x) and [PP](2)-InsP(4) were present at 15 pmol/mg (approx. 1.1 microM), 15 pmol/mg (approx. 1.1 microM) and 30 pmol/mg (approx. 2.2 microM) respectively, while the intracellular concentration of InsP(6) was 0.5 nmol/mg of protein (approx. 36 microM). Disruption of aps1 resulted in a 52% decrease in Ap(6)A hydrolase activity in vitro, no detectable change in the intracellular Ap(5)A concentration, and 3-fold increased intracellular concentrations of PP-Ins P(5) and [PP](x)-InsP(x). Disruption of aps1 resulted in no detectable change in morphology or growth rate in minimal or rich media at 30 degrees C. Overexpression of aps1 via two different plasmids that resulted in 60% and 6-fold increases above wild-type enzymic activity in vitro caused no detectable changes in the intracellular concentrations of [PP](2)-InsP(4), [PP](x)-InsP(x) or PP-InsP(5), but paradoxical increases of approx. 2.5- and 55-fold respectively in the intracellular Ap(5)A concentration. Overexpression of aps1 also resulted in a reduced growth rate and in morphological changes, including swollen, rounded and multiseptate cells. No phenotypic changes or changes in intracellular Ap(5)A occurred upon overexpression of aps1 E93Q, which encodes a mutated Aps1 lacking significant enzymic activity. We conclude that Aps1 degrades PP-InsP(5) and [PP](x)-InsP(x) in vivo.