To quantify the diffusion constant of small molecules in the plant cell wall, fluorescence from carboxyfluorescein (CF) in the intact roots of Arabidopsis thaliana was recorded. Roots were immersed ...in a solution of the fluorescent dye and viewed through a confocal fluorescence microscope. These roots are sufficiently transparent that much of the apoplast can be imaged. The diffusion coefficient, Dcw, of CF in the cell wall was probed using two protocols: fluorescence recovery after photobleaching and fluorescence loss following perfusion with dye-free solution. Diffusion coefficients were obtained from the kinetics of the fluorescent transients and modelling apoplast geometry. Apoplastic diffusion constants varied spatially in the root. In the elongation zone and mature cortex, Dcw=(3.2±1.4)x10⁻¹¹ m² s⁻¹, whereas in mature epidermis, Dcw=(2.5±0.7)x10⁻¹² m² s⁻¹, at least an order of magnitude lower. Relative to the diffusion coefficient of CF in water, these represent reductions by approximately 1/15 and 1/195, respectively. The low value for mature epidermis is correlated with a suberin-like permeability barrier that was detected with either autofluorescence or berberine staining. This study provides a quantitative estimate of the permeability of plant cell walls to small organic acids--a class of compounds that includes auxin and other plant hormones. These measurements constrain models of solute transport, and are important for quantitative models of hormone signalling during plant growth and development.
Osmosis is the flow of solvent across a semipermeable membrane from a region of lower to higher solute concentration. It is of central importance in plant and animal physiology and finds many uses in ...industry. A survey of published papers, web resources, and current textbooks reveals that numerous misconceptions about osmosis continue to be cited and taught. To clarify these issues, we re-derive the thermodynamics of osmosis using the canonical formalism of statistical mechanics and go on to discuss the main points that continue to lead to misunderstandings.
In Arabidopsis, lateral roots originate from pericycle cells deep within the primary root. New lateral root primordia (LRP) have to emerge through several overlaying tissues. Here, we report that ...auxin produced in new LRP is transported towards the outer tissues where it triggers cell separation by inducing both the auxin influx carrier LAX3 and cell‐wall enzymes. LAX3 is expressed in just two cell files overlaying new LRP. To understand how this striking pattern of LAX3 expression is regulated, we developed a mathematical model that captures the network regulating its expression and auxin transport within realistic three‐dimensional cell and tissue geometries. Our model revealed that, for the LAX3 spatial expression to be robust to natural variations in root tissue geometry, an efflux carrier is required—later identified to be PIN3. To prevent LAX3 from being transiently expressed in multiple cell files, PIN3 and LAX3 must be induced consecutively, which we later demonstrated to be the case. Our study exemplifies how mathematical models can be used to direct experiments to elucidate complex developmental processes.
Emergence of a new lateral root primordium through the outer layers of the parental root requires the sequential auxin‐mediated induction of two auxin transporters. This positive feedback regulatory loop coordinates patterned gene expression in outer tissues.
Synopsis
Emergence of a new lateral root primordium through the outer layers of the parental root requires the sequential auxin‐mediated induction of two auxin transporters. This positive feedback regulatory loop coordinates patterned gene expression in outer tissues.
The emergence of lateral roots through several tissues requires the precise regulation of gene expression in overlaying cells to trigger cell separation.
Auxin derived from new lateral root primordia induces a positive feedback loop in the outer tissues by promoting the expression of the auxin influx transporter LAX3.
A mathematical model based on realistic 3D geometries predicted the involvement of an auxin efflux carrier that was later identified to be PIN3.
The model also revealed that PIN3 must be expressed before LAX3 to ensure a ‘robust’ pattern of LAX3 induction in just two overlaying cortical cell files, thereby delimiting cell separation.
Measuring Proteome Dynamics in Vivo Rachdaoui, Nadia; Austin, Leanne; Kramer, Eric ...
Molecular & cellular proteomics,
December 2009, 20091201, 2009-12-00, Letnik:
8, Številka:
12
Journal Article
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Proteomics investigations typically yield information regarding static gene expression profiles. The central issues that limit the study of proteome dynamics include how to (i) administer a labeled ...amino acid in vivo, (ii) measure the isotopic labeling of a protein(s) (which may be low), and (iii) reliably interpret the precursor/product labeling relationships. In this study, we demonstrate the potential of quantifying proteome dynamics by coupling the administration of stable isotopes with mass spectrometric assays. Although the direct administration of a labeled amino acid(s) is typically used to measure protein synthesis, we explain the application of labeled water, comparing 2H2O versus H218O for measuring albumin biosynthesis in vivo. This application emphasizes two distinct advantages of using labeled water over a labeled amino acid(s). First, in long term studies (e.g. days or weeks), it is not practical to continuously administer a labeled amino acid(s); however, in the presence of labeled water, organisms will generate labeled amino acids. Second, to calculate rates of protein synthesis in short term studies (e.g. hours), one must utilize a precursor/product labeling ratio; when using labeled water it is possible to reliably identify and easily measure the precursor labeling (i.e. water). We demonstrate that labeled water permits studies of protein synthesis (e.g. albumin synthesis in mice) during metabolic “steady-state” or “non-steady-state” conditions, i.e. integrating transitions between the fed and fasted state or during an acute perturbation (e.g. following a meal), respectively. We expect that the use of labeled water is applicable to wide scale investigations of proteome dynamics and can therein be used to obtain a functional image of gene expression in vivo.
Vessel ligation using energy-based surgical devices is steadily replacing conventional closure methods during minimally invasive and open procedures. In exploring the molecular nature of ...thermally-induced tissue bonds, novel applications for surgical resection and repair may be revealed. This work presents an analysis of the influence of unbound water and hydrophilic glycosaminoglycans on the formation and resilience of vascular seals
via
: (a) changes in pre-fusion tissue hydration, (b) the enzymatic digestion of glycosaminoglycans (GAGs) prior to fusion and (c) the rehydration of vascular seals following fusion. An 11% increase in pre-fusion unbound water led to an 84% rise in vascular seal strength. The digestion of GAGs prior to fusion led to increases of up to 82% in seal strength, while the rehydration of native and GAG-digested vascular seals decreased strengths by 41 and 44%, respectively. The effects of increased unbound water content prior to fusion combined with the effects of seal rehydration after fusion suggest that the heat-induced displacement of tissue water is a major contributor to tissue adhesion during energy-based vessel sealing. The effects of pre-fusion GAG-digestion on seal integrity indicate that GAGs are inhibitory to the bond formation process during thermal ligation. GAG digestion may allow for increased water transport and protein interaction during the fusion process, leading to the formation of stronger bonds. These findings provide insight into the physiochemical nature of the fusion bond, its potential for optimization in vascular closure and its application to novel strategies for vascular resection and repair.
ABSTRACT We update the method of the Holmberg & Flynn study, including an updated model of the Milky Way's interstellar gas, radial velocities, an updated reddening map, and a careful statistical ...analysis, to bound the allowed surface density and scale height of a dark disk. We pay careful attention to the self-consistency of the model, including the gravitational influence of the dark disk on other disk components, and to the net velocity of the tracer stars. We find that the data set exhibits a non-zero bulk velocity in the vertical direction as well as a displacement from the expected location at the Galactic midplane. If not properly accounted for, these features would bias the bound toward low dark disk mass. We therefore perform our analysis two ways. In the first, using the traditional method, we subtract the mean velocity and displacement from the tracers' phase space distributions. In the second method, we perform a non-equilibrium version of the HF method to derive a bound on the dark disk parameters for an oscillating tracer distribution. Despite updates in the mass model and reddening map, the traditional method results remain consistent with those of HF2000. The second, non-equilibrium technique, however, allows a surface density as large as 14 M pc − 2 (and as small as 0 M pc − 2 ), demonstrating much weaker constraints. For both techniques, the bound on surface density is weaker for larger scale height. In future analyses of Gaia data it will be important to verify whether the tracer populations are in equilibrium.
Rheumatoid arthritis (RA) affects millions world-wide. While anti-TNF treatment is widely used to reduce disease progression, treatment fails in ∼one-third of patients. No biomarker currently exists ...that identifies non-responders before treatment. A rigorous community-based assessment of the utility of SNP data for predicting anti-TNF treatment efficacy in RA patients was performed in the context of a DREAM Challenge (http://www.synapse.org/RA_Challenge). An open challenge framework enabled the comparative evaluation of predictions developed by 73 research groups using the most comprehensive available data and covering a wide range of state-of-the-art modelling methodologies. Despite a significant genetic heritability estimate of treatment non-response trait (h(2)=0.18, P value=0.02), no significant genetic contribution to prediction accuracy is observed. Results formally confirm the expectations of the rheumatology community that SNP information does not significantly improve predictive performance relative to standard clinical traits, thereby justifying a refocusing of future efforts on collection of other data.
INTERSTELLAR GAS AND A DARK DISK Kramer, Eric David; Randall, Lisa
The Astrophysical journal,
10/2016, Letnik:
829, Številka:
2
Journal Article
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ABSTRACT We introduce a potentially powerful method for constraining or discovering a thin dark matter disk in the Milky Way. The method relies on the relationship between the midplane densities and ...scale heights of interstellar gas being determined by the gravitational potential, which is sensitive to the presence of a dark disk. We show how to use the interstellar gas parameters to set a bound on a dark disk and discuss the constraints suggested by the current data. However, current measurements for these parameters are discordant, with the uncertainty in the constraint being dominated by the molecular hydrogen midplane density measurement, as well as by the atomic hydrogen velocity dispersion measurement. Magnetic fields and cosmic ray pressure, which are expected to play a role, are uncertain as well. The current models and data are inadequate to determine the disk's existence, but taken at face value, may favor its existence depending on the gas parameters used.
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