A role of extracellular signaling and <i>rpoS</i> in the density-dependent survival kinetics.

<p>(A) A role of extracellular signaling: a high density of exponentially-growing cells (<i>N</i>_CFU ≈ 7·10⁸/ml) was transferred to a fresh medium without glycerol. <i>N</i>_CFU of cells in the fresh medium (green triangles) decreases similarly to that from the previous experiment (solid blue squares, re-plotted from <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.g001" target="_blank">Fig. 1</a>). Next, a spent medium was prepared from a culture of a high density of cells. <i>N</i>_CFU of cells at low density in the spent medium (green inverse triangles) decreases similarly to that from the previous experiments (solid red circles, re-plotted from <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.g001" target="_blank">Fig. 1</a>). The results indicate that extracellular signaling does not play a role for the density-dependent kinetics. See the text for details. (B) A role of <i>rpoS</i>: Under starvation, <i>N</i>_CFU of the Δ<i>rpoS</i> strain (open symbols) decreases faster than that of the wild type strain (solid symbols, re-plotted from <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.g001" target="_blank">Fig. 1</a>); compare the slope of the dotted line −μ₀^ΔrpoS (= −0.035 hr ^-1) and the slope of the dashed line −<i>μ</i>₀ (= −0.018 hr ^-1). See also <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.s007" target="_blank">S6 Fig</a> for <i>N</i>_CFU of other densities of the Δ<i>rpoS</i> strain. Importantly, in the low cell-density cultures (e.g., open red circles), the periods during which <i>N</i>_CFU is maintained are much shorter for the Δ<i>rpoS</i> strain (brown region) than for the wild type strain (green region); note that here the brown and green regions are approximately determined as regions where the survival kinetics does not follow exponentially decay. This indicates that <i>rpoS</i> plays an important role for the wild type strain to maintain <i>N</i>_CFU for extended periods of time in low density under starvation.</p

Survival Kinetics of Starving Bacteria Is Biphasic and Density-Dependent

<div><p>In the lifecycle of microorganisms, prolonged starvation is prevalent and sustaining life during starvation periods is a vital task. In the literature, it is commonly assumed that survival kinetics of starving microbes follows exponential decay. This assumption, however, has not been rigorously tested. Currently, it is not clear under what circumstances this assumption is true. Also, it is not known when such survival kinetics deviates from exponential decay and if it deviates, what underlying mechanisms for the deviation are. Here, to address these issues, we quantitatively characterized dynamics of survival and death of starving <i>E</i>. <i>coli</i> cells. The results show that the assumption – starving cells die exponentially – is true only at high cell density. At low density, starving cells <i>persevere</i> for extended periods of time, before dying rapidly exponentially. Detailed analyses show intriguing quantitative characteristics of the <i>density-dependent and biphasic</i> survival kinetics, including that the period of the perseverance is inversely proportional to cell density. These characteristics further lead us to identification of key underlying processes relevant for the perseverance of starving cells. Then, using mathematical modeling, we show how these processes contribute to the density-dependent and biphasic survival kinetics observed. Importantly, our model reveals a thrifty strategy employed by bacteria, by which upon sensing impending depletion of a substrate, the limiting substrate is conserved and utilized later during starvation to delay cell death. These findings advance quantitative understanding of survival of microbes in oligotrophic environments and facilitate quantitative analysis and prediction of microbial dynamics in nature. Furthermore, they prompt revision of previous models used to analyze and predict population dynamics of microbes.</p></div

Upgrading the Storage Properties of Bio-oil by Adding a Compound Additive

A compound additive consisting of methanol, <i>N</i>,<i>N</i>-dimethylformamide (DMF), and acetone was obtained with the A-Optimal mixture design of Design-Expert. How the solvent effected the stability of bio-oil was analyzed on the basis of viscosity, moisture content, and pH. Bio-oil with the optimal compound additive (1 wt % methanol, 5.064 wt % DMF, and 1.940 wt % acetone) had a low viscosity and moisture content and high pH after aging (80 °C for 24 h). The corresponding property values were 4.36 mm²/s, 24.03%, and 4.49, respectively, and the result was better than bio-oil with a single solvent. Gas chromatography–mass spectrometry (GC–MS) analysis revealed that the phenol contents in all of the compounds in bio-oil were high. After aging, the contents of sugars and esters increased and several chemical compounds, such as 2-ethoxy-5-(1-propen-1-yl) and 5-hydroxy-2-methylbenzaldehyde, disappeared in bio-oil with the compound additive. Elemental analysis showed that the contents of O and N increased after the addition of the optimal compound additive. The compound additive exerted a positive effect on the bio-oil during storage

A mechanistic account of the density-dependent, biphasic survival kinetics.

<p>(A) Cells consume substrates for cell growth and the substrate concentration decreases in the medium (green line). When the concentration decreases to the levels affecting the rate of cell growth, RpoS accumulates (blue line) [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.ref026" target="_blank">26</a>,<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.ref027" target="_blank">27</a>]. RpoS represses cell growth (red line) [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.ref030" target="_blank">30</a>–<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.ref032" target="_blank">32</a>], forming negative feedback. In the feedback scheme, at low substrate levels, RpoS strongly represses cell growth and hence, substrate consumption, allowing cells to <i>conserve</i> a small amount of the substrate before it is completely depleted by cell growth. See the text for details. (B) This feedback predicts that as the substrate concentration is reduced, the growth arrest occurs at a non-zero substrate concentration <i>S</i>₁, i.e., <i>λ</i> = 0 at <i>S</i> = <i>S</i>₁ > 0. This prediction agrees with previous studies [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.ref033" target="_blank">33</a>–<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.ref035" target="_blank">35</a>]. Importantly, further studies show that although the growth rate of the population is zero at <i>S</i> = <i>S</i>₁, the substrate consumption rate is not zero; see [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.ref036" target="_blank">36</a>] for review. This is commonly known as maintenance requirement; it requires continuous influx of the substrate to maintain a constant population size (<i>λ</i> = 0). If the influx of the substrate is less than the level needed for the maintenance, <i>λ</i> < 0 (green region) [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.ref037" target="_blank">37</a>,<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.ref038" target="_blank">38</a>]. Our model indicates that <i>λ</i>(0) = − <i>μ</i>₀; see the text for details. As a comparison, the relation of <i>λ</i> and <i>S</i> in the Δ<i>rpoS</i> strain is shown as a dashed line. Note that at intermediate substrate concentrations, <i>λ</i> of Δ<i>rpoS</i> strain is higher than that of the wild type strain [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.ref030" target="_blank">30</a>–<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.ref032" target="_blank">32</a>]. Also, note that when the substrate is completely exhausted, the culture of the Δ<i>rpoS</i> strain loses viability more rapidly than the wild type strain (see [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.ref018" target="_blank">18</a>,<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.ref025" target="_blank">25</a>] and <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.g002" target="_blank">Fig. 2B</a>); thus, the value of <i>λ</i>(0) of Δ<i>rpoS</i> strain should be less than that of the wild type strain. (C, D) At the onset of growth arrest (time zero in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.s002" target="_blank">S1B Fig</a>), <i>S</i> = <i>S</i>₁; see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.g004" target="_blank">Fig. 4B</a>. Without additional influx of the substrate, <i>S</i> will continue to decrease over time due to the consumption for the maintenance (cyan line in green region in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.g004" target="_blank">Fig. 4C</a>). Following the relation between <i>λ</i> and <i>S</i> depicted in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.g004" target="_blank">Fig. 4B</a>, <i>λ</i> will continue to decrease over time too. This will result in gradual decrease of <i>N</i>_CFU (cyan line in green region in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.g004" target="_blank">Fig. 4D</a>). At some point (<i>T</i>₀), the substrate gets completely depleted (orange line in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.g004" target="_blank">Fig. 4C</a>) and <i>N</i>_CFU decreases exponentially at a fixed rate of <i>λ</i> (0) afterwards (orange line in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.g004" target="_blank">Fig. 4D</a>). For the culture with higher cell-densities, <i>S</i> will decrease faster because the substrate is consumed by more cells, leading to shorter periods of the first phase. Quantitative formulation of these processes straightforwardly leads to a mathematical solution equal to the empirical formulas (Eqs (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.e003" target="_blank">3</a>) and (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.e004" target="_blank">4</a>)). The solid lines in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.g001" target="_blank">Fig. 1</a> and <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004198#pcbi.1004198.s003" target="_blank">S2 Fig</a> show the fits of the solution to the data. See the text for details.</p

In the allergen stimulated group DCs most genes with significant change in transcription (DE) had altered methylation either in the promoter (14%), CpG island (22%) or both (38%) (of all overalpping DMR-DE).

<p>Only 26% of the genes had changes elsewhere in the body of the transcript.</p

Number of transcripts differentially methylated and differentially expressed between asthma-at-risk DCs and controls.

<p>Number of transcripts differentially methylated and differentially expressed between asthma-at-risk DCs and controls.</p

Interaction network of transcripts with significant change in DNA methylation at birth that show significant transcriptional change later in life upon the first encounter with allergen.

<p>Interacting factors are depicted in various shapes depending on their biological nature, connecting arrows indicate known links. Blue circles indicate transcripts down-regulated in asthma-at-risk DCs, red – up-regulated.</p

Transcripts showing both DNA methylation and expression changes between naïve normal and asthma-at-risk DCs form a small interaction network focused on regulation of a pleiotropic cytokine IL-6.

<p>Interacting factors are depicted in various shapes depending on their biological nature, connecting arrows indicate known links. Blue circles indicate transcripts down-regulated in asthma-at-risk DCs, red – up-regulated.</p

Preparation of a Cellulosic Photosensitive Hydrogel for Tubular Tissue Engineering

Since the concept of tissue engineering was proposed, biocompatible hydrogel materials have attracted the attention of researchers. With the help of three-dimensional (3D) printing technology, precise shaping of hydrogels can be realized. In this paper, we synthesized a cellulosic photosensitive acrylamide (AM)/N,N-methylenebisacrylamide (MBA) hydrogel. With the high-efficiency water-soluble photoinitiator TPO@Tw developed by our research group, the efficient photocuring cross-linking process of the hydrogel can be realized under 405 nm visible light. In consideration of the viscosity, curing mass, curing depth, and break distance of the hydrogel, we screened out hydroxypropyl cellulose (HPC) as the preferred tackifier of the material. The addition of HPC greatly improved the mechanical properties of the hydrogel. The compressive modulus of the optimal sample AM-HPC-5 increased by 709.2% and the tensile strength increased by 76.7% compared with the blank control group. By adding a PEGDA shell to the surface of the material, the water retention capacity of the hydrogel was effectively improved. The water loss rate was greatly reduced. The 3D wooden-pile structure model was printed by a DIW 3D printer. Further, through coaxial extrusion, the microtubule structure that may be applied in tissue engineering was obtained. Cell experiment results showed high biocompatibility of the hydrogel. NIH 3T3 cells could adhere and grow on the surface of microtubules

Enhancing Coimmobilization Capacity of Schwertmannite for Arsenic and Cadmium through pH Elevation after Chemical Oxidation

Schwertmannite (Sch) is a promising environmental functional material for remediation of arsenic pollution, particularly arsenite [As(III)], due to its unique adsorption mechanism. However, its application in metal–metalloid cocontamination is greatly limited by its ineffective immobilization of cationic metals. In this study, a preparation method of chemical oxidation–pH elevation was proposed to optimize the immobilization capacity of schwertmannite for As and cadmium [Cd(II)], which referred to promoting solution pH to neutral conditions after FeSO4–H2O2 chemical oxidation. The resultant schwertmannite mixture (Sch-M) had a slightly increased Fe content (by 14.2–17.7%) and a reduced sulfate content (by 24.5–42.1%) compared to Sch. Sch-M displayed stronger mineral phase stability under anaerobic Fe(II)-catalyzed condition. The adsorption capacity of Sch-M for As(III) was basically consistent with that of Sch (172.9–211.3 vs 196.5 mg/g) and reached 19.7–22.4 mg/g for Cd(II) at pH 6.5. Sch-M performed better stabilization effects for metals and metalloids in a contaminated soil than zerovalent iron. In addition, its passivation ability was resistant to acidic conditions (pH 2.6). The practical application of the Sch-based environmental functional material in the remediation of metal(loid)-contaminated soils is worthy of in-depth study