Measured vs. predicted values from Model 3a (universal D and species-specific μ).

<p>Dash lines are 1∶1. The model explains between-species variation in all four cases (area- and mass-based Amax and Rdark). The amount of within-species variation explained is greatest for Rdark_area (Figure 1a) and least for Amax_mass (Figure 1d). Units for per-area Amax and Rdark are µmol CO₂ m⁻² s⁻¹, and units for per-mass Amax and Rdark are 10⁻⁴ µmol CO₂ g⁻¹ s⁻¹. Species code: GB = gray birch, WA = white ash, SM = sugar maple, WP = white pine, EH = eastern hemlock.</p

Predicted per-area leaf photosynthetic capacity (Amax_area) and dark respiration rate (Rdark_area) vs. observed values.

<p>The model (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091798#pone.0091798.e002" target="_blank">Equation 2</a> in main text) assumes that each leaf's Amax_area (or Rdark_area) is equal to a species-specific constant per-mass Amax (or Rdark) times the leaf's mass:area ratio (LMA). Symbols marked by small grey dots indicate shade leaves of sun grown trees. Species code: GB = gray birch, WA = white ash, SM = sugar maple, WP = white pine, EH = eastern hemlock, AB = American beech.</p

Relationship between normalized Amax or Rdark (measured value divided by species mean full-sun value) and light.

<p>Species code: GB = gray birch, WA = white ash, SM = sugar maple, WP = white pine, EH = eastern hemlock.</p

Species-Independent Down-Regulation of Leaf Photosynthesis and Respiration in Response to Shading: Evidence from Six Temperate Tree Species

<div><p>The ability to down-regulate leaf maximum net photosynthetic capacity (Amax) and dark respiration rate (Rdark) in response to shading is thought to be an important adaptation of trees to the wide range of light environments that they are exposed to across space and time. A simple, general rule that accurately described this down-regulation would improve carbon cycle models and enhance our understanding of how forest successional diversity is maintained. In this paper, we investigated the light response of Amax and Rdark for saplings of six temperate forest tree species in New Jersey, USA, and formulated a simple model of down-regulation that could be incorporated into carbon cycle models. We found that full-sun values of Amax and Rdark differed significantly among species, but the rate of down-regulation (proportional decrease in Amax or Rdark relative to the full-sun value) in response to shade was not significantly species- or taxon-specific. Shade leaves of sun-grown plants appear to follow the same pattern of down-regulation in response to shade as leaves of shade-grown plants. Given the light level above a leaf and one species-specific number (either the full-sun Amax or full-sun Rdark), we provide a formula that can accurately predict the leaf's Amax and Rdark. We further show that most of the down regulation of per unit area Rdark and Amax is caused by reductions in leaf mass per unit area (LMA): as light decreases, leaves get thinner, while per unit mass Amax and Rdark remain approximately constant.</p></div

Relationships between Amax and Rdark.

<p>The left panel shows area-based rates, and the right panel shows mass-based rates. Symbols marked by small grey dots indicate shade leaves of sun grown trees. Species code: GB = gray birch, WA(P) = white ash sampled at the Princeton site, WA(S) = white ash sampled at the Stokes site, SM = sugar maple, WP = white pine, EH = eastern hemlock, AB = American beech.</p

Relationship between leaf mass area ratio (LMA, mg/cm²) and leaf-level irradiance.

<p>For both angiosperm and conifer species, LMA can be expressed as a linear function of light (L, % of full sun) when light is less than 30%. For angiosperm species, the expression is LMA = 0.163*L+1.997 (R² = 0.85, P<<0.001); and the expression for conifer species is LMA = 0.233 *L+6.044 (R² = 0.45, P<<0.001). The plateau values of LMA when light is above about 30% are 6.83 mg/cm² for angiosperm species, and 12.64 mg/cm² for conifer species. Species code: GB = gray birch, WA = white ash, SM = sugar maple, WP = white pine, EH = eastern hemlock.</p

Maximum likelihood estimates (MLE) and 95% confidence limits for parameters in Model 3a.

<p>Units for per-area Amax and Rdark are µmol CO₂ m⁻² s⁻¹, and units for per-mass Amax and Rdark are 10⁻⁴ µmol CO₂ g⁻¹ s⁻¹.</p

Comparison of models of leaf maximum net photosynthetic capacity (Amax) and dark respiration rate (Rdark) in response to light level.

<p>The models here are the nine possible combinations of, (1) a single value of μ (i.e., full-sun Amax or Rdark) shared by all species, (2) separate μ for deciduous and conifer trees, (3) species-specific μ; and (a) a single value of D for all species, (b) separate D for deciduous and conifer species, (c) species-specific D. The data are normalized either by area or by mass (norm). The number of parameters (df) of each model includes the variance of the error term in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091798#pone.0091798.e001" target="_blank">Equation (1)</a>. R² is the coefficient of determination describing the overall fit of the model to data; and the Akaike Information Criterion (aic.ncor) is sample size-corrected following Bolker <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091798#pone.0091798-Bolker1" target="_blank">[35]</a>, , where k is the number of parameters, and n is the sample size. The AIC index without sample size-corrected showed the same results. The best model(s) (lowest aic.ncor) is highlighted in bold.</p

Activation of ferritinophagy is required for the RNA-binding protein ELAVL1/HuR to regulate ferroptosis in hepatic stellate cells

<p>Ferroptosis is a recently recognized form of regulated cell death that is characterized by lipid peroxidation. However, the molecular mechanisms regulating ferroptosis are largely unknown. In this study, we report that the RNA-binding protein ELAVL1/HuR plays a crucial role in regulating ferroptosis in liver fibrosis. Upon exposure to ferroptosis-inducing compounds, ELAVL1 protein expression was remarkably increased through the inhibition of the ubiquitin-proteasome pathway. <i>ELAVL1</i> siRNA led to ferroptosis resistance, whereas <i>ELAVL1</i> plasmid contributed to classical ferroptotic events. Interestingly, upregulated ELAVL1 expression also appeared to increase autophagosome generation and macroautophagic/autophagic flux, which was the underlying mechanism for ELAVL1-enhanced ferroptosis. Autophagy depletion completely impaired ELAVL1-mediated ferroptotic events, whereas autophagy induction showed a synergistic effect with ELAVL1. Importantly, ELAVL1 promoted autophagy activation via binding to the AU-rich elements within the F3 of the 3ʹ-untranslated region of <i>BECN1/Beclin1</i> mRNA. The internal deletion of the F3 region abrogated the ELAVL1-mediated <i>BECN1</i> mRNA stability, and, in turn, prevented ELAVL1-enhanced ferroptosis. In mice, treatment with sorafenib alleviated murine liver fibrosis by inducing hepatic stellate cell (HSC) ferroptosis. HSC-specific knockdown of <i>ELAVL1</i> impaired sorafenib-induced HSC ferroptosis in murine liver fibrosis. Noteworthy, we retrospectively analyzed the effect of sorafenib on HSC ferroptosis in advanced fibrotic patients with hepatocellular carcinoma receiving sorafenib monotherapy. Attractively, ELAVL1 upregulation, ferritinophagy activation, and ferroptosis induction occurred in primary human HSCs from the collected human liver tissue. Overall, these results reveal novel molecular mechanisms and signaling pathways of ferroptosis, and also identify ELAVL1-autophagy-dependent ferroptosis as a potential target for the treatment of liver fibrosis.</p> <p><b>Abbreviations:</b> ACTA2/alpha-SMA: actin, alpha 2, smooth muscle, aorta; ACTB/beta-actin: actin beta; ARE: AU-rich element; ATG: autophagy related; BDL: bile duct ligation; BECN1: beclin 1; BSO: buthionine sulfoximine; COL1A1: collagen type I alpha 1 chain; ELAVL1/HuR: ELAV like RNA binding protein 1; FDA: fluorescein diacetate; FTH1: ferritin heavy chain 1; GOT1/AST: glutamic-oxaloacetic transaminase 1; GPT/ALT: glutamic–pyruvic transaminase; GPX4: glutathione peroxidase 4; GSH: glutathione; HCC: hepatocellular carcinoma; HSC: hepatic stellate cell; LCM: laser capture microdissection; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; MDA: malondialdehydep; NCOA4: nuclear receptor coactivator 4; PTGS2: prostaglandin-endoperoxide synthase 2; ROS: reactive oxygen species; SQSTM1/p62: sequestosome 1; TBIL: total bilirubin; TEM: transmission electron microscopy; TGFB1: trasforming growth factor beta 1; UTR: untranslated region; VA-Lip-<i>ELAVL1</i>-siRNA: vitamin A-coupled liposomes carrying <i>ELAVL1</i>-siRNA. </p

Appendix A. Description of study sites.

Description of study sites