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  • 1
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    A-to-I RNA editing in the earliest-diverging Eumetazoan phyla (2017)
    Oxford University Press
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Molecular Biology and Evolution 34 (2017): 1890-1901, doi:10.1093/molbev/msx125.
    Description: The highly conserved ADAR enzymes, found in all multicellular metazoans, catalyze the editing of mRNA transcripts by the deamination of adenosines to inosines. This type of editing has two general outcomes: site specific editing, which frequently leads to recoding, and clustered editing, which is usually found in transcribed genomic repeats. Here, for the first time, we looked for both editing of isolated sites and clustered, non-specific sites in a basal metazoan, the coral Acropora millepora during spawning event, in order to reveal its editing pattern. We found that the coral editome resembles the mammalian one: it contains more than 500,000 sites, virtually all of which are clustered in non-coding regions that are enriched for predicted dsRNA structures. RNA editing levels were increased during spawning and increased further still in newly released gametes. This may suggest that editing plays a role in introducing variability in coral gametes.
    Description: This work was supported by the Australian Research Council (to PK), the European Research Council (grant 311257), the I-CORE Program of the Planning and Budgeting Committee in Israel (grants 41/11 and 1796/12), and the Israel Science Foundation (1380/14).
    Keywords: RNA editing ; ADAR ; Evolution ; Coral
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
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    Heterogeneity of competition at decameter scale: patches of high canopy leaf area in a shade-intolerant larch stand transpire less yet are more sensitive to drought (2015)
    Oxford University Press
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    Publication Date: 2015-06-04
    Description: Small differences in the sensitivity of stomatal conductance to light intensity on leaf surfaces may lead to large differences in total canopy transpiration ( E C ) with increasing canopy leaf area ( L ). Typically, the increase of L would more than compensate for the decrease of transpiration per unit of leaf area ( E L ), resulting in concurrent increase of E C . However, highly shade-intolerant species, such as Larix principis-rupprechtii Mayr., may be so sensitive to increased shading that such compensation is not complete. We hypothesized that in such a stand, windfall-induced spatial variation at a decameter scale would result in greatly reduced E L in patches of high L leading to lower E C than low competition patches of sparse canopy. We further hypothesized that quicker extraction of soil moisture in patches of lower competition will result in earlier onset of drought symptoms in these patches. Thus, patches of low L will transition from light to soil moisture as the factor dominating E L . This process should progressively homogenize E C in the stand even as the variation of soil moisture is increasing. We tested the hypotheses utilizing sap flux of nine trees, and associated environmental and stand variables. The results were consistent with only some of the expectations. Under non-limiting soil moisture, E L was very sensitive to the spatial variation of L , decreasing sharply with increasing L and associated decrease of mean light intensity on leaf surfaces. Thus, under the conditions of ample soil moisture maximum E C decreased with increasing patch-scale L . Annual E C and biomass production also decreased with L , albeit more weakly. Furthermore, variation of E C among patches decreased as average stand soil moisture declined between rain events. However, contrary to expectation, high L plots which transpired less showed a greater E L sensitivity to decreasing stand-scale soil moisture, suggesting a different mechanism than simple control by decreasing soil moisture. We offer potential explanations to the observed phenomenon. Our results demonstrate that spatial variation of L at decameter scale, even within relatively homogeneous, single-species, even-aged stands, can produce large variation of transpiration, soil moisture and biomass production and should be considered in 1-D soil–plant–atmosphere models.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 3
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    Heavy metal resistance in halophilic Bacteria and Archaea (2016)
    Oxford University Press
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    Publication Date: 2016-06-30
    Description: Heavy metals are dense chemicals with dual biological role as micronutrients and intoxicants. A few hypersaline environmental systems are naturally enriched with heavy metals, while most metal-contaminated sites are a consequence of human activities. Numerous halotolerant and moderately halophilic Bacteria possess metal tolerance, whereas a few archaeal counterparts share similar features. The main mechanisms underlying heavy metal resistance in halophilic Bacteria and Archaea include extracellular metal sequestration by biopolymers, metal efflux mediated by specific transporters and enzymatic detoxification. Biotransformation of metals by halophiles has implications both for trace metal turnover in natural saline ecosystems and for development of novel bioremediation strategies.
    Keywords: Physiology & Biochemistry
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Stem compression reversibly reduces phloem transport in Pinus sylvestris trees (2015)
    Oxford University Press
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    Publication Date: 2015-10-23
    Description: Manipulating tree belowground carbon (C) transport enables investigation of the ecological and physiological roles of tree roots and their associated mycorrhizal fungi, as well as a range of other soil organisms and processes. Girdling remains the most reliable method for manipulating this flux and it has been used in numerous studies. However, girdling is destructive and irreversible. Belowground C transport is mediated by phloem tissue, pressurized through the high osmotic potential resulting from its high content of soluble sugars. We speculated that phloem transport may be reversibly blocked through the application of an external pressure on tree stems. Thus, we here introduce a technique based on compression of the phloem, which interrupts belowground flow of assimilates, but allows trees to recover when the external pressure is removed. Metal clamps were wrapped around the stems and tightened to achieve a pressure theoretically sufficient to collapse the phloem tissue, thereby aiming to block transport. The compression's performance was tested in two field experiments: a 13 C canopy labelling study conducted on small Scots pine ( Pinus sylvestris L.) trees [2–3 m tall, 3–7 cm diameter at breast height (DBH)] and a larger study involving mature pines (~15 m tall, 15–25 cm DBH) where stem respiration, phloem and root carbohydrate contents, and soil CO 2 efflux were measured. The compression's effectiveness was demonstrated by the successful blockage of 13 C transport. Stem compression doubled stem respiration above treatment, reduced soil CO 2 efflux by 34% and reduced phloem sucrose content by 50% compared with control trees. Stem respiration and soil CO 2 efflux returned to normal within 3 weeks after pressure release, and 13 C labelling revealed recovery of phloem function the following year. Thus, we show that belowground phloem C transport can be reduced by compression, and we also demonstrate that trees recover after treatment, resuming C transport in the phloem.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 5
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    Hydraulic time constants for transpiration of loblolly pine at a free-air carbon dioxide enrichment site (2013)
    Oxford University Press
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    Publication Date: 2013-02-21
    Description: The impact of stored water on estimates of transpiration from scaled sap flux measurements was assessed in mature Pinus taeda (L.) at the Duke Free-Air CO 2 Enrichment (FACE) site. We used a simple hydraulic model with measurements of sap flux ( J ) at breast height and the base of the live crown for 26 trees over 6 months to examine the effects of elevated CO 2 (eCO 2 ) and fertilization (N F ) treatments, as well as temporal variation in soil moisture ( M ( t ) ), on estimates of the hydraulic time constant (). At low M ( t ) , there was little (〈12%) difference in of different treatments. At high M ( t ) , differences were much greater, with reductions of 27, 52 and 34% in eCO 2 , N F and eCO 2 x N F respective to the control. Incorporating with these effects into the analysis of a larger data set of previous J measurements at this site (1998–2008) improved agreement between modeled and measured values in 92% of cases. However, a simplified calibration of that neglected treatment and soil moisture effects performed more dependably, improving agreement in 98% of cases. Incorporating had the effect of increasing estimates of reference stomatal conductance at 1 kPa vapor pressure deficit (VPD) and saturating photosynthetic active radiation (PAR) an average of 12–14%, while increasing estimated sensitivities to VPD and PAR. A computationally efficient hydraulic model, such as the one presented here, incorporated into a hierarchical model of stomatal conductance presents a novel approach to including hydraulic time constants in estimates of stomatal responses from long-term sap flux data sets.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 6
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    The effects of elevated CO2 and nitrogen fertilization on stomatal conductance estimated from 11 years of scaled sap flux measurements at Duke FACE (2013)
    Oxford University Press
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    Publication Date: 2013-02-21
    Description: In this study, we employ a network of thermal dissipation probes (TDPs) monitoring sap flux density to estimate leaf-specific transpiration ( E L ) and stomatal conductance ( G S ) in Pinus taeda (L.) and Liquidambar styraciflua L. exposed to +200 ppm atmospheric CO 2 levels (eCO 2 ) and nitrogen fertilization. Scaling half-hourly measurements from hundreds of sensors over 11 years, we found that P. taeda in eCO 2 intermittently (49% of monthly values) decreased stomatal conductance ( G S ) relative to the control, with a mean reduction of 13% in both total E L and mean daytime G S . This intermittent response was related to changes in a hydraulic allometry index ( A H ), defined as sapwood area per unit leaf area per unit canopy height, which decreased a mean of 15% with eCO 2 over the course of the study, due mostly to a mean 19% increase in leaf area ( A L ). In contrast, L. styraciflua showed a consistent (76% of monthly values) reduction in G S with eCO 2 with a total reduction of 32% E L , 31% G S and 23% A H (due to increased A L per sapwood area). For L. styraciflua , like P. taeda , the relationship between A H and G S at reference conditions suggested a decrease in G S across the range of A H . Our findings suggest an indirect structural effect of eCO 2 on G S in P. taeda and a direct leaf level effect in L. styraciflua . In the initial year of fertilization, P. taeda in both CO 2 treatments, as well as L. styraciflua in eCO 2 , exhibited higher G S with N F than expected from shifts in A H , suggesting a transient direct effect on G S . Whether treatment effects on mean leaf-specific G S are direct or indirect, this paper highlights that long-term treatment effects on G S are generally reflected in A H as well.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 7
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    Increased resin flow in mature pine trees growing under elevated CO2 and moderate soil fertility (2012)
    Oxford University Press
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    Publication Date: 2012-06-23
    Description: Warmer climates induced by elevated atmospheric CO 2 (eCO 2 ) are expected to increase damaging bark beetle activity in pine forests, yet the effect of eCO 2 on resin production—the tree's primary defense against beetle attack—remains largely unknown. Following growth-differentiation balance theory, if extra carbohydrates produced under eCO 2 are not consumed by respiration or growth, resin production could increase. Here, the effect of eCO 2 on resin production of mature pines is assessed. As predicted, eCO 2 enhanced resin flow by an average of 140% ( P = 0.03) in canopy dominants growing in low-nitrogen soils, but did not affect resin flow in faster-growing fertilized canopy dominants or in carbohydrate-limited suppressed individuals. Thus, pine trees may become increasingly protected from bark beetle attacks in an eCO 2 climate, except where they are fertilized or are allowed to become overcrowded.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 8
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    Uncertainty analysis of forest carbon sink forecast with varying measurement errors: a data assimilation approach (2011)
    Oxford University Press
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    Publication Date: 2011-11-24
    Description: Aims Accurate forecast of ecosystem states is critical for improving natural resource management and climate change mitigation. Assimilating observed data into models is an effective way to reduce uncertainties in ecological forecasting. However, influences of measurement errors on parameter estimation and forecasted state changes have not been carefully examined. This study analyzed the parameter identifiability of a process-based ecosystem carbon cycle model, the sensitivity of parameter estimates and model forecasts to the magnitudes of measurement errors and the information contributions of the assimilated data to model forecasts with a data assimilation approach. Methods We applied a Markov Chain Monte Carlo method to assimilate eight biometric data sets into the Terrestrial ECOsystem model. The data were the observations of foliage biomass, wood biomass, fine root biomass, microbial biomass, litter fall, litter, soil carbon and soil respiration, collected at the Duke Forest free-air CO 2 enrichment facilities from 1996 to 2005. Three levels of measurement errors were assigned to these data sets by halving and doubling their original standard deviations. Important Findings Results showed that only less than half of the 30 parameters could be constrained, though the observations were extensive and the model was relatively simple. Higher measurement errors led to higher uncertainties in parameters estimates and forecasted carbon (C) pool sizes. The long-term predictions of the slow turnover pools were affected less by the measurement errors than those of fast turnover pools. Assimilated data contributed less information for the pools with long residence times in long-term forecasts. These results indicate the residence times of C pools played a key role in regulating propagation of errors from measurements to model forecasts in a data assimilation system. Improving the estimation of parameters of slow turnover C pools is the key to better forecast long-term ecosystem C dynamics.
    Print ISSN: 1752-993X
    Electronic ISSN: 1752-9921
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Modelling understorey light for seedling regeneration in continuous cover forestry canopies (2011)
    Oxford University Press
    In: Forestry
    Details
    Publication Date: 2011-11-24
    Description: Continuous cover forestry (CCF) aims at enhancing stand structural diversity and favouring natural regeneration. To give guidance on how to manage a CCF stand to achieve seedling growth below canopy, an estimate of light transmittance is required. So far, in the UK, only stand-level parameters have been used by managers to predict the understorey light in CCF stands. We assessed a UK Sitka spruce stand undergoing transformation to CCF and measured canopy transmittance using hemispherical pictures. Stand-level characteristics were found to be highly stand specific and not appropriate to predict seedling growth in CCF stands. We parameterized a detailed light model (4C-A-RTM) and a simple one-layer turbid medium model (BL). A sensitivity analysis was performed to test the effect of key stand structural parameters on the modelled transmittance. Measured transmittance from hemispherical photographs was used to validate the models. Both models tended to underestimate canopy transmittance but were positively related to current-year growth of the below canopy seedlings ( R 2 = 0.92, P 〈 0.001). Comparison of the two models showed that the 4C-A-RTM provided a better estimation of light transmittance across observed canopy structural differences. Furthermore, the inclusion of stand characteristics in the 4C-A-RTM is likely to confer greater applicability across stands.
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 10
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    Message from the Editor-in-Chief (2012)
    Oxford University Press
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    Publication Date: 2012-03-02
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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