Sobol\u27 sensitivity analysis of the Holocene Peat Model: What drives carbon accumulation in peatlands?

Understanding the development of northern peatlands and their carbon accumulation dynamics is crucial in order to confidently integrate northern peatlands into global carbon cycle models. To achieve this, northern peatland models are becoming increasingly complex and now include feedback processes between peat depth, decomposition, hydrology, and vegetation composition and productivity. Here we present results from a global sensitivity analysis performed to assess the behavior and parameter interaction of a peatland simulation model. A series of simulations of the Holocene Peat Model were performed with different parameter combinations in order to assess the role of parameter interactions on the simulated total carbon mass after 5000 years of peatland development. The impact of parameter uncertainty on the simulation results is highlighted, as is the importance of multiple parameter interactions. The model sensitivity indicates that peat physical properties play an important role in peat accumulation; these parameters are poorly constrained by observations and should be a focus of future research. Furthermore, the results show that autogenic processes are able to produce a wide range of peatland development behaviors independently of any external environmental changes

Exploring the limits of knowledge on boreal peatland development using a new model: the Holocene Peatland Model

The Holocene Peatland Model (HPM) (Frolking et al. 2009, Frolking et al. in prep.) is a recently developed tool integrating up-to-date knowledge on peatland dynamics that explores peatland development and carbon dynamics on a millennial timescale. HPM combines the water and carbon cycles with net primary production and peat decomposition and takes the multiple feedbacks into account. The model remains simple and few site-specific inputs are needed. HPM simulates the transient development of the peatland and delivers peat age, peat depth, peat composition, carbon accumulation and water table depth for each simulated year. Evaluating the ability of the model to reproduce peatland development can be achieved in several manners. Commonly one could choose to compare simulations results with observations from field data. However, we argue that the overall response of the model does not give much information about the value of the model design. Modelling of peatlands dynamics requires a lot of information regarding the behaviour of a peatland system within its environment (including allogenic changes in climate, hydrological conditions, nutrient availability or autogenic processes such as microtopographical effects). The actual state of knowledge does not cover all processes, interactions or feedbacks and a lot of peatland properties are neither well defined nor measured yet, so that estimates have been needed to build the model. The work presented here aims at analyzing the role of the model parameterization on the simulation results. To do so, a sensitivity analysis is performed with a Monte-Carlo analysis and with help of the GUI-HDMR software (Ziehn and Tomlin, 2009). This method ranks the parameters and combinations of them according to their influence on simulation results. The results will emphasize how the simulation is sensitive to the parameter values. First, the distribution of outputs gives insight into the possible responses of the simulation to HPM’s assemblage of current knowledge. Second, the importance of some parameters on simulation results points out certain gaps in the current understanding of peatland dynamics. Thus, this study helps determine some avenues that should be explored in future in order to improve peatlands dynamics understanding

Accumulation du carbone dans les tourbières boréales : analyse de sensibilité et intégration de données paléoécologiques

Les tourbières nordiques, sont des écosystèmes humides ayant la particularité de produire plus de matière organique qu'elles n'en décomposent. Elles ont ainsi accumulé de formidables quantités de carbone depuis le début de la dernière déglaciation. C'est pour cette raison qu'elles représentent un intérêt particulier pour la modélisation du climat global. En effet, contenant environ un tiers du carbone des sols tout en ne couvrant qu'environ 3% de la surface terrestre, les tourbières émettent également de grandes quantités de méthane, qui a un pouvoir de réchauffement climatique 23 fois plus important que le dioxyde de carbone. Afin de pouvoir intégrer ces différents facteurs dans les modèles globaux du climat et d'estimer leur incidence sur le cycle global du carbone, il est nécessaire de mieux connaitre la dynamique du carbone dans les tourbières elles-mêmes. Les tourbières nordiques ont la capacité d'archiver des informations rapportant les différents changements qu'elles ont subis depuis leur développement. Ces changements incluent les changements climatiques régionaux, qui ont affecté leur végétation et la dynamique du carbone, mais aussi des changements autogènes, c'est-à-dire propres à leur dynamique interne. Il est donc nécessaire de prendre en compte ces différents facteurs en vue de reproduire leur dynamique. Cette thèse a pour objectif d'évaluer la connaissance de la dynamique du carbone dans les tourbières par le biais de l'évaluation du Holocene Peat Model (Frolking et al. 2010). Ce modèle comprend une description des processus d'accumulation, de décomposition, du bilan hydrique et une représentation de la végétation par 12 groupes fonctionnels de plantes ainsi que les boucles de rétroaction entre ces différents processus. Son évaluation a été effectuée en deux étapes. Dans un premier temps, une analyse de sensibilité a permis de déceler les paramètres du modèle ayant une influence sur la quantité totale de carbone dans les simulations, puis les interactions entre les paramètres ont également été analysées. Les résultats montrent que certains paramètres représentent des sources d'incertitude importantes et devraient être l'objet de plus amples recherches (tels que la conductivité hydraulique, le gradient d'anoxie, certains paramètres contrôlant le bilan hydrique et la densité sèche). De plus, parmi les milliers de simulations effectuées, on observe que plusieurs types de développements des tourbières sont possibles, bien que la méthodologie mette l'emphase sur les processus autogènes et contraigne les processus allogènes à un régime de précipitation et une productivité primaire nette (PPN, servant d'indicateur climatique) constants. Par ailleurs, il apparaît que les sphaignes ont une influence sur le type de développement de la tourbière, ce qui affecte par conséquent l'accumulation du carbone. Dans un second temps, le modèle est calibré pour deux sites de la région de la Baie James au Québec. Il s'agit de deux tourbières ombrotrophes ouvertes ayant des caractéristiques écohydrologiques et des taux d'accumulation de carbone différents. Pour chacun de ces sites, deux simulations sont réalisées : la première est basée sur une reconstruction des précipitations et la seconde sur une reconstruction des niveaux de nappe phréatique. Il est notable que les résultats des simulations révèlent des périodes durant lesquelles les tourbières présentent des pertes nettes de carbone. En comparant les résultats des simulations avec les taux d'accumulation de carbone et les résultats des analyses de macrorestes végétaux, on constate que le modèle reproduit, de façon générale, les variations observées dans ces séries de données. De plus, il est conclu que ce modèle peut être utilisé comme outil d'identification des causes de variations de l'assemblage végétal. Bien que de certains processus doivent être étudiés plus avant afin de limiter les incertitudes du modèle, cette thèse a permis d'établir la validité des concepts de dynamique du carbone dans les tourbières en intégrant l'évaluation des dynamiques d'échelle globale et locale.\ud ______________________________________________________________________________ \ud MOTS-CLÉS DE L’AUTEUR : Tourbière, modélisation, évaluation, analyse de sensibilité, forçage, fonction de transfert

A new model of Holocene peatland net primary production, decomposition, water balance, and peat accumulation

Peatland carbon and water cycling are tightly coupled, so dynamic modeling of peat accumulation over decades to millennia should account for carbon-water feedbacks. We present initial results from a new simulation model of long-term peat accumulation, evaluated at a wellstudied temperate bog in Ontario, Canada. The Holocene Peat Model (HPM) determines vegetation community composition dynamics and annual net primary productivity based on peat depth (as a proxy for nutrients and acidity) and water table depth. Annual peat (carbon) accumulation is the net balance above- and below-ground productivity and litter/peat decomposition – a function of peat hydrology (controlling depth to and degree of anoxia). Peat bulk density is simulated as a function of degree of humification, and affects the water balance through its influence on both the growth rate of the peat column and on peat hydraulic conductivity and the capacity to shed water. HPM output includes both time series of annual carbon and water fluxes, peat height, and water table depth, as well as a final peat profile that can be “cored” and compared to field observations of peat age and macrofossil composition. A stochastic 8500-yr, annual precipitation time series was constrained by a published Holocene climate reconstruction for southern Quebec. HPM simulated 5.4 m of ´ peat accumulation (310 kg C m−2 ) over 8500 years, 6.5% of total NPP over the period. Vascular plant functional types accounted for 65% of total NPP over 8500 years but only 35% of the final (contemporary) peat mass. Simulated age-depth and carbon accumulation profiles were compared to a radiocarbon dated 5.8 m, c.9000-yr core. The simulated core was younger than observations at most depths, but had a similar overall trajectory; carbon accumulation rates were generally higher in the simulation and were somewhat more variable than observations. HPM results were sensitive to centuryscale anomalies in precipitation, with extended drier periods (precipitation reduced ∼10%) causing the peat profile to lose carbon (and height), despite relatively small changes in NP

Water table fluctuations and carbon accumulation of a fen and a bog in the James Bay Lowlands of Quebec, Canada

An important work regarding northern hemisphere peatland modeling is currently being processed. One of the first steps of this work is to understand the relationship between different components of the peatland system and to analyse the way unspecific peatland systems react to water table fluctuations in terms of accumulation and decomposition that we present in this article. We chose distinct sampling sites within a large region including boreal and subarctic ecosystems in the Bay James lowlands, northern Québec, Canada. Two fens were selected in the subarctic region and two bogs in the boreal region. These sites have different geographical, climatological and ecological features (ex. pH, nutrient availability and species compositions). Fens and bogs behaviours in matter of decomposition and accumulation thus follow different patterns. The analyses of cores for theses sites allow the comparison and the quantification of the differences between subarctic and boreal sites. Five cores were analysed against Testate amoebae every 2cm for the short cores and every 4cm for the long core. These cores are also dated with 210 Pb and 14C. Loss on ignition analysis was performed with the resolution of 1cm for each core. The use of a transfer function with the results of the Testate amoebae analysis allowed reconstruction of water table fluctuations from 7500 years BP to the present. This reconstruction gives us an insight into the humidity regime of the system. This information is compared to the carbon accumulation sequences to evaluate the response of the system to changes in water table position. This research shows response range between sites and quantifies the range of the water table fluctuation inducing an imbalance of the system. This information will be of significant importance for the development of the peatland dynamics modeling

Identification of novel genes potentially involved in somatic embryogenesis in chicory (Cichorium intybus L.)

<p>Abstract</p> <p>Background</p> <p>In our laboratory we use cultured chicory (<it>Cichorium intybus</it>) explants as a model to investigate cell reactivation and somatic embryogenesis and have produced 2 chicory genotypes (K59, C15) sharing a similar genetic background. K59 is a responsive genotype (embryogenic) capable of undergoing complete cell reactivation <it>i.e</it>. cell de- and re-differentiation leading to somatic embryogenesis (SE), whereas C15 is a non-responsive genotype (non-embryogenic) and is unable to undergo SE. Previous studies <abbrgrp><abbr bid="B1">1</abbr></abbrgrp> showed that the use of the β-D-glucosyl Yariv reagent (β-GlcY) that specifically binds arabinogalactan-proteins (AGPs) blocked somatic embryo production in chicory root explants. This observation indicates that β-GlcY is a useful tool for investigating somatic embryogenesis (SE) in chicory. In addition, a putative AGP (DT212818) encoding gene was previously found to be significantly up-regulated in the embryogenic K59 chicory genotype as compared to the non-embryogenic C15 genotype suggesting that this AGP could be involved in chicory re-differentiation <abbrgrp><abbr bid="B2">2</abbr></abbrgrp>. In order to improve our understanding of the molecular and cellular regulation underlying SE in chicory, we undertook a detailed cytological study of cell reactivation events in K59 and C15 genotypes, and used microarray profiling to compare gene expression in these 2 genotypes. In addition we also used β-GlcY to block SE in order to identify genes potentially involved in this process.</p> <p>Results</p> <p>Microscopy confirmed that only the K59, but not the C15 genotype underwent complete cell reactivation leading to SE formation. β-GlcY-treatment of explants blocked <it>in vitro </it>SE induction, but not cell reactivation, and induced cell wall modifications. Microarray analyses revealed that 78 genes were differentially expressed between induced K59 and C15 genotypes. The expression profiles of 19 genes were modified by β-GlcY-treatment. Eight genes were both differentially expressed between K59 and C15 genotypes during SE induction and transcriptionally affected by β-GlcY-treatment: <it>AGP </it>(DT212818), <it>26 S proteasome AAA ATPase subunit 6 </it>(<it>RPT6</it>), <it>remorin </it>(<it>REM</it>), <it>metallothionein-1 </it>(<it>MT1</it>), two non-specific lipid transfer proteins genes (<it>SDI-9 and DEA1</it>), <it>3-hydroxy-3-methylglutaryl-CoA reductase </it>(<it>HMG-CoA reductase</it>), and <it>snakin 2 </it>(<it>SN2</it>). These results suggest that the 8 genes, including the previously-identified <it>AGP </it>gene (DT212818), could be involved in cell fate determination events leading to SE commitment in chicory.</p> <p>Conclusion</p> <p>The use of two different chicory genotypes differing in their responsiveness to SE induction, together with β-GlcY-treatment represented an efficient tool to discriminate cell reactivation from the SE morphogenetic pathway. Such an approach, together with microarray analyses, permitted us to identify several putative key genes related to the SE morphogenetic pathway in chicory.</p

Overexpression of Protein Kinase C Confers Protection Against Antileukemic Drugs by Inhibiting the Redox-Dependent Sphingomyelinase Activation

ABSTRACT Induction of apoptosis by chemotherapeutic drugs involves the sphingomyelin-ceramide (SM-CER) pathway. This signaling is critically dependent on reactive oxygen species (ROS) generation and p53/p56 Lyn activation. In this study, we have investigated the influence of protein kinase C (PKC) overexpression on the SM-CER pathway in U937 human leukemia cell line. We show that PKC overexpression resulted in delayed apoptosis and significant resistance to both 1-␤-D-arabinofuranosylcytosine (ara-C) and daunorubicin (DNR), but there was no significant protection against cell-permeant C 6 -CER. Moreover, PKC overexpression abrogated drug-induced neutral sphingomyelinase stimulation and CER generation by inhibiting ROS production. We further investigated p53/p56 Lyn activation in PKC-overexpressing U937 cells treated with ara-C or DNR. We demonstrate that PKC inhibited p53/p56 Lyn phosphorylation and stimulation in drug-or H 2 O 2 -treated cells, suggesting that p53/p56 Lyn redox regulation is altered in PKC-overexpressing cells. Finally, we show that PKC-overexpressing U937 cells displayed accelerated H 2 O 2 detoxification. Altogether, our study provides evidence for the role of PKC in the negative regulation of drug-induced SM-CER pathway

Randomised pharmacokinetic trial of rifabutin with lopinavir/ritonavir-antiretroviral therapy in patients with HIV-associated tuberculosis in Vietnam.

BACKGROUND: Rifampicin and protease inhibitors are difficult to use concomitantly in patients with HIV-associated tuberculosis because of drug-drug interactions. Rifabutin has been proposed as an alternative rifamycin, but there is concern that the current recommended dose is suboptimal. The principal aim of this study was to compare bioavailability of two doses of rifabutin (150 mg three times per week and 150 mg daily) in patients with HIV-associated tuberculosis who initiated lopinavir/ritonavir-based antiretroviral therapy in Vietnam. Concentrations of lopinavir/ritonavir were also measured. METHODS: This was a randomized, open-label, multi-dose, two-arm, cross-over trial, conducted in Vietnamese adults with HIV-associated tuberculosis in Ho Chi Minh City (Clinical trial registry number NCT00651066). Rifabutin pharmacokinetics were evaluated before and after the introduction of lopinavir/ritonavir -based antiretroviral therapy using patient randomization lists. Serial rifabutin and 25-O-desacetyl rifabutin concentrations were measured during a dose interval after 2 weeks of rifabutin 300 mg daily, after 3 weeks of rifabutin 150 mg daily with lopinavir/ritonavir and after 3 weeks of rifabutin 150 mg three times per week with lopinavir/ritonavir. RESULTS: Sixteen and seventeen patients were respectively randomized to the two arms, and pharmacokinetic analysis carried out in 12 and 13 respectively. Rifabutin 150 mg daily with lopinavir/ritonavir was associated with a 32% mean increase in rifabutin average steady state concentration compared with rifabutin 300 mg alone. In contrast, the rifabutin average steady state concentration decreased by 44% when rifabutin was given at 150 mg three times per week with lopinavir/ritonavir. With both dosing regimens, 2 - 5 fold increases of the 25-O-desacetyl- rifabutin metabolite were observed when rifabutin was given with lopinavir/ritonavir compared with rifabutin alone. The different doses of rifabutin had no significant effect on lopinavir/ritonavir plasma concentrations. CONCLUSIONS: Based on these findings, rifabutin 150 mg daily may be preferred when co-administered with lopinavir/ritonavir in patients with HIV-associated tuberculosis. TRIAL REGISTRATION: ClinicalTrials.gov NCT00651066

Aspects of microbial communities in peatland carbon cycling under changing climate and land use pressures

This is the final version. Available on open access from the Finnish Peatland Society via the DOI in this record. Globally, major efforts are being made to restore peatlands to maximise their resilience to anthropogenic climate change, which puts continuous pressure on peatland ecosystems and modifies the geography of the environmental envelope that underpins peatland functioning. A probable effect of climate change is reduction in the waterlogged conditions that are key to peatland formation and continued accumulation of carbon (C) in peat. C sequestration in peatlands arises from a delicate imbalance between primary production and decomposition, and microbial processes are potentially pivotal in regulating feedbacks between environmental change and the peatland C cycle. Increased soil temperature, caused by climate warming or disturbance of the natural vegetation cover and drainage, may result in reductions of long-term C storage via changes in microbial community composition and metabolic rates. Moreover, changes in water table depth alter the redox state and hence have broad consequences for microbial functions, including effects on fungal and bacterial communities especially methanogens and methanotrophs. This article is a perspective review of the effects of climate change and ecosystem restoration on peatland microbial communities and the implications for C sequestration and climate regulation. It is authored by peatland scientists, microbial ecologists, land managers and non-governmental organisations who were attendees at a series of three workshops held at The University of Manchester (UK) in 2019–2020. Our review suggests that the increase in methane flux sometimes observed when water tables are restored is predicated on the availability of labile carbon from vegetation and the absence of alternative terminal electron acceptors. Peatland microbial communities respond relatively rapidly to shifts in vegetation induced by climate change and subsequent changes in the quantity and quality of below-ground C substrate inputs. Other consequences of climate change that affect peatland microbial communities and C cycling include alterations in snow cover and permafrost thaw. In the face of rapid climate change, restoration of a resilient microbiome is essential to sustaining the climate regulation functions of peatland systems. Technological developments enabling faster characterisation of microbial communities and functions support progress towards this goal, which will require a strongly interdisciplinary approach.Natural Environment Research Council (NERC

Role des antigenes HLA classe I dans la susceptibilite a la cytotoxine naturelle NK/LAK

SIGLECNRS T Bordereau / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc