Carbon and nitrogen allocation in Lolium perenne in response to elevated atmospheric CO2 with emphasis on soil carbon dynamics

The effect of elevated CO2 on the carbon and nitrogen distribution within perennial ryegrass (L. perenne L.) and its influence on belowground processes were investigated. Plants were homogeneously 14C-labelled in two ESPAS growth chambers in a continuous 14C-CO2 atmosphere of 350 and 700 L L-1 CO2 and at two soil nitrogen regimes, in order to follow the carbon flow through all plant and soil compartments.After 79 days, elevated CO2 increased the total carbon uptake by 41 and 21% at low (LN) and high nitrogen (HN) fertilisation, respectively. Shoot growth remained unaffected, whereas CO2 enrichment stimulated root growth by 46% and the root/soil respiration by 111%, irrespective of the nitrogen concentration. The total 14C-soil content increased by 101 and 28% at LN and HN, respectively. The decomposition of the native soil organic matter was not affected either by CO2 or by the nitrogen treatment.Elevated CO2 did not change the total nitrogen uptake of the plant either at LN or at HN. Both at LN and HN elevated CO2 significantly increased the total amount of nitrogen taken up by the roots and decreased the absolute and relative amounts translocated to the shoots.The amount of soil nitrogen immobilised by micro-organisms and the size of the soil microbial biomass were not affected by elevated CO2, whereas both were significantly increased at the higher soil N content.Most striking was the 88% increase in net carbon input into the soil expressed as: 14C-roots plus total 14C-soil content minus the 12C-carbon released by decomposition of native soil organic matter. The net carbon input into the soil at ambient CO2 corresponded with 841 and 1662 kg ha-1 at LN and HN, respectively. Elevated CO2 increased these amounts with an extra carbon input of 950 and 1056 kg ha-1. Combined with a reduced decomposition rate of plant material grown at elevated CO2 this will probably lead to carbon storage in grassland soils resulting in a negative feed back on the increasing CO2 concentration of the atmosphere.     

The Growth and Carbon Economy of Selection Lines of Lolium perenne cv. S23 with Differing Rates of Dark Respiration: 2. Grown as Young Plants from Seed

Young plants of two selection lines of Lolium perenne cv. S23with ‘fast’ and ‘slow’ rates of ‘maturetissue’ respiration were individually grown from seed,together with plants of S23, their common parent, in 9.2 cmpots in a controlled environment at 20/15 °C day/night temperatures. No significant differences were found between the genotypesin leaf extension and tiller production during this early stageof their growth. They did differ however, by an average of 26%,in the rate of dark respiration of fully expanded leaf laminae.The use of a simple model demonstrated that such a differencein respiration could alone account for the different rates ofdry matter production shown by the selection lines when grownas young crops from seed. Possible penalties of ‘slow’respiration are also considered. Lolium perenne L., ryegrass, respiration, maintenance respiration, stimulated swards, leaf growth, tiller production, carbon economy     

Comparing Population Patterns to Processes: Abundance and Survival of a Forest Salamander following Habitat Degradation

Habitat degradation resulting from anthropogenic activities poses immediate and prolonged threats to biodiversity, particularly among declining amphibians. Many studies infer amphibian response to habitat degradation by correlating patterns in species occupancy or abundance with environmental effects, often without regard to the demographic processes underlying these patterns. We evaluated how retention of vertical green trees (CANOPY) and coarse woody debris (CWD) influenced terrestrial salamander abundance and apparent survival in recently clearcut forests. Estimated abundance of unmarked salamanders was positively related to CANOPY ( _Canopy  = 0.21 (0.02–1.19; 95% CI), but not CWD ( _CWD  = 0.11 (−0.13–0.35) within 3,600 m² sites, whereas estimated abundance of unmarked salamanders was not related to CANOPY ( _Canopy  = −0.01 (−0.21–0.18) or CWD ( _CWD  = −0.02 (−0.23–0.19) for 9 m² enclosures. In contrast, apparent survival of marked salamanders within our enclosures over 1 month was positively influenced by both CANOPY and CWD retention ( _Canopy  = 0.73 (0.27–1.19; 95% CI) and _CWD  = 1.01 (0.53–1.50). Our results indicate that environmental correlates to abundance are scale dependent reflecting habitat selection processes and organism movements after a habitat disturbance event. Our study also provides a cautionary example of how scientific inference is conditional on the response variable(s), and scale(s) of measure chosen by the investigator, which can have important implications for species conservation and management. Our research highlights the need for joint evaluation of population state variables, such as abundance, and population-level process, such as survival, when assessing anthropogenic impacts on forest biodiversity.     

A proteomic and targeted metabolomic approach to investigate change in Lolium perenne roots when challenged with glycine

A combined proteomic and isotope tracer approach was used to investigate the impact of supplying N as glycine to roots of Lolium perenne. Initially, ammonium nitrate was supplied to all plants, after which half received glycine as their sole N source, while the remainder continued to receive ammonium nitrate. Plants supplied with glycine acquired less N than those receiving the mineral source, resulting in reduced root nitrate concentrations. The amino acid complement of roots was also strongly affected by the form of N supplied, and 15N labelling indicated that the biochemical fate of acquired N in roots was dependent on the form of N available for uptake. Proteomic analysis of Lolium roots indicated that 6% of 627 root proteins resolved on 2D gels changed in abundance in response to the form of N applied. Multivariate analysis of protein abundance clearly discriminated the proteomes of L. perenne roots as a function of treatment applied. Seven affected proteins were identified (mostly by protein homology with sequenced species), including methionine adenosyltransferase, an enzyme involved in glycine metabolism. Although some changes in root amino acid and protein complements were due to responses to reduced N supply, both the distinct fate of 15N tracers and the abundances of identified proteins could be attributed specifically to the form of N available to roots. The results demonstrate the potential of targeted proteomic approaches to identify functioning of plants where more traditional methods cannot resolve multiple, co-incident biological interactions and element fluxes.     

Molecular genecology of temperature response in Lolium perenne: 1. preliminary analysis to reduce false positives

Molecular genecology is the study of geographical clines in frequencies of molecular markers and their relationship to ecological clines in environmental conditions. This study outlines the principles underlying the selection of populations, focusing on avoiding 'false positives'- noncausal correlations between allele frequency and the environment. The principles are illustrated by identifying a set of populations of Lolium perenne for the study of temperature responses. The selected set of populations encompasses a 20 degrees C range in mean January temperature. Their freezing tolerance shows a linear trend with winter temperature, LT50 decreasing by 0.25 degrees C for each 1 degrees C reduction in mean January temperature.     

Response to Selection for Dark Respiration Rate of Mature Leaves in Lolium perenne and its Effects on Growth of Young Plants and Simulated Swards

Selections for slow and for fast rate of dark respiration ofmature leaves were made from within Lolium perenne cv. S23.Selected parents were pair-crossed to provide 15 F₁ familieswith slow respiration and 15 with fast. Dark respiration was inherited and families with contrastingrates were subjected to sequentially harvested growth analysesfrom the third leaf stage to that of 95 per cent light interceptionin a growth room. Seven periods of regrowth of simulated swardsof the families were then recorded. During development of theprimary canopy, growth of the selections did not differ untilthe final harvest interval. At this stage slow respiration familieshad faster (P < 0.05) net assimilation rate and greater plantdry weight (P < 0.05) and leaf area index (P < 0.05) thanthe fast respiration group. Relative growth rate followed thesame trend. In the swards after each regrowth dry matter yieldof the slow respiration group was greater than that of the fast. In another experiment, simulated swards of six slow respirationfamilies yielded more than swards of six fast respiration familiesover sequential regrowth periods in a glasshouse from May toNovember: S23 was intermediate. Differences were most duringAugust and September. Crop growth rate at each harvest correlated(P < 0.05 or P < 0.01) with previously determined leafrespiration at 25 °C. Leaf protein levels in August weaklycorrelated (r = +0.57, P < 0.05) with respiration rate perunit dry weight but there was a significant residual negativecorrelation (r = –0.67, P < 0.05) between the rateper unit protein and growth at that time. Results are discussedin relation to the concept of ‘maintenance-relàted’respiration. Lolium perenne L., perennial ryegrass, respiration, maintenance respiration, relative growth rate, leaf area ratio     

Impact of Gene Dosage on Gene Expression,Biological Processes and Survival in Cervical Cancer: A Genome-Wide Follow-Up Study

We investigated the role of tumor copy number (CN)–altered genome (CN-AG) in the carcinogenesis of cervical cancer (CC), especially its effect on gene expression, biological processes, and patient survival. Fifty-nine human papillomavirus 16 (HPV16)-positive CCs were investigated with microarrays–31 for mapping CN-AG and 55 for global gene expression, with 27 CCs in common. Five-year survival was investigated in 55 patients. Deletions and amplifications >2.5 Mb were defined as CN alterations. The %CN-AG varied from 0 to 32.2% (mean = 8.1±8.9). Tumors were classified as low (mean = 0.5±0.6, n = 11), medium (mean = 5.4±2.4, n = 10), or high (mean = 19.2±6.6, n = 10) CN. The highest %CN-AG was found in 3q, which contributed an average of 55% of all CN alterations. Genome-wide, only 5.3% of CN-altered genes were deregulated directly by gene dosage. In contrast, the rate in fully duplicated 3q was twice as high. Amplification of 3q explained 23.2% of deregulated genes in whole tumors (r² = 0.232, p = 0.006; analysis of variance), including genes located in 3q and other chromosomes. A total of 862 genes were deregulated exclusively in high-CN tumors, but only 22.9% were CN altered. This suggests that the remaining genes are not deregulated directly by gene dosage, but by mechanisms induced in trans by CN-altered genes. Anaphase-promoting complex/cyclosome (APC/C)-dependent proteasome proteolysis, glycolysis, and apoptosis were upregulated, whereas cell adhesion and angiogenesis were downregulated exclusively in high-CN tumors. The high %CN-AG and upregulated gene expression profile of APC/C-dependent proteasome proteolysis were associated with poor patient survival (p<0.05, log-rank test). Along with glycolysis, they were linearly associated with FIGO stage (r>0.38, p<0.01, Spearman test). Therefore, inhibition of APC/C-dependent proteasome proteolysis and glycolysis could be useful for CC treatment. However, whether they are indispensable for tumor growth remains to be demonstrated.     

Fate of fructose supplied to leaf sheaths after defoliation of Lolium perenne L.: assessment by 13C-fructose labelling

The role of fructans from leaf sheaths for the refoliation of Lolium perenne after severe defoliation was assessed by following the fate of (13)C-fructose supplied to leaf sheaths at the time of defoliation. At the end of the 4 h labelling period on defoliated plants, 77% of the (13)C incorporated was still located in leaf sheaths. Only 4% and 0.9% were, respectively, allocated to stem and roots, while 18% was imported by the growing leaves where (13)C was allocated first to the proximal part of the leaf growth zone (0-10 mm). In all tissues, the most highly (13)C-labelled carbohydrates was not fructose but sucrose. In leaf sheaths, (13)C-loliose was produced. In the leaf growth zone (0-20 mm), fructans were simultanously synthesized from (13)C entering the leaves and degraded. The export of (13)C from leaf sheaths continued during the first day of regrowth but stopped afterwards. There was no net loss of C from (13)C-fructose over the first 2 d of regrowth. The role of fructans and loliose is discussed as well as the physiological mechanisms contributing to defoliation tolerance in L. perenne.     

Growth of Ryegrass (Lolium perenne L.) Exposed to SO2: I. EFFECTS ON PHOTOSYNTHESIS AND RESPIRATION

The effects of exposure to SO₂ (50 and 400 µg m^–3SO₂) on the growth, photosynthesis, and respiration of perennialryegrass (Lolium perenne L.) cv. S23 were examined in two successivegrowth periods of 29 and 22 d. At the higher concentration ofSO₂, there was some visible injury of the leaves and specificleaf area was reduced, but yield, net photosynthesis, and darkrespiration of the plants were not significantly affected byexposure. The treatment was also without effect on the transpirationcoefficient of the plants and their number of tillers. The plantsexposed to the lower concentration of SO₂ showed no signs ofinjury and did not differ in any of the measured characteristicsfrom plants grown in SO₂-free air. Content of S in the shootsincreased linearly with the concentration of SO₂, the additionalS being found in the sulphate fraction whilst organic S wasunchanged. The results are discussed in relation to earlierfindings that yield of ryegrass exposed to SO₂ may be reducedwithout visible signs of injury.     

A demonstration of a 1:1 correspondence between chiasma frequency and recombination using a Lolium perenne/Festuca pratensis substitution

A single chromosome of the grass species Festuca pratensis has been introgressed into Lolium perenne to produce a diploid monosomic substitution line 2n = 2x = 14. The chromatin of F. pratensis and L. perenne can be distinguished by genomic in situ hybridization (GISH), and it is therefore possible to visualize the substituted F. pratensis chromosome in the L. perenne background and to study chiasma formation in a single marked bivalent. Recombination occurs freely in the F. pratensis/L. perenne bivalent, and chiasma frequency counts give a predicted map length for this bivalent of 76 cM. The substituted F. pratensis chromosome was also mapped with 104 EcoRI/Tru91 and HindIII/Tru91 amplified fragment length polymorphisms (AFLPs), generating a marker map of 81 cM. This map length is almost identical to the map length of 76 cM predicted from the chiasma frequency data. The work demonstrates a 1:1 correspondence between chiasma frequency and recombination and, in addition, the absence of chromatid interference across the Festuca and Lolium centromeres.     

Growth of Ryegrass (Lolium perenne L.) Exposed to SO2: III. EFFECTS ON FREE AND STORAGE CARBOHYDRATE CONCENTRATIONS

Exposure of ryegrass (Lolium perenne L.) cv. S23 to 0, 50, and400 µg m^–3 SO₂ for an initial 29 d (first harvest),and for an additional 22 d period of regrowth (second harvest),resulted in distinct alterations in carbohydrate metabolismat each harvest. At the first harvest, exposure to 50 µgm^–3 increased concentrations of free and total carbohydrates,whereas exposure to 400 µg m^–3 resulted in concentrationshardly different from those in control plants. At both SO₂ concentrations,more assimilate was retained as free carbohydrate rather thanas storage carbohydrate. Comparison of assimilate distributionat the end of the light, and at the end of the dark period atthe first harvest led to the conclusion that light-mediatedmetabolism is more sensitive to SO₂ exposure than dark metabolism,and that assimilate distribution might be controlled by at leasttwo processes exhibiting different SO₂ sensitivities.     

StochPy: A Comprehensive,User-Friendly Tool for Simulating Stochastic Biological Processes

Single-cell and single-molecule measurements indicate the importance of stochastic phenomena in cell biology. Stochasticity creates spontaneous differences in the copy numbers of key macromolecules and the timing of reaction events between genetically-identical cells. Mathematical models are indispensable for the study of phenotypic stochasticity in cellular decision-making and cell survival. There is a demand for versatile, stochastic modeling environments with extensive, preprogrammed statistics functions and plotting capabilities that hide the mathematics from the novice users and offers low-level programming access to the experienced user. Here we present StochPy (Stochastic modeling in Python), which is a flexible software tool for stochastic simulation in cell biology. It provides various stochastic simulation algorithms, SBML support, analyses of the probability distributions of molecule copy numbers and event waiting times, analyses of stochastic time series, and a range of additional statistical functions and plotting facilities for stochastic simulations. We illustrate the functionality of StochPy with stochastic models of gene expression, cell division, and single-molecule enzyme kinetics. StochPy has been successfully tested against the SBML stochastic test suite, passing all tests. StochPy is a comprehensive software package for stochastic simulation of the molecular control networks of living cells. It allows novice and experienced users to study stochastic phenomena in cell biology. The integration with other Python software makes StochPy both a user-friendly and easily extendible simulation tool.     

Temperature Sensitivity of Photosynthesis in Lolium perenne Swards: A Comparison of Two Methods for Deriving Photosynthetic Parameters from in vivo Measurements

The seasonal variation in photosynthetic rate of grass swards is partly the result of changes in the environment and partly the result of changes in the photosynthetic capacity of the sward itself. We evaluated two types of photosynthesis equations regarding their capacity to analyse seasonal and short-term temperature effects on photosynthesis of ryegrass (Lolium perenne L.). Intact cores of a field-grown ryegrass sward were taken to the laboratory 10 d after cutting for measurement of photosynthesis under controlled conditions. This was done during two four-week periods, in summer and autumn. Net photosynthetic rate (P _N) of the sward was lower in autumn than in summer. Both a simple negatively exponential photosynthesis irradiance-response curve and the Farquhar equations for photosynthesis were applied to the in vivo canopy measurements. Application of the irradiance-response curve showed that irradiance-saturated gross photosynthetic rate increased linearly with increasing temperature and was higher in summer than in autumn. The initial radiation use efficiency did not differ between the seasons but decreased with the temperature rise. This explains the observation that total canopy photosynthetic rate decreased after short-term temperature increases in both seasons. The parameters in Farquhar equations that represent the temperature sensitivity of the maximum electron transport rate and of the Michaelis-Menten constants for CO₂ and O₂ fixation could not be quantified satisfactorily. Parameterisation of the Farquhar equations was hampered by a lack of robust information on many biochemical parameters, and the use of simple empirical response-functions may be preferable in the case of in vivo canopy measurements on grass swards.     

A Hydroponic System for Growing Gnotobiotic Vs. Sterile Plants to Study Phytoremediation Processes

In some phytoremediation studies it is desirable to separate and define the specific contribution of plants and root-colonizing bacteria towards contaminant removal. Separating the influence of plants and associated bacteria is a difficult task for soil root environments. Growing plants hydroponically provides more control over the biological factors in contaminant removal. In this study, a hydroponic system was designed to evaluate the role of sterile plant roots, rhizodeposition, and root-associated bacteria in the removal of a model contaminant, phenol. A strain of Pseudomonas pseudoalcaligenes that grows on phenol was inoculated onto plant roots. The introduced biofilm persisted in the root zone and promoted phenol removal over non-augmented controls. These findings indicate that this hydroponic system can be a valuable tool for phytoremediation studies that investigate the effects of biotic and abiotic factors on pollution remediation.     

The International Heart Transplant Survival Algorithm (IHTSA): A New Model to Improve Organ Sharing and Survival

Background

Heart transplantation is life saving for patients with end-stage heart disease. However, a number of factors influence how well recipients and donor organs tolerate this procedure. The main objective of this study was to develop and validate a flexible risk model for prediction of survival after heart transplantation using the largest transplant registry in the world.

Methods and Findings

We developed a flexible, non-linear artificial neural networks model (IHTSA) and classification and regression tree to comprehensively evaluate the impact of recipient-donor variables on survival over time. We analyzed 56,625 heart-transplanted adult patients, corresponding to 294,719 patient-years. We compared the discrimination power with three existing scoring models, donor risk index (DRI), risk-stratification score (RSS) and index for mortality prediction after cardiac transplantation (IMPACT). The accuracy of the model was excellent (C-index 0.600 [95% CI: 0.595–0.604]) with predicted versus actual 1-year, 5-year and 10-year survival rates of 83.7% versus 82.6%, 71.4% – 70.8%, and 54.8% – 54.3% in the derivation cohort; 83.7% versus 82.8%, 71.5% – 71.1%, and 54.9% – 53.8% in the internal validation cohort; and 84.5% versus 84.4%, 72.9% – 75.6%, and 57.5% – 57.5% in the external validation cohort. The IHTSA model showed superior or similar discrimination in all of the cohorts. The receiver operating characteristic area under the curve to predict one-year mortality was for the IHTSA: 0.650 (95% CI: 0.640–0.655), DRI 0.56 (95% CI: 0.56–0.57), RSS 0.61 (95% CI: 0.60–0.61), and IMPACT 0.61 (0.61–0.62), respectively. The decision-tree showed that recipients matched to a donor younger than 38 years had additional expected median survival time of 2.8 years. Furthermore, the number of suitable donors could be increased by up to 22%.

Conclusions

We show that the IHTSA model can be used to predict both short-term and long-term mortality with high accuracy globally. The model also estimates the expected benefit to the individual patient.     

The Discovery of Medicines from Plants: A Current Biological Perspective1

The Discovery of Medicines from Plants: A Current Biological Perspective. The last 50 years have seen tremendous innovations in the process of discovering novel bioactive compounds from plants. Every stage of the natural products discovery and development pipeline has seen major advances, so as a result, today it is possible to evaluate large numbers of plant extracts efficiently and in more effective ways against a wider array of disease targets. Despite all of these technological advances and numerous large-scale discovery efforts, the number of new drugs developed as natural products from plants to reach the market has been surprisingly low, very different from the continuing productive discovery work from microbes. The innovations in the discovery process are reviewed, possible explanations for low success of recent discovery efforts are explored, and an effort is made to estimate the future potential of plants as a discovery resource. It may be that the low rate of discovery during this developmental period of natural products discovery is a consequence of technological limitations of the discovery process rather than a lack of interesting compounds in plants, and that even when necessary assumptions are taken into account, conservative estimates would indicate great potential for the discovery of new drugs from plants.