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Catalytic bio–chemo and bio–bio tandem oxidation reactions for amide and carboxylic acid synthesis
(2014)
A catalytic toolbox for three different water-based one-pot cascades to convert aryl alcohols to amides and acids and cyclic amines to lactams, involving combination of oxidative enzymes (monoamine oxidase, xanthine dehydrogenase, galactose oxidase and laccase) and chemical oxidants (TBHP or CuI(cat)/H2O2) at mild temperatures, is presented. Mutually compatible conditions were found to afford products in good to excellent yields.
In Australia, the rabbit haemorrhagic disease virus (RHDV) has been used since 1996 to reduce numbers of introduced European rabbits (Oryctolagus cuniculus) which have a devastating impact on the native Australian environment. RHDV causes regular, short disease outbreaks, but little is known about how the virus persists and survives between epidemics. We examined the initial spread of RHDV to show that even upon its initial spread, the virus circulated continuously on a regional scale rather than persisting at a local population level and that Australian rabbit populations are highly interconnected by virus-carrying flying vectors. Sequencing data obtained from a single rabbit population showed that the viruses that caused an epidemic each year seldom bore close genetic resemblance to those present in previous years. Together, these data suggest that RHDV survives in the Australian environment through its ability to spread amongst rabbit subpopulations. This is consistent with modelling results that indicated that in a large interconnected rabbit meta-population, RHDV should maintain high virulence, cause short, strong disease outbreaks but show low persistence in any given subpopulation. This new epidemiological framework is important for understanding virus-host co-evolution and future disease management options of pest species to secure Australia's remaining natural biodiversity.
Recent advances in high-throughput omics techniques render it possible to decode the function of genes by using the "guilt-by-association" principle on biologically meaningful clusters of gene expression data. However, the existing frameworks for biological evaluation of gene clusters are hindered by two bottleneck issues: (1) the choice for the number of clusters, and (2) the external measures which do not take in consideration the structure of the analyzed data and the ontology of the existing biological knowledge. Here, we address the identified bottlenecks by developing a novel framework that allows not only for biological evaluation of gene expression clusters based on existing structured knowledge, but also for prediction of putative gene functions. The proposed framework facilitates propagation of statistical significance at each of the following steps: (1) estimating the number of clusters, (2) evaluating the clusters in terms of novel external structural measures, (3) selecting an optimal clustering algorithm, and (4) predicting gene functions. The framework also includes a method for evaluation of gene clusters based on the structure of the employed ontology. Moreover, our method for obtaining a probabilistic range for the number of clusters is demonstrated valid on synthetic data and available gene expression profiles from Saccharomyces cerevisiae. Finally, we propose a network-based approach for gene function prediction which relies on the clustering of optimal score and the employed ontology. Our approach effectively predicts gene function on the Saccharomyces cerevisiae data set and is also employed to obtain putative gene functions for an Arabidopsis thaliana data set.
The photosynthetic carbon metabolism, including the Calvin-Benson cycle, is the primary pathway in C-3-plants, producing starch and sucrose from CO2. Understanding the interplay between regulation and efficiency of this pathway requires the development of mathematical models which would explain the observed dynamics of metabolic transformations. Here, we address this question by casting the existing models of Calvin-Benson cycle and the end-product processes into an analysis framework which not only facilitates the comparison of the different models, but also allows for their ranking with respect to chosen criteria, including stability, sensitivity, robustness and/or compliance with experimental data. The importance of the photosynthetic carbon metabolism for the increase of plant biomass has resulted in many models with various levels of detail. We provide the largest compendium of 15 existing, well-investigated models together with a comprehensive classification as well as a ranking framework to determine the best-performing models for metabolic engineering and planning of in silica experiments. The classification can be additionally used, based on the model structure, as a tool to identify the models which match best the experimental design. The provided ranking is just one alternative to score models and, by changing the weighting factor, this framework also could be applied for selection of other criteria of interest.
Attachment of phages to host cells, followed by phage DNA ejection, represents the first stage of viral infection of bacteria. Salmonella phage P22 has been extensively studied, serving as an experimental model for bacterial infection by phages. P22 engages bacteria by binding to the sugar moiety of lipopolysaccharides using the viral tailspike protein for attachment. While the structures of the N-terminal particle-binding domain and the major receptor-binding domain of the tailspike have been analyzed individually, the three-dimensional organization of the intact protein, including the highly conserved linker region between the two domains, remained unknown. A single amino-acid exchange in the linker sequence made it possible to crystallize the full-length protein. Two crystal structures of the linker region are presented: one attached to the N-terminal domain and the other present within the complete tailspike protein. Both retain their biological function, but the mutated full-length tailspike displays a retarded folding pathway. Fitting of the full-length tailspike into a published cryo-electron microscopy map of the P22 virion requires an elastic distortion of the crystal structure. The conservation of the linker suggests a role in signal transmission from the distal tip of the molecule to the phage head, eventually leading to DNA ejection.
In plants, SNF1-related kinase (SnRK1) responds to the availability of carbohydrates as well as to environmental stresses by down-regulating ATP consuming biosynthetic processes, while stimulating energy-generating catabolic reactions through gene expression and post-transcriptional regulation. The functional SnRK1 complex is a heterotrimer where the catalytic alpha subunit associates with a regulatory beta subunit and an activating gamma subunit. Several different metabolites as well as the hormone abscisic acid (ABA) have been shown to modulate SnRK1 activity in a cell- and stimulus-type specific manner. It has been proposed that tissue- or stimulus-specific expression of adapter proteins mediating SnRK1 regulation can at least partly explain the differences observed in SnRK1 signaling. By using yeast two-hybrid and in planta bi-molecular fluorescence complementation assays we were able to demonstrate that proteins containing the domain of unknown function (DUF) 581 could interact with both isoforms of the SnRK1 alpha subunit (AKIN10/11) of Arabidopsis. A structure/function analysis suggests that the DUF581 is a generic SnRK1 interaction module and co-expression with DUF581 proteins in plant cells leads to reallocation of the kinase to specific regions within the nucleus. Yeast two-hybrid analyses suggest that SnRK1 and DUF581 proteins share common interaction partners inside the nucleus. The analysis of available microarray data implies that expression of the 19 members of the DUF581 encoding gene family in Arabidopsis is differentially regulated by hormones and environmental cues, indicating specialized functions of individual family members. We hypothesize that DUF581 proteins could act as mediators conferring tissue- and stimulus-type specific differences in SnRK1 regulation.
In eukaryotes, regulated protein turnover is required during many cellular processes, including defense against pathogens. Ubiquitination and degradation of ubiquitinated proteins via the ubiquitin proteasome system (UPS) is the main pathway for the turnover of intracellular proteins in eukaryotes. The extensive utilization of the UPS in host cells makes it an ideal pivot for the manipulation of cellular processes by pathogens. Like many other Gram-negative bacteria, Xanthomonas species secrete a suite of type-III effector proteins (T3Es) into their host cells to promote virulence. Some of these T3Es exploit the plant UPS to interfere with immunity. This review summarizes T3E examples from the genus Xanthomonas with a proven or suggested interaction with the host UPS or UPS-like systems and also discusses the apparent paradox that arises from the presence of T3Es that inhibit the UPS in general while others rely on its activity for their function.
Redox modulation of protein activity by thioredoxins (TRXs) plays a key role in cellular regulation. Thioredoxin z (TRX z) and its interaction partner fructokinase-like protein 1 (FLN1) represent subunits of the plastid-encoded RNA polymerase (PEP), suggesting a role of both proteins in redox regulation of chloroplast gene expression. Loss of TRX z or FLN1 expression generates a PEP-deficient phenotype and renders the plants incapable to grow autotrophically. This study shows that PEP function in trx z and fln1 plants can be restored by complementation with redox-inactive TRX z C106S and FLN1 C(105/106)A protein variants, respectively. The complemented plants showed wild-type levels of chloroplast gene expression and were restored in photosynthetic capacity, indicating that redox regulation of PEP through TRX z/FLN1 per se is not essential for autotrophic growth. Promoter-reporter gene studies indicate that TRX z and FLN1 are expressed during early phases of leaf development while expression ceases at maturation. Taken together, our data support a model in which TRX z and FLN1 are essential structural components of the PEP complex and their redox activity might only play a role in the fine tuning of PEP function.
Elucidating the genetic basis of morphological changes in evolution remains a major challenge in biology [1-3]. Repeated independent trait changes are of particular interest because they can indicate adaptation in different lineages or genetic and developmental constraints on generating morphological variation [4-6]. In animals, changes to "hot spot" genes with minimal pleiotropy and large phenotypic effects underlie many cases of repeated morphological transitions [4-8]. By contrast, only few such genes have been identified from plants [8-11], limiting cross-kingdom comparisons of the principles of morphological evolution. Here, we demonstrate that the REDUCED COMPLEXITY (RCO) locus [12] underlies more than one naturally evolved change in leaf shape in the Brassicaceae. We show that the difference in leaf margin dissection between the sister species Capsella rubella and Capsella grandiflora is caused by cis-regulatory variation in the homeobox gene RCO-A, which alters its activity in the developing lobes of the leaf. Population genetic analyses in the ancestral C. grandiflora indicate that the more-active C. rubella haplotype is derived from a now rare or lost C. grandiflora haplotype via additional mutations. In Arabidopsis thaliana, the deletion of the RCO-A and RCO-B genes has contributed to its evolutionarily derived smooth leaf margin [12], suggesting the RCO locus as a candidate for an evolutionary hot spot. We also find that temperature-responsive expression of RCO-A can explain the phenotypic plasticity of leaf shape to ambient temperature in Capsella, suggesting a molecular basis for the well-known negative correlation between temperature and leaf margin dissection.
Polyadenylation of pre-mRNAs by poly(A) polymerase (PAPS) is a critical process in eukaryotic gene expression. As found in vertebrates, plant genomes encode several isoforms of canonical nuclear PAPS enzymes. In Arabidopsis thaliana these isoforms are functionally specialized, with PAPS1 affecting both organ growth and immune response, at least in part by the preferential polyadenylation of subsets of pre-mRNAs. Here, we demonstrate that the opposite effects of PAPS1 on leaf and flower growth reflect the different identities of these organs, and identify a role for PAPS1 in the elusive connection between organ identity and growth patterns. The overgrowth of paps1 mutant petals is due to increased recruitment of founder cells into early organ primordia, and suggests that PAPS1 activity plays unique roles in influencing organ growth. By contrast, the leaf phenotype of paps1 mutants is dominated by a constitutive immune response that leads to increased resistance to the biotrophic oomycete Hyaloperonospora arabidopsidis and reflects activation of the salicylic acid-independent signalling pathway downstream of ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1)/PHYTOALEXIN DEFICIENT4 (PAD4). These findings provide an insight into the developmental and physiological basis of the functional specialization amongst plant PAPS isoforms.
Diatom diversity in lakes of northwest Yakutia (Siberia) was investigated by microscopic and genetic analysis of surface and cored lake sediments, to evaluate the use of sedimentary DNA for paleolimnological diatom studies and to identify obscure genetic diversity that cannot be detected by microscopic methods. Two short (76 and 73 bp) and one longer (577 bp) fragments of the ribulose 1,5-bisphosphate carboxylase/oxygenase (rbcL) gene, encoding the large subunit of the rbcL, were used as genetic markers. Diverse morphological assemblages of diatoms, dominated by small benthic fragilarioid taxa, were retrieved from the sediments of each lake. These minute fragilarioid taxa were examined by scanning electron microscopy, revealing diverse morphotypes in Staurosira and Staurosirella from the different lakes. Genetic analyses indicated a dominance of haplotypes that were assigned to fragilarioid taxa and less genetic diversity in other diatom taxa. The long rbcL_577 amplicon identified considerable diversification among haplotypes clustering within the Staurosira/Staurosirella genera, revealing 19 different haplotypes whose spatial distribution appears to be primarily related to the latitude of the lakes, which corresponds to a vegetation and climate gradient. Our rbcL markers are valuable tools for tracking differences between diatom lineages that are not visible in their morphologies. These markers revealed putatively high genetic diversity within the Staurosira/Staurosirella species complex, at a finer scale than is possible to resolve by microscopic determination. The rbcL markers may provide additional reliable information on the diversity of barely distinguishable minute benthic fragilarioids. Environmental sequencing may thus allow the tracking of spatial and temporal diversification in Siberian lakes, especially in the context of diatom responses to recent environmental changes, which remains a matter of controversy.
Resurrection species are a group of land plants that can tolerate extreme desiccation of their vegetative tissues during harsh drought stress, and still quickly often within hours regain normal physiological and metabolic functions following rehydration. At the molecular level, this desiccation tolerance is attributed to basal cellular mechanisms including the constitutive expression of stress-associated genes and high levels of protective metabolites present already in the absence of stress, as well as to transcriptome and metabolome reconfigurations rapidly occurring during the initial phases of drought stress. Parts of this response are conferred by unique metabolites, including a diverse array of sugars, phenolic compounds, and polyols, some of which accumulate to high concentrations within the plant cell. In addition to drought stress, these metabolites are proposed to contribute to the protection against other abiotic stresses and to an increased oxidative stress tolerance. Recently, extracts of resurrection species and particular secondary metabolites therein were reported to display biological activities of importance to medicine, with e.g. antibacterial, anticancer, antifungal, and antiviral activities, rendering them possible candidates for the development of novel drug substances as well as for cosmetics. Herein, we provide an overview of the metabolite composition of resurrection species, summarize the latest reports related to the use of natural products from resurrection plants, and outline their potential for medical applications. (C) 2014 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/).
Although temporal heterogeneity is a well-accepted driver of biodiversity, effects of interannual variation in land-use intensity (LUI) have not been addressed yet. Additionally, responses to land use can differ greatly among different organisms; therefore, overall effects of land-use on total local biodiversity are hardly known. To test for effects of LUI (quantified as the combined intensity of fertilization, grazing, and mowing) and interannual variation in LUI (SD in LUI across time), we introduce a unique measure of whole-ecosystem biodiversity, multidiversity. This synthesizes individual diversity measures across up to 49 taxonomic groups of plants, animals, fungi, and bacteria from 150 grasslands. Multidiversity declined with increasing LUI among grasslands, particularly for rarer species and aboveground organisms, whereas common species and belowground groups were less sensitive. However, a high level of interannual variation in LUI increased overall multidiversity at low LUI and was even more beneficial for rarer species because it slowed the rate at which the multidiversity of rare species declined with increasing LUI. In more intensively managed grasslands, the diversity of rarer species was, on average, 18% of the maximum diversity across all grasslands when LUI was static over time but increased to 31% of the maximum when LUI changed maximally over time. In addition to decreasing overall LUI, we suggest varying LUI across years as a complementary strategy to promote biodiversity conservation.
Monoclonal antibodies (mAbs) are engineered immunoglobulins G (IgG) used for more than 20 years as targeted therapy in oncology, infectious diseases and (auto-)immune disorders. Their protein nature greatly influences their pharmacokinetics (PK), presenting typical linear and non-linear behaviors.
While it is common to use empirical modeling to analyze clinical PK data of mAbs, there is neither clear consensus nor guidance to, on one hand, select the structure of classical compartment models and on the other hand, interpret mechanistically PK parameters. The mechanistic knowledge present in physiologically-based PK (PBPK) models is likely to support rational classical model selection and thus, a methodology to link empirical and PBPK models is desirable. However, published PBPK models for mAbs are quite diverse in respect to the physiology of distribution spaces and the parameterization of the non-specific elimination involving the neonatal Fc receptor (FcRn) and endogenous IgG (IgGendo). The remarkable discrepancy between the simplicity of biodistribution data and the complexity of published PBPK models translates in parameter identifiability issues.
In this thesis, we address this problem with a simplified PBPK model—derived from a hierarchy of more detailed PBPK models and based on simplifications of tissue distribution model. With the novel tissue model, we are breaking new grounds in mechanistic modeling of mAbs disposition: We demonstrate that binding to FcRn is indeed linear and that it is not possible to infer which tissues are involved in the unspecific elimination of wild-type mAbs. We also provide a new approach to predict tissue partition coefficients based on mechanistic insights: We directly link tissue partition coefficients (Ktis) to data-driven and species-independent published antibody biodistribution coefficients (ABCtis) and thus, we ensure the extrapolation from pre-clinical species to human with the simplified PBPK model. We further extend the simplified PBPK model to account for a target, relevant to characterize the non-linear clearance due to mAb-target interaction.
With model reduction techniques, we reduce the dimensionality of the simplified PBPK model to design 2-compartment models, thus guiding classical model development with physiological and mechanistic interpretation of the PK parameters. We finally derive a new scaling approach for anatomical and physiological parameters in PBPK models that translates the inter-individual variability into the design of mechanistic covariate models with direct link to classical compartment models, specially useful for PK population analysis during clinical development.
Despite the success of highly active antiretroviral therapy (HAART) in the management of human immunodeficiency virus (HIV)-1 infection, virological failure due to drug resistance development remains a major challenge. Resistant mutants display reduced drug susceptibilities, but in the absence of drug, they generally have a lower fitness than the wild type, owing to a mutation-incurred cost. The interaction between these fitness costs and drug resistance dictates the appearance of mutants and influences viral suppression and therapeutic success. Assessing in vivo viral fitness is a challenging task and yet one that has significant clinical relevance. Here, we present a new computational modelling approach for estimating viral fitness that relies on common sparse cross-sectional clinical data by combining statistical approaches to learn drug-specific mutational pathways and resistance factors with viral dynamics models to represent the host-virus interaction and actions of drug mechanistically. We estimate in vivo fitness characteristics of mutant genotypes for two antiretroviral drugs, the reverse transcriptase inhibitor zidovudine (ZDV) and the protease inhibitor indinavir (IDV). Well-known features of HIV-1 fitness landscapes are recovered, both in the absence and presence of drugs. We quantify the complex interplay between fitness costs and resistance by computing selective advantages for different mutants. Our approach extends naturally to multiple drugs and we illustrate this by simulating a dual therapy with ZDV and IDV to assess therapy failure. The combined statistical and dynamical modelling approach may help in dissecting the effects of fitness costs and resistance with the ultimate aim of assisting the choice of salvage therapies after treatment failure.
Patterns of past vegetation changes over time and space can help facilitate better understanding of the interactions among climate, ecosystem, and human impact. Biome changes in China over the last 22,000 yr (calibrated radiocarbon date, a BP) were numerically reconstructed by using a standard approach of pollen-plant functional type-biome assignment (biomization). The biomization procedure involves pollen data from 2434 surface sites and 228 fossil sites with a high quality of pollen count and C-14 dating, 51 natural and three anthropogenic plant functional types (PFTs), as well as 19 natural and one anthropogenic biome. Surface pollen-based reconstruction of modern natural biome patterns is in good agreement (74.4%) with actual vegetation distribution in China. However, modem large-scale anthropogenic biome reconstruction has not been successful based on the current setup of three anthropogenic PFTs (plantation, secondary, and disturbed PFT) because of the limitation of non-species level pollen identification and the difficulty in the clear assignment of disturbed PFTs. The non-anthropogenic biome distributions of 44 time slices at 500-year intervals show large-scale discrepant and changed vegetation patterns from the last glacial maximum (LGM) to the Holocene throughout China. From 22 ka BP to 19 ka BP, temperate grassland, xerophytic shrubland, and desert dominated northern China, whereas cold or cool forests flourished in central China. Warm-temperate evergreen forests were restricted to far southern China, and tropical forests were absent During 18.5 ka BP to 12 ka BP, cold, cool, and dry biomes extended to some parts of northern, westem, and eastern China. Warm-temperate evergreen and mixed forests gradually expanded to occupy the whole of southern China. A slight northward shift of forest biomes occurred from 15 ka BP to 12 lea BP. During 11.5 ka BP to 9 ka BP, temperate grassland and shrubland gradually stretched to northern and western China. Cold and cool forests widely expanded into northern and central China, as well as in the northern margin of South China along with temperate deciduous forest. Since the early mid-Holocene (approximately 8.5 ka BP to 5.5 ka BP), all forest biomes shifted northward at the expense of herbaceous and shrubby biomes. Simultaneously, cold and cool forest biomes occupied the marginal areas of the Tibetan Plateau and the high mountains in western China. During the middle to late Holocene, from 5 ka to the present, temperate grassland and xerophytic shrubland expanded to the south and east, whereas temperate deciduous forests slightly shifted southward. After 3 lea BP, forest biomes were absent in western China and on the Tibetan plateau surface. Dramatic biome shifts from the LGM to the Holocene were observed in the forest-grassland ecotone and transitional zones between temperate and subtropical climates, between subtropical and tropical regions, and in the mountainous margins of the eastern Tibetan Plateau. Evidence showed more human disturbances during the late Holocene. More pollen records and historical documents are therefore further needed to understand fully the human disturbance-induced large-scale forest changes. In addition, more classifications of anthropogenic biome or land cover, more distinct assignment of pollen taxa to anthropogenic PFTs, and more effective numerical and/or mechanistic techniques in building large-scale human disturbances are required. (C) 2014 Elsevier B.V. All rights reserved.
Protein-metal coordination complexes are well known as active centers in enzymatic catalysis, and to contribute to signal transduction, gas transport, and to hormone function. Additionally, they are now known to contribute as load-bearing cross-links to the mechanical properties of several biological materials, including the jaws of Nereis worms and the byssal threads of marine mussels. The primary aim of this thesis work is to better understand the role of protein-metal cross-links in the mechanical properties of biological materials, using the mussel byssus as a model system. Specifically, the focus is on histidine-metal cross-links as sacrificial bonds in the fibrous core of the byssal thread (Chapter 4) and L-3,4-dihydroxyphenylalanine (DOPA)-metal bonds in the protective thread cuticle (Chapter 5).
Byssal threads are protein fibers, which mussels use to attach to various substrates at the seashore. These relatively stiff fibers have the ability to extend up to about 100 % strain, dissipating large amounts of mechanical energy from crashing waves, for example. Remarkably, following damage from cyclic loading, initial mechanical properties are subsequently recovered by a material-intrinsic self-healing capability. Histidine residues coordinated to transition metal ions in the proteins comprising the fibrous thread core have been suggested as reversible sacrificial bonds that contribute to self-healing; however, this remains to be substantiated in situ. In the first part of this thesis, the role of metal coordination bonds in the thread core was investigated using several spectroscopic methods. In particular, X-ray absorption spectroscopy (XAS) was applied to probe the coordination environment of zinc in Mytilus californianus threads at various stages during stretching and subsequent healing. Analysis of the extended X-ray absorption fine structure (EXAFS) suggests that tensile deformation of threads is correlated with the rupture of Zn-coordination bonds and that self-healing is connected with the reorganization of Zn-coordination bond topologies rather than the mere reformation of Zn-coordination bonds. These findings have interesting implications for the design of self-healing metallopolymers.
The byssus cuticle is a protective coating surrounding the fibrous thread core that is both as hard as an epoxy and extensible up to 100 % strain before cracking. It was shown previously that cuticle stiffness and hardness largely depend on the presence of Fe-DOPA coordination bonds. However, the byssus is known to concentrate a large variety of metals from seawater, some of which are also capable of binding DOPA (e.g. V). Therefore, the question arises whether natural variation of metal composition can affect the mechanical performance of the byssal thread cuticle. To investigate this hypothesis, nanoindentation and confocal Raman spectroscopy were applied to the cuticle of native threads, threads with metals removed (EDTA treated), and threads in which the metal ions in the native tissue were replaced by either Fe or V. Interestingly, replacement of metal ions with either Fe or V leads to the full recovery of native mechanical properties with no statistical difference between each other or the native properties. This likely indicates that a fixed number of metal coordination sites are maintained within the byssal thread cuticle – possibly achieved during thread formation – which may provide an evolutionarily relevant mechanism for maintaining reliable mechanics in an unpredictable environment.
While the dynamic exchange of bonds plays a vital role in the mechanical behavior and self-healing in the thread core by allowing them to act as reversible sacrificial bonds, the compatibility of DOPA with other metals allows an inherent adaptability of the thread cuticle to changing circumstances. The requirements to both of these materials can be met by the dynamic nature of the protein-metal cross-links, whereas covalent cross-linking would fail to provide the adaptability of the cuticle and the self-healing of the core. In summary, these studies of the thread core and the thread cuticle serve to underline the important and dynamic roles of protein-metal coordination in the mechanical function of load-bearing protein fibers, such as the mussel byssus.
Savanna rangelands worldwide are threatened by shrub encroachment, i.e. the increase of woody plant species at the cost of perennial grasses, causing a strong decline in the productivity of domestic livestock production. Although recent studies indicate that fire might be of great importance for semi-arid and arid savanna dynamics, it is largely not applied in the management of semi-arid rangelands especially with regard to woody plant control. We used the eco-hydrological savanna model EcoHyD to simulate the effects of different fire management strategies on semi-arid savanna vegetation and to assess their longterm suitability for semi-arid rangeland management. Simulation results show that prescribed fires, timed to kill tree seedlings prevented shrub encroachment for a broad range of livestock densities while the possible maximum long-term cattle densities on the simulated semi-arid rangeland in Namibia increased by more than 30%. However, when grazing intensity was too high, fire management failed in preventing shrub encroachment.
Our findings indicate that with regard to fire management a clear distinction between mesic and more arid savannas is necessary: While the frequency of fires is of relevance for mesic savannas, we recommend a fire management focussing on the timing of fire for semi-arid and arid savannas. (C) 2014 Elsevier Ltd. All rights reserved.
The structure, interpretation and parameterization of classical compartment models as well as physiologically-based pharmacokinetic (PBPK) models for monoclonal antibody (mAb) disposition are very diverse, with no apparent consensus. In addition, there is a remarkable discrepancy between the simplicity of experimental plasma and tissue profiles and the complexity of published PBPK models. We present a simplified PBPK model based on an extravasation rate-limited tissue model with elimination potentially occurring from various tissues and plasma. Based on model reduction (lumping), we derive several classical compartment model structures that are consistent with the simplified PBPK model and experimental data. We show that a common interpretation of classical two-compartment models for mAb disposition-identifying the central compartment with the total plasma volume and the peripheral compartment with the interstitial space (or part of it)-is not consistent with current knowledge. Results are illustrated for the monoclonal antibodies 7E3 and T84.66 in mice.
In ecology, biodiversity-ecosystem functioning (BEE) research has seen a shift in perspective from taxonomy to function in the last two decades, with successful application of trait-based approaches. This shift offers opportunities for a deeper mechanistic understanding of the role of biodiversity in maintaining multiple ecosystem processes and services. In this paper, we highlight studies that have focused on BEE of microbial communities with an emphasis on integrating trait-based approaches to microbial ecology. In doing so, we explore some of the inherent challenges and opportunities of understanding BEE using microbial systems. For example, microbial biologists characterize communities using gene phylogenies that are often unable to resolve functional traits. Additionally, experimental designs of existing microbial BEE studies are often inadequate to unravel BEE relationships. We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. We conclude that such trait-based approaches are a promising framework to increase the understanding of microbial BEE relationships and thus generating systematic principles in microbial ecology and more generally ecology.
This study examines a natural, rapid, fivefold increase in dissolved organic carbon (DOC) concentrations in a temperate shallow lake, describing the processes by which increased DOC resulted in anoxic conditions and altered existing carbon cycling pathways. High precipitation for two consecutive years led to rising water levels and the flooding of adjacent degraded peatlands. Leaching from the flooded soils provided an initial increase in DOC concentrations (from a 2010 mean of 12 +/- 1 mg L-1 to a maximum concentration of 53 mg L-1 by June 2012). Increasing water levels, DOC, and phytoplankton concentrations reduced light reaching the sediment surface, eliminating most benthic primary production and promoting anoxia in the hypolimnion. From January to June 2012 there was a sudden increase in total phosphorus (from 57 mg L-1 to 216 mg L-1), DOC (from 24.6 mg L-1 to 53 mg L-1), and iron (from 0.12 mg L-1 to 1.07 mg L-1) concentrations, without any further large fluxes in water levels. We suggest that anoxic conditions at the sediment surface and flooded soils produced a dramatic release of these chemicals that exacerbated brownification and eutrophication, creating anoxic conditions that persisted roughly 6 months below a water depth of 1 m and extended periodically to the water surface. This brownification-anoxia feedback loop resulted in a near-complete loss of macroinvertebrate and fish populations, and increased surface carbon dioxide (CO2) emissions by an order of magnitude relative to previous years.
In winter 2009/10, a sudden under-ice bloom of heterotrophic bacteria occurred in the seasonally ice-covered, temperate, deep, oligotrophic Lake Stechlin (Germany). Extraordinarily high bacterial abundance and biomass were fueled by the breakdown of a massive bloom of Aphanizomenon flos-aquae after ice formation. A reduction in light resulting from snow coverage exerted a pronounced physiological stress on the cyanobacteria. Consequently, these were rapidly colonized, leading to a sudden proliferation of attached and subsequently of free-living heterotrophic bacteria. Total bacterial protein production reached 201 mg C L-1 d(-1), ca. five times higher than spring-peak values that year. Fluorescence in situ hybridization and denaturing gradient gel electrophoresis at high temporal resolution showed pronounced changes in bacterial community structure coinciding with changes in the physiology of the cyanobacteria. Pyrosequencing of 16S rRNA genes revealed that during breakdown of the cyanobacterial population, the diversity of attached and free-living bacterial communities were reduced to a few dominant families. Some of these were not detectable during the early stages of the cyanobacterial bloom indicating that only specific, well adapted bacterial communities can colonize senescent cyanobacteria. Our study suggests that in winter, unlike commonly postulated, carbon rather than temperature is the limiting factor for bacterial growth. Frequent phytoplankton blooms in ice-covered systems highlight the need for year-round studies of aquatic ecosystems including the winter season to correctly understand element and energy cycling through aquatic food webs, particularly the microbial loop. On a global scale, such knowledge is required to determine climate change induced alterations in carbon budgets in polar and temperate aquatic systems.
Zooplankton carcasses are ubiquitous in marine and freshwater systems, implicating the importance of non-predatory mortality, but both are often overlooked in ecological studies compared with predatory mortality. The development of several microscopic methods allows the distinction between live and dead zooplankton in field samples, and the reported percentages of dead zooplankton average 11.6 (minimum) to 59.8 (maximum) in marine environments, and 7.4 (minimum) to 47.6 (maximum) in fresh and inland waters. Common causes of non-predatory mortality among zooplankton include senescence, temperature change, physical and chemical stresses, parasitism and food-related factors. Carcasses resulting from non-predatory mortality may undergo decomposition leading to an increase in microbial production and a shift in microbial composition in the water column. Alternatively, sinking carcasses may contribute significantly to vertical carbon flux especially outside the phytoplankton growth seasons, and become a food source for the benthos. Global climate change is already altering freshwater ecosystems on multiple levels, and likely will have significant positive or negative effects on zooplankton non-predatory mortality. Better spatial and temporal studies of zooplankton carcasses and non-predatory mortality rates will improve our understanding of this important but under-appreciated topic.
Light excitation of humic matter generates reactive oxygen species (ROS) in surface waters of aquatic ecosystems. Abundant ROS generated in humic matter rich lakes include singlet oxygen (O-1(2)) and hydrogen peroxide (H2O2). Because these ROS differ in half-life time and toxicity, we compared their effects on microbial activity (C-14-Leucine incorporation) and bacterial community composition (BCC) in surface waters of humic Lake Grosse Fuchskuhle (North-eastern Germany). For this purpose, experiments with water samples collected from the lake were conducted in July 2006, September 2008 and August 2009. Artificially increased O-1(2) and H2O2 concentrations inhibited microbial activity in water samples to a similar extent, but the effect of the respective ROS on BCC varied strongly. BCC analysis by 16S rRNA gene clone libraries and RT-PCR DGGE revealed ROS specific changes in relative abundance and activity of major bacterial groups and composition of dominating phylotypes. These changes were consistent in the three experiments performed in different years. The relative abundance of Polynucleobacter necessarius, Limnohabitans-related phylotypes (Betaproteobacteria), and Novosphingobium acidiphilum (Alphaproteobacteria) increased or was not affected by photo-sensitized O-1(2) exposure, but decreased after H2O2 exposure. The opposite pattern was found for Actinobacteria of the freshwater AcI-B cluster which were highly sensitive to O-1(2) but not to H2O2 exposure. Furthermore, group-specific RT-PCR DGGE analysis revealed that particle-attached P. necessarius and Limnohabitans-related phylotypes exhibit higher resistance to O-1(2) exposure compared to free-living populations. These results imply that O-1(2) acts as a factor in niche separation of closely affiliated Polynucleobacter and Limnohabitans-related phylotypes. Consequently, oxidative stress caused by photochemical ROS generation should be regarded as an environmental variable determining abundance, activity, and phylotype composition of environmentally relevant bacterial groups, in particular in illuminated and humic matter rich waters.
Dissolved organic carbon (DOC) concentrations - mainly of terrestrial origin - are increasing worldwide in inland waters. Heterotrophic bacteria are the main consumers of DOC and thus determine DOC temporal dynamics and availability for higher trophic levels. Our aim was to study bacterial carbon (C) turnover with respect to DOC quantity and chemical quality using both allochthonous and autochthonous DOC sources. We incubated a natural bacterial community with allochthonous C (C-13-labeled beech leachate) and increased concentrations and pulses (intermittent occurrence of organic matter input) of autochthonous C (phytoplankton lysate). We then determined bacterial C consumption, activities, and community composition together with the C flow through bacteria using stable C isotopes. The chemical analysis of single sources revealed differences in aromaticity and low-and high-molecular-weight substance fractions (LMWS and HMWS, respectively) between allochthonous and autochthonous C sources. Both DOC sources (allochthonous and autochthonous DOC) were metabolized at a high bacterial growth efficiency (BGE) around 50%. In treatments with mixed sources, rising concentrations of added autochthonous DOC resulted in a further, significant increase in bacterial DOC consumption of up to 68% when nutrients were not limiting. This rise was accompanied by a decrease in the humic substance (HS) fraction and an increase in bacterial biomass. Changes in DOC concentration and consumption in mixed treatments did not affect bacterial community composition (BCC), but BCC differed in single vs. mixed incubations. Our study highlights that DOC quantity affects bacterial C consumption but not BCC in nutrient-rich aquatic systems. BCC shifted when a mixture of allochthonous and autochthonous C was provided simultaneously to the bacterial community. Our results indicate that chemical quality rather than source of DOC per se (allochthonous vs. autochthonous) determines bacterial DOC turnover.
Fungi and bacteria are the major organic matter (OM) decomposers in aquatic ecosystems. While bacteria are regarded as primary mineralizers in the pelagic zone of lakes and oceans, fungi dominate OM decomposition in streams and wetlands. Recent findings indicate that fungal communities are also active in lakes, but little is known about their diversity and interactions with bacteria. Therefore, the decomposer niche overlap of saprotrophic fungi and bacteria was studied on pollen (as a seasonally recurring source of fine particulate OM) by performing microcosm experiments with three different lake types. Special emphasis was placed on analysis of fungal community composition and diversity. We hypothesized that (I) pollen select for small saprotrophic fungi and at the same time for typical particle-associated bacteria; (II) fungal communities form specific free-living and attached sub-communities in each lake type; (III) the ratio between fungi or bacteria on pollen is controlled by the lake's chemistry. Bacteria-to-fungi ratios were determined by quantitative PCR (qPCR), and bacterial and fungal diversity were studied by clone libraries and denaturing gradient gel electrophoresis (DGGE) fingerprints. A protease assay was used to identify functional differences between treatments. For generalization, systematic differences in bacteria-to-fungi ratios were analyzed with a dataset from the nearby Baltic Sea rivers. High abundances of Chytridiomycota as well as occurrences of Cryptomycota and yeast-like fungi confirm the decomposer niche overlap of saprotrophic fungi and bacteria on pollen. As hypothesized, microbial communities consistently differed between the lake types and exhibited functional differences. Bacteria-to-fungi ratios correlated well with parameters such as organic carbon and pH. The importance of dissolved organic carbon and nitrogen for bacteria-to-fungi ratios was supported by the Baltic Sea river dataset. Our findings highlight the fact that carbon-to-nitrogen ratios may also control fungal contributions to OM decomposition in aquatic ecosystems.
A mesocosm experiment was conducted to investigate the impact of rising fCO(2) on the build-up and decline of organic matter during coastal phytoplankton blooms. Five mesocosms (similar to 38 mA(3) each) were deployed in the Baltic Sea during spring (2009) and enriched with CO2 to yield a gradient of 355-862 A mu atm. Mesocosms were nutrient fertilized initially to induce phytoplankton bloom development. Changes in particulate and dissolved organic matter concentrations, including dissolved high-molecular weight (> 1 kDa) combined carbohydrates, dissolved free and combined amino acids as well as transparent exopolymer particles (TEP), were monitored over 21 days together with bacterial abundance, and hydrolytic extracellular enzyme activities. Overall, organic matter followed well-known bloom dynamics in all CO2 treatments alike. At high fCO(2,) higher Delta POC:Delta PON during bloom rise, and higher TEP concentrations during bloom peak, suggested preferential accumulation of carbon-rich components. TEP concentration at bloom peak was significantly related to subsequent sedimentation of particulate organic matter. Bacterial abundance increased during the bloom and was highest at high fCO(2). We conclude that increasing fCO(2) supports production and exudation of carbon-rich components, enhancing particle aggregation and settling, but also providing substrate and attachment sites for bacteria. More labile organic carbon and higher bacterial abundance can increase rates of oxygen consumption and may intensify the already high risk of oxygen depletion in coastal seas in the future.
Zooplankton support distinct bacterial communities in high concentrations relative to the surrounding water, but little is known about how the compositions and functionalities of these bacterial communities change through time in relation to environmental conditions. We conducted a year-long field study of bacterial communities associated with common zooplankton groups as well as free-living bacterial communities in the York River, a tributary of Chesapeake Bay. Bacterial community genetic fingerprints and their carbon substrate usage were examined by denaturing gradient gel electrophoresis (DGGE) of amplified 16S rDNA and by Biolog EcoPlates, respectively. Zooplankton-associated communities were genetically distinct from free-living bacterial communities but utilized a similar array of carbon substrates. On average, bacteria associated with different zooplankton groups were genetically more similar to each other within each month (65.4% similarity) than to bacterial communities of the same zooplankton group from different months (28 to 30% similarity), which suggests the importance of ambient environmental conditions in shaping resident zooplankton-associated bacterial communities. Monthly changes in carbon substrate utilization were less variable for zooplankton-associated bacteria than for free-living bacteria, suggesting that the zooplankton microhabitat is more stable than the surrounding water and supports specific bacterial groups in the otherwise unfavorable conditions in the water column.
Actinobacteria of the acI lineage are often the numerically dominant bacterial phylum in surface freshwaters, where they can account for >50% of total bacteria. Despite their abundance, there are no described isolates. In an effort to obtain enrichment of these ubiquitous freshwater Actinobacteria, diluted freshwater samples from Lake Grosse Fuchskuhle, Germany, were incubated in 96-well culture plates. With this method, a successful enrichment containing high abundances of a member of the lineage acI was established. Phylogenetic classification showed that the acIActinobacteria of the enrichment belonged to the acI-B2 tribe, which seems to prefer acidic lakes. This enrichment grows to low cell densities and thus the oligotrophic nature of acI-B2 was confirmed.
We investigated the systems response of metabolism and growth after an increase in irradiance in the nonsaturating range in the algal model Chlamydomonas reinhardtii. In a three-step process, photosynthesis and the levels of metabolites increased immediately, growth increased after 10 to 15 min, and transcript and protein abundance responded by 40 and 120 to 240 min, respectively. In the first phase, starch and metabolites provided a transient buffer for carbon until growth increased. This uncouples photosynthesis from growth in a fluctuating light environment. In the first and second phases, rising metabolite levels and increased polysome loading drove an increase in fluxes. Most Calvin-Benson cycle (CBC) enzymes were substrate-limited in vivo, and strikingly, many were present at higher concentrations than their substrates, explaining how rising metabolite levels stimulate CBC flux. Rubisco, fructose-1,6-biosphosphatase, and seduheptulose-1,7-bisphosphatase were close to substrate saturation in vivo, and flux was increased by posttranslational activation. In the third phase, changes in abundance of particular proteins, including increases in plastidial ATP synthase and some CBC enzymes, relieved potential bottlenecks and readjusted protein allocation between different processes. Despite reasonable overall agreement between changes in transcript and protein abundance (R-2 = 0.24), many proteins, including those in photosynthesis, changed independently of transcript abundance.
Polyadenylation is a decisive 3’ end processing step during the maturation of pre-mRNAs. The length of the poly(A) tail has an impact on mRNA stability, localization and translatability. Accordingly, many eukaryotic organisms encode several copies of canonical poly(A) polymerases (cPAPs). The disruption of cPAPs in mammals results in lethality. In plants, reduced cPAP activity is non-lethal. Arabidopsis encodes three nuclear cPAPs, PAPS1, PAPS2 and PAPS4, which are constitutively expressed throughout the plant. Recently, the detailed analysis of Arabidopsis paps1 mutants revealed a subset of genes that is preferentially polyadenylated by the cPAP isoform PAPS1 (Vi et al. 2013). Thus, the specialization of cPAPs might allow the regulation of different sets of genes in order to optimally face developmental or environmental challenges.
To gain insights into the cPAP-based gene regulation in plants, the phenotypes of Arabidopsis cPAPs mutants under different conditions are characterized in detail in the following work. An involvement of all three cPAPs in flowering time regulation and stress response regulation is shown. While paps1 knockdown mutants flower early, paps4 and paps2 paps4 knockout mutants exhibit a moderate late-flowering phenotype. PAPS1 promotes the expression of the major flowering inhibitor FLC, supposedly by specific polyadenylation of an FLC activator. PAPS2 and PAPS4 exhibit partially overlapping functions and ensure timely flowering by repressing FLC and at least one other unidentified flowering inhibitor. The latter two cPAPs act in a novel regulatory pathway downstream of the autonomous pathway component FCA and act independently from the polyadenylation factors and flowering time regulators CstF64 and FY. Moreover, PAPS1 and PAPS2/PAPS4 are implicated in different stress response pathways in Arabidopsis. Reduced activity of the poly(A) polymerase PAPS1 results in enhanced resistance to osmotic and oxidative stress. Simultaneously, paps1 mutants are cold-sensitive. In contrast, PAPS2/PAPS4 are not involved in the regulation of osmotic or cold stress, but paps2 paps4 loss-of-function mutants exhibit enhanced sensitivity to oxidative stress provoked in the chloroplast. Thus, both PAPS1 and PAPS2/PAPS4 are required to maintain a balanced redox state in plants. PAPS1 seems to fulfil this function in concert with CPSF30, a polyadenylation factor that regulates alternative polyadenylation and tolerance to oxidative stress.
The individual paps mutant phenotypes and the cPAP-specific genetic interactions support the model of cPAP-dependent polyadenylation of selected mRNAs. The high similarity of the polyadenylation machineries in yeast, mammals and plants suggests that similar regulatory mechanisms might be present in other organism groups. The cPAP-dependent developmental and physiological pathways identified in this work allow the design of targeted experiments to better understand the ecological and molecular context underlying cPAP-specialization.
Growth of plant organs relies on cell proliferation and expansion. While an increasingly detailed picture about the control of cell proliferation is emerging, our knowledge about the control of cell expansion remains more limited. We demonstrate the internal-motor kinesin AtKINESIN-13A (AtKIN13A) limits cell expansion and cell size in Arabidopsis thaliana, ion atkinl3a mutants forming larger petals with larger cells. The homolog, AtKINESIN-13B, also affects cell expansion and double mutants display growth, gametophytic and early embryonic defects, indicating a redundant role of he two genes. AtKIN13A is known to depolymerize microtubules and influence Golgi motility and distribution. Consistent his function, AtKIN13A interacts genetically with ANGUSTIFOLIA, encoding a regulator of Golgi dynamics. Reduced AtIGN13A activity alters cell wall structure as assessed by Fourier-transformed infrared-spectroscopy and triggers signalling he THESEUS1-dependent cell-wall integrity pathway, which in turn promotes the excess cell expansion in the atkinl3a mutant. Thus, our results indicate that the intracellular activity of AtKIN13A regulates cell expansion and wall architecture via THESEUS1, providing a compelling case of interplay between cell wall integrity sensing and expansion.
Leaves and floral organs grow to distinct, species-specific sizes and shapes. Research over the last few years has increased our understanding of how genetic pathways modulate cell proliferation and cell expansion to determine these sizes and shapes. In particular, the timing of proliferation arrest is an important point of control for organ size, and work on the regulators involved is showing how this control is achieved mechanistically and integrates environmental information. We are also beginning to understand how growth differs in different organs to produce their characteristic shapes, and how growth is integrated between different tissues that make up plant organs. Lastly, components of the general machinery in eukaryotic cells have been identified as having important roles in growth control.
Background: The identification of brassinosteroid (BR) deficient and BR insensitive mutants provided conclusive evidence that BR is a potent growth-promoting phytohormone. Arabidopsis mutants are characterized by a compact rosette structure, decreased plant height and reduced root system, delayed development, and reduced fertility. Cell expansion, cell division, and multiple developmental processes depend on BR. The molecular and physiological basis of BR action is diverse. The BR signalling pathway controls the activity of transcription factors, and numerous BR responsive genes have been identified. The analysis of dwarf mutants, however, may to some extent reveal phenotypic changes that are an effect of the altered morphology and physiology. This restriction holds particularly true for the analysis of established organs such as rosette leaves. Results: In this study, the mode of BR action was analysed in established leaves by means of two approaches. First, an inhibitor of BR biosynthesis (brassinazole) was applied to 21-day-old wild-type plants. Secondly, BR complementation of BR deficient plants, namely CPD (constitutive photomorphogenic dwarf)-antisense and cbb1 (cabbage1) mutant plants was stopped after 21 days. BR action in established leaves is associated with stimulated cell expansion, an increase in leaf index, starch accumulation, enhanced CO2 release by the tricarboxylic acid cycle, and increased biomass production. Cell number and protein content were barely affected. Conclusion: Previous analysis of BR promoted growth focused on genomic effects. However, the link between growth and changes in gene expression patterns barely provided clues to the physiological and metabolic basis of growth. Our study analysed comprehensive metabolic data sets of leaves with altered BR levels. The data suggest that BR promoted growth may depend on the increased provision and use of carbohydrates and energy. BR may stimulate both anabolic and catabolic pathways.
Phosphoglucomutase (PGM) catalyses the interconversion of glucose 1-phosphate (G1P) and glucose 6-phosphate (G6P) and exists as plastidial (pPGM) and cytosolic (cPGM) isoforms. The plastidial isoform is essential for transitory starch synthesis in chloroplasts of leaves, whereas the cytosolic counterpart is essential for glucose phosphate partitioning and, therefore, for syntheses of sucrose and cell wall components. In Arabidopsis two cytosolic isoforms (PGM2 and PGM3) exist. Both PGM2 and PGM3 are redundant in function as single mutants reveal only small or no alterations compared to wild type with respect to plant primary metabolism. So far, there are no reports of Arabidopsis plants lacking the entire cPGM or total PGM activity, respectively. Therefore, amiRNA transgenic plants were generated and used for analyses of various parameters such as growth, development, and starch metabolism. The lack of the entire cPGM activity resulted in a strongly reduced growth revealed by decreased rosette fresh weight, shorter roots, and reduced seed production compared to wild type. By contrast content of starch, sucrose, maltose and cell wall components were significantly increased. The lack of both cPGM and pPGM activities in Arabidopsis resulted in dwarf growth, prematurely die off, and inability to develop a functional inflorescence. The combined results are discussed in comparison to potato, the only described mutant with lack of total PGM activity.
Steroidal glycoalkaloids (SGAs) are nitrogen-containing secondary metabolites of the Solanum species, which are known to have large chemical and bioactive diversity in nature. While recent effort and development on LC/MS techniques for SGA profiling have elucidated the main pathways of SGA metabolism in tomato, the problem of peak annotation still remains due to the vast diversity of chemical structure and similar on overlapping of chemical formula. Here we provide a case study of peak classification and annotation approach by integration of species and tissue specificities of SGA accumulation for provision of comprehensive pathways of SGA biosynthesis. In order to elucidate natural diversity of SGA biosynthesis, a total of 169 putative SGAs found in eight tomato accessions (Solanum lycopersicum, S. pimpinellifolium, S. cheesmaniae, S. chmielewskii, S. neorickii, S. peruvianum, S. habrochaites, S. pennellii) and four tissue types were used for correlation analysis. The results obtained in this study contribute annotation and classification of SGAs as well as detecting putative novel biosynthetic branch points. As such this represents a novel strategy for peak annotation for plant secondary metabolites.
Changes in carbon flow and sink/source activities can affect floral, architectural, and reproductive traits of plants. In potato, overexpression (OE) of the purple acid phosphatase 2 of Arabidopsis (AtPAP2) resulted in earlier flowering, faster growth rate, increased tubers and tuber starch content, and higher photosynthesis rate. There was a significant change in sucrose, glucose and fructose levels in leaves, phloem and sink biomass of the OE lines, consistent with an increased expression of sucrose transporter 1 (StSUT1). Furthermore, the expression levels and enzyme activity of sucrose-phosphate synthase (SPS) were also significantly increased in the OE lines. These findings strongly suggest that higher carbon supply from the source and improved sink strength can improve potato tuber yield. (C) 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
In leaves of two starch-related single-knockout lines lacking either the cytosolic transglucosidase (also designated as disproportionating enzyme 2, DPE2) or the maltose transporter (MEX1), the activity of the plastidial phosphorylase isozyme (PHS1) is increased. In both mutants, metabolism of starch-derived maltose is impaired but inhibition is effective at different subcellular sites. Two constitutive double knockout mutants were generated (designated as dpe2-1 x phs1a and mex1 x phs1b) both lacking functional PHS1. They reveal that in normally grown plants, the plastidial phosphorylase isozyme participates in transitory starch degradation and that the central carbon metabolism is closely integrated into the entire cell biology. All plants were grown either under continuous illumination or in a light-dark regime. Both double mutants were compromised in growth and, compared with the single knockout plants, possess less average leaf starch when grown in a light-dark regime. Starch and chlorophyll contents decline with leaf age. As revealed by transmission electron microscopy, mesophyll cells degrade chloroplasts, but degradation is not observed in plants grown under continuous illumination. The two double mutants possess similar but not identical phenotypes. When grown in a light-dark regime, mesophyll chloroplasts of dpe2-1 x phs1a contain a single starch granule but under continuous illumination more granules per chloroplast are formed. The other double mutant synthesizes more granules under either growth condition. In continuous light, growth of both double mutants is similar to that of the parental single knockout lines. Metabolite profiles and oligoglucan patterns differ largely in the two double mutants.
Leaf senescence is a developmentally controlled process, which is additionally modulated by a number of adverse environmental conditions. Nitrogen shortage is a well-known trigger of precocious senescence in many plant species including crops, generally limiting biomass and seed yield. However, leaf senescence induced by nitrogen starvation may be reversed when nitrogen is resupplied at the onset of senescence. Here, the transcriptomic, hormonal, and global metabolic rearrangements occurring during nitrogen resupply-induced reversal of senescence in Arabidopsis thaliana were analysed. The changes induced by senescence were essentially in keeping with those previously described; however, these could, by and large, be reversed. The data thus indicate that plants undergoing senescence retain the capacity to sense and respond to the availability of nitrogen nutrition. The combined data are discussed in the context of the reversibility of the senescence programme and the evolutionary benefit afforded thereby. Future prospects for understanding and manipulating this process in both Arabidopsis and crop plants are postulated.
Climate change will increasingly affect the natural habitat and diet of polar bears (Ursus maritimus). Understanding the energetic needs of polar bears is therefore important. We developed a theoretical method for estimating polar bear food consumption based on using the highly recalcitrant polychlorinated biphenyl (PCB) congener, 2,2',4,4',55-hexaCB (CB153) in bear adipose tissue as an indicator of food intake. By comparing the CB153 tissue concentrations in wild polar bears with estimates from a purposely designed individual-based model, we identified the possible combinations of field metabolic rates (FMR) and CB153 deposition efficiencies in East Greenland polar bears. Our simulations indicate that if 30% of the CB153 consumed by polar bear individuals were deposited into their adipose tissue, the corresponding FMR would be only two times the basal metabolic rate. In contrast, if the modelled CB153 deposition efficiency were 10%, adult polar bears would require six times more energy than that needed to cover basal metabolism. This is considerably higher than what has been assumed for polar bears in previous studies though it is similar to FMRs found in other marine mammals. An implication of this result is that even relatively small reductions in future feeding opportunities could impact the survival of East Greenland polar bears.