Modelling Nutrient Uptake by Individual Hyphae of Arbuscular Mycorrhizal Fungi: Temporal and Spatial Scales for an Experimental Design

Arbuscular mycorrhizas, associations between plant roots and soil fungi, are ubiquitous among land plants. Arbuscular mycorrhizas can be beneficial for plants by overcoming limitations in nutrient supply. Hyphae, which are long and thin fungal filaments extending from the root surface into the soil, increase the volume of soil accessible for plant nutrient uptake. However, no models so far specifically consider individual hyphae. We developed a mathematical model for nutrient uptake by individual fungal hyphae in order to assess suitable temporal and spatial scales for a new experimental design where fungal uptake parameters are measured on the single hyphal scale. The model was developed based on the conservation of nutrients in an artificial cylindrical soil pore (capillary tube) with adsorbing wall, and analysed based on parameter estimation and non-dimensionalisation. An approximate analytical solution was derived using matched asymptotic expansion. Results show that nutrient influx into a hypha from a small capillary tube is characterized by three phases: Firstly, uptake rapidly decreases as the hypha takes up nutrients, secondly, the depletion zone reaches the capillary wall and thus uptake is sustained by desorption of nutrients from the capillary wall, and finally, uptake goes to zero after nutrients held on the capillary wall have been completely depleted. Simulating different parameter regimes resulted in recommending the use of capillaries filled with hydrogel instead of water in order to design an experiment operating over measurable time scales.     

Nutrient Uptake by ‘Alamo’ Switchgrass Used as an Energy Crop

Field studies were conducted in 2000 and 2001 to examine yields and nutrient removal by Alamo switchgrass (Panicum virgatum L.) grown at eight locations within five states in the upper southeastern USA. Plots, which had been established for >5 years as part of a larger study, were cut either once (late fall) or twice (midsummer and late fall). Plots cut once received 50 kg N per hectare per year, while twice-cut plots received 100 kg N per hectare per year. Nutrient concentrations of and nutrient removal by harvested biomass were determined. Partitioning of nutrients into leaf and stem fractions was determined at the time of the midsummer harvest in 2000. Biomass production during 2000 and 2001 averaged 15.9 Mg/ha per year across all sites and was as high as 21.7 Mg/ha per year at one site. Two cuttings plus the additional 50 kg N per hectare did not generally increase seasonal yields; and, in one quite productive location, that management caused a yield reduction. Nitrogen removal with two cuts was much higher than with a single cut due largely to the higher N content in the midsummer harvest. Over the 2 years, twice as much N was removed with the two annual cuts as with one cut. Nitrogen removal exceeded the amounts of N applied in both managements, suggesting N was being supplied via mineralization or other processes. Phosphorus removal also increased significantly with the two-cut management. Seasonal K and Ca removals were more similar between the two managements. Nitrogen and P concentrations generally declined basipetally in tillers, with older leaves and internodes having lower concentrations of both nutrients. Potassium was more uniformly distributed than N throughout the tiller components (leaf and stem). Calcium was higher in older leaf blades. Levels of soil P, K, and Ca at most locations appeared not to be limiting biomass production and were adequate for long-term productivity.     

Explicit Separation of Growth and Motility in a New Tumor Cord Model

We investigate a new model of tumor growth in which cell motility is considered an explicitly separate process from growth. Bulk tumor expansion is modeled by individual cell motility in a density-dependent diffusion process. This model is implemented in the context of an in vivo system, the tumor cord. We investigate numerically microscale density distributions of different cell classes and macroscale whole tumor growth rates as functions of the strength of transitions between classes. Our results indicate that the total tumor growth follows a classical von Bertalanffy growth profile, as many in vivo tumors are observed to do. This provides a quick validation for the model hypotheses. The microscale and macroscale properties are both sensitive to fluctuations in the transition parameters, and grossly adopt one of two phenotypic profiles based on their parameter regime. We analyze these profiles and use the observations to classify parameter regimes by their phenotypes. This classification yields a novel hypothesis for the early evolutionary selection of the metastatic phenotype by selecting against less motile cells which grow to higher densities and may therefore induce local collapse of the vascular network.     

Modeling and Estimation of Kinetic Parameters and Replicative Fitness of HIV-1 from Flow-Cytometry-Based Growth Competition Experiments

Growth competition assays have been developed to quantify the relative fitness of HIV-1 mutants. In this article, we develop mathematical models to describe viral/cellular dynamic interactions in the assay system from which the competitive fitness indices or parameters are defined. In our previous HIV-viral fitness experiments, the concentration of uninfected target cells was assumed to be constant (Wu et al. 2006). But this may not be true in some experiments. In addition, dual infection may frequently occur in viral fitness experiments and may not be ignorable. Here, we relax these two assumptions and extend our earlier viral fitness model (Wu et al. 2006). The resulting models then become nonlinear ODE systems for which closed-form solutions are not achievable. In the new model, the viral relative fitness is a function of time since it depends on the target cell concentration. First, we studied the structure identifiability of the nonlinear ODE models. The identifiability analysis showed that all parameters in the proposed models are identifiable from the flow-cytometry-based experimental data that we collected. We then employed a global optimization approach (the differential evolution algorithm) to directly estimate the kinetic parameters as well as the relative fitness index in the nonlinear ODE models using nonlinear least square regression based on the experimental data. Practical identifiability was investigated via Monte Carlo simulations.     

Nitrogen and α-Ketoglutaric Acid Application Modulate Grain Yield,Aroma, Nutrient Uptake and Physiological Attributes in Fragrant Rice

Journal of Plant Growth Regulation - The present study was conducted to assess the effects of nitrogen (N) and α-ketoglutaric acid application morpho-physiological attributes, aroma...     

Impact of the Invasive Alien Plant Solidago Giganteaon Primary Productivity, Plant Nutrient Content and Soil Mineral Nutrient Concentrations

Invasion by alien plants can alter ecosystem processes and soil properties. In this study, we compared aboveground productivity, nutrient pools in standing biomass and topsoil (0–0.10 m) mineral nutrient concentrations between plots invaded by Early Goldenrod (Solidago gigantea) and adjacent, uninvaded, vegetation at five sites in Belgium. The five sites were characterised by a resident perennial herbaceous vegetation and spanned a wide range in soil fertility level and floristic composition. Invaded stands consistently had higher (2–3-fold) aboveground productivity and lower mineral element concentrations in standing phytomass. Nutrient pools (calculated as concentration × phytomass) was ca. twice higher in invaded plots, suggesting that S. gigantea might enhance nutrient cycling rates. Impacts on topsoil chemistry were surprisingly modest, with slightly higher nutrient concentrations under the invader. A noticeable exception was phosphorus, which showed higher concentrations of ammonium acetate-extractable fraction in invaded plots in four of five sites. It appears that S. gigantea does not significantly contribute to nutrient uplift from deep soil layers to topsoil, possibly because it does not root much deeper compared to resident vegetation.Equally contributing authors: S. Vanderhoeven, N. Dassonville     

Uptake and processing of DNA by Acinetobacter calcoaceticus – a review

In natural transformation, DNA in the form of macromolecular fragments can be translocated across the cell envelope of prokaryotic microorganisms. During the past two decades, several, largely mutually contradictory, hypotheses have been forwarded to explain the molecular mechanism and bioenergetics of this translocation process. Other biomacromolecules are translocated across the bacterial cell envelope as well, such as polysaccharides and proteins, the latter for instance in the process of the assembly of type-IV pili. This brings up the question whether or not common components are involved.Here, we review analyses of DNA translocation in Acinetobacter calcoaceticus, a Gram-negative eubacterium that is able to migrate through twitching motility, and also shows a high frequency of natural transformation. DNA uptake in this organism is an energy-dependent process. Upon entry into the cells, the DNA fragments are integrated into the resident chromosome when a sufficiently large region of mutual homology is available (200 to 400 bp). However, this process is rather inefficient, and on the average 500 bp of each incoming fragment is degraded through exonuclease activity. Upon covalent attachment of a bulky protein molecule to the transforming DNA, the DNA-translocation machinery becomes blocked in further translocation activity.Since A. calcoaceticus is not well suited for transposon mutagenesis, a random mutagenesis procedure has been developed, based on the ligation of an antibiotic-resistance marker to random fragments of chromosomal DNA. This method was used to generate several mutants impaired in the natural transformation process. Three of these have been characterized in detail. No components, common to the translocation of macromolecules through the cell envelope of Acinetobacter, have been detected in this screen.     

The Effects and Mechanisms of Mitochondrial Nutrient α-Lipoic Acid on Improving Age-Associated Mitochondrial and Cognitive Dysfunction: An Overview

We have identified a group of nutrients that can directly or indirectly protect mitochondria from oxidative damage and improve mitochondrial function and named them “mitochondrial nutrients”. The direct protection includes preventing the generation of oxidants, scavenging free radicals or inhibiting oxidant reactivity, and elevating cofactors of defective mitochondrial enzymes with increased Michaelis–Menten constant to stimulate enzyme activity, and also protect enzymes from further oxidation, and the indirect protection includes repairing oxidative damage by enhancing antioxidant defense systems either through activation of phase 2 enzymes or through increase in mitochondrial biogenesis. In this review, we take α-lipoic acid (LA) as an example of mitochondrial nutrients by summarizing the protective effects and possible mechanisms of LA and its derivatives on age-associated cognitive and mitochondrial dysfunction of the brain. LA and its derivatives improve the age-associated decline of memory, improve mitochondrial structure and function, inhibit the age-associated increase of oxidative damage, elevate the levels of antioxidants, and restore the activity of key enzymes. In addition, co-administration of LA with other mitochondrial nutrients, such as acetyl-l-carnitine and coenzyme Q10, appears more effective in improving cognitive dysfunction and reducing oxidative mitochondrial dysfunction. Therefore, administrating mitochondrial nutrients, such as LA and its derivatives in combination with other mitochondrial nutrients to aged people and patients suffering from neurodegenerative diseases, may be an effective strategy for improving mitochondrial and cognitive dysfunction.     

γ-Aminobutyric Acid Uptake by Sympathetic Ganglia

EXOGENOUS γ-aminobutyric acid (GABA) accumulates against a concentration gradient in isolated mammalian nervous tissue^1–3 and mixes with GABA stored in the tissue⁴. Thus, neurones which use GABA as an inhibitory transmitter might be identified by locating sites of accumulation of radioactively-labelled GABA using autoradiography^5–7, assuming that exogenous GABA is only taken up into neurones already containing GABA. A correlation between GABA uptake and endogenous content has been noted in slices from different parts of the brain³ and in different nerve-ending fractions^8–10. These experiments, however, do not show whether GABA can be accumulated in nerve tissue totally devoid of “gabanergic” neurones. To test this, we have measured the uptake of GABA by isolated sympathetic ganglia. The principal transmitter in the ganglion is acetylcholine while the postganglionic neurones are mainly adrenergic. By analogy with the brain, the ganglion contains negligible amounts of GABA, glutamic decarboxylase or GABA-transaminase^11,12.     

Can Growth Form Classification Predict Litter Nutrient Dynamics and Decomposition Rates in Lowland Wet Forest?

This study investigates whether it is possible to simplify the complex influence of numerous species on leaf litter decomposition in a diverse tropical forest using functional classifications to predict litter quality, decomposition rate, and nutrient dynamics during decomposition, over a 2-yr period. Thirty-three lowland tropical forest plant species from contrasting growth forms (canopy trees, pioneer trees, lianas, palms, herbs) were studied. Twelve of 18 indices of litter quality varied significantly among growth forms, with canopy trees and palms showing lower litter quality than pioneer trees and herbs. Canopy leaves decomposed more slowly than understory leaves. Decomposition rate and mass loss trended greater ( P <0.1) in herbs and pioneer trees compared with other growth forms. There were no significant differences between monocots and dicots, and no phylogenetic signal for decomposition was observed. Significant correlations between continuous litter quality variables and decomposition rate were observed with correlation coefficients up to 0.72. Litter lignin:Mg, P concentration, and lignin:K, were the litter quality variables most related to decomposition rate. All elements showed significant negative correlations between initial litter concentration and percent remaining, but many elements showed significant correlation between percent element remaining and initial concentrations of other elements, indicating a stoichiometric balance between these elements during decomposition. The results show that although classification by growth form and canopy position are helpful for considering the ecosystem implications of changing community composition, litter quality traits provide additional predictive power for estimating the effects of species change on decomposition.
Abstract in Spanish is available at http://www.blackwell-synergy.com/loi/btp     

Expression and Secretion of Bifidobacterium adolescentis Amylase by Bifidobacterium Longum

Bifidobacterium adolescentis Int-57 (INT57), isolated from human feces, secretes an amylase. We have shot-gun cloned, sequence analyzed and expressed the gene encoding this amylase in B. longum. The sequenced 2477 bp fragment was homologous to other extracellular amylases. The encoded protein was predicted to be composed of 595 amino acids with a molecular weight of 64 kDa, and was designated AmyB. Highly conserved amylase domains were found in AmyB. The signal sequence and cleavage site was predicted by sequence analysis. AmyB was subcloned into pBES2, a novel E. coli–Bifidobacterium shuttle vector, to construct pYBamy59. Subsequently, B. longum, with no apparent amylase activity, was transformed with pYBamy59. More than 90% of the amylase activity was detected in the culture broth. This approach may open the way for the development of more efficient expression and secretion systems for Bifidobacterium. Both authors contributed equally Received 17 June 2005; Revisions requested 13 July 2005 and 26 September 2005; Revisions received 12 September 2005 and 8 November 2005; Accepted 11 November 2005     

Role of Zinc–Lysine on Growth and Chromium Uptake in Rice Plants under Cr Stress

Journal of Plant Growth Regulation - Chromium (Cr) is a very toxic heavy metal present in agricultural soils. Soils contaminated with Cr are the major source of Cr entrance into the food chain. The...     

Growth and genotype × environment interactions in Betula pendula: can tree genetic variation be maintained by small-scale forest ground heterogeneity?

Forest ground heterogeneity can affect interactions among tree species and control the assembly of local forest communities. Less is known of the effects of spatial heterogeneity on the maintenance of tree genetic variation through small-scale genotype × environment (G × E) interactions. We measured growth variation within and among 17 Betula pendula genotypes, planted in a clear-cut forest site through the summers 2009–2011. We assessed the spatial heterogeneity at two scales: among forest stands having history of the same or different tree species combinations (treated as replicate blocks), and along a gradient of within-block forest density, revealed by the stump density. To add a temporal perspective, we distinguished between old (cut 50 years earlier) and new stumps (cut one year earlier). The broad-sense heritabilities for growth were 0.093–0.055 and the coefficients of genotypic variation 0.37–0.21 in 2009–2011. The growth difference among the genotypes was 3.5–5.5 fold, significant in all years, and the rank of genotype means correlated positively between the years. The most favourable block had 106 % higher growth than the least favourable block and the amount of total variation explained by block increased from 0.4 % in 2009 to 6.9 % in 2011. Genotype × block interaction was marginally significant in 2009, but not later. Similarly, the response of growth to old stump density in sapling vicinity varied among the genotypes in 2009, but not later. In 2010 and 2011, the mean growth increased by 50–91 % along the old stump density gradient. Our results suggest that despite creating significant variation in sapling growth the small-scale forest ground heterogeneity, which reflects the recent forest history, may not significantly contribute to the maintenance of genetic variation in B. pendula populations.     

Nutrient requirements of in vitro cultured Halophila ovalis and Posidonia coriacea: nitrogen source

Axenic cultures of Posidonia coriacea and Halophila ovalis were established to investigate the effect of nitrogen addition and the optimum concentration of MS (Murashige and Skoog Physiol Plant 15:473–497, 1962) macronutrients, micronutrients and organics. Chlorophyll content and dissolved oxygen of H. ovalis was optimal at the control concentration of macronutrients (half strength MS). Below and above this concentration, growth of this species was compromised. A similar effect was observed for H. ovalis growth in response to MS micronutrient. However, changing the MS vitamins concentration had no impact on the growth of H. ovalis or P. coriacea. Leaf and root numbers of H. ovalis were highest in the treatment with the most nitrogen (50.6 mM). Root architecture of H. ovalis was affected by nitrogen source; shorter roots without root hairs were produced when NH₄NO₃ was present in the media. Longer roots with root hairs were produced when the cultures were grown in the absence of NH₄NO₃. P. coriacea growth did not exceed that of the control for any of the treatments. The response of H. ovalis to nutrient addition suggests its opportunistic nature, whereas the lack of response by P. coriacea suggests there may be some other limiting factor. This study shows that the proposed formulation of ½ strength MS can be suitable for both H. ovalis and P. coriacea.     

Tyrosine Phosphorylation of β-Catenin and Plakoglobin Enhanced by Hepatocyte Growth Factor and Epidermal Growth Factor in Human Carcinoma Cells

The effect of hepatocyte growth factor /scatter factor (HGF/SF) and epidermal growth factor (EGF) on cadherin-mediated adhesion of human carcinoma cells was studied. HGF/SF induced scattering of colonic adenocarcinoma HT29 and gastric adenocarcinomas MKN7 and MKN74 cells. Likewise, EGF induced scattering of HT29 and MKN7 cells. These cells expressed E-cadherin, which was concentrated at cell-cell contact sites. When the scattering of these cells was induced by HGF/SF or EGF, the E-cadherin concentration at cell-cell boundaries tended to decrease. Irnmunoblotting analyses, however, demonstrated that these growth factor treatments did not alter the expression of E-cadherin and E-cadherin-associated proteins, α- and β-catenin and plakoglobin. β-Catenin, plakoglobin and an unidentified 115-kDa molecule associated with E-cadherin were found to be phosphorylated at tyrosine residues, and these phosphorylations were enhanced by the growth factor treatments. These results suggest that HGF/SF and EGF may modulate the function of the cadherin-catenin system via tyrosine phosphorylation of cadherin-associated proteins.     

N,N′-Dicyclohexylcarbodiimide Inhibition of Dunaliella Growth,and Restoration by Some Adenine Nucleotides and Plant Growth Regulators

N,N′-Dicyclohexylcarbodiimide (DCCD), an inhibitor of membrane-bound ATPase, strongly inhibited the growth, as measured by an increase in cell number, of Dunaliella tertiolecta. However, this inhibition was reversed by simultaneous application of adenosine 5′-triphosphate (ATP) or adenosine 2′-monophosphate (2′-AMP). Adenosine and adenosine 5′-diphosphate (ADP) were ineffective in restroration of the DCCD-inhibited growth. Gibberellin A₃ (GA₃) and 2,4- dichlorophenoxyacetic acid (2,4-D) also reversed the inhibition of DCCD on D. tertiolecta growth, although these plant growth regulators did not promote an increase in cell number.     

Impact of Subunit Composition on the Uptake of α-Crystallin by Lens and Retina

Misfolded protein aggregation, including cataract, cause a significant amount of blindness worldwide. α-Crystallin is reported to bind misfolded proteins and prevent their aggregation. We hypothesize that supplementing retina and lens with α-crystallin may help to delay disease onset. The purpose of this study was to determine if αB-crystallin subunits containing a cell penetration peptide (gC-tagged αB-crystallin) facilitate the uptake of wild type αA-crystallin (WT-αA) in lens and retina. Recombinant human αB-crystallin was modified by the addition of a novel cell penetration peptide derived from the gC gene product of herpes simplex virus (gC-αB). Recombinant gC-αB and wild-type αA-crystallin (WT-αA) were purified from E. coli over-expression cultures. After Alexa-labeling of WT-αA, these proteins were mixed at ratios of 1:2, 1:5 and 1:10, respectively, and incubated at 37°C for 4 hours to allow for subunit exchange. Mixed oligomers were subsequently incubated with tissue culture cells or mouse organ cultures. Similarly, crystallin mixtures were injected into the vitreous of rat eyes. At various times after exposure, tissues were harvested and analyzed for protein uptake by confocal microscopy or flow cytometry. Chaperone-like activity assays were performed on α-crystallins ratios showing optimal uptake using chemically-induced or heat induced substrate aggregation assays. As determined by flow cytometry, a ratio of 1:5 for gC-αB to WT-αA was found to be optimal for uptake into retinal pigmented epithelial cells (ARPE-19). Chaperone-like activity assays demonstrated that hetero-oligomeric complex of gC-αB to WT-αA (in 1:5 ratio) retained protein aggregation protection. We observed a significant increase in protein uptake when optimized (gC-αB to WT-αA (1:5 ratio)) hetero-oligomers were used in mouse lens and retinal organ cultures. Increased levels of α-crystallin were found in lens and retina following intravitreal injection of homo- and hetero-oligomers in rats.