Markov modelling of immunological and virological states in HIV-1 infected patients

The purpose of this study was to evaluate the evolution of HIV infected patients and to bring out some significant factors associated with this pathology. The main criteria revealing the State of illness is viral load measurement (VL). However the CD4 lymphocytes also represent an important marker as these reflect the State of the immune reservoir. Many studies have been carried out in this field and different models have been proposed with a view to a better understanding of this disease. Multi State Markov models defined in terms of CD4 counts, or in terms of viral load, have proved to be very useful tools for modelling HIV disease progression. The model we have developed in this study is based on both the CD4 lymphocytes counts and VL. Markov models are characterized by transition intensities. In this paper we explored several structures in succession. First, we used a homogeneous continuous time Markov process with four states defined by crossed values of CD4 and VL in a given patient at a given time. Then, the effect of certain covariates on the infection process was introduced into the model via the transition intensity functions, as with a Cox regression model. Since the hypothesis of homogeneity may be unrealistic in certain cases, we also considered piecewise homogeneous Markov models. Finally, the effects of covariates and time were combined in a piecewise homogeneous model with a covariate. We applied these methods to data from 1313 HIV-infected patients included in the NADIS cohort.     

Does Solid-state <Superscript>15</Superscript>N NMR Spectroscopy Detect all Soil Organic Nitrogen?

Virtually all of the N detected by ¹⁵N cross polarization (CP) NMR spectra of four HF-treated soil clay fractions is amide N. However, the intensity of this ¹⁵N CP NMR signal (per unit N) is 27–57% lower than detected for a wheat protein, gliadin. There are two possible explanations – either the amide N in the soil clay fractions produces proportionately less NMR signal than does the amide N in gliadin, or part of the N in the soil clay fractions produces little or no NMR signal. The cross polarization dynamics of the gliadin amide resonance and amide resonances detected for the soil clay fractions are very similar and thus should produce similar amounts of signal, ruling out the first possibility. Therefore up to half or even more of the organic N in these soil clay fractions must be in a form that is insensitive to NMR detection. For a model compound (caffeine), non-protonated heterocyclic N produced less than 20% of the signal of an equivalent amount of amide N in gliadin. Results from several ¹³C NMR techniques provide further evidence that much of the undetected N in the soil clay fractions may be heterocyclic.     

Carbon and nitrogen sources influence the ligninolytic enzyme activity of <Emphasis Type="Italic">Trametes versicolor</Emphasis>

Among carbon sources studied, cellobiose and mannitol provided the highest laccase (Lac) activity (648 and 742 U1^-1, respectively) of Trametes versicolor 775 while glucose gave maximum manganese peroxidase (MnP) and peroxidase activities (44 and 114U1^-1, respectively). Citrus fruit peel as growth substrate enhanced Lac activity 7-fold when compared to the medium with cellobiose, whereas grape vine sawdust increased MnP and peroxidase activity up to 148 and 677U1^-1, respectively.     

Nitrogen outputs from fecal and urine deposition of small mammals: implications for nitrogen cycling

The contribution of small mammals to nitrogen cycling could have repercussions for the producer community in the maintaining or perhaps magnifying of nitrogen availability. Our objective was to model nitrogen outputs (deposition of feces and urine) of small mammals in an old-field ecosystem and estimate the amount of fecal and urinary nitrogen deposited annually. To address this objective, we used models from laboratory studies and combined these with data from field studies to estimate dietary nitrogen and monthly and annual nitrogen outputs from fecal and urine deposition of five rodent species. The models accounted for monthly fluctuations in density and biomass of small-mammal populations. We estimated that the minimal amount of nitrogen deposited by rodents was 1.0 (0.9–1.1) and 2.7 (2.6–2.9) kg Nha⁻¹ year⁻¹ from feces and urine, respectively, for a total contribution of 3.7 (3.5–4.0) kg Nha⁻¹ year⁻¹. Hispid cotton rats (Sigmodon hispidus) accounted for >75% of the total nitrogen output by small mammals. Our estimates of annual fecal and urinary nitrogen deposited by rodents were comparable to nitrogen deposits by larger herbivores and other nitrogen fluxes in grassland ecosystems and should be considered when assessing the potential effects of herbivory on terrestrial nitrogen cycles.     

Translocation of 15N indicates nitrogen recycling in the mat-forming lichen Cladonia portentosa

Nitrogen translocation was measured in Cladonia portentosa during 2 yr growth in Scottish heathland. Translocation was predicted to occur if N is resorbed from senescent basal tissue and recycled within the thallus. (15)N was introduced into either the lower (TU thalli) or upper (TD thalli) 25 mm of 50-mm-long thalli as (15)N-NH(4) (+), (15)N-NO(3) (-) or (15)N-glycine. Labelled thalli were placed within intact lichen cushions, either upright (TU) or inverted (TD). Vertical distribution of label was quantified immediately following labelling and after 1 and 2 yr. Independently of the form of introduced label, (15)N migrated upwards in TU thalli, with new growth being a strong sink. Sink regions for (15)N during year 1 (including new growth) became sources of (15)N translocated to new growth in year 2. Upward migration into inverted bases was minimal in TD thalli, but was again marked in new growth that developed from inverted apices. Relocation of N to regions of growth could facilitate internal N recycling, a process postulated to explain the ecological success of mat-forming lichens.     

Characterization of transgenic poplar with ectopic expression of pine cytosolic glutamine synthetase under conditions of varying nitrogen availability

The present study addresses the hypothesis that enhanced expression of glutamine synthetase (GS) in transgenic poplar, characterized by the ectopic expression of pine cytosolic GS, results in an enhanced efficiency of nitrogen (N) assimilation and enhanced growth. Transgenic and control poplar were supplied with low and high N levels and the role of ectopic expression of the pine GS in growth and N assimilation was assessed by using amino acid analysis, (15)N enrichment, biochemical analyses, and growth measurements. While leaves of transgenic poplar contained 85% less (P < 0.01) free ammonium than leaves of nontransgenic control plants, leaves of transgenics showed increases in the levels of free glutamine and total free amino acids. Transgenic poplar lines also displayed significant increases in growth parameters when compared with controls grown under both low (0.3 mm) and high (10 mm) nitrate conditions. Furthermore, (15)N-enrichment experiments showed that 27% more (P < 0.05) (15)N was incorporated into structural compounds in transgenic lines than in nontransgenic controls. Using the methods described here, we present direct evidence for increased N assimilation efficiency and growth in GS transgenic lines.     

Growth and biomass of mycorrhizal mycelia in coniferous forests along short natural nutrient gradients

Hybridization may lead to unique phytochemical expression in plant individuals. Hybrids may express novel combinations or extreme concentrations of secondary metabolites or, in some cases, produce metabolites novel to both parental species. Here we test whether there is evidence for extreme metabolite expression or novelty in F1 hybrids between Senecio aquaticus and Senecio jacobaea. Hybridization is thought to occur frequently within Senecio, and hybridization might facilitate secondary metabolite diversification within this genus. Parental species express different quantities of several classes of compounds known to be involved in antiherbivore defence, including pyrrolizidine alkaloids, chlorogenic acid, flavonoids and benzoquinoids. Hybrids demonstrate differential expression of some metabolites, producing lower concentrations of amino acids, and perhaps flavonoids, than either parental species. Despite evidence for quantitative hybrid novelty in this system, NMR profiling did not detect any novel compounds among the plant groups studied. Metabolomic profiling is a useful technique for identifying qualitative changes in major metabolites according to plant species and/or genotype, but is less useful for identifying small differences between plant groups, or differences in compounds expressed in low concentrations.     

Decline of acid-sensitive plant species in heathland can be attributed to ammonium toxicity in combination with low pH

The effects of increasing ammonium concentrations in combination with different pH levels were studied on five heathland plant species to determine whether their occurrence and decline could be attributed to ammonium toxicity and/or pH levels. Plants were grown in growth media amended with four different ammonium concentrations (10, 100, 500 and 1000 micromol l(-1)) and two pH levels resembling acidified (pH 3.5 or 4) and weakly buffered (pH 5 or 5.5) situations. Survival of Antennaria dioica and Succisa pratensis was reduced by low pH in combination with high ammonium concentrations. Biomass decreased with increased ammonium concentrations and decreasing pH levels. Internal pH of the plants decreased with increasing ammonium concentrations. Survival of Calluna vulgaris, Deschampsia flexuosa and Gentiana pneumonanthe was not affected by ammonium. Moreover, biomass increased with increasing ammonium concentrations. Biomass production of G. pneumonanthe reduced at low pH levels. A decline of acid-sensitive species in heathlands was attributed to ammonium toxicity effects in combination with a low pH.