Evaluating 50 years of time-series soil radiocarbon data: towards routine calculation of robust C residence times

In 1959, Athol Rafter began a substantial programme of monitoring the flow of ¹⁴C produced by atmospheric thermonuclear tests through New Zealand’s atmosphere, biosphere and soil. By building on the original measurements through ongoing sampling, a database of over 500 soil radiocarbon measurements spanning 50 years has now been compiled. The datasets, including an 11-point time series, allow strong focus on the robust quantification of residence times ranging from years to decades. We describe key aspects of the dataset, including the ability to identify critical assumptions inherent in calculating soil C residence times. The 3 most critical assumptions relate to: (1) the proportion of old C (“fraction passive”), (2) the lag time between photosynthesis and C entering the modeled pool, and (3) changes in the rates of C input (i.e., steady state). We demonstrate the ability to compare residence times in contrasting sites, such Andisols and non-Andisols, and the ability to calculate residence times across a range of soil depths. We use ¹⁴C in a two-box model to quantify soil carbon turnover parameters in deforested dairy pastures under similar climate in the Tokomaru silt loam (non-Andisol) versus the Egmont black loam (Andisol), originally sampled in 1962, 1965 and 1969, and resampled again in 2008. The ¹⁴C-based residence times of the main soil C pool in surface soil (~8 cm) are ~9 years in the Tokomaru soils compared to ~17 years for the Egmont soils. This difference represents nearly a doubling of soil C residence time, and roughly explains the doubling of the soil C stock. Passive soil C comprises 15% of the soil C pool in Tokomaru soils versus 27% in Egmont soils. A similar difference in residence times is found in a second surface soil comparison between the Bruntwood soil (Andisol) and the Te Kowhai soil (non-Andisol) with residence times of 18 and 27 years, respectively. The comparisons support evidence that C dynamics do differ in Andisols versus non-Andisols, as a result of both the mineral allophane and Al complexation. Expanding our calculations beyond surface soil, we show that thickening the calculation depth by combining horizons allows robust residence times to be calculated at a range of depths. Overall, the large and systematically collected dataset demonstrate that soil C residence times of the main soil C pool can be routinely calculated using ¹⁴C wherever samples collected 10 or more years apart in New Zealand grassland soils are available, and presumably under similar circumstances in other soils worldwide.     

CORRESPONDENCE BETWEEN PHYLOGENY AND MORPHOLOGY OF SNOWELLA SPP. AND WORONICHINIA NAEGELIANA,CYANOBACTERIA COMMONLY OCCURRING IN LAKES1

In this study, the first reported isolates of the genera Snowella and Woronichinia were characterized by 16S rRNA gene sequencing and morphological analysis. Phylogenetic studies and sequences for these genera were not available previously. By botanical criteria, the five isolated strains were identified as Snowella litoralis (Häyrén) Komárek et Hindák Snowella rosea (Snow) Elenkin and Woronichinia naegeliana (Unger) Elenkin. This study underlines the identification of freshly isolated cultures, since the Snowella strains lost the colony structure and were not identifiable after extended laboratory cultivation. In the 16S rRNA gene analysis, the Snowella strains formed a monophyletic cluster, which was most closely related to the Woronichinia strain. Thus, our results show that the morphology of the genera Snowella and Woronichinia was in congruence with their phylogeny, and their phylogeny seems to support the traditional botanical classification of these genera. Furthermore, the genera Snowella and Woronichinia occurred commonly and might occasionally be the most abundant cyanobacterial taxa in mainly oligotrophic and mesotrophic Finnish lakes. Woronichinia occurred frequently and also formed blooms in eutrophic Czech reservoirs.     

Fluorescent ligands for adenosine receptors

Interest is increasing in developing fluorescent ligands for characterization of adenosine receptors (ARs), which hold a promise of usefulness in the drug discovery process. The size of a strategically labeled AR ligand can be greatly increased after the attachment of a fluorophore. The choice of dye moiety (e.g. Alexa Fluor 488), attachment point and linker length can alter the selectivity and potency of the parent molecule. Fluorescent derivatives of adenosine agonists and antagonists (e.g. XAC and other heterocyclic antagonist scaffolds) have been synthesized and characterized pharmacologically. Some are useful AR probes for flow cytometry, fluorescence correlation spectroscopy, fluorescence microscopy, fluorescence polarization, fluorescence resonance energy transfer, and scanning confocal microscopy. Thus, the approach of fluorescent labeled GPCR ligands, including those for ARs, is a growing dynamic research field.     

Long-term decrease in VLA-4 expression and functional impairment of dendritic cells during natalizumab therapy in patients with multiple sclerosis

Myeloid and plasmacytoid dendritic cells (mDCs, pDCs) are central to the initiation and the regulation of immune processes in multiple sclerosis (MS). Natalizumab (NTZ) is a humanized monoclonal antibody approved for the treatment of MS that acts by blocking expression of VLA-4 integrins on the surface of leukocytes. We determined the proportions of circulating DC subsets and analyzed expression of VLA-4 expression in 6 relapsing-remitting MS patients treated with NTZ for 1 year. VLA-4 expression levels on pDCs and mDCs decreased significantly during follow-up. In vitro coculture of peripheral blood mononuclear cells and pDCs, with different doses of NTZ in healthy controls (HC) and MS patients showed dose-dependent down-regulation of VLA-4 expression levels in both MS patients and HC, and reduced functional ability to stimulate antigen-specific T-lymphocyte responses. The biological impact of NTZ may in part be attributable to inhibition of transmigration of circulating DCs into the central nervous system, but also to functional impairment of interactions between T cells and DC.     

The stochastic logistic model with correlated carrying capacities reproduces beta-diversity metrics of microbial communities

The large taxonomic variability of microbial community composition is a consequence of the combination of environmental variability, mediated through ecological interactions, and stochasticity. Most of the analysis aiming to infer the biological factors determining this difference in community structure start by quantifying how much communities are similar in their composition, trough beta-diversity metrics. The central role that these metrics play in microbial ecology does not parallel with a quantitative understanding of their relationships and statistical properties. In particular, we lack a framework that reproduces the empirical statistical properties of beta-diversity metrics. Here we take a macroecological approach and introduce a model to reproduce the statistical properties of community similarity. The model is based on the statistical properties of individual communities and on a single tunable parameter, the correlation of species’ carrying capacities across communities, which sets the difference of two communities. The model reproduces quantitatively the empirical values of several commonly-used beta-diversity metrics, as well as the relationships between them. In particular, this modeling framework naturally reproduces the negative correlation between overlap and dissimilarity, which has been observed in both empirical and experimental communities and previously related to the existence of universal features of community dynamics. In this framework, such correlation naturally emerges due to the effect of random sampling.     

The ontogeny of the olfactory system in ceratophryid frogs (Anura,Ceratophryidae)

The aquatic‐to‐terrestrial shift in the life cycle of most anurans suggests that the differences between the larval and adult morphology of the nose are required for sensory function in two media with different physical characteristics. However, a better controlled test of specialization to medium is to compare adult stages of terrestrial frogs with those that remain fully aquatic as adults. The Ceratophryidae is a monophyletic group of neotropical frogs whose diversification from a common terrestrial ancestor gave rise to both terrestrial (Ceratophrys, Chacophrys) and aquatic (Lepidobatrachus) adults. So, ceratophryids represent an excellent model to analyze the morphology and possible changes related to a secondary aquatic life. We describe the histomorphology of the nose during the ontogeny of the Ceratophryidae, paying particular attention to the condition in adult stages of the recessus olfactorius (a small area of olfactory epithelium that appears to be used for aquatic olfaction) and the eminentia olfactoria (a raised ridge on the floor of the principal cavity correlated with terrestrial olfaction). The species examined (Ceratophrys cranwelli, Chacophrys pierottii, Lepidobatrachus laevis, and L. llanensis) share a common larval olfactory organ composed by the principal cavity, the vomeronasal organ and the lateral appendix. At postmetamorphic stages, ceratophryids present a common morphology of the nose with the principal, middle, and inferior cavities with characteristics similar to other neobatrachians at the end of metamorphosis. However, in advanced adult stages, Lepidobatrachus laevis presents a recessus olfactorius with a heightened (peramorphic) development and a rudimentary (paedomorphic) eminentia olfactoria. Thus, the adult nose in Lepidobatrachus laevis arises from a common developmental ‘terrestrial’ pathway up to postmetamorphic stages, when its ontogeny leads to a distinctive morphology related to the evolutionarily derived, secondarily aquatic life of adults of this lineage.     

Are capuchin monkeys (Cebus apella) inequity averse?

It has been reported that capuchin monkeys reject a less preferred food (LPF) when they see a partner capuchin receive a more preferred food (PF) for performing the same task. This behaviour was taken as evidence of 'inequity aversion', but an alternative hypothesis is that capuchins reject the LPF because of the mere presence of the PF. We tested this hypothesis in a paradigm, which consisted of presenting two different foods (one PF and one LPF) on a tray and allowing the capuchin to take only the LPF. Refusals to initiate the trial and refusals to take and eat the LPF were higher when the PF was hidden (hiding condition) and when the PF was accumulated in sight but out of reach of the subject (accumulation condition) compared to when two pieces of LPF were placed on the tray (control condition). Interestingly, the subject behaved as in the control condition when its partner was given and ate the PF (partner condition). We argue that capuchins' refusals were due to the frustration of seeing and not obtaining the PF, and that seeing the partner eating increases the LPF acceptance.     

Juvenile hormone catabolism and oviposition in the codling moth, Cydia pomonella, as functions of age, mating status, and hormone treatment.

In vitro catabolism of juvenile hormone (JH) in haemolymph of adult female Cydia pomonella was ascribed mainly to juvenile hormone esterase (JHE) activity. No significant differences were noted between virgin and mated females 0-96 h post-emergence. Changes in JHE activity did not appear dependent upon fluctuations in JH titre; conversely, changes in JHE activity could not explain the changes in JH titres. Maximal JHE activity was recorded at 24 h (331.47 +/- 47.25 pmol/h/microl; 355.93 +/- 36.68 pmol/h/microl, virgin; mated insects, respectively) and preceded the peak in JH titres at 48 h. Topical application of JH II (10 ng-10 microg) or fenoxycarb (50 ng) enhanced JHE activity up to 640 and 56%, respectively. Treatment upon emergence with 10 microg JH II induced enzymic activity for less than 24 h, and when 10 microg JH II or 50 ng fenoxycarb were applied, circulating JH titres returned to control levels within 24 h. Oviposition was highly sensitive to exogenous JH and declined significantly with dosages >100 pg. To allow a degree of oocyte maturation before JH treatment, the hormone was administered at 6, 12, 24, or 48 h post-emergence and/or females were mated. Neither measure "protected" the system; oviposition declined immediately after JH application.     

Effect of hepatocyte growth factor on assembly of zonula occludens-1 protein at the plasma membrane

Hepatocyte growth factor (HGF) is a paracrine cytokine that influences epithelial morphogenesis by modulating cell–cell adhesion and cell polarity. We have examined the role of HGF in the tight junction (TJ) formation. We followed the assembly and disassembly at the plasma membrane of the major component of the TJ, zonula occludens-1 (ZO-1) protein, after HGF treatment. We applied HGF to the basolateral compartment of MDCK cell monolayers grown on transwell filters to analyze the effect of HGF on polarized cells. Confocal laser scanning microscopy showed that HGF caused a marked reduction of ZO-1 at the lateral sites and a concomitant increase in the cytoplasm. We used the calcium switch assay to analyze the effect of HGF in early TJ development. In MDCK cells cultured in low calcium levels, ZO-1 is distributed intracellularly. The presence of HGF greatly retarded the movement of ZO-1 from the cytosol to the membrane after restoration of normal (1.8 mM) calcium levels for 1.5 and 3 hr. The presence of HGF during the calcium switch caused increased tyrosine phosphorylation of β-catenin. The incubation of MDCK cells with vanadate, a potent tyrosine-specific phosphatase inhibitor, also affected the ZO-1 localization at the plasma membrane during the calcium switch. This was concomitant with increased tyrosine phosphorylation of β-catenin. These results suggest that HGF affects the TJ assembly, and this phenomenon may be important in loosening of intercellular junctions and migration of epithelial cells during HGF-induced morphogenesis. J. Cell. Physiol. 176:465–471, 1998. © 1998 Wiley-Liss, Inc.     

Identification of essential operons with a rhamnose-inducible promoter in Burkholderia cenocepacia

Scanning of bacterial genomes to identify essential genes is of biological interest, for understanding the basic functions required for life, and of practical interest, for the identification of novel targets for new antimicrobial therapies. In particular, the lack of efficacious antimicrobial treatments for infections caused by the Burkholderia cepacia complex is causing high morbidity and mortality of cystic fibrosis patients and of patients with nosocomial infections. Here, we present a method based on delivery of the tightly regulated rhamnose-inducible promoter P(rhaB) for identifying essential genes and operons in Burkholderia cenocepacia. We demonstrate that different levels of gene expression can be achieved by using two vectors that deliver P(rhaB) at two different distances from the site of insertion. One of these vectors places P(rhaB) at the site of transposon insertion, while the other incorporates the enhanced green fluorescent protein gene (e-gfp) downstream from P(rhaB). This system allows us to identify essential genes and operons in B. cenocepacia and provides a new tool for systematically identifying and functionally characterizing essential genes at the genomic level.