Walter’s two-layer hypothesis revisited: back to the roots!

Walter (Jahrb Wiss Bot 87:750–860, 1939) proposed a two-layer hypothesis, an equilibrium explanation for coexistence of savanna trees and grasses. This hypothesis relies on vertical niche partitioning and assumed that grasses are more water-use efficient than trees and use subsurface water while trees also have access to deeper water sources. Thus, in open savannas, grasses were predicted to predominate because of their water use efficiency and access to subsurface water. This hypothesis has been a prominent part of the savanna literature since first proposed. We review the literature on Walter’s hypothesis and reconsider his original intentions. Walter intended this hypothesis to be restricted to dry savannas. In his opinion, mesic and humid savannas were controlled by biotic factors and disturbances. We surveyed the global savanna literature for records of vertical niche partitioning by grasses and trees. We find that, within the scope of Walter’s original intentions, this hypothesis works remarkably well, and in some cases is appropriate for deserts as well as for dry temperate systems and even some mesic savannas.     

The relationship of nucleotide polymorphism, recombination rate and selection in wild tomato species

We analyzed the effects of mating system and recombination rate on single nucleotide polymorphisms using 14 single-copy nuclear loci from single populations of five species of wild tomatoes (Solanum section Lycopersicon). The taxa investigated comprise two self-compatible (SC) and three self-incompatible (SI) species. The observed reduction in nucleotide diversity in the SC populations compared to the SI populations is much stronger than expected under the neutral effects of the mating system on effective population size. Importantly, outgroup sequences available for 11 of the 14 loci yield strong positive correlations between silent nucleotide diversity and silent divergence, indicative of marked among-locus differences in mutation rates and/or selective constraints. Furthermore, using a physical estimate of local recombination rates, we find that silent nucleotide diversity (but not divergence) is positively correlated with recombination rate in two of the SI species. However, this correlation is not nearly as strong as in other well-characterized species (in particular, Drosophila). We propose that nucleotide diversity in Lycopersicon is dominated mainly by differences in neutral mutation rates and/or selective constraints among loci, demographic processes (such as population subdivision), and background selection. In addition, we hypothesize that the soil seed bank plays an important role in the maintenance of the large genetic diversity in the SI species (in particular L. peruvianum).     

A simple method for predicting the functional differentiation of duplicate genes and its application to MIKC-type MADS-box genes

A simple statistical method for predicting the functional differentiation of duplicate genes was developed. This method is based on the premise that the extent of functional differentiation between duplicate genes is reflected in the difference in evolutionary rate because the functional change of genes is often caused by relaxation or intensification of functional constraints. With this idea in mind, we developed a window analysis of protein sequences to identify the protein regions in which the significant rate difference exists. We applied this method to MIKC-type MADS-box proteins that control flower development in plants. We examined 23 pairs of sequences of floral MADS-box proteins from petunia and found that the rate differences for 14 pairs are significant. The significant rate differences were observed mostly in the K domain, which is important for dimerization between MADS-box proteins. These results indicate that our statistical method may be useful for predicting protein regions that are likely to be functionally differentiated. These regions may be chosen for further experimental studies.     

Role of glomerular proteoglycans in IgA nephropathy

Mesangial matrix expansion is a prominent feature of the most common form of glomerulonephritis, IgA nephropathy (IgAN). To find molecular markers and improve the understanding of the disease, the gene and protein expression of proteoglycans were investigated in biopsies from IgAN patients and correlated to clinical and morphological data. We collected and microdissected renal biopsies from IgAN patients (n = 19) and from healthy kidney donors (n = 14). Patients were followed for an average time of 4 years and blood pressure was according to target guidelines. Distinct patterns of gene expression were seen in glomerular and tubulo-interstitial cells. Three of the proteoglycans investigated were found to be of special interest and upregulated in glomeruli: perlecan, decorin and biglycan. Perlecan gene expression negatively correlated to albumin excretion and progress of the disease. Abundant decorin protein expression was found in sclerotic glomeruli, but not in unaffected glomeruli from IgAN patients or in controls. Transforming growth factor beta (TGF-β), known to interact with perlecan, decorin and biglycan, were upregulated both on gene and protein level in the glomeruli. This study provides further insight into the molecular mechanisms involved in mesangial matrix expansion in IgAN. We conclude that perlecan is a possible prognostic marker for patients with IgAN. In addition, the up-regulation of biglycan and decorin, as well as TGF-β itself, indicate that regulation of TGF-β, and other profibrotic markers plays a role in IgAN pathology.     

Facing multiple enemies: parasitised hosts respond to predator kairomones

During their lifetime most organisms are exposed to various enemies influencing their victims in multiple direct and indirect ways. Most studies concentrate on the effects of one enemy at a time, thereby not taking into account that in nature organisms are often simultaneously exposed to more than one enemy. We conducted a life-history experiment to investigate the simultaneous effects of predators (fish, Leuciscus idus) and parasites (microparasite, Caullerya mesnili) on their victim (Daphnia galeata). D. galeata were exposed to predator kairomones, parasites or both. D. galeata are able to sense the presence of fish predators via chemical cues (= kairomones). Both fish predator kairomones and microparasite infections influence the life history of Daphnia. Some of the effects of fish predator kairomones are directly opposed to microparasite effects; fecundity, for example, is increased in the presence of fish kairomones and decreased in Daphnia parasitised with C. mesnili. We investigated the influence of both threats on age at maturity, body size at different adult instars, fecundity and survival of one D. galeata clone. In the presence of fish kairomones, all D. galeata matured significantly earlier and increased the number of eggs in the second brood significantly. Parasitised D. galeata matured significantly earlier than non-parasitised ones in the absence and presence of fish kairomones. An infection with the microparasite C. mesnili led to significantly lower clutch sizes at the second adult instar, to significantly smaller body sizes from adult instar three onwards and to significantly reduced survival. No significant interaction effect between the responses to fish presence and to parasite infection was found for any of the investigated life-history traits. The lack of interaction effects between the exposure to predator kairomones and parasite infection was most likely due to the different timing of the effects. Fish kairomones affected D. galeata early in its life history whereas C. mesnili increased in its effects over time. Our results show that parasitised D. galeata are able to exhibit life-history responses to fish predator presence early in their lives. Thus, D. galeata parasitised with C. mesnili have a similar chance as non-parasitised D. galeata to escape from fish predation via life-history changes. Since older parasitised D. galeata are smaller, they may have an even better chance to escape visual predators under actual predation.     

Fine Mapping the Spatial Distribution and Concentration of Unlabeled Drugs within Tissue Micro-Compartments Using Imaging Mass Spectrometry

Readouts that define the physiological distributions of drugs in tissues are an unmet challenge and at best imprecise, but are needed in order to understand both the pharmacokinetic and pharmacodynamic properties associated with efficacy. Here we demonstrate that it is feasible to follow the in vivo transport of unlabeled drugs within specific organ and tissue compartments on a platform that applies MALDI imaging mass spectrometry to tissue sections characterized with high definition histology. We have tracked and quantified the distribution of an inhaled reference compound, tiotropium, within the lungs of dosed rats, using systematic point by point MS and MS/MS sampling at 200 µm intervals. By comparing drug ion distribution patterns in adjacent tissue sections, we observed that within 15 min following exposure, tiotropium parent MS ions (mass-to-charge; m/z 392.1) and fragmented daughter MS/MS ions (m/z 170.1 and 152.1) were dispersed in a concentration gradient (80 fmol-5 pmol) away from the central airways into the lung parenchyma and pleura. These drug levels agreed well with amounts detected in lung compartments by chemical extraction. Moreover, the simultaneous global definition of molecular ion signatures localized within 2-D tissue space provides accurate assignment of ion identities within histological landmarks, providing context to dynamic biological processes occurring at sites of drug presence. Our results highlight an important emerging technology allowing specific high resolution identification of unlabeled drugs at sites of in vivo uptake and retention.     

Does nitrogen transfer between plants confound 15N-based quantifications of N2 fixation?

Background and aims

Transfer of fixed N from legumes to non-legume reference plants may alter the ¹⁵N signature of the reference plant as compared to the soil N available to the legume. This study investigates how N transfer influences the result of ¹⁵N-based N₂ fixation measurements.

Methods

We labelled either legumes or non-legumes with ¹⁵N and performed detailed analyses of ¹⁵N enrichment in mixed plant communities in the field. The results were used in a conceptual model comparing how different N transfer scenarios influenced the ¹⁵N signatures of legumes and reference plants, and how the resulting N₂ fixation estimate was influenced by using reference plants in pure stand or in mixture with the legume.

Results

Based on isotopic signatures, N transfer was detected in all directions: from legume to legume, from legume to non-legume, from non-legume to legume, from non-legume to non-legume. In the scenario of multidirectional N transfer, N₂ fixation was overestimated by using a reference plant in pure stand.

Conclusions

Fixed N transferred to neighbouring reference plants modifies the ¹⁵N signature of the soil N available both to the reference plant and the N₂-fixing legume. This provides strong support for using reference plants growing in mixture with the legumes for reliable quantifications of N₂ fixation.     

Patterns of molecular genetic variation among cat breeds

Genetic variation in cat breeds was assessed utilizing a panel of short tandem repeat (STR) loci genotyped in 38 cat breeds and 284 single-nucleotide polymorphisms (SNPs) genotyped in 24 breeds. Population structure in cat breeds generally reflects their recent ancestry and absence of strong breed barriers between some breeds. There is a wide range in the robustness of population definition, from breeds demonstrating high definition to breeds with as little as a third of their genetic variation partitioning into a single population. Utilizing the STRUCTURE algorithm, there was no clear demarcation of the number of population subdivisions; 16 breeds could not be resolved into independent populations, the consequence of outcrossing in established breeds to recently developed breeds with common ancestry. These 16 breeds were divided into 6 populations. Ninety-six percent of cats in a sample set of 1040 were correctly assigned to their classified breed or breed group/population. Average breed STR heterozygosities ranged from moderate (0.53; Havana, Korat) to high (0.85; Norwegian Forest Cat, Manx). Most of the variation in cat breeds was observed within a breed population (83.7%), versus 16.3% of the variation observed between populations. The hierarchical relationships of cat breeds is poorly defined as demonstrated by phylogenetic trees generated from both STR and SNP data, though phylogeographic grouping of breeds derived completely or in part from Southeast Asian ancestors was apparent.