A new spineless species of Vella (Brassicaceae) from the high mountains of south-eastern Spain

Vella castrilensis sp. nov. is described from the high mountains of Granada and Jaén provinces (south-eastern Iberian Peninsula), where it grows on calcareous soils. It is a hexaploid (2 n  = 68) spineless dwarf shrub, woody at the base, with oblong-lanceolate, entire to shallowly dentate leaves and fruit with an acute tongue-shaped stylar segment and strongly reticulate-nerved valves. The characteristic unique combination of vegetative, karyological and reproductive features of V. castrilensis is not present in any described taxon of the genus, and warrants recognition at the species rank. Affinities and differences with other related taxa are discussed. Phylogenetic, biogeographical, bioclimatic, ecological data and conservation proposals are also reported.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 149 , 121–128.     

Parallel evolution of genes and languages in the Caucasus region

We analyzed 40 single nucleotide polymorphism and 19 short tandem repeat Y-chromosomal markers in a large sample of 1,525 indigenous individuals from 14 populations in the Caucasus and 254 additional individuals representing potential source populations. We also employed a lexicostatistical approach to reconstruct the history of the languages of the North Caucasian family spoken by the Caucasus populations. We found a different major haplogroup to be prevalent in each of four sets of populations that occupy distinct geographic regions and belong to different linguistic branches. The haplogroup frequencies correlated with geography and, even more strongly, with language. Within haplogroups, a number of haplotype clusters were shown to be specific to individual populations and languages. The data suggested a direct origin of Caucasus male lineages from the Near East, followed by high levels of isolation, differentiation, and genetic drift in situ. Comparison of genetic and linguistic reconstructions covering the last few millennia showed striking correspondences between the topology and dates of the respective gene and language trees and with documented historical events. Overall, in the Caucasus region, unmatched levels of gene-language coevolution occurred within geographically isolated populations, probably due to its mountainous terrain.     

The coexistence of Bosmina and Ceriodaphnia in a south Andes lake

1. The coexistence of Bosmina and Ceriodaphnia was studied in relation to phytoplankton succession in a small lake (Laguna Ezquerra) in the araucanian region of Argentina. 2. The study involved field sampling and single species cultures of each of the two cladocerans in lake water under laboratory conditions. 3. Ceriodaphnia showed a unimodal cycle while Bosmina had a bimodal pattern during 4 months of coexistence. Ceriodaphnia exhibited a direct relationship between clutch size and biovolume of edible algae, whereas Bosmina's fecundity was related to the density of flagellates. 4. We found that the fecundity of these species responded differently to laboratory and field conditions. The fecundity of Ceriodaphnia followed the same pattern in both the field and laboratory, whereas Bosmina showed higher fecundity values in laboratory experiments. 5. Our results are in good agreement with predictions derived from Northern Hemisphere studies, indicating that food-limited populations of daphnids and Bosmina can coexist for extended periods in spatially homogeneous environments. 6. The variation in food availability, measured as biovolume of edible algae, determines the loss of Ceriodaphnia and the persistence of Bosmina.     

Do metacommunity mass effects predict changes in species incidence and abundance?

Metacommunity matrices contain data on species incidence or abundance across sites, compactly portraying community composition and how it varies over sites. We constructed models based on an initial metacommunity matrix of either species incidence or abundance to test whether such data suffice to predict subsequent changes in incidence or abundance at each site. The models reflect both species and site mass effects in using products of the row and column totals to predict the incidence or abundance of each species expected at each site. We tested these models against empirical data on vascular plant incidence and abundance collected from two sets of forested sites in both the 1950s and 2000s. Predictions from these models parallel observed changes in species incidence and abundance in these distinctly different metacommunities and differ greatly from null model predictions. The abundance model shows greater power than the incidence model reflecting its higher information content. Predictions were more accurate for the more diverse forests of southern Wisconsin that are changing quickly in response to succession and fragmentation. Simulations show that these results are robust but sensitive to sampling intensity. Because these models require no data on site conditions or species’ characteristics, they provide a useful baseline to assess more complex models based on species’ functional traits, local site conditions, or landscape context. They may also prove useful to conservation biologists seeking to predict local population declines and extinction risks.     

Staurosporine-induced apoptotic water loss is cell- and attachment-specific

Apoptotic volume decrease (AVD) is a characteristic cell shrinkage observed during apoptosis. There are at least two known processes that may result in the AVD: exit of intracellular water and splitting of cells into smaller fragments. Although AVD has traditionally been attributed to water loss, direct evidence for that is often lacking. In this study, we quantified intracellular water in staurosporine-treated cells using a previously described optical microscopic technique that combines volume measurements with quantitative phase analysis. Water loss was observed in detached HeLa and in adherent MDCK but not in adherent HeLa cells. At the same time, adherent HeLa and adherent MDCK cells exhibited visually similar apoptotic morphology, including fragmentation and activation of caspase-3. Morphological changes and caspase activation were prevented by chloride channel blockers DIDS and NPPB in both adherent and suspended HeLa cells, while potassium channel blocker TEA was ineffective. We conclude that staurosporine-induced dehydration is not a universal cell response but depends on the cell type and substrate attachment and can only be judged by direct water measurements. The effects of potassium or chloride channel blockers do not always correlate with the AVD.     

Relationship between boron and calcium in the N2-fixing legume–rhizobia symbiosis

Because boron (B) and calcium (Ca²⁺) seem to have a strong effect on legume nodulation and nitrogen fixation, rhizobial symbiosis with leguminous plants, grown under varying concentrations of both nutrients, was investigated. The study of early pre‐infection events included the capacity of root exudates to induce nod genes, and the degree of adsorption of bacteria to the root surface. Both phenomena were inhibited by B deficiency, and increased by addition of Ca²⁺, resulting in an increase of the number of nodules. The infection and invasion steps were investigated by fluorescence microscopy in pea nodules harbouring a Rhizobium leguminosarum strain that constitutively expresses green fluorescent protein. High Ca²⁺ enhanced cell and tissue invasion by Rhizobium, which was highly inhibited after B deficiency. This was combined with an increased B concentration in nodules of plants grown on B‐free medium and supplemented with high Ca²⁺ concentrations, and that can be attributed to an increased B import to the nodules. Histological examination of indeterminate (pea) and determinate (bean) nodules showed an altered nodule anatomy at low B content of the tissue. The moderate increase in nodular B due to additional Ca²⁺ was not sufficient to prevent the abnormal cell wall structure and the aberrant distribution of pectin polysaccharides in B‐deficient treatments. Overall results indicate that the development of the symbiosis depends of the concentration of B and Ca²⁺, and that both nutrients are essential for nodule structure and function.     

Dispersal to predator‐free space counterweighs fecundity costs in alate aphid morphs

1. Specialisation in dispersal by alate aphids often imposes constraints on other functions, particularly a reduction in fecundity due to wing development. Short‐distance flight from patches of high population density to uninfested plants may provide temporary predator‐free space, compensating for low fecundity. However, this theoretical prediction has not been explored experimentally. 2. To test this hypothesis, a field cage experiment was conducted in which Aphis glycines populations initiated with controlled proportions of apterous and alate individuals were exposed to predation, while predator‐free space was accessible only through flight. It was predicted that an investment in alate individuals would benefit a population under predation, regardless of associated costs to fecundity. 3. As expected, a strong trade‐off was observed between fecundity and wing development. However, populations initiated with a fixed proportion of alate and apterous individuals showed no reductions in final population size compared with populations initiated with apterous individuals exclusively. Moreover, the initial presence of alate individuals in the populations increased aphid prevalence (i.e. proportion of plants colonised). Similarly, both increased population size and prevalence were observed when predator‐free space was accessible through flight, as opposed to when it was inaccessible. 4. These results show that despite high costs to fecundity, an investment in alate individuals is neither beneficial nor detrimental to population size when predator‐free space is accessible, but increases aphid prevalence. It is concluded that prevalence might provide an ecological advantage important enough to warrant the production of alate morphs under intense predation.     

Modulatory effects of interferon‐γ and interleukin‐4 on cellular immune responses against Hypoderma lineatum antigens

This study investigates the in vitro modulatory effects of interferon‐γ (IFN‐γ) and interleukin‐4 (IL‐4) on both proliferative bovine T cell responses and IL‐10 production induced by different antigens [crude larval extract and the purified fractions hypodermin A, B and C (HyA, HyB, HyC)] obtained from first instars of Hypoderma lineatum (Diptera: Oestridae), alone or in the presence of the mitogen concanavalin A. Incubation with the different parasitic antigens resulted in significant inhibition of T cell proliferation and IL‐10 production, which, in general, did not revert after the addition of IFN‐γ and IL‐4. In the absence of antigens, IL‐4 induced significant inhibition of mitogen‐induced T cell responses. Exogenous IFN‐γ exhibited an inhibitory effect on cell proliferation in the presence of the purified fractions HyB and HyC. These in vitro data suggest that far from neutralizing the effects of larval antigens, the addition of IFN‐γ potentiates their anti‐proliferative activity; by contrast, IL‐4 had no consistent effects on proliferative responses to Hypoderma. IL‐4 provoked an increment of IL‐10 levels in supernatants of HyB‐stimulated cells. In conclusion, exogenous IFN‐γ and IL‐4 were unable to counteract the suppressor effects of H. lineatum antigens.     

NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation

Nested effects models have been used successfully for learning subcellular networks from high-dimensional perturbation effects that result from RNA interference (RNAi) experiments. Here, we further develop the basic nested effects model using high-content single-cell imaging data from RNAi screens of cultured cells infected with human rhinovirus. RNAi screens with single-cell readouts are becoming increasingly common, and they often reveal high cell-to-cell variation. As a consequence of this cellular heterogeneity, knock-downs result in variable effects among cells and lead to weak average phenotypes on the cell population level. To address this confounding factor in network inference, we explicitly model the stimulation status of a signaling pathway in individual cells. We extend the framework of nested effects models to probabilistic combinatorial knock-downs and propose NEMix, a nested effects mixture model that accounts for unobserved pathway activation. We analyzed the identifiability of NEMix and developed a parameter inference scheme based on the Expectation Maximization algorithm. In an extensive simulation study, we show that NEMix improves learning of pathway structures over classical NEMs significantly in the presence of hidden pathway stimulation. We applied our model to single-cell imaging data from RNAi screens monitoring human rhinovirus infection, where limited infection efficiency of the assay results in uncertain pathway stimulation. Using a subset of genes with known interactions, we show that the inferred NEMix network has high accuracy and outperforms the classical nested effects model without hidden pathway activity. NEMix is implemented as part of the R/Bioconductor package ‘nem’ and available at www.cbg.ethz.ch/software/NEMix.