Biophysical properties of Saccharomyces cerevisiae and their relationship with HOG pathway activation

Parameterized models of biophysical and mechanical cell properties are important for predictive mathematical modeling of cellular processes. The concepts of turgor, cell wall elasticity, osmotically active volume, and intracellular osmolarity have been investigated for decades, but a consistent rigorous parameterization of these concepts is lacking. Here, we subjected several data sets of minimum volume measurements in yeast obtained after hyper-osmotic shock to a thermodynamic modeling framework. We estimated parameters for several relevant biophysical cell properties and tested alternative hypotheses about these concepts using a model discrimination approach. In accordance with previous reports, we estimated an average initial turgor of 0.6 ± 0.2 MPa and found that turgor becomes negligible at a relative volume of 93.3 ± 6.3% corresponding to an osmotic shock of 0.4 ± 0.2 Osm/l. At high stress levels (4 Osm/l), plasmolysis may occur. We found that the volumetric elastic modulus, a measure of cell wall elasticity, is 14.3 ± 10.4 MPa. Our model discrimination analysis suggests that other thermodynamic quantities affecting the intracellular water potential, for example the matrix potential, can be neglected under physiological conditions. The parameterized turgor models showed that activation of the osmosensing high osmolarity glycerol (HOG) signaling pathway correlates with turgor loss in a 1:1 relationship. This finding suggests that mechanical properties of the membrane trigger HOG pathway activation, which can be represented and quantitatively modeled by turgor.     

Rounding up the usual suspects: a standard target‐gene approach for resolving the interfamilial phylogenetic relationships of ecribellate orb‐weaving spiders with a new family‐rank classification (Araneae,Araneoidea)

We test the limits of the spider superfamily Araneoidea and reconstruct its interfamilial relationships using standard molecular markers. The taxon sample (363 terminals) comprises for the first time representatives of all araneoid families, including the first molecular data of the family Synaphridae. We use the resulting phylogenetic framework to study web evolution in araneoids. Araneoidea is monophyletic and sister to Nicodamoidea rank. n. Orbiculariae are not monophyletic and also include the RTA clade, Oecobiidae and Hersiliidae. Deinopoidea is paraphyletic with respect to a lineage that includes the RTA clade, Hersiliidae and Oecobiidae. The cribellate orb‐weaving family Uloboridae is monophyletic and is sister group to a lineage that includes the RTA Clade, Hersiliidae and Oecobiidae. The monophyly of most Araneoidea families is well supported, with a few exceptions. Anapidae includes holarchaeids but the family remains diphyletic even if Holarchaea is considered an anapid. The orb‐web is ancient, having evolved by the early Jurassic; a single origin of the orb with multiple “losses” is implied by our analyses. By the late Jurassic, the orb‐web had already been transformed into different architectures, but the ancestors of the RTA clade probably built orb‐webs. We also find further support for a single origin of the cribellum and multiple independent losses. The following taxonomic and nomenclatural changes are proposed: the cribellate and ecribellate nicodamids are grouped in the superfamily Nicodamoidea rank n. (Megadictynidae rank res. and Nicodamidae stat. n. ). Araneoidea includes 17 families with the following changes: Araneidae is re‐circumscribed to include nephilines , Nephilinae rank res., Arkyidae rank n. , Physoglenidae rank n. , Synotaxidae is limited to the genus Synotaxus, Pararchaeidae is a junior synonym of Malkaridae ( syn. n. ), Holarchaeidae of Anapidae ( syn. n. ) and Sinopimoidae of Linyphiidae ( syn. n. ).     

Diffusional conductances to CO2 as a target for increasing photosynthesis and photosynthetic water-use efficiency

A key objective for sustainable agriculture and forestry is to breed plants with both high carbon gain and water-use efficiency (WUE). At the level of leaf physiology, this implies increasing net photosynthesis (A _N) relative to stomatal conductance (g _s). Here, we review evidence for CO₂ diffusional constraints on photosynthesis and WUE. Analyzing past observations for an extensive pool of crop and wild plant species that vary widely in mesophyll conductance to CO₂ (g _m), g _s, and foliage A _N, it was shown that both g _s and g _m limit A _N, although the relative importance of each of the two conductances depends on species and conditions. Based on Fick’s law of diffusion, intrinsic WUE (the ratio A _N/g _s) should correlate on the ratio g _m/g _s, and not g _m itself. Such a correlation is indeed often observed in the data. However, since besides diffusion A _N also depends on photosynthetic capacity (i.e., V _c,max), this relationship is not always sustained. It was shown that only in a very few cases, genotype selection has resulted in simultaneous increases of both A _N and WUE. In fact, such a response has never been observed in genetically modified plants specifically engineered for either reduced g _s or enhanced g _m. Although increasing g _m alone would result in increasing photosynthesis, and potentially increasing WUE, in practice, higher WUE seems to be only achieved when there are no parallel changes in g _s. We conclude that for simultaneous improvement of A _N and WUE, genetic manipulation of g _m should avoid parallel changes in g _s, and we suggest that the appropriate trait for selection for enhanced WUE is increased g _m/g _s.     

The influence of the O-antigen and the capsular polysaccharide on the establishment of PlCmts lysogeny in Klebsiella pneumoniae

The O-antigen of the lipopolysaccharide in Klebsiella pneumoniae caused a significant reduction in the frequency of establishment of PlCmts lysogeny, while the capsular polysaccharide showed no effect on this frequency. The bacterial receptor for PlCmts are the lipopolysaccharide-core oligosaccharides, the results suggest that K. pneumoniae strains with an O-antigen in their lipopolysaccharide have a poorly accessible lipopolysaccharide-core (the PlCmts bacterial receptor), while K. pneumoniae strains lacking the O-antigen have a highly accessible lipopolysaccharide-core. The accessibility of the receptor is independent of the K antigen (capsular polysaccharide).     

Distinguishing dung from blue, red and yellow-backed duikers through noninvasive genetic techniques

Dung counts have been widely used to estimate duiker abundance and densities in tropical African forests. However, one of the major limitations of this method is that species' identification of dung based on morphological characteristics is extremely difficult in most cases. Some authors made the assumption that dung pellets could at least be distinguishable between the blue duiker, the red duikers and the yellow-backed duiker. However, this study is the first attempt to test the reliability of field identification. In this study, we suggest a method based on a noninvasive genetic protocol to identify duiker species. The comparison of field and genetic identifications shows that only dung from Cephalophus silvicultor was identified in the field without error. The rate of error for red duikers and the blue duiker is high and any attempt to distinguish among those species will result in wrong estimations for each species. We recommend the use of DNA tests to ensure reliable species' identification when duiker censuses based on dung counts are used. This methodological input will probably strengthen the dung count technique and increase its reliability for duiker species abundance estimations and spatial distribution studies.     

Predicting rat presence on small islands

We analyzed data on presence or absence of 156 vascular plant species on 14 islets of the Cabrera National Park archipelago and found a significant correlation between rat presence and floristic composition. By contrast, island area, island height, and storm exposition seem to have no effect on species composition. We chose a subset of plants favoured or depressed by rat presence for a non-linear principal component analysis and evaluated successfully the usefulness of such a subset in predicting rat presence using a randomization method. To optimally allocate resources, rat eradication campaigns should be focused in islets displaying rat-free vegetation type.     

Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi

Oxidative phosphorylation is among the most conserved mitochondrial pathways. However, one of the cornerstones of this pathway, the multi-protein complex NADH : ubiquinone oxidoreductase (complex I) has been lost multiple independent times in diverse eukaryotic lineages. The causes and consequences of these convergent losses remain poorly understood. Here, we used a comparative genomics approach to reconstruct evolutionary paths leading to complex I loss and infer possible evolutionary scenarios. By mining available mitochondrial and nuclear genomes, we identified eight independent events of mitochondrial complex I loss across eukaryotes, of which six occurred in fungal lineages. We focused on three recent loss events that affect closely related fungal species, and inferred genomic changes convergently associated with complex I loss. Based on these results, we predict novel complex I functional partners and relate the loss of complex I with the presence of increased mitochondrial antioxidants, higher fermentative capabilities, duplications of alternative dehydrogenases, loss of alternative oxidases and adaptation to antifungal compounds. To explain these findings, we hypothesize that a combination of previously acquired compensatory mechanisms and exposure to environmental triggers of oxidative stress (such as hypoxia and/or toxic chemicals) induced complex I loss in fungi.     

Spatial heterogeneity in water velocity drives leaf litter dynamics in streams

1. Stream hydro-morphology refers to the heterogeneous distribution of hydrologic conditions that occur above a complex benthic surface such as a streambed.
2. We hypothesised that hydro-morphological conditions will influence the retention, re-distribution, and microbial-driven decomposition of leaf litter inputs in stream ecosystems because each process varies with overlying water velocity.
3. We tested this hypothesis using: (1) the spatial distribution of water velocity within a stream reach as a surrogate of stream hydro-morphology; (2) leaf tracer (i.e. Ginkgo biloba L.) additions with serial recovery to examine the relationship between benthic retention and overlying velocity; and (3) measurements of leaf litter decomposition (i.e. Alnus glutinosa [L.] Gaertn.) under different water velocity conditions.
4. Results demonstrate that water velocity exerts a significant influence on the retention and re-distribution of leaf litter inputs within the reach. The observed range of water velocity (from c. 0 to 0.92 cm/s) also strongly influences the range of leaf litter decomposition rates (0.0076–0.0222/day).
5. Our findings illustrate that water velocity influences leaf litter dynamics in streams by controlling leaf litter transport, retention and re-distribution as well as how leaves decompose within recipient stream reaches. Ultimately, the results show that the efficiency of leaf litter inputs in supporting stream ecosystem function is dependent on the hydro-morphological characteristics of the receiving stream ecosystems.

     

Patient-specific respiratory models using dynamic 3D MRI: Preliminary volunteer results

Organ and tumour motion has a significant impact on the planning and delivery of radiotherapy treatment. At present imaging modality such as four-dimensional computer tomography (4DCT) cannot be used to measure the variability of motion between different respiratory cycles. To create reliable motion models, one needs to acquire volumetric data sets of the lungs with sufficient sampling of the breathing cycle. In this paper we investigate the use of highly parallel MRI to acquire such data. A 32 channel coil in conjunction with a balanced SSFP sequence and a SENSE factor of 6 were used to acquire volumetric data sets in five healthy volunteers. The acquisition was repeated for seven series of different breathing patterns. The data acquired was of sufficient spatial resolution (5 × 5 × 5 mm³) and image quality to carry out automated non-rigid registration. The acquisition rate (c.a. 2 volumes per second) allowed for a meaningful sampling of the different respiratory curves that were automatically obtained from the skin surface motion. This acquisition technique should provide images of high enough quality to create statistical respiratory models.