The effect of area on local and regional elevational patterns of species richness

Aim To calculate the degree to which differences between local and regional elevational species richness patterns can be accounted for by the effects of regional area. Location Five elevational transects in Costa Rica, Ecuador, La Réunion, Mexico and Tanzania. Methods We sampled ferns in standardized field plots and collated regional species lists based on herbarium and literature data. We then used the Arrhenius function S = cA^z to correct regional species richness (S) for the effect of area (A) using three slightly different approaches, and compared the concordance of local and regional patterns prior to and after accounting for the effect of area on regional richness using linear regression analyses. Results We found a better concordance between local and regional elevational species richness after including the effect of area in the majority of cases. In several cases, local and regional patterns are very similar after accounting for area. In most of the cases, the maximum regional richness shifted to a higher elevation after accounting for area. Different approaches to correct for area resulted in qualitatively similar results. Main conclusions The differences between local and regional elevational richness patterns can at least partly be accounted for by area effects, suggesting that the underlying causes of elevational richness patterns might be the same at both spatial scales. Values used to account for the effect of area differ among the different study locations, showing that there is no generally applicable elevational species–area relationship.     

Distinguishing positive selection from neutral evolution: boosting the performance of summary statistics

Summary statistics are widely used in population genetics, but they suffer from the drawback that no simple sufficient summary statistic exists, which captures all information required to distinguish different evolutionary hypotheses. Here, we apply boosting, a recent statistical method that combines simple classification rules to maximize their joint predictive performance. We show that our implementation of boosting has a high power to detect selective sweeps. Demographic events, such as bottlenecks, do not result in a large excess of false positives. A comparison to other neutrality tests shows that our boosting implementation performs well compared to other neutrality tests. Furthermore, we evaluated the relative contribution of different summary statistics to the identification of selection and found that for recent sweeps integrated haplotype homozygosity is very informative whereas older sweeps are better detected by Tajima's π. Overall, Watterson's was found to contribute the most information for distinguishing between bottlenecks and selection.     

Proteomics of corynebacteria: From biotechnology workhorses to pathogens

Corynebacteria belong to the high G+C Gram-positive bacteria (Actinobacteria) and are closely related to Mycobacterium and Nocardia species. The best investigated member of this group of almost seventy species is Corynebacterium glutamicum, a soil bacterium isolated in 1957, which is used for the industrial production of more than two million tons of amino acids per year. This review focuses on the technical advances made in proteomics approaches during the last years and summarizes applications of these techniques with respect to C. glutamicum metabolic pathways and stress response. Additionally, selected proteome applications for other biotechnologically important or pathogenic corynebacteria are described.     

High-Flux Hemodialysis and High-Volume Hemodiafiltration Improve Serum Calcification Propensity

BackgroundCalciprotein particles (CPPs) may play an important role in the calcification process. The calcification propensity of serum (T₅₀) is highly predictive of all-cause mortality in chronic kidney disease patients. Whether T₅₀ is therapeutically improvable, by high-flux hemodialysis (HD) or hemodiafiltration (HDF), has not been studied yet.MethodsWe designed a cross-sectional single center study, and included stable prevalent in-center dialysis patients on HD or HDF. Patients were divided into two groups based on dialysis modality, were on a thrice-weekly schedule, had a dialysis vintage of > 3 months and vascular access providing a blood flow rate > 300 ml/min. Calcification propensity of serum was measured by the time of transformation from primary to secondary CPP (T₅₀ test), by time-resolved nephelometry.ResultsWe included 64 patients, mean convective volume was 21.7L (SD 3.3L). In the pooled analysis, T₅₀ levels increased in both the HD and HDF group with pre- and post-dialysis (mean (SD)) of 244(64) - 301(57) and 253(55) - 304(61) min respectively (P = 0.43(HD vs. HDF)). The mean increase in T₅₀ was 26.29% for HD and 21.97% for HDF patients (P = 0.61 (HD vs. HDF)). The delta values (Δ) of calcium, phosphate and serum albumin were equal in both groups. Baseline T₅₀ was negatively correlated with phosphate, and positively correlated with serum magnesium and fetuin-A. The ΔT₅₀ was mostly influenced by Δ phosphate (r = -0.342; P = 0.002 HD and r = -0.396; P<0.001 HDF) in both groups.ConclusionsHD and HDF patients present with same baseline T50 calcification propensity values pre-dialysis. Calcification propensity is significantly improved during both HD and HDF sessions without significant differences between both modalities.     

Implementation and Evaluation of a Fully Automated Multiplex Real-Time PCR Assay on the BD Max Platform to Detect and Differentiate Herpesviridae from Cerebrospinal Fluids

A fully automated multiplex real-time PCR assay—including a sample process control and a plasmid based positive control—for the detection and differentiation of herpes simplex virus 1 (HSV1), herpes simplex virus 2 (HSV2) and varicella-zoster virus (VZV) from cerebrospinal fluids (CSF) was developed on the BD Max platform. Performance was compared to an established accredited multiplex real time PCR protocol utilizing the easyMAG and the LightCycler 480/II, both very common devices in viral molecular diagnostics. For clinical validation, 123 CSF specimens and 40 reference samples from national interlaboratory comparisons were examined with both methods, resulting in 97.6% and 100% concordance for CSF and reference samples, respectively. Utilizing the BD Max platform revealed sensitivities of 173 (CI 95%, 88–258) copies/ml for HSV1, 171 (CI 95%, 148–194) copies/ml for HSV2 and 84 (CI 95%, 5–163) copies/ml for VZV. Cross reactivity could be excluded by checking 25 common viral, bacterial and fungal human pathogens. Workflow analyses displayed shorter test duration as well as remarkable fewer and easier preparation steps with the potential to reduce error rates occurring when manually assessing patient samples. This protocol allows for a fully automated PCR assay on the BD Max platform for the simultaneously detection of herpesviridae from CSF specimens. Singular or multiple infections due to HSV1, HSV2 and VZV can reliably be differentiated with good sensitivities. Control parameters are included within the assay, thereby rendering its suitability for current quality management requirements.     

A high‐resolution approach for the spatiotemporal analysis of forest canopy space using terrestrial laser scanning data

Forest canopies and tree crown structures are of high ecological importance. Measuring canopies and crowns by direct inventory methods is time‐consuming and of limited accuracy. High‐resolution inventory tools, in particular terrestrial laser scanning (TLS), is able to overcome these limitations and obtain three‐dimensional (3D) structural information about the canopy with a very high level of detail. The main objective of this study was to introduce a novel method to analyze spatiotemporal dynamics in canopy occupancy at the individual tree and local neighborhood level using high‐resolution 3D TLS data. For the analyses, a voxel grid approach was applied. The tree crowns were modeled through the combination of two approaches: the encasement of all crown points with a 3D α‐shape, which was then converted into a voxel grid, and the direct voxelization of the crown points. We show that canopy occupancy at individual tree level can be quantified as the crown volume occupied only by the respective tree or shared with neighboring trees. At the local neighborhood level, our method enables the precise determination of the extent of canopy space filling, the identification of tree–tree interactions, and the analysis of complementary space use. Using multitemporal TLS data recordings, this method allows the precise detection and quantification of changes in canopy occupancy through time. The method is applicable to a wide range of investigations in forest ecology research, including the study of tree diversity effects on forest productivity or growing space analyses for optimal tree growth. Due to the high accuracy of this novel method, it facilitates the precise analyses even of highly plastic individual tree crowns and, thus, the realistic representation of forest canopies. Moreover, our voxel grid framework is flexible enough to allow for the inclusion of further biotic and abiotic variables relevant to complex analyses of forest canopy dynamics.     

Synthetic circuits reveal how mechanisms of gene regulatory networks constrain evolution

Phenotypic variation is the raw material of adaptive Darwinian evolution. The phenotypic variation found in organismal development is biased towards certain phenotypes, but the molecular mechanisms behind such biases are still poorly understood. Gene regulatory networks have been proposed as one cause of constrained phenotypic variation. However, most pertinent evidence is theoretical rather than experimental. Here, we study evolutionary biases in two synthetic gene regulatory circuits expressed in Escherichia coli that produce a gene expression stripe—a pivotal pattern in embryonic development. The two parental circuits produce the same phenotype, but create it through different regulatory mechanisms. We show that mutations cause distinct novel phenotypes in the two networks and use a combination of experimental measurements, mathematical modelling and DNA sequencing to understand why mutations bring forth only some but not other novel gene expression phenotypes. Our results reveal that the regulatory mechanisms of networks restrict the possible phenotypic variation upon mutation. Consequently, seemingly equivalent networks can indeed be distinct in how they constrain the outcome of further evolution.     

Investigation of the dithiocarbamate-induced coupling of allylidene and carbonyl ligands on a tungsten center

Reaction of the allylidene tungsten complex [W(CPhCHCHMe)Br₂(CO)₂(4-picoline)] (1) with the dithiocarbamates MS₂CNR₂ (a: M=Na, R=Et; b: M=Na, R=Me; c: M=Li, R=Ph) in THF at 50 °C affords the vinylketene tungsten complexes [W(S₂CNR₂)₂(OCCPhCHCHMe)(CO)] (2a–c). At lower temperatures, four reaction intermediates (3–6) may be discerned. Spectroscopic studies indicate that these compounds contain η⁴-allyldithiocarbamate ligands which are generated by addition of dithiocarbamate across the metal-carbon double bond of the allylidene-tungsten unit in 1. The structures of [W(S₂CNEt₂)₂(OCCPhCHCHMe)(CO)] (2a) and of one intermediate, [W(η⁴-Et₂NCS₂CPhCHCHMe)(S₂CNEt₂)(CO)₂] (5a) were elucidated by X-ray crystallography.     

Structural Fold and Binding Sites of the Human Na-Phosphate Cotransporter NaPi-II

Phosphate plays essential biological roles and its plasma level in humans requires tight control to avoid bone loss (insufficiency) or vascular calcification (excess). Intestinal absorption and renal reabsorption of phosphate are mediated by members of the SLC34 family of sodium-coupled transporters (NaPi-IIa,b,c) whose membrane expression is regulated by various hormones, circulating proteins, and phosphate itself. Consequently, NaPi-II proteins are also potentially important pharmaceutical targets for controlling phosphate levels. Their crucial role in P_i homeostasis is underscored by pathologies resulting from naturally occurring SLC34 mutations and SLC34 knockout animals. SLC34 isoforms have been extensively studied with respect to transport mechanism and structure-function relationships; however, the three-dimensional structure is unknown. All SLC34 transporters share a duplicated motif comprising a glutamine followed by a stretch of threonine or serine residues, suggesting the presence of structural repeats as found in other transporter families. Nevertheless, standard bioinformatic approaches fail to clearly identify a suitable template for molecular modeling. Here, we used hydrophobicity profiles and hidden Markov models to define a structural repeat common to all SLC34 isoforms. Similar approaches identify a relationship with the core regions in a crystal structure of Vibrio cholerae Na⁺-dicarboxylate transporter VcINDY, from which we generated a homology model of human NaPi-IIa. The aforementioned SLC34 motifs in each repeat localize to the center of the model, and were predicted to form Na⁺ and P_i coordination sites. Functional relevance of key amino acids was confirmed by biochemical and electrophysiological analysis of expressed, mutated transporters. Moreover, the validity of the predicted architecture is corroborated by extensive published structure-function studies. The model provides key information for elucidating the transport mechanism and predicts candidate substrate binding sites.