Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses

Because biological processes can result in different loci having different evolutionary histories, species tree estimation requires multiple loci from across multiple genomes. While many processes can result in discord between gene trees and species trees, incomplete lineage sorting (ILS), modeled by the multi-species coalescent, is considered to be a dominant cause for gene tree heterogeneity. Coalescent-based methods have been developed to estimate species trees, many of which operate by combining estimated gene trees, and so are called "summary methods". Because summary methods are generally fast (and much faster than more complicated coalescent-based methods that co-estimate gene trees and species trees), they have become very popular techniques for estimating species trees from multiple loci. However, recent studies have established that summary methods can have reduced accuracy in the presence of gene tree estimation error, and also that many biological datasets have substantial gene tree estimation error, so that summary methods may not be highly accurate in biologically realistic conditions. Mirarab et al. (Science 2014) presented the "statistical binning" technique to improve gene tree estimation in multi-locus analyses, and showed that it improved the accuracy of MP-EST, one of the most popular coalescent-based summary methods. Statistical binning, which uses a simple heuristic to evaluate "combinability" and then uses the larger sets of genes to re-calculate gene trees, has good empirical performance, but using statistical binning within a phylogenomic pipeline does not have the desirable property of being statistically consistent. We show that weighting the re-calculated gene trees by the bin sizes makes statistical binning statistically consistent under the multispecies coalescent, and maintains the good empirical performance. Thus, "weighted statistical binning" enables highly accurate genome-scale species tree estimation, and is also statistically consistent under the multi-species coalescent model. New data used in this study are available at DOI: http://dx.doi.org/10.6084/m9.figshare.1411146, and the software is available at https://github.com/smirarab/binning.     

The Effect of Winter Sowing,Chemical, and Nano-Fertilizer Sources on Oil Content and Fatty Acids of Dragon’s Head (Lallemantia iberica Fischer & C.A. Meyrefeer)

Journal of Plant Growth Regulation - Dragon’s head is a multifunctional plant with diverse applications so that all its parts, including its leaves and seeds, have nutritional value. For the...     

Allosteric modulation of zinc speciation by fatty acids

Background

Serum albumin is the major protein component of blood plasma and is responsible for the circulatory transport of a range of small molecules that include fatty acids, hormones, metal ions and drugs. Studies examining the ligand-binding properties of albumin make up a large proportion of the literature. However, many of these studies do not address the fact that albumin carries multiple ligands (including metal ions) simultaneously in vivo. Thus the binding of a particular ligand may influence both the affinity and dynamics of albumin interactions with another.

Scope of review

Here we review the Zn^2 + and fatty acid transport properties of albumin and highlight an important interplay that exists between them. Also the impact of this dynamic interaction upon the distribution of plasma Zn^2 +, its effect upon cellular Zn^2 + uptake and its importance in the diagnosis of myocardial ischemia are considered.

Major conclusions

We previously identified the major binding site for Zn^2 + on albumin. Furthermore, we revealed that Zn^2 +-binding at this site and fatty acid-binding at the FA2 site are interdependent. This suggests that the binding of fatty acids to albumin may serve as an allosteric switch to modulate Zn^2 +-binding to albumin in blood plasma.

General significance

Fatty acid levels in the blood are dynamic and chronic elevation of plasma fatty acid levels is associated with some metabolic disorders such as cardiovascular disease and diabetes. Since the binding of Zn^2 + to albumin is important for the control of circulatory/cellular Zn^2 + dynamics, this relationship is likely to have important physiological and pathological implications. This article is part of a Special Issue entitled Serum Albumin.     

Effect of thymoquinone and Nigella sativa seeds oil on lipid peroxidation level during global cerebral ischemia-reperfusion injury in rat hippocampus

It has been previously reported that Nigella sativa oil (NSO) and thymoquinone (TQ), active constituent of N. sativa seeds oil, may prevent oxidative injury in various models. Therefore, we considered the possible effect of TQ and NSO on lipid peroxidation level following cerebral ischemia-reperfusion injury (IRI) in rat hippocampus. Male NMRI rats were divided into nine groups, namely, sham, control, ischemia and ischemia treated with NSO or TQ. TQ (2.5, 5 and 10 mg/kg), NSO (0.048, 0.192 and 0.384 mg/kg), phenytoin (50 mg/kg, as positive control) and saline (10 ml/kg, as negative control) were injected intraperitoneally immediately after reperfusion and the administration was continued every 24h for 72 h after induction of ischemia. The transient global cerebral ischemia was induced using four-vessel-occlusion method for 20 min. Lipid peroxidation level in hippocampus portion was measured as malondialdehyde (MDA) based on its reaction with thiobarbituric acid (TBA) following ischemic insult. The transient global cerebral ischemia induced a significant increase in TBA reactive substances (TBARS) level (p<0.001), in comparison with sham-operated animal. Pretreatment with TQ and NSO were resulted a significant decrease in MDA level as compared with ischemic group (66.9+/-1.5 vs. 297+/-2.5 nmol/g tissue for TQ, 10 mg/kg; p<0.001 and 153.5+/-1.3 nmol/g tissue for NSO, 0.384 mg/kg; p<0.001). Using a reversed-phase HPLC system, the amount of TQ in NSO was also quantified and was 0.58% w/w. These results suggest that TQ and NSO may have protective effects on lipid peroxidation process during IRI in rat hippocampus.     

Evaluation of solid polymeric organic materials for use in bioreactive sediment capping to stimulate the degradation of chlorinated aliphatic hydrocarbons

In situ bioreactive capping is a promising technology for mitigation of surface water contamination by discharging polluted groundwater. Organohalide respiration (OHR) of chlorinated ethenes in bioreactive caps can be stimulated through incorporation of solid polymeric organic materials (SPOMs) that provide a sustainable electron source for organohalide respiring bacteria. In this study, wood chips, hay, straw, tree bark and shrimp waste, were assessed for their long term applicability as an electron donor for OHR of cis-dichloroethene (cDCE) and vinyl chloride (VC) in sediment microcosms. The initial release of fermentation products, such as acetate, propionate and butyrate led to the onset of extensive methane production especially in microcosms amended with shrimp waste, straw and hay, while no considerable stimulation of VC dechlorination was obtained in any of the SPOM amended microcosms. However, in the longer term, short chain fatty acids accumulation decreased as well as methanogenesis, whereas high dechlorination rates of VC and cDCE were established with concomitant increase of Dehalococcoides mccartyi and vcrA and bvcA gene numbers both in the sediment and on the SPOMs. A numeric simulation indicated that a capping layer of 40 cm with hay, straw, tree bark or shrimp waste is suffice to reduce the groundwater VC concentration below the threshold level of 5 μg/l before discharging into the Zenne River, Belgium. Of all SPOMs, the persistent colonization of tree bark by D. mccartyi combined with the lowest stimulation of methanogenesis singled out tree bark as a long-term electron donor for OHR of cDCE/VC in bioreactive caps.     

Impact of pre-incubation time of silk fibroin scaffolds in culture medium on cell proliferation and attachment

Cell behaviours such as proliferation and attachment can be affected by the length of pre-incubation period of the scaffolds in the culture medium for long term. The aim of this study was to investigate the long term pre-incubation of 3D silk fibroin scaffolds in complete culture medium on cell attachment and proliferation. After the preparation of silk fibroin scaffolds by the technique of freeze drying, the scaffolds were pre-incubated in complete culture medium for 2 d, 6 d or 10 d before apical papilla stem cells (SCAP) seeding. Modifications of the scaffold surface and wettability were examined by FE-SEM and water contact angle, respectively. Results showed a decrease both in roughness and water contact angle as pre-incubation time increases. DNA measurement after 18 h and 10 d cell seeding showed a significant increase of DNA concentration which represents better attachment and proliferation with pre-incubation time increase. Qualitative examination, live&dead assay or H&E staining method after 30 h and 10 d cell seeding respectively, indicated that pre-incubation of scaffolds has time dependent effect on cell proliferation and attachment. This suggests that improvement of cell attachment and proliferation may be mediated by differences in the amount of wettability (decreased water contact angle) after exposure of scaffold to culture medium for long term which, in turn, causes more protein adsorption in the surface of silk fibroin scaffold (decreased roughness).     

Interspecific Gene Flow Shaped the Evolution of the Genus Canis

1. Download high-res image (233KB)
2. Download full-size image