Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches

Simultaneous molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics and species delimitation studies. In these investigations, multiple sequence alignments consist of both intra‐ and interspecies samples (mixed samples). As a result, the phylogenetic trees contain interspecies, interpopulation and within‐population divergences. Bayesian relaxed clock methods are often employed in these analyses, but they assume the same tree prior for both inter‐ and intraspecies branching processes and require specification of a clock model for branch rates (independent vs. autocorrelated rates models). We evaluated the impact of a single tree prior on Bayesian divergence time estimates by analysing computer‐simulated data sets. We also examined the effect of the assumption of independence of evolutionary rate variation among branches when the branch rates are autocorrelated. Bayesian approach with coalescent tree priors generally produced excellent molecular dates and highest posterior densities with high coverage probabilities. We also evaluated the performance of a non‐Bayesian method, RelTime, which does not require the specification of a tree prior or a clock model. RelTime's performance was similar to that of the Bayesian approach, suggesting that it is also suitable to analyse data sets containing both populations and species variation when its computational efficiency is needed.     

A Highlights from MBoC Selection: β1 integrin regulates Arg to promote invadopodial maturation and matrix degradation

β1 integrin has been shown to promote metastasis in a number of tumor models, including breast, ovarian, pancreatic, and skin cancer; however, the mechanism by which it does so is poorly understood. Invasive membrane protrusions called invadopodia are believed to facilitate extracellular matrix degradation and intravasation during metastasis. Previous work showed that β1 integrin localizes to invadopodia, but its role in regulating invadopodial function has not been well characterized. We find that β1 integrin is required for the formation of mature, degradation-competent invadopodia in both two- and three-dimensional matrices but is dispensable for invadopodium precursor formation in metastatic human breast cancer cells. β1 integrin is activated during invadopodium precursor maturation, and forced β1 integrin activation enhances the rate of invadopodial matrix proteolysis. Furthermore, β1 integrin interacts with the tyrosine kinase Arg and stimulates Arg-dependent phosphorylation of cortactin on tyrosine 421. Silencing β1 integrin with small interfering RNA completely abrogates Arg-dependent cortactin phosphorylation and cofilin-dependent barbed-end formation at invadopodia, leading to a significant decrease in the number and stability of mature invadopodia. These results describe a fundamental role for β1 integrin in controlling actin polymerization–dependent invadopodial maturation and matrix degradation in metastatic tumor cells.     

The effect of peptidoglycan enriched diets on antimicrobial peptide gene expression in rainbow trout (Oncorhynchus mykiss)

The aim of this study was to investigate the effect of feeding rainbow trout (Oncorhynchus mykiss) peptidoglycan (PG) enriched diets on antimicrobial peptide (AMP) gene expression. Fish were divided into 5 groups and fed diets containing 0, 5, 10, 50 and 100 mg PG/Kg, and sampled 1, 7 and 14 days later. The expression of eight AMP genes (four defensins, two cathelicidins and two liver expressed AMPs) was determined in skin, gill, gut and liver, tissues important for first lines of defence or production of acute phase proteins. Up-regulation of many AMPs was found after feeding the PG enriched diets, with sequential expression seen over the time course studied, where defensins were typically expressed early and cathelicidins and LEAPs later on. A number of clear differences in AMP responsiveness between the tissues examined were also apparent. Of the four PG concentrations used, 5 mg PG/Kg did not always elicit AMP gene induction or to the same degree as seen with the other diets. The three higher dose groups generally showed similar trends although differences in fold change were more pronounced in the 50 and 100 mg PG/Kg groups. Curiously several AMPs were down-regulated after 14 days of feeding in gills, gut and liver. Nevertheless, overall the PG enriched diets had a positive effect on AMP expression. Further investigations now need to be undertaken to confirm whether this higher AMP gene expression correlates with protection against common bacterial diseases and if PG enriched diets have value as a means to temporarily boost the piscine immune system.     

Facilitating Establishment of Advance Regeneration of Pterocarpus santalinus L.—An Endangered Tree Species from India

Red sanders (Pterocarpus santalinus L.) is an endangered and endemic tropical tree species from India in need of restoration. This study evaluated options for improving establishment of its advance regeneration in degraded forests. Using randomized complete block design, the effect of silvicultural treatments involving prescribed fire, in combination with disking, singling, disking with singling, and control (no treatment) on survival and growth of advanced regeneration were evaluated for a period of 2 years. Results indicate that the treatments served to ameliorate microsite conditions resulting in better survival and growth. Seedlings with fewer coppice shoots, treatments with a singling component, and treatments with disking component showed better survival and growth. The number and height of other neighboring seedlings and trees also influenced seedling establishment. Seedlings showed significantly higher survival results in the prescribed fire with disking (disking with prescribed burn [DPB]: 96%) and prescribed fires with disking and singling (singling plus disking with prescribed burn [SDPB]: 94%) treatments. Similarly, tall seedlings and those with larger root collar diameters accrued significantly higher volume growth in DPB (87%) and SDPB (97%) treatments. Although seedlings showed similar increments in DPB and SDPB treatments, better survival due to singling indicated the latter as the best option. In dense regeneration areas, preferential treatment of the taller and larger stump‐sized seedlings and, in limited regeneration areas that of smaller seedlings, may yield better results. Additionally, removal of competing vegetation and canopy opening may also help establishment of young regeneration. The results of this study have applications for restoration of endangered species in other tropical dry deciduous ecosystems worldwide.     

The Use of Ice to Enrich the Environment of Pigs Housed Indoors

Pigs used in research are often housed in barren environments. The effects of ice as a simple enrichment tool for newly weaned pigs were investigated. Four replicates of 120 pigs were separated into 3 groups. One group was given free access to blocks of ice (ice group), another group had access to Classic Kong toys (Kong group), and a 3rd group did not receive any enrichment (control group). The behavior of each group was observed every 5 min from 08:00 hr to 12:00 hr during 4 consecutive days. Pigs were motivated to explore the ice blocks (4.85% ± 1.34) over the Classic Kong toys (2.03% ± 0.59). No differences in other behaviors were found between treatments. Ice is an effective and easy-to-replace enrichment device. Blocks of ice can be used as enrichment devices for pigs housed in research facilities.     

Breeding systems in two species of the genus Helleborus (Ranunculaceae)

ABSTRACT

The results of various types of manual and free pollination are reported in Helleborus bocconei and Helleborus foetidus, two sympatric species of the understorey of submediterranean woods that flower in January–March and are pollinated by bumble-bees of the genus Bombus. Both species were found to be partially self-compatible even if at different rates; geitonogamy seems to be more frequent in H. foetidus and spontaneous self-pollination does not usually occur for morphological reasons, and the species are not apomictic. Efficiency in seed production after free pollination was very high indicating that in spite of harsh climatic condition, there were no limitations imposed by pollen or pollinators.     

Which comes first: Renal inflammation or oxidative stress in spontaneously hypertensive rats?

The present study was undertaken to identify whether inflammation or oxidative stress is the primary abnormality in the kidney in spontaneously hypertensive rats (SHR). Renal inflammation and oxidative stress were evaluated in 2- and 3-week-old prehypertensive SHR and age-matched genetically normotensive control Wistar-Kyoto (WKY) rats. Blood pressure was similar in WKY and SHR rats at 2 and 3 weeks, of age. Renal inflammation (macrophage and nuclear factor-κB) was elevated in SHR at 3 weeks, but not at 2 weeks, of age compared with age-matched WKY rats. Renal oxidative stress (nitrotyrosine, 8-hydroxy-2′-deoxyguanosine and p47phox) was also clearly elevated in 3-week-old SHR compared with age-matched WKY rats. Additionally, NADPH oxidase subunit p47phox was found elevated in 2-week-old SHR compared to age-matched WKY rats. Moreover, antioxidant (N-acetyl-l-cysteine and Tempol) treatment reduced renal inflammation in prehypertensive SHR. We therefore conclude that the oxidative stress appears before inflammation as a primary abnormality in the kidney in prehypertensive SHR.     

Comparing DNA Extraction Methods for Analysis of Botanical Materials Found in Anti-Diabetic Supplements

A comparative performance evaluation of DNA extraction methods from anti-diabetic botanical supplements using various commercial kits was conducted, to determine which produces the best quality DNA suitable for PCR amplification, sequencing and species identification. All plant materials involved were of suboptimal quality showing various levels of degradation and therefore representing real conditions for testing herbal supplements. Eight different DNA extraction methods were used to isolate genomic DNA from 13 medicinal plant products. Two methods for evaluation, DNA concentration measurements that included absorbance ratios as well as PCR amplifiability, were used to determine quantity and quality of extracted DNA. We found that neither DNA concentrations nor commonly used UV absorbance ratio measurements at A ₂₆₀/A ₂₈₀ between 1.7 and 1.9 are suitable for globally predicting PCR success in these plant samples, and that PCR amplifiablity itself was the best indicator of extracted product quality. However, our results suggest that A ₂₆₀/A ₂₈₀ ratios below about 1.3 and above 2.3 indicated a DNA quality too poor to amplify. Therefore, A ₂₆₀/A ₂₈₀ measurements are not useful to identify samples that likely will amplify but can be used to exclude samples that likely will not amplify reducing the cost for unnecessarily subjecting samples to PCR. The two Nucleospin^® plant II kit extraction methods produced the most pure and amplifiable genomic DNA extracts. Our results suggest that there are clear, discernable differences between extraction methods for low quality plant samples in terms of producing contamination-free, high-quality genomic DNA to be used for further analysis.