Rejecting strictly allopatric speciation on a continental island: prolonged postdivergence gene flow between Taiwan (Leucodioptron taewanus,Passeriformes Timaliidae) and Chinese (L. canorum canorum) hwameis

Allopatry is conventionally considered the geographical mode of speciation for continental island organisms. However, strictly allopatric speciation models that assume the lack of postdivergence gene flow seem oversimplified given the recurrence of land bridges during glacial periods since the late Pliocene. Here, to evaluate whether a continental island endemic, the Taiwan hwamei (Leucodioptron taewanus, Passeriformes Timaliidae) speciated in strict allopatry, we used weighted‐regression‐based approximate Bayesian computation (ABC) to analyse the genetic polymorphism of 18 neutral nuclear loci (total length: 8500 bp) in Taiwan hwamei and its continental sister species, the Chinese hwamei (L. canorum canorum). The nonallopatry model was found to fit better with observed genetic polymorphism of the two hwamei species (posterior possibility = 0.82). We also recovered unambiguous signals of nontrivial bidirectional postdivergence gene flow (N_em » 1) between Chinese hwamei and Taiwan hwamei until 0.5 Ma. Divergence time was estimated to be 3.5 to 2 million years earlier than that estimated from mitochondrial cytochrome b sequences. Finally, using the inferred nonallopatry model to simulate genetic variation at 24 nuclear genes examined showed that the adiponectin receptor 1 gene may be under divergent adaptation. Our findings imply that the role of geographical barrier may be less prominent for the speciation of continental island endemics, and suggest a shift in speciation studies from simply correlating geographical barrier and genetic divergence to examining factors that facilitate and maintain divergence, e.g. differential selection and sexual selection, especially in the face of interpopulation gene flow.     

Predicting Flow Reversals in a Computational Fluid Dynamics Simulated Thermosyphon Using Data Assimilation

A thermal convection loop is a annular chamber filled with water, heated on the bottom half and cooled on the top half. With sufficiently large forcing of heat, the direction of fluid flow in the loop oscillates chaotically, dynamics analogous to the Earth’s weather. As is the case for state-of-the-art weather models, we only observe the statistics over a small region of state space, making prediction difficult. To overcome this challenge, data assimilation (DA) methods, and specifically ensemble methods, use the computational model itself to estimate the uncertainty of the model to optimally combine these observations into an initial condition for predicting the future state. Here, we build and verify four distinct DA methods, and then, we perform a twin model experiment with the computational fluid dynamics simulation of the loop using the Ensemble Transform Kalman Filter (ETKF) to assimilate observations and predict flow reversals. We show that using adaptively shaped localized covariance outperforms static localized covariance with the ETKF, and allows for the use of less observations in predicting flow reversals. We also show that a Dynamic Mode Decomposition (DMD) of the temperature and velocity fields recovers the low dimensional system underlying reversals, finding specific modes which together are predictive of reversal direction.     

A phenome-guided drug repositioning through a latent variable model

Background

The phenome represents a distinct set of information in the human population. It has been explored particularly in its relationship with the genome to identify correlations for diseases. The phenome has been also explored for drug repositioning with efforts focusing on the search space for the most similar candidate drugs. For a comprehensive analysis of the phenome, we assumed that all phenotypes (indications and side effects) were inter-connected with a probabilistic distribution and this characteristic may offer an opportunity to identify new therapeutic indications for a given drug. Correspondingly, we employed Latent Dirichlet Allocation (LDA), which introduces latent variables (topics) to govern the phenome distribution.

Results

We developed our model on the phenome information in Side Effect Resource (SIDER). We first developed a LDA model optimized based on its recovery potential through perturbing the drug-phenotype matrix for each of the drug-indication pairs where each drug-indication relationship was switched to “unknown” one at the time and then recovered based on the remaining drug-phenotype pairs. Of the probabilistically significant pairs, 70% was successfully recovered. Next, we applied the model on the whole phenome to narrow down repositioning candidates and suggest alternative indications. We were able to retrieve approved indications of 6 drugs whose indications were not listed in SIDER. For 908 drugs that were present with their indication information, our model suggested alternative treatment options for further investigations. Several of the suggested new uses can be supported with information from the scientific literature.

Conclusions

The results demonstrated that the phenome can be further analyzed by a generative model, which can discover probabilistic associations between drugs and therapeutic uses. In this regard, LDA serves as an enrichment tool to explore new uses of existing drugs by narrowing down the search space.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-267) contains supplementary material, which is available to authorized users.     

Sugarcane borer (Lepidoptera: Crambidae) management threshold assessment on four sugarcane cultivars

This research assesses the potential for using different economic injury thresholds in management of a key insect pest on susceptible and resistant commercially produced cultivars of sugarcane (Saccharum spp. hybrids). In a 2-yr sugarcane borer, Diatraea saccharalis (F.) (Lepidoptera: Crambidae), study involving four commercially produced sugarcane cultivars and four insecticide treatment thresholds, 'LCP 85-384' and 'HoCP 91-555' were the most susceptible based on percentage of bored internodes compared with the more resistant 'HoCP 85-845' and 'CP 70-321'. In 2001, the 10% infested stalks threshold was not as effective as the 5% early season-10% late season and 5% full season for HoCP 91-555. Based on D. saccharalis injury under natural infestation conditions, susceptible cultivars seem to require a lower infestation threshold than the more resistant cultivars to achieve adequate injury reduction. Among yield components, only the theoretical recoverable sugar per stalk was significantly increased by applying insecticides. With the resistant HoCP 85-845, differences were not detected for percentage of bored internodes among treated versus untreated management regimes. The resistant HoCP 85-845 had higher levels of fiber in our study; however, no clear pattern on resistance mechanisms was established, because the resistant cultivar CP 70-321 had comparatively low levels of fiber. The development of cultivar-specific thresholds is expected to lower the amount of insecticide used for D. saccharalis management in the sugarcane industry, reduce selection pressure, and delay the development of insecticide resistance.     

The discovery of an orally efficacious positive allosteric modulator of the calcium sensing receptor containing a dibenzylamine core

The discovery of a series of novel and orally efficacious type II calcimimetics, developed from the lead compound 1, is described herein. Compound 22 suppressed plasma PTH levels relative to vehicle when dosed orally in a rat pharmacodynamic model.     

The Endoplasmic Reticulum Is a Reservoir for WAVE/SCAR Regulatory Complex Signaling in the Arabidopsis Leaf

During plant cell morphogenesis, signal transduction and cytoskeletal dynamics interact to locally organize the cytoplasm and define the geometry of cell expansion. The WAVE/SCAR (for WASP family verprolin homologous/suppressor of cyclic AMP receptor) regulatory complex (W/SRC) is an evolutionarily conserved heteromeric protein complex. Within the plant kingdom W/SRC is a broadly used effector that converts Rho-of-Plants (ROP)/Rac small GTPase signals into Actin-Related Protein2/3 and actin-dependent growth responses. Although the components and biochemistry of the W/SRC pathway are well understood, a basic understanding of how cells partition W/SRC into active and inactive pools is lacking. In this paper, we report that the endoplasmic reticulum (ER) is an important organelle for W/SRC regulation. We determined that a large intracellular pool of the core W/SRC subunit NAP1, like the known positive regulator of W/SRC, the DOCK family guanine nucleotide-exchange factor SPIKE1 (SPK1), localizes to the surface of the ER. The ER-associated NAP1 is inactive because it displays little colocalization with the actin network, and ER localization requires neither activating signals from SPK1 nor a physical association with its W/SRC-binding partner, SRA1. Our results indicate that in Arabidopsis (Arabidopsis thaliana) leaf pavement cells and trichomes, the ER is a reservoir for W/SRC signaling and may have a key role in the early steps of W/SRC assembly and/or activation.The W/SRC (for WASP family verprolin homologous/suppressor of cAMP receptor regulatory complex) and Actin-Related Protein (ARP)2/3 complex are part of an evolutionarily conserved Rho-of-Plants (ROP)/Rac small GTPase signal transduction cascade that controls actin-dependent morphogenesis in a wide variety of tissues and developmental contexts (Smith and Oppenheimer, 2005; Szymanski, 2005; Yalovsky et al., 2008). Many of the components and regulatory relationships among the complexes were discovered based on the stage-specific cell-swelling and -twisting phenotypes of the distorted class of Arabidopsis (Arabidopsis thaliana) trichome mutants (Szymanski et al., 1999; Zhang et al., 2005, 2008; Djakovic et al., 2006; Le et al., 2006; Uhrig et al., 2007). However, in both maize (Zea mays) and Arabidopsis, W/SRC and/or ARP2/3 are required for normal pavement cell morphogenesis (Frank and Smith, 2002; Mathur et al., 2003b; Brembu et al., 2004). Compared with other Arabidopsis pavement cell mutants, the shape defects of the distorted group are relatively mild. However, the distorted mutants and spike1 (spk1) differ from most other morphology mutants in that they display gaps in the shoot epidermis, most frequently at the interface of pavement cells and stomata (Qiu et al., 2002; Le et al., 2003; Li et al., 2003; Mathur et al., 2003b; Zhang et al., 2005; Djakovic et al., 2006). The cell gaps may reflect either uncoordinated growth between neighboring cells or defective cortical actin-dependent secretion of polysaccharides and/or proteins that promote cell-cell adhesion (Smith and Oppenheimer, 2005; Hussey et al., 2006; Leucci et al., 2007).In tip-growing cells, there is a strict requirement for actin to organize the trafficking and secretion activities of the cell to restrict growth to the apex. In Arabidopsis, the W/SRC-ARP2/3 pathway is not an essential tip growth component, because null alleles of both W/SRC and ARP2/3 subunits do not cause noticeable pollen tube or root hair phenotypes (Le et al., 2003; Djakovic et al., 2006). However, reverse genetic analysis of the W/SRC subunit BRK1 and ARP2/3 in the tip-growing protonemal cells of Physcomitrella patens revealed the obvious importance of this pathway (Harries et al., 2005; Perroud and Quatrano, 2008). Along similar lines, in two different legume species, W/SRC subunits are required for a normal root nodulation response to symbiotic bacteria (Yokota et al., 2009; Miyahara et al., 2010), indicating a conditional importance for this pathway in root hair growth. These genetic studies centered on the W/SRC and ARP2/3 pathways, in addition to those that involve a broader collection of actin-based morphology mutants (Smith and Oppenheimer, 2005; Blanchoin et al., 2010), are defining important cytoskeletal proteins and new interactions with the endomembrane system during morphogenesis. However, it is not completely clear how unstable actin filaments and actin bundle networks dictate the growth patterns of cells (Staiger et al., 2009).The difficulty of understanding the functions of specific actin arrays can be explained, in part, by the fact that plant cells that employ a diffuse growth mechanism have highly unstable cortical actin filaments and large actin bundles that do not have a geometry that obviously relates to the direction of growth or a specific subcellular activity (Blanchoin et al., 2010). This is in contrast to the cortical endocytic actin patches in yeast (Saccharomyces cerevisiae; Evangelista et al., 2002; Kaksonen et al., 2003) and cortical meshworks in the lamellipodia of crawling cells (Pollard and Borisy, 2003) that reveal subcellular locations where actin works to locally control membrane dynamics. In thick-walled plant cells, the magnitude of the forces that accompany turgor-driven cell expansion exceed those that could be generated by actin polymerization by orders of magnitude (Szymanski and Cosgrove, 2009). Localized cell wall loosening or the assembly of an anisotropic cell wall generates asymmetric yielding responses to turgor-induced stress (Baskin, 2005; Cosgrove, 2005). Therefore, the actin-based control of cell boundary dynamics is indirect, and the actin cytoskeleton influences cell shape change, in part, by actin and/or myosin-dependent trafficking of hormone transporters (Geldner et al., 2001) and organelles (Prokhnevsky et al., 2008), including those that control the localized delivery of protein complexes and polysaccharides that pattern the cell wall (Leucci et al., 2007; Gutierrez et al., 2009). In this scheme for actin-based growth control, the actin network dynamically rearranges at spatial scales that span from approximately 1- to 10-µm subcellular domains that may locally position organelles (Cleary, 1995; Gibbon et al., 1999; Szymanski et al., 1999) to the more than 100-µm actin bundle networks that operate at the spatial scales of entire cells (Gutierrez et al., 2009; Dyachok et al., 2011). It is clear from the work of several laboratories that the W/SRC and ARP2/3 protein complexes are required to organize cortical actin and actin bundle networks in trichomes (Szymanski et al., 1999; Le et al., 2003; Deeks et al., 2004; Zhang et al., 2005) and cylindrical epidermal cells (Mathur et al., 2003b; Dyachok et al., 2008, 2011). A key challenge now is to understand how plant cells deploy these approximately 10- to 20-nm heteromeric protein complexes to influence the patterns of growth at cellular scales.The genetic and biochemical control of ARP2/3 is complicated, but this is a tractable problem in plants, because the pathway is relatively simple compared with most other species in which it has been characterized. For example, in organisms ranging from yeast to humans, there are multiple types of ARP2/3 activators, protein complexes, and pathways that activate ARP2/3 (Welch and Mullins, 2002; Derivery and Gautreau, 2010). However, the maize and Arabidopsis genomes encode only WAVE/SCAR homologous proteins that can potently activate ARP2/3 (Frank et al., 2004; Basu et al., 2005). Detailed genetic and biochemical analyses of the WAVE/SCAR gene family in Arabidopsis demonstrated that the plant activators function interchangeably within the context of the W/SRC and define the lone pathway for ARP2/3 activation (Zhang et al., 2008). Bioinformatic analyses are consistent with a prominent role for W/SRC in the angiosperms, because in general, WASH complex subunits, which are structurally similar to WAVE/SCAR proteins, are largely absent from the higher plant genomes, while WAVE/SCAR genes are highly conserved (Kollmar et al., 2012).The components and regulatory schemes of the W/SRC-ARP2/3 pathway in Arabidopsis and P. patens are conserved compared with vertebrate species that employ these same protein complexes (Szymanski, 2005). For example, mutant complementation tests indicate that human W/SRC and ARP2/3 complex subunits can substitute for the Arabidopsis proteins (Mathur et al., 2003b). Furthermore, biochemical assays of Arabidopsis W/SRC (Basu et al., 2004; El-Assal et al., 2004; Frank et al., 2004; Le et al., 2006; Uhrig et al., 2007) and ARP2/3 assembly (Kotchoni et al., 2009) have shown that the binary interactions among W/SRC subunits and ARP2/3 complex assembly mechanisms are indistinguishable from those that have been observed for human W/SRC (Gautreau et al., 2004) and yeast ARP2/3 (Winter et al., 1999). After an initial period of controversy concerning the biochemical control of W/SRC, it is now apparent that vertebrate W/SRC (Derivery et al., 2009; Ismail et al., 2009), like the ARP2/3 complex (Machesky et al., 1999), is intrinsically inactive and requires positive regulation by Rac and other factors to fully activate ARP2/3 (Ismail et al., 2009; Lebensohn and Kirschner, 2009; Chen et al., 2010). Although overexpression of dominant negative ROP mutants causes trichome swelling and a reduced trichome branch number (Fu et al., 2002), the involvement of ROPs in trichome morphogenesis has been difficult to prove with a loss-of-function ROP allele because so many ROPs are expressed in this cell type (Marks et al., 2009). Existing reports on ROP loss-of-function mutants demonstrate the importance of pavement cell morphogenesis but do not document a trichome phenotype (Fu et al., 2005; Xu et al., 2010). A recent report describes a clever strategy to generate ROP loss-of-function lines that used the ectopic expression of ROP-specific bacterial toxins. There was a strong association between inducible expression of the toxins and the appearance of trichomes with severe trichome swelling and reduced branch number phenotypes (Singh et al., 2012). Although the exact mechanism of ROP-dependent control of W/SRC remains to be determined, the results described above in combination with the detection of direct interactions between the ROPGEF SPK1, active forms of ROP, and W/SRC subunits (Basu et al., 2004, 2008; Uhrig et al., 2007) strongly suggest that W/SRC is a ROP effector complex.The major challenge in the field now is to better understand the cellular control of W/SRC and how the complex is partitioned into active and inactive pools. In mammalian cells that crawl on a solid substrate, current models propose that a cytosolic pool of inactive WAVE/SCAR proteins and W/SRC is locally recruited and activated at specific plasma membrane surfaces in response to signals from some unknown Rac guanine nucleotide-exchange factor (GEF), protein kinase, and/or lipid kinase (Oikawa et al., 2004; Lebensohn and Kirschner, 2009; Chen et al., 2010). However, in Drosophila melanogaster neurons (Bogdan and Klämbt, 2003) and cultured human melanoma cells (Steffen et al., 2004), there are large pools of W/SRC with a perinuclear or organelle-like punctate localization that has no obvious relationship to cell shape or motility, raising uncertainty about the cellular mechanisms of W/SRC activation and the importance of different subcellular pools of the complex.In plants, cell fractionation experiments indicate that SCAR1 and ARP2/3 have an increased association with membranes compared with their animal counterparts (Dyachok et al., 2008; Kotchoni et al., 2009). In tip-growing moss protonemal cells, both the W/SRC subunit BRK1 and ARP2/3 localize to a population of unidentified organelles within the apical zone (Perroud and Quatrano, 2008). Similar live-cell imaging experiments in Arabidopsis reported a plasma membrane localization for SCAR1 and BRK1 in a variety of shoot epidermal and root cortex, and their accumulation at young trichome branch tips and at three-way cell wall junctions may define subcellular domains for W/SRC-ARP2/3-dependent actin filament nucleation at the plasma membrane (Dyachok et al., 2008). However, to our knowledge, active W/SRC, defined here as the fraction of W/SRC that colocalizes with ARP2/3 or actin, has not been reported in plants, and the plasma membrane is not necessarily the only organelle involved in W/SRC regulation. For example, the reported accumulation of BRK1 and SCAR1 at three-way cell wall junctions has a punctate appearance at the cell cortex that may not simply correspond to the plasma membrane (Dyachok et al., 2008). Also, in young stage 4 trichomes, there was an uncharacterized pool of intracellular SCAR1, but not BRK1, that localized to relatively large punctate structures (Dyachok et al., 2008). The endoplasmic reticulum (ER) may also be involved in W/SRC regulation. The ER-localized DOCK family ROPGEF SPK1 (Zhang et al., 2010) physically associates with multiple W/SRC proteins (Uhrig et al., 2007; Basu et al., 2008) and, based on genetic criteria, is an upstream, positive regulator of the W/SRC-ARP2/3 pathway (Basu et al., 2008). In the leaf, one function of SPK1 is to promote normal trafficking between the ER and Golgi; however, arp2/3 mutants do not share ER-stress phenotypes with spk1 (Zhang et al., 2010), making it unclear if SPK1 and the ER are directly involved in W/SRC signaling.This paper focuses on the localization and control of the W/SRC subunit NAP1/GNARLED/NAPP/HEM1/2. Arabidopsis NAP1 directly interacts with the ROP/Rac effector subunit SRA1/PIROGI/KLUNKER/PIRP (Basu et al., 2004; El-Assal et al., 2004; Uhrig et al., 2007). Based on the equally severe syndrome of nap1 and arp2/3 null phenotypes, and double mutant analyses, the only known function of NAP1 is to positively regulate ARP2/3 (Brembu et al., 2004; Deeks et al., 2004; El-Din El-Assal et al., 2004; Li et al., 2004). The vertebrate SRA1-NAP1 dimer is important for W/SRC assembly (Gautreau et al., 2004) and forms an extended physical surface that trans-inhibits the C-terminal ARP2/3-activating domain of WAVE/SCAR (Chen et al., 2010). The plant NAP1 and SRA1 proteins share end-to-end amino acid conservation with their vertebrate homologs and may form a heterodimer with similar functions (Basu et al., 2004; El-Assal et al., 2004; Uhrig et al., 2007). We report here that Arabidopsis NAP1 is strongly associated with ER membranes. In a detailed series of localization experiments, we detect a complicated intracellular distribution of NAP1 among the ER, the nucleus, and unidentified submicrometer punctae. A large pool of ER-associated NAP1 is inactive, based on the low level of colocalization with actin.Its accumulation on the ER does not require activating signals from either SPK1 or SRA1. These data indicate that the ER is a reservoir for W/SRC signaling and suggest that early steps in the positive regulation of NAP1 and the W/SRC occur on the ER surface.     

Utilization of Inhaled Corticosteroids for Infants with Bronchopulmonary Dysplasia

Objective

To determine demographic and clinical variables associated with inhaled corticosteroid administration and to evaluate between-hospital variation in inhaled steroid use for infants with bronchopulmonary dysplasia (BPD).

Design

Retrospective Cohort Study.

Setting

Neonatal units of 35 US children''s hospitals; as recorded in the Pediatric Health Information System (PHIS) database.

Patients

1429 infants with evolving BPD at 28 days who were born at <29 weeks gestation with birth weight <1500 grams, admitted within the first 7 postnatal days, and discharged between January 2007–June 2011.

Results

Inhaled steroids were prescribed to 25% (n = 352) of the cohort with use steadily increasing during the first two months of hospitalization. The most frequently prescribed steroid was beclomethasone (n = 194, 14%), followed by budesonide (n = 125, 9%), and then fluticasone (n = 90, 6%). Birth gestation <24 weeks, birth weight 500–999 grams, and prolonged ventilation all increased the adjusted odds of ever receiving inhaled corticosteroids (p<0.05). Wide variations between hospitals in the frequency of infants ever receiving inhaled steroids (range: 0–60%) and the specific drug prescribed were noted. This variation persisted, even after controlling for observed confounders.

Conclusions

Inhaled corticosteroid administration to infants with BPD is common in neonatal units within U.S. Children''s hospitals. However, its utilization varies markedly between centers from no treatment at some institutions to the majority of infants with BPD being treated at others. This supports the need for further research to identify the benefits and potential risks of inhaled steroid usage in infants with BPD.     

Discovery and optimization of a novel series of GPR142 agonists for the treatment of type 2 diabetes mellitus

The discovery and initial optimization of a series of phenylalanine based agonists for GPR142 is described. The structure-activity-relationship around the major areas of the molecule was explored to give agonists 90 times more potent than the initial HTS hit in a human GPR142 inositol phosphate accumulation assay. Removal of CYP inhibition by exploration of the pyridine A-ring is also described.