On testing biological data for the presence of a boundary

Under the boundary line model for a biological data set, where one variable is a biological response (e.g. crop yield) to an independent variable (e.g. available water content of the soil), we interpret the upper (or lower) boundary on a plot of the dependent variable (ordinate) against the independent variable (abscissa) as representing the maximum (or minimum) possible response for a given value of the independent variable. This concept has been widely used in soil science, agronomy and plant physiology; but it has been subject to criticism. In particular, no methods that are used to analyse the boundary line quantify the evidence that the envelope of the plot represents a boundary (in the sense of some limiting response to the independent variable) rather than simply being a fringe of extreme values of no intrinsic biological interest. In this article, we present a novel procedure that tests a data set for evidence of a boundary by considering its statistical properties in the region of the proposed boundary. The method is demonstrated using both simulated and real data sets.     

Plate 463. Hibbertia Cuneiformis Dilleniaceae

The shrubby Hibbertia cuneiformis (Labill.) Smith ( Dilleniaceae ) is described and illustrated. Its history and cultivation are discussed.     

Chromosomal character optimization

A method is presented to optimize chromosomal data on a cladogram. This procedure simultaneously considers variation at the nucleotide and locus levels including nucleotide substitution, insertion and deletion, locus insertions and deletion, and gene rearrangement. Locus labeling is not a requirement of the procedure and such annotation will result from the dynamic homology analysis of the chromosome data. An example of complete arthropod mtDNA sequences is presented.     

Multiple alignment by aligning alignments

MOTIVATION: Multiple sequence alignment is a fundamental task in bioinformatics. Current tools typically form an initial alignment by merging subalignments, and then polish this alignment by repeated splitting and merging of subalignments to obtain an improved final alignment. In general this form-and-polish strategy consists of several stages, and a profusion of methods have been tried at every stage. We carefully investigate: (1) how to utilize a new algorithm for aligning alignments that optimally solves the common subproblem of merging subalignments, and (2) what is the best choice of method for each stage to obtain the highest quality alignment. RESULTS: We study six stages in the form-and-polish strategy for multiple alignment: parameter choice, distance estimation, merge-tree construction, sequence-pair weighting, alignment merging, and polishing. For each stage, we consider novel approaches as well as standard ones. Interestingly, the greatest gains in alignment quality come from (i) estimating distances by a new approach using normalized alignment costs, and (ii) polishing by a new approach using 3-cuts. Experiments with a parameter-value oracle suggest large gains in quality may be possible through an input-dependent choice of alignment parameters, and we present a promising approach for building such an oracle. Combining the best approaches to each stage yields a new tool we call Opal that on benchmark alignments matches the quality of the top tools, without employing alignment consistency or hydrophobic gap penalties. AVAILABILITY: Opal, a multiple alignment tool that implements the best methods in our study, is freely available at http://opal.cs.arizona.edu.     

NHERF-1 and the cytoskeleton regulate the traffic and membrane dynamics of G protein-coupled receptors

The sodium-hydrogen exchange regulatory factor 1 (NHERF-1/EBP50) interacts with the C terminus of several G protein-coupled receptors (GPCRs). We examined the role of NHERF-1 and the cytoskeleton on the distribution, dynamics, and trafficking of the beta(2)-adrenergic receptor (beta(2)AR; a type A receptor), the parathyroid hormone receptor (PTH1R; type B), and the calcium-sensing receptor (CaSR; type C) using fluorescence recovery after photobleaching, total internal reflection fluorescence, and image correlation spectroscopy. beta(2)AR bundles were observed only in cells that expressed NHERF-1, whereas the PTH1R was localized to bundles that parallel stress fibers independently of NHERF-1. The CaSR was never observed in bundles. NHERF-1 reduced the diffusion of the beta(2)AR and the PTH1R. The addition of ligand increased the diffusion coefficient and the mobile fraction of the PTH1R. Isoproterenol decreased the immobile fraction but did not affect the diffusion coefficient of the beta(2)AR. The diffusion of the CaSR was unaffected by NHERF-1 or the addition of calcium. NHERF-1 reduced the rate of ligand-induced internalization of the PTH1R. This phenomenon was accompanied by a reduction of the rate of arrestin binding to PTH1R in ligand-exposed cells. We conclude that some GPCRs, such as the beta(2)AR, are attached to the cytoskeleton primarily via the binding of NHERF-1. Others, such as the PTH1R, bind the cytoskeleton via several interacting proteins, one of which is NHERF-1. Finally, receptors such as the CaSR do not interact with the cytoskeleton in any significant manner. These interactions, or the lack thereof, govern the dynamics and trafficking of the receptor.     

Quantitative magnetic resonance spectroscopy reveals a potential relationship between radiation-induced changes in rat brain metabolites and cognitive impairment

To test the efficacy of magnetic resonance spectroscopy (MRS) in identifying radiation-induced brain injury, adult male Fischer 344 rats received fractionated whole-brain irradiation (40 or 45 Gy given in 5-Gy fractions twice a week for 4 or 4.5 weeks, respectively); control rats received sham irradiation. Twelve and 52 weeks after whole-brain irradiation, rats were subjected to high-resolution MRI and proton MRS. No apparent lesions or changes in T(1)- or T(2)-weighted images were noted at either time. This is in agreement with no gross changes being found in histological sections from rats 50 weeks postirradiation. Analysis of the MR spectra obtained 12 weeks after fractionated whole-brain irradiation also failed to show any significant differences (P > 0.1) in the concentration of brain metabolites between the whole-brain-irradiated and sham-irradiated rats. In contrast, analysis of the MR spectra obtained 52 weeks postirradiation revealed significant differences between the irradiated and sham-irradiated rats in the concentrations of several brain metabolites, including increases in the NAA/tCr (P < 0.005) and Glx/tCr (P < 0.001) ratios and a decrease in the mI/tCr ratio (P < 0.01). Although the cognitive function of these rats measured by the object recognition test was not significantly different (P > 0.1) between the irradiated and sham-irradiated rats at 14 weeks postirradiation, it was significantly different (P < 0.02) at 54 weeks postirradiation. These findings suggest that MRS may be a sensitive, noninvasive tool to detect changes in radiation-induced brain metabolites that may be associated with the radiation-induced cognitive impairments observed after prolonged fractionated whole-brain irradiation.     

Historical linguistics as a sequence optimization problem: the evolution and biogeography of Uto‐Aztecan languages

Language origins and diversification are vital for mapping human history. Traditionally, the reconstruction of language trees has been based on cognate forms among related languages, with ancestral protolanguages inferred by individual investigators. Disagreement among competing authorities is typically extensive, without empirical grounds for resolving alternative hypotheses. Here, we apply analytical methods derived from DNA sequence optimization algorithms to Uto‐Aztecan languages, treating words as sequences of sounds. Our analysis yields novel relationships and suggests a resolution to current conflicts about the Proto‐Uto‐Aztecan homeland. The techniques used for Uto‐Aztecan are applicable to written and unwritten languages, and should enable more empirically robust hypotheses of language relationships, language histories, and linguistic evolution.     

POY version 5: phylogenetic analysis using dynamic homologies under multiple optimality criteria

We present POY version 5, an open source program for the phylogenetic analysis of diverse data types including qualitative, aligned sequences, unaligned sequences, genomic data, and user‐defined sequences. In addition to the maximum‐parsimony optimality criterion supported by POY4, POY5 supports several types of maximum likelihood as well as posterior probability. To make these analyses feasible, new heuristic search algorithms and parallelization options have been implemented for all criteria.     

Live Imaging of Inorganic Phosphate in Plants with Cellular and Subcellular Resolution

Despite variable and often scarce supplies of inorganic phosphate (Pi) from soils, plants must distribute appropriate amounts of Pi to each cell and subcellular compartment to sustain essential metabolic activities. The ability to monitor Pi dynamics with subcellular resolution in live plants is, therefore, critical for understanding how this essential nutrient is acquired, mobilized, recycled, and stored. Fluorescence indicator protein for inorganic phosphate (FLIPPi) sensors are genetically encoded fluorescence resonance energy transfer-based sensors that have been used to monitor Pi dynamics in cultured animal cells. Here, we present a series of Pi sensors optimized for use in plants. Substitution of the enhanced yellow fluorescent protein component of a FLIPPi sensor with a circularly permuted version of Venus enhanced sensor dynamic range nearly 2.5-fold. The resulting circularly permuted FLIPPi sensor was subjected to a high-efficiency mutagenesis strategy that relied on statistical coupling analysis to identify regions of the protein likely to influence Pi affinity. A series of affinity mutants was selected with dissociation constant values of 0.08 to 11 mm, which span the range for most plant cell compartments. The sensors were expressed in Arabidopsis (Arabidopsis thaliana), and ratiometric imaging was used to monitor cytosolic Pi dynamics in root cells in response to Pi deprivation and resupply. Moreover, plastid-targeted versions of the sensors expressed in the wild type and a mutant lacking the PHOSPHATE TRANSPORT4;2 plastidic Pi transporter confirmed a physiological role for this transporter in Pi export from root plastids. These circularly permuted FLIPPi sensors, therefore, enable detailed analysis of Pi dynamics with subcellular resolution in live plants.Phosphorus is an essential element that plants acquire and assimilate in the form of inorganic phosphate (Pi). This macronutrient is a component of numerous metabolites and macromolecules, including ATP, nucleic acids, and phospholipids, and serves key roles in energy transfer reactions, signal transduction processes, and regulation of enzyme activities. Of fundamental importance to plants, Pi also serves critical roles in photosynthesis as both a substrate for ATP synthesis through photophosphorylation and a regulator in the partitioning of fixed carbon between the starch and Suc biosynthetic pathways.In many soils, particularly those used for low-input agriculture, the amounts of Pi available to plants are limiting for growth and productivity (Vance et al., 2003). Most of the Pi in soils is unavailable, because it is immobilized through formation of insoluble complexes or exists in organic forms, such as phytate, that plants cannot use directly (Schachtman et al., 1998). As a result, concentrations of free Pi in soil solution range from 1 to 10 μm, whereas cells require Pi in the millimolar range (Bieleski, 1973).To acclimate to Pi limitation, plants have evolved mechanisms to enhance Pi acquisition and also, mobilize, recycle, and conserve internal stores. These mechanisms include secretion of organic acids and phosphatases (Vance et al., 2003), increased growth of lateral roots and root hairs (Bates and Lynch, 2000; Péret et al., 2011), production of high-affinity Pi transporters at the root-soil interface (Misson et al., 2004; Shin et al., 2004), formation of symbiotic association with mycorrhizal fungi, which enhances Pi scavenging capabilities (Javot et al., 2007), modification of metabolic pathways (Plaxton and Tran, 2011), and altered patterns of Pi translocation between organs and transport between subcellular compartments (Walker and Sivak, 1986; Mimura, 1999; Raghothama, 1999). Substantial insights have been gained into the underlying biochemical identities and regulatory strategies for such adaptive responses, including those related to sensing and signaling of Pi status (Rouached et al., 2010; Chiou and Lin, 2011; Plaxton and Tran, 2011; Jain et al., 2012; Liu et al., 2014; Zhang et al., 2014). However, a thorough understanding of their respective mechanisms and how these are integrated is limited by the inability to assess intracellular Pi concentrations with high spatial and temporal resolution.Genetically encoded fluorescent sensors or biosensors have proven to be powerful tools for monitoring metabolites and ions in vivo, because their expression and subcellular targeting can be manipulated and fluorescence imaging is nondestructive (Lalonde et al., 2005; Okumoto et al., 2012). Sensor proteins are fusions of a ligand binding domain or protein with one or two fluorescent proteins (e.g. GFP and related variants). Sensors with a single fluorescent protein report ligand-dependent changes in conformation as changes in fluorescence intensity, whereas sensors with two fluorescent proteins can yield changes in fluorescence resonance energy transfer (FRET), which can be quantified through ratiometric imaging. FRET-based sensors have been used in live plants to assess a variety of analytes, including Glc, maltose, Suc, Gln, calcium, zinc, and pH (Deuschle et al., 2006; Chaudhuri et al., 2008, 2011; Kaper et al., 2008; Rincón-Zachary et al., 2010; Adams et al., 2012; Gjetting et al., 2012, 2013; Krebs et al., 2012).Gu et al. (2006) engineered a FRET-based Pi sensor named fluorescence indicator protein for inorganic phosphate (FLIPPi) that consists of a cyanobacterial inorganic phosphate binding protein (PiBP) fused to enhanced cyan fluorescent protein (eCFP) and enhanced yellow fluorescent protein (eYFP) and showed the use of one of these sensors for monitoring cytosolic Pi in cultured animal cells. In this study, we generated a series of second generation FLIPPi sensors that were modified and optimized for use in live plants. Substitution of eYFP with a circularly permuted (cp) form of the fluorescent protein Venus (cpVenus; Nagai et al., 2002, 2004) greatly increased the magnitude of Pi-dependent FRET responses. In keeping with the initial nomenclature, Pi sensors constructed with cpVenus were designated cpFLIPPi. We also used a targeted mutagenesis approach to obtain cpFLIPPi sensors with Pi binding affinities that spanned the physiological range of most cell compartments and expressed these in Arabidopsis (Arabidopsis thaliana). Confocal microscopy coupled with ratiometric analysis or acceptor photobleaching detected changes in cytosolic Pi levels in root epidermal cells in response to Pi starvation, and these changes were fully reversed by Pi replenishment. Plastid-localized versions of the same sensors expressed in wild-type plants and mutants lacking the PHOSPHATE TRANSPORT4;2 (PHT4;2) plastidic Pi transporter (Irigoyen et al., 2011) were used to confirm a role for this transporter in the export of Pi from root plastids. These results show the use of cpFLIPPi sensors for monitoring Pi distributions with both cellular and subcellular resolutions in live plants.     

The Response of the Alpine Dwarf Shrub Salix herbacea to Altered Snowmelt Timing: Lessons from a Multi-Site Transplant Experiment

Climate change is altering spring snowmelt patterns in alpine and arctic ecosystems, and these changes may alter plant phenology, growth and reproduction. To predict how alpine plants respond to shifts in snowmelt timing, we need to understand trait plasticity, its effects on growth and reproduction, and the degree to which plants experience a home-site advantage. We tested how the common, long-lived dwarf shrub Salix herbacea responded to changing spring snowmelt time by reciprocally transplanting turfs of S. herbacea between early-exposure ridge and late-exposure snowbed microhabitats. After the transplant, we monitored phenological, morphological and fitness traits, as well as leaf damage, during two growing seasons. Salix herbacea leafed out earlier, but had a longer development time and produced smaller leaves on ridges relative to snowbeds. Longer phenological development times and smaller leaves were associated with reduced sexual reproduction on ridges. On snowbeds, larger leaves and intermediate development times were associated with increased clonal reproduction. Clonal and sexual reproduction showed no response to altered snowmelt time. We found no home-site advantage in terms of sexual and clonal reproduction. Leaf damage probability depended on snowmelt and thus exposure period, but had no short-term effect on fitness traits. We conclude that the studied populations of S. herbacea can respond to shifts in snowmelt by plastic changes in phenology and leaf size, while maintaining levels of clonal and sexual reproduction. The lack of a home-site advantage suggests that S. herbacea may not be adapted to different microhabitats. The studied populations are thus unlikely to react to climate change by rapid adaptation, but their responses will also not be constrained by small-scale local adaptation. In the short term, snowbed plants may persist due to high stem densities. However, in the long term, reduction in leaf size and flowering, a longer phenological development time and increased exposure to damage may decrease overall performance of S. herbacea under earlier snowmelt.