Optimization of PCR conditions to amplify microsatellite loci in the bunchgrass lizard (Sceloporus slevini) genomic DNA

<p>Abstract</p> <p>Background</p> <p>Microsatellites, also called Simple Sequence Repeats (SSRs), repetitions of nucleotide motifs of 1-5 bases, are currently the markers of choice due to their abundant distribution in the genomes, and suitability for high-throughput analysis. A total of five different primer pairs were optimized for polymerase chain reaction (PCR) to amplify microsatellite loci in total genomic DNA of bunchgrass lizards (<it>Sceloporus slevini</it>) collected from three sites in southeastern Arizona; the Sonoita Plain, Chiricahua Mountains and Huachuca Mountains.</p> <p>Findings</p> <p>The primers used for current investigation were originally designed for the Eastern Fence Lizard (<it>Sceloporus undulatus</it>). Five primer pairs were selected based on annealing temperatures for optimizing the PCR conditions to amplify with bunchgrass lizards. Different concentrations of DNA and annealing temperature were optimized. While keeping other reagents constant, a DNA concentration, 37.5 ng in the final reaction volume and PCR conditions of an initial denaturation of 94°C for five minutes, an annealing temperature of 55°C and final extension of 72°C for four minutes gave the best amplification for all the primer pairs.</p> <p>Conclusions</p> <p>Modifying the standard protocol for annealing temperatures and final extension time increases the success of cross amplification of specific microsatellite loci in the bunchgrass lizard. A loading volume of 5 ul DNA at a concentration of 10 ng/ul and a 2% agarose for gel electrophoresis were observed the best for cross amplification of selected five primer pairs on bunch grass lizard.</p> <p>Trial Registration</p> <p>The research was conducted with Arizona Game and Fish Department scientific collecting permits SP565256, SP657407 & SP749119 to Dr. Christian A d'Orgeix.</p

TRY plant trait database – enhanced coverage and open access

Plant traits - the morphological, anatomical, physiological, biochemical and phenological characteristics of plants - determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits - almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Synthesis and characterization of iridium polypyridyl complexes with ester groups with potential applications in covalent attachment to metal oxide surfaces

We report the synthesis and characterization of two iridium polypyridyl complexes, [Ir(deeb)(2)Cl-2](PF6) and [Ir(deeb)(2)(dpp)](PF6)(3), where deeb diethyl-2,2'-bipyridine-4,4'-dicarboxylate and dpp = 2,3-bis(2-pyridyl) pyrazine. From H-1 NMR spectral data, the two deeb ligands are attached to Ir cis to each other. Mass spectra contain fragmentation patterns of the (M-PF6)(+) and (M-3PF(6))(3+) molecular ions for [Ir(deeb)(2)Cl-2](PF6) and [Ir(deeb)(2)(dpp)](PF6)(3), respectively. The electronic absorption spectrum of [Ir(deeb)(2)Cl-2](PF6) shows maxima at 308nm and 402 nm, which are assigned as (1)pi -> pi* and metal-to-ligand charge transfer transitions, respectively. [Ir(deeb)(2)(dpp)](P(F)6)(3) exhibits peaks due to (1)pi -> pi* transitions at 322nm and 334 nm. [Ir(deeb)(2)Cl-2](PF6) has emission peaks at 538nm in acetonitrile and 567nm in the solid state, with lifetimes of 1.71 mu s and 0.35 mu s, respectively. [Ir(deeb)(2)Cl-2](PF6) has an unusually higher quantum yield than analogous compounds. [Ir(deeb)(2)(dpp)](PF6)(3) has emission peaks at 540nm in acetonitrile and 599nm in the solid state with lifetimes of 1.23 mu s and 0.14 mu s, respectively. Cyclic voltammetry of [Ir(deeb)(2)Cl-2](PF6) yields two reversible couples at -0.72 and -0.87V versus Ag/AgCl, both corresponding to deeb ligand reductions, and a quasi-reversible couple at -1.48V corresponding to Ir3+/+ reduction. Electrochemical reduction of [Ir(deeb)(2)(dpp)](PF6)(3) yields couples at -0.38, -0.54, -0.71, and -1.33 V, assigned as deeb(0/-), deeb(0/-), dpp(0/-), and Ir3+/+ reductions, respectively