bluuebunny/crossref_metadata_2025 huggingface dataset:
Defect-mediated phonon dynamics in TaS2 and WSe2
Authors: Cremons Daniel R. , Plemmons Dayne A. , Flannigan David J.
Published: May 2017

We report correlative crystallographic and morphological studies of defect-dependent phonon dynamics in single flakes of 1T-TaS2 and 2H-WSe2 using selected-area diffraction and bright-field imaging in an ultrafast electron microscope. In both materials, we observe in-plane speed-of-sound acoustic-phonon wave trains, the dynamics of which (i.e., emergence, propagation, and interference) are strongly dependent upon discrete interfacial features (e.g., vacuum/crystal and crystal/crystal interfaces). In TaS2, we observe cross-propagating in-plane acoustic-phonon wave trains of differing frequencies that undergo coherent interference approximately 200 ps after initial emergence from distinct interfacial regions. With ultrafast bright-field imaging, the properties of the interfering wave trains are observed to correspond to the beat frequency of the individual oscillations, while intensity oscillations of Bragg spots generated from selected areas within the region of interest match well with the real-space dynamics. In WSe2, distinct acoustic-phonon dynamics are observed emanating and propagating away from structurally dissimilar morphological discontinuities (vacuum/crystal interface and crystal terrace), and results of ultrafast selected-area diffraction reveal thickness-dependent phonon frequencies. The overall observed dynamics are well-described using finite element analysis and time-dependent linear-elastic continuum mechanics.
Unconventional generation of optical vortex beam using axicon pair and a birefringent lens: Validation of plasmonic excitation
Authors: Banerjee Jayeta , Ray Mina
Published: May 2017

We generate a nondiffracted Bessel beam using an axicon. A simple setup is presented to generate a zero order Bessel beam. Moreover, we introduce certain modifications in this optical setup for unconventional generation of an optical vortex beam using an axicon pair and a birefringent lens. An optical vortex beam with a topological charge of 1 is generated, and the corresponding spiral pattern has been demonstrated, which confirms the presence of orbital angular momentum in the optical vortex beam. Further, plasmonic excitation is validated using both zero order and first order Bessel beams. Our approach to confirm the presence of surface plasmon resonance relies on the use of a Wollaston prism. We are able to separately identify the coupling of surface plasmons with the p-polarized components via the absence of the corresponding annular beam.
Polarimetric analysis of stress anisotropy in nanomechanical silicon nitride resonators
Authors: Capelle T. , Tsaturyan Y. , Barg A. , Schliesser A.
Published: May 2017

We realise a circular gray-field polariscope to image stress-induced birefringence in thin (sub-micron thick) silicon nitride membranes and strings. This enables quantitative mapping of the orientation of principal stresses and stress anisotropy, complementary to, and in agreement with, finite element modeling. Furthermore, using a sample with a well-known stress anisotropy, we extract a value for the photoelastic (Brewster) coefficient of silicon nitride, C ≈ (3.4 ± 0.1) × 10−6 MPa−1. We explore possible applications of the method to analyse and quality-control stressed membranes with phononic crystal patterns.
Force spectroscopy unveils hidden protein-folding states
Authors: Miller Johanna L.
Published: May 2017

Specially developed short, bendy cantilevers may be the key to accessing biomolecular dynamics.
An electron–proton collider could bridge the gap between the LHC and its successor
Authors: Feder Toni
Published: May 2017

Whether the CERN facility goes ahead will depend on community support for it in the next European strategy for particle physics.
eadem figura manet: Measuring morphological convergence in diplocentrid scorpions (Arachnida : Scorpiones : Diplocentridae) under a multilocus phylogenetic framework
Authors: Santibáñez-López Carlos E. , Kriebel Ricardo , Sharma Prashant P.
Published: May 2017

Morphology still plays a key role in the systematics and phylogenetics of most of the scorpion families and genera, including the Diplocentridae Karsch, 1880. The monophyly of this family, and the monophyly of its two subfamilies is supported by morphological characters; however, neither hypothesis has been tested using molecular data. The lack of a molecular phylogeny has prevented the study of the evolution of morphology within the family. Here, we examine the morphological evolution of several key character systems in diplocentrid systematics. We tested the monophyly of the Diplocentridae, and subsequently the validity of its two subfamilies using a five-locus phylogeny. We examined the variation and evolution of the shape of the carapace, the external surface of the pedipalp patella and the retrolateral surface of the pedipalp chelae of males and females. We also examined the phylogenetic signal of discrete and continuous characters previously reported. We show that Diplocentridae is monophyletic, but Nebinae is nested within Diplocentrinae. Therefore, Nebinae is synonymised with Diplocentrinae (new synonymy). Finally, we show that a new character system proposed here, tarsal spiniform and macrosetal counts, retains high phylogenetic signal and circumscribes independently evolving substructures within this character system.
Large-area spatial disaggregation of a mosaic of conventional soil maps: evaluation over Western Australia
Authors: Holmes K. W. , Griffin E. A. , Odgers N. P.
Published: May 2017

Conventional soil maps may be the best available source for spatial soil information in data-limited areas, including individual soil properties. Spatial disaggregation of these maps, or mapping the unmapped soil components, offers potential for transforming them into spatially referenced soil class distributions. We used an automated, iterative classification tree approach to spatially disaggregate a patchwork of soil surveys covering Western Australia (2.5 × 106 km2) to produce raster surfaces of soil class occurrence. The resulting rasters capture the broad spatial patterns of dominant soils and harmonise soil class designations across most survey boundaries. More than 43 000 archived profiles were used to evaluate the accuracy of the rasters. In 20% of cases, the predicted soil class with the highest probability matched that recorded for the profile; when any of the three highest probability soil classes predicted were considered correct, the global accuracy was 40%. The accuracy increased to 71% when the rasters were reassembled to represent a higher level in the soil classification system. The predicted surfaces retained features related to the mapping intensity of the original surveys and generally had higher prediction accuracy of profile soil class where the surface geochemistry was more homogeneous. The best indicator of prediction accuracy was how common the profile soil class was in the original mapping (94% variance explained); profile observations collected during soil survey may be biased towards rare soils, making them less suitable for validation or modelling directly from point data.
Derivation of terrain covariates for digital soil mapping in Australia
Authors: Gallant John C. , Austin Jenet M.
Published: May 2017

Digital soil mapping is founded on the availability of covariates that are used as surrogates for the spatial patterns in soil properties. One important subset of covariates represents the patterns due to terrain, and these are typically derived from a digital elevation model at a suitable resolution. When each digital soil mapping exercise requires the calculation of terrain covariates, there is a clear potential for inconsistent methods and for choosing the covariates that are easiest to derive rather than those that are most relevant. The creation of open repositories of relevant terrain covariates that are correctly derived avoids these problems and fosters the application of digital soil mapping and other modelling activities that benefit from landscape properties. This paper describes the creation of a suite of commonly used terrain covariates from the 1-arcsecond (~30 m) resolution digital elevation models for Australia that were released through CSIRO’s Data Access Portal and the TERN Data Discovery Portal. The methods used to derive the terrain covariates are described and their characteristics are identified.
Past, present, and future of Palenquero creole
Authors: Moñino Yves
Published: May 2017

This article examines the current usage of the creole language of Palenque. To properly contextualize the topic in time and space, the study presents various aspects of Palenquero language and culture, linking them with the history and language use of other Afro-Colombian communities. I present an overview of Palenque’s oral history, which is then assessed in light of colonial archival records. Thereafter, attention is turned to the genesis and composition of the creole, in an effort to demonstrate that it must be considered a Neo-Romance vernacular, regardless of its rather minor linguistic African legacy. That legacy is traceable to a single sub-Saharan language, i.e. Kikongo. An attempt is made to offer a hypothesis for the unexpected uniformity of this African substrate. The sociolinguistic description of Palenque’s creole and Spanish bilingualism is at the core of this study. An effort is made to describe Palenqueros’ self-perception of their past and current language use. I claim that today’s relatively small proportion of fluent creole speakers, and the teaching of Palenquero as an L2 in Palenque’s secondary school, are two outward signs that the prospects for the creole’s survival are slim. This I argue in spite of recent community-based efforts to revitalize the creole, which has received support from UNESCO’s declaration in 2008 of Palenque as “Masterpiece of the Intangible Heritage of Humanity.” Finally, a theoretical analysis of orality, oral literature and “orature” will lead to a proposal to revitalize the use of the creole language.
The emerging need for methods appropriate to study dynamic systems
Authors: MacIntyre Peter D. , MacKay Emily , Ross Jessica , Abel Esther
Published: May 2017

There is a pressing need to develop methodology to study complex dynamic systems. In this chapter we review 12 specific methods that offer solutions to the methodological challenges presented by a dynamic approach. Specific methods include several qualitative interview designs, longitudinal cluster analysis, Q-methodology, the trajectory equifinality model, the idiodynamic method, latent growth modelling, and change point analysis. The collection of methods provides an overview of qualitative, quantitative, and mixed-methods approaches that have been applied to the study of complex dynamic systems. Each reviewed procedure has been applied to the study of motivation for language learning and demonstrates how to take account of multiple timescales, initial conditions, and dynamic stability among other issues. Even as methods are being refined, novel research findings are emerging. The lasting impact of Complexity Theory on the field of second language development depends on closing the present gap between metaphorical and/or theoretical development and specific research methods.
Lost in state space?
Authors: Lowie Wander
Published: May 2017

Since we can only make the observations our method allows us, we will have to adjust our method of investigation to the phenomena and questions we are interested in within the context and timescale of our focus. If we want to test hypotheses about the grand sweep effects of factors affecting language use at one moment in time, traditional group studies using statistics based on the Gaussian distribution are the most appropriate method. But if we are interested in investigating the changing relations in complex adaptive or dynamical systems, we should use nonlinear analyses of longitudinal data in which the denseness of the observations is adjusted to the expected rate of development. The resulting time series can then be analyzed using techniques that allow nonlinearity of the relations and that value variability as containing meaningful information. However, while there is general consensus about the requirements for traditional research in terms of the choice of parametric or nonparametric statistics, desirable power, effect sizes, and other conventions, the requirements and conventions for complexity research are not set. With the increasing popularity of complex dynamic approaches to second language development, and with more and more researchers applying complexity methodology, there is an urgent need for quality norms for this type of research. In this contribution I will make a modest proposal to some quality criteria in complexity research.
A neuropsycholinguistic approach to complexity
Authors: Köpke Barbara
Published: May 2017

Research on bilingualism has considerably changed our view of language processing, one of the main contributions being a growing awareness of the instability of language systems. While Complexity Theory claims that there is no stability whatsoever, I will argue that there are moments in the life of a language user when language systems are specifically prone to change and discuss three such cases: changes in language use patterns leading to language attrition, adding a new language to the language system, and adaptation to acquired language disorders such as aphasia. Adopting a neuropsycholinguistic approach that compares different situations of typical and disordered language use and takes into account insights from neurosciences, this discussion demonstrates the brain’s adaptive potential when it is faced with structural disorganization or with environmental changes. Furthermore, and very much in line with predictions from Complexity Theory, the findings discussed suggest that language is probably less independent from other cognitive skills than previously thought.
Energy conservation in SLA
Authors: Han ZhaoHong , Bao Gang , Wiita Paul
Published: May 2017

This chapter takes a system view on second language (L2) development. However, unlike proponents of Complex Dynamic Systems Theory (CDST) viewing the developmental system as ever dynamic without a finite state, we take up a long-standing observation about a signature L2 phenomenon, inter-learner differential attainment, and theorize about its ontology. Drawing on a fundamental physics law, the Law of Conservation of Energy – importantly, not only conceptually but also mathematically – we lay out the key parameters and their interactional relationship in engineering L2 differential attainment. The parameters include aptitude, motivation, L2 input, and L1-TL distance, all of them interacting over time vis-à-vis the developmental positioning of the learner once s/he enters the field of learning, another concept key to the system view we expound in this chapter. The resulting theory, Energy Conservation Theory in L2 or ECT-L2, promises broad descriptive, explanatory, and predictive powers. We discuss the theory in conjunction with CDST, arguing for their complementarity.
Use of Electricity to Sedate Lake Trout for Intracoelomic Implantation of Electronic Transmitters
Authors: Faust Matthew D. , Vandergoot Christopher S. , Hostnik Eric T. , Binder Thomas R. , Mida Hinderer Julia L. , Ives Jessica T. , Krueger Charles C.
Published: May 2017

Use of telemetry data to inform fisheries conservation and management is becoming increasingly common; as such, fish typically must be sedated before surgical implantation of transmitters into the coelom. Given that no widely available, immediate-release chemical sedative currently exists in North America, we investigated the feasibility of using electricity to sedate Lake Trout Salvelinus namaycush long enough for an experienced surgeon to implant an electronic transmitter (i.e., 180 s). Specifically, our study objectives were to determine (1) whether some combination of electrical waveform characteristics (i.e., duty cycle, frequency, voltage, and pulse type) could sedate Lake Trout for at least 180 s; and (2) whether Lake Trout that were sequentially exposed to continuous DC and pulsed DC had greater rates of spinal injury and short-term mortality than control fish. A Portable Electrosedation System unit was used to sedate hatchery and wild Lake Trout. Dual-frequency pulsed-DC and two-stage approaches successfully sedated Lake Trout and had similar induction and recovery times. Lake Trout sedated using the two-stage approach did not have survival rates or spinal abnormalities that were significantly different from those of control fish. We concluded that electricity was a viable alternative to chemical sedatives for sedating Lake Trout before surgical implantation of an electronic transmitter, but we suggest that Lake Trout and other closely related species (e.g., Arctic Char Salvelinus alpinus) may require morphotype-specific electrical waveforms due to their morphological diversity.

Received January 28, 2017; accepted April 24, 2017 Published online June 20, 2017
Effects of Feeding Frequencies on the Growth, Plasma Biochemistry, and Liver Glycogen of Jade Perch Scortum barcoo in a Recirculating System
Authors: Al-Khafaji Firas M , Romano Nicholas , Amin S M Nurul , Fadel Abdalbast H I , Ebrahimi Mahdi , Karami Ali , Arshad Aziz
Published: May 2017

Jade Perch Scortum barcoo having an initial average weight of 7.28 ± 0.13 g (mean ± SE) were cultured in a recirculating system at different feeding frequencies that included one, two, three, or four meals a day at 5% body weight per day. Treatments were performed in triplicate using 65 fish in each replicate. After 72 d, the survival, growth, feeding efficiencies, body indices, plasma biochemistry, whole-body proximate composition, and muscle cholesterol were measured while histological sections of the liver were stained for glycogen with periodic acid Schiff. Results showed that growth was best when fish were fed three times a day, which was significantly higher than those fed one, two or four times a day. Feeding efficiencies were significantly better for fish fed two or three times a day. Plasma glucose, plasma cholesterol, periodic acid Schiff staining intensity of the liver, and hepatosomatic index were significantly higher for fish fed three times a day compared with once a day. Whole-body crude protein was significantly lower for fish fed once a day compared with treatments of two or four times a day. Muscle cholesterol tended to increase with increasing feeding frequencies, but the results were not significant. No significant treatment effect was detected on the plasma mineral content. Based on a feeding rate of 5% body weight/d, it is recommended that feedings are divided into three meals a day to increase available energy for optimal growth.
Natural Competence Rates Are Variable Among Xylella fastidiosa Strains and Homologous Recombination Occurs In Vitro Between Subspecies fastidiosa and multiplex
Authors: Kandel Prem P. , Almeida Rodrigo P. P. , Cobine Paul A. , De La Fuente Leonardo
Published: May 2017

Xylella fastidiosa, an etiological agent of emerging crop diseases around the world, is naturally competent for the uptake of DNA from the environment that is incorporated into its genome by homologous recombination. Homologous recombination between subspecies of X. fastidiosa was inferred by in silico studies and was hypothesized to cause disease emergence. However, no experimental data are available on the degree to which X. fastidiosa strains are capable of competence and whether recombination can be experimentally demonstrated between subspecies. Here, using X. fastidiosa strains from different subspecies, natural competence in 11 of 13 strains was confirmed with plasmids containing antibiotic markers flanked by homologous regions and, in three of five strains, with dead bacterial cells used as source of donor DNA. Recombination frequency differed among strains and was correlated to growth rate and twitching motility. Moreover, intersubspecific recombination occurred readily between strains of subsp. fastidiosa and multiplex, as demonstrated by movement of antibiotic resistance and green fluorescent protein from donor to recipient cells and confirmed by DNA sequencing of the flanking arms of recombinant strains. Results demonstrate that natural competence is widespread among X. fastidiosa strains and could have an impact in pathogen adaptation and disease development.
Multiple P450s and Variation in Neuronal Genes Underpins the Response to the Insecticide Imidacloprid in a Population ofDrosophila melanogaster
Authors: Denecke Shane , Fusetto Roberto , Martelli Felipe , Giang Alex , Battlay Paul , Fournier-Level Alexandre , O’Hair Richard A. , Batterham Philip
Published: May 2017

Insecticide resistance is an economically important example of evolution in response to intense selection pressure. Here, the genetics of resistance to the neonicotinoid insecticide imidacloprid is explored using the Drosophila Genetic Reference Panel, a collection of inbredDrosophila melanogastergenotypes derived from a single population in North Carolina. Imidacloprid resistance varied substantially among genotypes, and more resistant genotypes tended to show increased capacity to metabolize and excrete imidacloprid. Variation in resistance level was then associated with genomic and transcriptomic variation, implicating several candidate genes involved in central nervous system function and the cytochrome P450sCyp6g1andCyp6g2.CRISPR-Cas9 mediated removal ofCyp6g1suggested that it contributed to imidacloprid resistance only in backgrounds where it was already highly expressed.Cyp6g2, previously implicated in juvenile hormone synthesis via expression in the ring gland, was shown to be expressed in metabolically relevant tissues of resistant genotypes.Cyp6g2overexpression was shown to both metabolize imidacloprid and confer resistance. These data collectively suggest that imidacloprid resistance is influenced by a variety of previously known and unknown genetic factors.
Cells from the same lineage switch from reduction to enhancement of size variability inArabidopsissepals
Authors: Tsugawa Satoru , Hervieux Nathan , Kierzkowski Daniel , Routier-Kierzkoswska Anne-Lise , Sapala Aleksandra , Hamant Olivier , Smith Richard S. , Roeder Adrienne H. K. , Boudaoud Arezki , Li Chun-Biu
Published: May 2017

Organs form with remarkably consistent sizes and shapes during development, whereas a high variability in size and growth is observed at cell level. Given this contrast, it is unclear how such consistency at organ scale can emerge from cellular behavior. We examine the growth of cell lineages, or groups of cells that are the progeny of a single mother cell. At early stages of the lineage, we find that initially smaller lineages grow faster than the larger ones reducing variability in lineage size, a phenomenon we refer to as size uniformization. In contrast at later stages of the lineage, size variability is enhanced when initially larger cell lineages grow faster than the smaller ones. Our results imply that the cell lineage changes its growth pattern at a tipping point. Finally, we found that the growth heterogeneity of individual cells within a lineage is correlated with fast growth of the lineage. Consequently, fast growing lineages show greater cell growth heterogeneity, leading to uniformization in lineage size. Thus, cellular variability in growth contributes toward decreasing variability of cell lineages throughout the sepal.
Bistablity in Fluorescence from a purple non-sulfur bacteria
Authors: Bose Anirban , Raja Sufi O , Ray Sanhita , Dasgupta Anjan Kr
Published: May 2017

Bistable optical emission has been observed for photosynthetic purple non-sulfur bacteriaRhodobacter capsulatusSB1003. The microbes respond to UV excitation (at 395nm) in a bifurcating way one branch corresponding to increase and the other corresponding to diminishing fluorescent emission in the range 590-685nm.The switching between such bifurcating branches can be observed when parameters like concentration, temperature are varied or static magnetic field is applied. Thus switching from amplification to reduction occurs if fluorophore concentration lowered. Again if temperature is lowered a steady quenching (instead of amplification) of fluorescence is observed. However presence of magnetic field of the order of 0.5 T reverts this and once again the systems resumes its fluoresence amplifying state. We propose that aggregation of bacterial porphyrin and regulation of such aggregation by photon excitation may explain this bistablity. Possible ecological implication of the photosynthetic bistability is suggested.
Geographical co-occurrence of butterfly species: The importance of niche filtering by host plant species
Authors: Nakadai Ryosuke , Hashimoto Koya , Iwasaki Takaya , Sato Yasuhiro
Published: May 2017

The relevance of interspecific resource competition in the context of community assembly by herbivorous insects is a well-known topic in ecology. Most previous studies focused on local species assemblies, that shared host plants. Few studies evaluated species pairs within a single taxon when investigating the effects of host plant sharing at the regional scale. Herein, we explore the effect of plant sharing on the geographical co-occurrence patterns of 232 butterflies distributed across the Japanese archipelago; we use two spatial scales (10 × 10 km and 1 × 1 km grids) to this end. We considered that we might encounter one of two predictable patterns in terms of the relationship between co-occurrence and host sharing among butterflies. On the one hand, host sharing might promote distributional exclusivity attributable to interspecific resource competition. On the other hand, sharing of host plants may promote co-occurrence attributable to filtering by resource niche. At both grid scales, we found significant negative correlations between host use similarity and distributional exclusivity. Our results support the hypothesis that the butterfly co-occurrence pattern across the Japanese archipelago is better explained by filtering via resource niche rather than interspecific resource competition.
New tools and approaches to newborn screening: ready to open Pandora's box?
Authors: Ficicioglu Can
Published: May 2017

The landscape of newborn screening (NBS) is changing as new tools are developed. We must acknowledge that NBS is a very important and extraordinarily positive initiative especially for rare and serious inherited disorders; however, lessons learned from current NBS should guide the future of NBS as we enter the era of “omics” that will expand NBS for many other genetic disorders. In this article, I will first discuss new tools such as genomics and metabolomics for NBS. I will then turn to assessing how best to take advantage of new technical developments while considering the best interests of patients and the success of newborn screening.
Lipid Extraction from Yeast Cells
Authors: Knittelfelder Oskar L. , Kohlwein Sepp D.
Published: May 2017

The diversity of lipid molecules in biological tissues makes their analysis an experimental challenge. Not only do lipids differ greatly in their chemical structures and biophysical properties, but they also occur in greatly varying concentrations in living cells. Accordingly, even for an organism with a relatively simple lipidome such as yeast, multiple extraction and analysis protocols have been developed because none of them allows comprehensive and quantitative determination of all the diverse molecular lipid species. Here we describe an extraction procedure that results in good yields of neutral lipids and glycerophospholipids from yeast. The resulting samples are suitable for analysis by thin-layer chromatography, gas chromatography/mass spectrometry, or high-performance liquid chromatography.
Thin-Layer Chromatography to Separate Phospholipids and Neutral Lipids from Yeast
Authors: Knittelfelder Oskar L. , Kohlwein Sepp D.
Published: May 2017

Thin-layer chromatography (TLC) is a versatile technique for the separation of lipid classes. It provides excellent resolution, can be used for both preparative and analytical applications, and does not require expensive equipment. Here we describe the use of different solvent systems to separate yeast phospholipids and neutral lipids by TLC in one dimension. Resolved lipid species are visualized by iodine vapor or by charring after treatment with sulfuric acid and manganese chloride. Neither of these staining techniques yields a quantitative readout because the mixture of various lipids in yeast affects iodine absorption and charring efficiency; standard curves are required to obtain semiquantitative estimates of the relative lipid composition.
4-Thiouridine Labeling to Analyze mRNA Turnover in Schizosaccharomyces pombe
Authors: Mata Juan , Wise Jo Ann
Published: May 2017

Traditionally, the half-lives of mRNAs were measured after inhibition of transcription to allow decay of the preexisting population. The protocol presented here is a more recently developed strategy in which mRNA turnover is analyzed by measuring the decline in levels of newly synthesized RNA labeled with 4-thiouridine (4sU) during a brief pulse. After RNA extraction, the 4sU is biotinylated and the labeled species are purified using streptavidin beads. DNA microarrays can then be used to compare this population with total RNA, allowing half-lives to be calculated.
Shipment of Live Preimplantation-Stage Mouse Embryos
Authors: Behringer Richard , Gertsenstein Marina , Nagy Kristina Vintersten , Nagy Andras
Published: May 2017

Sharing genetically modified mouse models is a very important part of collaboration between researchers. Shipping live animals around the world is inconvenient, expensive, and cumbersome because of the variety of international regulations and paperwork. The issue of health status differences between animal facilities is of great importance; traditionally, imported animals are quarantined to determine their health status and avoid the introduction of undesirable pathogens. The shipment of preimplantation-stage embryos for immediate transfer into pseudopregnant recipients upon arrival is a commonly used method for transportation. Time coordination on both sides is critical in this case, but the shipment can be done by any courier and the container does not need to be returned. This protocol has been used since the early 1990s to rederive dozens of mouse strains.
Direct and Indirect Cell-Based Enzyme-Linked Immunosorbent Assay
Authors: Kohl Thomas O. , Ascoli Carl A.
Published: May 2017

The direct cell-based enzyme-linked immunosorbent assay (ELISA) has developed into a popular alternative immunoassay for the rapid detection of expressed cell-surface antigens or receptors. It is used to determine cell surface antigen expression profiles using existing reporter-labeled antibodies. The target specificity of newly developed antibodies can be determined by the indirect approach, which screens hybridoma supernatants for antibody reactivity against the target antigen of interest. The cell-based ELISA acts as a surrogate for the identification of immunohistochemistry-reactive (IHC) antibodies and aids in hybridoma-derived antibody identification, which is used for further ELISA development. Briefly, cells are adsorbed onto the microtiter plate surface and then fixed. Next, either hybridoma supernatant or reporter-labeled antibody is added and allowed to bind, followed by a washing step to remove unbound antibodies. For the indirect approach—during the screening of hybridoma supernatant—a reporter-labeled species-specific secondary antibody is added. For either approach, the next step is the addition of substrate. Substrate hydrolysis is proportional to the level of cell-surface antigen expression and can be measured using a microplate reader. Cell-based ELISAs have detection sensitivities comparable to quantitative analyses by flow cytometry and can be developed in multiplex format using different reporters for the analysis of cell populations.
Derivation of Mouse Embryonic Stem (ES) Cell Lines Using Small-Molecule Inhibitors of Erk and Gsk3 Signaling (2i)
Authors: Nichols Jennifer , Jones Kenneth
Published: May 2017

The efficiency of embryonic stem (ES) cell derivation is very high if embryos are incubated, from the eight-cell stage, in the presence of the two inhibitors of signaling via the Erk and Gsk3 pathways (PD0325901 and CHIR99021, respectively, known as “2i”). The success rate may vary, depending on the quality of the embryos and the speed with which they are processed, but it is not unusual to obtain ES cell lines from all embryos allocated to the study, even from the least permissive strains. Furthermore, ES cells can be efficiently obtained from any complex genetic mouse model or for in vitro analysis and additional genetic manipulation in any background of choice.
Library Quantification Using PicoGreen Fluorometry
Authors: Mardis Elaine , McCombie W. Richard
Published: May 2017

This protocol describes the quantification of DNA using PicoGreen and a fluorometer to determine the concentration of DNA sample for downstream processing. Because dye-based methods will not detect degraded or short DNA fragments, PicoGreen requires DNAs ≥50 bp, but can less reliably detect fragments as small as 20 bp.
Identification of SNPs involved in regulating a novel alternative transcript of P450 CYP6ER1 in the brown planthopper
Authors: Liang Zhi‐Kun , Pang Rui , Dong Yi , Sun Zhong‐Xiang , Ling Yan , Zhang Wen‐Qing
Published: May 2017

Cytochrome P450‐mediated metabolic resistance is one of the major mechanisms involved in insecticide resistance. Although the up‐regulation of cytochrome P450 plays a vital role in insecticide metabolism, the molecular basis for the transcriptional regulation of cytochrome P450 remains largely unknown. The P450 gene CYP6ER1, has been reported to confer imidacloprid resistance to the brown planthopper, Nilaparvata lugens. Here, we identified a novel alternative transcript of CYP6ER1 (transcript A2) that had different expression patterns between resistant and susceptible populations, and was more stable after insecticide induction. The promoter of this transcript was sequenced and multiple single nucleotide polymorphisms (SNPs) were detected in individuals from susceptible and resistant field‐collected populations. Resistant alleles of four SNPs were found to significantly enhance the promoter activity of the CYP6ER1 transcript A2. Electrophoretic mobility shift assays (EMSAs) revealed that these SNPs might regulate the binding of transcription factors to the promoter. Our findings provide novel evidence regarding the transcriptional regulation of a metabolic resistance‐related gene and may be useful to understand the resistance mechanism of N. lugens in the field.
Functional characterization of a Niemann–Pick type C2 protein in the parasitoid wasp Microplitis mediator
Authors: Zheng Yao , Wang Shan‐Ning , Peng Yong , Lu Zi‐Yun , Shan Shuang , Yang Ye‐Qing , Li Rui‐Jun , Zhang Yong‐Jun , Guo Yu‐Yuan
Published: May 2017

Niemann–Pick type C2 (NPC2) is a type of small soluble protein involved in lipid metabolism and triglyceride accumulation in vertebrates and arthropods. Recent studies have determined that NPC2 also participates in chemical communication of arthropods. In this work, two novel NPC2 proteins (MmedNPC2a and MmedNPC2b) in Microplitis mediator were identified. Real‐time quantitative PCR (qPCR) analysis revealed that MmedNPC2a was expressed higher in the antennae than in other tissues of adult wasps compared with MmedNPC2b. Subsequent immunolocalization results demonstrated that NPC2a was located in the lymph cavities of sensilla placodea. To further explore the binding characterization of recombinant MmedNPC2a to 54 candidate odor molecules, a fluorescence binding assay was performed. It was found MmedNPC2a could not bind with selected fatty acids, such as linoleic acid, palmitic acid, stearic acid and octadecenoic acid. However, seven cotton volatiles, 4‐ethylbenzaldehyde, 3,4‐dimethylbenzaldehyde, β‐ionone, linalool, m‐xylene, benzaldehyde and trans‐2‐hexen‐1‐al showed certain binding abilities with MmedNPC2a. Moreover, the predicted 3D model of MmedNPC2a was composed of seven β‐sheets and three pairs of disulfide bridges. In this model, the key binding residues for oleic acid in CjapNPC2 of Camponotus japonicus, Lue68, Lys69, Lys70, Phe97, Thr103 and Phe127, are replaced with Phe85, Ser86, His87, Leu113, Tyr119 and Ile143 in MmedNPC2a, respectively. We proposed that MmedNPC2a in M. mediator may play roles in perception of plant volatiles.
Gender‐related differences in antiplatelet treatment patterns and outcome: Insights from the GReekAntiPlatElet Registry
Authors: Xanthopoulou Ioanna , Davlouros Periklis , Deftereos Spyridon , Hamilos Michalis , Sitafidis George , Kanakakis Ioannis , Vavouranakis Manolis , Goudevenos John , Lekakis John , Alexopoulos Dimitrios
Published: May 2017

Aims

Data on the clinical impact of gender in “real‐life” patients with acute coronary syndrome (ACS) undergoing percutaneous coronary intervention (PCI), receiving clopidogrel, prasugrel, or ticagrelor are limited. We aimed to investigate sex‐based differences in clinical outcome of those patients.

Methods

In a prospective, observational, multicenter, cohort study, 2047 patients were recruited into the GReekAntiPlatElet (GRAPE) Registry and were followed up until 1 year for major adverse cardiovascular events (MACE, composite of death, nonfatal myocardial infarction, urgent revascularization, and stroke) and bleeding events (Bleeding Academic Research Consortium [BARC] classification).

Results

Women (n=360, 17.6%) were more frequently administered clopidogrel (rather than novel P2Y12 receptor antagonists) at PCI hospital and at discharge. MACE occurred in 9.2% and 8.1% of women and men, respectively and did not differ significantly by gender. Rate of observed bleeding BARC any type was 57.2% and 44.4% in women and men, respectively. Following adjustment, only differences in BARC any type and BARC type 1 events remained significant, with higher rates observed between women: hazard ratio (95% confidence interval) 1.51 (1.23‐1.85) and 1.58 (1.27‐1.96), respectively, P<.001 for both.

Conclusions

In a contemporary “real‐life” cohort of patients with ACS treated with PCI and focusing on antiplatelet treatment 1‐year ischemic outcome does not differ by gender, while women do present more frequently not actionable bleeding events.
Molecular recognition of a carboxy pyridostatin toward G‐quadruplex structures: Why does it prefer RNA?
Authors: Rocca Roberta , Talarico Carmine , Moraca Federica , Costa Giosuè , Romeo Isabella , Ortuso Francesco , Alcaro Stefano , Artese Anna
Published: May 2017

The pyridostatin (PDS) represents the lead compound of a family of G‐quadruplex (G4) stabilizing synthetic small molecules based on a N,N′‐bis(quinolinyl)pyridine‐2,6‐dicarboxamide scaffold. Its mechanism of action involves the induction of telomere dysfunction by competing for binding with telomere‐associated proteins, such as human POT1. Recently, through a template‐directed “in situ” click chemistry approach, a PDS derivative, the carboxypyridostatin (cPDS), was discovered. It has the peculiarity to exhibit high molecular specificity for RNA over DNA G4, while PDS is a good generic RNA and DNA G4‐interacting small molecule. Structural data on the binding modes of these compounds are not available, and the selectivity mode of cPDS toward TERRA G4 is unknown too. Therefore, this work is aimed at rationalizing the selectivity of cPDS versus TERRA G4 by means of molecular dynamics and docking simulations, coupled to better understand the binding mode of these compounds to telomeric G4 structures.

The comprehensive analysis of cPDS binding mode and its conformational behavior demonstrates the importance of the ligand conformation properties coupled with a remarkable solvation contribution. This work is expected to provide valuable clues for further rational design of novel and selective TERRA G4 binders.
Airflow obstruction, cognitive function and mortality in a US national cohort: NHANES‐III
Authors: Odeyemi Yewande E. , Meda Edris , Ogundipe Funmilola , Russ Ebony , Mehari Alem , Obisesan Thomas , Gillum Richard F.
Published: May 2017

Objective

To test the hypothesis that cognitive impairment increases mortality independent of airflow obstruction.

Materials and Methods

In 1988‐1994 the Third National Health and Nutrition Examination Survey (NHANES III) measured forced expiratory volume in the first second (FEV1) and the forced vital capacity (FVC) and selected items on cognitive function with mortality follow‐up. For this survival analysis 4365 persons aged 60 and over with complete data formed the analytic sample.

Results

The FEV1/FVC less than the lower limit of predicted ratio (LLP) defined airflow obstruction and Composite Cognitive Function Score (CCF) ≤4, cognitive impairment. The percentage who died during follow up was 67% among those with neither FEV1/FVC < LLP nor CCF ≤4, 82% with FEV1/FVC < LLP only, 85% with CCF score ≤4 only and 93% with both FEV1/FVC LLP and CCF score ≤4 (P < .001). Weighted Cox proportional hazards regression revealed an increased hazard ratio (HR) in persons with FEV1/FVC <LLP only and in persons with CCF ≤4 only, respectively, compared with persons with neither. FEV1/FVC ratio < LLP remained a significant predictor of mortality with an interaction between FEV1/FVC ratio < LLP and CCF ≤4 (P = .051).

Conclusion

Elderly persons with either airflow obstruction or cognitive impairment or both had increased all‐cause mortality when compared to those with neither after adjusting for confounders. However, cognitive impairment was not a predictor of increased mortality independent of airflow obstruction.
Morphology and Molecular Phylogeny of Two New Ciliates, Holostichides heterotypicus n. sp. and Holosticha muuiensis n. sp. (Ciliophora: Urostylida)
Authors: Kim Kang‐San , Jung Jae‐Ho , Min Gi‐Sik
Published: May 2017

Two new urostylid species, Holostichides heterotypicus n. sp. and Holosticha muuiensis n. sp., were discovered in South Korea. Morphological and phylogenetic analyses were carried out to confirm that these species are new to science. Holostichides heterotypicus is mainly characterized by the following combination of features: 110–205 μm long in vivo; 5–10 frontoterminal cirri; 6–8 midventral pairs with 2–3 midventral cirral rows; cortical granules present; four bipolar dorsal kineties; and 6–9 caudal cirri. Ontogenetic features of H. heterotypicus are similar to those of H. typicus. Phylogenetic analyses revealed that H. heterotypicus was distantly separated from bakuellid genera Apobakuella, Bakuella, Metaurostylopsis, and Neobakuella. This result is supported by the following features: transverse cirri (present in the other four bakuellids vs. absent in Holostichides) and caudal cirri (absent in the other four bakuellids vs. present in Holostichides). Holosticha muuiensis n. sp. is mainly distinguished from its congeners by the following combination of features: 100–185 long in vivo; shortened undulating membrane; cortical granules lacking; contractile vacuole absent; 51–66 adoral zone of membranelles; 42–60 macronuclear nodules; and five bipolar dorsal kineties. In the phylogenetic tree, Holosticha muuiensis n. sp. clustered with a Holosticha group (containing Holosticha diademata, Holosticha foissneri, and Holosticha heterofoissneri).
Nuclear Features of the Heterotrich Ciliate Blepharisma americanum: Genomic Amplification, Life Cycle, and Nuclear Inclusion
Authors: Wancura Megan M. , Yan Ying , Katz Laura A. , Maurer‐Alcalá Xyrus X.
Published: May 2017

Blepharisma americanum, a member of the understudied ciliate class Heterotrichea, has a moniliform somatic macronucleus that resembles beads on a string. Blepharisma americanum is distinguishable by its pink coloration derived from the autofluorescent pigment blepharismin and tends to have a single somatic macronucleus with 3–6 nodes and multiple germline micronuclei. We used fluorescence confocal microscopy to explore the DNA content and amplification between the somatic and germline nuclei of B. americanum through its life cycle. We estimate that the DNA content of the macronucleus and micronucleus are 43 ± 8 Gbp and 83 ± 16 Mbp respectively. This correlates with an approximate DNA content difference of 500‐fold from micronucleus to macronucleus and a macronuclear ploidy of ~1,100 N as compared to the presumably diploid micronucleus. We also investigate a previously reported macronuclear inclusion, which is present sporadically across all life cycle stages; this inclusion looks as if it contains blepharismin based on its fluorescent properties, but its function remains unknown. We also provide additional detail to our understanding of life cycles changes in B. americanum by analyses of fluorescent images. Overall, the data analyzed here contribute to our understanding of the diversity of nuclear architecture in ciliates by providing details on the highly polyploid somatic macronucleus of B. americanum.
Correlation between oral fluid and plasma oxytetracycline concentrations after intramuscular administration in pigs
Authors: Gajda A. , Jablonski A. , Gbylik – Sikorska M. , Posyniak A.
Published: May 2017

The penetration of oxytetracycline (OTC) into the oral fluid and plasma of pigs and correlation between oral fluid and plasma were evaluated after a single intramuscular (i.m.) dose of 20 mg/kg body weight of long‐acting formulation. The OTC was detectable both in oral fluid and plasma from 1 hr up to 21 day after drug administration. The maximum concentrations (Cmax) of drug with values of 4021 ± 836 ng/ml in oral fluid and 4447 ± 735 ng/ml in plasma were reached (Tmax) at 2 and 1 hr after drug administration respectively. The area under concentration–time curve (AUC), mean residence time (MRT) and the elimination half‐life (t1/2β) were, respectively, 75613 ng × hr/ml, 62.8 hr and 117 hr in oral fluid and 115314 ng × hr/ml, 31.4 hr and 59.2 hr in plasma. The OTC concentrations were remained higher in plasma for 48 hr. After this time, OTC reached greater level in oral fluid. The strong correlation (r = .92) between oral fluid and plasma OTC concentrations was observed. Concentrations of OTC were within the therapeutic levels for most sensitive micro‐organism in pigs (above MIC values) for 48 hr after drug administration, both in the plasma and in oral fluid.
Structure and Process: Examining the Interaction between Bureaucratic Organization and Analytical Requirements
Authors: Shapiro Stuart
Published: May 2017

Attempts by politicians to control bureaucratic decisions include both structural (how is the agency making the decision organized?) and procedural (what rules must they follow when making the decision?). But how do these two modes of influence interact? This article examines the interaction between bureaucratic structure and one procedural control, the requirement that agencies conduct an analysis of their decisions prior to their issuance. I look at this interaction in the context of two types of analysis, cost‐benefit analysis and environmental impact assessment. I interview 16 individuals in each field and draw from their experiences of conducting and reviewing more than a thousand analyses. The conduct of analysis is affected by where analysts are placed in agencies. In particular, independence of analysts has a trade‐off. The more independent analysts are, the more likely they can challenge preferred decisions in their agency. But independent analysts are brought into decisions later and their independence may limit their long‐term impacts on agency culture. Despite this trade‐off, analysts expressed a clear preference for independence. The interaction between different controls of bureaucratic behavior is a potentially fruitful line for further research.