bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of the Implementation of Barcode Technology and an Electronic Medication Administration Record on Adverse Drug Events
Authors: Truitt Erin , Thompson Ross , Blazey-Martin Deborah , Nisai Danna , Salem Deeb
Published: June 2016

Background

Hospitals have attempted to reduce adverse drug events (ADEs) by investing in new technologies, but data regarding their efficacy are lacking.

Objectives

This study evaluates the effects of the implementation of barcode medication administration (BCMA) and electronic medication administration record (eMAR) technology on the profile of ADEs in a hospital setting.

Methods

We conducted a before-and-after study examining the effects of the implementation of BCMA and eMAR technology on the profile of ADEs at a 400-bed academic medical center by using incident reports. We compared reported ADEs in pre- and post-implementation periods of 5 months to determine whether there was a reduction in the rate of ADEs within medication use phases. We further examined the severity of errors and described changes in the distribution of types of errors.

Results

A total of 775 electronic error-reporting system reports were included in this study: 397 (51%) in the pre-implementation period and 378 (49%) in the post-implementation period. The rate of ADEs significantly decreased from 0.26% to 0.20% after implementation of the technology (relative risk [RR], 0.78; 95% CI, 0.67–0.89). The rate of transcription errors decreased from 0.089% to 0.036% (RR, 0.40; 95% CI, 0.30–0.54), which was largely attributed to reduction of “wrong time” errors. The rate of administration errors was identical in both groups at 0.017% (RR, 0.98; 95% CI 0.58–1.66). The mean severity level of administration errors significantly decreased from 4.44 to 3.23 ( p = .005).

Conclusion

The implementation of eMAR and BCMA technology improved patient safety by decreasing the overall rate of ADEs and the rate of transcription errors. These technologies also reduced the harmful impact to patients caused by administration errors.
American cultural myth and the orphan archetype
Authors: Morris Robert B.
Published: June 2016

The following article defines and explores the power of myth in shaping societal attitudes. The author discusses cultural myth as it pertains to a nation’s self-image and conception of its past. The American cultural myth is examined in detail to help discover the roots of unsustainable aspects of American thinking. The author discusses the history of the North American colonies, challenges faced by early settlers, and the belief systems that formed the roots of the American cultural myth. The article goes on to explore how early events brought about the evolution of the legendary American cowboy and how the cowboy mythos is closely tied to the hero’s journey and psychological development. The author maintains that the Puritan mindset, the cowboy ideal and present-day circumstances have forged a national psyche resembling the Jungian orphan archetype. The author’s hope is that by understanding the root causes of some of the nation’s difficulties we may begin healing many of the spiritual wounds of the past and set off on a path towards stronger and healthier community bonds.
Priorización de valores en estudiantes jóvenes y mayores en el contexto de la crisis económica
Authors: Hernández Serrano María José , Parra Nieto Gabriel , Pérez Grande María Dolores
Published: June 2016

El cambio de valores en la sociedad postmoderna nos sitúa ante un debate recurrente sobre una posible brecha generacional entre jóvenes y mayores. La postmodernidad, el aumento del individualismo y el relativismo contrastan hoy con las necesidades que plantean la situación económica y la reformulación de las prioridades axiológicas. Ante las circunstancias actuales, cuestionamos si la crisis mundial no ha venido a homogeneizar en cierta medida los valores de jóvenes y mayores, al vivir ambos etapas de socialización en contextos de mayor escasez e inseguridad. El objetivo de este estudio es comparar las similitudes y diferencias en la apreciación de los valores de ambas cohortes, según la escala RVS (Rokeach). En los resultados encontramos considerables semejanzas en los valores básicos que priorizan ambos grupos. Pero también se sigue evidenciando en los jóvenes un mayor índice de postmodernismo al presentar una mayor pluralidad y diversificación hacia valores más individualistas e intrapersonales.
Justificación filosófica de la educación en valores éticos y cívicos en la educación formal. Análisis crítico de la LOMCE
Authors: Gracia Calandín Javier , Gozálvez Vicent
Published: June 2016

En este trabajo partimos de los planteamientos de la nueva LOMCE para remontarnos al sentido y justificación filosófica de cada uno de los valores éticos que a nuestro juicio han de ser atendidos en la educación como ejes vertebradores de la misma. En primer lugar, llamamos la atención sobre algunas contradicciones en la nueva LOMCE. Posteriormente, exploramos el fundamento filosófico de los valores éticos en la educación. Para ello proponemos el enfoque hermenéutico para desentrañar los valores éticos. Es en el tercero y más extenso apartado donde ahondamos en el fundamento filosófico de los diferentes valores éticos en los que a nuestro juicio debe basarse una educación que busque la formación cívica y el pleno desarrollo de la personalidad humana, tal como se defiende en textos constitucionales y en las declaraciones internacionales de derechos fundamentales.
Identificando os factores de influência da compra por impulso em adolescentes portugueses
Authors: Lins Samuel , Poeschl Gabrielle , Eberhardt Ana
Published: June 2016

A compra por impulso tem sido uma área vastamente pesquisada, entretanto, raras investigações têm sido realizadas em Portugal e particularmente com o público adolescente. Esta pesquisa teve o objectivo de identificar factores influenciadores da compra impulsiva (variáveis sociodemográficas, práticas sociais e hábitos online, variáveis psicológica, de influência grupal e valores). Participaram 238 adolescentes portugueses (117 rapazes e 121 raparigas, com idade média de 15.43 anos) da cidade do Porto (Portugal). Os resultados mostram que o sexo de pertença não influência a compra por impulso, e que a frequência de visitas a centros comerciais por mês, o prazer nas compras, a importância atribuída à marca, a tendência a gastar mais na presença de amigos e o materialismo nas compras têm uma correlação positiva com a compra por impulso, enquanto os valores de bem-estar profissional apresentam uma relação negativa. Os resultados corroboram a literatura e contribuem para compreender melhor o comportamento de compra impulsiva em Portugal.
Functional time series analysis of age-specific fertility rates: visualizing the change in the age-pattern of fertility in India
Authors: Deb Mallika , Chakrabarty Tapan Kumar
Published: June 2016

Functional Time Series Analysis (FTSA) is carried out in this article to uncover the temporal variations in the age pattern of fertility in India. Attempt is made to find whether there is any typical age pattern in the nationâ€™s fertility across the reproductive age groups. If so, how do we characterize the role of changing age pattern of fertility across reproductive age groups in the nationâ€™s fertility transition? We have used region-specific (rural-urban) and country level data series on Age-Specific Fertility Rates (ASFRs) available from Sample Registration System (SRS), India during 1971-2013. Findings of this study are very impressive. It is observed that the youngest age group of women in 15-19 years has contributed to the maximum decline in fertility with a substantially accelerated pace during the period of study. The major changes in fertility rates among Indian women dominated by the rural representation occur at the ages after 30. Further, the study also suggests that the future course of demographic transition in India from third phase to the fourth phase of replacement fertility would depend on the degree and pace of decline among the rural women aged below 30 years.
Hepatic and Gastrointestinal Manifestations in Rheumatic and Connective Tissue Diseases
Authors: Shimoda Shinji , Chong Yong , Akahoshi Mitsuteru , Niiro Hiroaki , Tsukamoto Hiroshi
Published: June 2016

Digestive diseases and digestive symptoms are among the most universal diseases in everyday clinical care. However, digestive diseases accompanying rheumatic and connective tissue diseases are often onset with a background of complicated pathologies. Therefore, it is necessary to distinguish these at an early stage and carry out treatment according to the pathology. It is necessary to give specialized support upon precise medical interviews and physical examinations along with making diagnoses by standard clinical and graphic examinations.
Lambert‐Eaton Myasthenic Syndrome: A Review
Authors: Matsumoto Hideyuki , Ugawa Yoshikazu
Published: June 2016

Lambert‐Eaton myasthenic syndrome (LEMS) is an auto‐immune disorder caused by neuromuscular transmission failure, and is a representative pre‐neuromuscular junctional disorder. The auto‐immune antibody is anti‐P/Q‐type voltage‐gated calcium channel (P/Q‐type VGCC) antibody detected in approximately 80 to 90% of LEMS patients. Approximately 60% of LEMS patients have small cell lung cancer (SCLC), approximately 10% of patients have other malignant tumors, and the remaining 30% have no malignancy. Thus, the therapeutic strategy for LEMS depends on the presence of a malignant tumor. LEMS with a malignant tumor is also considered to be a representative paraneoplastic neurological syndrome. Recently, new chemotherapeutic drugs for malignant tumors including SCLC have been developed. In cases with no malignancy, several new immune‐mediated therapies have become available. Therefore, we can expect improved therapeutic responses for this disorder.
Frontostriatal Circuit Dynamics Correlate with Cocaine Cue-Evoked Behavioral Arousal during Early Abstinence
Authors: Smith Wesley C. , Rosenberg Matthew H. , Claar Leslie D. , Chang Victoria , Shah Sagar N. , Walwyn Wendy M. , Evans Christopher J. , Masmanidis Sotiris C.
Published: June 2016

It is thought that frontostriatal circuits play an important role in mediating conditioned behavioral responses to environmental stimuli that were previously encountered during drug administration. However, the neural correlates of conditioned responses to drug-associated cues are not well understood at the level of large populations of simultaneously recorded neurons, or at the level of local field potential (LFP) synchrony in the frontostriatal network. Here we introduce a behavioral assay of conditioned arousal to cocaine cues involving pupillometry in awake head-restrained mice. After just 24 h of drug abstinence, brief exposures to olfactory stimuli previously paired with cocaine injections led to a transient dilation of the pupil, which was greater than the dilation effect to neutral cues. In contrast, there was no cue-selective change in locomotion, as measured by the rotation of a circular treadmill. The behavioral assay was combined with simultaneous recordings from dozens of electrophysiologically identified units in the medial prefrontal cortex (mPFC) and ventral striatum (VS). We found significant relationships between cocaine cue-evoked pupil dilation and the proportion of inhibited principal cells in the mPFC and VS. Additionally, LFP coherence analysis revealed a significant correlation between pupillary response and synchrony in the 25–45 Hz frequency band. Together, these results show that pupil dilation is sensitive to drug-associated cues during acute stages of abstinence, and that individual animal differences in this behavioral arousal response can be explained by two complementary measures of frontostriatal network activity.
Dutch Skies, Global Laws
Authors: Achbari A. , van Lunteren F.
Published: June 2016

This essay examines the transformation of a local rule of thumb into a widely acknowledged meteorological law, generally known as Buys Ballot’s law. This law relates wind direction to atmospheric pressure. From 1857 to 1867, Christophorus Buys Ballot (1817–1890) actively lobbied in the international arena for his wind rule, which he regarded as a promising basis for a system of storm warnings. At the same time he was reluctant to generalize his rule beyond the Dutch boundaries or to make strong claims about its predictive nature. Initially he failed to interest foreign meteorologists in his work, partly because of a widespread scepticism with regard to meteorological predictions, and partly because some of his foreign colleagues favored competing theories. One of his main rivals in this respect was Robert Fitzroy, director of the British Meteorological Office, who had set up his own warning system. This practice provoked the wrath of the Royal Society, as its members regarded Fitzroy’s theories and the resulting predictions as unscientific. After his death the Society took the British Meteorological Office under its control and abolished the practice of storm warnings. The resulting wave of protests from people who felt they had benefitted from the warnings landed the Society in an awkward predicament. The warnings could only be reintroduced without losing face if they had a “scientific” basis, and therefore finding a sound basis for storm predictions became a matter of urgency. At last Buys Ballot found a willing ear for his campaign. A rapid verification of his wind rule in Britain sufficed for the introduction of the unprecedented expression “Buys Ballot’s law” in the Royal Society reports. From these authoritative reports the designation rapidly spread all over the world, thus becoming a current expression.
Materials Research, Super Batteries, and the Technopolitics of Electric Automobility
Authors: Eisler Matthew N.
Published: June 2016

The protracted commercialization of battery electric passenger vehicles is often ascribed to the failure of the automobile industry to embrace the latest power sources. In this article, I argue that the pace of progress in this context was instead dictated largely by the ways researchers constructed metrics of power source performance. Such processes can in turn be seen as issuing from the conflicting agendas of academic, industrial, and state research. Knowledge of advanced power sources historically tended to be generated not in the automobile industry but in the research laboratories of allied industries and especially in state-funded academic networks. Notable in this regard was materials science and engineering, which exerted an important epistemic influence on advanced power source and electric vehicle research and development. Materials researchers tended to select compounds for reactivity rather than safety and durability, giving rise to the idea of a super battery and leading them and others to treat power sources as essentially materials rather than parts of complex technological systems. This way of thinking prevented technologists from appreciating the physical limits of power sources in real-world applications, setting up crises of expectation at later stages of electric automobile research and development. In the gap between basic research and the exigencies of industrial technoscience, the imagined super-battery electric vehicle came to be mobilized for ends consonant with multiple entrenched interests.
Atoms in Agriculture
Authors: Curry Helen Anne
Published: June 2016

This paper explores the nature of scientific research and innovation at the intersection of technological systems via a study of atomic age plant breeding. I show how the well-established framework of “large technological systems” can be deployed to understand research dynamics in the Cold War life sciences, and further suggest that this framework might be useful in understanding still other areas of scientific research. I argue that the development of experimental tools and research programs dedicated to plant breeding via nuclear-derived technologies arose where researchers experienced the imperatives of innovation within two technological systems—nuclear and agricultural—simultaneously. In the absence of a significant infrastructure for nuclear agriculture, it was the mobility of innovations, the exchange of research tools and practices across experimental settings and research domains, which enabled nuclear-aided plant breeding to flourish for a time. As I show, understanding the dynamics of the technological systems in which researchers were embedded, including their interactions with other systems, is essential to understanding this unlikely area of research inquiry, the novel tools it relied upon, and the unusual scientific careers to which it gave rise.
Governing the Hazards of Climate
Authors: Henderson Gabriel
Published: June 2016

During the late 1970s, some members of the United States Congress introduced seminal legislation to ameliorate what they believed to be the economic costs of climatic change. Concerned that American society had become too sensitive to the stresses of even minor climatic fluctuations as manifest in recent weather-related crises, many felt that congressional legislation was necessary to foster greater cooperation between various groups—state climatologists; agricultural researchers; local, state, and federal policy makers; private and public industries. The hope was that greater coordination of the nation’s economic and scientific resources would stimulate a more flexible and resilient society, while allowing the implementation of a more service-driven approach to climate governance. Despite congressional urgency, however, the Carter Administration—specifically the Office of Management and Budget and the Office of Science and Technology Policy—challenged congressional efforts on the grounds that accommodating user needs was both scientifically unjustified and politically irresponsible. Relying heavily on what officials perceived to be the collective judgment of federal science administrators and agency heads, the Administration favored instead a more research-oriented climate program committed to improving the reliability of climate prediction and more effectively coordinating a national response. Even after President Carter reluctantly signed the National Climate Program Act in September 1978, the Administration nonetheless persisted in its effort to stifle the implementation of a service-oriented program.
A Plasmid Set for Efficient Bacterial Artificial Chromosome (BAC) Transgenesis in Zebrafish
Authors: Fuentes Fernando , Reynolds Eric , Lewellis Stephen W , Venkiteswaran Gayatri , Knaut Holger
Published: June 2016

Transgenesis of large DNA constructs is essential for gene function analysis. Recently, Tol2 transposase-mediated transgenesis has emerged as a powerful tool to insert bacterial artificial chromosome (BAC) DNA constructs into the genome of zebrafish. For efficient transgenesis, the genomic DNA piece in the BAC construct needs to be flanked by Tol2 transposon sites, and the constructs should contain a transgenesis marker for easy identification of transgenic animals. We report a set of plasmids that contain targeting cassettes that allow the insertion of Tol2 sites and different transgenesis markers into BACs. Using BACs containing these targeting cassettes, we show that transgenesis is as efficient as iTol2, that preselecting for expression of the transgenesis marker increases the transgenesis rate, and that BAC transgenics faithfully recapitulate the endogenous gene expression patterns and allow for the estimation of the endogenous gene expression levels.
Quantitative Assessment of Eye Phenotypes for Functional Genetic Studies UsingDrosophila melanogaster
Authors: Iyer Janani , Wang Qingyu , Le Thanh , Pizzo Lucilla , Grönke Sebastian , Ambegaokar Surendra S , Imai Yuzuru , Srivastava Ashutosh , Troisí Beatriz Llamusí , Mardon Graeme , Artero Ruben , Jackson George R , Isaacs Adrian M , Partridge Linda , Lu Bingwei , Kumar Justin P , Girirajan Santhosh
Published: June 2016

About two-thirds of the vital genes in the Drosophila genome are involved in eye development, making the fly eye an excellent genetic system to study cellular function and development, neurodevelopment/degeneration, and complex diseases such as cancer and diabetes. We developed a novel computational method, implemented as Flynotyper software (http://flynotyper.sourceforge.net), to quantitatively assess the morphological defects in the Drosophila eye resulting from genetic alterations affecting basic cellular and developmental processes. Flynotyper utilizes a series of image processing operations to automatically detect the fly eye and the individual ommatidium, and calculates a phenotypic score as a measure of the disorderliness of ommatidial arrangement in the fly eye. As a proof of principle, we tested our method by analyzing the defects due to eye-specific knockdown of Drosophila orthologs of 12 neurodevelopmental genes to accurately document differential sensitivities of these genes to dosage alteration. We also evaluated eye images from six independent studies assessing the effect of overexpression of repeats, candidates from peptide library screens, and modifiers of neurotoxicity and developmental processes on eye morphology, and show strong concordance with the original assessment. We further demonstrate the utility of this method by analyzing 16 modifiers of sine oculis obtained from two genome-wide deficiency screens of Drosophila and accurately quantifying the effect of its enhancers and suppressors during eye development. Our method will complement existing assays for eye phenotypes, and increase the accuracy of studies that use fly eyes for functional evaluation of genes and genetic interactions.
Genomic Selection in Multi-environment Crop Trials
Authors: Oakey Helena , Cullis Brian , Thompson Robin , Comadran Jordi , Halpin Claire , Waugh Robbie
Published: June 2016

Genomic selection in crop breeding introduces modeling challenges not found in animal studies. These include the need to accommodate replicate plants for each line, consider spatial variation in field trials, address line by environment interactions, and capture nonadditive effects. Here, we propose a flexible single-stage genomic selection approach that resolves these issues. Our linear mixed model incorporates spatial variation through environment-specific terms, and also randomization-based design terms. It considers marker, and marker by environment interactions using ridge regression best linear unbiased prediction to extend genomic selection to multiple environments. Since the approach uses the raw data from line replicates, the line genetic variation is partitioned into marker and nonmarker residual genetic variation (i.e., additive and nonadditive effects). This results in a more precise estimate of marker genetic effects. Using barley height data from trials, in 2 different years, of up to 477 cultivars, we demonstrate that our new genomic selection model improves predictions compared to current models. Analyzing single trials revealed improvements in predictive ability of up to 5.7%. For the multiple environment trial (MET) model, combining both year trials improved predictive ability up to 11.4% compared to a single environment analysis. Benefits were significant even when fewer markers were used. Compared to a single-year standard model run with 3490 markers, our partitioned MET model achieved the same predictive ability using between 500 and 1000 markers depending on the trial. Our approach can be used to increase accuracy and confidence in the selection of the best lines for breeding and/or, to reduce costs by using fewer markers.
Pollen Killer GeneS35Function Requires Interaction with an Activator That Maps Close toS24, Another Pollen Killer Gene in Rice
Authors: Kubo Takahiko , Yoshimura Atsushi , Kurata Nori
Published: June 2016

Pollen killer genes disable noncarrier pollens, and are responsible for male sterility and segregation distortion in hybrid populations of distantly related plant species. The genetic networks and the molecular mechanisms underlying the pollen killer system remain largely unknown. Two pollen killer genes, S24 and S35, have been found in an intersubspecific cross of Oryza sativa ssp. indica and japonica. The effect of S24 is counteracted by an unlinked locus EFS. Additionally, S35 has been proposed to interact with S24 to induce pollen sterility. These genetic interactions are suggestive of a single S24-centric genetic pathway (EFS–S24–S35) for the pollen killer system. To examine this hypothetical genetic pathway, the S35 and the S24 regions were further characterized and genetically dissected in this study. Our results indicated that S35 causes pollen sterility independently of both the EFS and S24 genes, but is dependent on a novel gene close to the S24 locus, named incentive for killing pollen (INK). We confirmed the phenotypic effect of the INK gene separately from the S24 gene, and identified the INK locus within an interval of less than 0.6 Mb on rice chromosome 5. This study characterized the genetic effect of the two independent genetic pathways of INK–S35 and EFS–S24 in indica–japonica hybrid progeny. Our results provide clear evidence that hybrid male sterility in rice is caused by several pollen killer networks with multiple factors positively and negatively regulating pollen killer genes.
Preparing for Winter: The Transcriptomic Response Associated with Different Day Lengths inDrosophila montana
Authors: Parker Darren J , Ritchie Michael G , Kankare Maaria
Published: June 2016

At northern latitudes, the most robust cue for assessing the onset of winter is the shortening of day lengths. Many species use day length as a cue to increase their cold tolerance and/or enter into diapause, but little is known about changes in gene expression that occur under different day lengths. We investigate the gene expression changes associated with differences in light/dark cycles in Drosophila montana, a northerly distributed species with a strong adult photoperiodic reproductive diapause. To examine gene expression changes induced by light both prior to and during diapause, we used both nondiapausing and diapausing flies. We found that the majority of genes that are differentially expressed between different day lengths in nondiapausing and diapausing flies differ. However, the biological processes involved were broadly similar. These included neuron development and metabolism, which are largely consistent with an increase in cold tolerance previously observed to occur in these flies. We also found that many genes associated with reproduction change in expression level between different day lengths, suggesting that D. montana use changes in day length to cue changes in reproduction both before and after entering into diapause. Finally, we also identified several interesting candidate genes for light-induced changes including Lsp2, para, and Ih.
Fungal Innate Immunity Induced by Bacterial Microbe-Associated Molecular Patterns (MAMPs)
Authors: Ipcho Simon , Sundelin Thomas , Erbs Gitte , Kistler H Corby , Newman Mari-Anne , Olsson Stefan
Published: June 2016

Plants and animals detect bacterial presence through Microbe-Associated Molecular Patterns (MAMPs) which induce an innate immune response. The field of fungal–bacterial interaction at the molecular level is still in its infancy and little is known about MAMPs and their detection by fungi. Exposing Fusarium graminearum to bacterial MAMPs led to increased fungal membrane hyperpolarization, a putative defense response, and a range of transcriptional responses. The fungus reacted with a different transcript profile to each of the three tested MAMPs, although a core set of genes related to energy generation, transport, amino acid production, secondary metabolism, and especially iron uptake were detected for all three. Half of the genes related to iron uptake were predicted MirA type transporters that potentially take up bacterial siderophores. These quick responses can be viewed as a preparation for further interactions with beneficial or pathogenic bacteria, and constitute a fungal innate immune response with similarities to those of plants and animals.
Organ Length Control by an ADAMTS Extracellular Protease inCaenorhabditis elegans
Authors: Shibata Yukimasa , Kawakado Yuri , Hori Noriyoshi , Tanaka Kota , Inoue Ryo , Takano Tomomi , Kubota Yukihiko , Nishiwaki Kiyoji
Published: June 2016

MIG-17, a secreted protease of the ADAMTS family, acts in the directed migration of gonadal distal tip cells (DTCs) through regulation of the gonadal basement membrane in Caenorhabditis elegans. Here, we show that MIG-17 is also required for the control of pharynx elongation during animal growth. We found that the pharynx was elongated in mig-17 mutants compared with wild type. MIG-17 localized to the pharyngeal basement membrane as well as to the gonadal basement membrane. The number of nuclei in the pharynx, and the pumping rate of the pharynx, were not affected in mig-17 mutants, suggesting that cells constituting the pharynx are elongated, although the pharynx functions normally in these mutants. In contrast to the control of DTC migration, MIG-18, a secreted cofactor of MIG-17, was not essential for pharynx length regulation. In addition, the downstream pathways of MIG-17 involving LET-2/type IV collagen, FBL-1/fibulin-1, and NID-1/nidogen, partly diverged from those in gonad development. These results indicate that basement membrane remodeling is important for organ length regulation, and suggest that MIG-17/ADAMTS functions in similar but distinct molecular machineries in pharyngeal and gonadal basement membranes.
The Histone Variant H3.3 Is Enriched atDrosophilaAmplicon Origins but Does Not Mark Them for Activation
Authors: Paranjape Neha P , Calvi Brian R
Published: June 2016

Eukaryotic DNA replication begins from multiple origins. The origin recognition complex (ORC) binds origin DNA and scaffolds assembly of a prereplicative complex (pre-RC), which is subsequently activated to initiate DNA replication. In multicellular eukaryotes, origins do not share a strict DNA consensus sequence, and their activity changes in concert with chromatin status during development, but mechanisms are ill-defined. Previous genome-wide analyses in Drosophila and other organisms have revealed a correlation between ORC binding sites and the histone variant H3.3. This correlation suggests that H3.3 may designate origin sites, but this idea has remained untested. To address this question, we examined the enrichment and function of H3.3 at the origins responsible for developmental gene amplification in the somatic follicle cells of the Drosophila ovary. We found that H3.3 is abundant at these amplicon origins. H3.3 levels remained high when replication initiation was blocked, indicating that H3.3 is abundant at the origins before activation of the pre-RC. H3.3 was also enriched at the origins during early oogenesis, raising the possibility that H3.3 bookmarks sites for later amplification. However, flies null mutant for both of the H3.3 genes in Drosophila did not have overt defects in developmental gene amplification or genomic replication, suggesting that H3.3 is not essential for the assembly or activation of the pre-RC at origins. Instead, our results imply that the correlation between H3.3 and ORC sites reflects other chromatin attributes that are important for origin function.
A Comprehensive Toolbox for Genome Editing in Cultured Drosophila melanogaster Cells
Authors: Kunzelmann Stefan , Böttcher Romy , Schmidts Ines , Förstemann Klaus
Published: June 2016

Custom genome editing has become an essential element of molecular biology. In particular, the generation of fusion constructs with epitope tags or fluorescent proteins at the genomic locus facilitates the analysis of protein expression, localization, and interaction partners at physiologic levels. Following up on our initial publication, we now describe a considerably simplified, more efficient, and readily scalable experimental workflow for PCR-based genome editing in cultured Drosophila melanogaster cells. Our analysis at the act5C locus suggests that PCR-based homology arms of 60 bp are sufficient to reach targeting efficiencies of up to 80% after selection; extension to 80 bp (PCR) or 500 bp (targeting vector) did not further improve the yield. We have expanded our targeting system to N-terminal epitope tags; this also allows the generation of cell populations with heterologous expression control of the tagged locus via the copper-inducible mtnDE promoter. We present detailed, quantitative data on editing efficiencies for several genomic loci that may serve as positive controls or benchmarks in other laboratories. While our first PCR-based editing approach offered only blasticidin-resistance for selection, we now introduce puromycin-resistance as a second, independent selection marker; it is thus possible to edit two loci (e.g., for coimmunoprecipitation) without marker removal. Finally, we describe a modified FLP recombinase expression plasmid that improves the efficiency of marker cassette FLP-out. In summary, our technique and reagents enable a flexible, robust, and cloning-free genome editing approach that can be parallelized for scale-up.
The SEB-1 Transcription Factor Binds to the STRE Motif in Neurospora crassa and Regulates a Variety of Cellular Processes Including the Stress Response and Reserve Carbohydrate Metabolism
Authors: Freitas Fernanda Zanolli , Virgilio Stela , Cupertino Fernanda Barbosa , Kowbel David John , Fioramonte Mariana , Gozzo Fabio Cesar , Glass N Louise , Bertolini Maria Célia
Published: June 2016

When exposed to stress conditions, all cells induce mechanisms resulting in an attempt to adapt to stress that involve proteins which, once activated, trigger cell responses by modulating specific signaling pathways. In this work, using a combination of pulldown assays and mass spectrometry analyses, we identified the Neurospora crassa SEB-1 transcription factor that binds to the Stress Response Element (STRE) under heat stress. Orthologs of SEB-1 have been functionally characterized in a few filamentous fungi as being involved in stress responses; however, the molecular mechanisms mediated by this transcription factor may not be conserved. Here, we provide evidences for the involvement of N. crassa SEB-1 in multiple cellular processes, including response to heat, as well as osmotic and oxidative stress. The Δseb-1 strain displayed reduced growth under these conditions, and genes encoding stress-responsive proteins were differentially regulated in the Δseb-1 strain grown under the same conditions. In addition, the SEB-1-GFP protein translocated from the cytosol to the nucleus under heat, osmotic, and oxidative stress conditions. SEB-1 also regulates the metabolism of the reserve carbohydrates glycogen and trehalose under heat stress, suggesting an interconnection between metabolism control and this environmental condition. We demonstrated that SEB-1 binds in vivo to the promoters of genes encoding glycogen metabolism enzymes and regulates their expression. A genome-wide transcriptional profile of the Δseb-1 strain under heat stress was determined by RNA-seq, and a broad range of cellular processes was identified that suggests a role for SEB-1 as a protein interconnecting these mechanisms.
N-Ethyl-N-Nitrosourea (ENU) Mutagenesis Reveals an Intronic Residue Critical forCaenorhabditis elegans3′ Splice Site Functionin Vivo
Authors: Itani Omar A , Flibotte Stephane , Dumas Kathleen J , Guo Chunfang , Blumenthal Thomas , Hu Patrick J
Published: June 2016

Metazoan introns contain a polypyrimidine tract immediately upstream of the AG dinucleotide that defines the 3′ splice site. In the nematode Caenorhabditis elegans, 3′ splice sites are characterized by a highly conserved UUUUCAG/R octamer motif. While the conservation of pyrimidines in this motif is strongly suggestive of their importance in pre-mRNA splicing, in vivo evidence in support of this is lacking. In an N-ethyl-N-nitrosourea (ENU) mutagenesis screen in Caenorhabditis elegans, we have isolated a strain containing a point mutation in the octamer motif of a 3′ splice site in the daf-12 gene. This mutation, a single base T-to-G transversion at the -5 position relative to the splice site, causes a strong daf-12 loss-of-function phenotype by abrogating splicing. The resulting transcript is predicted to encode a truncated DAF-12 protein generated by translation into the retained intron, which contains an in-frame stop codon. Other than the perfectly conserved AG dinucleotide at the site of splicing, G at the –5 position of the octamer motif is the most uncommon base in C. elegans 3′ splice sites, occurring at closely paired sites where the better match to the splicing consensus is a few bases downstream. Our results highlight both the biological importance of the highly conserved –5 uridine residue in the C. elegans 3′ splice site octamer motif as well as the utility of using ENU as a mutagen to study the function of polypyrimidine tracts and other AU- or AT-rich motifs in vivo.
A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination
Authors: Li Gang , Hillier LaDeana W , Grahn Robert A , Zimin Aleksey V , David Victor A , Menotti-Raymond Marilyn , Middleton Rondo , Hannah Steven , Hendrickson Sher , Makunin Alex , O’Brien Stephen J , Minx Pat , Wilson Richard K , Lyons Leslie A , Warren Wesley C , Murphy William J
Published: June 2016

High-resolution genetic and physical maps are invaluable tools for building accurate genome assemblies, and interpreting results of genome-wide association studies (GWAS). Previous genetic and physical maps anchored good quality draft assemblies of the domestic cat genome, enabling the discovery of numerous genes underlying hereditary disease and phenotypes of interest to the biomedical science and breeding communities. However, these maps lacked sufficient marker density to order thousands of shorter scaffolds in earlier assemblies, which instead relied heavily on comparative mapping with related species. A high-resolution map would aid in validating and ordering chromosome scaffolds from existing and new genome assemblies. Here, we describe a high-resolution genetic linkage map of the domestic cat genome based on genotyping 453 domestic cats from several multi-generational pedigrees on the Illumina 63K SNP array. The final maps include 58,055 SNP markers placed relative to 6637 markers with unique positions, distributed across all autosomes and the X chromosome. Our final sex-averaged maps span a total autosomal length of 4464 cM, the longest described linkage map for any mammal, confirming length estimates from a previous microsatellite-based map. The linkage map was used to order and orient the scaffolds from a substantially more contiguous domestic cat genome assembly (Felis catus v8.0), which incorporated ∼20 × coverage of Illumina fragment reads. The new genome assembly shows substantial improvements in contiguity, with a nearly fourfold increase in N50 scaffold size to 18 Mb. We use this map to report probable structural errors in previous maps and assemblies, and to describe features of the recombination landscape, including a massive (∼50 Mb) recombination desert (of virtually zero recombination) on the X chromosome that parallels a similar desert on the porcine X chromosome in both size and physical location.
Local Ancestry Inference in a Large US-Based Hispanic/Latino Study: Hispanic Community Health Study/Study of Latinos (HCHS/SOL)
Authors: Browning Sharon R , Grinde Kelsey , Plantinga Anna , Gogarten Stephanie M , Stilp Adrienne M , Kaplan Robert C , Avilés-Santa M Larissa , Browning Brian L , Laurie Cathy C
Published: June 2016

We estimated local ancestry on the autosomes and X chromosome in a large US-based study of 12,793 Hispanic/Latino individuals using the RFMix method, and we compared different reference panels and approaches to local ancestry estimation on the X chromosome by means of Mendelian inconsistency rates as a proxy for accuracy. We developed a novel and straightforward approach to performing ancestry-specific PCA after finding artifactual behavior in the results from an existing approach. Using the ancestry-specific PCA, we found significant population structure within African, European, and Amerindian ancestries in the Hispanic/Latino individuals in our study. In the African ancestral component of the admixed individuals, individuals whose grandparents were from Central America clustered separately from individuals whose grandparents were from the Caribbean, and also from reference Yoruba and Mandenka West African individuals. In the European component, individuals whose grandparents were from Puerto Rico diverged partially from other background groups. In the Amerindian ancestral component, individuals clustered into multiple different groups depending on the grandparental country of origin. Therefore, local ancestry estimation provides further insight into the complex genetic structure of US Hispanic/Latino populations, which must be properly accounted for in genotype-phenotype association studies. It also provides a basis for admixture mapping and ancestry-specific allele frequency estimation, which are useful in the identification of risk factors for disease.
Site-Directed Genome Knockout in Chicken Cell Line and Embryos Can Use CRISPR/Cas Gene Editing Technology
Authors: Zuo Qisheng , Wang Yinjie , Cheng Shaoze , Lian Chao , Tang Beibei , Wang Fei , Lu Zhenyu , Ji Yanqing , Zhao Ruifeng , Zhang Wenhui , Jin Kai , Song Jiuzhou , Zhang Yani , Li Bichun
Published: June 2016

The present study established an efficient genome editing approach for the construction of stable transgenic cell lines of the domestic chicken (Gallus gallus domesticus). Our objectives were to facilitate the breeding of high-yield, high-quality chicken strains, and to investigate gene function in chicken stem cells. Three guide RNA (gRNAs) were designed to knockout the C2EIP gene, and knockout efficiency was evaluated in DF-1 chicken fibroblasts and chicken ESCs using the luciferase single-strand annealing (SSA) recombination assay, T7 endonuclease I (T7EI) assay, and TA clone sequencing. In addition, the polyethylenimine-encapsulated Cas9/gRNA plasmid was injected into fresh fertilized eggs. At 4.5 d later, frozen sections of the embryos were prepared, and knockout efficiency was evaluated by the T7EI assay. SSA assay results showed that luciferase activity of the vector expressing gRNA-3 was double that of the control. Results of the T7EI assay and TA clone sequencing indicated that Cas9/gRNA vector-mediated gene knockdown efficiency was approximately 27% in both DF-1 cells and ESCs. The CRISPR/Cas9 vector was also expressed in chicken embryos, resulting in gene knockdown in three of the 20 embryos (gene knockdown efficiency 15%). Taken together, our results indicate that the CRISPR/Cas9 system can mediate stable gene knockdown at the cell and embryo levels in domestic chickens.
Quantitative Trait Locus Analysis of Mating Behavior and Male Sex Pheromones inNasoniaWasps
Authors: Diao Wenwen , Mousset Mathilde , Horsburgh Gavin J , Vermeulen Cornelis J , Johannes Frank , van de Zande Louis , Ritchie Michael G , Schmitt Thomas , Beukeboom Leo W
Published: June 2016

A major focus in speciation genetics is to identify the chromosomal regions and genes that reduce hybridization and gene flow. We investigated the genetic architecture of mating behavior in the parasitoid wasp species pair Nasonia giraulti and Nasonia oneida that exhibit strong prezygotic isolation. Behavioral analysis showed that N. oneida females had consistently higher latency times, and broke off the mating sequence more often in the mounting stage when confronted with N. giraulti males compared with males of their own species. N. oneida males produce a lower quantity of the long-range male sex pheromone (4R,5S)-5-hydroxy-4-decanolide (RS-HDL). Crosses between the two species yielded hybrid males with various pheromone quantities, and these males were used in mating trials with females of either species to measure female mate discrimination rates. A quantitative trait locus (QTL) analysis involving 475 recombinant hybrid males (F2), 2148 reciprocally backcrossed females (F3), and a linkage map of 52 equally spaced neutral single nucleotide polymorphism (SNP) markers plus SNPs in 40 candidate mating behavior genes revealed four QTL for male pheromone amount, depending on partner species. Our results demonstrate that the RS-HDL pheromone plays a role in the mating system of N. giraulti and N. oneida, but also that additional communication cues are involved in mate choice. No QTL were found for female mate discrimination, which points at a polygenic architecture of female choice with strong environmental influences.
A Genetic Map BetweenGossypium hirsutumand the Brazilian EndemicG. mustelinumand Its Application to QTL Mapping
Authors: Wang Baohua , Liu Limei , Zhang Dong , Zhuang Zhimin , Guo Hui , Qiao Xin , Wei Lijuan , Rong Junkang , May O Lloyd , Paterson Andrew H , Chee Peng W
Published: June 2016

Among the seven tetraploid cotton species, little is known about transmission genetics and genome organization in Gossypium mustelinum, the species most distant from the source of most cultivated cotton, G. hirsutum. In this research, an F2 population was developed from an interspecific cross between G. hirsutum and G. mustelinum (HM). A genetic linkage map was constructed mainly using simple sequence repeat (SSRs) and restriction fragment length polymorphism (RFLP) DNA markers. The arrangements of most genetic loci along the HM chromosomes were identical to those of other tetraploid cotton species. However, both major and minor structural rearrangements were also observed, for which we propose a parsimony-based model for structural divergence of tetraploid cottons from common ancestors. Sequences of mapped markers were used for alignment with the 26 scaffolds of the G. hirsutum draft genome, and showed high consistency. Quantitative trait locus (QTL) mapping of fiber elongation in advanced backcross populations derived from the same parents demonstrated the value of the HM map. The HM map will serve as a valuable resource for QTL mapping and introgression of G. mustelinum alleles into G. hirsutum, and help clarify evolutionary relationships between the tetraploid cotton genomes.