bluuebunny/crossref_metadata_2025 huggingface dataset:
AVALIAÇÃO PRELIMINAR DA TAXA DE SEDIMENTAÇÃO NA REGIÃO DE CULTIVO DE MOLUSCOS (Perna perna) NA ENSEADA DA ARMAÇAO - SC.
Authors: SCHETTINI C. A. , RESGALLA Jr. C. , KUROSHIMA K. N.
Published: October 2016

A atividade de cultivo do molusco Perna perna (Linnaeus, 1758) vêm crescendo de maneira expressiva ao longo do litoral do Estado de Santa Catarina nos últimos anos. Embora essa atividade apresente aspectos positivos em termos econômicos para as comunidades de pescadores arte¬sanais, ela também apresenta impactos ambientais para as regiões onde se desenvolve. Desses impactos, o aumento da taxa de sedimentação potencial é um dos efeitos comumente observados. A Enseada da Armação de ltapocoroy é um sistema abrigado do ataque de ondas provenientes do quadrante sul, e as correntes devido à maré raramente ultrapassam 0,1 m.s-1. Durante um período de 51 horas, de 30 de agosto até 1° de setembro de 1995, foi instalado um sistema de armadilhas de sedimentos abaixo de uma corda de cultivo localizada em uma região com 4 m de profundidade. O sistema ficou a 1 m acima do fundo. Esse sistema de armadilhas consiste de um flutuador com 4 tubos de PVC (armadilhas) com relação comprimento/diâmetro = 5, sendo colocado e retirado com o auxílio de mergulho autônomo. Em dois dos tubos foram adicionados 100 ml de uma solução de NaCI 50 %o, e nos outros dois tubos foram adicionados o mesmo volume de solução com formaldeído 5 %. O material retido nas armadilhas foi filtrado em filtro de fibra de vidro (poro = 0,45 gm), e desalinizado. A partir do material retido nos filtros foram analisados (1) a massa total retida, (2) organismos planctônicos com lupa, (3) carbono orgânico por titulação e (4) matéria orgânica total por combustão em mufla. A taxa de sedimentação potencial foi estimada pela relação massa retida (tempo de permanência . área da armadilha). Os resultados mostraram uma taxa de sedimentação média de 118 ± 65 g.rn-2.dia-1 (peso seco). Da massa retida, 17 % consiste de matéria orgânica total, sendo que dessa matéria orgânica, 24% é constituído de carbono orgânico, ou 4 % da massa total. Nos filtros foram encontrados zooplâncton apenas nas armadilhas com solução de formaldeído. A taxa de sedimentação potencial encontrada para a Enseada da Armação de ltapocoroy, 118 ± 65 g.m-2.dia-1, é superior à taxas encontradas em outras regiões de cultivo ao redor do mundo, no entanto deve ser considerada como uma abordagem inicial.
DIAGNÓSTICO SÓCIO-ECONÔMICO E CULTURAL NAS COMUNIDADES PESQUEIRAS ARTESANAIS DO LITORAL CENTRO-NORTE DO ESTADO DE SANTA CATARINA
Authors: MEDEIROS R. P. , POLETTE M. , VIZINHO S. C. , MACEDO C. X. , BORGES J. C.
Published: October 2016

A pesca artesanal é uma atividade tradicional na Zona Costeira do Estado de Santa Catarina, exercendo um importante papel histórico, social e econômico nesta região. Este estudo foi realizado no litoral Centro-Norte do Estado de Santa Catarina, incluindo 10 municípios: Barra Velha, Piçarras, Penha, Navegantes, ltajaí, Balneário Camboriú, Itapema, Porto Belo, Bombinhas e Tijucas, onde um diagnóstico e planejamento ambiental foi produzido. Para realizar este diagnóstico, foram realizadas 482 entrevistas com pescadores artesanais. Os resultados indicaram que a pesca de arrasto de camarão é a principal atividade pesqueira artesanal da área. Verificou-se também que, em geral, a pesca artesanal apresenta problemas importantes como a falta de fiscalização da atuação da frota industrial próxima à costa e a falta de uma política de apoio à pesca artesanal. Um outro sério problema é o desenvolvimento desordenado da orla marítima, anti¬gamente dominada por comunidades pesqueiras. Isto resultou numa diminuição do número de pescadores na comunidade e uma diminuição da rentabilidade da pesca. Soluções imediatas, como por exemplo, programas de extensão universitária, educação ambiental e uma reavaliação da política pesqueira devem ser realizadas antes que esta atividade desapareça do litoral Centro-Norte do Estado de Santa Catarina.
Los derechos humanos fundamentados mediante la legitimación y la moral jurídica.
Authors: Galán Galindo Astrid Rocío
Published: October 2016

El Estado colombiano está inmerso en el proceso de paz y posconflicto, si llegara a concretarse tal acuerdo, razón por la cual debe enfrentar una etapa de transición continua en la que se replanteen aspectos como el modelo de justicia que se ha venido aplicando y que terminará por modificar el sistema jurídico y las políticas públicas que hasta la fecha se han venido ejecutando. Es por ello que, a la hora de plantear políticas públicas cuyo objetivo sea la consecución de la paz, estas deben ser entendidas desde la esfera de la sana convivencia y la aceptación del otro. Todo aquello se lograría a partir de una evolución del sistema jurídico y cultural de la sociedad colombiana que permita incluir la moral jurídica, la cual, tiene como requisito fundamental el reconocimiento recíproco entre personas y se materializa con un sistema jurídico que abarque más allá de una simple protección a los derechos humanos. Lo anterior hace referencia a la pluricultural existente en todo el territorio nacional, por ejemplo, las minorías étnicas gitanas, afrodescendientes, etc. y a cómo deben ser incluidas de forma efectiva en un modelo social sostenible.
Perfil hematológico e bioquímico plasmático de camundongos após ingestão da planta Arrabidaea chica
Authors: Ferreira Fernanda Aires Guedes , Silva Fernando César , Carvalho Christopher Mateus , Costa Jaqueline Campos , Ferreira Júlia Maria Resende
Published: October 2016

A planta Arrabidaea chica (Humb. & Bonpl.) B. Verl. (família Bignoniaceae), conhecida como pariri é uma planta nativa das florestas tropicais e conhecida pelo seu amplo uso na medicina popular. O objetivo deste estudo foi verificar a ação de A. chica no aumento de parâmetros hematológicos e bioquímicos plasmáticos de camundongos (n=24) Swiss (Mus musculus) através do uso contínuo (ad libitum), durante 45 dias, de extratos aquoso e etanólico das folhas de A. chica. Ao fim do teste, foi feita uma avaliação clínica para avaliar condições físicas e a massa corporal dos camundongos, após o sangue dos animais foram coletados por punção cardíaca. Os resultados mostraram aumento (p<0,05) de hemácias, hemoglobina e plaquetas. O extrato etanólico apresentou maior eficiência que o extrato aquoso, apresentando aumento de 9,2% na concentração de hemácias, 4,4% na concentração de hemoglobina e 29,5% na concentração de plaquetas. Quanto ao perfil bioquímico plasmático, os camundongos apresentaram aumento (p<0,05) da enzima fosfatase alcalina indicando possível hepatoxicidade. Os resultados indicam A. chica como uma aliada fitoterápica durante tratamento de doenças sanguíneas.
Eletropolimerização de azul de metileno sobre carbono vítreo e estabilidade do filme de poli(azul de metileno)
Authors: Braun Walter Augusto , Kussler Roberto Christoph , Bagatini Marília , Hilgemann Maurício
Published: October 2016

Os polímeros condutores (CP) têm permeado muitos campos de pesquisa eletroquímica. O trabalho tem como objetivo estudar diferentes condições para a polimerização eletroquímica do azul de metileno (MB) sobre carbono vítreo e testar a estabilidade dos filmes poliméricos (PMB) formados, a fim de que possam a vir a ser usados como biomembranas. O estudo da eletropolimerização do MB foi feito através da técnica de voltametria cíclica, na faixa de potencial de -0,40 a +1,20 V, a uma velocidade de varredura de 50 mV s-1. Os parâmetros estudados para a eletropolimerização foram o o uso de diferentes soluções eletrolíticas, o potencial inicial aplicado e um pós-tratamento, que consistia em manter o filme polimérico em sua solução formadora por 24 h a 4 ºC. Para a avaliação da estabilidade dos filmes formados, voltamogramas cíclicos foram obtidos na faixa de potencial de -0,40 a +0,50 V, com uma velocidade de varredura de 50 mV s-1, em intervalos de 5 minutos entre cada leitura, utilizando uma solução de tampão acetato (pH 5,0) e NaNO3 0,1 mol L-1. Na maioria dos cenários testados, o sinal da corrente do PMB decai com o passar do tempo. No entanto, dentre as várias condições testadas, a que apresentou melhores resultados envolve deixar o eletrodo mergulhado na sua solução formadora, proporcionando que o monômero ainda presente no filme possa ser lixiviado de volta à solução, e garantindo um sinal estável com o passar do tempo.
A Fresh Look at P.Beatty III (P47) Towards an Integrative Study of an Early Christian Codex
Authors: Malik Peter
Published: October 2016

Chester Beatty Biblical Papyrus III is the earliest extensive manuscript of the Apocalypse of John. It has, however, received very little scholarly attention. This gap in our knowledge will be filled by the author’s current research, where physical and nontextual features are analysed in connection with scribal habits and textual characteristics. This preliminary article draws attention to two aspects where such an integrative method has proven particularly fruitful.
Recheneffiziente Trajektorienoptimierung für Fahrzeuge mittels quadratischem Programm
Authors: Gutjahr Benjamin , Pek Christian , Gröll Lutz , Werling Moritz
Published: October 2016

Die aus der Literatur bekannten Verfahren zur Optimierung von Fahrtrajektorien überfordern kurz und mittelfristig die
Fahrzeugsteuergeräte hinsichtlich ihrer Rechenleistung. Um auch neu aufkommenden Qualitätsanforderungen zu entsprechen,
nutzt die vorliegende Arbeit die aus der Literatur bekannten Vorteile der beschränkten, linear-quadratischen Optimierung
zur recheneffizienten Lösungsfindung gewinnbringend aus. Hierbei führt die ausgewählte Problemformulierung basierend auf
dem anwendungsspezifischem Einsatz von Schlupfvariablen zu funktionalen Weiterentwicklungen, sodass neben der
priorisierten Kollisionsvermeidung auch Aspekte natürlichen Fahrverhaltens auf besondere Weise berücksichtigt werden
können. Die Erprobung der umgesetzten Fahrzeuglängs- und -querführung im Realversuch verdeutlicht das große Potential
dieses Ansatzes für automatisierte Fahrfunktionen.
Fostering engagement with the Common European Framework of Reference for Languages and the European Language Portfolio: Learning from good practice in university language centres
Authors: Carson Lorna
Published: October 2016

This article begins with a brief overview of the aims and activities of the CercleS CEFR/ELP Focus Group. It goes on to report on some of the outcomes of the 2015 CercleS CEFR/ELP seminar hosted by the Centre for Language and Communication Studies at Trinity College Dublin. The five examples presented during the seminar’s plenary sessions are summarised, illustrating how the CEFR and ELP have been used in university language centres both to foster student engagement and reflection and to meet the increasingly urgent need for benchmarking language learning outcomes in higher education.
Aligning ESP courses with the Common European Framework of Reference for Languages
Authors: Athanasiou Androulla , Constantinou Elis Kakoulli , Neophytou Maro , Nicolaou Anna , Papadima Sophocleous Salomi , Yerou Christina
Published: October 2016

This article explains how the
From the learning diary to the ELP: An e-portfolio for autonomous language learning
Authors: Bertolotti Greta , Beseghi Micol
Published: October 2016

In 2011 the Language Centre of the University of Parma introduced a self-study programme aimed at creating an autonomy-inspired language learning environment. Students are actively engaged in the management of their own learning and co-directed by advisors and teachers in the phases of planning, monitoring and assessment. Reflective diary writing has played such a crucial role in the programme that it was decided to extend the learner diary and implement the ELP. The model used is an online version of the canonical ELP (Little and Perclová 2001), consisting of a language passport, a language biography and a dossier; it is based on the principles of reflective learning, self-assessment and learner autonomy (Little et al. 2011,
The classroom and beyond: Creating a learning environment to support learners of Japanese at CEFR levels A2.2 towards B1
Authors: Ijichi Nobuko
Published: October 2016

Japanese is a popular choice amongst higher education students on IWLPs (Institution-Wide Language Programmes), but the language presents challenges for many learners. Students on university elective programmes begin their courses with enthusiasm but often become discouraged and drop out at the post-beginner stage. Thus Japanese elective programmes in universities can be over-represented at beginner level but then tail off. There are many examples of good practice in teaching beginners Japanese but fewer models at higher levels. This activity report focuses on the development of a student learning environment suitable for Japanese at A2.2 towards B1 levels, incorporating classroom activities but also opportunities for learning in a “beyond the classroom” context. It is now widely accepted that the CEFR can provide much support and open up new opportunities. A common approach is to begin by defining appropriate “can do” descriptors, which can then be set as classroom objectives for learners. But very often there is not enough time or opportunity to use the language in the classroom. This report shows how classroom learning can be supplemented in contexts outside the institutional setting. Such contexts can provide real-world tasks, stimuli for interaction, a range of authentic documents, and culture discovery opportunities. All these support learning in a dynamic manner and ideally should link back to the CEFR’s “can do” objectives, which are identified in the core curriculum.
Copula–Induced Measures of Concordance
Authors: Fuchs Sebastian
Published: October 2016

We study measures of concordance for multivariate copulas and copulas that induce measures of
concordance. To this end, for a copula A, we consider the maps C → R given by

where C denotes the collection of all d–dimensional copulas, M is the Fréchet–Hoeffding upper bound, Π is the product copula, [. , .] : C × C → R is the biconvex form given by
[C, D] := ∫ [0,1]d C(u) dQD(u) with
the probability measure QD associated with the copula D, and ψΛ C → C is a transformation of copulas.
We present conditions on ψΛ and on A under which these maps are measures of concordance. The resulting
class of measures of concordance is rich and includes the well–known examples Spearman’s rho and Gini’s
gamma.
Quality assurance and standardization in view of non-invasive prenatal testing (NIPT)
Authors: Schenk Peter W.
Published: October 2016

The development and utilization of non-invasive prenatal tests have provided new and exciting challenges for quality assurance. Quality managers, scientists and technicians have been faced with the question of appropriate validation and quality controls for these innovative tests. Guidelines on quality assurance and quality control are still lacking and the need is growing inexorably. To integrate non-invasive prenatal tests into existing guidelines, attention must be paid to ISO standard 15189 which describes the requirements for medical laboratories and therefore diagnostic molecular genetics laboratories. Performing the test in an accredited molecular genetics laboratory according to ISO 15189 ensures the adherence to, and compliance with, all important principles. In this article, an overview of quality requirements applied to non-invasive prenatal testing is given from a quality manager’s point of view.
On unitary extensions and unitary
completions of topological monoids
Authors: Averbukh Boris G.
Published: October 2016

The concept of a unitary Cauchy net in an arbitrary Hausdorff topological monoid generalizes the
concept of a fundamental sequence of reals. We construct extensions of this monoid where all its unitary
Cauchy nets converge.
Language as Mechanisms for Interaction
Authors: Kempson Ruth , Cann Ronnie , Gregoromichelaki Eleni , Chatzikyriakidis Stergios
Published: October 2016

Language use is full of subsentential shifts of context, a phenomenon dramatically illustrated in conversation where non-sentential utterances displaying seamless shifts between speaker/hearer roles appear regularly. The hurdle this poses for standard assumptions is that every local linguistic dependency can be distributed across speakers, with the content of what they are saying and the significance of each conversational move emerging incrementally. Accordingly, we argue that the modelling of a psychologically-realistic grammar necessitates recasting the notion of natural language in terms of our ability for interaction with others and the environment, abandoning the competence-performance dichotomy as standardly envisaged. We sketch Dynamic Syntax, a model in which underspecification and incremental time-relative update is central, showing how interactive effects of conversation follow directly. Finally, we note the changing cognitive-science horizons to be explored once a language-as-action view is adopted.
What ellipsis can do for phases and what it can’t, but not how
Authors: Aelbrecht Lobke
Published: October 2016

The study of ellipsis, being a mismatch between form and meaning, has already proven to have consequences for our understanding of language in general, as it has helped us gain insights in other domains of the grammar. This paper focuses on one of these domains, namely the notion of Spell-Out and the theory of phases that has been developed within the Minimalist Program (Chomsky 1995,
Performance, Performativity, and the Medium of Poetry: W. B. Yeats’s “Among School Children”
Authors: Haekel Ralf
Published: October 2016

Performance theory has a long and complex history. Initiated by J. L. Austin’sHow To Do Things With Words, it has been critically discussed by Émile Benveniste, Jacques Derrida, and Paul de Man among others. Most recently, media studies and the concept of cultural techniques have added yet another facet to what originated in speech act theory. Although poetry with its musical dimension seems especially prone to be investigated in the field, this is rarely the case. After an overview of the relevant theoretical developments, I analyze William Butler Yeats’s “Among School Children” – with a special focus on its final verse “How can we know the dancer from the dance?” – as a powerful reflection on the performative nature of poetry in general.
Involvement of Brain-Enriched Guanylate Kinase-Associated Protein (BEGAIN) in Chronic Pain after Peripheral Nerve Injury
Authors: Katano Tayo , Fukuda Masafumi , Furue Hidemasa , Yamazaki Maya , Abe Manabu , Watanabe Masahiko , Nishida Kazuhiko , Yao Ikuko , Yamada Akihiro , Hata Yutaka , Okumura Nobuaki , Nakazawa Takanobu , Yamamoto Tadashi , Sakimura Kenji , Takao Toshifumi , Ito Seiji
Published: October 2016

Maintenance of neuropathic pain caused by peripheral nerve injury crucially depends on the phosphorylation of GluN2B, a subunit of the N-methyl-d-aspartate (NMDA) receptor, at Tyr1472 (Y1472) and subsequent formation of a postsynaptic density (PSD) complex of superficial spinal dorsal horn neurons. Here we took advantage of comparative proteomic analysis based on isobaric stable isotope tags (iTRAQ) between wild-type and knock-in mice with a mutation of Y1472 to Phe of GluN2B (Y1472F-KI) to search for PSD proteins in the spinal dorsal horn that mediate the signaling downstream of phosphorylated Y1472 GluN2B. Among several candidate proteins, we focused on brain-enriched guanylate kinase-associated protein (BEGAIN), which was specifically up-regulated in wild-type mice after spared nerve injury (SNI). Immunohistochemical analysis using the generated antibody demonstrated that BEGAIN was highly localized at the synapse of inner lamina II in the spinal dorsal horn and that its expression was up-regulated after SNI in wild-type, but not in Y1472F-KI, mice. In addition, alteration of the kinetics of evoked excitatory postsynaptic currents for NMDA but not those for α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors in spinal lamina II was demonstrated by BEGAIN deletion. We demonstrated that mechanical allodynia, a condition of abnormal pain induced by innocuous stimuli, in the SNI model was significantly attenuated in BEGAIN-deficient mice. However, there was no significant difference between naive wild-type and BEGAIN-knockout mice in terms of physiological threshold for mechanical stimuli. These results suggest that BEGAIN was involved in pathological pain transmission through NMDA receptor activation by the phosphorylation of GluN2B at Y1472 in spinal inner lamina II.
Black Feminist Reflections on Activism
Authors: Scott Karla D.
Published: October 2016

Often experienced but rarely theorized, black feminist activism can be exhausting and the emotional labor debilitating. Yet often in the name of being “good” and “strong” black women who are “down” for the cause and our people, we keep going even when it hurts. Doing so continues the legacy of domination by relentlessly caring for others at the expense of ourselves. To protect and preserve our physical, emotional, intellectual, and spiritual health as black women, we must ask: How can we repurpose our strength to lead and support demonstrations against social injustices without continually sacrificing our wellbeing? Focused on summer 2014, I explore how the aftermath of my mother's death and living amid the fires of Ferguson, MO—linked to the killing of Michael Brown—sparked the realization that self-care is critical for black feminist survival.
Absorption and distribution of estradiol from male seminal emissions during mating
Authors: deCatanzaro Denys , Pollock Tyler
Published: October 2016

Estradiol-17β (E2) plays critical roles in female maturation, sexual receptivity, ovulation and fertility. In many mammals, contact with males can similarly affect these female parameters, whereas male excretions contain significant quantities of E2. We administered radiolabeled estradiol ([3H]E2) to male mice in doses representing a small fraction of their endogenous E2. These males were paired with sexually receptive females, and radioactivity was traced into the females’ systems. In Experiment 1, males were given [3H]E2 at 24 and 1 h before mating. Male-to-female [3H]E2 transfer intensified with increasing numbers of intromissions and spiked in the uterus after insemination. In Experiment 2, sexually experienced young males received [3H]E2 at 72 and 24 h before mating, and all mated to ejaculation. The copulatory plug deposited in the female reproductive tract contained substantial levels of radioactivity. The uteri, other tissues and blood serum of females displayed radioactivity indicative of E2 transfer. In Experiment 3, radioactivity was observed 3 and 18 h after insemination in the females’ uteri and other tissues, including parts of the brain. In Experiment 4, we observed substantial levels of radioactivity in semen as well as the copulatory plugs retrieved from the females after mating. Transferred E2 could directly affect abundant estrogen receptors in the female reproductive tract without potential metabolism by the liver. Sexually transferred E2 may facilitate uterine preparation for blastocyst implantation. These data converge with several lines of evidence indicating that male-sourced E2 can transfer to proximate females in bioactive form, contributing to various mammalian pheromonal effects.
Evolutionary Genomics of Peach and Almond Domestication
Authors: Velasco Dianne , Hough Josh , Aradhya Mallikarjuna , Ross-Ibarra Jeffrey
Published: October 2016

The domesticated almond [Prunus dulcis (L.) Batsch] and peach [P. persica (Mill.) D. A. Webb] originated on opposite sides of Asia and were independently domesticated ∼5000 yr ago. While interfertile, they possess alternate mating systems and differ in a number of morphological and physiological traits. Here, we evaluated patterns of genome-wide diversity in both almond and peach to better understand the impacts of mating system, adaptation, and domestication on the evolution of these taxa. Almond has around seven times the genetic diversity of peach, and high genome-wide FST values support their status as separate species. We estimated a divergence time of ∼8 MYA (million years ago), coinciding with an active period of uplift in the northeast Tibetan Plateau and subsequent Asian climate change. We see no evidence of a bottleneck during domestication of either species, but identify a number of regions showing signatures of selection during domestication and a significant overlap in candidate regions between peach and almond. While we expected gene expression in fruit to overlap with candidate selected regions, instead we find enrichment for loci highly differentiated between the species, consistent with recent fossil evidence suggesting fruit divergence long preceded domestication. Taken together, this study tells us how closely related tree species evolve and are domesticated, the impact of these events on their genomes, and the utility of genomic information for long-lived species. Further exploration of this data will contribute to the genetic knowledge of these species and provide information regarding targets of selection for breeding application, and further the understanding of evolution in these species.
Transcriptome Analysis Reveals that Vitamin A Metabolism in the Liver Affects Feed Efficiency in Pigs
Authors: Zhao Yunxia , Hou Ye , Liu Fei , Liu An , Jing Lu , Zhao Changzhi , Luan Yu , Miao Yuanxin , Zhao Shuhong , Li Xinyun
Published: October 2016

Feed efficiency (FE) is essential for pig production. In this study, 300 significantly differentially expressed (DE) transcripts, including 232 annotated genes, 28 cis-natural antisense transcripts (cis-NATs), and 40 long noncoding RNAs (lncRNAs), were identified between the liver of Yorkshire pigs with extremely high and low FE. Among these transcripts, 25 DE lncRNAs were significantly correlated with 125 DE annotated genes at a transcriptional level. These DE genes were enriched primarily in vitamin A (VA), fatty acid, and steroid hormone metabolism. VA metabolism is regulated by energy status, and active derivatives of VA metabolism can regulate fatty acid and steroid hormones metabolism. The key genes of VA metabolism (CYP1A1, ALDH1A2, and RDH16), fatty acid biosynthesis (FASN, SCD, CYP2J2, and ANKRD23), and steroid hormone metabolism (CYP1A1, HSD17B2, and UGT2B4) were significantly upregulated in the liver of high-FE pigs. Previous study with the same samples indicated that the mitochondrial function and energy expenditure were reduced in the muscle tissue of high-FE pigs. In conclusion, VA metabolism in liver tissues plays important roles in the regulation of FE in pigs by affecting energy metabolism, which may mediate fatty acid biosynthesis and steroid hormone metabolism. Furthermore, our results identified novel transcripts, such as cis-NATs and lncRNAs, which are also involved in the regulation of FE in pigs.
Distinct and Overlapping Requirements for Cyclins A, B, and B3 inDrosophilaFemale Meiosis
Authors: Bourouh Mohammed , Dhaliwal Rajdeep , Rana Ketki , Sinha Sucheta , Guo Zhihao , Swan Andrew
Published: October 2016

Meiosis, like mitosis, depends on the activity of the cyclin dependent kinase Cdk1 and its cyclin partners. Here, we examine the specific requirements for the three mitotic cyclins, A, B, and B3 in meiosis of Drosophila melanogaster. We find that all three cyclins contribute redundantly to nuclear envelope breakdown, though cyclin A appears to make the most important individual contribution. Cyclin A is also required for biorientation of homologs in meiosis I. Cyclin B3, as previously reported, is required for anaphase progression in meiosis I and in meiosis II. We find that it also plays a redundant role, with cyclin A, in preventing DNA replication during meiosis. Cyclin B is required for maintenance of the metaphase I arrest in mature oocytes, for spindle organization, and for timely progression through the second meiotic division. It is also essential for polar body formation at the completion of meiosis. With the exception of its redundant role in meiotic maturation, cyclin B appears to function independently of cyclins A and B3 through most of meiosis. We conclude that the three mitotic cyclin-Cdk complexes have distinct and overlapping functions in Drosophila female meiosis.
Transcriptome Profiling in Rat Inbred Strains and Experimental Cross Reveals Discrepant Genetic Architecture of Genome-Wide Gene Expression
Authors: Kaisaki Pamela J , Otto Georg W , Argoud Karène , Collins Stephan C , Wallis Robert H , Wilder Steven P , Yau Anthony C Y , Hue Christophe , Calderari Sophie , Bihoreau Marie-Thérèse , Cazier Jean-Baptiste , Mott Richard , Gauguier Dominique
Published: October 2016

To test the impact of genetic heterogeneity on cis- and trans-mediated mechanisms of gene expression regulation, we profiled the transcriptome of adipose tissue in 20 inbred congenic strains derived from diabetic Goto–Kakizaki (GK) rats and Brown–Norway (BN) controls, which contain well-defined blocks (1–183 Mb) of genetic polymorphisms, and in 123 genetically heterogeneous rats of an (GK × BN)F2 offspring. Within each congenic we identified 73–1351 differentially expressed genes (DEGs), only 7.7% of which mapped within the congenic blocks, and which may be regulated in cis. The remainder localized outside the blocks, and therefore must be regulated in trans. Most trans-regulated genes exhibited approximately twofold expression changes, consistent with monoallelic expression. Altered biological pathways were replicated between congenic strains sharing blocks of genetic polymorphisms, but polymorphisms at different loci also had redundant effects on transcription of common distant genes and pathways. We mapped 2735 expression quantitative trait loci (eQTL) in the F2 cross, including 26% predominantly cis-regulated genes, which validated DEGs in congenic strains. A hotspot of >300 eQTL in a 10 cM region of chromosome 1 was enriched in DEGs in a congenic strain. However, many DEGs among GK, BN and congenic strains did not replicate as eQTL in F2 hybrids, demonstrating distinct mechanisms of gene expression when alleles segregate in an outbred population or are fixed homozygous across the entire genome or in short genomic regions. Our analysis provides conceptual advances in our understanding of the complex architecture of genome expression and pathway regulation, and suggests a prominent impact of epistasis and monoallelic expression on gene transcription.
Genomic, Transcriptomic, and Proteomic Analysis Provide Insights Into the Cold Adaptation Mechanism of the Obligate Psychrophilic Fungus Mrakia psychrophila
Authors: Su Yao , Jiang Xianzhi , Wu Wenping , Wang Manman , Hamid M Imran , Xiang Meichun , Liu Xingzhong
Published: October 2016

Mrakia psychrophila is an obligate psychrophilic fungus. The cold adaptation mechanism of psychrophilic fungi remains unknown. Comparative genomics analysis indicated that M. psychrophila had a specific codon usage preference, especially for codons of Gly and Arg and its major facilitator superfamily (MFS) transporter gene family was expanded. Transcriptomic analysis revealed that genes involved in ribosome and energy metabolism were upregulated at 4°, while genes involved in unfolded protein binding, protein processing in the endoplasmic reticulum, proteasome, spliceosome, and mRNA surveillance were upregulated at 20°. In addition, genes related to unfolded protein binding were alternatively spliced. Consistent with other psychrophiles, desaturase and glycerol 3-phosphate dehydrogenase, which are involved in biosynthesis of unsaturated fatty acid and glycerol respectively, were upregulated at 4°. Cold adaptation of M. psychrophila is mediated by synthesizing unsaturated fatty acids to maintain membrane fluidity and accumulating glycerol as a cryoprotectant. The proteomic analysis indicated that the correlations between the dynamic patterns between transcript level changes and protein level changes for some pathways were positive at 4°, but negative at 20°. The death of M. psychrophila above 20° might be caused by an unfolded protein response.
Proper Sterol Distribution Is Required for Candida albicans Hyphal Formation and Virulence
Authors: McCourt Paula , Liu Hsing-Yin , Parker Josie E , Gallo-Ebert Christina , Donigan Melissa , Bata Adam , Giordano Caroline , Kelly Steven L , Nickels Joseph T
Published: October 2016

Candida albicans is an opportunistic fungus responsible for the majority of systemic fungal infections. Multiple factors contribute to C. albicans pathogenicity. C. albicans strains lacking CaArv1 are avirulent. Arv1 has a conserved Arv1 homology domain (AHD) that has a zinc-binding domain containing two cysteine clusters. Here, we explored the role of the CaAHD and zinc-binding motif in CaArv1-dependent virulence. Overall, we found that the CaAHD was necessary but not sufficient for cells to be virulent, whereas the zinc-binding domain was essential, as Caarv1/Caarv1 cells expressing the full-length zinc-binding domain mutants, Caarv1C3S and Caarv1C28S, were avirulent. Phenotypically, we found a direct correlation between the avirulence of Caarv1/Caarv1, Caarrv1AHD, Caarv1C3S, and Caarv1C28S cells and defects in bud site selection, septa formation and localization, and hyphal formation and elongation. Importantly, all avirulent mutant strains lacked the ability to maintain proper sterol distribution. Overall, our results have established the importance of the AHD and zinc-binding domain in fungal invasion, and have correlated an avirulent phenotype with the inability to maintain proper sterol distribution.
CRISPR/Cas9-Mediated Genome Editing and Mutagenesis of EcChi4 in Exopalaemon carinicauda
Authors: Gui Tianshu , Zhang Jiquan , Song Fengge , Sun Yuying , Xie Shijun , Yu Kuijie , Xiang Jianhai
Published: October 2016

The development of the type II clustered regularly interspaced short palindromic repeats (CRISPR) system has resulted in the revolution of genetic engineering, and this technology has been applied in the genome editing of various species. However, there are no reports about target-specific genome editing in shrimp. In this research, we developed a microinjection method for the ridgetail white prawn Exopalaemon carinicauda and successfully applied CRISPR/Cas9 technology to the genome editing of E. carinicauda. Through coinjection of mRNA of Cas9 nuclease and gRNA specialized for E. carinicauda chitinase 4 (EcChi4), shrimps with indel mutations were obtained. Further analysis showed that the mutations could be transmitted to the next generation. This is the first time that site-specific genome editing has been successfully demonstrated in a decapod, and will further contribute to the study of functional genomics in decapods.
In Silico Whole Genome Sequencer and Analyzer (iWGS): a Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies
Authors: Zhou Xiaofan , Peris David , Kominek Jacek , Kurtzman Cletus P , Hittinger Chris Todd , Rokas Antonis
Published: October 2016

The availability of genomes across the tree of life is highly biased toward vertebrates, pathogens, human disease models, and organisms with relatively small and simple genomes. Recent progress in genomics has enabled the de novo decoding of the genome of virtually any organism, greatly expanding its potential for understanding the biology and evolution of the full spectrum of biodiversity. The increasing diversity of sequencing technologies, assays, and de novo assembly algorithms have augmented the complexity of de novo genome sequencing projects in nonmodel organisms. To reduce the costs and challenges in de novo genome sequencing projects and streamline their experimental design and analysis, we developed iWGS (in silicoWhole Genome Sequencer and Analyzer), an automated pipeline for guiding the choice of appropriate sequencing strategy and assembly protocols. iWGS seamlessly integrates the four key steps of a de novo genome sequencing project: data generation (through simulation), data quality control, de novo assembly, and assembly evaluation and validation. The last three steps can also be applied to the analysis of real data. iWGS is designed to enable the user to have great flexibility in testing the range of experimental designs available for genome sequencing projects, and supports all major sequencing technologies and popular assembly tools. Three case studies illustrate how iWGS can guide the design of de novo genome sequencing projects, and evaluate the performance of a wide variety of user-specified sequencing strategies and assembly protocols on genomes of differing architectures. iWGS, along with a detailed documentation, is freely available at https://github.com/zhouxiaofan1983/iWGS.
Extensive Epigenetic Changes Accompany Terminal Differentiation of Mouse Hepatocytes After Birth
Authors: Cannon Matthew V , Pilarowski Genay , Liu Xiuli , Serre David
Published: October 2016

DNA methylation is traditionally thought to be established during early development and to remain mostly unchanged thereafter in healthy tissues, although recent studies have shown that this epigenetic mark can be more dynamic. Epigenetic changes occur in the liver after birth, but the timing and underlying biological processes leading to DNA methylation changes are not well understood. We hypothesized that this epigenetic reprogramming was the result of terminal differentiation of hepatocyte precursors. Using genomic approaches, we characterized the DNA methylation patterns in mouse liver from E18.5 until adulthood to determine if the timing of the DNA methylation change overlaps with hepatocyte terminal differentiation, and to examine the genomic context of these changes and identify the regulatory elements involved. Out of 271,325 CpGs analyzed throughout the genome, 214,709 CpGs changed DNA methylation by more than 5% (e.g., from 5 to 10% methylation) between E18.5 and 9 wk of age, and 18,863 CpGs changed DNA methylation by more than 30%. Genome-scale data from six time points between E18.5 and P20 show that DNA methylation changes coincided with the terminal differentiation of hepatoblasts into hepatocytes. We also showed that epigenetic reprogramming occurred primarily in intergenic enhancer regions while gene promoters were less affected. Our data suggest that normal postnatal hepatic development and maturation involves extensive epigenetic remodeling of the genome, and that enhancers play a key role in controlling the transition from hepatoblasts to fully differentiated hepatocytes. Our study provides a solid foundation to support future research aimed at further revealing the role of epigenetics in stem cell biology.
Drosophila CG2469 Encodes a Homolog of Human CTR9 and Is Essential for Development
Authors: Chaturvedi Dhananjay , Inaba Mayu , Scoggin Shane , Buszczak Michael
Published: October 2016

Conserved from yeast to humans, the Paf1 complex participates in a number of diverse processes including transcriptional initiation and polyadenylation. This complex typically includes five proteins: Paf1, Rtf1, Cdc73, Leo1, and Ctr9. Previous efforts identified clear Drosophila homologs of Paf1, Rtf1, and Cdc73 based on sequence similarity. Further work showed that these proteins help to regulate gene expression and are required for viability. To date, a Drosophila homolog of Ctr9 has remained uncharacterized. Here, we show that the gene CG2469 encodes a functional Drosophila Ctr9 homolog. Both human and Drosophila Ctr9 localize to the nuclei of Drosophila cells and appear enriched in histone locus bodies. RNAi knockdown of Drosophila Ctr9 results in a germline stem cell loss phenotype marked by defects in the morphology of germ cell nuclei. A molecular null mutation of Drosophila Ctr9 results in lethality and a human cDNA CTR9 transgene rescues this phenotype. Clonal analysis in the ovary using this null allele reveals that loss of Drosophila Ctr9 results in a reduction of global levels of histone H3 trimethylation of lysine 4 (H3K4me3), but does not compromise the maintenance of stem cells in ovaries. Given the differences between the null mutant and RNAi knockdown phenotypes, the germ cell defects caused by RNAi likely result from the combined loss of Drosophila Ctr9 and other unidentified genes. These data provide further evidence that the function of this Paf1 complex component is conserved across species.
The GATOR1 Complex Regulates Metabolic Homeostasis and the Response to Nutrient Stress inDrosophila melanogaster
Authors: Wei Youheng , Reveal Brad , Cai Weili , Lilly Mary A
Published: October 2016

TORC1 regulates metabolism and growth in response to a large array of upstream inputs. The evolutionarily conserved trimeric GATOR1 complex inhibits TORC1 activity in response to amino acid limitation. In humans, the GATOR1 complex has been implicated in a wide array of pathologies including cancer and hereditary forms of epilepsy. However, the precise role of GATOR1 in animal physiology remains largely undefined. Here, we characterize null mutants of the GATOR1 components nprl2, nprl3, and iml1 in Drosophila melanogaster. We demonstrate that all three mutants have inappropriately high baseline levels of TORC1 activity and decreased adult viability. Consistent with increased TORC1 activity, GATOR1 mutants exhibit a cell autonomous increase in cell growth. Notably, escaper nprl2 and nprl3 mutant adults have a profound locomotion defect. In line with a nonautonomous role in the regulation of systemic metabolism, expressing the Nprl3 protein in the fat body, a nutrient storage organ, and hemocytes but not muscles and neurons rescues the motility of nprl3 mutants. Finally, we show that nprl2 and nprl3 mutants fail to activate autophagy in response to amino acid limitation and are extremely sensitive to both amino acid and complete starvation. Thus, in Drosophila, in addition to maintaining baseline levels of TORC1 activity, the GATOR1 complex has retained a critical role in the response to nutrient stress. In summary, the TORC1 inhibitor GATOR1 contributes to multiple aspects of the development and physiology of Drosophila.
Improvement of Predictive Ability by Uniform Coverage of the Target Genetic Space
Authors: Bustos-Korts Daniela , Malosetti Marcos , Chapman Scott , Biddulph Ben , van Eeuwijk Fred
Published: October 2016

Genome-enabled prediction provides breeders with the means to increase the number of genotypes that can be evaluated for selection. One of the major challenges in genome-enabled prediction is how to construct a training set of genotypes from a calibration set that represents the target population of genotypes, where the calibration set is composed of a training and validation set. A random sampling protocol of genotypes from the calibration set will lead to low quality coverage of the total genetic space by the training set when the calibration set contains population structure. As a consequence, predictive ability will be affected negatively, because some parts of the genotypic diversity in the target population will be under-represented in the training set, whereas other parts will be over-represented. Therefore, we propose a training set construction method that uniformly samples the genetic space spanned by the target population of genotypes, thereby increasing predictive ability. To evaluate our method, we constructed training sets alongside with the identification of corresponding genomic prediction models for four genotype panels that differed in the amount of population structure they contained (maize Flint, maize Dent, wheat, and rice). Training sets were constructed using uniform sampling, stratified-uniform sampling, stratified sampling and random sampling. We compared these methods with a method that maximizes the generalized coefficient of determination (CD). Several training set sizes were considered. We investigated four genomic prediction models: multi-locus QTL models, GBLUP models, combinations of QTL and GBLUPs, and Reproducing Kernel Hilbert Space (RKHS) models. For the maize and wheat panels, construction of the training set under uniform sampling led to a larger predictive ability than under stratified and random sampling. The results of our methods were similar to those of the CD method. For the rice panel, all training set construction methods led to similar predictive ability, a reflection of the very strong population structure in this panel.
Higher Objectives of Islamic Investment Products: Islamizing Indonesian Capital Market
Authors: Soemitra Andri
Published: October 2016

Indonesian capital market regulators have already accommodated Islamic products as one of Indonesian capital market products. Theoretically, Islamic investment promises three main benefits i.e. spiritual, financial, and social benefits. Realizing Islamic investment in the sense of those three main benefits needs serious effort. This paper discusses the perception of capital market investors. This study suggests that their opinion as to whether or not sharī‘ah capital market products had fulfilled their expectations of Islamic comprehensive objectives. Islamic capital market instruments are part of Islamic instruments. The Islamization of financial institutions and instruments in the modern era has emerged not only to meet Muslims’ need for financial activities but also as the medium to realize the higher objectives of Islam, i.e. maqāṣid al-sharī‘ah in economic and financial activities.DOI: 10.15408/sdi.v23i2.2408
The Reception of Seyyed Hossein Nasr’s Ideas within the Indonesian Intellectual Landscape
Authors: Widiyanto Asfa
Published: October 2016

This paper examines the appreciation and acceptance of Seyyed Hossein Nasr’s (b. 1933) ideas in the context of intellectual discourse in Indonesia. To do so, it investigates the translation of Nasr’s works into Indonesian, studies on Nasr’s thought, and quotations from Nasr’s works that emerge in the writings of some Indonesian intellectuals. It is especially the notions of Perennialism, “traditional Islam” and scientia sacra that throw light on the process by which his ideas have taken root and gained influence and acceptance in Indonesia. To be more specific, the article scrutinizes the impact of Nasr’s ideas and perspectives on the structure of thought of two Indonesian intellectuals, namely Nurcholish Madjid (1939-2005) and Komaruddin Hidayat (b. 1953). This paper also traces the roots of Nasr’s and Hidayat’s thought in the classical-medieval Islamic tradition, most specifically in Suhrawardi’s School of Illumination, and compares these with those of Madjid and Hidayat.DOI: 10.15408/sdi.v23i2.3002
Ḥizb al-‘Adālah wa al-Rafāhīyah (PKS) wa Siyāsāt al-Huwīyah al-Islāmīyah: Istiratijīyāt Kawādir al-Ḥizb li Ta’ṭīr Qaḍāyā Nukhabihim al-Fasādīyah al-Mālīyah
Authors: Saputra Rangga Eka
Published: October 2016

This article explains the mechanism of cadre engagement and militancy of Prosperous Justice Party (PKS), as the Islamist party in Indonesia. This study departs from the puzzle that despite their president, Luthfi Hasan Ishaaq, was accused for corruption crime ahead of elections in 2014, but the PKS’s vote still stable from the previous election period (2009). Since PKS is a party cadre, this study argues that the success of the PKS in maintaining the vote in the 2014 election was because of militancy and loyalty of their cadre in doing work collectively for the party. By using the framing approach in the field of social movement, this study concludes that the engagement and militancy of the PKS’s cadre have been influenced by their vigorous framing resources both ideology and identity, as well as the ability of party leaders in mobilizing those resources to their cadre at the lower levels.DOI: 10.15408/sdi.v23i2.3313