scholarly journals Re-annotation of eight Drosophila genomes

2018 ◽  
Vol 1 (6) ◽  
pp. e201800156 ◽  
Author(s):  
Haiwang Yang ◽  
Maria Jaime ◽  
Maxi Polihronakis ◽  
Kelvin Kanegawa ◽  
Therese Markow ◽  
...  
Keyword(s):  
Species Differences ◽  
Transcriptome Assembly ◽  
Model Organisms ◽  
The Core ◽  
Extant Species ◽  
Species Comparisons ◽  
Central Resource ◽  
Extensive Collection ◽  
The Many ◽  
Drosophila Grimshawi

The sequenced genomes of the Drosophila phylogeny are a central resource for comparative work supporting the understanding of the Drosophila melanogaster non-mammalian model system. These have also facilitated evolutionary studies on the selected and random differences that distinguish the thousands of extant species of Drosophila. However, full utility has been hampered by uneven genome annotation. We have generated a large expression profile dataset for nine species of Drosophila and trained a transcriptome assembly approach on D. melanogaster that best matched the extensively curated annotation. We then applied this to the other species to add more than 10000 transcript models per species. We also developed new orthologs to facilitate cross-species comparisons. We validated the new annotation of the distantly related Drosophila grimshawi with an extensive collection of newly sequenced cDNAs. This re-annotation will facilitate understanding both the core commonalities and the species differences in this important group of model organisms, and suggests a strategy for annotating the many forthcoming genomes covering the tree of life.

scholarly journals Reannotation of eight Drosophila genomes

2018 ◽  
Author(s):  
Haiwang Yang ◽  
Maria Jaime ◽  
Maxi Polihronakis ◽  
Kelvin Kanegawa ◽  
Therese Markow ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Transcriptome Assembly ◽  
Model Organisms ◽  
Extant Species ◽  
New Gene ◽  
Drosophila Phylogeny ◽  
Species Comparisons ◽  
Central Resource ◽  
Extensive Collection ◽  
Drosophila Grimshawi

AbstractThe sequenced genomes in the Drosophila phylogeny is a central resource for comparative work supporting the understanding of the Drosophila melanogaster non-mammalian model system. These have also facilitated studying the selected and random differences that distinguish the thousands of extant species of Drosophila. However, full utility has been hampered by uneven genome annotation. We have generated a large expression profile dataset for nine species of Drosophila and trained a transcriptome assembly approach on Drosophila melanogaster to develop a pipeline that best matched the extensively curated annotation. We then applied this to the other species to add tens of thousands of new gene models per species. We also developed new orthologs to facilitate cross-species comparisons. We validated the new annotation of the distantly related Drosophila grimshawi with an extensive collection of newly sequenced cDNAs. This reannoation will facilitate understanding both the core commonalities and the species differences in this important group of model organisms.

Computing Cores for Existential Rules with the Standard Chase and ASP

2020 ◽  
Author(s):  
Markus Krötzsch
Keyword(s):  
Large Class ◽  
Data Exchange ◽  
Answer Set Programming ◽  
Query Answering ◽  
Universal Model ◽  
The Core ◽  
Universal Models ◽  
General Terms ◽  
Special Cases ◽  
The Many

To reason with existential rules (a.k.a. tuple-generating dependencies), one often computes universal models. Among the many such models of different structure and cardinality, the core is arguably the “best”. Especially for finitely satisfiable theories, where the core is the unique smallest universal model, it has advantages in query answering, non-monotonic reasoning, and data exchange. Unfortunately, computing cores is difficult and not supported by most reasoners. We therefore propose ways of computing cores using practically implemented methods from rule reasoning and answer set programming. Our focus is on cases where the standard chase algorithm produces a core. We characterise this desirable situation in general terms that apply to a large class of cores, derive concrete approaches for decidable special cases, and generalise these approaches to non-monotonic extensions of existential rules.

AFRICAN WOMEN AND FORBIDDEN GROUNDS: FEMALE SEXUALITY AND SELF-DETERMINATION IN AFRICAN LITERATURE

Imbizo ◽  
2017 ◽  
Vol 7 (1) ◽  
pp. 40-54
Author(s):  
Oyeh O. Otu
Keyword(s):  
Female Sexuality ◽  
Sense Of Self ◽  
African Literature ◽  
The Other ◽  
Self Determination ◽  
African Women ◽  
The Core ◽  
The Many ◽  
The One ◽  
Sexual Repression

This article examines how female conditioning and sexual repression affect the woman’s sense of self, womanhood, identity and her place in society. It argues that the woman’s body is at the core of the many sites of gender struggles/ politics. Accordingly, the woman’s body must be decolonised for her to attain true emancipation. On the one hand, this study identifies the grave consequences of sexual repression, how it robs women of their freedom to choose whom to love or marry, the freedom to seek legal redress against sexual abuse and terror, and how it hinders their quest for self-determination. On the other hand, it underscores the need to give women sexual freedom that must be respected and enforced by law for the overall good of society.

scholarly journals The brain transcriptome of the wolf spider, Schizocosa ocreata

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Daniel Stribling ◽  
Peter L. Chang ◽  
Justin E. Dalton ◽  
Christopher A. Conow ◽  
Malcolm Rosenthal ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Model Organisms ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Wolf Spiders ◽  
Schizocosa Ocreata ◽  
Genomic Studies ◽  
The Brain

Abstract Objectives Arachnids have fascinating and unique biology, particularly for questions on sex differences and behavior, creating the potential for development of powerful emerging models in this group. Recent advances in genomic techniques have paved the way for a significant increase in the breadth of genomic studies in non-model organisms. One growing area of research is comparative transcriptomics. When phylogenetic relationships to model organisms are known, comparative genomic studies provide context for analysis of homologous genes and pathways. The goal of this study was to lay the groundwork for comparative transcriptomics of sex differences in the brain of wolf spiders, a non-model organism of the pyhlum Euarthropoda, by generating transcriptomes and analyzing gene expression. Data description To examine sex-differential gene expression, short read transcript sequencing and de novo transcriptome assembly were performed. Messenger RNA was isolated from brain tissue of male and female subadult and mature wolf spiders (Schizocosa ocreata). The raw data consist of sequences for the two different life stages in each sex. Computational analyses on these data include de novo transcriptome assembly and differential expression analyses. Sample-specific and combined transcriptomes, gene annotations, and differential expression results are described in this data note and are available from publicly-available databases.

scholarly journals Terra Madre 2006: Political Theater and Ritual Rhetoric in the Slow Food Movement

2008 ◽  
Vol 8 (2) ◽  
pp. 31-39 ◽  
Author(s):  
adrian peace
Keyword(s):  
Political Theater ◽  
The Political ◽  
Slow Food ◽  
Political Spectacle ◽  
The Core ◽  
Global Character ◽  
Secular Rituals ◽  
The Many ◽  
Mega Event ◽  
Food Movement

The biannual mega-event of Terra Madre is now established as the political flagship of the Slow Food movement. It assembles in Turin the leading cosmopolitan figures of this neo-tribal, post modern organization, along with several thousand of its ordinary members, who were drawn in 2006 from the ranks of food producers, cooks and academics. The most significant secular rituals of Terra Madre involve the theatrical celebration of its global character, beginning with the assembly of representatives from some 1600 ““food communities”” distributed throughout the world. Equally important are the many smaller scale activities in which the details of the movement's politics are articulated and embellished, at times in strikingly rhetorical ways. In this paper, which is based on ethnographic research, the theatrical and rhetorical qualities of Terra Madre as a political spectacle are explored in some detail. It is argued, in conclusion, that what is inadvertently exposed are some of the political myths which lie at the core of the Slow Food movement's contemporary philosophy.

Polycomb genes role in cancer pathophysiology is offering targets for therapeutics including gene therapy

2021 ◽  
Author(s):  
Moataz Dowaidar
Keyword(s):  
Catalytic Activity ◽  
Detailed Understanding ◽  
The Core ◽  
Chromatin Regulators ◽  
Genetic Modifications ◽  
Anti Cancer ◽  
The Many ◽  
The One ◽  
Context Specific ◽  
Study Context

Several phenotypes can come from transcription regulation. Sequence-specific transcription factors are needed to effectively execute transcriptional programs, however they are often not operating alone. Polycomb PcG proteins are a well-known class of chromatin regulators found in Drosophila melanogaster and other species, including humans. As time passed, the concept of a PCG gene or protein shifted from the original phenotypic meaning of mutant flies to the contemporary biochemical description. PCG genes and proteins are under investigation for their critical contributions to physiology and their cancer treatment potential. Adding additional PcG members, with substantial responsibilities in PRC modulation, has opened new routes of inquiry in the issue. It is still needed to discover the many PRC variations' roles and how their catalytic activity is controlled. This review covers mutually exclusive PRC2 variants and employs a technique like the one used for PRC1 variants. Based on current biochemical findings, these classifications are valid. More auxiliary PcG subunit research is needed for now. Moreover, it is unknown how many PRC cell variations occur (hypothetically, there could be more than 100 different PRC variants).In order to fully elucidate the new PcG proteins and complexes, it is necessary to perform comprehensive research. We must study context-specific genetic modifications to better provide remedies. Current anti-cancer drugs target mainly the core subunits and catalytic activity of PRC2 and PRC1, and understanding these functions is critical. Targeting each particular activity that has been deregulated might be rather beneficial. PCG proteins are involved in oncogenesis, tumor suppression, and development/congenital illness as well. PcG involvement in cancer, once revealed, would be intriguing. Successful and effective therapeutic therapies will be helped by a detailed understanding of the pathways that contain PcG proteins.

scholarly journals A practical guide to buildde-novoassemblies for single tissues of non-model organisms: the example of a Neotropical frog

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3702 ◽  
Author(s):  
Santiago Montero-Mendieta ◽  
Manfred Grabherr ◽  
Henrik Lantz ◽  
Ignacio De la Riva ◽  
Jennifer A. Leonard ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Cost Effective ◽  
Model Organisms ◽  
Rna Seq ◽  
Assembly Pipeline ◽  
Wide Variability ◽  
History Of ◽  
Inexperienced User

Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome and the transcriptome must be assembledde-novo. We used RNA-seq to obtain the transcriptomic profile forOreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome ofO. cruralis. We also present a pipeline to assist with pre-processing, assembling, evaluating and functionally annotating ade-novotranscriptome from RNA-seq data of non-model organisms. Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to buildde-novotranscriptome assemblies using readily available software and is freely available at:https://github.com/biomendi/TRANSCRIPTOME-ASSEMBLY-PIPELINE/wiki.

The Oxford Handbook of Virginia Woolf

2021 ◽  
Keyword(s):  
Secondary Students ◽  
Virginia Woolf ◽  
Magical Realism ◽  
Natural World ◽  
The Novel ◽  
Post Secondary ◽  
The Core ◽  
The Times ◽  
The Many ◽  
Hogarth Press

With thirty-nine original chapters from internationally prominent scholars, The Oxford Handbook of Virginia Woolf is designed for post-secondary students, scholars, and common readers. Feminist to the core, each chapter offers an overview that is at once fresh and thoroughly grounded in prior scholarship. Six parts focus on Woolf’s life, her texts, her experiments, her as a professional, her contexts, and her afterlife. Opening chapters on Woolf’s life address the powerful influences of family, friends, and home. Part II on her works moves chronologically, emphasizing Woolf’s practice of writing essays and reviews alongside her fiction. Chapters on Woolf’s experimentalism pay special attention to the literariness of Woolf’s writing, with opportunity to trace its distinctive watermark while ‘Professions of Writing’, invites readers to consider how Woolf worked in cultural fields including and extending beyond the Hogarth Press and the Times Literary Supplement. Part V on ‘Contexts’ moves beyond writing to depict her engagement with the natural world as well as the political, artistic, and popular culture of her time. The final part, ‘Afterlives’, demonstrates the many ways Woolf’s reputation continues to grow. Of particular note, chapters explore three distinct Woolfian traditions in fiction: the novel of manners, magical realism, and the feminist novel.

Managing Privilege as a Key to Inclusive Leadership

2012 ◽  
pp. 131-148
Author(s):  
Doug Harris ◽  
Kasia Ganko-Rodriguez
Keyword(s):  
Exponential Growth ◽  
Personal Growth ◽  
Employee Performance ◽  
Positive Outcomes ◽  
Inclusive Leadership ◽  
The Core ◽  
Diversity And Inclusion ◽  
The Many

The field of diversity and inclusion has experienced exponential growth over last 30 years. Yet, while these progressions have occurred, many of the core diversity and inclusion concepts have remained fairly stagnant. One critical example is around the concept of privilege. All of us find ourselves privileged in some way, but leaders in particular need to recognize and manage privilege to ensure inclusion in the workplace. Through personal examples and real stories, this chapter highlights the many positive outcomes leaders will experience by effectively managing privilege. These powerful outcomes include areas such as personal growth and effectiveness, more authentic relationships, increased levels of respect, expanded circle of influence, and maximized employee performance. To conclude, the authors look at the stages leaders go through before they are able to effectively manage this expanded view of privilege. These stages can be described as bliss, awareness, overprotection, enlightened, and ultimately managing privilege.

New Gender Relations in the Transforming IT-Industry of Malaysia

2010 ◽  
pp. 25-47
Author(s):  
Ulf Mellström
Keyword(s):  
It Industry ◽  
Spatial Practices ◽  
Critical Thought ◽  
Technology Studies ◽  
The Core ◽  
Gender And Technology ◽  
Femininity And Masculinity ◽  
And Gender ◽  
The Many ◽  
Opening Up

This chapter investigates how and why computer science in Malaysia is dominated by women. Drawing on recent critical interventions in gender and technology studies the paper aims at opening up for more culturally situated analyses of the gendering of technology or the technology of gendering with the Malaysian case exemplifying the core of the argument. The paper argues along four different strands of critical thought: (1) A critique of the ‘black-boxing’ of gender in gender and technology studies; (2) A critique of the Anglo-centric bias of gender and technology studies advocating more of context sensitivity and focus on the cultural embeddedness of gender and technology relations; (3) In line with that, also paying more attention to spatial practices and body politics in regard to race, class, and gender in gender and technology relations; 4. A critique of ‘western’ positional notions of gender configurations and opening up for more fluid constructions of gender identity including the many crossovers between relational and positional definitions of femininity and masculinity.

Sign in / Sign up

Export Citation Format

Share Document