scholarly journals Exploring the Use of Environmental DNA (eDNA) to Detect Animal Taxa in the Mesopelagic Zone

2021 ◽  
Vol 9 ◽  
Author(s):  
Annette F. Govindarajan ◽  
Rene D. Francolini ◽  
J. Michael Jech ◽  
Andone C. Lavery ◽  
Joel K. Llopiz ◽  
...  
Keyword(s):  
United States ◽  
Environmental Dna ◽  
Taxonomic Diversity ◽  
Great Promise ◽  
Sample Collection ◽  
Mesopelagic Zone ◽  
Reference Databases ◽  
Insight Into ◽  
Mesopelagic Species ◽  
Collection Time

Animal biodiversity in the ocean’s vast mesopelagic zone is relatively poorly studied due to technological and logistical challenges. Environmental DNA (eDNA) analyses show great promise for efficiently characterizing biodiversity and could provide new insight into the presence of mesopelagic species, including those that are missed by traditional net sampling. Here, we explore the utility of eDNA for identifying animal taxa. We describe the results from an August 2018 cruise in Slope Water off the northeast United States. Samples for eDNA analysis were collected using Niskin bottles during five CTD casts. Sampling depths along each cast were selected based on the presence of biomass as indicated by the shipboard Simrad EK60 echosounder. Metabarcoding of the 18S V9 gene region was used to assess taxonomic diversity. eDNA metabarcoding results were compared with those from net-collected (MOCNESS) plankton samples. We found that the MOCNESS sampling recovered more animal taxa, but the number of taxa detected per liter of water sampled was significantly higher in the eDNA samples. eDNA was especially useful for detecting delicate gelatinous animals which are undersampled by nets. We also detected eDNA changes in community composition with depth, but not with sample collection time (day vs. night). We provide recommendations for applying eDNA-based methods in the mesopelagic including the need for studies enabling interpretation of eDNA signals and improvement of barcode reference databases.

scholarly journals Anacapa Toolkit: an environmental DNA toolkit for processing multilocus metabarcode datasets

2018 ◽  
Author(s):  
Emily E. Curd ◽  
Zack Gold ◽  
Gaurav S Kandlikar ◽  
Jesse Gomer ◽  
Max Ogden ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sequence Data ◽  
Environmental Dna ◽  
Taxonomic Diversity ◽  
R Package ◽  
Community Diversity ◽  
Taxonomic Assignment ◽  
Lowest Common Ancestor ◽  
Reference Databases ◽  
Comprehensive Reference

Abstract1. Environmental DNA (eDNA) metabarcoding is a promising method to monitor species and community diversity that is rapid, affordable, and non-invasive. Longstanding needs of the eDNA community are modular informatics tools, comprehensive and customizable reference databases, flexibility across high-throughput sequencing platforms, fast multilocus metabarcode processing, and accurate taxonomic assignment. As bioinformatics tools continue to improve, addressing each of these demands within a single bioinformatics toolkit is becoming a reality.2. We present the modular metabarcode sequence toolkit Anacapa (https://github.com/limey-bean/Anacapa/), which addresses the above needs, allowing users to build comprehensive reference databases and assign taxonomy to raw multilocus metabarcode sequence data A novel aspect of Anacapa is our database building module, Creating Reference libraries Using eXisting tools (CRUX), which generates comprehensive reference databases for specific user-defined metabarcode loci. The Quality Control and Dereplication module sorts and processes multiple metabarcode loci and processes merged, unmerged and unpaired reads maximizing recovered diversity. Followed by amplicon sequence variants (ASVs) detection using DADA2. The Anacapa Classifier module aligns these ASVs to CRUX-generated reference databases using Bowtie2. Taxonomy is assigned to ASVs with confidence scores using a Bayesian Lowest Common Ancestor (BLCA) method. The Anacapa Toolkit also includes an R package, ranacapa, for automated results exploration through standard biodiversity statistical analysis.3. We performed a series of benchmarking tests to verify that the Anacapa Toolkit generates comprehensive reference databases that capture wide taxonomic diversity and that it can assign high-quality taxonomy to both MiSeq-length and Hi-Seq length sequence data. We demonstrate the value of the Anacapa Toolkit to assigning taxonomy to eDNA sequences from seawater samples from southern California including capability of this tool kit to process multilocus metabarcoding data.4. The Anacapa Toolkit broadens the exploration of eDNA and assists in biodiversity assessment and management by generating metabarcode specific databases, processing multilocus data, retaining all read types, and expanding non-traditional eDNA targets. Anacapa software and source code are open and available in a virtual container to ease installation.

Hamas and Civil Society in Gaza

2013 ◽  
Author(s):  
Sara Roy
Keyword(s):  
United States ◽  
Political Violence ◽  
West Bank ◽  
Gaza Strip ◽  
Social Institutions ◽  
The United States ◽  
Great Promise ◽  
Religious Congregations ◽  
Regional Dynamics ◽  
Second Intifada

Many in the United States and Israel believe that Hamas is nothing but a terrorist organization, and that its social sector serves merely to recruit new supporters for its violent agenda. Based on extensive fieldwork in the Gaza Strip and West Bank during the critical period of the Oslo peace process, this book shows how the social service activities sponsored by the Islamist group emphasized not political violence but rather community development and civic restoration. The book demonstrates how Islamic social institutions in Gaza and the West Bank advocated a moderate approach to change that valued order and stability, not disorder and instability; were less dogmatically Islamic than is often assumed; and served people who had a range of political outlooks and no history of acting collectively in support of radical Islam. These institutions attempted to create civic communities, not religious congregations. They reflected a deep commitment to stimulate a social, cultural, and moral renewal of the Muslim community, one couched not only—or even primarily—in religious terms. Vividly illustrating Hamas's unrecognized potential for moderation, accommodation, and change, the book also traces critical developments in Hamas' social and political sectors through the Second Intifada to today, and offers an assessment of the current, more adverse situation in the occupied territories. The Oslo period held great promise that has since been squandered. This book argues for more enlightened policies by the United States and Israel, ones that reflect Hamas' proven record of nonviolent community building. A new afterword discusses how Hamas has been affected by changing regional dynamics and by recent economic and political events in Gaza, including failed attempts at reconciliation with Fatah.

Excavating the Layers of Trauma in Homelands and Hostlands: Supporting Political Refugees in U.S. Schools

2021 ◽  
pp. 155545892199751
Author(s):  
Mehtap Akay ◽  
Reva Jaffe-Walter
Keyword(s):  
United States ◽  
Teacher Education ◽  
Education System ◽  
Home Country ◽  
The United States ◽  
Dominant Culture ◽  
Refugee Students ◽  
Political Refugees ◽  
Language And Education ◽  
Insight Into

This article details how a newly arrived Turkish refugee student navigates schooling in the United States. It highlights the trauma a purged Turkish families experience in their home country and their challenges as newcomers unfamiliar with their new country’s dominant culture, language, and education system. The case narrative provides insight into how children of Turkish political refugees are often overlooked in the context of U.S. schools, where teachers lack adequate training and supports. By illuminating one refugee family’s experiences in U.S. schools, the case calls for leaders to develop holistic supports and teacher education focused on the needs of refugee students.

scholarly journals »Heimat im Koffer.« – »Oder über das Emigrantendasein. (Falls nicht zu traurig).«

Aschkenas ◽  
2014 ◽  
Vol 24 (2) ◽  
Author(s):  
Joachim Schlör
Keyword(s):  
United States ◽  
New York ◽  
Popular Music ◽  
Everyday Life ◽  
The United States ◽  
National Socialist ◽  
Weimar Germany ◽  
Musical Traditions ◽  
German Jewish ◽  
Insight Into

AbstractThe idea to create and stage a play called »Heimat im Koffer« – »A home in the suitcase« – emerged, I presume, in Vienna shortly before Austria became part of National Socialist Germany in 1938: the plot involved the magical translocation of a typical Viennese coffeehouse, with all its inhabitants and with the songs they sang, to New York; their confrontation with American everyday life and musical traditions would create the humorous situations the authors hoped for. Since 1933, Robert Gilbert (Robert David Winterfeld, 1899–1978), the son of a famous Jewish musician and himself a most successful writer of popular music for film and operetta in Weimar Germany, found himself in exile in Vienna where he cooperated with the journalist Rudolf Weys (1898–1978) and the piano artist Hermann Leopoldi (1888–1959). Whereas Gilbert and Leopoldi emigrated to the United States and became a part of the German-Jewish and Austrian-Jewish emigré community of New York – summarizing their experience in a song about the difficulty to acquire the new language, »Da wär’s halt gut, wenn man Englisch könnt« (1943) – Weys survived the war years in Vienna. After 1945, Gilbert and Weys renewed their contact and discussed – in letters kept today within the collection of the Viennese Rathausbibliothek – the possibility to finally put »Heimat im Koffer« on stage. The experiences of exile, it turned out, proved to be too strong, and maybe too serious, for the harmless play to be realized, but the letters do give a fascinating insight into everyday-life during emigration, including the need to learn English properly, and into the impossibility to reconnect to the former life and art.

Practicing DNPs’ Perceptions of the DNP

2013 ◽  
Vol 6 (2) ◽  
pp. 91-97 ◽  
Author(s):  
Pamella Stoeckel ◽  
Cheryl Kruschke
Keyword(s):  
United States ◽  
Health Care ◽  
The United States ◽  
Added Value ◽  
Doctor Of Nursing Practice ◽  
Educational Preparation ◽  
Practice Nurses ◽  
Key Informant ◽  
Insight Into

This qualitative key informant study examined the emerging role of the doctor of nursing practice (DNP) degree to fill a gap in health care in the United States. Although the DNP degree was proposed to bring added value to the health care system, it is new with little research to confirm the assumption. This research addressed this need by phone interviews of 12 practicing DNPs in the United States. Questions asked of the participants focused on differences in role/practice as a DNP and challenges faced. The interviews were audiotaped, transcribed, and responses coded for themes. Five broad categories with relational themes emerged from the data of DNPs perceptions of their practices. The categories included educational preparation, practice settings, role acceptance, leadership, and challenges. The results of this study provide insight into the perceptions of practicing DNPs experiencing adjustment to practice as a DNP. These perceptions aid other DNPs and educators in preparing advance practice nurses for the future.

scholarly journals The State of Clinical Librarianship in Canada: a Review of the Literature, 1970–2013

2014 ◽  
Vol 34 (2) ◽  
pp. 69 ◽  
Author(s):  
Helen Halbert
Keyword(s):  
United States ◽  
Professional Training ◽  
Literature Search ◽  
The United States ◽  
Formative Period ◽  
Review Of The Literature ◽  
Job Titles ◽  
Medical Librarian ◽  
History Of ◽  
Insight Into

This paper examines the history of clinical librarianship in Canada from 1970 to 2013 as seen through the lens of practitioner narratives and published literature. While no reviews of clinical librarianship in Canada were found in the literature search, there were many project descriptions in articles and published reports that have provided insight into the field during its formative period in Canada from the 1970s. In addition to tracing narrative histories from 1970 to 2013, the author has continued to wonder why these important stories have never properly been told. Was it because the scope of clinical librarianship, its expected and embodied professional duties, was not regulated (as it is in the United States and United Kingdom)? Is it because the American Library Association accredited library schools in Canada do not offer appropriate curricula and professional training? It seems clear that some librarians in Canada were pioneers in the way that Gertrude Lamb was in the United States, but they did not call themselves clinical librarians. Consequently, they opted for more generic job titles such as medical librarian and health librarian. Whatever the reasons for this, it is within this framework that the author begins an exploration of clinical librarianship in Canada. The paper's aim is to provide a view into clinical librarianship in Canada back to the 1970s to ensure the story is properly told.

scholarly journals Overcoming limitations to environmental DNA studies: A coastal temperate reference sequence database for multiple chloroplast gene regions generated in a single assay.

2021 ◽  
Author(s):  
Nicole Foster ◽  
Kor-jent Dijk ◽  
Ed Biffin ◽  
Jennifer Young ◽  
Vicki Thomson ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Reference Sequence ◽  
Reference Database ◽  
Chloroplast Gene ◽  
Coastal Plants ◽  
Reference Databases ◽  
Targeted Capture ◽  
Comprehensive Reference

A proliferation in environmental DNA (eDNA) research has increased the reliance on reference sequence databases to assign unknown DNA sequences to known taxa. Without comprehensive reference databases, DNA extracted from environmental samples cannot be correctly assigned to taxa, limiting the use of this genetic information to identify organisms in unknown sample mixtures. For animals, standard metabarcoding practices involve amplification of the mitochondrial Cytochrome-c oxidase subunit 1 (CO1) region, which is a universally amplifyable region across majority of animal taxa. This region, however, does not work well as a DNA barcode for plants and fungi, and there is no similar universal single barcode locus that has the same species resolution. Therefore, generating reference sequences has been more difficult and several loci have been suggested to be used in parallel to get to species identification. For this reason, we developed a multi-gene targeted capture approach to generate reference DNA sequences for plant taxa across 20 target chloroplast gene regions in a single assay. We successfully compiled a reference database for 93 temperate coastal plants including seagrasses, mangroves, and saltmarshes/samphire’s. We demonstrate the importance of a comprehensive reference database to prevent species going undetected in eDNA studies. We also investigate how using multiple chloroplast gene regions impacts the ability to discriminate between taxa.

scholarly journals ATONEMENT THEORY REVISITED: CALVIN, BEZA, AND AMYRAUT ON THE EXTENT OF THE ATONEMENT

Perichoresis ◽  
2013 ◽  
Vol 11 (1) ◽  
pp. 51-75
Author(s):  
Matthew S. Harding
Keyword(s):  
United States ◽  
Seventeenth Century ◽  
The United States ◽  
Theological Method ◽  
Reformed Tradition ◽  
In Christ ◽  
Insight Into

ABSTRACT Throughout the bulk of the Reformed Tradition’s history within both Europe and the United States, most scholars have dismissed pastor and theologian Moïse Amyraut as a seventeenth century French heretic whose actions and theology led to the demise of the Huguenots in France. However, upon further introspection into Amyraut’s claims as being closer to Calvin (soteriologically) than his Genevan successors, one finds uncanny parallels in the scriptural commentaries and biblical insight into the expiation of Christ between Calvin and Amyraut. By comparing key scriptural passages concerning the atonement, this article demonstrates that Reformed theologian Moïse Amyraut in fact propagated a universal atonement theory which parallels Calvin’s, both men ascribing to biblical faithfulness, a (humanistic) theological method, and similar hermeneutic. As such, both Calvin and Amyraut scripturally contend that God desires and provided the means for the salvation of the whole world. Further, the article demonstrates that Calvin’s successor, Theodore de Beza, could not in fact make the same claims as Amyraut, this article demonstrating that Beza went beyond Calvin’s scriptural approach to Christ’s expiation. Therefore, this article supports a more centrist approach from within and outside the Reformed tradition by demonstrating that Calvin and Amyraut concentrically held to God’s gracious provision in Christ for the saving of the whole world, for those who would believe in Christ for salvation.

Nicholas Said

2021 ◽  
Author(s):  
Mohammed Bashir Salau
Keyword(s):  
United States ◽  
North America ◽  
Middle East ◽  
19Th Century ◽  
North Africa ◽  
The United States ◽  
Primary Sources ◽  
Sahara Desert ◽  
Insight Into

The two versions of the autobiography that Nicholas Said published offer insight into 19th-century conditions in five continents as well as insight into life as a child, slave, manservant, and teacher. As a child in the 1830s, Said was enslaved in Borno, marched across the Sahara Desert, and passed from hand to hand in North Africa and the Middle East. After serving as a slave in various societies, Said was freed by a Russian aristocrat in the late 1850s after accompanying the aristocrat in question to various parts of Europe. In the 1850s, Said also traveled as a manservant for a European traveler to South and North America. Ultimately he settled in the United States, where he authored two versions of his autobiography, served as a teacher and soldier, got married, and disappeared from sight. This article compares the two versions of the autobiography that Said published, provides an overview of Said’s life, charts the development of scholarly works on Said, and draws attention to the primary sources related to the study of Said and his autobiography.

Taiwan–Myanmar Relations within the Framework of the New Southbound Policy

2021 ◽  
pp. 1-31
Author(s):  
Kristina Kironska
Keyword(s):  
United States ◽  
Soft Power ◽  
The United States ◽  
Political Transformation ◽  
Military Rule ◽  
Political Relations ◽  
Trade War ◽  
The Relationship ◽  
Insight Into

Abstract This article combines the study of Taiwan’s New Southbound Policy with a case study of Taiwan–Myanmar relations from a perspective of political relations, economic cooperation, and Taiwan’s (un)recognisability in Myanmar—i.e. Taiwan’s soft power in Myanmar. The first part of the paper introduces the policy and compares it with the previous ones, and sheds light on Taiwan’s motivation to engage with Myanmar. It considers the ongoing trade war between the United States and China, due to which investment relocation from China is expected to sharply increase. The second part of the paper provides an insight into the relationship between Taiwan and Myanmar after Myanmar’s state-led political transformation from military rule and economic liberalisation since approximately 2010. It explains the main aspects and determinants of the relationship between two countries that share a neighbouring potential hegemon which they both wish to balance against.

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