bluuebunny/crossref_metadata_2025 huggingface dataset:
Black Atlantic (Dis)Entanglements: Langston Hughes, Richard Wright, and Spain
Authors: Soto Isabel
Published: June 2017

The work of Langston Hughes and Richard Wright provides a unique entry point into an under-studied area of Black Studies: the Spanish role in the construction of racial categories and racially determined practices. My essay examines how Hughe’s and Wright’s reactions to the Hispanophone world were mediated through the issue of race. While Hughes articulates a de-othering or entanglement with his surrounding space, Wright colludes in a historical process of racial differentiation of Spain and things Spanish. Hughes’s writings on the Spanish-speaking world and the 1936–1939 Civil War address issues of race and coloniality and precede current historiography’s recognition of the conflict as a racialized and colonial event. Wright, Hughes’s near contemporary and one-time co-author, provides an intriguing – if problematic – vision of Francoist Spain in his travelogPagan Spain, published some twenty years after Hughes left the war-torn country in 1937. If Hughes partakes of the Spanish (racial) reality and historical moment, Wright acquiesces in the Black Legend, the exceptionalizing Protestant response to the Iberian superpower of early modernity.
Heel-Raised Foot Posture Does Not Affect Trunk and Lower Extremity Biomechanics During a Barbell Back Squat in Recreational Weight lifters
Authors: Lee Szu-Ping , Gillis Carrie B. , Ibarra Javier J. , Oldroyd Derek F. , Zane Ryan S.
Published: June 2017

Lee, S-P, Gillis, CB, Ibarra, JJ, Oldroyd, DF, and Zane, RS. Heel-raised foot posture does not affect trunk and lower extremity biomechanics during a barbell back squat in recreational weight lifters. J Strength Cond Res 33(3): 606–614, 2019—It is claimed that weightlifting shoes with a raised heel may lead to a more upright trunk posture, and thus reduce the risk of back injuries during a barbell back squat. These proclaimed biomechanical effects have not been thoroughly investigated. The purpose of this study was to compare trunk and lower extremity biomechanics during barbell back squats in three foot postures. Fourteen recreational weight lifters (7 men and 7 women) between the ages of 18 and 50 years performed barbell back squats in three conditions (barefoot on a flat surface, barefoot on a heel-raised platform, and wearing heel-raised weightlifting shoes) at 80% of their 1 repetition maximum. Surface electromyography was used to assess the activation of the knee extensors and paraspinal muscles at L3 and T12 spinal levels. A 3D motion capture system and an electrogoniometer recorded the kinematics of the thoracic spine, lumbar spine, and knee during the back squat to a depth where the hip was at least at the same level to the knee. Results indicated that none of the heel-raised foot postures significantly affected trunk and lower extremity muscle activation (thoracolumbar paraspinal [p = 0.52], lumbar paraspinal [p = 0.179], knee extensor [p = 0.507]) or the trunk angles (thoracolumbar spine [p = 0.348], lumbar spine [p = 0.283]) during the squat. Our results demonstrated that during barbell back squats, heel-raised foot postures do not significantly affect spinal and knee extensor muscle activations, and trunk and knee kinematics. Heel-raised weightlifting shoes are unlikely to provide significant protection against back injuries for recreational weight lifters during the barbell back squat.
Sea surface microlayer in a changing ocean – A perspective
Authors: Wurl Oliver , Ekau Werner , Landing William M. , Zappa Christopher J.
Published: June 2017

The sea surface microlayer (SML) is the boundary interface between the atmosphere and ocean, covering about 70% of the Earth’s surface. With an operationally defined thickness between 1 and 1000 µm, the SML has physicochemical and biological properties that are measurably distinct from underlying waters. Recent studies now indicate that the SML covers the ocean to a significant extent, and evidence shows that it is an aggregate-enriched biofilm environment with distinct microbial communities. Because of its unique position at the air-sea interface, the SML is central to a range of global biogeochemical and climate-related processes. The redeveloped SML paradigm pushes the SML into a new and wider context that is relevant to many ocean and climate sciences.
Uso das vibrantes na aquisição do português como língua estrangeira por nativos americanos e espanhóis: implicações ao ensino
Authors: Dutra Alessandra
Published: June 2017

Seguindo os pressupostos teóricos da Sociolinguística Laboviana, o estudo propõe analisar o uso das vibrantes na aquisição do português como língua estrangeira por nativos americanos e espanhóis. Para isso, selecionamos os tipos de pesquisa bibliográfica, de campo e analítica e dividimos a fala de 11 nativos americanos e 11 espanhóis em estilos que vão dos informais até os mais formais. Os resultados mostraram que o contexto em que os informantes usam um fonema na língua nativa motiva o seu uso na aprendizagem do português. A aquisição dos fonemas do português é mais célere entre os informantes mais jovens e o uso de estruturas da língua materna dos informantes são mais frequentes em estilos de fala informais.********************************************************************Use of vibrant in the acquisition of Portuguese as a foreign language bynative American and Spanish speakers: implications for teachingAbstract: Based on the theoretical postulations of Labov’s Sociolinguistics, this study proposes to analyze the use of vibrant in the acquisition of the Portuguese as a foreign language by native Americans and Spanish speakers. For this purpose, it was selected types of bibliographical, field and analytics researches and, the speech from 11 American and 11 Spanish native speakers were divided in styles, which passes through informal to ones that are more formal. The results showed that the context, in which the informants use a phoneme in their native language, motivates its usage in learning Portuguese. The acquisition of phonemes of Portuguese is more rapid among the younger informants while the informant´s mother tongue structure usage is more common in informal speech styles. Keywords: Phonetics variation; Portuguese to foreign speakers; Linguistic and extra linguistics aspects
Mujeres, pandillas y violencia en Guatemala
Authors: Reséndiz Rivera Nelly Erandy
Published: June 2017

El objetivo general es analizar la participación de mujeres que pertenecen al Barrio 18 y a la Mara Salvatrucha en Guatemala. Para cumplir esta finalidad, se utilizaron los estudios de la violencia, la teoría feminista y el trabajo de campo en prisiones de menores de edad en el país mencionado. Las niñas, las adolescentes y las adultas en las pandillas son un subgrupo, el cual recibe de manera aguda las agresiones de sus compañeros. Ellas también son negadas cuando se recurre a una perspectiva androcéntrica o a una visión sexista del fenómeno. Los ataques contra las mujeres por serlo por parte de la sociedad en general, no logran eliminar que las homegirls aprovechen a la violencia para obtener recursos simbólicos y materiales para sobrevivir. Las dieciocheras y mareras modifican parcialmente los roles y los estereotipos de género, pero permanecen como actoras sociales y no como sujetas de la historia.
La libertad en la guerra: análisis del problema en tres obras de teatro de Jean Paul Sartre
Authors: Herrera Rodríguez Omar S.
Published: June 2017

El problema central por desarrollar en este trabajo es la relación entre la libertad y la guerra en la filosofía de Jean Paul Sartre, en cuanto que la guerra conlleva necesariamente la eliminación del Otro y el riesgo de la propia existencia, por ende, la eliminación potencial de la libertad en cuanto elemento ontológico fundamental y distintivo de los sujetos. Para ello realizo un análisis relacional de la propuesta sartriana expuesta en El Ser y la nada con el desarrollo que el autor ofrece en tres de sus obras de teatro: El diablo y el buen Dios, Los secuestrados de Altona y Las manos sucias; con el objetivo de mostrar el alcance crítico de Sartre contra la guerra como las posibilidades de generar en/desde la guerra, autoconsciencia y proyectos de resistencia en los sujetos.
Germanismos del catalán a partir del latín medieval
Authors: Jaime Moya Joan M.ª
Published: June 2017

En el presente artículo se pretende estudiar una serie de palabras catalanas de origen germánico, documentadas en el latín medieval de Cataluña antes de que éstas aparezcan en fuentes escritas ya directamente en romance.
Pulsed electromagnetic energy as an adjunct to physiotherapy for the treatment of acute low back pain: A randomised controlled trial
Authors: Anita Krammer , Horton Stuart , Tumilty Steve
Published: June 2017

The intention of this study was to investigate any additional benefits of pulsed electromagnetic energy used as an adjunct to routine physiotherapy for the treatment of acute non-specific low back pain. To address this aim, a single centre, double blinded, placebo controlled randomised control trial was conducted. Forty participants presenting to the University of Otago, School of Physiotherapy Clinic with acute non-specific low back pain (< 6 weeks) were recruited. The Oswestry Disability Index was employed as the primary outcome measure. Secondary outcomes included the Patient Specific Functional Scale and the Numeric Pain Rating Scale. Outcomes were collected at baseline, one week and four weeks (or discharge). Baseline characteristics exhibited no differences between groups. The group treated with active pulsed electromagnetic energy failed to demonstrate any significant additional improvements in Oswestry Disability Index, Patient Specific Functional Scale or Numeric Pain Rating Scale scores (p > 0.05). Irrespective of group allocation, all participants experienced significant improvements in Oswestry Disability Index, Patient Specific Functional Scale and Numeric Pain Rating Scale scores over both follow-up periods (p<0.05). Concisely, pulsed electromagnetic energy provides no significant additional benefit to physiotherapy in the treatment of acute non-specific low back pain.
ПРОБЛЕМЫ НАЛОГОВОЙ СИСТЕМЫ УКРАИНЫ
Authors: Мартыновский В. С. , Кулаковская Т. А. , Фарзетдинов Д. Ф.
Published: June 2017

В данной статье рассмотрены проблемы налоговой системы Украины и высоких ставок налогов, что приводит к увеличению доли теневой экономики. Рассмотрены налог на добавленную стоимость и налог на доходы физических лиц. Также были описаны методы по оптимизации налоговой системы.
ФОРМУВАННЯ РЕСУРСНОЇ СТРАТЕГІЇ ПІДПРИЄМСТВА
Authors: Коверга А. В. , Буренко Ю. О. , Крупіца І. В.
Published: June 2017

У статті запропоновано ресурсний підхід як основа реалізації функціональних стратегій підприємств харчової промисловості. На основі мікроекономічної теорії розроблені критерії та послідовність реалізації функціональних стратегій підприємств.
THE DEVELOPING TRENDS OF THE ITALIAN AND UKRAINIAN VITICULTURE AND WINERIES
Authors: Kalaman O. , Babenko K.
Published: June 2017

The world experience of viticulture development and winemaking is analyzed in this article. It is established that the experience of Italy is the most acceptable example for Ukrainian winegrowers. The analysis of wine industry development in Ukraine and Odessa region is carried out general. The dynamics of grape production and the processing of wine materials in different areas as well as the inside and outside factors making impact on development of wineries are also analyzed
Plagiarism: Misconduct Awareness on Novice Research within the Cyberworld
Authors: Lehobye Nafta Mokate
Published: June 2017

More often than not, there exists some form of infringement relating to the use of other authors' work. This is particularly so in instances in which novice authors make use of the information available within the cyber-digital environment. The article explains the meaning of plagiarism and describes the many manifestations thereof, with the primary aim of providing guidance to novice authors.
Editorial
Authors: Venter Francois
Published: June 2017

This issue deals with a selection of topics of environmental law. As it should be clear from the short tribute written by Margaret Beukes, the issue is devoted to Professor Elmien Bray, for many years a force in the emergence of South African environmental law.

Jonathan Verschuuren of Tilburg University expertly comments on the Dutch Crisis and Recovery Act, showing clearly why it is such a controversial piece of legislation: balancing economic recovery with sustainable development, sound principles of law, justice and crisis management is shown to be a very hard result to achieve by means of legislation.
0.1M EDTA-0.2M MgCl2-0.2M Ascorbate Buffer v1
Authors: John Seth , Bonnie Poulos not provided , Christine Schirmer not provided
Published: June 2017

Preparation of iron chloride resuspension buffer using disodium EDTA dihydrate and magnesium chloride in Tris buffer.
10g/L Fe Stock Solution v1
Authors: Sullivan Lab Matthew
Published: June 2017

10g/L Fe Stock Solution for Iron Chloride Precipitation of Viruses from Seawater Protocol.
16s Pyrotag PCR v1
Authors: Ochman Howard
Published: June 2017

Modified from H. Ochman protocol: Environ. Micro. 2009 Kunin, Engelbrekson Ochman & Hugenholtz
1M Tris v1
Authors: Alex Aitken Ms
Published: June 2017

This shows how to make 1M Tris.
T-maze phototaxis with LEDs v1
Authors: Brembs Björn
Published: June 2017

We use this protocol to test if flies have preferance for darkness or light (phototactic or non-phototactic response).
Buffered glutaraldehyde v1
Authors: Deng Li
Published: June 2017

Formulation for a phosphate-buffered 20% glutaraldehyde stock solution.
Phage Tangential Flow Filtration v1
Authors: Rohwar Forest
Published: June 2017

In tangential flow filtration (TFF), the sample is run parallel to the filter. Particles that are smaller than the pore size are pushed out through the holes (the filtrate). Particles that are larger than the pore size are retained inside the filter (the retentate). TFF is most effective when a reservoir is used so that the sample can be recycled through numerous times.
Primary trace metal stocks v1
Authors: Sullivan Lab Matthew
Published: June 2017

Preparation of trace metal stock solutions for cyanobacteria trace metal mixture (CTMM)
Iron Chloride Solution v1
Authors: Cunningham B.R. , J.R. Brum not provided , S.M. Schwenck not provided , M.B. Sullivan not provided , S.G. John not provided
Published: June 2017

For use in Wet-Mount Method for Enumeration of Aquatic Viruses
Manual setting of k-mer coverage peaks v1
Authors: not provided Afiahayati , Sato K not provided , Namiki T not provided , Hachiya T not provided , Tanaka H not provided , Sakakibara Y. not provided
Published: June 2017

Contrary to single-genome assemblers (e.g., Velvet and SOAPdenovo), MetaVelvet assumes metagenomics settings. Accordingly,k-mer coverage histogram might be multi-modal rather than uni-modal. Please note that the coverage peak parameters can largely affect MetaVelvet assembling results. Although simple and automatic peak detection algorithm is implemented inmeta-velvetg, we strongly recommend manual inspection ofk-mer coverage peaks and manual setting of the coverage peak parameters. For manually setting the coverage peak parameters, please execute the following procedures.
bioBakery Protocols v1
Authors: Huttenhower Curtis
Published: June 2017

This tutorial focuses on performing a comprehensive metagenomic analysis from whole-genome shotgun sequencing data for microbiome studies. It is divided in to different steps that use the following metagenomic, computational tools: MetaPhlAn, GraPhlAn, LEfSe, and HUMAnN. Our last addition to the PhlAn tools is PhyloPhlAn that can be used in metagenomics for phylgenetically and taxonomically place contigs assembled from whole metagenomic sequencing samples.This tutorial is also a step-by-step description of the metagenomic pipeline we used in our review paper about computational meta'omics(specifically Figure 4).
Flow cytometry analysis of diatoms and coccolithophores with diagnostic stains (via a BD Biosciences Accuri C6) v1
Authors: Nissimov Jozef
Published: June 2017

This general protocol can be used for assessing eukaryotic populations with various diagnostic stains (SYTOX for live/dead cells; DAF-FM for nitric oxide producing cells; DCFDA for reactive oxygen species; others). It is geared for samples that are ~5-10 µm in size, using a 70 µm orifice.
MTN100 with 1x NaCl v1
Authors: Sullivan Matthew
Published: June 2017

This mixture is is used with Cesium Chloride Dialysis for Viruses
Urea/SDS Solution v1
Authors: Corrier/Nathan VerBerkmoes Kristin
Published: June 2017

For use in "FASP Kit Protocol-OrNL Developed for Bacteriophage"
Pollak Trichrome Solution v1
Authors: Hall Sonia
Published: June 2017

Combine: 150mls Ethanol 150mls distilled water 3mls Glacial Acetic Acid Split into 4 beakers (approx 75mls each) and add a stir bar. Beaker 1 - Add: 0.5g Acid Fuchsin and 1.0g Ponceau 2R Beaker 2 - Add: 0.45g Light green, SF, yellowish Beaker 3 - Add: 0.75g Orange G and 1.5g Phosphotungstic acid Beaker 4 - Add: 1.5g Phosphomolybdic acid When each reagent is maximally dissolved, combine the 4 dyes and filter. Cover storage bottle in tin foil to reduce light exposure. Remake each month.
Metatranscriptomics sample preparation protocol w/ScriptSeq v1
Authors: DeLong Ed
Published: June 2017

This protocol is an update of the Metatranscriptomics protocol from DeLong lab 2012 which incorporates ScriptSeq v2 RNA library preparation. Part A: RNA extraction, DNase treatment, purification, and quantification. Part B: rRNA subtraction Part C: cDNA synthesis and Illumina library prep
Amplification of phage genes from lysates and environmental samples v1
Authors: Sullivan Matthew
Published: June 2017

From Sullivan M., Lindell D., Lee J., Thompson L., Bielawski J., Chisholm S. Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts.PLOS Biology, 2006 4(8):e234. Please see the published manuscript for additional information.
Filter drying procedure v1
Authors: Fuhrman Jed
Published: June 2017

For use in "SYBR Green Assay".
Whole protein extraction from tissues v1
Authors: Liu Vivian
Published: June 2017

This protocol is for whole protein extraction from tissues like kidney, liver ,musscle etc. Histone proteins which are tightly twisted on genomic DNA can also be extracted with this protocol.
NEXTflex™ mtDNA-Seq for cell samples v1
Authors: Scientific Bioo
Published: June 2017

The NEXTflex™ mtDNA-Seq Kit is designed to prepare single or paired-end DNA libraries of mitochondrial DNA (mtDNA) for sequencing using Illumina® platforms. The procedure isolates mitochondrial DNA from genomic DNA (gDNA) by selective digestion of linear nuclear DNA, followed by fragmentation of mtDNA and library preparation. Please see the full manualfor additional details. (Note: This is the procedure for Cell Samples; for Blood Samples, see this protocol.)
Antibody Purification (small scale) v1
Authors: Liu Vivian
Published: June 2017

This protocol described a easy procedure to purify anti-sera in small scale batch. Protein A or protein G beads can be used depending on the immunoglobulin types.
Viruses from Hypersaline Waters v1
Authors: M. Stedman Kenneth , Kate Porter not provided , and Mike L. Dyall-Smith not provided
Published: June 2017

This is a protocol from: Stedman,K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6:The isolation of viruses infecting Archaea.Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7 Please see the published manuscript for additional information.
Obtaining pure phage stock v1
Authors: Middelboe Mathias , Amy M. Chan not provided , and Sif K. Bertelsen not provided
Published: June 2017

Clearing zones on lawns of host bacteria potentially contain all lytic phages against the given host that were present in the original water sample. Little is still known about the occurrence and diversity of phages infecting specific hosts, but generally isolation procedures as those described above may reveal multiple phages against specific target bacteria (e.g., Comeau et al. 2006; Holmfeldt et al. 2007; Stenholm et al. 2008). It is therefore necessary to further isolate the phages to obtain specific stocks of single phages.
Clonal virus purification v1
Authors: Middelboe Mathias , Amy M. Chan not provided , and Sif K. Bertelsen not provided
Published: June 2017

For use in "Obtaining pure cyanophage stocks (liquid assay)"
High Efficiency, Homology-Directed Genome Editing in Caenorhabditis elegans Using CRISPR/Cas9 Ribonucleoprotein Complexes v1
Authors: Paix Alexandre , Andrew Folkmann not provided , Dominique Rasoloson not provided , Geraldine Seydoux not provided
Published: June 2017

This is a collection of protocols from: Paix A,Folkmann A,Rasoloson D, andSeydoux G (2015) High Efficiency, Homology-Directed Genome Editing in Caenorhabditis elegans Using CRISPR/Cas9 Ribonucleoprotein Complexes.Genetics genetics.115.179382; Early online July 17, 2015.doi:10.1534/genetics.115.179382 Please see the full manuscript for detail.
LB agar plate, 1.5% v2
Authors: Bien Harold
Published: June 2017

Preparation of both LB broth for growing bacteria and LB agar plates
Seydoux lab Cas9 preparation test: Tag gtbp?1 with eGFP or mCherry using dpy?10 co?CRISPR v1
Authors: Paix Alexandre , Andrew Folkmann not provided , Dominique Rasoloson not provided , Geraldine Seydoux not provided
Published: June 2017

This is a positive control experiment (to test protocol in your hands and/or activity of your home‐made Cas9): tag gtbp‐1 with eGFP or mCherry using dpy‐10 co‐CRISPR.. The protocol is from: Paix A,Folkmann A,Rasoloson D, andSeydoux G (2015) High Efficiency, Homology-Directed Genome Editing in Caenorhabditis elegans Using CRISPR/Cas9 Ribonucleoprotein Complexes.Genetics genetics.115.179382; Early online July 17, 2015.doi:10.1534/genetics.115.179382 Please see the full manuscript for detail.
Yeast Extract?Peptone?Glycerol +Antifolates (YPGly+ AF) Media v1
Authors: G. Alexander William , Drew T. Doering not provided , and Chris Todd Hittinger not provided
Published: June 2017

This recipe is from: Alexander WG, Doering DT,andHittinger CT (2014) High-Efficiency Genome Editing and Allele Replacement in Prototrophic and Wild Strains of Saccharomyces.Genetics 198:859-866;doi:10.1534/genetics.114.170118 See the full protocol for step-by-step YPGly+ AF preparation instructions.
DNA Extraction for college laboratory setting v1
Authors: M. Burnette III James , Susan R. Wessler not provided
Published: June 2017

This protocol is based on one described by Li et al. (2010) and has been modified to work in a college laboratory setting. The protocol is from: JamesM. Burnette III andSusan R. Wessler (2013) Transposing from the Laboratory to the Classroom to Generate Authentic Research Experiences for UndergraduatesGenetics193:367-375; doi:10.1534/genetics.112.147355 Students need approximately 1.5 hours to extract DNA from up to five samples and the protocol can be carried out over several class periods by stopping at steps 6 and 9. Please see the full manuscript for additional details.
Simultaneous measurement of grazing and viral lysis of phytoplankton v2
Authors: Brussaard Corina , Anne-Claire Baudoux not provided , Anna A. M. Noordeloos not provided , Marcel J. W. Veldhuis not provided
Published: June 2017

An alternate version to the protocol "Simultaneous measurement of grazing and viral lysis of phytoplankton v1"
General protocol for the concentration of virioplankton from a large volume (>20 L) water sample v1
Authors: Eric Wommack K. , Télesphore Sime-Ngando not provided , Danielle M. Winget not provided , Sanchita Jamindar not provided , and Rebekah R. Helton not provided
Published: June 2017

This protocoloutlines and evaluates the filtration steps needed for the preparation of samples (viral concentrates) containing a density of viral particles concentrated from large volumes of natural water samples.(Fig. 2A and B)
Anti-BrdU Staining Protocols v1
Authors: Miller Kelsey
Published: June 2017

Protocols for Anti-BrdU Staining Using DNAse with Surface and Fluorescent Proteins and Anti-BrdU Staining Using 70% Ethanol and 2N HCl
Anti-BrdU Staining Using 70% Ethanol and 2N HCl v1
Authors: Miller Kelsey
Published: June 2017

Anti-BrdU Staining Protocol Using 70% Ethanol and 2N HCl
Immunopurification — Small Scale using Epitope Tag Affinity Matrices v1
Authors: Miller Kelsey
Published: June 2017

Immunochemistry Protocols: Immunopurification ‐ (Small Scale) Using Anti‐Epitope Tag Affinity Matrices: Typically, immunoprecipitation of antigen from extracts of transfected mammalian cells requires between 1-5 μL of polyclonal antiserum, 5-100 μL of hybridoma tissue culture medium, or 1-3 μL of ascites. If more antibody is used than is necessary, nonspecific background will increase. The concentration of immunoglobulins in antiserum is approximately 6-8 mg/mL. Supernatant from cultured hybridoma cells typically contains 10-100 μg/mL immunoglobulin, and ascites fluid contains 5-7 mg/mL immunoglobulin.
MojoSort™ Positive Selection Columns Protocol v1
Authors: Miller Kelsey
Published: June 2017

BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This simple protocol consists of following the MojoSort™ protocol to label the cells with pre-diluted MojoSort™ reagents and using the columns as indicated by the manufacturer. Note: Due to the properties of our beads, it may be possible to use far fewer beads that with other commercial suppliers. We recommend a titration to find the best dilution factor. However, as a general rule, dilutions ranging from 1:3 to 1:20 for the Nanobeads can be used.
SAMfluoro™: SAM Methyltransferase Assay v1
Authors: not provided G-Biosciences
Published: June 2017

A Fluorescent, Continuous Enzyme Assay.
NUCLEIC dotMETRIC™ v1
Authors: not provided G-Biosciences
Published: June 2017

1µl Assay for detecting and measuring DNA, RNA & Oligos.
High sensitivity miRNA library preparation protocol by TailorMix miRNA Sample Preparation Kit (Version 2) T v1
Authors: Yip Karen
Published: June 2017

ThI high sensitivity miRNA library generation for the Illumina sequencing platform. Our enhanced reagent kit enables the discovery and profiling of small RNAs from a variety of sources including FFPE, exosome, serum, and whole blood. The TailorMix workflow is designed for ease of use, enabling library preparation a single day. Features: User Friendly Workflow: Libraries can be prepared in a single day. No Additional Reagents Necessary: All reaction enzymes and buffers are provided. Stress Free Gel Purification: TailorCut Gel Extraction Tool Set is included for easy gel excision and purification. Easy to Use: Reagents are supplied as ready-to-use mixtures which improves consistency and reproducibility. Ultra High Sensitivity: Prepare miRNA libraries from any source with as little as 10ng of total RNA input.
High sensitivity miRNA Illumina library preparation protocol by TailorMix miRNA Sample Preparation Kit (Version 2) v3
Authors: Yip Karen , Kelvin Chan not provided , Danny Lee not provided
Published: June 2017

This protocol is designed for high sensitivity miRNA library generation for the Illumina sequencing platform. Our protocol and the enhanced reagent kit enables the discovery and profiling of small RNAs from a variety of sources including FFPE, exosome, serum, and whole blood. The TailorMix workflow is designed for ease of use, enabling library preparation a single day. Features: User Friendly Workflow: Libraries can be prepared in a single day. No Additional Reagents Necessary: All reaction enzymes and buffers are provided. Stress Free Gel Purification: TailorCut Gel Extraction Tool Set is included for easy gel excision and purification. Easy to Use: Reagents are supplied as ready-to-use mixtures which improves consistency and reproducibility. Ultra High Sensitivity: Prepare miRNA libraries from any source with as little as 10ng of total RNA input.
OmniPrep™ Protocol Collection for High Quality Genomic DNA Extraction v1
Authors: not provided G-Biosciences
Published: June 2017

This is a collection of protocols for high quality genomic DNA extraction using the OmniPrep™ kit. Please refer to the appropriate protocol below depending on your application.
Collection of Protocols for XIT™ Genomic DNA Blood Kit v1
Authors: not provided G-Biosciences
Published: June 2017

This is a collection of G-Biosciences protocols using XIT™ Genomic DNA Blood Kit for the isolation of genomic DNA from fresh blood, bone marrow & buffy coat.
MegaLong™ Protocol for Isolation of >100kb Genomic DNA (Blood) v1
Authors: not provided G-Biosciences
Published: June 2017

MegaLong™ isolates high molecular weight (>100kb) genomic DNA from a variety of samples, including animal tissues, cultured cells, whole blood, bacterial and yeast. The protocol described here is for bloodsamples. Please refer to the appropriate protocol, depending on your application.
Autoclave Frankfurter Fiesta v1
Authors: not provided Proro , Melted Mint Forums not provided
Published: June 2017

This protocol is part of the VERVE holiday drive to collect exotic off-the-shelf laboratory recipes. More detailshere.
Spot-on-lawn (halo) assay for screening enrichment cultures and isolates for viruses v1
Authors: M. Stedman Kenneth , Kate Porter not provided , and Mike L. Dyall-Smith not provided
Published: June 2017

This protocol is based on Schleper et al. (1992) as modified by Stedman et al. (2003). This is a protocol from: Stedman,K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6:The isolation of viruses infecting Archaea.Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7 Please see the published manuscript for additional information.
Ice-cold Effervescent Lab Apple v1
Authors: Silva Elizabeth
Published: June 2017

This protocol is part of the VERVE holiday drive to collect exotic off-the-shelf laboratory recipes. More detailshere. (Image: Frosty apple, Olga Filonenko, CC BY-SA)
VBRC Base By Base: Export a sequence selection to a different file v1
Authors: Tang Nick
Published: June 2017

Viral Bioinformatic Resource Centre Provide databases of viral genomic information. Please check theOrganismsmenu to see which viruses we support: we’re now focusing on large DNA viruses The VOCs (Virus Orthologous Clusters) database is at the heart of our system. The database links directly to integrated tools for comparative analyses. VOCs sorts genes into ortholog clusters (e.g. RNA polymerase) to simplify data retrieval. Provide easy access to the genes, gene families, and genomes of the different virus families. via a unique series of powerful Java tools that support multiple computer platforms (seeVBRC Tools menu). design and build software to tackle specific bioinformatics/virology problems, often in collaboration with virologists. Rally the research community to provide expert curation of these viral genomes by: Adding value to GenBank sequences through enhancing and updating genome annotations Linking to research reviews/papers for the research community. Collaborate with researchers to help on specific bioinformatics problems, e.g. Custom searches of the databases Building new features into our tools Help with genome annotation
Script P2: Contig Assembly v1
Authors: GC Hannigan , Grice EA not provided , et al. not provided
Published: June 2017

This protocol provides a method for assembly of metagenomic data using the Ray assembly toolkit and the subsequent analysis of contig statistics. Based on the publication: Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome."mBio6.5 (2015): e01578-15.
Running "16sblaster" at iPlant v1
Authors: Youens-Clark Ken
Published: June 2017

See upcoming paper by Watts, Hurwitz, Youens-Clark. Code is freely available atGithub.
Yeast DAPI Staining v1
Authors: Cone Alan
Published: June 2017

Stains the nucleus of budding or fission yeast with DAPI in order to see it with a fluorescence microscope.
Script R9: Plotting Microbial Taxonomy from MEGAN v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocol outlines the analysis used to plot MEGAN taxonomic assignments. Based on the methods from the following publication: Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome."mBio6.5 (2015): e01578-15.
Script R10: Whole Metagenome Beta Diversity v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocoloutlines the beta-diversity analysis that we performed on the whole metagenome samples. We measured the signifiance of the dissimilarity between samples that were grouped by biological occlusion status, microenvironment (sebaceous, moist, etc), and sampling time point. Here we also describe our intrapersonal vs interpersonal dissimilarity measurements. Based on methods from the following publication: Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome."mBio6.5 (2015): e01578-15.
Script R12: Functional Analysis v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocoloutlines the analysis used to plot KEGG functional annotation.
Stellaris® RNA FISH Protocol for Brain v1
Authors: Biosearch Technologies LGC
Published: June 2017

Stellaris® RNA FISH protocol for fresh frozen mouse brain
Viruses Purification of Perkinsus spp. v1
Authors: LAZARE Mathieu
Published: June 2017

The purpose of this protocol is to isolate and characterize viruses that infect P.olseni, P.marinus.
CviJI Storage Buffer v1
Authors: DUNIGAN AND IRINA AGARKOVA DAVID
Published: June 2017

For use in CviJI Purification From IL-3A Virus Infected NC64A Chlorella.
1X CviJI Assay Buffer v1
Authors: DUNIGAN AND IRINA AGARKOVA DAVID
Published: June 2017

For use in CviJI Purification From IL-3A Virus Infected NC64A Chlorella.
Transformation of supercompetent cells v2
Authors: Lunt Dave
Published: June 2017

Protocol to prepare E. coli supercompetent cells to transform with plasmid/ligation. This protocol is originally derived from Hanahan, D. (1983) J. Mol. Biol. 166:557-580 with somechanges. This version works exceptionally well for cloning PCR products where the number of colonies is not expected to be as high as from some ligations. These cells outperform commercially purchased supercompetent cells in my hands.
DNA extraction from plants v1
Authors: Stam Remco
Published: June 2017

Widely used protocol to extract DNA from plant leaves. Many versions circulate on the web, this is the version as we use it. It works well on maize, tomato and probably many other plants.
Assembling Viral Metagenomic Data with SPAdes (Cyverse) v1
Authors: Bolduc Benjamin
Published: June 2017

Assemblingactual reads from the Ocean Sampling Day (2014)usingSPAdes, an assembler implemented in Cyverse.
Quality Control of Reads Using Trimmomatic (Cyverse) v1
Authors: Bolduc Benjamin
Published: June 2017

A collection of protocols designed to guide the user in processing a viral metagenome from raw sequence data to assembly, and subsequent analysis. The user usesactual reads fromOcean Sampling Day (2014)and processes them entirely within Cyverse, a NSF-supported cyberinfrastructure. Quality trimming of reads is important!
Isolation and isotopic labeling of bacteria v1
Authors: Terrado Ramon
Published: June 2017

This protocol describes how to isolate bacteria in order to label its biomass using 13C-glucose and 15N-ammonia. The first steps aim to isolate candidate bacteria that are able of growing on the chosen substrates for isotopic labeling. The protocol was applied to the isolation of bacetria from freshwater algal cultures, although it can be applied to natural samples. The M9 media used in the protocol is based on the media from Marley, Lu and Bracken (2001). References: Marley, J., Lu, M., & Bracken, C. (2001). A method for efficient isotopic labeling of recombinant proteins. Journal of Biomolecular Nmr, 20(1), 71–75.
Isotopic labeling of freshwater mixotrophic algae using isotopic labeled heat-killed bacteria v1
Authors: terrado Ramon
Published: June 2017

This protocol aims to achieve an isotopic labeling of mixotrophic algae using 15Nand 13Clabeled heat-killed bacteria. It was developped to be used with the mixorophic chrysophyteOchromonas to asses the sources of carbon and nitrogen of this algae when growing mixotrophically .Sources of nitrogen and carbon in the media used were reduced to 1 inorganic source (NH4Cl for nitrogen and bicarbonate for carbon) and 1 organic source (heat-killed bacteria); media used for Ochromonas growth was modified accordingly to reflect this. Downstream analysis of isotopic labeled Ochromonas includebulk IRMS measurements or nanoSIMS measurements.
ASP12A Recipe for culturing Aureococcus anophagefferens v2
Authors: Gann Eric
Published: June 2017

Defined Medium for Aureococcus anophagefferens
On-Column DNase I Treatment for ISOLATE II Biofluids RNA Kit v1
Authors: not provided Bioline
Published: June 2017

The ISOLATE II Biofluids RNA Kit isolates total RNA with minimal amounts of genomic DNA contamination using the supplied Genomic DNA Removal Column. However, additional DNase I treatment may be required in certain cases e.g. the amount of genomic DNA in the sample exceeds the capacity of the Genomic DNA Removal Column, or performing a highly sensitive application. An alternative additional DNase I treatment protocol is: DNase I Treatment of Purified RNA in Solution. This optional protocol can be used for additional removal of residual DNA that may affect sensitive downstream applications.
ISOLATE II Biofluids RNA Kit v1
Authors: not provided Bioline
Published: June 2017

The ISOLATE II Biofluids RNA Kit is specially developed for the rapid phenol-free isolation of high quality total RNA from biofluids and viruses. Total RNA can be purified from blood, plasma, serum and other types of biofluids such as saliva, urine, semen and cerebrospinal fluid (CSF). Viral RNA can be isolated from the same sample sources, as well as cultured cells and tissue. The kit isolates all sizes of RNA from large mRNA, viral RNA and ribosomal RNA (rRNA) down to small RNAs such as microRNA (miRNA) and short interfering RNA (siRNA).
MG_HW7: Taxonomic Classification Using Centrifuge v1
Authors: Thornton James
Published: June 2017

This protocol provides a procedure to generate taxonomic data from assembled contigs using centrifuge.
MG_HW7: Taxonomic Classification Using Centrifuge v3
Authors: Thornton James
Published: June 2017

This protocol provides a procedure to generate taxonomic data from assembled contigs using centrifuge.
MPN (Most Probable Number) assay for infectivity of algal viruses v1
Authors: Zimmerman Amy
Published: June 2017

Purpose: To quantify infectious viruses and evaluate the infectivity of a viral sample. Summary: 50 µL of serially-diluted (10-3 to 10-10) virus sample is added to 150 µL of exponentially growing host cells in triplicate 96-well microplates and incubated at normal growth conditions for ~2 weeks. Cell lysis is assessed every few days qualitatively by visual inspection and quantitatively by measuring optical density on a microplate reader. The MPN of infective viruses in each concentrate is estimated from the proportion of virus-positive (i.e., lysed) wells using the MPN_ver4.xls Excel spreadsheet from Jarvis, B., Wilrich, C., and P.-T. Wilrich (2010), Journal of Applied Microbiology 109 (2010), 1660 – 1667. Percent infectivity is then calculated by comparing the MPN-estimated abundance of infective viruses to the abundance of virus-like particles (VLPs) determined by flow cytometry analysis.
Nile Red prepared in acetone v1
Authors: Allen Elizabeth
Published: June 2017

Nile Red is prepared in acetone to make a working concentration of 1000 ug/mL. It should be stored at 4°C in the dark.
Sytoxgreen staining (DNA stain, for flow cytometry) v1
Authors: Miller Darach
Published: June 2017

Amalgam from various places.
How to copy from host to guest machine v1
Authors: Thornton James
Published: June 2017

Short instructions on how to allow copying and pasting to the virtual machine.
Half strength MS (+ B5 vits and 1% sucrose) growth medium v1
Authors: Arsuffi Giulia
Published: June 2017

Steps to make half strength MS + B5 vitamins solid growth medium (w/ 1% sucrose) for standard Marchantia tissue culture.
Setting up Experimental Cultures for Large-scale One-step Phage Infection of Cyanobacteria v1
Authors: Giuliani Sarah
Published: June 2017

Experiment purpose is to monitor the time-course of a large-scale infection of host cyanobacteria by phage under variable media conditions and obtain samples for proteomic and transcriptomic analysis. As a minimum, prepare 12 sample bottles for cells infected with phage and control phage lysate, under 2 different media treatments, with triplcates of each unique Phage/Treatment combination.
Sampling for qEXT and MPN assays: Large-scale One-step Phage Infection of Cyanobacteria v3
Authors: Giuliani Sarah
Published: June 2017

Experiment purpose is to monitor the time-course of a large-scale infection of host cyanobacteria by phage under variable media conditions and obtain samples for proteomic and transcriptomic analysis. 15 Hourly Timepoints: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 Sampling is for qPCR assay to determine total extracellular phage (qEXT), and for MPN (most probable number) assay to determine % phage infectivity. For qEXT and MPN sampling,250 µL of each sample in duplicates were collected and filtered through a 0.2 µm, 96-well filter plate, for each time point. The flow through filtrate containing phage was stored at 4°C as the sample to analyze.
ECOGEO 'Omics Training: 4.3 Binning Module - Anvi'o v2
Authors: Murat Eren A.
Published: June 2017

This is the hands-on interactive component to the ECOGEO Workshop Module on Binning.
ECOGEO 'Omics Training: 4.4 Phylogenetics v2
Authors: Dombrowski and Kiley Seitz Nina
Published: June 2017

Provides a short introduction to phylogenetics and how to build a phylogenetic tree from concatenated ribosomal marker proteins. Open this protocol inside the virtual machine (details in 'Start Instructions') for easy copy, paste of commands into the command line terminal window.
SpinOUT™ for Desalting and Buffer Exchange of Peptide and Protein Samples v1
Authors: not provided G-Biosciences
Published: June 2017

This is a collection of G-Biosciences protocols: SpinOUT™ for Desalting & Buffer Exchange of Peptide & Protein Samples. (Cat. # 786-170 to 786-173, 786-703 to 786-708, 786-865 to 786-869)
Rye B Agar v1
Authors: Stam Remco
Published: June 2017

This Agar medium can be used for the cultivation of Phytophthora infestans. It is particularly suitable to induce sporulation of Phytophthora on plate. For long term storage on plate, Rye B agar is recommended. This protocal has been copied from http://www.plantpath.cornell.edu/Fry/ Original reference: Caten, C. E. and J. L. Jinks. 1968. Spontaneous variability of single isolates of Phytophthora infestans. I. Cultural variation. Can. J. Bot. 46: 329-348.
Agrobacterium mediated transformation of Marchantia spores v3
Authors: Sauret-Gueto Susana
Published: June 2017

This method produces random integration of DNA into the genome of Marchantia. The technique relies on the capacity of Agrobacterium tumefasciens to transfer DNA to plants. This DNA can be specified as it is flanked by sequences of DNA called the Right and Left Border (RB & LB), named as a whole as the T-DNA. The original tumour-inducing (Ti) plasmid from Agrobacterium was adapted to a binary plasmid system allowing easy cloning of the T-DNA part of the system in E. coli before being electroplated into Agrobacterium and then transfection into plants by infection. This protocol is based onIshizaki et al., 2008, optimised in Jim Haseloff lab,Plant Sciences, University of Cambridge, by Nuri Purswani and Bernardo Pollak. At the moment Linda Silvestri and Susana Sauret-Gueto are seeing on further optimisation, including feedback from other researchers working in Marchantia, like Bo Xu.
Cultivation / Spore Production for Alternaria Solani v1
Authors: Stam Remco
Published: June 2017

Protocol for the cultivatio of Alternaria Solani. This protocol has been used for many years at the chair of Phytopathology at the Technical University of Munich. SNA Medium was first described by Nirenberg in 1981.
Agrobacterium mediated transformation of Marchantia spores v5
Authors: Sauret-Gueto Susana
Published: June 2017

This method produces random integration of DNA into the genome of Marchantia. The technique relies on the capacity of Agrobacterium tumefasciens to transfer DNA to plants. This DNA can be specified as it is flanked by sequences of DNA called the Right and Left Border (RB & LB), named as a whole as the T-DNA. The original tumour-inducing (Ti) plasmid from Agrobacterium was adapted to a binary plasmid system allowing easy cloning of the T-DNA part of the system in E. coli before being electroplated into Agrobacterium and then transfection into plants by infection. This protocol is based onIshizaki et al., 2008, optimised in Jim Haseloff lab,Plant Sciences, University of Cambridge, by Nuri Purswani and Bernardo Pollak. At the moment Linda Silvestri and Susana Sauret-Gueto are seeing on further optimisation, including feedback from other researchers working in Marchantia, like Bo Xu.
Preparing AQUIL Media v1
Authors: Wasson Alexis
Published: June 2017

Procedure in order to prepare EDTA media (also known as Aquil).
FlowCam Standard Operating Procedure v1
Authors: Harris Jacob
Published: June 2017

The FlowCam can be used to take quick cell density measurements of liquid samples.
Create "abe487" Github repo v3
Authors: Youens-Clark Ken
Published: June 2017

The imageis the Github logo.
C_HW2: Makefile, command line exercises with yeast v7
Authors: Youens-Clark Ken
Published: June 2017

Yeast is a well-characterized genome due to its small size and historical significance in genetics. The websitehttp://yeastgenome.org/ is a dedicated resource for yeast genomics. For this exercise, I want you to create a "Makefile" that will execute this entire pipeline if I type "make."
Plant cell protoplast isolation v1
Authors: Burgess Steven
Published: June 2017

A protocol for isolation of protoplast from plant cells adapted from Yoo et al. 2007 (http://www.nature.com/nprot/journal/v2/n7/full/nprot.2007.199.htm). Procedure was optimized for use on Arabidopsis thaliana tissue.
C_HW2: Makefile, command line exercises with yeast v9
Authors: Youens-Clark Ken
Published: June 2017

Yeast is a well-characterized genome due to its small size and historical significance in genetics. The websitehttp://yeastgenome.org/ is a dedicated resource for yeast genomics. For this exercise, I want you to create a "Makefile" that will execute this entire pipeline if I type "make."
Fungal DNA Lysis Buffer v1
Authors: Taranto Adam
Published: June 2017

Lysis buffer for extraction of DNA from fungal material. Contains ionic and non-ionic detergents. Contains RNAse-A. Composition: NaCl 150mM EDTA pH 8.0 1 mM Tris BasepH 8.0 10 mM Polyvinylpolypyrrolidone (PVPP) 2% IGEPAL-CA630 0.5% Sodium deoxycholate 0.5% SDS 1% RNAse-A 100 µg/mL
JetSeq™ DNA Library Preparation Kit v1
Authors: not provided Bioline
Published: June 2017

This protocol is for the JetSeqTM DNA Library Preparation Kit. The kit is designed to generate high-quality next generation sequencing (NGS) libraries suitable for sequencing on Illumina MiSeqTM, NextSeqTM or HiSeqTM instruments.