bluuebunny/crossref_metadata_2025 huggingface dataset:
Fingerprinting aquatic virus communities using denaturing gradient gel electrophoresis (DGGE) v1
Authors: Sandaa Ruth-Anne , Steven M. Short not provided , and Declan C. Schroeder not provided
Published: June 2017

Using DGGE, similar-sized PCR products that differ in nucleotide composition (sequence) can be separated in denaturing gradient gels. Denaturing gradient gels are created using acrylamide (structural material) solutions that contain different amounts of denaturants (urea and formamide), such that the highest concentration of denaturants is at the bottom of the gel and the lowest concentration is at the top. As dsDNA fragments differing in sequence migrate into the gel during electrophoresis, they encounter increasing concentrations of denaturants, and each fragment partially melts (i.e., double-stranded regions dissociate into single-stranded) at a different place in the gel depending on its sequence. Because the electrophoretic mobility of partially melted DNA fragments is greatly reduced compared to dsDNA, same-sized DNA fragments with different sequences focus at different positions in these gels. Because PCR with universal primers can be used to amplify related, but different, DNA sequences, and different sequences focus at different positions in a denaturing gradient gel, DGGE can be used to produce a unique banding pattern, or fingerprint, for each PCR product amplified from different microbial communities.
Separate different viral genome sizes v1
Authors: Sandaa Ruth-Anne , Steven M. Short not provided , and Declan C. Schroeder not provided
Published: June 2017

For use in "Fingerprinting aquatic virus communities using PFGE"
70% Ethanol v1
Authors: Baker Andrew
Published: June 2017

Mix 7 parts of 100% Ethanol (200-proof) and 3 parts MilliQ water.
FLVP assays v1
Authors: M. Comeau and Rachel T. Noble André
Published: June 2017

The following continued adaptation of Hennes et al. (1995) is a result of FLVP assay optimizations for the Vibrio alginolyticus PWH3a-phage P1 phage-host system (PHS) for use with SYBR Green I stain. Novices to microscopy would benefit from reading Wen et al. (2004) for details on preparing and storing slides using SYBR Green I stain. This protocol is a modification of the standard slide preparation techniques for bacteria and viruses in aquatic samples (see Suttle and Fuhrman 2010, this volume).
Ethanol Fixation Protocol v1
Authors: Miller Kelsey
Published: June 2017

Cell Fixation and Permeabilization Protocol Using 70% Ethanol
Anti-Neu5Gc Antibody Kit Protocols v1
Authors: Miller Kelsey
Published: June 2017

Anti-Neu5Gc Antibody Kit Protocols for Flow Cytometry, ELISA, and Western blot.
Anti-Neu5Gc Antibody Kit Protocol - ELISA v1
Authors: Miller Kelsey
Published: June 2017

This protocol is essentially the same as a standard ELISA protocol, with one major exception – all animal compounds must be avoided in buffers, etc. because they contain Neu5Gc, which will interfere with antibody activity and result in misleading data. Essentially, the glycoconjugate to be evaluated is immobilized on an ELISA plate and exposed to a primary antibody. The antibody provided in this kit has been shown to identify as little as 5 pmol of Neu5Gc per microgram glycoprotein, which is at or below the current detection limit for conventional DMB HPLC analysis. An advantage of the ELISA procedure is that it confirms the presence of Neu5Gc on the glycoconjugate of interest, but use caution, as it also reacts with solution/media that contains glycoconjugate.
MojoSort™ Nanobeads No Wash Protocol v1
Authors: Miller Kelsey
Published: June 2017

The cells targeted by the Nanobeads are either selected or depleted by incubating your sample with the directly conjugated magnetic particles. The magnetically labeled fraction is retained by the use of a magnetic separator. After collection of the targeted cells, downstream applications include functional assays, gene expression, phenotypic characterization, etc.
OmniPrep™ for Fungus v1
Authors: not provided G-Biosciences
Published: June 2017

High Quality Genomic DNA Extraction from Fungal Samples
MojoSort™ Human CD4 T Cell Selection Protocol v1
Authors: Miller Kelsey
Published: June 2017

This protocol has been optimized to remove washing steps after antibody and nanobeads incubation, resulting in a shorter and more convenient protocol. This procedure is optimized for the isolation of 107 to 2 x 108 cells per tube. If working with fewer cells keep volumes as indicated for 107 cells. For best results, optimize the conditions to your specific cell number and tissue. Prepare fresh MojoSort™ Buffer solution by diluting the 5X concentrate with sterile distilled water. Product description and procedure summary: This kit is designed for the sequential positive selection of CD4+ T cells from human peripheral blood mononuclear cells (PBMCs). Human monocytes express both CD14 and CD4. When using only CD4 Nanobeads for positive selection of human CD4 T cells, monocytes could be isolated along with the T cells. If this monocyte fraction does not impact your application, there is no need to address it. However, not including this population may be required. Thus, the first step in this kit is the depletion of CD14+ cells using a combination of biotin anti-human CD14 and Streptavidin Nanobeads. The second step is the positive selection of the CD4 T cells using directly conjugated CD4 Nanobeads. After collection of the targeted cells, downstream applications include functional assays, gene expression, phenotypic characterization, etc.
OmniPrep™ For High Quality Genomic DNA Extraction From Nucleated Blood Cells (Bird, Fish, Frog) v1
Authors: not provided G-Biosciences
Published: June 2017

The OmniPrep™ kit isolates high quality genomic DNA from many different species and tissue types including animal, plant, bacteria, yeast, fungi, whole blood, and cells in culture. DNA can be isolated from samples high in polysaccharides or other contaminants that are difficult to remove from the DNA preparations. This protocol is for use with nucleated blood cells (bird, fish, frog). Please refer to the appropriate protocol depending on your application.
OmniPrep™ For High Quality Genomic DNA Extraction From Gram-Positive Bacteria v1
Authors: not provided G-Biosciences
Published: June 2017

The OmniPrep™ kit isolates high quality genomic DNA from many different species and tissue types including animal, plant, bacteria, yeast, fungi, whole blood, and cells in culture. DNA can be isolated from samples high in polysaccharides or other contaminants that are difficult to remove from the DNA preparations. This protocol is for use with gram-positive bacteria. Please refer to the appropriate protocol depending on your application.
OmniPrep™ For High Quality Genomic DNA Extraction From Solid Tissue (Fresh or Frozen) v1
Authors: not provided G-Biosciences
Published: June 2017

The OmniPrep™ kit isolates high quality genomic DNA from many different species and tissue types including animal, plant, bacteria, yeast, fungi, whole blood, and cells in culture. DNA can be isolated from samples high in polysaccharides or other contaminants that are difficult to remove from the DNA preparations. This protocol is for use with solid tissue samples (see the Guidelines for large tissue samples of 10-50mg). Please refer to the appropriate protocol depending on your application.
MegaLong™ Protocols Collection for Isolation of >100kb Genomic DNA v1
Authors: not provided G-Biosciences
Published: June 2017

This is a collection of G-Biosciences MegaLong™ protocols for the isolation of >100kb Genomic DNA . MegaLong™ isolates high molecular weight (>100kb) genomic DNA from a variety of samples, including animal tissues, cultured cells, whole blood, bacterial and yeast.Please refer to the appropriate protocol below, depending on your application.
Isolation of Mitochondria from Soft Tissues (Liver or Brain) using the FOCUS™ Mitochondria Kit v1
Authors: not provided G-Biosciences
Published: June 2017

This protocol is part of theFOCUS™ Mitochondria Kit collection. Please refer to the appropriate protocol depending on your application.
TRIS acetate phosphate (TAP) medium v1
Authors: Burgess Steven
Published: June 2017

TAP medium is the most widely used for growth of the green alga Chlamydomonas reinhardtii. Note the presence of acetate effects the photosynthetic ability of the alga and minimal medium should be used instead if quantifying effects of mutations or inhibitors on photosynthesis. Source: from Gorman, D.S., and R.P. Levine (1965) Proc. Natl. Acad. Sci. USA 54, 1665-1669. http://www.chlamycollection.org/TAP.html
Fractionation of Light and Heavy Mitochondria by Gradient Cushion (FOCUS™ SubCell Kit) v1
Authors: not provided G-Biosciences
Published: June 2017

This is part of the collection ofFOCUS™ SubCell protocols for the enrichment of subcellular fractions. Please refer to the appropriate protocol depending on your application.
Subcellular Fractionation from Liver or Brain Soft Tissues (FOCUS™ SubCell Kit) v1
Authors: not provided G-Biosciences
Published: June 2017

This is part of the collection ofFOCUS™ SubCell protocols for the enrichment of subcellular fractions. Please refer to the appropriate protocol depending on your application.
Thanksgiving Dinner Autoclave Style v1
Authors: not provided Priorclave
Published: June 2017

This protocol is part of the VERVE holiday drive to collect exotic off-the-shelf laboratory recipes. More detailshere. Timing is everything when preparing a large meal. Unfortunately, for the truly epic holiday meals – like Thanksgiving – there never seems to be enough oven space to ensure everything arrives at the table steaming. Something has always cooled, collapsed, or coagulated before the turkey is ready to carve. This is where the autoclave comes in: It’s built to hold loads at around 250 degrees Fahrenheit, and since it subjects them to twice normal atmospheric pressure, it tends to cut cooking times in half. Autoclave cook-time for a small to mid-sized turkey should be less than 2 hours. Wanna impress the in-laws this year? Bring home your favorite tabletop food-grade autoclave (not your Priorclave, though; those are research-grade autoclaves!) and put it to use on the big day.
Chloroplast Isolation from Diatoms v1
Authors: Dreux Chappell P. , Bethany D. Jenkins not provided
Published: June 2017

A protocol to separate chloroplasts from diatom cells using ammonium fluoride to permeate the silica frustrule and a percoll gradient to separate the plastid from other cellular components.
Isolation of Haloviruses from Natural 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.
The Isolation of Viruses Infecting Archaea v1
Authors: M. Stedman Kenneth , Kate Porter not provided , and Mike L. Dyall-Smith not provided
Published: June 2017

These are protocols 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.
VBRC Base By Base: View gene annotations 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
VBRC Base By Base: Search for a sequence motif, either exact (regular expression search) or inexact (fuzzy motif search) 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
Investigating biotin-BSM binding to streptavidin (that in turn is bound to dS-OEG-biotin) on QCM-D sensors v1
Authors: Linderberg Victoria
Published: June 2017

This protocol is used for investigating biotin-BSM binding to streptavidin on QCM-D sensors.
PCPipe: Protein clustering with SIMAP annotations v1
Authors: Hurwitz Bonnie , Ken Youens-Clark not provided
Published: June 2017

PCPipe is a protein-clustering tool. The input is a set of ORFs and a FASTAfile with already clustered ORFs. The process entails: Use cd-hit-2d to compare the inputpeptides to previously clustered proteins The result isa file with input proteins that clustered to existing clusters and those that did not Use the unclustered peptides and self-cluster them via cd-hit Take a representative sequence from each novelcluster, and use "blastp"to compare to SIMAP. Use the resulting SIMAP "feature_id" to look up the SIMAP features, merging the query results with the protein ID into a tab-delimited annotations file Provide the user with twocluster files and the annotations for the new clusters based on the representative sequence Code is freely available atGithub.
NYCIII Culture Media for Gardnerella vaginalis and other fastidious anaerobes v1
Authors: Perry Justin , Cory Weimer not provided , Warren G Lewis not provided , Lewis Lab not provided
Published: June 2017

NYCIII (en-why-see-three) culture media Suitable for the culture of Gardnerella vaginalis
Script R7: Intra and Inter Personal Dissimilarity v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocoloutlines the analysis used for intra and interpersonal diversity of the virome and whole metagenome using the Bray Curtis dissimilarity metric. We visualize the differences as bar plots and calculate the statistical significance of the differences using a t-test. 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.
Quick Protocol for Monarch® DNA Gel Extraction Kit (NEB #T1020) v1
Authors: England Biolabs New
Published: June 2017

This is thequickversion of the Monarch® DNA Gel Extraction Kit Protocol (NEB #T1020). For the full protocol, please clickhere.
Quick Protocol for Monarch® Plasmid Miniprep Kit (NEB #T1010) v1
Authors: England Biolabs New
Published: June 2017

This is the quick version of the Monarch® Plasmid DNA Miniprep Kit Protocol (NEB #T1010). For the full protocol, please clickhere.
Stellaris® RNA FISH Sequential IF + FISH in Adherent Cells Protocol v1
Authors: Biosearch Technologies LGC
Published: June 2017

Stellaris RNA FISH protocol for sequential labeling with IF and RNA FISH in adherent cells.
9 ?L reaction mix v1
Authors: D. Weynberg Karen , Elisha M. Wood-Charlson not provided , Curtis A. Suttle not provided , and Madeleine J. H. van Oppen not provided
Published: June 2017

For use in Generating viral metagenomes from the coral holobiont.
Reconditioning PCR amplification of the SISPA primer denaturing cycles v1
Authors: D. WEYNBERG KAREN , ELISHA M. WOOD-CHARLSON not provided , CURTIS A. SUTTLE not provided , AND MADELEINE J. H. VAN OPPEN not provided
Published: June 2017

For use in Generating viral metagenomes from the coral holobiont.
30.0% Acrylamide stock solution (30.0:0.8) v1
Authors: Dunigan and Irina Agarkova David
Published: June 2017

For use in Polyacrylamide Gel System For Electrophoresis Of Proteins.
Stacking gel buffer (4X) v1
Authors: DUNIGAN AND IRINA AGARKOVA DAVID
Published: June 2017

For use in Polyacrylamide Gel System For Electrophoresis Of Proteins.
Tris-glycine buffer v1
Authors: Burnton Stanton
Published: June 2017

Tris-glycine buffer solution
Viruses Purification of Perkinsus spp. v2
Authors: LAZARE Mathieu
Published: June 2017

The purpose of this protocol is to isolate and characterize viruses that infect P.olseni, P.marinus.
Viruses Purification of Perkinsus spp. v3
Authors: LAZARE Mathieu
Published: June 2017

The purpose of this protocol is to isolate and characterize viruses that infect P.olseni, P.marinus.
Running gel buffer (10X) v1
Authors: DUNIGAN AND IRINA AGARKOVA DAVID
Published: June 2017

For use in Polyacrylamide Gel System For Electrophoresis Of Proteins.
Viral metagenomic analysis on Cabbage Patch Kids v2
Authors: Burnton Stanton
Published: June 2017

This protocol is a parody of an existing scientific journal article and is intended to showcase the features available on the protocols.io platform in order for VERVE Net members to developefuture protocols. While the viral metagenomic analysis on Cabbage Patch Kids is impossible to perform, due to the real-world non-existant nature of Cabbage Patch kids, the sourcedarticle isMetagenomic analysis of viruses associated with field-grown and retail lettuce identifies human and animal virusesand the "Material and methods" section has been adapted from using actual lettuce data toa metagenomic protocol for Cabbage Patch Kids.
CviJI Buffer B v1
Authors: DUNIGAN AND IRINA AGARKOVA DAVID
Published: June 2017

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

For use in CviRI Purification From XZ-6E Virus Infected NC64A Chlorella.
The abundance and taxonomy of microbes in our meals for three diet types v1
Authors: Luo Qianwen
Published: June 2017

Thistutorial was based off of the paper The microbes we eat: abundance and taxonomy of microbes consumed in a day's worth of meals for three diet types.The article provides those interested in bioinformatics, food science, or microbiology information about how to test the abundance and taxonomy of microbes in our daily meals. The step by step procedures covers how the author run this experiment. Source: Lang JM, Eisen JA, Zivkovic AM. (2014) The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types. PeerJ2:e659.https://peerj.com/articles/659/
Identifying Viral Sequences Using VirSorter (Cyverse) v1
Authors: Bolduc Benjamin
Published: June 2017

Identifying putative viral sequences from SPAdes-assembled datafrom the Ocean Sampling Day (2014)metagenomic datasets using VirSorter.
Applying vContact to Viral Sequences and Visualizing the Output (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.
K-mer-based host screening v2
Authors: Hurwitz Bonnie , Ken Youens-Clark not provided
Published: June 2017

K-mer-based approaches to determining sequence similiarity can befaster than traditional use of BLAST. This application usesJellyfishto index host FASTA files, then uses the mode value (default 2)of the number of matching k-mers (default k=20) from the input sequenceto determine whether the sequence is similar enough to the host sequence to be rejected. The output of the app is: "screened" directory containing the sequences from each file that were found to be dissimlar to the host "rejected" directory containing the sequence from each file that were too similar to the host "jf" directory containing Jellyfish indexes of each "host" file (useful for later runs with other files to skip recreating) "kmer" directory containing k-mers of query sequences and ".loc" file showing the number of ".kmer" lines associated to each sequence Code is freely available atGithub.
Immunofluorescence Staining v1
Authors: not provided BioLegend , Inc. not provided
Published: June 2017

This is a collection of BioLegend protocols for Immunofluorescence Staining.
T Cell Activation with anti-CD3? Antibodies v1
Authors: not provided BioLegend , Inc. not provided
Published: June 2017

This is a collection of BioLegend T Cell Activation with anti-CD3ε Antibodies protocols, for human andmouse.
Sampling for extracellular phage quantification by qPCR and MPN assays v4
Authors: Giuliani Sarah
Published: June 2017

Sampling is for qPCR assay to determine total extracellular phage (qEXT), and for MPN (most probable number) assay to determine infective phage concentration. Samples containing phage and cells arefiltered through a 0.2µm membrane in 96-well format to remove cells; filtrate fraction is saved for later analysis.
Sampling for RNA / Protein/ dissolved nutrients from phage infection experiments v2
Authors: Giuliani Sarah
Published: June 2017

Thissampling protocol is designed to collect two fractions: cell pellets and cell-free filtered supernatants. The cell pellets are used for gene expression analyses by RNA-Seq and proteomics. The cell-free fraction is used for analysis of dissolved analytes (e.g. N, P, DOC). Volumes are based on our experience with cyanobacterial cultures at cell densities ~ 5E7/ml. For more/less concentrated cultures, adjust volumes accordingly.
C_HW4 (tac) v2
Authors: Youens-Clark Ken
Published: June 2017

Create a script that is the reverse of ‘cat’ in that it will print the lines from a given input file in reverse order: $ cat input.txt foo bar baz quux $ ./tac.pl6 input.txt quux baz bar foo The script should accept a single unnamed “input” argument that should be a file. If provided no arguments or an argument that is not an existing file, the script should produce a “usage” statement: $ ./tac.pl6 Usage: ./tac.pl6  $ ./tac.pl6 this-does-not-exist Usage: ./tac.pl6  If given an input that does not exist, it should print a usage statement. A passing test suite should look like this: $ make test ./test.pl6 1..3 ok 1 - No args gives usage ok 2 - Bad arg gives usage ok 3 - Correct output If you “make jabber,” you should see this: And the mome raths outgrabe. All mimsy were the borogoves, Did gyre and gimble in the wabe; 'Twas brillig, and the slithy toves He chortled in his joy. O frabjous day! Callooh! Callay!' Come to my arms, my beamish boy! "And, has thou slain the Jabberwock? He went galumphing back. He left it dead, and with its head The vorpal blade went snicker-snack! One, two! One, two! And through and through And burbled as it came! Came whiffling through the tulgey wood, The Jabberwock, with eyes of flame, And, as in uffish thought he stood, And stood awhile in thought. So rested he by the Tumtum tree, Long time the manxome foe he sought -- He took his vorpal sword in hand: The frumious Bandersnatch!" Beware the Jubjub bird, and shun The jaws that bite, the claws that catch! "Beware the Jabberwock, my son! And the mome raths outgrabe. All mimsy were the borogoves, Did gyre and gimble in the wabe: 'Twas brillig, and the slithy toves JABBERWOCKY -- Lewis Carroll
Lysate Preparation from Biofluids/Viruses Collected with Nasal or Throat Swabs v1
Authors: not provided Bioline
Published: June 2017

The steps for preparing the lysate are different depending on the starting material. Please ensure you follow the correct procedure for your starting material (see the section Disrupting and Homogenizing Starting Materials and the different lysate preparation protocols here). The subsequent steps detailed in Genomic DNA removal and total RNA purification are the same in all cases. This protocol is designed for the isolation of all sizes of RNA (including miRNA) from a wide variety of biofluids derived from all human and animal sources collected with nasal or throat swabs. Follow this protocol for isolating RNA from viruses collected with nasal or throat swabs.
Lysate Preparation from Viruses in Mammalian Tissue v1
Authors: not provided Bioline
Published: June 2017

The steps for preparing the lysate are different depending on the starting material. Please ensure you follow the correct procedure for your starting material (see the section Disrupting and Homogenizing Starting Materials and the different lysate preparation protocols here). The subsequent steps detailed in Genomic DNA removal and total RNA purification are the same in all cases. This protocol describes the isolation of viral RNA from small amounts of tissue (up to 20 mg for most types of tissue).
Optiprep gradient preparation for virus separation v1
Authors: Gilg Ilana
Published: June 2017

The purpose of this protocol is to generate Optiprep gradients for isolating viruses
CZV8CS - liquid medium for fungal culture v1
Authors: Mead Oliver
Published: June 2017

prepare 100 mL per 250 mL flask for each overnight culture for CZV8CS - liquid media for flask culture prepare 100 mL per 250 mL flask for each overnight culture for 100 mL: 300 mL Czapek-Dox liquid medium 4.54 g 13.62 g centrifuged V8 juice 20 mL 60 mL add H20 to 95 mL 285 mL adjust to pH 6.0 transfer to transfer to flask(s) and autoclave add 5 mL sterile complete supplement to media after autoclaving Complete Supplement (CS) Bacto-casamino acids 20 g/l Bacto-peptone 20 g/l Bacto-yeast extract 20g/l Adenine 3 g/l 9 Biotin 0.02 g/l Nicotinic acid 0.02 g/l P-aminobenzoic acid 0.02 g/l 10 Pyridoxine 0.02 g/l Thiamine 0.02 g/l
Memasukkan foto ke dalam photo frame v1
Authors: Irawan Hendy
Published: June 2017

Cara memasukkan foto mentah (raw) ke dalamphoto frame yang sudah disiapkan dalam format PowerPoint, agar siap dipublikasi di media sosial dan situs web.
Local BLAST database v1
Authors: Seshadri and Georgios Pavlopoulos Rekha
Published: June 2017

BLAST (Basic Local Alignment Search Tool) is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences (Wikipedia). http://www.hypothesisjournal.com/wp-content/uploads/2011/08/boutros-3-1-fig2.png Compare tara_med_examplegenome protein sequences to a custom collection of carbon fixation related genes (downloaded from KEGG) Collection contains marker genes for: CBB, Wood-Ljundahl, reductive TCA, 3-hydroxypropionate, 3-hydroxypropionate/4-hydroxybutyrate As a cyanobacteria - which carbon fixation pathway?
Protoplast Isolation - Incubation Buffer v1
Authors: Burgess Steven
Published: June 2017

Instructions to make 50 mL of incubation buffer for protoplast isolation. Adapted from Yoo et al. 2007http://www.nature.com/nprot/journal/v2/n7/full/nprot.2007.199.html
Sueoka's High Salt Medium v1
Authors: Burgess Steven
Published: June 2017

Sueoka's High Salt Medium is used for photoautotrophic growth of the green alga Chlamydomonas reinhardtii. The medium is also known as HS or HSM. Source: Sueoka, N. (1960) Proc. Natl. Acad. Sci. USA 46, 83-91. http://www.chlamycollection.org/Sueoka.html
Murashige and Skoog (MS) medium v1
Authors: Burgess Steven
Published: June 2017

Murashige and Skoog medium (or MSO or MS0 (MS-zero)) is a plant growth medium used in the laboratories for cultivation of plant cell culture. MSO was invented by plant scientists Toshio Murashige and Folke K. Skoog in 1962 during Murashige's search for a new plant growth regulator. A number behind the letters MS is used to indicate the sucrose concentration of the medium. For example, MS0 contains no sucrose and MS20 contains 20 g/l sucrose. Along with its modifications, it is the most commonly used medium in plant tissue culture experiments in laboratorium.[1] Source: http://cshprotocols.cshlp.org/content/2010/2/pdb.rec12142.full?text_only=true
Nile Red Staining of Drosophila Larval Tissues v1
Authors: Allen Elizabeth
Published: June 2017

Thisprotocol isused to stain late larvalDrosophilalipid droplets in fat bodies and intestines with Nile Red, which emits fluorescence in the 552/636 nm range.
Qiime Commands v1
Authors: Dsouza Melissa
Published: June 2017

Commands for hands-on component for Qiime are found in guidelines.
Sampling to Monitor Fluorescence during Cell Lysis: 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. 15 Hourly Timepoints: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 (unfiltered) 8 Even-hour Timepoints: 0, 2, 4, 6, 8, 10, 12, 14 (filtered) Sampling is for monitoring the fluorescence vs. time and tracking the real-time progression of the phage infection. For Fluorescence measurement,20 µl of sample was taken from each experiment bottle and diluted 10X in ASW in a 96-well plate for both filtered and unfiltered samples. The plate was read with the program “chla + phyco_onestep.prt” on the Tecan plate reader, which reads fluorescence at 680 nm (excitation 440 nm) for chlorophyll a and reads fluorescence at 577 nm (excitation at 544 nm) for phycoerythrin.
ECOGEO 'Omics Training: 4.1 Assembly v2
Authors: Aylward Frank , Daniel Mende not provided
Published: June 2017

Provides a short introduction to MEGAHIT, IDBA-UD, and SPAdes assemblers, a demo on Prodigal Gene Caller, and determining % of reads and contig coverage using Bowtie2 short read aligner. Open this protocol inside the virtual machine (details in 'Start Instructions') for easy copy, paste of commands into the command line terminal window.
Agrobacterium mediated transformation of Marchantia spores v2
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 and it has been 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, and into HT methods like AgarTrap
Command line exercises with yeast v1
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.
Transfection of Cas9 RNP (ribonucleoprotein) into adherent cells using the Lipofectamine® RNAiMAX v1
Authors: England BioLabs New , Inc. not provided
Published: June 2017

Cas9 nuclease may be usedin vivoto create targeted genome modifications. There are several ways in which to introduce Cas9-guide RNA complexes into cells. Here we present a method for the transfection of Cas9 RNP’s into HEK293 FT cells using Thermo Fisher Lipofectamine® RNAiMAX. This is a ‘reverse transfection’ method that uses a final concentration of 10 nM RNP per transfection in a 96-well culture plate.
Command line exercises with yeast v2
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.
Chlorophyll Extraction in Cyanobacteria v1
Authors: Schmelling Nicolas
Published: June 2017

This protocol should be used for chlorophyll extraction in cyanobacteria. The equation for calculating the exact chlorophyll content can be found at the end of this document. You might want to measure the optical density (OD) of you cyanobacteria culture at 750 nm. Use BG11 medium or water as the reference solution. You might need the OD of your culture to normalize the cholorphyll concentration to the number of cyanobacteria. Calculate chlorophyll content Chl [µg/ml] = OD665nm x 13.9 [µg/ml] x dilution factor of culture
Cleaning for new teflon (PFA/FEP/PTFE) v1
Authors: John Seth
Published: June 2017

Protocol for cleaning new and old teflon products.
Western Blot v1
Authors: Cone Alan
Published: June 2017

How the Ju Lab does Western Blots
MojoSort™ Mouse NK Cell Isolation Kit Protocol v1
Authors: Miller Kelsey
Published: June 2017

This procedure is optimized for the isolation of 107 to 2 x 108 cells per tube. If working with fewer than 107 cells, keep volumes as indicated for 107 cells. For best results, optimize the conditions to your specific cell number and tissue. Prepare fresh MojoSort™ Buffer solution by diluting the 5X concentrate with sterile distilled water. The purity of the CD3- CD49b+ NK Cell fraction typically ranges from 80 to 90%. Removal of dead cells is highly recommended prior to cell isolation. Dead cells can be removed using appropriate centrifugation media or other methods. Product description and procedure summary: The kit is designed for the isolation of mouse NK cells from lymphoid tissues. Target cells are depleted by incubating the sample with the biotin antibody cocktail followed by incubation with magnetic Streptavidin Nanobeads. The magnetically labeled fraction is retained by the use of a magnetic separator. The untouched cells are collected. These are the cells of interest; do not discard the liquid. Some of the downstream applications include functional assays, gene expression, phenotypic characterization, etc.
RefSeqMash 0.0.2 v2
Authors: Youens-Clark Ken
Published: June 2017

RefSeqMash uses the MinHash (http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x) algorithm to characterize the genera/species/strains present in metagenomic samples by comparing the reads to ~11K known RefSeq genomes.
MG_HW5: Mapping reads with Bowtie2 v1
Authors: Thornton James
Published: June 2017

This protocol provides a procedure for mapping reads to co-assembled contigs using Bowtie2.
MojoSort™ Mouse CX3CR1 Selection Kit Protocol v1
Authors: Miller Kelsey
Published: June 2017

This procedure is optimized for the isolation of 106 cells per test. If working with fewer than 106cells, keepvolumes as indicated for 106cells. For best results, optimize the conditions to your specific cell number andtissue. Prepare fresh MojoSort™ Buffer solution by diluting the 5X concentrate with sterile distilled water. Product description and procedure summary:Target cells are positively selected or depleted by incubating the sample with the biotin anti‐mouse CX3CR1antibody followed by incubation with magnetic Streptavidin Nanobeads. The magnetically labeled fraction isretained by the use of a magnetic separator. These are the CX3CR1+ cells, do not discard them if those are thecells of interest. Some of the downstream applications include functional assays, gene expression, phenotypiccharacterization, etc.
SensiFAST™ Probe Hi-ROX One-Step Kit v1
Authors: not provided Bioline
Published: June 2017

The SensiFAST™ Probe Hi-ROX One-Step Kit has been formulated for highly reproducible first-strand cDNA synthesis and subsequent real-time PCR in a single tube. The kit is formulated for use with probe-detection technology, including TaqMan®, Scorpions® and molecular beacon probes. A combination of the latest advances in buffer chemistry together with a reverse transcriptase and hot-start DNA polymerase system, ensures that SensiFAST Probe Hi-ROX One-Step Kit produces fast, highly-specific and ultra-sensitive one-step real-time RT-PCR. The SensiFAST Probe Hi-ROX One-Step Kit consists of a 2x SensiFAST Probe Hi-ROX One-Step mix, separate reverse transcriptase and RiboSafe RNase Inhibitor.
SensiFAST™ Protocols v1
Authors: not provided Bioline
Published: June 2017

This is a collection of Bioline protocols for the SensiFAST™ Kits. Please refer to the appropriate protocol, depending on your application.
MG_HW9: Getting started with Anvi'o v1
Authors: Eren and Bonnie Hurwitz Murat
Published: June 2017

Adapted fromhttp://merenlab.org/2016/06/22/anvio-tutorial-v2/
Marchantia Protoplast Isolation v1
Authors: Boehm Christian
Published: June 2017

Marchantia protoplast preparation (adapted from Bopp and Vicktor 1988)
Pre-stain protocol for GreenGlo™ Safe DNA Dye, 20,000X in Water v1
Authors: Scientific Denville
Published: June 2017

GreenGlo ™, 20,000X in Water, is a non-carcinogenic and non-toxic alternative to Ethidium bromide used for the detection of nucleic acids in agarose gels. It is as sensitive as Ethidium bromide. There is no toxic DMSO as GreenGlo ™ is supplied in water. GreenGlo ™ has fluorescence excitation maxima at 295 nm and 490 nm. The fluorescence emission maxima is similar to EtBr when bound to DNA – at 530 nm.
SQK-MAP005 protocol for library preparation for Nanopore sequencing v1
Authors: Istace Benjamin , Anne Friedrich not provided , Léo dAgata not provided , Sébastien Faye not provided , Emilie Payen not provided , Odette Beluche not provided , Claudia Caradec not provided , Sabrina Davidas not provided , Corinne Cruaud not provided , Gianni Liti not provided , Arnaud Lemainque not provided , Stefan Engelen not provided , Patrick Wincker not provided , Joseph Schacherer not provided , Jean-Marc Aury not provided
Published: June 2017

This protocol describes the library preparation for Nanopore sequencing according to the SQK-MAP005 protocol. It accompanies the GigaScience publication: Benjamin Istace, et al. (2017) De novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer. GigaScience...
Total Chlorophyll a Measurements by Spectrophotometer v1
Authors: Steven Wilhelm Dr.
Published: June 2017

Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol. Adapted from Wetzel and Likens 2000. Limnological Analyses, Springer NY
Трансформация органов власти Казанской губернии после Февральской революции
Authors: Миронова Елена Валерьевна
Published: June 2017

Статья посвящена проблеме реорганизации власти в Казанской губернии после событий февраля 1917 г. в России. В общих чертах реорганизация была закончена весной, но отдельные изменения в системе управления продолжались до Октябрьской революции. Актуальность статьи определяется недостаточной изученностью трансформации власти в регионах и, в частности в Казанской губернии.

На основании материалов периодической печати и архивных документов изучены становление и развитие как новых институтов власти на местах — комиссаров Временного правительства, комитетов общественной безопасности и Советов, так и развитие прежних органов самоуправления — земств и городских дум. Основной институт власти, на который опиралось Временное правительство, — комиссары — оказался неспособным проводить требуемую политику. Органы самоуправления в течение весны 1917 г. сделали попытку демократизации. В их состав были введены представители низов, но, не обладая необходимым опытом управления, они продолжали подчиняться буржуазии и землевладельцам, стоявшим во главе этих учреждений. Советы, как и комиссары, должны были удовлетворять чаяниям крестьян и пролетариев, а также бороться с зажиточной частью населения, не хотевшей усиления революции. Совет крестьянских депутатов губернии занял радикальную позицию и прямо нарушал постановления правительства.

Автор сделал вывод, что местные органы управления, проводя неуверенную политику Временного правительства, не смогли удовлетворить потребности населения в решении земельного и продовольственного вопросов, обеспечении безопасности. В итоге буржуазия и дворянство потеряли авторитет и уступили позиции выходцам из «низов». Последние и пришли к власти в результате Октябрьской революции 1917 г. 
Проблема гармонии природы в творчестве Н. А. Заболоцкого: философский и религиозный контекст
Authors: Казакова Ирина Борисовна
Published: June 2017

В русской литературе XX в. едва ли найдется поэт, более напряженно размышлявший о сущности и предназначении природы, чем Николай Алексеевич Заболоцкий (1903–1958). Его стихи содержат целостный взгляд на окружающий мир и поэтому могут рассматриваться как выражение определенной философии природы. Целью статьи является анализ темы гармонии природы в творчестве Заболоцкого, выявление роли тех или иных философских и религиозных концепций в формировании взглядов поэта на проблему.

В натурфилософской поэзии Н. А. Заболоцкого природная жизнь рассматривается как гармоничная и дисгармоничная одновременно. Это можно объяснить присутствием в творчестве поэта двух концепций гармонии и, соответственно, двух способов решения проблемы дисгармонии. Первая концепция восходит к неоплатонической традиции, приверженцами которой были И. В. Гете — один из наиболее близких Н. А. Заболоцкому по своему мировоззрению поэтов — и представители романтической эстетики. Согласно этой концепции дисгармония в универсуме, проявляющаяся или в виде физического несовершенства, или в виде морального зла, — это частность, не нарушающая предустановленного мирового порядка.

Вторая концепция близка православной точке зрения на природу как динамическую реальность, которая постепенно совершенствуется, избавляется от дисгармонических явлений и движется к идеальному гармоничному состоянию — деификации. Ключевую роль в этом процессе играет человечество, которое, вступив в разлад с Богом, нарушило и природную гармонию, поэтому теперь люди должны помочь природе избавиться от противоречий. Мысли о деификации дополняются в поэтическом мире Н. А. Заболоцкого идеей научного прогресса в духе К. Э. Циолковского, В. И. Вернадского и философии космизма.

Для выражения идеи природной гармонии Н. А. Заболоцкий пользуется образностью, восходящей к пифагорейскому учению о музыке небесных сфер. Поэт не соединяет обе концепции в одно непротиворечивое учение, и присутствие в его творчестве двух точек зрения на проблему дисгармонии природы свидетельствует о сложности его мировоззрения, о насыщенном философском и культурном контексте его творчества.
Is the publishing landscape of bioprinting research going to change?
Authors: CHUA Chee Kai
Published: June 2017

Bioprinting as a new and emerging research field is now gaining momentum. Figure 1 was generated from Scopus by using bioprinting as the search keyword. It shows the trend of the number of published docu-ments (article or review) per year. There are 361 documents in total and 103 are published in the most recent year.
Desterritorialização e Perda da Aura: uma análise da cronica de Jose Fernandes
Authors: Da Silva Rosimeire Soares , Rodrigues Maria Aparecida
Published: June 2017

Resumo: este estudo, de cunho teórico, objetiva demonstrar como a crônica de José Fernandes, por se tratar de um objeto artístico literário contemporâneo, promove nova leitura mediante a desterritorialização e perda parcial da aura. Sobre isso, questiona-se: a crônica, em seu processo evolutivo e em meio à era da reprodutibilidade artística, perdeu a aura? Foi emancipada? Para tanto, este estudo está ancorado na teoria estética de Benjamim, territorialização e desterritorialização de Deleuze e Guatarri; cronotopo e dialogismo de Bakhtin. Como recorte metodológico, utilizou-se a pesquisa teórica com abordagem qualitativa e ênfase no conceito de arte como fenômeno estético-discursivo, passível de interpretação crítica. E no que se refere ao modo de tratamento do objeto de estudo, trata-se de uma pesquisa bibliográfica com amplitude descritivo-explicativa. Assim, a crônica de JF nega alguns postulados a respeito desse tipo de narrativa curta e se configura como o Fiat criador enquanto gênero ficcional.

Palavras-chave: Crônica Contemporânea. Aura. Desterritorialização.
A Literatura e seus Desafios: o que dura em tempos líquidos?
Authors: Coimbra Rosicley Andrade
Published: June 2017

Resumo: o objetivo deste artigo é refletir sobre alguns aspectos da modernidade e sobre os principais desafios da literatura diante daquilo que Zygmunt Bauman chamou de tempos líquidos. Partindo das reflexões de Bauman intentamos pensar como a literatura tem reagido em face dos vários aspectos desses tempos fluídos. Para tanto levantamos as seguintes indagações: Quais as estratégias da literatura diante da efemeridade das coisas do presente? Quais valores a literatura tem conseguido preservar? E quais outros desafios a literatura tem enfrentado? E, em meio a toda uma mixórdia de acontecimentos cotidianos, como o indivíduo se comporta? Estas são questões norteadoras para reflexões que estão longe de uma resposta, uma vez que a modernidade possui facetas cambiantes e semoventes, características de sua ambivalência. Sob a perspectiva dos aspectos mencionados, pretendemos pensar também como a literatura tem tratado temas como: o presente, o amor, o espaço, a experiência e a si própria.

Palavras-chave: Modernidade. Literatura. Reflexões. Desafios.
Capitalism, Microfinance and Democracy
Authors: Kharbanda Sakshi
Published: June 2017

The paper looks at the relationship between neoliberal thought of economics and microfinance. Applying the principles of embedded neoliberal economics to microfinance suggests that the government and markets do not exist in solidarity. They can both grow and sink together. Both are required to fulfill each other's requirements to sustain in a nation state. This paper suggests that market oriented economy, can be mediated through the government by bringing in changes to the institutions that can help markets grow and by also molding the nature of relationship it shares with the society. On the other hand, Markets have to incorporate the cultural, social and local knowledge to use it to their advantage. Economic sphere cannot work on its own regulations and by itself completely. The aim of neoliberal proponents shall not be to create same homogeneous conditions wherever they go to operate. Rather diversity should be studied closely to devise the best methods to deal with different contexts and societies. The paper first analyses the relationship between different types of capitals (Physical and Social) with Microfinance and development and then knits them together with the thread of democracy.
Editorial
Authors: Sengupta Mousumi
Published: June 2017

No Abstract.