bluuebunny/crossref_metadata_2025 huggingface dataset:
ДОСЛІДЖЕННЯ ТЕХНОЛОГІЧНИХ АСПЕКТІВ ВИРОБНИЦТВА ХЛІБА ІЗ ДИСПЕРГОВАНОЇ ЗЕРНОВОЇ МАСИ З ВИКОРИСТАННЯМ ДОДАТКОВОЇ ПІДГОТОВКИ СИРОВИНИ
Authors: МИКОЛЕНКО С. Ю. , СОКОЛОВ В. Ю. , ПЕНЬКОВА В. В.
Published: June 2017

У статті описані основні тенденції щодо розвитку харчової промисловості у напрямку створення функціональних продуктів, здатних замінити рафіновані продукти масового споживання та висвітлені основні проблеми, які виникають при виробництві цільнозернового хліба. Розглянуто становище ринку виробництва продуктів функціонального призначення в Україні та потенційну користь від використання периферичних частин зернівки у таких продуктах. Здійснено огляд наукових праць, спрямованих на розробку і покращення якості цільнозернових продуктів функціонального призначення. Описано технологічні особливості виробництва хліба із диспергованої зернової маси та висвітлено основні технологічні проблеми, які потребують вирішення. Метою роботи була розробка рецептур і визначення оптимальних технологічних параметрів виробництва хліба із диспергованого зерна пшениці при застосуванні плазмохімічно активованої води для замочування зерна та приготування тіста. Досліджено вплив складу і кількості рецептурних компонентів на якість хліба із пророщеного зерна пшениці. За результатами дослідження підібрано оптимальну рецептуру для хліба із диспергованої зернової маси.  Запропоновано використання плазмохімічно активованої води у якості інтенсифікатора біохімічних процесів та антисептика у технології виробництва продукції з диспергованої пророщеної зернової сировини. Визначено  вплив тривалості замочування зерна на якість готових виробів та встановлено особливості формування якості хліба із диспергованої зернової маси при використанні води, підданої дії контактної нерівноважної плазми. Представлені результати комплексної оцінки якості досліджуваних зразків хліба. Розглянуто вплив плазмохімічно активованої води на активність амілолітичних ферментів і прискорення протікання біологічних процесів у зернівці. Показано вплив води, підданої дії контактної нерівноважної плазми на газоутворюючу здатність тіста. Доведено доцільність використання плазмохімічно активованої води для підвищення якості хліба із пророщеного зерна пшениці та суттєве скорочення тривалості його виробництва.
ВИРОБНИЦТВО І ЯКІСТЬ ГРЕЧАНИХ ПРОДУКТІВ
Authors: ЖИГУНОВ Д. О. , СОЦ С. М. , ДРОЗДОВ А. Ю.
Published: June 2017

В даний час зростають потреби населення в нових продуктах харчування, які характеризуються екологічною чистотою і здоровим напрямком. Одним з таких продуктів є гречана крупа, отримана із зерна гречки. При вирощуванні гречки не застосовуються хімічні добрива, що робить її екологічно чистою. Україна знаходиться в трійці світових лідерів виробників гречки. Ця культура переважно споживається в країнах, де її виробляють, також в останні роки новий поштовх світового споживання гречки дають розвинені азіатські країни. На сьогодні існуючі технології виробництва гречаної крупи, є дуже складними і енергоємними, вимагають великої кількості обладнання. При цьому якість і вихід готової продукції не реалізують потенційні можливості, закладені в зерні. В статті наведено удосконалену технологію виробництва гречаної крупи, яка включає наступні етапи: очищення зерна від домішок, попереднє розділення зерна гречки на потоки, роздільне пропарювання різних за крупністю потоків, розділення потоків на фракції, диференціацію режимів лущення і обробки та контроль. Особливістю розробленої технології є можливість пропарювання кожної фракції зерна гречки окремо: для крупніших фракцій передбачені більш жорсткіші режими – тиск пари 0,30-0,35 МПа, тривалість пропарювання 5-7 хв.; для дрібніших фракцій менш жорсткіші режими – тиск пари 0,25-0,30 МПа, тривалість пропарювання 4-6 хв. Такий диференціальний підхід дозволяє максимально зберегти термолабільні біологічно активні речовини та підвищити вихід і якість готової продукції.  За даною технологією передбачено отримання трьох сортів гречаної крупи, вирівняною за кольором та крупністю: ядриця відібрана вищого ґатунку, ядриця першого ґатунку та дрібна ядриця. Вихід при переробці зерна гречки вирощеного в Україні складає: для ядриці відібраної вищого ґатунку – 35-40%; для ядриця першого ґатунку – 25-30%; для дрібної ядриці  – 4-8%. Кожен вид отриманої крупи за запропонованою технологією має свого споживача та свою ціну. Така технологія дозволить істотно підвищити приваблювання переробки зерна гречки і поширити попит населення на гречані продукти
f-атоми складності функцій Морса на замкнених оріорієнтованих двовимірних многовидах
Authors: Пришляк О. О. , Скочко Д. М.
Published: June 2017

В роботі було досліджено та знайдено всі можливі f-атоми складност 4 функцій Морса на замкнених орієнтованих двовимірних многовидах.
Голоморфно-проективнi перетворення та конформно-келеровi многовиди
Authors: Черевко Є. В.
Published: June 2017

Розглянуто голоморфно-проективнi вiдображення та можливiсть Ёх iснування на локально конформно-келерових многовидах. Отримана система рiвнянь типу Коши, що є визачальною для групи конформно голоморфно-проективних iнфiнiтезимальних перетворень.
Трійки нескінченних ітерацій гіперпросторів max-плюс опуклих множин
Authors: Савченко Александр Григорьевич , Заричный Михаил Михайлович
Published: June 2017

Досліджується геометрія нескінченних ітерованих гіперпросторів компактних max-плюс опуклих множин, їх поповнень та компактифікацій.
О поверхностях пространства Минковского со стационарными значениями кривизны грассманова образа
Authors: Grechneva Marina , Stegantseva Polina
Published: June 2017

В данной работе рассматриваются классы поверхностей (времениподобные и пространственноподобные) пространства Минковского ^1R_4 со стационарными значениями кривизны грассманова многообразия PG(2,4) вдоль площадок, касательных к их грассманову образу Г^2
Застосування просторів-склеювачів до класифікації Бера відображень однієї змінної
Authors: Karlova Olena
Published: June 2017

Ми вводимо поняття (локально) слабкого простору-склеювача і розглядаємо застосування склеювачів до берівської класифікації відображень з класів Лебеґа, а також фрагментовних відображень.
A new curvature-like tensor in an almost contact Riemannian manifold
Authors: Matsumoto Koji
Published: June 2017

In a M. Prvanović’s paper [5], we can find a new curvature-like tensor in an almost Hermitian manifold.In this paper, we define a new curvature-like tensor, named contact holomorphic Riemannian, briefly (CHR), curvature tensor in an almost contactRiemannian manifold. Then, using this tensor, we mainly research (CHR)-curvature tensor in a Kenmotsu and a Sasakian manifold. We introducethe flatness of a (CHR)-curvature tensor and show that a Kenmotsu anda Sasakian manifold with a flat (CHR)-curvature tensor is flat, see Theorems3.1 and 4.1. Next, we introduce the notion of an (CHR)-n-Einstein inan almost contact Riemannian manifold. In particular, in a Sasakian or aKenmotsu manifold, a (CHR)-n-Einstein manifold is n-Einstein, see Theorem5.3. Finally, from this tensor, we introduce a notion of a (CHR)-spaceform in an almost contact Riemannian manifold. In particular, if a Kenmotsuand a Sasakian manifold are (CHR)-space form, then the (CHR)-curvaturetensor satisfies a special equation, see Theorems 6.2 and 7.1.
A Future Perspective on Constitutional Stability
Authors: De Klerk Frederik Willem
Published: June 2017

The 2nd of February next year will be the twentieth anniversary of the beginning of the transformation process that led to the establishment of our present non-racial constitutional democracy.  The previous year when I had addressed the National Party caucus after my unexpected election as leader of the party, I stressed the need to take a quantum leap to break out of the political and economic dead-end street in which we found ourselves.  The overwhelming reaction was "jump FW, jump!".
'n Toekomstige Perspektief op Grondwetlike Stabiliteit
Authors: De Klerk Frederik Willem
Published: June 2017

van die proses van transformasie, wat gelei het tot die instelling van ons huidige nie-rassige grondwetlike demokrasie.  Die vorige jaar, toe ek die koukus van die Nasionale Party toegespreek het ná my onverwagte verkiesing tot leier van die party, het ek klem gelê op die noodsaaklikheid om ŉ kwantumsprong te neem om weg te breek van die politieke en ekonomiese doodloopstraat waarin ons onsself bevind het.  Die oorweldigende reaksie was "spring FW, spring!".
Editorial
Authors: Venter Francois
Published: June 2017

Former State President F W de Klerk, an alumnus of Potchefstroom, delivered the seventh lecture in a series bearing his name last year in October. Some of the other lectures in the series were published in PER (2004(2), 2005(1), 2009(2). We are proud to publish Mr de Klerk's presentation in this issue as an oratio in which he stated that "the Constitution is the indispensable basis of our national unity and our best and abiding hope for continued freedom, prosperity and stability," but simultaneously felt constrained to identify seven threats to which the Constitution was exposed
Public Interest Environmental Litigation: Recent Cases Raise Possible Obstacles
Authors: Kidd Michael
Published: June 2017

Despite the broadening of locus standi in environmental cases by both Section 38 of the Constitution of the Republic of South Africa, 1996, and Section 32 of the National Environmental Management Act 107 of 1998, two recent cases suggest that the pre-constitutional approach to locus standi still holds sway in our Courts.  Moreover, failure to recognise the environmental right in Section 24 of the Constitution may be an impediment to applicants' ability to bring an interdict application successfully.  Correct use of the relevant constitutional provisions ought to obviate such problems, but alternatives are suggested.  In the course of the article, it is suggested that the rule in Patz v Greene is no longer relevant and should be consigned to the history books.
Qiagen MinElute Gel Extraction v1
Authors: Crone Michael
Published: June 2017

MinElute columns can also be used on any vacuum manifold with luer connectors (e.g., QIAvac 24 Plus or QIAvac 6S with Luer Adapters). The following protocol is designed to extract and purify DNA of 70 bp to 4 kb from standard or low-melt agarose gels in TAE or TBE buffer using vacuum-driven processing resulting in high end-concentrations of DNA. Up to 400 mg agarose can be processed per MinElute column.
Resuspension Buffer P1 v1
Authors: not provided Qiagen
Published: June 2017

This is a 0.05M Tris-Cl (pH 8.0), 0.01M EDTA resuspension buffer containing RNase A
Treatments and Preservation of Seawater Samples for FISH v1
Authors: Poulos Bonnie , Jenn Brum not provided , Elke Allers not provided , Christine Schirmer not provided
Published: June 2017

This protocol gives a method for treatment and preservation of seawater samples that will be subject to fluorescence in situ hybridization (FISH). Samples are used with fluorescent probes to determine what populations of bacteria or other microbes are present. The filters may also be used to simply count the number of microbes in a sample. Requires varying amounts of 10µm or 200µm filtrate (up to 11.5L for open ocean depth profile) as shown in Table I.
0.7% Agarose v1
Authors: Sullivan Matthew
Published: June 2017

.
Cesium Chloride Gradients v1
Authors: Sullivan Matthew
Published: June 2017

The usefulness of cesium chloride (CsCl) step gradients and continuous gradients for the separation of viruses is based on the differing buoyant densities of viruses, bacteria, and extracellular debris. This protocol provides a method for Cesium Chloride and DNA Extraction for Viruses (See guidelines for DNA Extraction).
Protocol for SYBR Counts of Cyanophages and Bacteria v1
Authors: Fu and Matt Sullivan Ross
Published: June 2017

Purpose: to determine the concentration of DNA-containing particles in a given sample; useful in finding cell counts or phage titers.
SYBR Gold Working Stock 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
Luminex Bead Coupling v1
Authors: Meyer Aaron
Published: June 2017

We use this process to create our own Luminex assays from standard ELISA reagents.
Modified KAPA Express Extract v1
Authors: Crone Michael
Published: June 2017

KAPA Express Extract is a novel thermostable protease and buffer system that allows for the extraction of PCR-ready DNA from various tissue types in as little as 10 min. This protocol uses half the normal reaction mix.
Cloning with NEB Instant Sticky-end Ligase Master Mix (M0370) v1
Authors: Bien Harold
Published: June 2017

Taken directly from NEB's website, this is the protocol for using their optimized sticky-end ligation and transformation. For more information, see https://www.neb.com/products/m0370-instant-sticky-end-ligase-master-mix. Instant Sticky-end Ligase Master Mix is a ready-to-use 2X solution of T4 DNA ligase and a proprietary ligation enhancer in an optimized reaction buffer. Specifically formulated to rapidly ligate cohesive-end (2–4 bp) substrates and improve transformation, the mix simplifies reaction set-up and provides an optimized ratio of enzyme and buffer components. No thawing of the master mix is required as it maintains a liquid state during storage at -20°C* and no incubation time is necessary to achieve ligation efficiencies sufficient for successful sub-cloning of sticky-end substrates. Just add the master mix to DNA with compatible ends, mix and transform; thereby reducing the valuable time needed for routine ligations. Ligations for subcloning can be carried out in small volumes with low concentrations, allowing users to conserve precious DNA samples, and be used directly to transform many strains of chemically competent E. coli without dilution. * Freezers vary in their actual internal temperature. Our testing demonstrates that the master mix is liquid at -20°C. Freeze-thaw testing at -70°C has confirmed that the performance after 20 freeze/thaw cycles is close to the original mix. Product Source Purified from an E. coli strain containing a recombinant gene encoding T4 DNA Ligase. Reaction Volume Definition 1X Instant Sticky-end Ligase Master Mix with DNA substrates in a 10 μl reaction volume. A 10 μl reaction contains 1800 cohesive end units of T4 DNA Ligase.
Discovering novel genetic polymorphism using VIROME v1
Authors: Bhavsar Jaysheel , Shawn Polson not provided , K. Eric Wommack not provided
Published: June 2017

This tutorial explains how to use VIROME to discover novel genetic polymorphism from viral metagenome shotgun data. Wommack, K. E., J. Bhavsar, S. W. Polson, J. Chen, M. Dumas, S. Srinivasiah, M. Furman, S. Jamindar, and D. J. Nasko. 2012. VIROME: a standard operating procedure for analysis of viral metagenome sequences. Standards in Genomic Sciences 6:427-439 [PMC3558967] See site for more information.
Concentrating Viruses via PEG precipitation v1
Authors: Nissimov Jozef
Published: June 2017

Concentrating Viruses via PEG precipitation
Gel Electrophoresis v1
Authors: J. Cone Alan
Published: June 2017

Separates molecules based on size. Great for checking DNA after a Restriction Digest.
BG-11 Medium for Freshwater Cyanobacteria v1
Authors: Deng Li
Published: June 2017

This medium is used successfully for most cyanobacteria. Vitamin B12 may be added for those species that require it. Use f/2 vitamin solution.
SYBR Green Assay v1
Authors: Patel Anand , Rachel T Noble not provided , Joshua A Steele not provided , Michael S Schwalbach not provided , Ian Hewson not provided , Jed A Fuhrman not provided
Published: June 2017

The protocol provides an inexpensive, rapid (30 min) and reliable technique for obtaining counts of viruses and prokaryotes simultaneously. The method is from: Patel A, Noble RT, Steele JA, Schwalbach MS, Hewson I, Fuhrman JA.Virus and prokaryote enumeration from planktonic aquatic environments by epifluorescence microscopy with SYBR Green I. Nat Protoc. 2007;2(2):269-76. Please see the full manuscript for more details.
Tangential flow filtration (TFF) concentration of phytoplankton v1
Authors: Vaulot Daniel
Published: June 2017

Concentrate phytoplankton samples about 100-fold typically from 5L down to 20 mL. Takes about 1 hour per sample. Samples can be used for flow cytometry sorting or for cultures. Enrichment by TFF usually keep growing for a longer time than unconcentrate samples. Reference Marie, D., Shi, X.L., Rigaut-Jalabert, F. & Vaulot, D. (2010). Use of flow cytometric sorting to better assess the diversity of small photosynthetic eukaryotes in the English Channel. FEMS Microbiology Ecology. 72. p.pp. 165–178.
Fixation of marine samples for flow cytometry analysis v1
Authors: Vaulot Daniel
Published: June 2017

Protocol to fix marine samples for flow cytometry analysis of phtoplankton and bacteria with SYBR-Green. Fix at least 2 samples per depth sampled and at least 6 to 10 depths per vertical profile Reference Marie, D., Rigaut-Jalabert, F. & Vaulot, D. (2014). An improved protocol for flow cytometry analysis of phytoplankton cultures and natural samples. Cytometry. 85. p.pp. 962–968.
Immunoprecipitation Lysis Buffer v1
Authors: Liu Vivian
Published: June 2017

This lysis buffer is strong enough for lysis most cell lines and wild enough to keep protein interactions. It has been tested on mouse embryonic stem cells, cancer cell lines and overexpressed cells.
Phytoplankton and bacteria filtration v1
Authors: Middelboe Mathias , Amy M. Chan not provided , and Sif K. Bertelsen not provided
Published: June 2017

For use in "Isolation of cyanophages by liquid bioassays"
One-step growth experiments (bacteriophages) v1
Authors: Middelboe Mathias , Amy M. Chan not provided , and Sif K. Bertelsen not provided
Published: June 2017

The life cycle of phages can be characterized by one-step growth experiments, which are designed in a way that allows only a single infection cycle to take place (i.e., no re-infections occurring by phages produced during the experiment).
Plate Amplification v1
Authors: Middelboe Mathias , Amy M. Chan not provided , and Sif K. Bertelsen not provided
Published: June 2017

For use in "Obtaining pure cyanophage stock: plaque purification"
Preparation of reagents v1
Authors: A. Suttle and Jed A. Fuhrman Curtis
Published: June 2017

For Enumeration of virus particles in aquatic or sediment samples by epifluorescence microscopy protocol.
Basic electron microscopy of aquatic viruses v1
Authors: Ackermann and Mikal Heldal Hans-W.
Published: June 2017

This protocol is from: Hans-W. Ackermann and Mikal Heldal. 2010. Chapter 18:Basic electron microscopy of aquatic viruses.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 full manuscript for additional details.
Internal Epitope Tagging of Proteins Using Transposon Tn7 v1
Authors: E. Zordan Rebecca , Brian J. Beliveau not provided , Jonathan A. Trow not provided , Nancy L. Craig not provided , and Brendan P. Cormack not provided
Published: June 2017

This is a protocol for in vitro transposon mutagenesis for introduction of internal epitope tags. It is from: Zordan RE, Beliveau BJ, Trow JA, Craig NL, and Cormack BP (2015) Avoiding the Ends: Internal Epitope Tagging of Proteins Using Transposon Tn7. Genetics 200:47-58; doi:10.1534/genetics.114.169482 Please see the full manuscript for additional details. This protocol delineates the steps to perform a small (20μl) “‐enzyme” negative control reaction and a large (80μl) “+ enzyme” experimental mutagenesis reaction in parallel. The enzymes and buffers are mixed together in a master mix (5.5‐reaction sized, to account for pipetting error) and later split into appropriate reaction sizes.
Extracting DNA from viruses embedded in agarose v1
Authors: F. Steward and Alexander I. Culley Grieg
Published: June 2017

If one wishes to have a stock of high molecular weight viral DNA that can be stored for long periods of time with minimal shearing or degradation, the viruses can be embedded in agarose before extraction. Extraction of embedded cells is the standard procedure for sizing the genomes of bacteria andyeast by PFGE (Sambrook and Russell 2001), and a similar protocol can be used for embedded viruses (Rohozinski et al. 1989; Lanka et al. 1993; Wommack et al. 1999; Sandaa et al. 2010, this volume). This is a protocol from: Steward, G. F. and A. I. Culley. 2010. Chapter 16: Extraction and purification of nucleic acids from viruses.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.
Transform Stratagene's XL-10 Gold Ultracompetent cells v1
Authors: Bien Harold
Published: June 2017

Protocol for transforming XL-10 GOld Ultracompetent cells from Stratagene (now Agilent). Protocol adopted from manufacturer's instructions.
Embedding yeast colonies for light and electron microscopy v1
Authors: Piccirillo Sarah , Melissa G. White not provided , Jeffrey C. Murphy not provided , Douglas J. Law not provided , Saul M. Honigberg and
Published: June 2017

The following is a modification of a Scherz R., 2001 method forcolony embedding. The protocol described here is from: Sarah Piccirillo,et. al. The Rim101p/PacC Pathway and Alkaline pH Regulate Pattern Formation in Yeast Colonies(2010) Genetics184:707-716; doi:10.1534/genetics.109.113480 Please see the full manuscript for additional details.
Generating Cas9-mediated fluorescent protein knock-ins with a self-excising selection cassette (SEC) v1
Authors: J. Dickinson Daniel , Ariel M. Pani not provided , Jennifer K. Heppert not provided , Christopher D. Higgins and Bob Goldstein not provided
Published: June 2017

This protocols is from: Daniel J. Dickinson, et al. (2015) Streamlined genome engineering with a self-excising drug selection cassette.Genetics; Early online June 3, 2015,doi:10.1534/genetics.115.178335 Please see the full manuscriptor additional details. Also, updates are available on the author's website.
Fingerprinting aquatic virus communities using pulsed field gel electrophoresis (PFGE) v1
Authors: Sandaa Ruth-Anne , Steven M. Short not provided , and Declan C. Schroeder not provided
Published: June 2017

The viral concentrate used for PFGE analysis must be molded into plugs, followed by lysis of the virus particles to release their DNA. It is possible to run solution-based preparation of viral DNA for PFGE (Steward 2001); however, large DNA molecules (>100 kb) are extremely sensitive to mechanical shearing in aqueous solution (Bouchez and Camilleri 1997). The consensus is that lysis inside viral plugs prevents mechanical shearing of the DNA, resulting in more discrete PFGE bands. Intact viral genomes are then separated by size by PFGE. After separation, the banding pattern is visualized by staining with a fluorescent DNA stain. This banding pattern provides a visual record of the genome size distribution that can be used for qualitative and quantitative comparisons between samples.
Generation of DNA fragments by DNase digestion v1
Authors: H. Wilson and Declan Schroeder William
Published: June 2017

Generation of DNA fragments by DNase digestion involves digesting DNA for a range of times, then picking the time that gives optimal-sized DNA fragments (typically 1000–4000 bp).
1% SDS in DNA Buffer v1
Authors: Baker Andrew
Published: June 2017

This buffer is used to stabilize samples for archiving and subsequentgenomic DNA extraction. SDS is dissolved to a concentration of 1% (w/v) in DNAB (DNA buffer: 0.4 M NaCl +0.05 MEDTA in MilliQ water). The buffer may need to be warmed for SDS to completely dissolve. Tissue samples areadded to small aliquots of 1% SDS in DNAB and heated to 65°C for 60-90 minutes. They are then stable at room temperature and ready for extraction of genomic DNA.
Viral and bacterial isolates, propagation and preparation of stocks v1
Authors: M. Comeau and Rachel T. Noble André
Published: June 2017

The following procedure is an adaptation of the original FLVP protocol from Hennes et al. (1995) for use with SYBR Green I stain. Normally, this protocol will take 2 days given that the softening of the viral pellet is an overnight step. However, if the viral pellet redissolves quickly, it can be accomplished in 1 day.
Pellet resuspension v1
Authors: M. Comeau and Rachel T. Noble André
Published: June 2017

For use in Viral and bacterial isolates, propagation and preparation of stocks.
Western Blotting Protocols (Collection) v1
Authors: not provided BioLegend , Inc. not provided
Published: June 2017

This is a collection of Western Blotting protocols from BioLegend. Please use the appropriate protocol, depending on your application.
MojoSort™ Streptavidin Nanobeads Protocol v1
Authors: Miller Kelsey
Published: June 2017

The cells targeted by the Streptavidin Nanobeads are either selected or depleted by incubating your sample with the magnetic particles after incubating with a biotin-conjugated antibody or antibody cocktail. 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.
Immunofluorescent Staining of Foxp3 in Frozen Sections v1
Authors: Miller Kelsey
Published: June 2017

T regulatory cells (also known as Tregs or Regulatory T cells) are essential cells inthe immune system that suppress immune responses of other cells, designed tolimit excessive reactions and prevent autoimmunity. Tregs are characterized by theexpression of CD4, CD25, and Foxp3, while lacking CD127. CD4+Foxp3+ regulatoryT cells have been referred to as “naturally-occurring” regulatory T cells to distinguishthem from “suppressor” T cell populations that are generated in vitro. While othervariants of suppressive T cells do exist, such as CD8 suppressor cells, Th3 and Tr-1 cells,Tregs are classically defined as CD4+CD25+Foxp3+ cells. Here, we provide a protocolfor immunofluorescent staining of FOXP3 in frozen sections, adapted from a protocolfrom Dr. Matthias Hardtke-Wolenski, Medizinische Hochschule Hannover. This protocolhas been successfully used on mouse spleen, liver, and skin sections.
High sensitivity miRNA Illumina library preparation protocol by TailorMix miRNA Sample Preparation Kit (Version 2) v4
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™ For High Quality Genomic DNA Extraction From Paraffin-Embedded Tissue 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 parafin-embedded tissue. Please refer to the appropriate protocol depending on your application.
High sensitivity (low input) miRNA Illumina library preparation protocol by TailorMix miRNA Sample Preparation Kit (Version 2) v5
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™ For High Quality Genomic DNA Extraction From Body Fluids 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 body fluids(includingCSF, plasma, saliva, serum, sputum, synovial fluid, urine and whole blood). Please refer to the appropriate protocol depending on your application.
Cryopreservation v1
Authors: Hessen-Schmidt Sarah
Published: June 2017

Cryopreservation of cells in 50% glycerol
MegaLong™ Protocol for Isolation of >100kb Genomic DNA (Bacterial DNA) 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 bacteral DNAsamples. Please refer to the appropriate protocol, depending on your application.
Subcellular Fractionation from Animal Cells (FOCUS™ SubCell Kit) v1
Authors: not provided G-Biosciences
Published: June 2017

This protocol is for processing 20x106 cells (or ~100µl wet cell pellet). It can be scaled up and down accordingly. 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.
Collection of FOCUS™ SubCell Protocols For the Enrichment of Subcellular Fractions v1
Authors: not provided G-Biosciences
Published: June 2017

This is a collection of G-Biosciences FOCUS™ SubCell protocols for the enrichment of subcellular fractions. Please refer to the appropriate protocol depending on your application.
Cleaning of the Nuclear Fraction (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.
Electron Microscopy of Haloviruses 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.
Detection of Lysogeny in Marine Environments v1
Authors: H. Paul and Markus Weinbauer John
Published: June 2017

These are protocols from: Paul, J. H., and M. Weinbauer. 2010. Detection of lysogeny in marineenvironments, p. 30–33. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual ofAquatic Viral Ecology. ASLO. Please see the published manuscript for additional information.
Script P1: Pre-Processing Samples v1
Authors: GD Hannigan , Grice EA not provided , et al. not provided
Published: June 2017

This protocol provides methods for quality control of metagenomic data. Included is adapter trimming, quality trimming, decontamination, negative control removal, and pre-processing results. Based on the methods found in 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 P3: Open Reading Frame Prediction v1
Authors: GC HANNIGAN , GRICE EA not provided , ET AL not provided
Published: June 2017

This protocol provides a method for predicting the locations of the open reading frames (ORFs) using the Glimmer3 toolkit. Methods 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.
Script P5: Diversity v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocol provides a method to predict phage community diversity using the algorithm PHACCS.Sequencing of viral communities often results in a high percent of unknown reads, largely due to our incomplete reference databases. To address this unknown factor of viromes, the algorithm PHACCS (PHAge Communities from Contig Spectra) was developed to predict virus community alpha diversity without the use of taxonomic references. 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 P6: HPyV Detection v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocol provides a method for detecting Human Polyomaviruses (HPyVs) in our virome and whole metagenome datasets. For genome reference, download the HPyV genomes (in fasta format) from NCBI (nucleotide) using the search terms "Human Polyomavirus" AND "Complete Genome". This is used in the rest of the analyses.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.
Attaching biotin to Bovine Submaxillary Mucin (BSM) and purifying BSM-biotin v1
Authors: Linderberg Victoria
Published: June 2017

This protocol describes how to attach biotin to Bovine Serum Mucin (BSM). The procedure uses a botin-NHS molecule to attach biotin to amines in the mucin proteins.
Script P7: Assigning Whole Metagenome Taxonomy v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocol provides a method for assigning whole metagenome taxonomy using MetaPhlAn and MEGAN toolkits. 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 R3: Quality Control Statistics v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocoloutlines the quality control analysis measuring the percent relative abundance of 16S rRNA levels in the virome and whole metagenome, as well as the number of virome sequences mapping to the whole metagenome, and vice versa. These measures are used to validate the quality of the sequence datasets. 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.
K-mer-based host screening v1
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.
Script P11: Functional Analysis v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocol provides method for KEGG Analysis, Gene Ontology Analysis, and Operational Protein Family Analysis. 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 R11: Replication Cycle v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This section outlines the analyses we used in our replication cycle section of our report. We first predict how many contigs are potentially of the temperate replication cycle and display this information using a Euler diagram. We then use a relative abundance approach by visualizing the percent of temperate phages present at each site. We end by visualizing the relative abundances of bacteria annotations of the phage contigs. 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.
Stellaris® RNA FISH 96 Well Glass Bottom Plate Protocol v1
Authors: Biosearch Technologies LGC
Published: June 2017

This protocol is specifically designed for high throughput applications of Stellaris in 96 well glass bottom plates.
Stellaris® RNA FISH FFPE (Paraffin-Embedded Tissue) Protocol v1
Authors: Biosearch Technologies LGC
Published: June 2017

Stellaris RNA FISH protocol for formalin-fixed, paraffin-embedded (FFPE) tissue.
Unix and Bioinformatics v1
Authors: Tully Benjamin
Published: June 2017

This protocol details the use of various unix commands commonly used in bioinformatics.
Definitive guide to western blot v1
Authors: Dunigan and Irina Agarkova David
Published: June 2017

Western blotting uses specific antibodies to identify proteins that have been separated based on size by gel electrophoresis. The immunoassay uses a membrane made of nitrocellulose or PVDF (polyvinylidene fluoride). The gel is placed next to the membrane and application of an electrical current induces the proteins to migrate from the gel to the membrane. The membrane can then be further processed with antibodies specific for the target of interest, and visualized using secondary antibodies and detection reagents.
Detecting Fungal Infections in Almonds v1
Authors: Cadena Carolina
Published: June 2017

This protocol is based on the study done by two members of the Biological and Agricultural Engineering department at UC Davis which analyzes the ability of infrared spectroscopy to detect fungal infections in almonds. The methods section of this article was adapted to fit the protocols.io format.Source: “Detection of fungal infection in almond kernels using near-infrared reflectance spectroscopy”. Pei-Shih Liang, David C. Slaughter, Alejandro Ortega-Beltran, Themis J. Michailides. Biosystems Engineering, Volume 137, September 2015, Pages 64–72
CviRI Buffer B v1
Authors: DUNIGAN AND IRINA AGARKOVA DAVID
Published: June 2017

For use in CviRI Purification From XZ-6E Virus Infected NC64A Chlorella.
Isotopic labeling of freshwater mixotrophic algae using isotopic labeled inorganic nitrogen and carbon v1
Authors: Terrado Ramon
Published: June 2017

This protocol aims to achieve an isotopic labeling of mixotrophic algae using 15NH4Cl and 13C-bicarbonate. 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.
RNA (and optional DNA) extraction from environmental samples (filters) v1
Authors: Hu Sarah
Published: June 2017

This protocol describes the extraction process of RNA and/or DNA from marine environmental samples. Samples are assumed to be collected via filtering sample seawater onto filters. Filters are then flash frozen in the first lysis buffer. The protocol describes the steps used to lyse and separate material from filters and use the lysate for RNA and/or DNA extraction using Qiagen extraction kits (e.g. https://www.qiagen.com/us/shop/Sample-Technologies/Combined-Sample-Technologies/). Downstream RNA and DNA is used for molecular analyses such as tag sequencing (16S or 18S), (meta)genomic, or (meta)transcriptomic applications.List of materials needed before starting is inGuidelines.
Mapping Metagenomic Reads to Reference Sequences (Cyverse) v2
Authors: Bolduc Benjamin
Published: June 2017

Mapping metagenomic reads fromOcean Sampling Day (OSD) 2014 against NCBI's ViralRefSeq alongside viral sequences identified from the Tara Oceans survey using VirSorter.
Activation and Intracellular Staining of Whole Blood: For the Detection of Intracellular Cytokines and Other Intracellular Targets v1
Authors: not provided BioLegend , Inc. not provided
Published: June 2017

This is part of BioLegend's, "Intracellular Flow Cytometry Staining Protocol: For the Detection of Intracellular Cytokines and Other Intracellular Targets".
Sampling for Flow Cytometry (FCM) v2
Authors: Giuliani Sarah
Published: June 2017

Collect and preserve samplesfor flow cytometry analysis. This protocol can be used for labculture experiments or field samples.
MG_HW6: Gene Calls with Prodigal v3
Authors: Thornton James
Published: June 2017

This protocol provides the procedure to generate gene calls on your contigs using Prodigal.
ELISA protocol v1
Authors: not provided ELISAassays
Published: June 2017

Assay protocol for pre-coated ELISA plate to measure protein concentration
Lysate Preparation from Viruses in Cultured Cells Growing in a Monolayer 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 for the isolation of integrated viral RNA from mammalian cells growing in culture.
CZV8CS- top agar for fungal protoplast transformation v1
Authors: Mead Oliver
Published: June 2017

CZV8-top agar 100 mL per transformation 200 mL Czapek-Dox liquid 4.54 g 9.08 g agar 0.75 g 1.5 g sorbitol 18.22 g 36.44 g centrifuged V8 juice 20 mL 40 mL add H2O to 100 mL 200 mL adjust to pH 6.0 with NaOH split batch in 2 (½ for plating protoplasts, ½ for overlay) autoclave
MG_HW7: Taxonomic Classification Using Centrifuge v2
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 v5
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 v6
Authors: Thornton James
Published: June 2017

This protocol provides a procedure to generate taxonomic data from assembled contigs using centrifuge.
Import data peserta ke Google Contacts v1
Authors: Irawan Hendy
Published: June 2017

Dengan melakukan import data teman-teman sesama peserta ke Gmail/Google Contacts, maka Anda dapat dengan mudah menghubungi teman-temanpeserta lainnya, melalui telepon, SMS, WhatsApp, Telegram, maupun email. File yang dibutuhkan: File CSV Google Contacts - ada di Dropbox bersama
Assembly Introduction v1
Authors: Aylward and Daniel Mende Frank
Published: June 2017

Provides a short introduction of using the MEGAHIT, IDBA-UD, and SPAdes assemblers.
Propagation of marine eukaryotic viruses (Prasinoviruses) v1
Authors: Zimmerman Amy
Published: June 2017

Purpose: To reproducibly generate fresh preparations of virus for independent experiments. Summary: Fresh virus sample for an experiment is generated by a primary infection of exponentially growing host cells from a master stock of virus. The infected host is allowed to lyse until the culture is cleared. The lysate is filtered to remove any large cellular debris, then the viral-size fraction is concentrated from the filtered lysate and washed with buffer using a centrifugal concentrator. The viral concentrate is stored at 4°C protected from light and should be used for an experiment within 1-2 days. On the day of (or the day before) the experiment, an MPN assay should be set up to assess infectivity of the fresh viral concentrate.
Nitrogen-upshift, chemostat to batch mode v1
Authors: Miller Darach
Published: June 2017

The aim of this protocol is to describe how to do a very reproducible upshift of a nitrogen-limited yeast culture to nitrogen non-limited conditions. In order to do this with enough cells to make inefficient analysis (ie RATEseq) feasible, we start in the chemostat for high-cell counts.
Rye A Agar v1
Authors: Stam Remco
Published: June 2017

This Agar medium can be used for the cultivation of Phytophthora infestans. It is particularly suitable for long term maintenaince of Phytophthora on plate. To induce sporulation 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.
Sampling for RNA / Protein/ DOM/ PO4: 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. 9 Hourly Timepoints: 0, 1, 2, 3, 4, 6, 8, 10, 14 Sampling is to collect supernatant fractions to determine total dissolved phosphate and soluble reactive phosphate (TDP/SRP) for analysis of inorganic phosphate concentration and phosphate in dissolved organic material (DOM); and to collect pellets to isolate RNA for transcriptomics and proteins for proteomics.
SNA medium v1
Authors: Stam Remco
Published: June 2017

Growth Medium used for Alternaria Solani cultivation First described: Nirenberg 1981
Electroporation of Cas9 RNP (ribonucleoprotein) into adherent cells using the Neon® Electroporation 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 introduction of Cas9 RNP’s into HEK293 FT cells using the Thermo Fisher Neon Electroporation System. This method uses a final concentration of 20 nM RNP per transfection in a 24-well culture plate.