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Authors: Nicolas Schmelling
Group: M4455 - Synthetische Biologie und Biotechnologie
Summary: 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 need the OD of your culture to normalize the cholorphyll concentration to the number of cyanobacteria.Calculate chlorophyll content (adapted from Lichtenthaler 1978)Chl [µg/ml] = OD665nm x 13.9 [µg/ml] x dilution factor of cultureYou can take less than 1 ml, but note the dilution factor for the calculation later on, e.g. :1 ml sample = dilution factor of 1500 µl sample = dilution factor of 2100 µl sample = dilution factor of 10
Proper citation: Nicolas Schmelling 2019. Chlorophyll Extraction in Cyanobacteria. protocols.io dx.doi.org/10.17504/protocols.io.ywvfxe6 Copy
Authors: Biswapriya Misra, Michael Olivier
Group: Metabolomics Protocols & Workflows
Summary: This protocol provides details on preparation of human and non-human primate blood plasma/ serum extraction, and derivatization for GC-MS based metabolomics data acquisition.
Proper citation: Biswapriya Misra, Michael Olivier 2019. Metabolite Extraction and Derivatization of Plasma/ Serum Samples for High Resolution GC-MS- based Metabolomics. protocols.io dx.doi.org/10.17504/protocols.io.723hqgn Copy
Authors: Sophie Adler, Kirstie Whitaker, Mira Semmelroch, Konrad Wagstyl
Summary: The MELD Project is an international collaboration aiming to create open-access, robust and generalisable tools for FCD detection. To this end, we will train a neural network classifier on MRI features from FCD patients from multiple centres worldwide.Protocol 3 provides instructions on how to quality control the FreeSurfer reconstructions.These instructions are based on the freely available protocols on the ENIGMA-epilepsy website http://enigma.ini.usc.eduWe are very grateful to Derrek Hibar, Neda Jahanshad, Roberto Toro, Jerod Rasmussen, Theo van Erp, Esther Walton and Stefan Ehrlich who wrote the orginal ENIGMA protocols and offered them with an unlimited license without warranty! The main change is correct co-registration of FLAIR to T1 is now checked.
Proper citation: Sophie Adler, Kirstie Whitaker, Mira Semmelroch, Konrad Wagstyl 2018. MELD Protocol 3 - FreeSurfer Quality Control. protocols.io dx.doi.org/10.17504/protocols.io.pdadi2e Copy
Authors: Louise Lantier
Group: Mouse Metabolic Phenotyping Centers
Summary: The Promethion from Sable Systems (Las Vegas, NV) assesses several key metabolic characteristics of mice such as energy expenditure, preferred metabolic substrate, meal patterns, activity, live body mass. These are measured by individually housing the mice in the Promethion System cages for several days during which numerous parameters are continuously measured (food and water intake, weight, activity, O² and CO²).
Proper citation: Louise Lantier 2019. Vandy – Energy Balance with Promethion. protocols.io dx.doi.org/10.17504/protocols.io.yzxfx7n Copy
Authors: Parham Jabbarzadeh Kaboli, patimah Ismail, King-Hwa Ling
Summary: To MD analysis for one of our previous results of docking, for example to analyze the drug/target, almost 40 steps are required to finalize the MD results.The following protocol is according to our own experience in this project and was improved so that the errors were solved during the projects.
Proper citation: Parham Jabbarzadeh Kaboli, patimah Ismail, King-Hwa Ling 2018. Molecular Dynamics (MD) Simulations, step by step protocol. protocols.io dx.doi.org/10.17504/protocols.io.mztc76n Copy
Authors: Steven Wilhelm
Group: Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), CyanoHABs
Summary: Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol.Adapted from Nanodrop ND-1000 User Manual
Proper citation: Steven Wilhelm 2017. Nanodrop Spectrophotometer (ND-1000) for Nucleic Acid. protocols.io dx.doi.org/10.17504/protocols.io.id2ca8e Copy
Authors: Bernardo Mainou
Summary: Fluorescent labeling of reovirus virions with succinimidyl ester-conjugated fluorescent probes
Proper citation: Bernardo Mainou 2017. Fluorescent Labeling of Reovirus with Succinimidyl Ester Dyes. protocols.io dx.doi.org/10.17504/protocols.io.kqhcvt6 Copy
Authors: Kiichi Hirota, Yoshiyuki Matsuo
Proper citation: Kiichi Hirota, Yoshiyuki Matsuo 2018. Quantitative reverse transcriptase-PCR analysis. protocols.io dx.doi.org/10.17504/protocols.io.v7ne9me Copy
Authors: Rekha Seshadri
Group: ECOGEO
Summary: Explore and compare two strains of Dehalococcoides mccartyi to discover putative gene(s) responsible for complete dechlorination of PCE to nontoxic end product, ethylene.
Proper citation: Rekha Seshadri 2016. Functional Annotation & Beyond with Integrated Microbial Genomes (IMG). protocols.io dx.doi.org/10.17504/protocols.io.fb4biqw Copy
Authors: Eliza Harris
Group: Ecophysiology
Summary: Protocol: Bachelor and Master thesis students
Proper citation: Eliza Harris 2019. Bachelor/Masters thesis protocol. protocols.io dx.doi.org/10.17504/protocols.io.7brhim6 Copy
Authors: aronpeter92 , Sándor D. Attila, Andrei D. Mihalca
Proper citation: aronpeter92 , Sándor D. Attila, Andrei D. Mihalca 2021. Materials and Methods: First report of the bat fly species Basilia italica in Romania. protocols.io dx.doi.org/10.17504/protocols.io.bi2ykgfw Copy
Authors: Vidur Sabharwal
Proper citation: Vidur Sabharwal 2019. Setting up a liquid culture and harvesting C.elegans. protocols.io dx.doi.org/10.17504/protocols.io.xcpfivn Copy
Authors: Jason Kim
Group: Mouse Metabolic Phenotyping Centers
Summary: Summary:
This experiment provides the quantification of multiple cytokines and chemokines using multiplexed-Luminex technology based on beads containing specific antibodies. Serum cytokine levels reflect chronic or acute inflammation, and circulating cytokines and chemokines are altered in obesity.
Cytokines Panel I include IL-1α, IL-1β, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, KC (IL-8 homologue), IL-9, IL-10 (interleukin-10), IL-12 (p40), IL-12 (p70), IL-13, IL-15, IL-17A, TNFα (tumor necrosis factor alpha), IFNγ (interferon gamma), IP-10 (interferon gamma-induced protein 10; CXCL-10), Eotaxin (CCL-11), G-CSF (granulocyte colony stimulating factor), GM-CSF (granulocyte macrophage colony stimulating factor), LIF (leukemia inhibitory factor), LIX (LPS- induced CXC chemokine), MCP-1 (monocyte chemotactic protein-1; CCL-2), M-CSF (macrophage colony stimulating factor), MIG (monokine induced by gamma interferon; CXCL- 9), MIP-1α (macrophage inflammatory protein alpha; CCL-3), MIP-1β (macrophage inflammatory protein beta; CCL-4), and MIP-2/RANTES (macrophage inflammatory protein 2- alpha; CXCL-2).
A service can be requested for all or any combination of listed cytokines/chemokines for customized multiplexed Luminex assay.
Proper citation: Jason Kim 2019. U Mass - Electrolytes. protocols.io dx.doi.org/10.17504/protocols.io.xwafpae Copy
Authors: Yuan Zhenya
Summary: This protocol refer to a study having the aim to study on the variation of gut microbiota in preterm infants in the process of feeding intolerance after birth.
In this study, fecal samples were collected from the preterm infants for several times and performed on the bacterial DNA extraction,PCR amplification in the lab, and 16S rRNA sequencing on the Miseq PE300 of the Illumina Platform.
Proper citation: Yuan Zhenya 2019. Protocol of sampling of feces in preterm infants. protocols.io dx.doi.org/10.17504/protocols.io.tn4emgw Copy
Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol outlines our alpha diversity analyses of the virome (from PHACCS) and whole metagenome (from MetaPhlan OTU table). We start by comparing the virome and whole metagenome alpha diversity values, and then look at the differences in virome and whole metagenome diversity between skin sites. 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." mBio 6.5 (2015): e01578-15.
Proper citation: HANNIGAN GD, GRICE EA, ET AL. 2016. Script R5: Virome Alpha Diversity. protocols.io dx.doi.org/10.17504/protocols.io.eimbcc6 Copy
Authors: peijun he
Group: Coronavirus Method Development Community, XPRIZE Rapid Covid Testing, Highfield Diagnostics
Summary: Coronavirus Lateral Flow Assay (LFA) operation protocol
Proper citation: peijun he 2020. Coronavirus Lateral Flow Assay (LFA) operation protocol. protocols.io dx.doi.org/10.17504/protocols.io.bksjkwcn Copy
Authors: Anna Behle
Group: Axmann Lab
Summary: Protocol for separating total RNA using denaturing formaldehyde agarose gel electrophoresis.This method can be used to separate larger RNAs in a range of 400-6000 nt, either for quality control or downstream Northern Blot Analysis.
Proper citation: Anna Behle 2017. Denaturing formaldehyde agarose gel-electrophoresis. protocols.io dx.doi.org/10.17504/protocols.io.gtsbwne Copy
Authors: Nick Tang
Group: VERVE Net, Upton-Lab
Summary: Viral Bioinformatic Resource CentreProvide databases of viral genomic information. Please check the Organisms menu 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 (see VBRC 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
Proper citation: Nick Tang 2016. VBRC Base By Base: Search for a sequence motif, either exact (regular expression search) or inexact (fuzzy motif search). protocols.io dx.doi.org/10.17504/protocols.io.eczbax6 Copy
Authors: Roey Angel
Group: SoWa RI Anaerobic and Molecular Microbiology (public)
Summary: This protocol describes a procedure for sampling plant roots in the field for future DNA and RNA extraction for microbiome analysis. The protocol is deliberately designed to be simple and requires no electronic equipment. Root samples are preserved in LifeGuard Soil Preservation Solution for protecting against nucleic acid degradation.
Proper citation: Roey Angel 2018. Field sampling of root-associated microbes for DNA/RNA extraction. protocols.io dx.doi.org/10.17504/protocols.io.qprdvm6 Copy
Authors: Virginia Sanchez
Summary: International and national studies on dating violence have concluded about the higher involvement of adolescents and youths in comparison to adult couples. At the same time, prevention programs have resulted more successful in adolescent population than in older ages, yielding promising results regarding the reduction of aggressive behaviour. However, despite these encouraging results, evidence-based universal prevention programs are still scarce among the scientific community, particularly in Spain. This project aims to contribute to the body of knowledge of evidence-based interventions developing, implementing and evaluating the efficacy of a Cluster-Randomized Control Trial Dating Violence Prevention Program. The program will integrate the characteristics and peculiarities of the phenomenon when it happens in the teenage years; risk and protective factors of dating violence will be considered and included in the design of the intervention program; the program will involve school member staff and will be partially sustained on peer-led learning. The results of this study will contribute to increasing the number of evaluated prevention programs to reduce dating violence in adolescence, which may be used by teachers and policymakers. By doing this, the project is therefore expected to contribute to the scientific and educational community with a psychoeducational model that could be incorporated into the educational policies.
Proper citation: Virginia Sanchez 2018. The Dat-e Adolescence Prevention Program Protocol: A Cluster Randomizedcontrol Trial. protocols.io dx.doi.org/10.17504/protocols.io.tp8emrw Copy
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