Volume: 3 Issue: 12 —BIO-PROTOCOL

Biochemistry

Paper Chromatography as Exemplified by Separation of Urocanic Acid and Deaminohistidine Author: Alexander V. Bogachev, date: 06/20/2013, view: 9190, Q&A: 0

Paper chromatography is an ancient technique to separate low molecular mass compounds based on their distribution between mobile phase (solvent) and stationary phase (cellulose and cellulose-bound water). Paper chromatography has been largely replaced by thin layer chromatography and high performance liquid chromatography as the latter methods ...

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Cell Biology

Calcium Mobilization Assay to Measure the Activity of Gq-coupled Receptors Author: Hamiyet Unal, date: 06/20/2013, view: 20283, Q&A: 0

Calcium mobilization assay is a cell-based second messenger assay to measure the calcium flux associated with Gq-protein coupled receptor activation or inhibition. The method utilizes a calcium sensitive fluorescent dye that is taken up into the cytoplasm of most cells. In some cell lines in which organic-anion transporters are particularly active ...

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LC3B Labeling on Terrestrial Isopod Adipocytes Authors: Christine Braquart-Varnier, Maryline Raimond and Mathieu Sicard, date: 06/20/2013, view: 8749, Q&A: 0

The LC3B protein plays a critical role in autophagy. Normally, this protein resides in the cytosol, but following cleavage and lipidation with phosphatidylethanolamine, LC3B associates with the phagophore. This localization can be used as a general marker for autophagic membranes. To visualize the LC3B, we used the LC3B Antibody Kit for Autophagy ...

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Developmental Biology

Labeling of Precursor Granule Cells in the Cerebellum by ex vivo Electroporation Author: Aya Ito-Ishida, date: 06/20/2013, view: 12642, Q&A: 1

This protocol will be useful to introduce the genes of interest into the cerebellar granule cells at early stages of development. Since the granule cell precursors are localized in the external granule layer before migration, DNA plasmids can be specifically incorporated into the granule cells by injecting DNA solution into the cerebellar fissures ...

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Microbiology

Amino Acid Transport Assays in Resting Cells of Lactococcus lactis Authors: Hein Trip and Juke S. Lolkema, date: 06/20/2013, view: 7335, Q&A: 0

Many bacteria are auxotrophic for at least a number of amino acids for which they lack the biosynthetic pathways. The organisms are still able to grow in media containing free amino acids as the sole source of amino acid when transport systems for the free amino acids are present in the cytoplasmic membrane. A range of transport systems for ...

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Macromolecular Biosynthesis Assay for Evaluation of Influence of an Antimicrobial on the Synthesis of Macromolecules Authors: Justyna Nowakowska, Nina Khanna and Regine Landmann, date: 06/20/2013, view: 9553, Q&A: 0

One of the most compelling approaches in the discovery of novel antimicrobials is screening of natural sources. In our publication we report on the activity of a compound 8-hydroxyserrulat-14-en-19-oic acid (EN4), a diterpene isolated from the Australian plant Eremophila neglecta. We evaluate its applicability for treatment of ...

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EdU labeling of Trypanosome Cells and Their Kinetoplast DNA (kDNA) Author: Jianyang Wang, date: 06/20/2013, view: 8330, Q&A: 0

Trypanosome mitochondrial genome, known as Kinetoplast DNA (kDNA), is a massive network of interlocked DNA rings. The studies of kDNA replication and architecture are of major significance since kDNA is a valid drug target. However, DNA in procyclic trypanosomes can not be labeled with tracer concentrations of ³[H]-thymidine, possibly ...

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IFN-α Inhibition Assay in vitro Author: Kathrin Gibbert, date: 06/20/2013, view: 8085, Q&A: 0

During viral infections Interferon-α (IFN-α) is expressed by infected host cells. IFN-α binds to its receptor (IFNAR1/2), which leads to the activation of downstream signaling via JAK-STAT. This signaling cascade results in the expression of several hundred different genes, so called interferon-stimulated gene, which lead to an antiviral state of ...

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Measurement of IFN-α Subtype Concentrations (Virus-free, Cell-based Bioassay) Author: Kathrin Gibbert, date: 06/20/2013, view: 7035, Q&A: 0

The induction of type I IFN is the immediate host response against viral infections. Type I IFNs belong to a multigene family including up to 14 different IFN-α subtypes and one IFN-β. They are highly conserved and bind the same receptor (IFNAR1/2) with varying affinities, although they differ in their biological activities.

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Molecular Biology

Structural Based Strategy for Predicting Transcription Factor Binding Sites Authors: Beisi Xu, Yongmei Wang, Haojun Liang and Guohui Li, date: 06/20/2013, view: 7363, Q&A: 0

Scanning through genomes for potential transcription factor binding sites (TFBSs) is becoming increasingly important in this post-genomic era. The position weight matrix (PWM) is the standard representation of TFBSs utilized when scanning through sequences for potential binding sites. Many transcription factor (TF) motifs are short and highly ...

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Plant Science

Hairy Root Transformation in Lotus japonicus Authors: Satoru Okamoto, Emiko Yoro, Takuya Suzaki and Masayoshi Kawaguchi, date: 06/20/2013, view: 15761, Q&A: 2

In L. japonicus, hairy root transformation is the very useful technique to generate transformed root systems in a short term. This protocol was previously described (Kumagai and Kouchi, 2003) with some modifications. After the infection of Agrobacterium rhizogenes, L. japonicus develops not only transformed but also ...

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Stable Transformation in Lotus japonicus Authors: Takema Sasaki, Takuya Suzaki and Masayoshi Kawaguchi, date: 06/20/2013, view: 12730, Q&A: 1

This is a protocol to produce stable transgenic plants in Lotus japonicus, which is established based on methods previously reported (Handberg and Stougaard, 1992; Stiller et al., 1997; Thkjaer et al., 1998) with some modifications. In this protocol, hygromycin is used to select transgenic plants.

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Growth Assay and Detection of TRP and Indole Derivatives in Piriformospora indica Culture Supernatant by LC-MS/MS Authors: Magdalena Hilbert, Lars M. Voll, Jörg Hofmann and Alga Zuccaro, date: 06/20/2013, view: 10666, Q&A: 0

The mutualistic root endophyte Piriformospora indica colonizes a wide range of plants and the colonization of root cells by this fungus is very often associated with beneficial effects to its host, such as growth promotion and increased biotic and abiotic stress tolerance. These traits may be based on general mechanisms and signaling ...

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Indole Derivative Feeding Test and Detection of TRP and Indole derivatives by Thin Layer Chromatography Authors: Magdalena Hilbert, Lars M. Voll, Jörg Hofmann and Alga Zuccaro, date: 06/20/2013, view: 8699, Q&A: 0

The mutualistic root endophyte Piriformospora indica colonizes a wide range of plants and the colonization of root cells by this fungus is very often associated with beneficial effects to its host, such as growth promotion and increased biotic and abiotic stress tolerance. These traits could be based on general mechanisms and signaling ...

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Systems Biology

RNA-Seq Library Generation from Rare Human Cells Isolated by FACS Authors: Sofia Gkountela and Amander T. Clark, date: 06/20/2013, view: 10611, Q&A: 0

High throughput RNA Sequencing has revolutionized transcriptome analyses. However, most available protocols require micrograms of RNA rendering this technique not feasible for analyzing small numbers of cells, including precious rare cell types isolated from human tissues or organs. Here, we used an RNA Amplification System and describe a method ...

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Past Issues in 2013

Volume: 3 Issue: 12

Biochemistry

Cell Biology

Developmental Biology

Microbiology

Molecular Biology

Plant Science

Systems Biology