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Past Issues in Bio-protocol

Volume: 5 Issue: 8April 20, 2015

  • All fields (13)
  • Biochemistry (2)
  • Microbiology (4)
  • Molecular Biology (2)
  • Plant Science (5)

Biochemistry

13C Kinetic Labeling and Extraction of Metabolites from Adherent Mammalian Cells Authors:  Parul Mehrotra, Najmuddin Saquib and Kanury V. S. Rao, date: 04/20/2015, view: 3032, Q&A: 0
Fluctuations in metabolite levels in mammalian cells are the most direct form of readout of the cellular metabolic state. The current protocol describes a method for pulse labeling and subsequent isolation of metabolites from adherent mammalian cells. The isolated metabolites can be identified and quantified by mass-spectrometry, allowing for ...
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Measurement of Nucleotide Triphosphate Sugar Transferase Activity via Generation of Pyrophosphate Authors:  Kaisei Maeda, Rei Narikawa and Masahiko Ikeuchi, date: 04/20/2015, view: 3088, Q&A: 0
Nucleotide triphosphate (NTP) transferases (EC. 2. 7. 7. X) transfer a nucleoside monophosphate moiety from NTP to another substrate. NTP sugar transferases form a large member of the NTP transferase. There are many variations for the substrate combination of the NTP sugar transferases. It is important to measure the precise enzymatic activity of ...
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Microbiology

In vitro Drug Susceptibility Assay for HBV Using Southern Blotting Authors:  Sung Hyun Ahn, Yong Kwang Park and Kyun-Hwan Kim, date: 04/20/2015, view: 2715, Q&A: 0
Antiviral agents for the suppression of hepatitis B virus (HBV) have been used for treating chronic hepatitis B. However, the emergence of drug-resistant HBV is still a major problem for antiviral treatment. To identify and characterize the drug-resistant HBV, the construction of HBV replicon and in vitro drug susceptibility assay are ...
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Introduction and Sequencing of Patient-isolated HBV RT Sequences into the HBV 1.2-mer Replicon Authors:  Sung Hyun Ahn, Yong Kwang Park and Kyun-Hwan Kim, date: 04/20/2015, view: 2444, Q&A: 0
Antiviral agents for the suppression of hepatitis B virus (HBV) have been used for treating chronic hepatitis B. However, the emergence of drug-resistant HBV is still a major problem for antiviral treatment. To identify and characterize the drug-resistant HBV, the construction of HBV replicon and in vitro drug susceptibility assay are ...
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Biotinylation and Purification of Surface-exposed Helicobacter pylori Proteins Authors:  Bradley J. Voss and Timothy L. Cover, date: 04/20/2015, view: 2503, Q&A: 0
Interactions between pathogenic bacteria and host cells are often mediated by proteins found on the surfaces of the bacteria. The Gram-negative bacterium Helicobacter pylori is predicted to produce at least 50 surface-exposed outer membrane proteins, but there has been relatively little progress in experimentally analyzing the ...
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Isolation of Heterocysts from Anabaena sp. PCC 7120 Authors:  Maria Ermakova and Yagut Allahverdiyeva, date: 04/20/2015, view: 3557, Q&A: 0
During combined nitrogen step-down, filaments of cyanobacterium Anabaena sp. PCC 7120 differentiate about 5-10% of vegetative photosynthetic cells into heterocysts, the specialized cells for N2 fixation (Walk, 1996). Heterocysts have a thick cell wall reducing permeation of O2 and consist of two additional layers ...
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Molecular Biology

Random DNA Binding Selection Assay (RDSA) Authors:  Yafei Wang and Meizhong Luo, date: 04/20/2015, view: 2329, Q&A: 0
Protein-DNA interaction is a very important cellular process, by which regulation of DNA biological function, usually gene expression, is exerted. The method of random DNA binding selection assay (RDSA) can be used to identify DNA elements bound by proteins with DNA-binding activities. This method is based on the enrichment of the target DNA ...
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DNA Slot Blot Repair Assay Authors:  Jeong-Min Park and Tae-Hong Kang, date: 04/20/2015, view: 4775, Q&A: 0
Ultraviolet (UV) irradiation induces helix distorting photolesions such as cyclobutane pyrimidine dimers (CPD) and pyrimidine-pyrimidone (6-4) photoproducts (6-4PP) which threaten genomic integrity if unrepaired. In mammals, nucleotide excision repair (NER) is the only pathway that removes UV-induced DNA damages. Here we describe DNA slot blot ...
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Plant Science

In Gel Detection of Lipase Activity in Crude Plant Extracts (Olea europaea) Authors:  Agnieszka Zienkiewicz, Juan David Rejón, Krzysztof Zienkiewicz, Antonio Jesus Castro and Maria Isabel Rodríguez-García, date: 04/20/2015, view: 2267, Q&A: 0
Here, we provide a detailed protocol describing a SDS-PAGE based procedure to assay in gel neutral lipase activity. Total protein extracts are separated by SDS-PAGE and gels are treated with lipase substrate-α-naphthyl palmitate. This long-chain fatty acid ester is hydrolysed by lipases present in the gel. The product resulting from this reaction ...
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Measuring the Arsenic Content and Speciation in Different Rice Tissues Authors:  E. Marie Muehe, Andreas Kappler, Christina Chaban and Birgit Daus, date: 04/20/2015, view: 2598, Q&A: 0
Arsenic (As) plays an important role in rice production as vast soils used for rice cultivation contain As. To understand how rice plants deal with inorganic As (III) and As (V) and organic As in their tissue, it is important to obtain specific information on how much and what species of As are present in which tissue of the rice plant. The ...
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Real-time Analysis of Lateral Root Organogenesis in Arabidopsis Authors:  Peter Marhavý and Eva Benková, date: 04/20/2015, view: 2900, Q&A: 0
Plants maintain capacity to form new organs such as leaves, flowers, lateral shoots and roots throughout their postembryonic lifetime. Lateral roots (LRs) originate from a few pericycle cells that acquire attributes of founder cells (FCs), undergo series of anticlinal divisions, and give rise to a few short initial cells. After initiation, ...
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Measuring Arabidopsis, Tomato and Barley Leaf Relative Water Content (RWC) Authors:  Nir Sade, Eyal Galkin and Menachem Moshelion, date: 04/20/2015, view: 3320, Q&A: 0
Measuring leaf relative water content (RWC) is a reliable and simple way to assess the water status of a leaf without any need for special equipment. Similar to leaf water potential, leaf RWC gives a strong indication of the plant’s response to different environmental conditions; yet RWC has been shown to be a more stable parameter than leaf water ...
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In vitro Reconstitution Assay of miRNA Biogenesis by Arabidopsis DCL1 Authors:  Tian Wang, Claudia Castillo-González, Lan You, Rui Li, Liwei Wen, Hongliang Zhu and Xiuren Zhang, date: 04/20/2015, view: 2543, Q&A: 0
microRNAs (miRNAs) are small non-coding RNAs, regulating most if not all, biological processes in eukaryotic organisms. miRNAs are initially processed from primary transcripts (pri-miRNAs) to produce miRNA precursors (pre-miRNAs), that are further processed into miRNA and its complementary strands (miRNA/*). In Arabidopsis, and possibly other ...
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