Volume: 6 Issue: 13 —BIO-PROTOCOL

Biochemistry

An Improved and Simplified Radial Gel Diffusion Assay for the Detection of Xylanase Activity Authors: Raviraj M. Kalunke, Ilaria Moscetti, Silvio Tundo and Renato D’Ovidio, date: 07/05/2016, view: 5379, Q&A: 0

Xylanase (E.C. 3.2.1.8) degrades β-1, 4 xylan by cleaving β-1, 4 glycosidic linkages randomly, resulting in the generation of xylose and xylo-oligosaccharides. Xylanases are produced by organisms including fungi, bacteria, yeast, marine algae, protozoans, snails, crustaceans and insects. Xylanases present considerable industrial interest for their ...

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Cancer Biology

High Fat Diet-induced Breast Cancer Model in Rat Authors: Meng Ju Wu and Chun Ju Chang, date: 07/05/2016, view: 4917, Q&A: 0

Obesity has been linked to breast cancer progression but the underlying mechanisms remain obscure. Being overweight or obese for a woman at the time she is diagnosed with breast cancer is linked to a high risk of recurrence regardless of treatment factors. In rodents, high body weight is also associated with increased incidence of spontaneous and ...

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Cell Biology

Isolation and Primary Culture of Adult Mouse Cardiac Fibroblasts Authors: Maria Patapia Zafeiriou, Claudia Noack and Laura Cecilia Zelarayan, date: 07/05/2016, view: 10852, Q&A: 1

Fibroblasts are often used as a feeder layer for progenitor or stem cells in co-culture systems. In the heart fibroblasts are important for cardiac development, homeostasis, and remodelling. They provide cardiomyocytes and progenitor cells not only with nutrition but also secrete extracellular matrix that forms the microenvironment that ensures ...

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Subchromoplast Fractionation Protocol for Different Solanaceae Fruit Species Authors: Marilise Nogueira, Harriet Berry, Rebecca Nohl, Martin Klompmaker, Alexandra Holden and Paul D. Fraser, date: 07/05/2016, view: 5266, Q&A: 0

Macromolecules, proteins, lipids, and other small molecules, such as carotenoids can be studied within different tissues and organelles using an array of in vitro and in vivo methodologies. In the case of tomato and other fleshy fruit the predominant organelle in ripe fruit is the chromoplast. The characteristic feature of this ...

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T Cell Transfer Model of Colitis Authors: Wen Pan, Shu Zhu, Dai Dai, Yuanjia Tang, Yihong Yao and Nan Shen, date: 07/05/2016, view: 9635, Q&A: 0

Inflammatory bowel disease (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC) is mainly caused by disordered immune regulation and dysregulated intestinal microbiota. Here we present the T cell transfer model which has extensively used in many studies to identify the regulatory T cell function in gut inflammation. Naïve T cells only ...

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Developmental Biology

Aorta Ring Assay Authors: Jing Jin, Xinyang Hu, Ling Zhang and Jian'an Wang, date: 07/05/2016, view: 8264, Q&A: 1

Angiogenesis is the nature and pathological process of blood vessel growth from pre-existing vascular buds. It plays an important role in cancer and cardiovascular disease. The aorta ring assay is an approach to study angiogenesis. In this experiment, we used the aorta of rat as the study material, cleaned the surrounding tissue of aorta and cut ...

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Immunology

Measurement of mRNA Decay in Mouse Embryonic Fibroblasts Authors: Lian-Qun Qiu, Wi S. Lai, Deborah J. Stumpo and Perry J. Blackshear, date: 07/05/2016, view: 7251, Q&A: 0

mRNA stability control is a critical step in the post-transcriptional regulation of gene expression. Actinomycin D, an antibiotic initially used as an anti-cancer drug, has turned out to be a convenient tool for studying the turnover rates of transcripts in cells, due to its inhibition of mRNA synthesis. Here, we describe a protocol for the ...

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Mouse Embryonic Fibroblast Cell Culture and Stimulation Authors: Lian-Qun Qiu, Wi S. Lai, Deborah J. Stumpo and Perry J. Blackshear, date: 07/05/2016, view: 12217, Q&A: 0

Culture of mouse embryonic fibroblast (MEF) cells represents a powerful system to test gene function due to their easy accessibility, rapid growth rates, and the possibility of a large number of experiments. Fibroblasts are a group of heterogeneous resident cells of mesenchymal origin that have various locations, diverse appearances and ...

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Molecular Biology

Estimation of the Chromosomal Copy Number in Synechococcus elongatus PCC 7942 Authors: Satoru Watanabe and Hirofumi Yoshikawa, date: 07/05/2016, view: 4908, Q&A: 0

Cyanobacteria are prokaryotic organisms that perform oxygenic photosynthesis. Freshwater cyanobacteria, such as Synechococcus elongatus PCC 7942 and Synechocystis sp. PCC 6803, are model organisms for the study of photosynthesis, gene regulation, and biotechnological applications because they are easy to manipulate ...

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Neuroscience

Locomotion Activity Measurement in an Open Field for Mice Authors: Levente Gellért and Dániel Varga, date: 07/05/2016, view: 11261, Q&A: 0

The Open Field (OF) paradigm is one of the most known primary behavioral tests to evaluate locomotion and exploration. Altered OF behaviour is relatively simple to observe, but understanding and explaining the reasons for the observed changes is a complex task. Generally, there are two factors, which determine the behavior in this paradigm; one, a ...

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Denervation of Mouse Lower Hind Limb by Sciatic and Femoral Nerve Transection Authors: Yuval Rinkevich, Daniel T. Montoro, Ethan Muhonen, David Lo, Masakazu Hasegawa, Clement D. Marshall, Graham G. Walmsley, Andrew Connolly, Irving L. Weissman and Michael T. Longaker, date: 07/05/2016, view: 9479, Q&A: 0

The requirement and influence of the peripheral nervous system on tissue replacement in mammalian appendages remain largely undefined. Reports from salamander models of appendage regeneration (Singer, 1952; Singer, 1947; Kumar et al., 2007), and of human clinical skin and nail problems associated with spinal cord injury patients (Stover ...

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Plant Science

Identification of Natural Hybrids by SSR Markers in Mussaenda Authors: Zhonglai Luo, Tingting Duan, Shuai Yuan, Shi Chen, Xiufeng Bai and Dianxiang Zhang, date: 07/05/2016, view: 5361, Q&A: 0

Detection of natural hybrids is of great significance for plant taxonomy, reproductive biology, and population genetic studies. Compared with methods depending on morphological characters, molecular markers provide reliable and much more accurate results. This protocol describes approaches employing microsatellite (SSR) markers to identify ...

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Chromosome Dosage Analysis in Plants Using Whole Genome Sequencing Authors: Ek Han Tan, Luca Comai and Isabelle M. Henry, date: 07/05/2016, view: 6593, Q&A: 0

Relative chromosome dosage, i.e., increases or decreases in the number of copies of specific chromosome regions in one sample versus another, can be determined using aligned read-counts from Illumina sequencing (Henry et al., 2010). The following protocol was used to identify the different classes of aneuploids that ...

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Indirect Immunofluorescence Assay in Chlamydomonas reinhardtii Authors: Takashi Yamano and Hideya Fukuzawa, date: 07/05/2016, view: 7196, Q&A: 0

Determining the protein localization is essential to elucidate its in vivo function. Fluorescence-tagged proteins are widely used for it, but it is sometimes difficult to express tagged proteins in Chlamydomonas. Alternatively, indirect immunofluorescence assay is also one of the widely used methods and many reports determining ...

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Stem Cell

Retinal Differentiation of Mouse Embryonic Stem Cells Author: Anna La Torre, date: 07/05/2016, view: 8422, Q&A: 5

Groundbreaking studies from Dr. Yoshiki Sasai’s laboratory have recently introduced novel methods to differentiate mouse and human Embryonic Stem Cells (mESCs and hESCs) into organ-like 3D structures aimed to recapitulate developmental organogenesis programs (Eiraku et al., 2011; Eiraku and Sasai, 2012; Nakano et al., 2012; ...

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Past Issues in 2016

Volume: 6 Issue: 13

Biochemistry

Cancer Biology

Cell Biology

Developmental Biology

Immunology

Molecular Biology

Neuroscience

Plant Science

Stem Cell