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Volume:4  Issue:21

November 05, 2014

Immunology

Binding Affinity Measurement of Antibodies from Crude Hybridoma Samples by SPR

Authors: Dorin Mlaki Ndao
Dorin Mlaki NdaoAffiliation: AC Immune SA, Lausanne, Switzerland
Bio-protocol author page: a1751
David T. Hickman
David T. HickmanAffiliation: AC Immune SA, Lausanne, Switzerland
Bio-protocol author page: a1752
María Pilar López-Deber
María Pilar López-DeberAffiliation: AC Immune SA, Lausanne, Switzerland
Bio-protocol author page: a1753
Aurélien Davranche
Aurélien DavrancheAffiliation: AC Immune SA, Lausanne, Switzerland
Bio-protocol author page: a1754
Andrea Pfeifer
Andrea PfeiferAffiliation: AC Immune SA, Lausanne, Switzerland
Bio-protocol author page: a1755
 and Andreas Muhs
Andreas MuhsAffiliation: AC Immune SA, Lausanne, Switzerland
For correspondence: andreas.muhs@acimmune.com
Bio-protocol author page: a1756
date: 11/5/2014, 4561 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1276 

[Abstract] Surface Plasmon Resonance (SPR) is widely used to generate kinetic and affinity information on specific interactions between biomolecules. This technique is label-free and monitors the binding event in real-time. It is generally used for characterization ...

Article identifier: bio-protocol.org/e1276

Isolation and In vitro Activation of Mouse Peyer’s Patch Cells from Small Intestine Tissue

Authors: Claudia Pastori
Claudia PastoriAffiliation: Division of Immunology, San Raffaele Scientific Institute, Milan, Italy
Bio-protocol author page: a1763
 and Lucia Lopalco
Lucia LopalcoAffiliation: Division of Immunology, San Raffaele Scientific Institute, Milan, Italy
For correspondence: lopalco.lucia@hsr.it
Bio-protocol author page: a1764
date: 11/5/2014, 4463 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1282 

[Abstract] The lumen of gastrointestinal tract is exposed to several potentially pathogenic microorganisms, thus it is extremely relevant to understand how immunosurveilance can be established. Peyer’s Patches (PPs) are oval or round lymphoid nodules that protrude ...

Article identifier: bio-protocol.org/e1282

Microbiology

Measurement of Proton-driven Antiport in Escherichia coli

Authors: Scarlett R. Holdsworth
Scarlett R. HoldsworthAffiliation: Institute for Global Food Security, Queen’s University Belfast, Belfast, UK
Bio-protocol author page: a1759
 and Christopher J. Law
Christopher J. LawAffiliation: Institute for Global Food Security, Queen’s University Belfast, Belfast, UK
For correspondence: c.law@qub.ac.uk
Bio-protocol author page: a1760
date: 11/5/2014, 2603 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1278 

[Abstract] Secondary active transport of substrates across the inner membrane is vital to the bacterial cell. Of the secondary active transporter families, the ubiquitous major facilitator superfamily (MFS) is the largest and most functionally diverse (Reddy et ...

Article identifier: bio-protocol.org/e1278

Measurement of the Electrogenicity of Bile Salt/H+ Antiport in Escherichia coli

Authors: Scarlett R. Holdsworth
Scarlett R. HoldsworthAffiliation: Institute for Global Food Security, Queen’s University Belfast, Belfast, UK
Bio-protocol author page: a1759
 and Christopher J. Law
Christopher J. LawAffiliation: Institute for Global Food Security, Queen’s University Belfast, Belfast, UK
For correspondence: c.law@qub.ac.uk
Bio-protocol author page: a1760
date: 11/5/2014, 2205 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1279 

[Abstract] The transmembrane proton gradient (ΔpH) is the primary source of energy exploited by secondary active substrate/H+ antiporters to drive the electroneutral transport of substrates across the Escherichia coli (E. coli) inner membrane. Such electroneutral ...

Article identifier: bio-protocol.org/e1279

Purification and Detection of a PDGA Depolymerase from Pusillimonas noertemannii

Authors: David Negus
David NegusAffiliation: University College London School of Pharmacy, London, UK
For correspondence: d.negus@ucl.ac.uk
Bio-protocol author page: a1761
 and Peter W. Taylor
Peter W. TaylorAffiliation: University College London School of Pharmacy, London, UK
Bio-protocol author page: a1762
date: 11/5/2014, 2464 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1280 

[Abstract] The purification of a target protein from a complex mixture of proteins is a challenging undertaking. If the target protein has been previously characterised, then information such as subcellular location, function, molecular weight and pI can be used ...

Article identifier: bio-protocol.org/e1280

Accelerated Storage Stability Testing of a Potential Anti-Anthrax Therapeutic, EnvD

Authors: David Negus
David NegusAffiliation: University College London School of Pharmacy, London, UK
For correspondence: d.negus@ucl.ac.uk
Bio-protocol author page: a1761
 and Peter W. Taylor
Peter W. TaylorAffiliation: University College London School of Pharmacy, London, UK
Bio-protocol author page: a1762
date: 11/5/2014, 2245 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1281 

[Abstract] The purpose of stability testing is to determine how the properties of a particular therapeutic vary with time under the influence of specific environmental factors. Information regarding the long-term stability of therapeutics can be extrapolated by ...

Article identifier: bio-protocol.org/e1281

Stable Transformation of Cyanobacterium Synechocystis sp.

Author: Reinhard K Proels
Reinhard K ProelsAffiliation: Chair of Phytopathology, Technische Universität München, Freising, Germany
For correspondence: proels@wzw.tum.de
Bio-protocol author page: a1779
date: 11/5/2014, 3757 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1286 

[Abstract] Cyanobacteria are prokaryotes, which perform oxygenic photosynthesis. Among them, the unicellular cyanobacterium Synechocystis sp. PCC 6803 (hereafter Synechocystis) is a well characterized model system for studies on oxygenic photosynthesis, light signal ...

Article identifier: bio-protocol.org/e1286

Fractionation by Ultracentrifugation of Gram Negative Cytoplasmic and Membrane Proteins

Authors: Sara M Sandrini
Sara M SandriniAffiliation: Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
For correspondence: sms26@le.ac.uk
Bio-protocol author page: a1780
Richard Haigh
Richard HaighAffiliation: Department of Genetics, University of Leicester, Leicester, UK
Bio-protocol author page: a1781
 and Primrose P. E. Freestone
Primrose P. E. FreestoneAffiliation: Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
Bio-protocol author page: a1782
date: 11/5/2014, 5870 views, 1 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1287 

[Abstract] Protein fractionation is a useful separation process which divides membrane proteins (including those located in the outer and inner membrane) and cytoplasmic proteins into discrete fractions. Fractionation of proteins can simplify analysis of the numbers ...

Article identifier: bio-protocol.org/e1287

Neuroscience

An Experimental Model of Neonatal Nociceptive Stimulation in Rats

Authors: Jackeline Moraes Malheiros
Jackeline Moraes MalheirosAffiliation: Departamento de Fisiologia, Universidade Federal de São Paulo, São Paulo, Brazil
Bio-protocol author page: a1765
Cristiane Amaral
Cristiane AmaralAffiliation: Departamento de Fisiologia, Universidade Federal de São Paulo, São Paulo, Brazil
Bio-protocol author page: a1766
Ana Teresa S Leslie
Ana Teresa S LeslieAffiliation: Departamento de Pediatria, Universidade Federal de São Paulo, São Paulo, Brazil
Bio-protocol author page: a1767
Ruth Guinsburg
Ruth GuinsburgAffiliation: Departamento de Pediatria, Universidade Federal de São Paulo, São Paulo, Brazil
Bio-protocol author page: a1768
 and Luciene Covolan
Luciene CovolanAffiliation: Departamento de Fisiologia, Universidade Federal de São Paulo, São Paulo, Brazil
For correspondence: lcovolan@unifesp.br
Bio-protocol author page: a1769
date: 11/5/2014, 3423 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1283 

[Abstract] In order to survive, preterm and/or sick neonates need diagnostic and therapeutic measures that may cause discomfort, stress and pain during a critical period of intense growing and modeling of the central nervous system (Anand et al., 2013). Scientific ...

Article identifier: bio-protocol.org/e1283

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Pain Assessment Using the Rat and Mouse Formalin Tests

Authors: Nian Gong
Nian GongAffiliation: King’s Lab, Shanghai Jiao Tong University School of Pharmacy, Shanghai, China
Bio-protocol author page: a1783
Qian Huang
Qian HuangAffiliation: King’s Lab, Shanghai Jiao Tong University School of Pharmacy, Shanghai, China
Bio-protocol author page: a1784
Yuan Chen
Yuan ChenAffiliation: King’s Lab, Shanghai Jiao Tong University School of Pharmacy, Shanghai, China
Bio-protocol author page: a1785
Meng Xu
Meng XuAffiliation: King’s Lab, Shanghai Jiao Tong University School of Pharmacy, Shanghai, China
Bio-protocol author page: a1786
Shuai Ma
Shuai MaAffiliation: King’s Lab, Shanghai Jiao Tong University School of Pharmacy, Shanghai, China
Bio-protocol author page: a1787
 and Yong-Xiang Wang
Yong-Xiang WangAffiliation: King’s Lab, Shanghai Jiao Tong University School of Pharmacy, Shanghai, China
For correspondence: yxwang@sjtu.edu.cn
Bio-protocol author page: a1788
date: 11/5/2014, 7421 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1288 

[Abstract] The formalin test was originally developed by Dubuisson and Dennis (1977), and has since been extensively used to assess pain-related responses. Rats and mice are the most frequently used animal models, though other species including cats, rabbits, guinea ...

Article identifier: bio-protocol.org/e1288

Plant Science

Preparation of Multiplexed Small RNA Libraries From Plants

Authors: Kerrigan B. Gilbert
Kerrigan B. GilbertAffiliation: Donald Danforth Plant Science Center, Saint Louis, USA
Bio-protocol author page: a1745
Noah Fahlgren
Noah FahlgrenAffiliation: Donald Danforth Plant Science Center, Saint Louis, USA
Bio-protocol author page: a1746
Kristin D. Kasschau
Kristin D. KasschauAffiliation: Donald Danforth Plant Science Center, Saint Louis, USA
Bio-protocol author page: a1747
Elisabeth J. Chapman
Elisabeth J. ChapmanAffiliation: Donald Danforth Plant Science Center, Saint Louis, USA
Bio-protocol author page: a1748
James C. Carrington
James C. CarringtonAffiliation: Donald Danforth Plant Science Center, Saint Louis, USA
Bio-protocol author page: a1749
 and Alberto Carbonell
Alberto CarbonellAffiliation: Donald Danforth Plant Science Center, Saint Louis, USA
For correspondence: acarbonell@ibmcp.upv.es
Bio-protocol author page: a1750
date: 11/5/2014, 4851 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1275 

[Abstract] High-throughput sequencing is a powerful tool for exploring small RNA populations in plants. The ever-increasing output from an Illumina Sequencing System allows for multiplexing multiple samples while still obtaining sufficient data for small RNA discovery ...

Article identifier: bio-protocol.org/e1275

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Extraction of Total Proteins from Rice Plant

Authors: Da-Gin Lin
Da-Gin LinAffiliation: Department of Agronomy, National Chung-Hsing University, Taichung, Taiwan
Bio-protocol author page: a1757
 and Chang-Sheng Wang
Chang-Sheng WangAffiliation: Department of Agronomy, National Chung-Hsing University, Taichung, Taiwan
For correspondence: wangchansen@nchu.edu.tw
Bio-protocol author page: a1758
date: 11/5/2014, 9241 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1277 

[Abstract] This protocol provides an efficient method for preparation of high-quality proteins from rice leaves and grains. The method involves phenol extraction to separate proteins from the non-protein components such as polysaccharides, lipids and phenolic compounds ...

Article identifier: bio-protocol.org/e1277

Measurement of the Number of Peroxisomes

Authors: Michitaro Shibata
Michitaro ShibataAffiliation: Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
Bio-protocol author page: a1770
Kazusato Oikawa
Kazusato OikawaAffiliation: Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
Bio-protocol author page: a1771
Shoji Mano
Shoji ManoAffiliation: Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
Bio-protocol author page: a1772
 and Mikio Nishimura
Mikio NishimuraAffiliation: Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
For correspondence: mikion@nibb.ac.jp
Bio-protocol author page: a1773
date: 11/5/2014, 2834 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1284 

[Abstract] This is the detailed protocol for the measurement of the number of peroxisomes described by Shibata et al. (2013). It is difficult to count the number of organelles in a cell because of the thickness of plant leaves. To overcome this challenge, protoplasts ...

Article identifier: bio-protocol.org/e1284

In vitro Assay of the Glycosyltransferase Activity of a Heterologously Expressed Plant Protein

Authors: Carsten P Ade
Carsten P AdeAffiliation 1: Scion, Rotorua, New Zealand
Affiliation 2: School of Biological Sciences, The University of Auckland, Auckland, New Zealand
Present address: Department of Biochemistry and Molecular Biology, University of Wuerzburg, Wuerzburg, Germany
Bio-protocol author page: a1774
Felix Bemm
Felix BemmAffiliation: Department of Bioinformatics, University of Wuerzburg, Wuerzburg, Germany
Bio-protocol author page: a1775
James M J Dickson
James M J DicksonAffiliation: School of Biological Sciences, The University of Auckland, Auckland, New Zealand
Bio-protocol author page: a1776
Christian Walter
Christian WalterAffiliation: Scion, Rotorua, New Zealand
Bio-protocol author page: a1777
 and Philip J Harris
Philip J HarrisAffiliation: School of Biological Sciences, The University of Auckland, Auckland, New Zealand
For correspondence: p.harris@auckland.ac.nz
Bio-protocol author page: a1778
date: 11/5/2014, 3096 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1285 

[Abstract] Glycosyltransferases are carbohydrate active enzymes containing catalytic modules involved in catalysing the biosynthesis of glycosidic bonds in oligo- and polysaccharides and glycoconjugates. One of the most comprehensive collections of Carbohydrate ...

Article identifier: bio-protocol.org/e1285