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A peer-reviewed protocol journal. No publication fee; no access fee.
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Volume 9, 2019
Volume 8, 2018
Volume 7, 2017
Volume 6, 2016
Volume 5, 2015
Volume 4, 2014
Volume 3, 2013
Volume 2, 2012
Volume 1, 2011
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Biochemistry
Identification of Factors in Regulating a Protein Ubiquitination by Immunoprecipitation: a Case Study of TRF2 on Human REST4 Ubiquitination
Authors:
Wei Cui
and
Patrick Ovando-Roche
,
date:
07/05/2015,
view:
6924,
Q&A:
0
Ubiquitination is the first step of the ubiquitin-proteasome pathway that regulates cells for their homeostatic functions and is an enzymatic, protein post-translational modification process in which ubiquitin is transferred to a target protein substrate by a set of three ubiquitin enzymes (Weissman
et al.
, 2011; Bhattacharyya
et al.
...
More >>
Immunology
Animal Models of Corneal Injury
Authors:
Matilda F. Chan
and
Zena Werb
,
date:
07/05/2015,
view:
5839,
Q&A:
0
The cornea is an excellent model system to use for the analysis of wound repair because of its accessibility, lack of vascularization, and simple anatomy. Corneal injuries may involve only the superficial epithelial layer or may penetrate deeper to involve both the epithelial and stromal layers. Here we describe two well-established
in vivo
...
More >>
Confocal Imaging of Myeloid Cells in the Corneal Stroma of Live Mice
Authors:
Matilda F. Chan
and
Zena Werb
,
date:
07/05/2015,
view:
7176,
Q&A:
0
The accessibility and transparency of the cornea makes it a good tissue model for monitoring immunological responses using
in vivo
real time imaging analysis (Lee
et al.
, 2010; Tan
et al.
, 2013). These corneal qualities have also allowed for high-resolution
in vivo
imaging of non-ocular tissue transplanted into ...
More >>
Microbiology
Axenic Cultivation of Mycelium of the Lichenized Fungus,
Lobaria pulmonaria
(Peltigerales, Ascomycota)
Authors:
Carolina Cornejo
,
Christoph Scheidegger
and
Rosmarie Honegger
,
date:
07/05/2015,
view:
5675,
Q&A:
0
Lichens are symbiotic organisms consisting of a fungal partner (the mycobiont) and one or more algal or cyanobacterial partners (the photobiont); moreover lichen thalli comprise a plethora of epi- and endobiotic bacteria and non-lichenized fungi. Genetic markers are the most promising tools for the study of fungal diversity. However, applying ...
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Mouse Models of Uncomplicated and Fatal Malaria
Authors:
Brian W. Huang
,
Emily Pearman
and
Charles C. Kim
,
date:
07/05/2015,
view:
9317,
Q&A:
0
Mouse models have demonstrated utility in delineating the mechanisms underlying many aspects of malaria immunology and physiology. The most common mouse models of malaria employ the rodent-specific parasite species
Plasmodium berghei
,
P. yoelii
, and
P. chabaudi
, which elicit distinct pathologies and immune responses and ...
More >>
Complex
in vivo
Ligation Using Homologous Recombination and High-efficiency Plasmid Rescue from
Saccharomyces cerevisiae
Authors:
Gregory C. Finnigan
and
Jeremy Thorner
,
date:
07/05/2015,
view:
6590,
Q&A:
0
The protocols presented here allow for the facile generation of a wide variety of complex multipart DNA constructs (tagged gene products, gene fusions, chimeric proteins, and other variants) using homologous recombination and
in vivo
ligation in budding yeast (
Saccharomyces cerevisiae
). This method is straightforward, efficient ...
More >>
Assays to Assess Virulence of
Xanthomonas axonopodis
pv.
manihotis
on Cassava
Authors:
Megan Cohn
,
Mikel Shybut
,
Douglas Dahlbeck
and
Brian Staskawicz
,
date:
07/05/2015,
view:
5513,
Q&A:
0
Cassava (
Manihot esculenta
) is a root crop that provides calories for people living in more than 100 tropical and subtropical countries and serves as a raw material for processing into starch and biofuels as well as feed for livestock (Howeler
et al.
, 2013).
Xanthomonas axonopodis
pv.
manihotis (Xam)
, the causal ...
More >>
Neuroscience
Assessment of Olfactory Behavior in Mice: Odorant Detection and Habituation-Dishabituation Tests
Authors:
Ana Perez-Villalba
,
Mª José Palop
,
Francisco Pérez-Sánchez
and
Isabel Fariñas
,
date:
07/05/2015,
view:
6973,
Q&A:
0
Olfaction has adaptive value for rodents as it is essential for feeding and mating, the establishment of social and territorial relationships, or the detection of potential predators, among others (Apfelbach
et al.
, 2005). Sensory input from the olfactory mucosa is first processed in the main olfactory bulb (MOB), a telencephalic ...
More >>
A Mouse Model of Preterm Brain Injury after Hypoxia-Ischemia
Authors:
Anna-Maj Albertsson
and
Xiaoyang Wang
,
date:
07/05/2015,
view:
7154,
Q&A:
0
The rodent hypoxia-ischemia (HI) model, referred to as the Vannucci model, is the most commonly used model for studying perinatal hypoxic-ischemic brain injury (Zhu
et al.
, 2009; Vannucci and Hagberg, 2004). In the Vannucci model, brain injury is acquired by combining a permanent unilateral common carotid artery ligation with subsequent ...
More >>
Plant Science
Trichoderma harzianum
Root Colonization in
Arabidopsis
Authors:
Ana Alonso-Ramírez
,
Jorge Poveda
,
Ignacio Martín
,
Rosa Hermosa
,
Enrique Monte
and
Carlos Nicolás
,
date:
07/05/2015,
view:
5776,
Q&A:
0
Trichoderma
is a soil-borne fungal genus that includes species with a significant impact on agriculture and industrial processes. In this article we show a detailed protocol of
Trichoderma harzianum
(
T. harzianum
) root invasion procedure described by Alonso-Ramírez
et al.
(2014). Some
Trichoderma
...
More >>
Detection of Alternative Oxidase Expression in
Arabidopsis thaliana
Protoplasts Treated with Aluminium
Authors:
Jian Liu
,
Zhe Li
and
Da Xing
,
date:
07/05/2015,
view:
5186,
Q&A:
0
Aluminium (Al), a non-essential metal widespread in the environment that is known to be toxic to humans as well as to plants, can cause damage not only to the roots but also to the aerial parts of plants. Its toxicity has been recognized as one of the major factors that limit crop production on acid soil. Alternative oxidase, the respiratory ...
More >>
A Chemical Genetic Screening Procedure for
Arabidopsis thaliana
Seedlings
Authors:
Marta Bjornson
,
Xingshun Song
,
Abhaya Dandekar
,
Annaliese Franz
,
Georgia Drakakaki
and
Katayoon Dehesh
,
date:
07/05/2015,
view:
7303,
Q&A:
0
Unbiased screening approaches are powerful tools enabling identification of novel players in biological processes. Chemical genetic screening refers to the technique of using a reporter response, such as expression of luciferase driven by a promoter of interest, to discover small molecules that affect a given process when applied to plants. These ...
More >>
Protein Immunoprecipitation Using
Nicotiana benthamiana
Transient Expression System
Authors:
Fang Xu
,
Charles Copeland
and
Xin Li
,
date:
07/05/2015,
view:
12220,
Q&A:
0
Nicotiana benthamiana
(
N. benthamiana
) is a useful model system to transiently express protein at high level. This protocol describes in detail how to transiently express protein in
N. benthamiana
and how to carry out protein immunoprecipitation in this expression system. This protocol can be broadly used for ...
More >>
Quantification of Uric Acid or Xanthine in Plant Samples
Authors:
Oliver K. Hauck
and
Claus-Peter Witte
,
date:
07/05/2015,
view:
4551,
Q&A:
0
We developed this protocol to assay and quantify the content of uric acid or xanthine in various tissues of
Arabidopsis thaliana
mutant lines with defective urate oxidase or xanthine dehydrogenase1 and in their complementation and suppressor lines (Hauck
et al.
, 2014).
The protocol is based on a method developed by ...
More >>
Bean Pod Mottle Virus
(BPMV) Viral Inoculation Procedure in Common Bean (
Phaseolus vulgaris
L.)
Authors:
Stéphanie Pflieger
,
Sophie Blanchet
,
Chouaib Meziadi
,
Manon M.S. Richard
and
Valérie Geffroy
,
date:
07/05/2015,
view:
9332,
Q&A:
4
Viral vectors derived from the
Bean pod mottle virus
(BPMV) were shown to be highly efficient tools for functional studies in soybean (
Glycine max
) and common bean (
Phaseolus vulgaris
) (Zhang
et al.
, 2010; Diaz-Camino
et al.
, 2011; Pflieger
et al.
, 2013; Pflieger
et al.
, 2014). Indeed, ...
More >>
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