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About Us
For Authors
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Preparation Guidelines
Submit Manuscript
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Editorial Criteria
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Volume 11, 2021
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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
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Biochemistry
Membrane Lipid Screen to Identify Molecular Targets of Biomolecules
Authors:
John R. Jimah
,
Paul H. Schlesinger
and
Niraj H. Tolia
,
date:
08/05/2017,
view:
6358,
Q&A:
0
Proteins that bind to and disrupt cell membranes may target specific phospholipids. Here we describe a protocol to identify the lipid targets of proteins and biomolecules. First, we describe a screen to identify lipids in membranes that are specifically bound by the biomolecule of interest. Second, we describe a method for determining if the ...
More >>
Purification of FLAG-tagged Secreted Proteins from Mammalian Cells
Authors:
Eisuke Itakura
,
Changchun Chen
and
Mario de Bono
,
date:
08/05/2017,
view:
7677,
Q&A:
0
This protocol describes a method for purifying glycosylated FLAG-tagged secreted proteins with disulfide bonds from mammalian cells. The purified products can be used for various applications, such as ligand binding assays.
More >>
Separation and Purification of Glycosaminoglycans (GAGs) from
Caenorhabditis elegans
Authors:
Tabea Dierker
and
Lena Kjellén
,
date:
08/05/2017,
view:
8633,
Q&A:
1
The nematode
Caenorhabditis elegans
is a popular model organism for studies of developmental biology, neurology, ageing and other fields of basic research. Because many developmental processes are regulated by glycosaminoglyans (GAGs) on cell surfaces and in the extracellular matrix, methods to isolate and analyze
C. elegans
GAGs ...
More >>
Isolation of Keratan Sulfate Disaccharide-branched Chondroitin Sulfate E from
Mactra chinensis
Authors:
Kyohei Higashi
and
Toshihiko Toida
,
date:
08/05/2017,
view:
5151,
Q&A:
0
Glycosaminoglycans (GAGs) including chondroitin sulfate (CS), dermatan sulfate (DS), heparin (HP), heparan sulfate (HS) and keratan sulfate (KS) are linear, sulfated repeating disaccharide sequences containing hexosamine and uronic acid (or galactose in the case of KS). Recently, a keratan sulfate (KS) disaccharide [GlcNAc
6S
...
More >>
Cancer Biology
RNA Interference Screening to Identify Proliferation Determinants in Breast Cancer Cells
Authors:
Yong-Wei Zhang
,
Rochelle E. Nasto
,
Sandra A. Jablonski
,
Ilya G Serebriiskii
,
Rishi Surana
,
Joseph Murray
,
Michael Johnson
,
Rebecca B. Riggins
,
Robert Clarke
,
Erica A. Golemis
and
Louis M. Weiner
,
date:
08/05/2017,
view:
6108,
Q&A:
0
RNAi screening technology has revealed unknown determinants of various biological signaling pathways in biomedical studies. This protocol provided detailed information about how to use RNAi screening to identify proliferation determinants in breast tumor cells. siRNA-based libraries targeting against Estrogen receptor (ER)-network, including 631 ...
More >>
Microbiology
Analysis of
N
-acetylmuramic acid-6-phosphate (MurNAc-6P) Accumulation by HPLC-MS
Authors:
Marina Borisova
and
Christoph Mayer
,
date:
08/05/2017,
view:
6114,
Q&A:
0
We describe here in detail a high-performance liquid chromatography-mass spectrometry (HPLC-MS)-based method to determine
N
-acetylmuramic acid-6-phosphate (MurNAc-6P) in bacterial cell extracts. The method can be applied to both Gram-negative and Gram-positive bacteria, and as an example we use
Escherichia coli
cells in this ...
More >>
Advanced Design of Minimalistic Dumbbell-shaped Gene Expression Vectors
Authors:
Xiaoou Jiang
and
Volker Patzel
,
date:
08/05/2017,
view:
6755,
Q&A:
0
Minimal DNA vectors exclusively comprising therapeutically relevant sequences hold great promise for the development of novel therapeutic regimen. Dumbbell-shaped vectors represent non-viral non-integrating DNA minimal vectors which have entered an advanced stage of clinical development (Hardee
et al.
, 2017). Spliceable introns and DNA ...
More >>
Measurement of Energy-dependent Rhodamine 6G Efflux in Yeast Species
Authors:
Yvetta Gbelska
,
Nora Toth Hervay
,
Vladimira Dzugasova
and
Alexandra Konecna
,
date:
08/05/2017,
view:
6253,
Q&A:
0
Rhodamine 6G is a highly fluorescent dye often used to determine the transport activity of yeast membrane efflux pumps. The ATP-binding cassette transporter
Kl
Pdr5p confers resistance to several unrelated drugs in
Kluyveromyces lactis
.
Kl
Pdr5p also extrudes rhodamine 6G (R6G) from intact yeast cells in an ...
More >>
Selection of Genetically Modified Bacteriophages Using the CRISPR-Cas System
Authors:
Miriam Manor
and
Udi Qimron
,
date:
08/05/2017,
view:
7879,
Q&A:
0
We present a CRISPR-Cas based technique for deleting genes from the T7 bacteriophage genome. A DNA fragment encoding homologous arms to the target gene to be deleted is first cloned into a plasmid. The T7 phage is then propagated in
Escherichia coli
harboring this plasmid. During this propagation, some phage genomes undergo homologous ...
More >>
Liposome Disruption Assay to Examine Lytic Properties of Biomolecules
Authors:
John R. Jimah
,
Paul H. Schlesinger
and
Niraj H. Tolia
,
date:
08/05/2017,
view:
9448,
Q&A:
0
Proteins may have three dimensional structural or amino acid features that suggest a role in targeting and disrupting lipids within cell membranes. It is often necessary to experimentally investigate if these proteins and biomolecules are able to disrupt membranes in order to conclusively characterize the function of these biomolecules. Here, we ...
More >>
Observation of Pneumococcal Phase Variation in Colony Morphology
Authors:
Jing Li
,
Juanjuan Wang
,
Fangfang Jiao
and
Jing-Ren Zhang
,
date:
08/05/2017,
view:
6997,
Q&A:
0
Streptococcus pneumoniae
(pneumococcus) is an important human pathogen that causes pneumonia, meningitis, sepsis, and otitis media. This bacterium normally resides in the nasopharynx as a commensal, but sometimes disseminates to sterile sites of humans and causes local or systemic inflammation. This biphasic behavior of
S. pneumoniae
...
More >>
Digestion of Peptidoglycan and Analysis of Soluble Fragments
Authors:
Ryan E. Schaub
and
Joseph P. Dillard
,
date:
08/05/2017,
view:
9239,
Q&A:
0
Peptidoglycan (murein) is a vital component of the cell wall of nearly all bacteria, composed of sugars linked by short peptides. This protocol describes the purification of macromolecular peptidoglycan from cultured bacteria and the analysis of enzyme-digested peptidoglycan fragments using high performance liquid chromatography (HPLC). Digested ...
More >>
A Protocol of Using White/Red Color Assay to Measure Amyloid-induced Oxidative Stress in
Saccharomyces cerevisiae
Authors:
Vidhya Bharathi
,
Amandeep Girdhar
and
Basant K Patel
,
date:
08/05/2017,
view:
8352,
Q&A:
0
The yeast
Saccharomyces cerevisiae
(
S. cerevisiae
) harboring
ade1
or
ade2
mutations manifest red colony color phenotype on rich yeast medium YPD. In these mutants, intermediate metabolites of adenine biosynthesis pathway are accumulated. Accumulated intermediates, in the presence of reduced glutathione, are ...
More >>
CRISPR/Cas9 Gene Editing in the Marine Diatom
Phaeodactylum tricornutum
Authors:
Marianne Nymark
,
Amit Kumar Sharma
,
Marthe C. G. Hafskjold
,
Torfinn Sparstad
,
Atle M. Bones
and
Per Winge
,
date:
08/05/2017,
view:
9128,
Q&A:
0
The establishment of the CRISPR/Cas9 technology in diatoms (Hopes
et al.
, 2016; Nymark
et al.
, 2016) enables a simple, inexpensive and effective way of introducing targeted alterations in the genomic DNA of this highly important group of eukaryotic phytoplankton. Diatoms are of interest as model microorganisms in a variety of ...
More >>
Molecular Biology
Improving CRISPR Gene Editing Efficiency by Proximal dCas9 Targeting
Authors:
Fuqiang Chen
,
Xiao Ding
,
Yongmei Feng
,
Timothy Seebeck
,
Yanfang Jiang
and
Gregory D Davis
,
date:
08/05/2017,
view:
6760,
Q&A:
0
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) systems function as an adaptive immune system in bacteria and archaea for defense against invading viruses and plasmids (Barrangou and Marraffini, 2014). The effector nucleases from some class 2 CRISPR-Cas systems have been repurposed for heterologous ...
More >>
Neuroscience
Extraction of Soluble and Insoluble Protein Fractions from Mouse Brains and Spinal Cords
Author:
Oliver Wirths
,
date:
08/05/2017,
view:
20298,
Q&A:
1
The current protocol details the preparation of soluble and insoluble protein lysates from mouse brain or spinal cord samples. In detail, tissue homogenization and sequential protein extraction are described. This procedure yields soluble and insoluble protein extracts that can be further processed in down-stream applications like ELISA or Western ...
More >>
Preparation of Crude Synaptosomal Fractions from Mouse Brains and Spinal Cords
Author:
Oliver Wirths
,
date:
08/05/2017,
view:
10218,
Q&A:
0
The current protocol describes the preparation of crude synaptosomal fractions from mouse brain or spinal cord samples. In detail, a sequential protocol yielding crude synaptosomal and light membrane fractions is provided. This fast and easy method might be sufficient to assess the amount of synaptic proteins in down-steam applications like ...
More >>
Plant Science
Polyamine and Paraquat Transport Assays in
Arabidopsis
Seedling and Callus
Authors:
Haoxi Chai
,
Yun Shen
and
Huazhong Shi
,
date:
08/05/2017,
view:
5040,
Q&A:
0
Polyamines (PAs) are polycationic compounds found in all living organisms and play crucial roles in growth and survival. We here show the ‘Polyamine and paraquat (PQ) transport assay’ protocol, which can be used to examine the uptake activity of PA/PQ transporters. We have used this protocol to demonstrate that PUT3 in
Arabidopsis
is a ...
More >>
Overrepresentation Analyses of Differentially Expressed Genes in the Smut Fungus
Ustilago bromivora
during Saprophytic and
in planta
Growth
Authors:
Angelika Czedik-Eysenberg
,
Franziska Rabe
,
Heinz Ekker
,
Carmen Czepe
and
Armin Djamei
,
date:
08/05/2017,
view:
6320,
Q&A:
0
We have established the
Ustilago bromivora
–
Brachypodium
spp. interaction as a new model pathosystem for biotrophic fungal plant infections of the head smut type (Rabe
et al.
, 2016). In this protocol, the methodology used for comparing gene expression between saprophytic and
in planta
growth of the fungus is ...
More >>
Isolation of Cytosol, Microsome, Free Polysomes (FPs) and Membrane-bound Polysomes (MBPs) from
Arabidopsis
Seedlings
Authors:
Yonghui Zhao
and
Shengben Li
,
date:
08/05/2017,
view:
7972,
Q&A:
0
The plant endomembrane system plays vital roles for synthesis, modification and secretion of proteins and lipids. From the classic view, only mRNAs encoding secreted proteins could be targeted to the endoplasmic reticulum (ER) for translation via a co-translational translocation manner, however, recently this model has been challenged by ...
More >>
Wheat Coleoptile Inoculation by
Fusarium graminearum
for Large-scale Phenotypic Analysis
Authors:
Lei-Jie Jia
,
Wan-Qiu Wang
and
Wei-Hua Tang
,
date:
08/05/2017,
view:
7561,
Q&A:
0
The ascomycete fungus
Fusarium graminearum
is a destructive fungal pathogen of wheat, barley and maize. Although reverse genetics and homologous recombination gene deletion methods have generated thousands of gene deletion mutants of
F. graminearum
, evaluating virulence of these fungal mutants is still a rate-limiting step. Here ...
More >>
Isolation of Guard-cell Enriched Tissue for RNA Extraction
Authors:
Pirko Jalakas
,
Dmitry Yarmolinsky
,
Hannes Kollist
and
Mikael Brosche
,
date:
08/05/2017,
view:
12134,
Q&A:
0
This is a protocol for isolation of guard cell enriched samples from
Arabidopsis thaliana
plants for RNA extraction. Leaves are blended in ice-water and filtered through nylon mesh to obtain guard cell enriched fragments. With guard cell enriched samples, gene expression analysis can be done,
e.g.
, comparing different gene ...
More >>
Stem Cell
Differentiation of Human Induced Pluripotent Stem Cells (iPS Cells) and Embryonic Stem Cells (ES Cells) into Dendritic Cell (DC) Subsets
Authors:
Stephanie Sontag
,
Malrun Förster
,
Kristin Seré
and
Martin Zenke
,
date:
08/05/2017,
view:
10944,
Q&A:
0
Induced pluripotent stem cells (iPS cells) are engineered stem cells, which exhibit properties very similar to embryonic stem cells (ES cells; Takahashi and Yamanaka, 2016). Both iPS cells and ES cells have an extraordinary self-renewal capacity and can differentiate into all cell types of our body, including hematopoietic stem/progenitor cells ...
More >>
Primary Culture System for Germ Cells from
Caenorhabditis elegans
Tumorous Germline Mutants
Authors:
Alexandra S. Vagasi
,
Mohammad M. Rahman
,
Snehal N. Chaudhari
and
Edward T. Kipreos
,
date:
08/05/2017,
view:
6558,
Q&A:
0
The
Caenorhabditis elegans
germ line is an important model system for the study of germ stem cells. Wild-type
C. elegans
germ cells are syncytial and therefore cannot be isolated in
in vitro
cultures. In contrast, the germ cells from tumorous mutants can be fully cellularized and isolated intact from the mutant animals. ...
More >>
Mouse Müller Cell Isolation and Culture
Authors:
Xiao Liu
,
Luosheng Tang
and
Yongqing Liu
,
date:
08/05/2017,
view:
7862,
Q&A:
0
Müller cells are the major supportive and protective glial cells across the retina. Unlike in fish, they have lost the capacity to regenerate the retina in mammals. But, mammalian Müller cells still retain certain retinal stem cell properties with various degree of self-renewal and differentiation potentials, and thereby held a merit in cell-based ...
More >>
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