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About Us
For Authors
Submission Procedure
Preparation Guidelines
Submit Manuscript
Editorial Process
Editorial Criteria
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A peer-reviewed protocol journal. No publication fee; no access fee.
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Volume 11, 2021
Volume 10, 2020
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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Biophysics
Optogenetic Tuning of Protein-protein Binding in Bilayers Using LOVTRAP
Authors:
Doug Tischer
and
Orion D. Weiner
,
date:
09/05/2020,
view:
2040,
Q&A:
0
Modern microscopy methods are powerful tools for studying live cell signaling and biochemical reactions, enabling us to observe when and where these reactions take place from the level of a cell down to single molecules. With microscopy, each cell or molecule can be observed both before and after a given perturbation, facilitating better inference ...
More >>
Cell Biology
An
in vitro
DNA Sensor-based Assay to Measure Receptor-specific Adhesion Forces of Eukaryotic Cells and Pathogens
Authors:
Maurizio Wack
,
Tina Wiegand
,
Friedrich Frischknecht
and
E. Ada Cavalcanti-Adam
,
date:
09/05/2020,
view:
1311,
Q&A:
0
Motility of eukaryotic cells or pathogens within tissues is mediated by the turnover of specific interactions with other cells or with the extracellular matrix. Biophysical characterization of these ligand-receptor adhesions helps to unravel the molecular mechanisms driving migration. Traction force microscopy or optical tweezers are typically ...
More >>
Quantitative Kinetic Analyses of Histone Turnover Using Imaging and Flow Cytometry
Authors:
Hanae Sato
,
Robert H. Singer
and
John M. Greally
,
date:
09/05/2020,
view:
1255,
Q&A:
0
Dynamic histone changes occur as a central part of chromatin regulation. Deposition of histone variants and post-translational modifications of histones are strongly associated with properties of chromatin status. Characterizing the kinetics of histone variants allows important insights into transcription regulation, chromatin maintenance and ...
More >>
Developmental Biology
Fluorescent Polysome Profiling in
Caenorhabditis elegans
Authors:
Dan Shaffer
and
Jarod A Rollins
,
date:
09/05/2020,
view:
1456,
Q&A:
0
An important but often overlooked aspect of gene regulation occurs at the level of protein translation. Many genes are regulated not only by transcription but by their propensity to be recruited to actively translating ribosomes (polysomes). Polysome profiling allows for the separation of unbound 40S and 60S subunits, 80S monosomes, and actively ...
More >>
Immunology
Flow-cytometric Detection of Low-level Reactive Oxygen Species in Cell Lines and Primary Immune Cells
Authors:
Kevin Bode
,
Corinna Link
,
Peter H. Krammer
and
Heiko Weyd
,
date:
09/05/2020,
view:
2259,
Q&A:
0
Depending on its concentration and cellular origin the production of reactive oxygen species (ROS) in the organism serves a variety of functions. While high concentrations during an oxidative burst are used to fight pathogens, low to moderate amounts of ROS act as signaling molecules important for several physiological processes such as regulation ...
More >>
Multiplication and Growth Inhibition Activity Assays for the Zoonotic Malaria Parasite,
Plasmodium knowlesi
Authors:
Franziska Mohring
,
Thomas A. Rawlinson
,
Simon J. Draper
and
Robert W. Moon
,
date:
09/05/2020,
view:
1912,
Q&A:
0
Malaria remains a major cause of morbidity and mortality globally. Clinical symptoms of the disease arise from the growth and multiplication of
Plasmodium
parasites within the blood of the host. Thus
in vitro
assays to determine how drug, antibody and genetic perturbations affect the growth rate of
Plasmodium
parasites ...
More >>
Microbiology
Live-cell Imaging by Super-resolution Confocal Live Imaging Microscopy (SCLIM): Simultaneous Three-color and Four-dimensional Live Cell Imaging with High Space and Time Resolution
Authors:
Kazuo Kurokawa
and
Akihiko Nakano
,
date:
09/05/2020,
view:
2112,
Q&A:
0
Many questions in cell biology can be solved by state-of-the-art technology of live cell imaging. One good example is the mechanism of membrane traffic, in which small membrane carriers are rapidly moving around in the cytoplasm to deliver cargo proteins between organelles. For directly visualizing the events in membrane trafficking system, ...
More >>
A High-throughput Interbacterial Competition Platform
Authors:
Hsiao-Han Lin
and
Erh-Min Lai
,
date:
09/05/2020,
view:
1334,
Q&A:
0
Contact-dependent interbacterial competition is a common strategy used by bacteria to fight for their ecological niches. Interbacterial competition is monitored by a competition assay involving co-culturing the attacker and the recipient bacterial cells on agar, followed by recovery of the surviving recipient cells. Conventional interbacterial ...
More >>
Screening Method for CRISPR/Cas9 Inhibition of a Human DNA Virus: Herpes Simplex Virus
Authors:
Werner M. Neuhausser
,
Hyung S. Oh
,
Pierce Eggan
,
Magdalena Angelova
,
Rory Kirchner
,
Kevin C. Eggan
and
David M. Knipe
,
date:
09/05/2020,
view:
2160,
Q&A:
0
The efficiency of cleavage of individual CRISPR/Cas9-sgRNAs remains difficult to predict based on the CRISPR target sequence alone. Different intracellular environments (dependent on cell type or cell cycle state for example) may affect sgRNA efficiency by altering accessibility of genomic DNA through DNA modifications such as epigenetic marks and ...
More >>
Molecular Biology
BRIDGE: An Open Platform for Reproducible Protein-Ligand Simulations and Free Energy of Binding Calculations
Authors:
Tharindu Senapathi
,
Christopher B. Barnett
and
Kevin J. Naidoo
,
date:
09/05/2020,
view:
2794,
Q&A:
2
Protein-ligand binding prediction is central to the drug-discovery process. This often follows an analysis of genomics data for protein targets and then protein structure discovery. However, the complexity of performing reproducible protein conformational analysis and ligand binding calculations, using vetted methods and protocols can be a ...
More >>
Nonenzymatic RNA-templated Synthesis of N3′→P5′ Phosphoramidate DNA
Authors:
Derek K. O'Flaherty
,
Lijun Zhou
and
Jack W. Szostak
,
date:
09/05/2020,
view:
1601,
Q&A:
0
The RNA world hypothesis describes a scenario where early life forms relied on RNA to govern both inheritance and catalyze useful chemical reactions. Prior to the emergence of enzymes capable of replicating the RNA genome, a nonenzymatic replication process would have been necessary to initiate Darwinian Evolution. However, the one-pot ...
More >>
Neuroscience
The Peak Interval Procedure in Rodents: A Tool for Studying the Neurobiological Basis of Interval Timing and Its Alterations in Models of Human Disease
Authors:
Fuat Balcı
and
David Freestone
,
date:
09/05/2020,
view:
903,
Q&A:
0
Animals keep track of time intervals in the seconds to minutes range with, on average, high accuracy but substantial trial-to-trial variability. The ability to detect the statistical signatures of such timing behavior is an indispensable feature of a good and theoretically-tractable testing procedure. A widely used interval timing procedure is the ...
More >>
Measuring Breathing Patterns in Mice Using Whole-body Plethysmography
Authors:
Patricia Prada-Dacasa
,
Andrea Urpi
,
Laura Sánchez-Benito
,
Patrizia Bianchi
and
Albert Quintana
,
date:
09/05/2020,
view:
1846,
Q&A:
0
Respiratory dysfunction is among the main cause of severe and fatal pathologies worldwide. The use of effective experimental models and methodologies for the study of the pulmonary pathophysiology is necessary to prevent, control and cure these diseases. Plethysmography, a technique for the assessment of lung function, has been widely applied in ...
More >>
Identification of Socially-activated Neurons
Authors:
Mary L. Phillips
and
Lucas Pozzo-Miller
,
date:
09/05/2020,
view:
1947,
Q&A:
0
Determining the neuronal circuitry responsible for specific behaviors is a major focus in the field of neurobiology. Activity-dependent immediate early genes (IEGs), transcribed and translated shortly after neurons discharge action potentials, have been used extensively to either identify or gain genetic access to neurons and brain regions ...
More >>
Plant Science
Efficient
Agrobacterium
-mediated Transformation of the Elite–
Indica
Rice Variety Komboka
Authors:
Van T. Luu
,
Melissa Stiebner
,
Paula Emmerich Maldonado
,
Sandra Valdés
,
Didier Marín
,
Gerardo Delgado
,
Virginia Laluz
,
Lin-Bo Wu
,
Paul Chavarriaga
,
Joe Tohme
,
Inez H. Slamet-Loedin
and
Wolf B. Frommer
,
date:
09/05/2020,
view:
3511,
Q&A:
0
Genetic transformation is crucial for both investigating gene functions and for engineering of crops to introduce new traits. Rice (
Oryza sativa
L.) is an important model in plant research, since it is the staple food for more than half of the world’s population. As a result, numerous transformation methods have been developed for both
...
More >>
An Efficient Inoculation Technique to Assess the Pathogenicity of
Pantoea
Species Associated to Bacterial Blight of Rice
Authors:
Kossi Kini
,
Raoul Agnimonhan
,
Issa Wonni
and
Drissa Silue
,
date:
09/05/2020,
view:
1235,
Q&A:
0
Bacteria blight diseases of rice due to several genera of pathogenic bacteria are one of the major constraints worldwide for rice production. The disease can be best managed through host plant resistance sources. For most of these bacteria such as
Xanthomonas oryzae
pv.
oryzae
,
X. oryzae
pv.
oryzicola
,
...
More >>
Ratiometric Measurement of Protein Abundance after Transient Expression of a Transgene in
Nicotiana benthamiana
Authors:
Aashima Khosla
and
David C. Nelson
,
date:
09/05/2020,
view:
1917,
Q&A:
0
Ratiometric reporters are tools to dynamically measure the relative abundance of a protein of interest. In these systems, a target protein fused to a fluorescent or bioluminescent reporter is expressed with fixed stoichiometry to a reference protein fused to a second reporter. Both fusion proteins are encoded on a single transcript but are ...
More >>
Stem Cell
Integration of Human Induced Pluripotent Stem Cell (hiPSC)-Derived Neurons into Rat Brain
Authors:
Xiling Yin
,
Ted M. Dawson
and
Valina L. Dawson
,
date:
09/05/2020,
view:
1406,
Q&A:
0
Human neuron transplantation offers novel opportunities for modeling human neurologic diseases and potentially replacement therapies. However, the complex structure of the human cerebral cortex, which is organized in six layers with tightly interconnected excitatory and inhibitory neuronal networks, presents significant challenges for
in vivo
...
More >>
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