• Volume 12, 2022
  • 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


PRODIGY: A Contact-based Predictor of Binding Affinity in Protein-protein Complexes Authors:  Anna Vangone and Alexandre M. J. J. Bonvin, date: 02/05/2017, view: 10651, Q&A: 0
Biomolecular interactions between proteins regulate and control almost every biological process in the cell. Understanding these interactions is therefore a crucial step in the investigation of biological systems and in drug design. Many efforts have been devoted to unravel principles of protein-protein interactions. Recently, we introduced a ...
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Cancer Biology

In vitro Assessment of RNA Polymerase I Activity Author:  Marzia Govoni, date: 02/05/2017, view: 7561, Q&A: 0
In eukaryotic cells transcriptional processes are carried out by three different RNA polymerases: RNA polymerase I which specifically transcribes ribosomal RNA (rRNA), RNA polymerase II which transcribes protein-coding genes to yield messenger RNAs (mRNAs) and small RNAs, while RNA polymerase III transcribes the genes for transfer RNAs and for the ...
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Polysome Fractionation to Analyze mRNA Distribution Profiles Authors:  Amaresh C. Panda, Jennifer L. Martindale and Myriam Gorospe, date: 02/05/2017, view: 26752, Q&A: 5
Eukaryotic cells adapt to changes in external or internal signals by precisely modulating the expression of specific gene products. The expression of protein-coding genes is controlled at the transcriptional and post-transcriptional levels. Among the latter steps, the regulation of translation is particularly important in cellular processes that ...
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Production, Purification and Crystallization of a Prokaryotic SLC26 Homolog for Structural Studies Authors:  Yung-Ning Chang, Farooque R. Shaik, Yvonne Neldner and Eric R. Geertsma, date: 02/05/2017, view: 8264, Q&A: 0
The SLC26 or SulP proteins constitute a large family of anion transporters that are ubiquitously expressed in pro- and eukaryotes. In human, SLC26 proteins perform important roles in ion homeostasis and malfunctioning of selected members is associated with diseases. This protocol details the production and crystallization of a prokaryotic SLC26 ...
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Determination of the in vitro Sporulation Frequency of Clostridium difficile Authors:  Adrianne N. Edwards and Shonna M. McBride, date: 02/05/2017, view: 7500, Q&A: 0
The anaerobic, gastrointestinal pathogen, Clostridium difficile, persists within the environment and spreads from host-to-host via its infectious form, the spore. To effectively study spore formation, the physical differentiation of vegetative cells from spores is required to determine the proportion of spores within a population of C. ...
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Force Measurement on Mycoplasma mobile Gliding Using Optical Tweezers Authors:  Masaki Mizutani and Makoto Miyata, date: 02/05/2017, view: 7144, Q&A: 0
Dozens of Mycoplasma species, belonging to class Mollicutes form a protrusion at a pole as an organelle. They bind to solid surfaces through the organelle and glide in the direction by a unique mechanism including repeated cycles of bind, pull, and release with sialylated oligosaccharides on host animal cells. The mechanical ...
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Analysis of the Virulence of Uropathogenic Escherichia coli Strain CFT073 in the Murine Urinary Tract Authors:  Anna Waldhuber, Manoj Puthia, Andreas Wieser, Catharina Svanborg and Thomas Miethke , date: 02/05/2017, view: 9812, Q&A: 0
This urinary tract infection model was used to monitor the efficacy of a new virulence factor of the uropathogenic Escherichia coli strain CFT073 in vivo. The new virulence factor which we designated TIR-containing protein C (TcpC) blocks Toll-like receptor signaling and the NLRP3 inflammasome signaling cascade by interacting ...
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Enriching Acidophilic Fe(II)-oxidizing Bacteria in No-flow, Fed-batch Systems Authors:  Yizhi Sheng, Bradley Kaley and William D. Burgos, date: 02/05/2017, view: 8226, Q&A: 0
Low-pH microbial Fe(II) oxidation occurs naturally in some Fe(II)-rich acid mine drainage (AMD) ecosystems across so-called terraced iron formations. Indigenous acidophilic Fe(II)-oxidizing bacterial communities can be incorporated into both passive and active treatments to remove Fe from the AMD solution. Here, we present a protocol of enriching ...
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Molecular Biology

Synthetic Lethality Screens Using RNAi in Combination with CRISPR-based Knockout in Drosophila Cells Authors:  Benjamin E. Housden, Hilary E. Nicholson and Norbert Perrimon, date: 02/05/2017, view: 10119, Q&A: 0
A synthetic lethal interaction is a type of genetic interaction where the disruption of either of two genes individually has little effect but their combined disruption is lethal. Knowledge of synthetic lethal interactions can allow for elucidation of network structure and identification of candidate drug targets for human diseases such as cancer. ...
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Heterochronic Pellet Assay to Test Cell-cell Communication in the Mouse Retina Authors:  Nobuhiko Tachibana, Dawn Zinyk, Randy Ringuette, Valerie Wallace and Carol Schuurmans, date: 02/05/2017, view: 9491, Q&A: 0
All seven retinal cell types that make up the mature retina are generated from a common, multipotent pool of retinal progenitor cells (RPCs) (Wallace, 2011). One way that RPCs know when sufficient numbers of particular cell-types have been generated is through negative feedback signals, which are emitted by differentiated cells and must reach ...
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Cued Rat Gambling Task Authors:  Michael M. Barrus and Catharine A. Winstanley, date: 02/05/2017, view: 12107, Q&A: 0
The ability of salient cues to serve as powerful motivators has long been recognized in models of drug addiction, but little has been done to investigate their effects on complex decision making. The Cued rat Gambling Task (CrGT) is an operant behavioural task which pairs salient, audiovisual cues with the delivery of sucrose pellet rewards on ...
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Plant Science

Miniature External Sapflow Gauges and the Heat Ratio Method for Quantifying Plant Water Loss Author:  Robert Paul Skelton, date: 02/05/2017, view: 8022, Q&A: 0
External sapflow sensors are a useful tool in plant ecology and physiology for monitoring water movement within small stems or other small plant organs. These gauges make use of heat as a tracer of water movement through the stem and can be applied in both a laboratory and a field setting to generate data of relatively high temporal resolution. ...
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Expression and Purification of the GRAS Domain of Os-SCL7 from Rice for Structural Studies Authors:  Shengping Li, Yanhe Zhao and Yunkun Wu, date: 02/05/2017, view: 7145, Q&A: 0
GRAS proteins, named after the first three members GAI, RGA and SRC, has been found in 294 embryophyta species and is represented by 1,035 sequences. They belong to a plant-specific protein family and play essential roles in plant growth and development. Proteins in this family are defined as minimally containing a conserved GRAS domain, which is ...
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Stem Cell

A Streamlined Method for the Preparation of Growth Factor-enriched Thermosensitive Hydrogels from Soft Tissue Authors:  Christopher J. Poon, Shaun S. Tan, Sholeh W. Boodhun, Keren M. Abberton and Wayne A. Morrison, date: 02/05/2017, view: 7119, Q&A: 0
Hydrogels are an ideal medium for the expansion of cells in three dimensions. The ability to induce cell expansion and differentiation in a controlled manner is a key goal in tissue engineering. Here we describe a detailed method for producing hydrogels from soft tissues with an emphasis on adipose tissue. In this method, soluble, extractable ...
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Systems Biology

Bioinformatic Analysis for Profiling Drug-induced Chromatin Modification Landscapes in Mouse Brain Using ChlP-seq Data Authors:  Yong-Hwee Eddie Loh, Jian Feng, Eric Nestler and Li Shen, date: 02/05/2017, view: 10135, Q&A: 0
Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is a powerful technology to profile genome-wide chromatin modification patterns and is increasingly being used to study the molecular mechanisms of brain diseases such as drug addiction. This protocol discusses the typical procedures involved in ChIP-seq data ...
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