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Article
Open AccessStable diffusion gradients in microfluidic conduits bounded by fluid walls
Assays mimicking in vitro the concentration gradients triggering biological responses like those involved in fighting infections and blood clotting are essential for biomedical research. Microfluidic assays pr...
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Article
Open AccessPredicting flows through microfluidic circuits with fluid walls
The aqueous phase in traditional microfluidics is usually confined by solid walls; flows through such systems are often predicted accurately. As solid walls limit access, open systems are being developed in wh...
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Article
Open AccessMicrofluidics with fluid walls
Microfluidics has great potential, but the complexity of fabricating and operating devices has limited its use. Here we describe a method — Freestyle Fluidics — that overcomes many key limitations. In this met...
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Article
Open AccessBiocompatibility of fluids for multiphase drops-in-drops microfluidics
This paper addresses the biocompatibility of fluids and surfactants in the context of microfluidics and more specifically in a drops-in-drops system for mammalian cell based drug screening. In the drops-in-dro...
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Article
Open AccessFormation of droplet interface bilayers in a Teflon tube
Droplet-interface bilayers (DIBs) have applications in disciplines ranging from biology to computing. We present a method for forming them manually using a Teflon tube attached to a syringe pump; this method i...
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Article
Isolation of the protein and RNA content of active sites of transcription from mammalian cells
Transcription factories contain all three mammalian RNA polymerases, each actively transcribing a different subset of genes. This protocol describes how to isolate large factory fragments for the analysis of a...
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Article
Open AccessTNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning
The rearrangement of nucleosomes along the DNA fiber profoundly affects gene expression, but little is known about how signalling reshapes the chromatin landscape, in three-dimensional space and over time, to ...
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Article
Open AccessEnhancers and silencers: an integrated and simple model for their function
Regulatory DNA elements such as enhancers, silencers and insulators are embedded in metazoan genomes, and they control gene expression during development. Although they fulfil different roles, they share speci...
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Article
The proteomes of transcription factories containing RNA polymerases I, II or III
The question of whether transcription factories containing RNA polymerases exist has been controversial, owing to the fact that they have not been isolated previously. Now, a method to carefully isolate these ...
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Article
Non-specific (entropic) forces as major determinants of the structure of mammalian chromosomes
Four specific forces (H-bonds, van der Waals forces, hydrophobic and charge interactions) shape the structure of proteins, and many biologists assume they will determine the shape of all structures in the cell...
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Chapter
Dynamic Chromatin Loops and the Regulation of Gene Expression
Although we have a draft sequence of the human genome, little is known about how the chromatin fiber is packed in three-dimensional (3D) space, or how packing affects function (Jackson 2003). We know packing play...
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Article
Different populations of RNA polymerase II in living mammalian cells
RNA polymerase II is responsible for transcription of most eukaryotic genes, but, despite exhaustive analysis, little is known about how it transcribes natural templates in vivo. We studied polymerase dynamics in...
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Article
Open AccessThe functional organization of mitochondrial genomes in human cells
We analyzed the organization and function of mitochondrial DNA in a stable human cell line (ECV304, which is also known as T-24) containing mitochondria tagged with the yellow fluorescent protein.
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Protocol
Approaches for Monitoring Nuclear Translation
The nuclear membrane is the defining feature of eukaryotes. It divides the cell into two functionally specialized compartments, and it is widely assumed that translation is restricted to only one: the cytoplas...
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Article
Predicting three-dimensional genome structure from transcriptional activity
We would like to be able to predict how genomes are folded in the cell from the primary DNA sequence. A model for the three-dimensional structure of all genomes is presented; it is based on the structure of th...
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Article
Stable correction of a genetic deficiency in human cells by an episome carrying a 115 kb genomic transgene
Persistent expression of a transgene at therapeutic levels is required for successful gene therapy, but many small vectors with heterologous promoters are prone to vector loss and transcriptional silencing. Th...
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Chapter
The nucleoskeleton and the topology of transcription
Transcription is conventionally believed to occur by passage of a mobile polymerase along a fixed template. Evidence for this model is derived almost entirely from material prepared using hypotonic salt concen...
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Article
Characterization of hypoxanthine-guanine phosphoribosyl transferase in man-mouse somatic cell hybrids by an improved electrophoretic method
The hypoxanthine-guanine phosphoribosyl transferase (HGPRT) activity in a group of man-mouse somatic cell hybrids, produced by Sendai virus-mediated cell fusion and HAT selection, has been analyzed by a new el...
