Microgels and apparatus for PAGE of nucleic acids in one or two dimensions.

We describe a system for horizontal 1D or 2D PAGE comprising an apparatus and microgels. There is no buffer outside the gel, making handling and sample loading easy. Specially designed electrodes on all four sides allow 2D electrophoresis without gel rotation.

Impact of different ChIP-Seq protocols on DNA integrity and quality of bioinformatics analysis results.

Different ChIP-Seq protocols may have a significant impact on the final outcome in terms of quality, number and distribution of called peaks. Sample DNA undergoes a long procedure before the final sequencing step, and damaged DNA can result in excessive mismatches in the alignment with reference genome. In this letter, we present the effect of well-defined modifications (timing of formaldehyde crosslink reversal, brand of the sonicator) of standard ChIP-Seq protocol on parallel samples derived from the same cell line correlating the initial DNA quality control metrics to the final bioinformatics analysis results.

Sequence specificity of single-stranded DNA-binding proteins: a novel DNA microarray approach.

We have developed a novel DNA microarray-based approach for identification of the sequence-specificity of single-stranded nucleic-acid-binding proteins (SNABPs). For verification, we have shown that the major cold shock protein (CspB) from Bacillus subtilis binds with high affinity to pyrimidine-rich sequences, with a binding preference for the consensus sequence, 5'-GTCTTTG/T-3'. The sequence was modelled onto the known structure of CspB and a cytosine-binding pocket was identified, which explains the strong preference for a cytosine base at position 3.

Comparative proteomic analysis using samples obtained with laser microdissection and saturation dye labelling.

Comparative proteomic methods are rapidly being applied to many different biological systems including complex tissues. One pitfall of these methods is that in some cases, such as oncology and neuroscience, tissue complexity requires isolation of specific cell types and sample is limited. Laser microdissection (LMD) is commonly used for obtaining such samples for proteomic studies.

The use of nucleic acid tools for target validation in central nervous system therapy.

The main challenge facing target validation today comes from the ongoing genomics revolution, which is generating an unprecedented number of potential targets. Existing technologies, such as mouse knockouts, are struggling to provide the throughput now required. Nucleic acid tools including antisense, RNA interference, ribozymes and aptamers offer a potentially higher throughput means of manipulating gene expression and thus validating targets in complex biological systems such as the central nervous system.

An endochitinase A from Vibrio carchariae: cloning, expression, mass and sequence analyses, and chitin hydrolysis.

We provide evidence that chitinase A from Vibrio carchariae acts as an endochitinase. The chitinase A gene isolated from V. carchariae genome encodes 850 amino acids expressing a 95-kDa precursor.

The potential of antisense as a CNS therapeutic.

Antisense offers a precise and specific means of knocking down expression of a target gene, and is a major focus of research in neuroscience and other areas. It has application as a tool in gene function and target validation studies and is emerging as a therapeutic technology in its own right. It has become increasingly obvious, however, that there are a number of hurdles to overcome before antisense can be used effectively in the CNS, most notably finding suitable nucleic acid chemistries and an effective delivery vehicle to transport antisense oligonucleotides (AS-ODNs) across the blood-brain barrier (BBB) to their site of action.

Enhanced long-term potentiation in the hippocampus of rats expressing mutant presenillin-1 is age related.

Electrophysiological recordings were made from Fischer rats engineered to express the human presenilin 1 gene carrying the M146V mutation. Extracellular recordings of field excitatory post-synaptic potential (EPSPs) were made to investigate EPSP properties, paired pulse responses, posttetanic potentiation, and long-term potentiation in the stratum radiatum and dentate gyrus of hippocampal slices maintained in vitro. Transgenic rats aged approximately 6 months showed no differences from their wild-type littermates in any of these properties.