Biomedical subjects

Jonathan P L Cox

Publications and source records attributed to Jonathan P L Cox.

4 recordsLinked to original sources

PubMed2005

Isolation of C15: a novel antibody generated by phage display against mesenchymal stem cell-enriched fractions of adult human marrow.

Adult bone marrow stroma contains a source of mesenchymal stem cells (MSC) that have the capacity to self-renew and differentiate into multiple stromal lineages. These rare cells can be visualised indirectly by the formation of heterogeneous colonies, containing stem cells and their differentiated progeny in long-term culture. If MSC and their associated progenitor and precursor populations are to reach their full therapeutic potential, markers will be required to identify and characterize specific bone marrow stromal subsets. We sought to use phage display to generate antibodies against bone marrow mononuclear cells (BMMNC) enriched for colony forming cells. Initially, we identified our target cell population by comparing the colony forming efficiency (CFE) of CD49a-positive, STRO-1-positive and CD45-negative BMMNC subpopulations with unseparated BMMNC. Selection with anti-CD49a gave the greatest enrichment (19-fold) of colony forming cells and in light of these findings, we generated phage antibodies against CD49a-positive BMMNC by simultaneous positive/negative selection. A dominant clone (C15), generated after 3 rounds of selection, has been isolated and sequenced, then characterized for cell and tissue specificity. Sequence analysis showed that the V(H) and V(L) gene segments of C15 aligned most closely to the VH26/DP-47 and IGLV3S1/DPL16 germline V segments found in the synthetic repertoire. C15 bound to 4% of freshly isolated BMMNC and localized to osteoblastic cells and proximal marrow cells in areas of active bone formation in sections of osteophyte. C15 binding was upregulated in cultured bone marrow stromal cells (BMSC) and was also detected on bone-derived cell lines. This report demonstrates that phage display is a powerful tool for the isolation of antibodies against rare cell populations, and provides a platform for the future application of this technology in the search for antigens on MSC and other rare cell populations.

Adult↗

PubMed2004

Dynamic polyhedral models of globular proteins.

We have devised several mechanical models of globular proteins by approximating them to various polyhedra (dodecahedron, truncated octahedron, icosahedron, truncated icosahedron). The models comprise hollow blocks linked together in a flexible chain. Between blocks there is a set of several reversible, weak magnetic interactions such that when the chain is agitated, it will fold into a stable polyhedral structure about the size of a hand. Folding may be followed in real time with a video camera. Key to the success of the folding process is the lightness of the chain. Several side chains may also be added to the blocks such that they come together to create a polyhedral core when the chain folds. The models have a number of similarities to globular proteins: each chain folds into a unique, but dynamic, three-dimensional structure; the instructions that determine this structure are built into the configuration of blocks; and it is difficult to predict this structure given the unfolded block configuration. Furthermore, the chains fold quickly, generally in less than a minute, several pathways are involved, and these pathways progress through elements of "native" structure. In particular, the models emphasize the importance of restricted conformational mobility in assisting the chain to fold, and also in eliminating undesirable interactions. Because of these similarities to globular proteins, we believe that the polyhedral models will, with continued development, be helpful in understanding the protein folding process, while at the same time acting as valuable educational visual aids. They might also inspire the construction of new types of microscopic, self-assembling devices.

Animals↗

PubMed2003

Methylated DNA labels for marking objects.

We recently described a method for digitally labelling objects with DNA. Here we show that, using DNA methyltransferases to create polymorphic DNA templates, it is possible to significantly increase the number of labels that can be generated by this method. Nine double-stranded DNA templates of different length were methylated with either M.HaeIII or M.AluI methyltransferase, or both. Different mixtures of methylated and unmethylated versions of this template set were used to 'invisibly' label paper. The mixtures were eluted from the paper and the methylated status of the templates in each mixture successfully determined, and the labels read, by digestion with the complementary restriction endonuclease, followed by a polymerase chain reaction and agarose gel electrophoresis. One methylated DNA label was read after it had been left on paper for two months.

Archaeal Proteins↗

PubMed2003

Some possible codes for encrypting data in DNA.

Three codes are reported for storing written information in DNA. We refer to these codes as the Huffman code, the comma code and the alternating code. The Huffman code was devised using Huffman's algorithm for constructing economical codes. The comma code uses a single base to punctuate the message, creating an automatic reading frame and DNA which is obviously artificial. The alternating code comprises an alternating sequence of purines and pyrimidines, again creating DNA that is clearly artificial. The Huffman code would be useful for routine, short-term storage purposes, supposing--not unrealistically--that very fast methods for assembling and sequencing large pieces of DNA can be developed. The other two codes would be better suited to archiving data over long periods of time (hundreds to thousands of years).

Algorithms↗