Towards in vitro vascularisation of collagen-GAG scaffolds.

Collagen-glycosaminoglycan scaffolds that have been used clinically for skin regeneration have also shown significant promise for other applications in tissue engineering. However, regeneration of thicker tissues with the aid of implanted biomaterials is likely to depend on, or be accelerated by, the ability to establish rapid vascularisation of the implant. The present study aims to establish a nascent vascular network in vitro within a CG scaffold as a first step towards that goal. Mesenchymal stem cells (MSCs) were chosen as primary vasculogenic candidate cells and a culture medium that promoted maximal network formation on Matrigel by these cells was selected. MSCs seeded in the CG scaffold formed networks of cord-like structures after one to two weeks in the presence of the vasculogenic medium; similar structures were formed by aortic endothelial cells (ECs) cultured for comparison. Gene expression analysis suggested that the MSCs began to adopt an endothelial phenotype, with RNA for PECAM and VCAM rising while that for alpha-smooth muscle actin fell. However there was no increase in Tie-2 and vWF expression. Addition of smooth muscle cells (SMCs) as a potential perivascular stabilising component did not have a noticeable effect on MSC-derived networks, although it enhanced EC-derived structures.

Gene expression by marrow stromal cells in a porous collagen-glycosaminoglycan scaffold is affected by pore size and mechanical stimulation.

Marrow stromal cell (MSC) populations, which are a potential source of undifferentiated mesenchymal cells, and culture scaffolds that mimic natural extracellular matrix are attractive options for orthopaedic tissue engineering. A type I collagen-glycosaminoglycan (CG) scaffold that has previously been used clinically for skin regeneration was recently shown to support expression of bone-associated proteins and mineralisation by MSCs cultured in the presence of osteogenic supplements. Here we follow RNA markers of osteogenic differentiation in this scaffold. We demonstrate that transcripts of the late stage markers bone sialoprotein and osteocalcin are present at higher levels in scaffold constructs than in two-dimensional culture, and that considerable gene induction can occur in this scaffold even in the absence of soluble osteogenic supplements. We also find that bone-related gene expression is affected by pore size, mechanical constraint, and uniaxial cyclic strain of the CG scaffold. The data presented here further establish the CG scaffold as a potentially valuable substrate for orthopaedic tissue engineering and for research on the mechanical interactions between cells and their environment, and suggest that a more freely-contracting scaffold with larger pore size may provide an environment more conducive to osteogenesis than constrained scaffolds with smaller pore sizes.

RNA editing in Physarum mitochondria: assays and biochemical approaches.

Mitochondrial RNAs in the myxomycete Physarum polycephalum differ from the templates from which they are transcribed in defined ways. Most transcripts contain nucleotides that are not present in their respective genes. These "extra" nucleotides are added during RNA synthesis by an unknown mechanism. Other differences observed between Physarum mitochondrial RNAs and the mitochondrial genome include nucleotide deletions, C to U changes, and the replacement of one nucleotide for another at the 5' end of tRNAs. All of these alterations are remarkably precise and highly efficient in vivo. Many of these editing events can be replicated in vitro, and here we describe both the in vitro systems used to study editing in Physarum mitochondria and the assays that have been developed to assess the extent of editing of RNAs generated in these systems at individual sites.

Morphological and functional differentiation of HSG cells: role of extracellular matrix and trpc 1.

A human salivary intercalated duct cell line (HSG) is capable of morphological change to acinar-type cells, and of salivary amylase (AMY1) expression, by culturing on basement membrane extracts (BME). The aim of this study was to determine the critical conditions for functional and morphological differentiation of HSG cells and to establish if the processes are related. Cells were grown on BMEs that had different protein concentrations and growth factor content, and then examined with respect to morphology and AMY1 expression. To investigate the role of intracellular calcium in amylase expression, a pcDNA3.1-TRPC1alpha construct was used to overexpress htrp1alpha, which mediates the store-operated calcium entry in HSG cells. Expression of the AMY1, TRPC1alpha and beta genes was quantified by means of real time RT-PCR. Growth factor-reduced BME (12.8 mg/ml) induced multicellular acinar structures with lumen formation but without stimulation of either AMY1 or TRPC1. HSG cells cultured on higher concentration BME (17.5 or 16.4 mg/ml) formed reticular networks. AMY1 expression increased both on growth factor-reduced BME (17.5 mg/ml: 3.0-fold, P < 0.001) and on regular BME (16.4 mg/ml: 3.7-fold, P < 0.001) accompanied by a slight increase in expression of TRPC1alpha and TRPC1beta. Overexpression of htrp1alpha did not cause any significant changes in AMY expression, though it attenuated the BME (17.5 mg/ml)-induced AMY1 upregulation. Overall, the higher protein concentration BME favors amylase expression in HSG cells, whereas the lower concentration causes marked morphological changes.

Unexpectedly complex editing patterns at dinucleotide insertion sites in Physarum mitochondria.

Many of the RNAs transcribed from the mitochondrial genome of Physarum polycephalum are edited by the insertion of nonencoded nucleotides, which are added either singly or as dinucleotides. In addition, at least one mRNA is also subject to substitutional editing in which encoded C residues are changed to U residues posttranscriptionally. We have shown previously that the predominant type of editing in these organelles, the insertion of nonencoded single C residues, occurs cotranscriptionally at the growing end of the RNA chain. However, less is known about the timing of dinucleotide addition, and it has been suggested that these insertions occur at a later stage in RNA maturation. Here we examine the addition of both single nucleotides and dinucleotides into nascent RNAs synthesized in vitro and in vivo. The distribution of added nucleotides within individual cloned cDNAs supports the hypothesis that all insertion sites are processed at the same time relative to transcription. In addition, the patterns of partial editing and misediting observed within these nascent RNAs suggest that separate factors may be required at a subset of dinucleotide insertion sites and raise the possibility that in vivo, nucleotides may be added to RNA and then changed posttranscriptionally.

Chimeric templates and assays used to study physarum cotranscriptional insertional editing in vitro.

RNAs made in the mitochondrion of Physarum polycephalum are edited relative to their template by the precise addition of nonencoded nucleotides, while they are being synthesized. This insertional editing has been reproduced in vitro during run-on extension of RNAs initiated in vivo, within partially purified mitochondrial transcription elongation complexes (mtTECs), but it does not occur when the mitochondrial polymerase initiates transcription on exogenous cloned DNA. This chapter describes in vitro transcription systems in which mtTEC RNAs are elongated on repositioned parts of the genome or exogenous DNA, in order to investigate how the nontemplated insertions are directed. Restriction enzyme digestion and DNA ligation are used to generate the chimeric templates, and the RNA products are analyzed directly by nuclease dissection (S1 protection followed by RNase T1 digestion) or by reverse transcriptase-polymerase chain reaction (RT-PCR) followed by restriction enzyme analysis or cloning and sequencing.

Editing site recognition and nucleotide insertion are separable processes in Physarum mitochondria.

Insertional RNA editing in Physarum polycephalum is a complex process involving the specific addition of non-templated nucleotides to nascent mitochondrial transcripts. Since all four ribonucleotides are substrates for the editing activity(s), both the site of insertion and the identity of the nucleotide to be added at a particular position must be specified, but the signals for these events have yet to be elucidated. Here we report the occurrence of sporadic errors in RNAs synthesized in vitro. These mistakes, which include omission of encoded nucleotides as well as misinsertions, occur only on templates that support editing. The pattern of these misediting events indicates that editing site recognition and nucleotide addition are separable events, and that the recognition step involves features of the mitochondrial template that are required for editing. The larger deletions lack all templated nucleotides between editing sites, suggesting that the transcription/editing apparatus can "jump" from one insertion site to another, perhaps mediated by interactions with editing determinants, while smaller omissions most likely reflect misalignment of the transcript upon resumption of templated RNA synthesis.

Cotranscriptional editing of Physarum mitochondrial RNA requires local features of the native template.

RNAs in the mitochondrion of Physarum polycephalum are edited by the precise cotranscriptional addition of non-encoded nucleotides. Here we describe experiments to address the basis of editing specificity using a series of chimeric templates generated by either rearranging the DNA present in editing-competent mitochondrial transcription elongation complexes (mtTECs) or linking it to exogenous DNA. Notably, run-on transcripts synthesized from rearranged mtTECs are edited at the natural sites, even when different genes are ligated together, yet exogenous, deproteinized DNA does not support editing. Furthermore, the accuracy of nucleotide insertion in chimeric RNAs argues that any cis-acting determinants of cytidine insertion are limited to small regions surrounding editing sites. Taken together, these observations strongly suggest that template-associated factors affect read-out of the mitochondrial genome.