PubMed Health⌕ Search

Biomedical subjects

Jennifer Kirkham

Publications and source records attributed to Jennifer Kirkham.

12 recordsLinked to original sources
PubMed2006

Collision events between RNA polymerases in convergent transcription studied by atomic force microscopy.

Atomic force microscopy (AFM) has been used to image, at single molecule resolution, transcription events by Escherichia coli RNA polymerase (RNAP) on a linear DNA template with two convergently aligned lambda(pr) promoters. For the first time experimentally, the outcome of collision events during convergent transcription by two identical RNAP has been studied. Measurement of the positions of the RNAP on the DNA, allows distinction of open promoter complexes (OPCs) and elongating complexes (EC) and collided complexes (CC). This discontinuous time-course enables subsequent analysis of collision events where both RNAP remain bound on the DNA. After collision, the elongating RNAP has caused the other (usually stalled) RNAP to back-track along the template. The final positions of the two RNAP indicate that these are collisions between an EC and a stalled EC (SEC) or OPC (previously referred to as sitting-ducks). Interestingly, the distances between the two RNAP show that they are not always at closest approach after 'collision' has caused their arrest.

DNA↗
PubMed2006

Studying silane mobility on hydrated mica using ambient AFM.

The mobility of the mono-functional aminosilane, aminopropyldimethylmethoxysilane (APDMMS), on mica has been investigated under ambient relative humidity (RH) using tapping-mode (TM) AFM. Silane layers were formed from vapour phase at various, controlled humidities and then imaged at ambient laboratory conditions (typically 30-40% RH). At low RH of formation (<25%) films without any resolvable sub-structure were formed, and these were stable to the imaging probe. At high RH of formation (>25%), where islands of phase II water are known to exist on mica, a two-phase domain structure was seen as two height levels and the surface area of the higher domains correlated with the RH. Sequential images taken over a 30-60 min time period show that these domains are mobile and at intermediate to high RH the domains coalesce under the influence of the scanning AFM tip. The results suggest the APDMMS resides at the air-water interface (rather than interacting with the mica) and that it preferentially interacts with the mobile phase II water as opposed to the phase I water tightly bound to the mica.

Journal Article↗
PubMed2006

Imaging RNA polymerase-amelogenin gene complexes with single molecule resolution using atomic force microscopy.

The AMELX gene encoding the enamel matrix protein, amelogenin, is located within (and in the opposite orientation to) the first intron of the ARHGAP6 gene, which encodes a GTPase-activating protein. The orientation of these two genes with respect to each other raises the possibility that they may undergo simultaneous convergent transcription during amelogenesis. The aim of this study was to use atomic force microscopy (AFM) to study a transcriptionally active amelogenin DNA template and to investigate the binding of RNA polymerase to convergently aligned promoters. Images of RNA polymerases stalled on DNA templates were obtained following incubation of the template with RNA polymerases and ribonucleotide triphosphates. A linear DNA template incorporating an intact rat amelogenin cDNA flanked by convergently aligned coliphage T7 and T3 promoters was constructed and shown to be transcriptionally active in vitro. Atomic force microscopy images of transcription complexes revealed globular structures, corresponding to single RNA polymerase molecules bound at specific locations on the DNA templates. These results indicate that AFM allows the visualization of individual RNA polymerases on DNA templates, offering a realistic approach to investigating the concept of convergent transcription of nested genes, which may lead to an understanding of whether the simultaneous expression of AMELX and ARHGAP6 is possible during the formation of tooth enamel.

Amelogenesis↗
PubMed2006

The effects of fluoride on the nanostructure and surface pK of enamel crystals: an atomic force microscopy study of human and rat enamel.

Atomic force microscopy (AFM) studies have revealed 30-40 nm-wide regular positively charged bands across maturation-stage rat enamel crystals. Low pH resolved these into positively charged spherical domains of approximately 30 nm diameter. Crystal surface pK values from adhesion force titrations were approximately 6.5. The effect of fluoride on this pK value and on the nanostructure of fluorosed human enamel crystals has not been reported. The nanostructure and surface chemistry (pK) of normal and fluorotic human and of fluoride-treated rat maturing enamel crystals was examined. Enamel was sectioned and polished, prior to examination, using AFM in height and friction modes. High-resolution height images revealed 30 nm-diameter spherical domains within crystals, arranged as layers of hexagons or as a shallow spiral. Fluorotic enamel showed similar, but less well ordered, nanodomains. These could represent an arrangement of original initiation sites or binding sites for modulating matrix proteins. Surface pK was derived from adhesion-force measurements between functionalized tips (OH or COOH) and crystal surfaces between pH 2 and pH 10. pK values of approximately 6.5 for normal crystals were reduced to approximately 5.5 after fluoride treatment. Reduction in surface pK by fluoride might indicate lowered protonation with possible effects on matrix protein binding.

Amelogenesis↗
PubMed2006

Evidence for direct amelogenin-target cell interactions using dynamic force spectroscopy.

Increasing evidence suggests that amelogenin, long held to be a structural protein of developing enamel matrix, may also have cell signaling functions. However, a mechanism for amelogenin cell signaling has yet to be described. The aim of the present study was to use dynamic chemical force spectroscopy to measure amelogenin interactions with possible target cells. Full-length amelogenin (rM179) was covalently attached to silicon nitride AFM tips. Synthetic RGD peptides and unmodified AFM tips were used as controls. Amelogenin-RGD cell binding force measurements were carried out using human periodontal ligament fibroblasts (HPDF) from primary explants and a commercially available osteoblast-like human sarcoma cell line as the targets. Results indicated a linear logarithmic dependence between loading rate and unbinding force for amelogenin-RGD target cells across the range of loading rates used. For RGD controls, binding events measured at 5.5 nN s-1 force loading rate resulted in a mean force of 60 pN. Values for amelogenin-fibroblast and amelogenin-osteoblast-like cell unbinding forces, measured at similar loading rates, were 50 and 55 pN, respectively. These data suggest that amelogenin interacts with potential target cells with forces characteristic of specific ligand-receptor binding, suggesting a direct effect for amelogenin at target cell membranes.

Amelogenin↗
PubMed2006

Intracellular nanosphere subunit assembly as revealed by amelogenin molecular cross-linking studies.

Enamel matrix comprises nanospheres predominantly composed of amelogenin. Studies have shown that recombinant amelogenin forms nanospheres similar to those formed in vivo, but it is unclear exactly how nanospheres assemble in vivo. Are amelogenin monomers secreted into the enamel matrix where they then self-assemble to form nanospheres, or does nanosphere assembly actually occur intracellularly? The aim of this study was to attempt to answer this question. Rat enamel organs were treated with the bifunctional cross-linker, dithio bis (succinimidyl propionate) (DSP), which cross-links primary amines lying in close molecular proximity. The key to this technique is the fact that DSP cross-links are later sensitive to reductive cleavage. The cross-linked proteins were first subjected to non-reducing sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) in the first dimension and then to reducing SDS-PAGE in the second dimension (so-called diagonal electrophoresis) followed by western blot probing with anti-amelogenin. The results indicated that intracellular amelogenin monomers are in close neighbor contact, forming complexes comprising up to six individual amelogenin monomers. We suggest that these initial complexes are prefabricated intracellularly before secretion. Once secreted, these prefabricated subunits assemble further to form the mature full-size nanospheres containing hundreds of individual amelogenins characteristic of enamel matrix.

Amelogenin↗
PubMed2005

Formation of aminosilane-functionalized mica for atomic force microscopy imaging of DNA.

Factors affecting the functionalization of mica with aminosilanes, in particular, aminopropyltriethoxysilane (APTES-mica), formed from the vapor phase have been systematically studied. The relative humidity (RH) during vapor deposition has been varied, and postdeposition treatment through baking has been used, as well as the comparison of mono and trifunctionality, to investigate how optimal surfaces for AFM imaging of DNA are formed. It is found that the stability of the APTES layers is a consequence of lateral polymerization and not covalent attachment to the mica substrate. At low RH (<25%), DNA adopts an open, well-resolved conformation, whereas at >25% RH, DNA surface-induced condensation occurs. Contact mode AFM scratching experiments show that two main structures of the silane layer exist at different humidity: a monolayer exists at RH < 25%, and a bilayer structure exists at RH > 25%. Finally, structural changes that these two layer types undergo after baking at 150 degrees C were investigated by AFM and X-ray photoelectron spectroscopy (XPS), and these now prevented DNA from binding to the APTES-mica, except in the presence of Mg(II) ions.

Aluminum Silicates↗
PubMed2005

Nested genes: biological implications and use of AFM for analysis.

A "nested" gene is located within the boundaries of a larger gene, often within an intron and in the opposite orientation. Such structures are common in bacteria and viruses, but have also been described in higher species as diverse as Drosophila and humans. Expression of nested and host genes may be simultaneously up-regulated due to use of common enhancers, or down-regulated through steric hindrance or interference caused by annealing of the complementary RNAs, leading to degradation. Methods for RNA analysis such as RT-PCR and in situ hybridization reveal the presence of specific mRNAs, but do not address regulation of expression within a single cell at a single genetic locus. Atomic force microscopy is a relatively new technology, which allows visualization of the movement of an RNA polymerase along a DNA template. The potential of this technology includes a greater molecular understanding of cellular decision making processes, leading to enhanced opportunities to intervene in disease progression through use of novel treatment modalities.

Animals↗
PubMed2004

Developing explanatory models of health inequalities in childhood dental caries.

OBJECTIVE: Long-term aim is to determine optimum interventions to reduce dental caries in children in disadvantaged communities and minimise the effects of exclusion from health care systems, of ethnic diversity, and health inequalities. DESIGN: Generation of initial explanatory models, study protocol and development of two standardised measures. First, to investigate how parental attitudes may impact on their children's oral health-related behaviours and second, to assess how dentists' attitudes may impact on the provision of dental care. SUBJECTS: Core research team, lead methodologists, 44 consortium members from 18 countries. To complete the development of the questionnaire, the initial set of items was administered to parents (n = 23) with children in nursery schools in Dundee, Scotland and sent to the same parents one week later. A standardised measure examining barriers to providing dental care for children aged 3 to 6 years was developed. 20 dentists working in primary dental care in Scotland completed the measure on two different occasions separated by one week. RESULTS: Explanatory models were developed. Family questionnaire: test-retest reliability excellent (r = 0.93 p < or = 0.001) with very good internal reliability (alpha = 0.89). Dentists questionnaire: excellent test-re-test reliability r = 0.88, (alpha = 0.90). CONCLUSIONS: Interaction between consortium members enhanced the validity of the questionnaires and protocols for different cultural locations. There were challenges in developing and delivering this multi-centre study. Experience gained will support the development of substantive trials and longitudinal studies to address the considerable international health disparity of childhood dental caries.

Attitude of Health Personnel↗
PubMed2003

Hydrostatic pressure modulates proteoglycan metabolism in chondrocytes seeded in agarose.

OBJECTIVE: To investigate the effect of isolated hydrostatic pressure on proteoglycan metabolism in chondrocytes. METHODS: Bovine articular chondrocytes cultured in agarose gels were subjected to 5 MPa hydrostatic pressure for 4 hours in either a static or a pulsatile (1 Hz) mode, and changes in glycosaminoglycan (GAG) synthesis, hydrodynamic size, and aggregation properties of proteoglycans and aggrecan messenger RNA (mRNA) levels were determined. RESULTS: The application of 5 MPa static pressure caused a significant increase in GAG synthesis of 11% (P < 0.05). Column chromatography showed that this increase in GAG synthesis was associated with large proteoglycans. In addition, semiquantitative reverse transcriptase-polymerase chain reaction showed a 4-fold increase in levels of aggrecan mRNA (P < 0.01). CONCLUSION: Hydrostatic pressure in isolation, which does not cause cell deformation, can affect proteoglycan metabolism in chondrocytes cultured in agarose gels, indicating an important role of hydrostatic pressure in the regulation of extracellular matrix turnover in articular cartilage.

Aggrecans↗
PubMed2003

Upregulation of aggrecan and type II collagen mRNA expression in bovine chondrocytes by the application of hydrostatic pressure.

The aim of this study was to investigate the effect of hydrostatic pressure on the expression of messenger ribonucleic acid (mRNA) for specific extracellular matrix proteins in chondrocytes. Chondrocytes obtained from bovine metatarsophalangeal joints were embedded in cylindrical 2% agarose gels. A novel experimental system was used to apply 5 MPa of static hydrostatic pressure to these chondrocytes for 4 hours. The application of hydrostatic pressure caused a significant increase in the level of aggrecan mRNA by almost four fold (p<0.01) as well as a 50% increase in the level of type II collagen mRNA (p<0.05). However, there was no significant change in the level of TIMP-1 mRNA. It was suggested that the application of hydrostatic pressure, in the absence of cell deformation, can bring about changes in the matrix components which may play an important role in the homeostasis and mechanical properties of articular cartilage.

Aggrecans↗