Biomedical subjects

Daniel J Graham

Publications and source records attributed to Daniel J Graham.

9 recordsLinked to original sources

PubMed2007

Comparison of native extracellular matrix with adsorbed protein films using secondary ion mass spectrometry.

In the past decade, the temperature-responsive behavior of poly(N-isopropyl acrylamide) (pNIPAM) has come to be recognized as a convenient method for the nondestructive harvest of confluent cell layers. Recently, we have utilized this nondestructive cell harvest method as a means to ascertain the nature of the extracellular matrix (ECM) secreted from cells. In this work, we compare the ECM obtained after cell liftoff to individual ECM proteins adsorbed directly onto RF-plasma-deposited pNIPAM (ppNIPAM). Using X-ray photoelectron spectroscopy, we find that the composition of ppNIPAM post-cell liftoff surfaces is consistent with those of the ppNIPAM post-protein adsorption surface, both of which differ from control surfaces. Using principal component analysis of positive-ion time-of-flight secondary ion mass spectrometry (ToF-SIMS) data, we show that the major ECM proteins examined can effectively be identified from their amino acid compositions. By comparing the positive-ion ToF-SIMS data from each of the ppNIPAM post-protein adsorption surfaces to that of ppNIPAM post-cell liftoff, we find that ppNIPAM post-cell liftoff surfaces are distinctly separate from fibronectin (FN). This result is consistent with our previous observation using immunoassay that FN is clearly associated with the cell sheet after low-temperature liftoff from ppNIPAM.

Acrylic Resins↗

PubMed2006

Can the theory of "whitening" explain the center-surround properties of retinal ganglion cell receptive fields?

To account for the spatial and temporal response properties of the retina, a number of studies have proposed that these properties serve to "whiten" the visual input. In particular, it has been argued that the sensitivity of retinal ganglion cells is matched to the spatial frequency spectrum of natural scenes, resulting in a flattened or "whitened" response spectrum across a range of frequencies. However, we argue that there are two distinct hypotheses regarding the flattening of the spectrum. The decorrelation hypothesis proposes that the magnitude of each ganglion cell tuning curve rises with spatial frequency, resulting in a flattened response spectrum for natural scene stimuli. With appropriate sampling, this scheme allows neighboring neurons to be uncorrelated with each other. The response equalization hypothesis proposes that the overall response magnitude of neurons increases with spatial frequency. The proposed goal of this model is to allow neurons with different receptive field sizes to produce the same average response to natural scenes. The response equalization hypothesis proposes an explanation for the relative gain of different ganglion cells and we show that this proposal fits well with published data. We suggest that both hypotheses are important in understanding the tuning and sensitivity of ganglion cells. However, using a simulation, both models are shown to be insufficient to explain the center-surround receptive field organization of ganglion cells. We discuss other factors, including representational sparseness, which could be related to the goals of ganglion cell spatial processing. We suggest three constraints needed to describe the basic linear properties of P-type ganglion cells: decorrelation, response equalization, and a minimal wiring or minimal size constraint.

Animals↗

PubMed2005

Cell sheet detachment affects the extracellular matrix: a surface science study comparing thermal liftoff, enzymatic, and mechanical methods.

This work compares the removal of bovine aortic endothelial cell (BAEC) monolayers via 1) low-temperature liftoff from a "smart polymer," plasma polymerized poly(N-isopropyl acrylamide) (ppNIPAM), 2) enzymatic digestion, and 3) mechanical dissociation from ppNIPAM surfaces. We examine the surfaces after cell removal by using X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (ToF-SIMS), immunostaining, and cell adhesion assay. Immunoassay results indicate that low-temperature liftoff nondestructively harvests the cell sheet and most of the underlying extracellular matrix (ECM), whereas enzymatic digestion and mechanical dissociation are damaging to both the cells and ECM. XPS results indicate that amide and alcohol groups attributed to proteins in the ECM are present on postliftoff surfaces. Principal component analysis (PCA) of ToF-SIMS data indicates that molecular ion fragments of amino acids are present on postliftoff surfaces. Finally, a cell adhesion assay seeding new cells on surfaces from which an initial layer of cells was removed via each of the three methods indicates that liftoff and mechanical dissociation leave behind surfaces that better promote cell adhesion. We conclude that the removal of BAEC cells via low-temperature liftoff from ppNIPAM-treated surfaces is less damaging to the ECM proteins remaining at the surface than the other methods.

Acrylamides↗

PubMed2005

Surface characterization of the extracellular matrix remaining after cell detachment from a thermoresponsive polymer.

The temperature-responsive behavior of poly(N-isopropyl acrylamide) (pNIPAM) directly affects the attachment and detachment of cells cultured on these surfaces. At culture temperatures, cells behave similarly to those on tissue culture polystyrene (TCPS), while at room temperature, cells cultured on pNIPAM spontaneously detach as a confluent sheet. In comparison, cells grown on TCPS remain attached indefinitely after the temperature drop, requiring enzymatic or mechanical removal. In this work, we present an examination of the response of bovine aortic endothelial cells (BAECs) and extracellular matrix (ECM) proteins to plasma polymerized NIPAM (ppNIPAM) surfaces using X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (ToF-SIMS), and immunostaining. Immunoassay results reveal that, although fibronectin, laminin, and collagen closely associate with the cell sheet, some collagen may be associated with the surface, as well. Our XPS results indicate that ppNIPAM surfaces after cell liftoff differ from their blank counterparts, the primary distinction being the presence of amide and alcohol species on ppNIPAM surfaces used for cell culture, possibly owing to the presence of a proteinaceous film. Finally, a comparison between ppNIPAM-treated surfaces used for cell culture versus control surfaces by principal component analysis of the ToF-SIMS data confirms that the surfaces differ; the presence of molecular ion fragments from amino acids (e.g., alanine, glycine, and proline) is the chief reason for this difference. Therefore, from our surface characterization of ppNIPAM-coated TCPS after cell liftoff, we conclude that although low-temperature liftoff of the BAEC monolayer is accompanied by the majority of the components of the ECM, some of the ECM proteins still remain at the surface.

Acrylic Resins↗

PubMed2003

Time-of-flight secondary ion mass spectrometry: techniques and applications for the characterization of biomaterial surfaces.

The surface of a biomaterial plays a critical role in the success of an implant. Much effort is currently being focused on controlling the chemistry at biomaterial surfaces to ensure favorable results in vivo. The successful tailoring of the surface chemistry will require a detailed surface characterization to verify that the desired changes have been made. This will include the ability to determine the composition, structure, orientation, and spatial distribution, of the molecules and chemical structures on the surface. TOF-SIMS is a powerful surface characterization technique that is able to address these requirements through both spectral analysis and direct chemical state imaging. The flexibility of the TOF-SIMS technique, and the wealth of data produced have generated much interest in its use for biomaterial characterization. This review discusses the strengths, weaknesses, and challenges of static TOF-SIMS for biomaterial surface characterization. First the basic principles of TOF-SIMS are introduced, giving an overview of the technique. Next, sample type, and other sample considerations are discussed. Then data interpretation is overviewed using examples from both spectral and imaging data. Finally, quantitative SIMS analysis is discussed and an outlook for TOF-SIMS analysis of biomaterials will be given.

Biocompatible Materials↗

PubMedDate not supplied

Information and organic molecules: structure considerations via integer statistics.

Information in relation to organic molecules was investigated in a previous work (Graham and Schacht, J. Chem. Inf. Comput. Sci. 2000, 40, 187). The topic is given further consideration here with the help of integer statistics. Discussed are the ramifications of an integer variable Omega(t) which quantifies the total number of binding complexions for an organic molecule. Offered is a statistical view of the maximum allowed number of independent regions D expressed by the molecule, dependent on Omega(t). We illustrate the distribution properties of D along with upper limit estimates of the regioinformation mu, also dependent on Omega(t). Integer statistics based on elementary number theory establish the key distribution properties of D and mu. In so doing, the traits distinguishing high regioinformation molecules are enumerated. The statistical approach encompasses all possible molecules and conditions, not just those reported to date in chemical databases. The aim is to view the regioinformation expressed by molecules in an alternative and general way.

Journal Article↗

PubMedDate not supplied

Information content in organic molecules: quantification and statistical structure via Brownian processing.

Information and organic molecules were the subject of two previous works from this lab (Graham and Schacht, J. Chem. Inf. Comput. Sci. 2000, 40, 187; Graham, J. Chem. Inf. Computer Sci. 2002, 42, 215). We delve further in this paper by examining organic structure graphs as objects of Brownian information processing. In so doing, tools are introduced which quantify and correlate molecular information to several orders. When the results are combined with energy data, an enhanced informatic view of covalent bond networks is obtained. The information properties of select molecules and libraries are illustrated. Notably, Brownian processing accommodates all possible compounds and libraries, not just ones registered in chemical databases. This approach establishes important features of the statistical structure underlying carbon chemistry.

Journal Article↗

PubMedDate not supplied

Information content in organic molecules: reaction pathway analysis via Brownian processing.

Carbon chemistry offers infinite possibilities for molecules as information carriers. Moreover, there is no boundary on the number of ways in which a carrier's information can change via a chemical reaction. Organic reaction pathways thus pose new types of informatic variables which compel characterization using Brownian methods. We apply the tools of the preceding paper to these variable types for select reactions and classes. Along the way, geometric descriptors are formulated which complement the structure graph sequences of chemistry texts and journals. In addition, the statistical structure underpinning carbon transformations is explored more deeply. Overall, this work brings to light several informatic principles of organic reactions. Knowledge of these can assist in synthetic designs on both large- and small-scales. Brownian methods are able to address the pathway structures of all organic reactions: those reported in the literature, explored in the lab, or in the developmental stage.

Journal Article↗

PubMedDate not supplied

Information content in organic molecules: aggregation states and solvent effects.

The information content of organic molecules has been the subject of a series of papers from this lab. The investigation continues as aggregation states and some of their attendant solvent effects are examined. An organic molecule operates as an information source not in a vacuum but rather in conjunction with one or more solvent compounds. Accordingly, solvents (ethanol, acetone, etc.) furnish both a source and a channel that modify molecular information. In this paper, Brownian techniques are developed further so as to quantify molecular information with aggregation states taken into account. Several applications follow concerning organic acid ionization in solution, tautomerization reactions, and molecular activity at biological receptor sites. The goal is to advance Brownian processing as a means of probing molecular information and its communication. To this end, practical examples are offered relating structure and function along informatic lines.

Acetic Acid↗