Biomedical subjects

Mark Ming-Cheng Cheng

Publications and source records attributed to Mark Ming-Cheng Cheng.

7 recordsLinked to original sources

PubMed2006

Physicochemically modified silicon as a substrate for protein microarrays.

Reverse phase protein microarrays (RPMA) enable high throughput screening of posttranslational modifications of important signaling proteins within diseased cells. One limitation of protein-based molecular profiling is the lack of a PCR-like intrinsic amplification system for proteins. Enhancement of protein microarray sensitivities is an important goal, especially because many molecular targets within patient tissues are of low abundance. The ideal array substrate will have a high protein-binding affinity and low intrinsic signal. To date, nitrocellulose-coated glass has provided an effective substrate for protein binding in the microarray format when using chromogenic detection systems. As fluorescent systems, such as quantum dots, are explored as potential reporter agents, the intrinsic fluorescent properties of nitrocellulose-coated glass slides limit the ability to image microarrays for extended periods of time where increases in net sensitivity can be attained. Silicon, with low intrinsic autofluorescence, is being explored as a potential microarray surface. Native silicon has low binding potential. Through titrated reactive ion etching (RIE), varying surface areas have been created on silicon in order to enhance protein binding. Further, via chemical modification, reactive groups have been added to the surfaces for comparison of relative protein binding. Using this combinatorial method of surface roughening and surface coating, 3-aminopropyltriethoxysilane (APTES) and mercaptopropyltrimethoxysilane (MPTMS) treatments were shown to transform native silicon into a protein-binding substrate comparable to nitrocellulose.

Adsorption↗

PubMed2006

Nanotechnologies for biomolecular detection and medical diagnostics.

Nanotechnology-based platforms for the high-throughput, multiplexed detection of proteins and nucleic acids in heretofore unattainable abundance ranges promise to bring substantial advances in molecular medicine. The emerging approaches reviewed in this article, with reference to their diagnostic potential, include nanotextured surfaces for proteomics, a two-particle sandwich assay for the biological amplification of low-concentration biomolecular signals, and silicon-based nanostructures for the transduction of molecular binding into electrical and mechanical signals, respectively.

Biopolymers↗

PubMed2006

Selective binding and enrichment for low-molecular weight biomarker molecules in human plasma after exposure to nanoporous silica particles.

The present manuscript describes a biomarker capturing strategy based on nanoporous silica particles. The method is shown to enrich the yield of species in the low-molecular weight proteome (LMWP), allowing detection of small peptides in the low-nanomolar range. Plasma samples were exposed to the silica particles, and the captured molecular species were profiled using MALDI-TOF. Mass spectra of the silica-treated human plasma samples showed a significant enrichment in MALDI-TOF protein profiles in the LMWP. Preliminary results indicated good level of reproducibility in plasma profiles with CVs on peak heights ranging from 6.3 to 14.7%. The MALDI-TOF signature changed significantly when the characteristics of the nanoporous silica were altered. The facile sample pretreatment before MS analysis, coupled to the potential for tailoring the surface properties of silica supports, hold promise for improving the recovery of low-abundance serum biomarkers.

Biomarkers↗

PubMed2006

Multiscale modeling of protein transport in silicon membrane nanochannels. Part 1. Derivation of molecular parameters from computer simulations.

We report in this account our efforts in the development of a novel multiscale simulation tool for integrated nanosystem design, analysis and optimization based on a three-tiered modeling approach consisting of (i) molecular models, (ii) atomistic molecular dynamics simulations, and (iii) dynamical models of protein transport at the continuum scale. In this work we used molecular simulations for the analysis of lysozyme adsorption on a pure silicon surface. The molecular modeling procedures adopted allowed (a) to elucidate the specific mechanisms of interaction between the biopolymer and the silicon surface, and (b) to derive molecular energetic and structural parameters to be employed in the formulation of a mathematical model of diffusion through silicon-based nanochannel membranes, thus filling the existing gap between the nano--and the macroscale.

Adsorption↗

PubMed2006

Multiscale modeling of protein transport in silicon membrane nanochannels. Part 2. From molecular parameters to a predictive continuum diffusion model.

Transport and surface interactions of proteins in nanopore membranes play a key role in many processes of biomedical importance. Although the use of porous materials provides a large surface-to-volume ratio, the efficiency of the operations is often determined by transport behavior, and this is complicated by the fact that transport paths (i.e., the pores) are frequently of molecular dimensions. Under these conditions, a protein diffusion can be slower than predicted from Fick law. The main contribution of this paper is the development of a mathematical model of this phenomenon, whose parameters are computed via molecular modeling, as described Part 1. Our multiscale modeling methodology, validated by using experimental results related to the diffusion of lysozyme molecules, constitutes an "ab initio" recipe, for which no experimental data are needed to predict the protein release, and can be tailored in principle to match any different protein and any different surface, thus filling gap between the nano and the macroscale.

Computer Simulation↗

PubMed2006

Nanoporous surfaces as harvesting agents for mass spectrometric analysis of peptides in human plasma.

Silica-based nanoporous surfaces have been developed in order to capture low molecular weight peptides from human plasma. Harvested peptides were subjected to mass spectrometric analysis by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a means of detecting and assessing the bound molecules. Peptide profiles consisting of about 70 peaks in the range 800-10,000 m/z were generated. The method could allow detection of small peptides at ng/mL concentration levels, either in standard solutions or in plasma. The same molecular cutoff effect was observed for mixtures of standard proteins and peptides incubated with silicon-based nanoporous surfaces.

Blood Proteins↗

PubMedDate not supplied

Fractionation of serum components using nanoporous substrates.

Numerous previously uncharacterized molecules resident within the low molecular weight circulatory proteome may provide a picture of the ongoing pathophysiology of an organism. Recently, proteomic signatures composed of low molecular weight molecules have been identified using mass spectrometry combined with bioinformatic algorithms. Attempts to sequence and identify the molecules that underpin the fingerprints are currently underway. The finding that many of these low molecular weight molecules may exist bound to circulating carrier proteins affords a new opportunity for fractionation and separation techniques prior to mass spectrometry-based analysis. In this study we demonstrate a method whereby nanoporous substrates may be used for the facile and reproducible fractionation and selective binding of the serum-based biomarker material, including subcellular proteins found within the serum. Aminopropyl-coated nanoporous silicon, when exposed to serum, can deplete serum of proteins and yield a serum with a distinct, altered MS profile. Additionally, aminopropyl-coated, nanoporous controlled-pore glass beads are able to bind a subset of serum proteins and release them with stringent elution. The eluted proteins have distinct MS profiles, gel electrophoresis profiles, and differential peptide sequence identities, which vary based on the size of the nanopores. These material surfaces could be employed in strategies for the harvesting and preservation of labile and carrier-protein-bound molecules in the blood.

Electrophoresis, Polyacrylamide Gel↗