Archive for the ‘Research Papers’ Category

Tim Newman’s Publications

Monday, April 12th, 2010

Correlating Cell Behavior with Tissue Topology in Embryonic Epithelia. PLoS One. April 2011
Correlating cell behavior with tissue topology in embryonic epithelia

Modeling Cell Rheology with the Subcellular Element Model
Modeling cell rheology with the Subcellular Element Model

Recently, the Subcellular Element Model (SEM) has been introduced, primarily to compute the dynamics of large numbers of three-dimensional deformable cells in multicellular systems. Within this model framework, each cell is represented by a collection of elastically coupled elements, interacting with one another via short-range potentials, and dynamically updated using over-damped Langevin dynamics. The SEM can also be used to represent a single cell in more detail, by using a larger number of subcellular elements exclusively identified with that cell. We have tested whether, in this context, the SEM yields viscoelastic properties consistent with those measured on single living cells. Employing virtual methods of bulk rheology and microrheology we find that the SEM successfully captures many cellular rheological properties at intermediate time scales and moderate strains, including weak power law rheology. In its simplest guise, the SEM cannot describe long-time/large-strain cell responses. Capturing these cellular properties requires extensions of the SEM which incorporate active cytoskeletal rearrangement. Such extensions will be the subject of a future publication.

Modeling cell rheology with the Subcellular Element Model (pdf)

Modeling Multicellular Systems using Sub-Cellular Elements (pdf)

Monday, April 12th, 2010

Author: T. J. Newman

We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and intercellular potentials. Advantages of the model include: i) adaptive cell-shape dynamics, ii) flexible accommodation of additional intracellular biology, and iii) the absence of an underlying grid. We present here a detailed description of the model, and use successive mean-¯eld approximations to connect it to more coarse-grained approaches, such as discrete cell-based algorithms and coupled partial differential equations. We also discuss efficient algorithms for encoding the model, and give an example of a simulation of an epithelial sheet. Given the biological flexibility of the model, we propose that it can be used effectively for modeling a range of multicellular processes, such as tumor dynamics and embryogenesis.

Modeling Multicellular systems using sub-cellular elements (pdf)

Automated Selection and Placement of Single Cells Using Vision-Based Feedback Control (pdf)

Tuesday, April 6th, 2010

Automated Selection and Placement of Single Cells Using Vision-Based Feedback Control

We present a robotic manipulation system for automated selection and transfer of individual living cells to analysis locations. We begin with a commonly used cell transfer technique using glass capillary micropipettes to aspirate and release living cells suspended in liquid growth media. Using vision-based feedback and closed-loop process control, two individual three-axis robotic stages position the micropipette tip in proximity to the cell of interest. The cell is aspirated and the tip is moved to a target location where the cell is dispensed. Computer vision is used to monitor and inspect the success of the dispensing process. In our initial application, the target cell destination is a microwell etched in a fused silica substrate. The system offers a robust and flexible technology for cell selection and manipulation. Applications for this technology include embryonic stem cells transfer, blastomere biopsy, cell patterning, and cell surgery.

Characterization of deep wet etching of fused silica glass for single cell and optical sensor deposition (pdf)

Tuesday, April 6th, 2010

Characterization of deep wet etching of fused silica glass for single cell and optical sensor deposition

The development of a high-throughput single-cell metabolic rate monitoring system relies onthe use of transparent substrate material for a single cell-trapping platform. The high opticaltransparency, high chemical resistance, improved surface quality and compatibility with thesilicon micromachining process of fused silica make it very attractive and desirable for thisapplication. In this paper, we report the results from the development and characterization of ahydrofluoric acid (HF) based deep wet-etch process on fused silica. The pin holes andnotching defects of various single-coated masking layers during the etching are characterizedand the most suitable masking materials are identified for different etch depths. Thedependence of the average etch rate and surface roughness on the etch depth, impurityconcentration and HF composition are also examined. The resulting undercut from the deepHF etch using various masking materials is also investigated. The developed and characterizedprocess techniques have been successfully implemented in the fabrication of micro-well arraysfor single cell trapping and sensor deposition. Up to 60 μm deep micro-wells have beenetched in a fused silica substrate with over 90{236bd5e292587b885399ce1fe93b84c86ca4f34851d3c4bf06f3f0da35a3ccbb} process yield and repeatability. To ourknowledge, such etch depth has never been achieved in a fused silica substrate by using anon-diluted HF etchant and a single-coated masking layer at room temperature.

A New Approach for Measuring Single-Cell Oxygen Consumption Rates (pdf)

Tuesday, April 6th, 2010

A New Approach for Measuring Single-Cell Oxygen Consumption Rates

A novel system that has enabled the measurement of single-cell oxygen consumption rates is presented. The experimental apparatus includes a temperature controlled environmental chamber, an array of microwells etched in glass, and a lid actuator used to seal cells in the microwells. Each microwell contains an oxygen sensitive platinum phosphor sensor used to monitor the cellular metabolic rates. Custom automation software controls the digital image data collection for oxygen sensor measurements, which are analyzed using an image-processing program to yield the oxygen concentration within each microwell versus time. Two proof-of-concept experiments produced oxygen consumption rate measurements for A549 human epithelial lung cancer cells of 5.39 and 5.27 fmol/min/cell, closely matching published oxygen consumption rates for bulk A549 populations.

Life-on-a-chip (pdf)

Tuesday, April 6th, 2010


Mechanistic studies of cellular processes are usually carried out with large populations of cells. However, parameters that are measured as averages of large populations can be misleading. For instance, an apparently linear response to a signal could, in fact, reflect an increasing number of cells in the population that have switched from ‘off’ to ‘on’, rather than a graded increase in response by all the cells. At present, the study of single cells is challenging, but new technologies mean it might soon be a reality.

Poster: The work of the Robert Ros team

Saturday, April 3rd, 2010

Rory Annual Meeting Poster (54×40) (png)

Rory Annual Meeting Poster (54×40) (pdf)

Poster: “Single Cell Tomography for Early Cancer Detection” Vivek Nandakumar, Laimonas Kelbauskas, Roger Johnson, Deirdre Meldrum

Wednesday, March 17th, 2010

Vivek Nandakumar, a graduate student working withDeirdre Meldrum, presented a poster of his work to the Arizona Microscopy and Microanalysis Society  (AIMS) annual meeting in March 2010.

viveknandakumar aims2010 PSOC (jpg)

Poster(Powerpoint): Single Cell Tomography for Early Cancer Detection

Poster (JPG):  Single Cell Tomography for Early Cancer Detection

Self-Assembled Water-Soluble Nucleic Acid Probe Tiles for Label-Free RNA Hybridization Assays (pdf)

Saturday, February 27th, 2010

Self-Assembled Water-Soluble Nucleic Acid Probe Tiles for Label-Free RNA Hybridization Assays

The DNA origami method, in which long, single-stranded DNA segments are folded into shapes by short staple segments, was used to create nucleic acid probe tiles that are molecular analogs of macroscopic DNA chips. One hundred trillion probe tiles were fabricated in one step and bear pairs of 20-nucleotide-long single-stranded DNA segments that act as probe sequences. These tiles can hybridize to their targets in solution and, after adsorption onto mica surfaces, can be examined by atomic force microscopy in order to quantify binding events, because the probe segments greatly increase in stiffness upon hybridization. The nucleic acid probe tiles have been used to study position-dependent hybridization on the nanoscale and have also been used for label-free detection of RNA.

The potential and challenges of nanopore sequencing (pdf)

Saturday, February 27th, 2010

The potential and challenges of nanopore sequencing


A nanopore-based device provides single-molecule detection and analytical capabilities that are achieved by electrophoretically driving molecules in solution through a nano-scale pore. The nanopore provides a highly confined space within which single nucleic acid polymers can be analyzed at high throughput by one of a variety of means, and the perfect processivity that can be enforced in a narrow pore ensures that the native order of the nucleobases in a polynucleotide is reflected in the sequence of signals that is detected. Kilobase length polymers (single-stranded genomic DNA or RNA) or small molecules (e.g., nucleosides) can be identified and characterized without amplification or labeling, a unique analytical capability that makes inexpensive, rapid DNA sequencing a possibility. Further research and development to overcome current challenges to nanopore identification of each successive nucleotide in a DNA strand offers the prospect of ‘third generation’ instruments that will sequence a diploid mammalian genome for ~$1,000 in ~24 h.