Multi-scale cellular engineering: From molecules to organ-on-a-chip.

Recent technological advances in cellular and molecular engineering have provided new insights into biology and enabled the design, manufacturing, and manipulation of complex living systems. Here, we summarize the state of advances at the molecular, cellular, and multi-cellular levels using experimental and computational tools. The areas of focus include intrinsically disordered proteins, synthetic proteins, spatiotemporally dynamic extracellular matrices, organ-on-a-chip approaches, and computational modeling, which all have tremendous potential for advancing fundamental and translational science. Perspectives on the current limitations and future directions are also described, with the goal of stimulating interest to overcome these hurdles using multi-disciplinary approaches

The transcriptional regulation of maspin : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Biochemistry at Massey University, Palmerston North, New Zealand

Maspin (mammary serine protease inhibitor) is a tumour suppressing member of the serpin superfamily. Maspin is expressed in normal breast and prostate cells, but reportedly down regulated during progression of cancer in these tissues. Maspin has been shown to inhibit cellular migration and invasion in vitro; while in vivo, maspin has been shown to inhibit tumour growth, metastasis, and angiogenesis. Maspin also plays a role in the sensitisation of cells to induced apoptosis. These functions of maspin are independent of serine protease inhibition; however the cellular mobility function is dependent on an intact reactive site loop. Despite this knowledge, the molecular mechanisms for all reported functions of maspin are currently unknown. Maspin is reported to be transcriptionally regulated: to date Ets, Ap1, and p53 transcription factors have been shown to activate transcription of maspin by binding directly to the promoter. Androgen is reported to be a negative regulator through the binding of the androgen receptor to a hormone response element within the promoter. This hormone response element is also responsible for an increase in maspin expression in response to tamoxifen, an anti-oestrogen drug. Transcriptional regulation of maspin has also been reported to be activated by other molecules, including gamma linolenic acid, manganese containing super-oxide dismutase, and nitric oxide, the mechanisms of regulation by these molecules is unknown. Loss of maspin expression in cancerous cells lines has been attributed to loss of one or more of the activating factors, and aberrant methylation of cytosine residues resulting in chromatin compaction. This study investigated the transcriptional regulation of maspin, with the aim of identifying transcriptional effectors important to the regulation of the gene. Identification of such factors may help identify a pathway in which maspin exerts its tumour suppressor functions. To this end, the maspin promoter was cloned and functional assays carried out. identifying several putative regions of the maspin promoter which may be important for the regulation of the gene. To date, the precise activator/repressor binding sites and the cognate proteins responsible for this regulation are unidentified

Genomic Analysis of Stress Response Against Arsenic in \u3cem\u3eCaenorhabditis elegans\u3c/em\u3e

Arsenic, a known human carcinogen, is widely distributed around the world and found in particularly high concentrations in certain regions including Southwestern US, Eastern Europe, India, China, Taiwan and Mexico. Chronic arsenic poisoning affects millions of people worldwide and is associated with increased risk of many diseases including arthrosclerosis, diabetes and cancer. In this study, we explored genome level global responses to high and low levels of arsenic exposure in Caenorhabditis elegans using Affymetrix expression microarrays. This experimental design allows us to do microarray analysis of dose-response relationships of global gene expression patterns. High dose (0.03%) exposure caused stronger global gene expression changes in comparison with low dose (0.003%) exposure, suggesting a positive dose-response correlation. Biological processes such as oxidative stress, and iron metabolism, which were previously reported to be involved in arsenic toxicity studies using cultured cells, experimental animals, and humans, were found to be affected in C. elegans. We performed genome-wide gene expression comparisons between our microarray data and publicly available C. elegans microarray datasets of cadmium, and sediment exposure samples of German rivers Rhine and Elbe. Bioinformatics analysis of arsenic-responsive regulatory networks were done using FastMEDUSA program. FastMEDUSA analysis identified cancer-related genes, particularly genes associated with leukemia, such as dnj-11, which encodes a protein orthologous to the mammalian ZRF1/MIDA1/MPP11/DNAJC2 family of ribosome-associated molecular chaperones. We analyzed the protective functions of several of the identified genes using RNAi. Our study indicates that C. elegans could be a substitute model to study the mechanism of metal toxicity using high-throughput expression data and bioinformatics tools such as FastMEDUSA

Shift-Symmetric Configurations in Two-Dimensional Cellular Automata: Irreversibility, Insolvability, and Enumeration

The search for symmetry as an unusual yet profoundly appealing phenomenon, and the origin of regular, repeating configuration patterns have long been a central focus of complexity science and physics. To better grasp and understand symmetry of configurations in decentralized toroidal architectures, we employ group-theoretic methods, which allow us to identify and enumerate these inputs, and argue about irreversible system behaviors with undesired effects on many computational problems. The concept of so-called configuration shift-symmetry is applied to two-dimensional cellular automata as an ideal model of computation. Regardless of the transition function, the results show the universal insolvability of crucial distributed tasks, such as leader election, pattern recognition, hashing, and encryption. By using compact enumeration formulas and bounding the number of shift-symmetric configurations for a given lattice size, we efficiently calculate the probability of a configuration being shift-symmetric for a uniform or density-uniform distribution. Further, we devise an algorithm detecting the presence of shift-symmetry in a configuration. Given the resource constraints, the enumeration and probability formulas can directly help to lower the minimal expected error and provide recommendations for system's size and initialization. Besides cellular automata, the shift-symmetry analysis can be used to study the non-linear behavior in various synchronous rule-based systems that include inference engines, Boolean networks, neural networks, and systolic arrays.Comment: 22 pages, 9 figures, 2 appendice

A Self-Organization Framework for Wireless Ad Hoc Networks as Small Worlds

Motivated by the benefits of small world networks, we propose a self-organization framework for wireless ad hoc networks. We investigate the use of directional beamforming for creating long-range short cuts between nodes. Using simulation results for randomized beamforming as a guideline, we identify crucial design issues for algorithm design. Our results show that, while significant path length reduction is achievable, this is accompanied by the problem of asymmetric paths between nodes. Subsequently, we propose a distributed algorithm for small world creation that achieves path length reduction while maintaining connectivity. We define a new centrality measure that estimates the structural importance of nodes based on traffic flow in the network, which is used to identify the optimum nodes for beamforming. We show, using simulations, that this leads to significant reduction in path length while maintaining connectivity.Comment: Submitted to IEEE Transactions on Vehicular Technolog

Complex Network Structure of Flocks in the Standard Vicsek Model

In flocking models, the collective motion of self-driven individuals leads to the formation of complex spatiotemporal patterns. The Standard Vicsek Model (SVM) considers individuals that tend to adopt the direction of movement of their neighbors under the influence of noise. By performing an extensive complex network characterization of the structure of SVM flocks, we show that flocks are highly clustered, assortative, and non-hierarchical networks with short-tailed degree distributions. Moreover, we also find that the SVM dynamics leads to the formation of complex structures with an effective dimension higher than that of the space where the actual displacements take place. Furthermore, we show that these structures are capable of sustaining mean-field-like orientationally ordered states when the displacements are suppressed, thus suggesting a linkage between the onset of order and the enhanced dimensionality of SVM flocks.Comment: 26 pages, 11 figures. To appear in J. Stat. Phy

Purification and functional characterisation of rhiminopeptidase A, a novel aminopeptidase from the venom of Bitis gabonica rhinoceros

This study describes the discovery and characterisation of a novel aminopeptidase A from the venom of B. g. rhinoceros and highlights its potential biological importance. Similar to mammalian aminopeptidases, rhiminopeptidase A might be capable of playing roles in altering the blood pressure and brain function of victims. Furthermore, it could have additional effects on the biological functions of other host proteins by cleaving their N-terminal amino acids. This study points towards the importance of complete analysis of individual components of snake venom in order to develop effective therapies for snake bites