Abstract
We have modeled and experimentally verified a microdroplet-based cell encapsulation process for various combinations of cell loading and target cell concentrations. Here, we explain theoretically and validate experimentally a model to isolate and pattern single target cells from heterogeneous mixtur...
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PMID: 21814548
PDF is available here.
Abstract
We synthesized a water-insoluble phospholipid polymer bearing a phenylboronic acid moiety (PMBV), which induces cell adhesion through a specific interaction with the glycoprotein, fibronectin. Surface plasmon resonance analysis revealed that fibronectin was adsorbed on the PMBV surface. When fibrobl...
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PMID: 20876952
PDF is available here.
Abstract
We show, by developing mathematical tools that merge control and information theory with physical chemistry, that seemingly mild constraints on these rates place severe limits on the ability to suppress molecular fluctuations. Specifically, the minimum standard deviation in abundances decreases with...
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PMID: 20829788
PDF is available here.
Abstract
We summarize how supercoiling is generated and review experimental and theoretical insights into supercoil relaxation. We distinguish between the passive dissipation of supercoils by diffusion and the active removal of supercoils by topoisomerase enzymes. We also review single-molecule studies that...
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PMID: 20723754
PDF is available here.
Abstract
We discuss how the active or passive induction of lipid-protein domain formation in membranes can alter membrane mechanics and thus affect processes such as the generation of curvature, the scission of buds and tubules, and lipid sorting.
Copyright 2010 Elsevier Inc. All rights rese...
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PMID: 20723749
PDF is available here.
Abstract
We discuss the sensitivity of the system with regard to the impedance sensor and describe the optical setup. The relevant parameters related to the experimental setup and sample preparation are discussed. The use of dielectrophoretic forces for particle manipulation is presented as a simple enabling...
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PMID: 19763464
PDF is available here.
Abstract
In mammalian cells, newly synthesized mRNAs undergo a pioneer round of translation that is important for mRNA quality control. Following maturation of messenger ribonucleoprotein particles during and after the pioneer round, steady-state cycles of mRNA translation generate most of th...
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PMID: 20691898
PDF is available here.
Abstract
The classical approach to the modeling of reality is founded upon its objectification. Although successful dealing with inanimate matter, objectification has proven to be much less successful elsewhere, sometimes to the point of paradox. This paper discusses an approach to the modeling of reality ba...
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PMID: 20587299
PDF is available here.
Abstract
Populations of cells are almost always heterogeneous in function and fate. To understand the plasticity of cells, it is vital to measure quantitatively and dynamically the molecular processes that underlie cell-fate decisions in single cells. Early events in cell signalling often occur within second...
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PMID: 20535203
PDF is available here.
Abstract
Present-day cellular systems biology is producing data on an unprecedented scale. This field has generated a renewed interest in the holistic, "system" character of cell structure-and-function. Underlying the data deluge, however, there is a clear and present need for a historical foundation. The or...
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PMID: 20200206
PDF is available here.
Abstract
We developed a continuous assay for the determination of TF procoagulant activity (PCA) in a cell-based system. We have shown the use of this assay at detecting agents that de-encrypt TF thereby leading to an increase in TF PCA in three cancer cell lines, namely, T24/83 bladder carcinoma cells and P...
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PMID: 20212456
PDF is available here.
Abstract
We applied gas chromatography-mass spectrometry metabolomics to analyze baby hamster kidney (BHK) cells of various cell ages cultivated in high-cell density perfusion reactors at both laboratory and manufacturing scales. Cell growth, metabolic activity and protein productivity measurements, which ar...
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PMID: 19914390
PDF is available here.
Abstract
I discuss how mathematical modeling relates quantitative measures of actin dynamics to the rates of underlying molecular level processes. The dynamic properties addressed include the rate of actin assembly at the leading edge of a moving cell, the disassembly rates of intracellular actin networks, t...
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PMID: 20462375
PDF is available here.
Abstract
We consider how NAD(+) metabolism plays important roles in the random patterns of aging, and also in the more programmatic aspects. The derivatives of NAD(+), such as reduced and oxidized forms of NAD(P)(+), play important roles in maintaining and regulating cellular redox state, Ca(2+) stores, DNA...
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PMID: 20307564
PDF is available here.
Abstract
We have shown that PLDs (phospholipases D) and their product, PA (phosphatidic acid), belong to the regulators of the secretory pathway in plants. We have also shown that specific NOXs (NADPH oxidases) producing ROS (reactive oxygen species) are involved in cell growth as exemplified by pollen tubes...
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PMID: 20298250
PDF is available here.
Abstract
The ability of a eukaryotic cell to resist deformation, to transport intracellular cargo and to change shape during movement depends on the cytoskeleton, an interconnected network of filamentous polymers and regulatory proteins. Recent work has demonstrated that both internal and external physical f...
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PMID: 20110992
PDF is available here.
Abstract
We have developed several techniques to achieve this goal with reasonable efforts. (1) Site-specific integration [molecular cut and paste mechanism (MCaP)] allows the generation of cell lines stably expressing the gene of interest within 4 weeks. In addition, these cell lines are characterised by a...
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PMID: 19763851
PDF is available here.
Abstract
We introduce here the concept of a 'lab-in-a-cell': the use of a single cell as a minimal and highly confined experimental unit, or experimentation in the simple, but still unequalled, platform provided by nature itself. LOC provides the appropriate format and set of tools for LIC experimentation, a...
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PMID: 19914725
PDF is available here.
Abstract
We give an overview and practical guide on how to acquire and analyze time-lapse sequences of dynamic microtubules in live cells by either fluorescently labeling entire microtubules or by utilizing proteins that specifically associate only with growing microtubule ends and summarize the strengths an...
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PMID: 20719263
PDF is available here.
Abstract
We describe methods to analyze the dynamic instability of microtubules in living cells by microscopy of microinjected or expressed fluorescent tubulin, time-lapse microscopy, and analysis of time-dependent microtubule length changes.
2010 Elsevier Inc. All rights reserved....
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PMID: 20719262
PDF is available here.
Abstract
We describe suitable specimen preparations, treatments with microtubule-depolymerizing drugs, and applicable settings on wide-field and confocal microscopy systems for four-dimensional time-lapse and fluorescence recovery after photobleaching analyses of microtubule dynamics.
2010 Elsevier Inc. All...
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PMID: 20719279
PDF is available here.
Abstract
We integrate this energetic concept inside the CPM. We simulate a cell differentiation inside a growing cell tissue. The results are the emergence of dynamic patterns coming from the consumption and production of energy. A model described by CA is less scalable than one described by a multi-agent sy...
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PMID: 20865555
PDF is available here.
Abstract
A simple setup is demonstrated for remote temperature monitoring of water, water-based media, and cells on a microscopic scale. The technique relies on recording changes in the shape of a stretching band of the hydroxyl group in liquid water at 3,100-3,700 cm(-1). Rather than direct measurements in...
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PMID: 20176524
PDF is available here.
Abstract
We review the models available in the literature, illustrating how the different assumptions impact upon both their accuracy and computational expense.The primary intentions are to provide a critical scientific review and a practical guide for researchers wishing to use such models in clinical appli...
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PMID: 21175401
PDF is available here.
Abstract
Models for electric field interactions with biological cells predict that pulses with durations shorter than the charging time of the outer membrane can affect intracellular structures. Experimental studies in which human cells were exposed to pulsed electric fields of up to 300 kV/cm amplitude, wit...
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PMID: 21133836
PDF is available here.
Abstract
We demonstrate a single-beam, high-throughput method where optical forces are applied anisotropically to stretch swollen erythrocytes in microfluidic flow. We also present numerical simulations of model spherical elastic cells subjected to optical forces and show that dual, opposing optical traps ar...
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PMID: 20799841
PDF is available here.
Abstract
Recently, understanding of many molecular interactions has progressed appreciably and cellular events once thought to be by-products of more important reactions or to be detrimental to cellular function are now known to be part of complex interactions of the cell with its environment. Numerous prote...
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PMID: 20515743
PDF is available here.
Abstract
This article reviews one of the most important post-translational protein modifiers--ubiquitin. The basic mechanisms of conjugation reactions of ubiquitin with substrate, factors influencing the ubiquitination and its role in regulation of different cellular processes have been considered.
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PMID: 21805857
PDF is available here.
Abstract
Atomic force microscope (AFM) has been used incrementally over the last decade in cell biology. Beyond its usefulness in high resolution imaging, AFM also has unique capabilities for probing the viscoelastic properties of living cells in culture and, even more, mapping the spatial distribution of ce...
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PMID: 20463929
PDF is available here.
Abstract
We know. The cell needs operational freedom and, thus, many motif-domain interactions might not be "hard-wired" through evolution, but instead may be like the Linux operating system, where symbolic links can point to files without duplication....
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PMID: 20571125
PDF is available here.
Abstract
Recent progress in bottom-up tissue engineering has demonstrated that three-dimensional tissue constructs with predefined architectures may be obtained by assembling shape-controlled hydrogels in multiphase reactor systems. Driven by the hydrophobic force between gel unit and liquid media, highly or...
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PMID: 20365184
PDF is available here.
Abstract
This paper reviews physical, experimental and epidemiological evidence for and against radiation hormesis and discusses implications with regards to radiation protection. The scientific community is still divided on the premise of radiation hormesis, with new literature published on a regular basis....
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PMID: 20169836
PDF is available here.
Abstract
The National Academy of Engineering selected 'Imaging' as one of the greatest engineering achievements of the 20th century (Greatest Engineering Achievements of the 20th Century. 2009 (cited 2008, November 10); available from: http://www.greatachievements.org/). The combination of different imaging...
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PMID: 20083856
PDF is available here.
Abstract
We study the morphogenetic field evolution yielding from an initial population of undifferentiated cells to diversified unicellular organisms as well as specialized eukaryotic cell types. The cells are represented as Julia sets and Pickover biomorphs, simulating the effect of Darwinian natural selec...
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PMID: 19596047
PDF is available here.
Abstract
Dielectrophoresis (DEP) is a technique which offers label-free measurement of cell electrophysiology by monitoring its movement in non-uniform electric fields. In this chapter, the theory underlying DEP is explored, as are the implications of the development of equipment for taking such measurements...
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PMID: 19763465
PDF is available here.
Abstract
We focus on the role of the Nm23-H1-h-Prune complex in cellular physiology, through an analysis of the balance between the 'bound' and 'non-bound' states of Nm23-H1 and h-Prune, whereby we speculate on the 'read-out' during cell homeostasis under non-balanced conditions. We have analysed the biochem...
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PMID: 19390954
PDF is available here.
Abstract
We developed multiscale fluorescence recovery after photobleaching (MS-FRAP) to address this deficiency. Diffusion measurements facilitated by MS-FRAP distinguish the diffusive hindrance of the interstitial versus cellular constituents in living tissue. Using multiscale diffusion measurements in viv...
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PMID: 19580771
PDF is available here.
Abstract
We discuss the idea that mitochondria provide the pool of PE necessary for the autophagosome biogenesis and we propose some possible experimental approaches aimed to explore this possibility....
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PMID: 19398041
PDF is available here.
Abstract
Self-consistent evaluations of the transmembrane potential (TMP) and possible membrane electroporation in spheroidal cells arising from an ultrashort, high-intensity pulse are reported. The present study couples the Laplace equation with Smoluchowski theory of pore formation, and uses double-shell m...
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PMID: 19258194
PDF is available here.
Abstract
Advances in biomarker discovery, synthetic biology and next-generation genomics promise to make designer cells a reality in the near future. Such cells can be engineered to report on diverse aspects of their physiology, potentially opening up new avenues of biological inquiry and enhancing our under...
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PMID: 19480631
PDF is available here.
Nathaniel D Heintzman,
Gary C Hon,
R David Hawkins,
Pouya Kheradpour,
Alexander Stark,
Lindsey F Harp,
Zhen Ye,
Leonard K Lee,
Rhona K Stuart,
Christina W Ching,
Keith A Ching,
Jessica E Antosiewicz-Bourget,
Hui Liu,
Xinmin Zhang,
Roland D Green,
Victor V Lobanenkov,
Ron Stewart,
James A Thomson,
Gregory E Crawford,
Manolis Kellis and
Bing Ren
Abstract
We have previously developed a chromatin-immunoprecipitation-based microarray method (ChIP-chip) to locate promoters, enhancers and insulators in the human genome. Here we use the same approach to identify these elements in multiple cell types and investigate their roles in cell-type-specific gene e...
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PMID: 19295514
PDF is available here.
Abstract
Galactic cosmic radiation is acknowledged as one of the major barriers to human space exploration. In space, astronauts are exposed to charged particles from Z = 1 (H) up to Z = 28 (Ni), but the probability of a hit to a specific single cell in the human body is low. Particle microbeams can deliver...
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PMID: 19346685
PDF is available here.
Abstract
We focus on selected protein trafficking events by which kidney epithelial cells regulate body fluid, ion and acid-base homeostasis in response to changes in physiological conditions. We discuss aquaporin 2 and G-protein-coupled receptors in fluid and ion balance, the vacuolar H(+)-adenosine triphos...
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PMID: 19170982
PDF is available here.
Abstract
A critical aspect in the development of biomaterials is the optimization of their surface properties to achieve an adequate cell response. In the present work, electrospun polycaprolactone nanofiber meshes (NFMs) are treated by radio-frequency (RF) plasma using different gases (Ar or...
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PMID: 19242938
PDF is available here.