At a glance: cellular biology for engineers

Engineering contributions have played an important role in the rise and evolution of cellular biology. Engineering technologies have helped biologists to explore the living organisms at cellular and molecular levels, and have created new opportunities to tackle the unsolved biological problems. There is now a growing demand to further expand the role of engineering in cellular biology research. For an engineer to play an effective role in cellular biology, the first essential step is to understand the cells and their components. However, the stumbling block of this step is to comprehend the information given in the cellular biology literature because it best suits the readers with a biological background. This paper aims to overcome this bottleneck by describing the human cell components as micro-plants that form cells as micro-bio-factories. This concept can accelerate the engineers' comprehension of the subject. In this paper, first the structure and function of different cell components are described. In addition, the engineering attempts to mimic various cell components through numerical modelling or physical implementation are highlighted. Next, the interaction of different cell components that facilitate complicated chemical processes, such as energy generation and protein synthesis, are described. These complex interactions are translated into simple flow diagrams, generally used by engineers to represent multi-component processes.     

Multiscale modeling of cellular systems in biology

Here we review eight different multiscale modeling efforts dealing with cellular systems in biology. The first two models focus on collagen based tissue, one dealing with the biomechanical properties of the tissue and the other focusing on how the dermis is remodeled in scar tissue formation. The next two models deal with first avascular tumor growth and then the role of the vasculature in tumor growth. We then consider two models which use the Immersed Boundary method to model tissue properties and cell–cell adhesion. Finally we conclude with two models with treatments of the Cellular Potts Model. The first models somitogenisis in the chick and the second links the Cellular Potts Model with the Keller–Segel model.     

Single-cell electrical lysis of erythrocytes detects deficiencies in the cytoskeletal protein network

The network of erythrocyte cytoskeletal proteins significantly influences erythrocyte physical and biological properties. Here we show that the kinetics of erythrocyte lysis during exposure to an electric field is sensitively correlated with defects in the cytoskeletal network. Histograms compiled from single-cell electrical lysis data show characteristics of erythrocyte populations that are deficient in a specific cytoskeletal protein, revealing the presence of cell subpopulations.     

Controllable and flexible cellular network for virus cell-to-cell spread

Cellular networks were constructed based on PEG modification and soft lithography, in which cell numbers and spatial distributions can be controlled. A micro-injector was combined with cellular networks to fix virus induced plaque and virus spread direction, by which virus cell-to-cell spread can be distinguished from cell-free spread.     

The impact of network biology in pharmacology and toxicology

With the need to investigate alternative approaches and emerging technologies in order to increase drug efficacy and reduce adverse drug effects, network biology offers a novel way of approaching drug discovery by considering the effect of a molecule and protein's function in a global physiological environment. By studying drug action across multiple scales of complexity, from molecular to cellular and tissue level, network-based computational methods have the potential to improve our understanding of the impact of chemicals in human health. In this review we present the available large-scale databases and tools that allow integration and analysis of such information for understanding the properties of small molecules in the context of cellular networks. With the recent advances in the omics area, global integrative approaches are necessary to cope with the massive amounts of data, and biomedical researchers are urged to implement new types of analyses that can lead to new therapeutic interventions with increased safety and efficacy compared with existing medications.     

Dynamic pore network model of surface heterogeneity in brine-filled porous media for carbon sequestration

Trapping of carbon in deep underground brine-filled reservoirs is a promising approach for the reduction of atmospheric greenhouse gas emissions. However, estimation of the amount of carbon dioxide (CO(2)) that can be captured in a given reservoir and the long-term storage stability remain a challenge. One difficulty lies in the estimation of local capillary pressure effects that arise from mineral surface heterogeneity inherent in underground geological formations. As a preliminary step to address this issue, we have performed dynamic pore network modelling (PNM) simulations of two-phase immiscible flow in two-dimensional structured porous media with contact angle heterogeneity under typical reservoir conditions. We begin by characterizing the network with a single, uniform contact angle. We then present saturation patterns for networks with homogeneous and heterogeneous contact angles distributions, based on two common reservoir minerals: quartz and mica, both of which have been well-characterized experimentally for their brine-CO(2) contact angles. At lower flow rates, we found moderately higher saturations for the heterogeneous networks than for the homogeneous ones. To characterize the fingering patterns, we have introduced R as the ratio of filled throats to the total network saturation. Based on this measure, the heterogeneous networks demonstrated thicker fingering patterns than the homogeneous networks. The computed saturation patterns demonstrate the importance of considering surface heterogeneity in pore-scale modelling of deep saline aquifers.     

Recent Advances in Plasmonic Nanostructures Applied for Label-free Single-cell Analysis

Cellular heterogeneity presents a major challenge in understanding the relationship between cells of particular genotype and response in disease. In order to characterize the cell-to-cell differences during the biochemical processes, single-cell analysis is necessary. Profiting from the unique localized surface plasmon resonance (LSPR) and Mie scattering, plasmonic nanostructures have revealed stable and adjustable scattering signals, avoiding photobleaching, blinking and autofluorescence phenomenon. These characterizations are propitious to the dynamic trace and biological image of single living cells. In this review, we discuss the recent advances in plasmonic nanostructures applied for label-free detection and monitoring of target cells at single-cell level by using three different techniques, surface-enhanced Raman scattering (SERS), surface-enhanced Infrared absorption spectroscopy (SEIRAS), and dark-field microscopy. Various avenues to design plasmonic probes combining spectra and imaging for single-cell analysis are demonstrated as well. We hope this review can highlight the superiority of plasmonic nanostructures in single cellular analysis, and further motivate the development of label-free cell analysis technique to elucidate cellular diversity and heterogeneity.     

Quantitative study of cellular heterogeneity in doxorubicin uptake and its pharmacological effect on cancer cells

Cellular heterogeneity in doxorubicin (DOX) uptake and its relationship with pharmacological effect on cancer cells were quantitatively investigated for the first time. An in vitro experimental model was established by treating human leukemia K562 and breast cancer MCF‐7 cells with different schedules of DOX with or without surface P‐glycoprotein (P‐gp) inhibitor verapamil (VER). The cellular heterogeneity in DOX uptake was quantitatively examined by single‐cell analysis using capillary electrophoresis coupled with laser‐induced fluorescence detection. The corresponding cytotoxic effect was tested by cellular morphology, 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyl‐tetrazolium and flow cytometry assays. The expression of cellular membrane surface P‐gp was determined by flow cytometry. Results showed that the cellular heterogeneity exists in DOX uptake. The single‐high DOX schedule leads to lower uptake heterogeneity and higher mean drug uptake. The cellular heterogeneity in DOX uptake was found to be negatively correlated with drug cytotoxicity and surface P‐gp expression, with r = ?0.7680 to ~ ?0.9587. VER reduces the cellular variation in DOX uptake, suggesting that surface P‐gp may be one of the causes of the cellular heterogeneity in DOX uptake. This research demonstrates the importance of quantitative study of cellular heterogeneity in drug uptake and its potential application in drug schedule design, response prediction and therapy modulation. Copyright © 2014 John Wiley & Sons, Ltd.     

Comprehensive mechanism and structure-sensitivity of ethanol oxidation on platinum: new transition-state searching method for resolving the complex reaction network

Ethanol oxidation on Pt is a typical multistep and multiselectivity heterogeneous catalytic process. A comprehensive understanding of this fundamental reaction would greatly benefit design of catalysts for use in direct ethanol fuel cells and the degradation of biomass-derived oxygenates. In this work, the reaction network of ethanol oxidation on different Pt surfaces, including close-packed Pt{111}, stepped Pt{211}, and open Pt{100}, is explored thoroughly with an efficient reaction path searching method, which integrates our new transition-state searching technique with periodic density functional theory calculations. Our new technique enables the location of the transition state and saddle points for most surface reactions simply and efficiently by optimization of local minima. We show that the selectivity of ethanol oxidation on Pt depends markedly on the surface structure, which can be attributed to the structure-sensitivity of two key reaction steps: (i) the initial dehydrogenation of ethanol and (ii) the oxidation of acetyl (CH3CO). On open surface sites, ethanol prefers C-C bond cleavage via strongly adsorbed intermediates (CH2CO or CHCO), which leads to complete oxidation to CO2. However, only partial oxidizations to CH3CHO and CH3COOH occur on Pt{111}. Our mechanism points out that the open surface Pt{100} is the best facet to fully oxidize ethanol at low coverages, which sheds light on the origin of the remarkable catalytic performance of Pt tetrahexahedra nanocrystals found recently. The physical origin of the structure-selectivity is rationalized in terms of both thermodynamics and kinetics. Two fundamental quantities that dictate the selectivity of ethanol oxidation are identified: (i) the ability of surface metal atoms to bond with unsaturated C-containing fragments and (ii) the relative stability of hydroxyl at surface atop sites with respect to other sites.     

Chelating agents for human diseases related to aluminium overload

The aim of this review is to give a general view on the current status of the role of aluminium in human health and disease. The main aspects of aluminium metabolism in humans are covered, summarizing the state of knowledge on the absorption, distribution, retention and excretion of aluminium, giving particular emphasis to the main metabolic pathways of this metal ion in different organs. Then the pathological consequences of aluminium overload in man, its role in neurodegenerative diseases and the emerging implication of this metal ions in different pathologies are treated. Finally, the function of different chelators utilized in clinical practice in the therapy of aluminium depending diseases is discussed and the latest studies on aluminium chelators are presented. Some emphasis is given to the parallelism between iron and aluminium chelators, and in particular interesting correlations between structural parameters of these two trivalent metal ions are presented.     

Use of neutron-energy moderation for resolving interferences in fast-neutron activation analysis

Four elements, vanadium, chromium, manganese and iron, have been determined in nickel-base samples after measurement of the intensity of two gamma-lines; the 0.85-MeV gamma-ray emitted by (56)Mn (produced from both Mn and Fe), and the 1.44-MeV gamma-ray from (52)V (arising from V and Cr). The two elements contributing to each gamma-peak were assayed separately from data obtained by irradiating each sample twice with neutrons of different energy distributions.     

Molecular mechanisms of polypeptide aggregation in human diseases

Protein aggregation is implicated in a plethora of neurodegenerative diseases. The proteins found to aggregate in these diseases are unrelated in their native structures and amino acid sequences, but form similar insoluble fibrils with characteristic cross-beta sheet morphologies called amyloid in the aggregated state. While both the mechanism of aggregation and the structure of the aggregates are not fully understood at the molecular level, recent studies provide strong support for the idea that protein aggregation into highly stable, insoluble amyloid structures is a general property of the polypeptide chain. For proteins with a unique native state, it is known that aggregation occurs under conditions that promote native-state destabilization in vitro and in vivo. Taken together, the results of several important recent investigations suggest three broad molecular frameworks that may underlie the conversion of normally soluble peptides and proteins into insoluble amyloid fibrils: (1) edge-strand hydrogen bonding, (2) domain-swapping, and (3) self-association of amyloidogenic fragments. We argue that these underlying scenarios are not mutually exclusive and may be protein-dependent - i.e., a protein with a high content of hinge-regions may aggregate via a runaway domain-swap, whereas a protein with a high content of amyloidogenic fragments may aggregate primarily by the self-association of these fragments. These different scenarios provide frameworks to understand the molecular mechanism of polypeptide aggregation.     

Some developments in reaction and solution microcalorimetry,with particular reference to its use in biochemistry and cellular biology

The field of isothermal microcalorimetry as applied to systems of interest for aqueous solution chemistry, biochemistry and in cellular biology is briefly reviewed. Some techniques recently developed in the author's laboratory are described.     

Reaction chemistry and collisional processes in multiple devices for resolving isobaric interferences in ICP-MS

A low-level review of the fundamentals of ion-molecule interactions is presented. These interactions are used to predict the efficiencies of collisional fragmentation, energy damping and reaction for a variety of neutral gases as a function of pressure in a rf-driven collision/reaction cell. It is shown that the number of collisions increases dramatically when the ion energies are reduced to near-thermal (< 0.1 eV), because of the ion-induced dipole and ion-dipole interaction. These considerations suggest that chemical reaction can be orders of magnitude more efficient at improving the analyte signal/background ratio than can collisional fragmentation. Considerations that lead to an appropriate selection of type of gas, operating pressure, and ion energies for efficient operation of the cell for the alleviation of spectral interferences are discussed. High efficiency (large differences between reaction efficiencies of the analyte and interference ions, and concomitant suppression of secondary chemistry) might be required to optimize the chemical resolution (determination of an analyte in the presence of an isobaric interference) when using ion-molecule chemistry to suppress the interfering ion. In many instances atom transfer to the analyte, which shifts the analytical m/z by the mass of the atom transferred, provides high chemical resolution, even when the efficiency of reaction is relatively low. Examples are given of oxidation, hydroxylation, and chlorination of analyte ions (V+, Fe+, As+, Se+, Sr+, Y+, and Zr+) to improve the capability of determination of complex samples. Preliminary results are given showing O-atom abstraction by CO from CaO+ to enable the determination of Fe in high-Ca samples.     

Extension of separation range in capillary isoelectric focusing for resolving highly basic biomolecules

The non-availability of commercial carrier ampholytes in the pH range greater than 11 has contributed to difficulties in focusing and resolving highly basic proteins/peptides using capillary isoelectric focusing (cIEF). Two different approaches, involving the use of N,N,N',N'-tetramethylethylenediamine (TEMED) and ampholyte 9-11, are investigated for their effects on the extension of separation range in cIEF. The addition of TEMED into pharmalyte 3-10 not only prevents the peptides/proteins from focusing in sections of the capillary beyond the detection point, but also extends the separation range to at least isoelectric point (pI) 12. The combination of ampholyte 9-11 with pharmalyte 3-10 surprisingly provides baseline resolution between bradykinin (pI 12) and cytochrome c (pI 10.3). The sample mixture, containing bradykinin, the high-pI protein calibration kit (pI 5.2-10.3), and cytochrome c digest, is employed to demonstrate the cIEF separation of proteins and peptides over a wide pH range of 3.7-12.