Live-cell System Research Articles

Identification of Potent and Selective CYP1A1 Inhibitors via Combined Ligand and Structure-Based Virtual Screening and Their in Vitro Validation in Sacchrosomes and Live Human Cells.

Target structure-guided virtual screening (VS) is a versatile, powerful, and inexpensive alternative to experimental high-throughput screening (HTS). To discover potent CYP1A1 enzyme inhibitors for cancer chemoprevention, a commercial library of 50 000 small molecules was utilized for VS guided by both ligand and structure-based strategies. For experimental validation, 300 ligands were proposed based on combined analysis of fitness scores from ligand based e-pharmacophore screening and docking score, prime MMGB/SA binding affinity and interaction pattern analysis from structure-based VS. These 300 compounds were screened, at 10 μM concentration, for in vitro inhibition of CYP1A1-Sacchrosomes (yeast-derived microsomal enzyme) in the ethoxyresorufin-O-de-ethylase assay. Thirty-two compounds displayed >50% inhibition of CYP1A1 enzyme activity at 10 μM. 2-Phenylimidazo-[1,2-a]quinoline (5121780, 119) was found to be the most potent with 97% inhibition. It also inhibited ∼95% activity of CYP1B1 and CYP1A2, the other two CYP1 enzymes. The compound 5121780 (119) showed high selectivity toward inhibition of CYP1 enzymes with respect to CYP2 and CYP3 enzymes (i.e., there was no detectable inhibition of CYP2D6/CYP2C9/CYP2C19 and CYP3A4 at 10 μM). It was further investigated in live CYP-expressing human cell system, which confirmed that compound 5121780 (119) potently inhibited CYP1A1, CYP1A2, CYP1B1 enzymes with IC50 values of 269, 30, and 56 nM, respectively. Like in Sacchrosomes, inhibition of CYP2D6/CYP2C9/CYP2C19 and CYP3A4 enzymes, expressed within live human cells, could hardly be detected at 10 μM. The compound 119 rescued CYP1A1 overexpressing HEK293 cells from CYP1A1 mediated benzo[a]pyrene (B[a]P) toxicity and also overcame cisplatin resistance in CYP1B1 overexpressing HEK293 cells. Molecular dynamics simulations of 5121780 (119) with CYP1 enzymes was performed to understand the interaction pattern to CYP isoforms. Results indicate that VS can successfully be used to identify promising CYP1A1 inhibitors, which may have potential in the development of novel cancer chemo-preventive agents.

Selective fluorescence sensing and quantification of uric acid by naphthyridine-based receptor in biological sample

Naphthyridine-based fluorescent probe H1 was synthesized and characterized for the quantification and selective detection of Uric Acid (UA) in live cell. In presence of UA, H1 forms the specific host-guest complex mainly through intermolecular hydrogen bonding and aromatic stacking which produces “turn-off” fluorescence. The probe and UA is found to be 1:1 stoichiometry on the basis of absorption and fluorescence titrations. The probe H1 has been shown to detect UA up to 0.6µM at pH 7.4. DFT-TDDFT calculations were performed in order to demonstrate the sensing mechanism and the electronic properties of the receptor-donor complex. The selectivity was evaluated in Vero cells in the presence of UA with other purine derivatives, structurally similar to UA. It was found to exhibit no cytotoxicity effect in tested concentration of H1 and good membrane permeability for the detection of UA in living cell system. The unknown concentration of UA in serum and urine can be measured easily using the fluorescence property of probe H1.

Organic Cyanide Decorated SERS Active Nanopipettes for Quantitative Detection of Hemeproteins and Fe3+ in Single Cells.

It is challenging to develop a robust nanoprobe for real-time operational and accurate detection of heavy metals in single cells. Fe-CN coordination chemistry has been well studied to determine the structural characteristics of hemeproteins by different techniques. However, the frequently used cyanide ligands are inorganic molecules that release cyanide anion under particular conditions and cause cyanide poisoning. In the present study, organic cyanide (4-mercaptobenzonitrile, MBN) was utilized for the first time in developing a facile nanoprobe based on surface-enhanced Raman scattering (SERS) for quantitative detection of hemeproteins (oxy-Hb) and trivalent iron (Fe3+) ions. The nanoprobe prepared by coating the glass capillary tip (100 nm) with a thin gold film, which enables highly localized study in living cell system. The cyanide stretching vibration in MBN was highly sensitive and selective to Fe3+ and oxy-Hb with excellent binding affinity (Kd 0.4 pM and 0.1 nM, respectively). The high sensitivity of the nanoprobe to analyte (Fe3+) was attributed to the two adsorption conformations (-SH and -CN) of MBN to the gold surface. Therefore, MBN showed an exceptional dual-peak (2126 and 2225 cm-1) behavior. Furthermore, the special Raman peaks of cyanide in 2100-2300 cm-1 (silent region of SERS spectra) are distinguishable from other biomolecules characteristic peaks. The selective detection of Fe3+ in both free and protein-bound states in aqueous solution is achieved with 0.1 pM and 0.08 μM levels of detection limits, respectively. Furthermore, practical applicability of fabricated nanoprobe was validated by detection of free Fe3+ in pretreated living HeLa cells by direct insertion of a SERS active nanoprobe. Regarding the appropriate precision, good reproducibility (relative standard deviation, RSD 7.2-7.6%), and recyclability (retain good Raman intensity even after three renewing cycles) of the method, the developed sensing strategy on a nanopipette has potential benefits for label-free, qualitative and quantitative recognition of heavy metal ions within nanoliter volumes.

A Simple Adaptable Blood-Brain Barrier Cell Model for Screening Matrix Metalloproteinase Inhibitor Functionality.

The blood-brain barrier is a multicellular and basement membrane unit that regulates molecular transport between the blood and central nervous system. Many cerebral pathologies, such as acute stroke and chronic vascular dementia, result in a disrupted blood-brain barrier, increasing its permeability and allowing the entry of potentially neurotoxic molecules. The activation of matrix metalloproteinases mediates further blood-brain barrier damage. The inhibition of matrix metalloproteinases is a potential strategy for stroke therapy. As inhibitors are developed, efficient context-specific screening methods will be required. Models of the blood-brain barrier have been extensively used to study neuropathologies and the effect of various treatment options.Herein, we describe a co-culture model of the blood-brain barrier composed of brain microvascular endothelial cells and astrocytes grown on an artificial basement membrane-coated membrane insert. Our cell model forms a barrier and is a simple first approximation of blood-brain barrier integrity. As currently developed, the model may be applied to testing the effect of matrix metalloproteinases and matrix metalloproteinase inhibitors on blood-brain barrier physiology and pathophysiology. The model is a quick and effective evaluation tool for generating nonclinical data in a living cell system before proceeding to animal models.

Eco-friendly synthesis of nitrogen-doped carbon nanodots from wool for multicolor cell imaging, patterning, and biosensing

We report an eco-friendly strategy for fabrication of nitrogen-doped carbon nanodots (N-CDs) and demonstrate their applications for multicolor cell imaging, patterning, and biosensing. N-CDs have been synthesized using wool as raw material via pyrolysis and microwave treatment, providing a green way for the production of N-CDs without the use of toxic/expensive solvents and starting materials. The prepared N-CDs exhibit exceptional advantages including high fluorescent quantum yield (22.5%), excellent biocompatibility, low toxicity, and satisfactory chemical stability. Depending on these superior properties, the N-CDs have been applied in multicolor bioimaging, patterning, and biosensing. Imaging of living cells has been observed with high resolution using N-CDs as a probe, which validates their use in imaging applications and their multicolor property in the living cell system. Additionally, the obtained N-CDs have been used as fluorescent inks for drawing luminescent patterns, showing favorable application in anti-counterfeit and optoelectronic dimensions. Most strikingly, the as-prepared N-CDs could visualize Fe3+ fluctuations in living cells with negligible autofluorescence based on their high sensitivity and selectivity detection for Fe3+ ions with a linear range of 0.1–10μM and a detection limit of 10nM.

Anaphase asymmetry and dynamic repositioning of the division plane during maize meiosis.

The success of an organism is contingent upon its ability to transmit genetic material through meiotic cell division. In plant meiosis I, the process begins in a large spherical cell without physical cues to guide the process. Yet, two microtubule-based structures, the spindle and phragmoplast, divide the chromosomes and the cell with extraordinary accuracy. Using a live-cell system and fluorescently labeled spindles and chromosomes, we found that the process self- corrects as meiosis proceeds. Metaphase spindles frequently initiate division off-center, and in these cases anaphase progression is asymmetric with the two masses of chromosomes traveling unequal distances on the spindle. The asymmetry is compensatory, such that the chromosomes on the side of the spindle that is farthest from the cell cortex travel a longer distance at a faster rate. The phragmoplast forms at an equidistant point between the telophase nuclei rather than at the original spindle mid-zone. This asymmetry in chromosome movement implies a structural difference between the two halves of a bipolar spindle and could allow meiotic cells to dynamically adapt to errors in metaphase and accurately divide the cell volume.

Chemical Composition, Antioxidant, Lipid Peroxidation Inhibition and Free Radical Scavenging Activities of Microwave Extracted Essential Oil from Allium sativum

Various chronicle diseases are associated with oxidative stress caused by free radicalsand reactive oxygen species in the living cell system. In the present study, the chemical composition and antioxidant capacity of Allium sativumessential oil (ASEO) were investigated using different scavenging models including 1,1-diphenyl-2-picryl hydrazyl (DPPH), nitric oxide, superoxide, and hydroxyl radicals. Also the ASEO was evaluated for its lipid peroxidation inhibition efficacy, reducing power ability and total phenolic contents. The ASEO was obtained by the hydrodistillation of the dried rhizomes of A. sativum using a microwave-assisted extraction technique. Gas chromatography-mass spectrometry analysis of the ASEO resulted in the determination of 17 different compounds, representing 92.46 % of the total oil. The major components in the ASEO were phenolics, saturated fatty acids, sugar alcohols, esters, hydrazine, quinoline and isoquinoline derivatives along with some other essential phytochemicals. The ASEO showed the antioxidant capacity as the inhibition of DPPH, nitric oxide, superoxide, and hydroxyl radicals by 72.06 %, 79.96 %, 72.66 %, and 71.21 %, respectively. Moreover, the ASEO displayed concentration-dependent reducing power ability and remarkable ferric ion-induced lipid peroxidation inhibitory effect in bovine brain extract. In addition, the ASEO yielded 5.75±0.21 mg/ g gallic acid equivalent phenolic content. The findings of the present study confirm the efficacy of A. sativumas a potential source of natural antioxidant.

Biocompatible multi-walled carbon nanotube–CdTe quantum dot–polymer hybrids for medical applications

Herein we report the synthesis of polymer coated quantum dots (QDs)–carbon nanotube composite material with high biocompatibility and low cellular toxicity. The synthesized multi-walled carbon nanotube (MWCNT)–QD-(-poly(glycidyl methacrylate)) (pGMA) hybrids were characterized using X-ray photoelectron spectroscopy, laser scanning confocal microscopy, transmission electron microscopy and scanning electron microscopy. The results showed that quantum dots were well-distributed on nanotube surfaces in high density. The toxicological assessments of QDs and MWCNT–QD–polymer hybrids in human mammary carcinoma cells and their fluorescence imaging in living cell system were carried out. MWCNT–QD–polymer hybrids possess intense red fluorescence signal under confocal microscopy and good fluorescence stability over 6-h exposure in living cell system. The toxicity comparison of QDs and MWCNT–QD–polymer hybrids has shown that the existence of PGMA thin coating on MWCNT–QD hybrid surface decreased the cellular toxicity and increased biocompatibility.

Toward Drug Repurposing in Epigenetics: Olsalazine as a Hypomethylating Compound Active in a Cellular Context

DNA hypomethylating drugs that act on DNA methyltransferase (DNMT) isoforms are promising anticancer agents. By using a well-characterized live-cell system to measure DNA methylation revisions (imprints), we characterize olsalazine, an approved anti-inflammatory drug, as a novel DNA hypomethylating agent. The cell-based screen used in this work is highly tractable, internally controlled, and well-suited for a drug repurposing strategy in epigenetics. Olsalazine very closely mimics the action of 5-aza-2'-deoxycytidine, a known hypomethylating drug, with minimal cytotoxicity at the concentrations tested. Olsalazine was identified by a rapid computer-guided similarity search of a database of approved drugs to a previously identified inhibitor of DNMTs.

Nitrogen‐Doped Carbon Dots: A Facile and General Preparation Method, Photoluminescence Investigation, and Imaging Applications

Carbon dots (Cdots) are an important probe for imaging and sensing applications because of their fluorescence property, good biocompatibility, and low toxicity. However, complex procedures and strong acid treatment are often required and Cdots suffer from low photoluminescence (PL) emission. Herein, a facile and general strategy using carbonization of precursors and then extraction with solvents is proposed for the preparation of nitrogen-doped Cdots (N-Cdots) with 3-(3,4-dihydroxyphenyl)-L-alanine (L-DOPA), L-histidine, and L-arginine as precursor models. After they are heated, the precursors become carbonized. Nitrogen-doped Cdots are subsequently extracted into N,N'-dimethylformamide (DMF) from the carbogenic solid. A core-shell structure of Cdots with a carbon core and the oxygen-containing shell was observed. Nitrogen has different forms in N-Cdots and oxidized N-Cdots. The doped nitrogen and low oxidation level in N-Cdots improve their emission significantly. The N-Cdots show an emission with a nitrogen-content-dependent intensity and Cdot-size-dependent emission-peak wavelength. Imaging of HeLa cells, a human cervical cancer cell line, and HepG2 cells, a human hepatocellular liver carcinoma line, was observed with high resolution using N-Cdots as a probe and validates their use in imaging applications and their multicolor property in the living cell system.

A modified fixed staining method for the simultaneous measurement of reactive oxygen species and oxidative responses

The generation of reactive oxygen species (ROS) in a live-cell system is routinely measured using the oxidation-sensitive fluorescent probe dichlorofluorescein (DCF). However, it is difficult to simultaneously monitor cellular oxidative responses and ROS generation in cells, and analyses of cellular oxidative responses are typically performed after ROS generation has been evaluated. In this study, we developed a modified fixed staining method that allows the simultaneous analysis of ROS generation and oxidative responses using standard immunostaining techniques. A microplate reader-based assay showed that of the fixatives tested, only methanol did not alter the hydrogen peroxide (H2O2)-mediated oxidation of the responsive dye 5-(and-6)-chloromethyl-2′,7′-dichlorodihydrofluorescein diacetate (CM-H2DCFDA), a chloromethyl derivative of H2DCFDA, or the fluorescence of oxidized DCF in vitro. Further in vivo assays using flow cytometry showed that both methanol and acetic acid maintained the fluorescence of oxidized DCF in H2O2-, antimycin A-, and serum starvation-treated human lung adenocarcinoma A549 cells and human microvascular endothelial HMEC-1 cells. Following acetic acid-based fixation, the ROS generation in starved HMEC-1 cells could be evaluated by flow cytometric analysis while simultaneously monitoring the phosphorylation status of p38 mitogen-activated protein kinase. Immunostaining also revealed the synchronization of ROS generation and the H2O2-induced phosphorylation of Src homology-2 domain-containing phosphatase2. This study describes a modified method that may be used in future biomedical investigations to simultaneously measure intracellular ROS production and cellular oxidative responses.

Characterization of a novel type of HIV-1 particle assembly inhibitor using a quantitative luciferase-Vpr packaging-based assay.

The HIV-1 auxiliary protein Vpr and Vpr-fusion proteins can be copackaged with Gag precursor (Pr55Gag) into virions or membrane-enveloped virus-like particles (VLP). Taking advantage of this property, we developed a simple and sensitive method to evaluate potential inhibitors of HIV-1 assembly in a living cell system. Two proteins were coexpressed in recombinant baculovirus-infected Sf9 cells, Pr55Gag, which formed the VLP backbone, and luciferase fused to the N-terminus of Vpr (LucVpr). VLP-encapsidated LucVpr retained the enzymatic activity of free luciferase. The levels of luciferase activity present in the pelletable fraction recovered from the culture medium correlated with the amounts of extracellular VLP released by Sf9 cells assayed by conventional immunological methods. Our luciferase-based assay was then applied to the characterization of betulinic acid (BA) derivatives that differed from the leader compound PA-457 (or DSB) by their substituant on carbon-28. The beta-alanine-conjugated and lysine-conjugated DSB could not be evaluated for their antiviral potentials due to their high cytotoxicity, whereas two other compounds with a lesser cytotoxicity, glycine-conjugated and ε-NH-Boc-lysine-conjugated DSB, exerted a dose-dependent negative effect on VLP assembly and budding. A fifth compound with a low cytotoxicity, EP-39 (ethylene diamine-conjugated DSB), showed a novel type of antiviral effect. EP-39 provoked an aberrant assembly of VLP, resulting in nonenveloped, morula-like particles of 100-nm in diameter. Each morula was composed of nanoparticle subunits of 20-nm in diameter, which possibly mimicked transient intermediates of the HIV-1 Gag assembly process. Chemical cross-linking in situ suggested that EP-39 favored the formation or/and persistence of Pr55Gag trimers over other oligomeric species. EP-39 showed a novel type of negative effect on HIV-1 assembly, targeting the Pr55Gag oligomerisation. The biological effect of EP-39 underlined the critical role of the nature of the side chain at position 28 of BA derivatives in their anti-HIV-1 activity.

Efficient assembly of multi-walled carbon nanotube-CdSe/ZnS quantum dot hybrids with high biocompatibility and fluorescence property

CdSe/ZnS core-shell quantum dots (QDs) were efficiently tethered onto polyamidoamine dendrimer-modified multi-walled carbon nanotubes (MWCNTs) by covalent linkage and mercapto-mediated assembly. The obtained MWCNT-QD hybrids were both photophysically and morphologically characterized. The QDs are well-distributed on single nanotube surface in high density and the assembly of QDs onto MWCNTs does not change the fluorescence emission wavelength of QDs but significantly decreases the emission density. Cytotoxicity of MWCNT-QD hybrids to HeLa cells and their fluorescence property in living cell system were evaluated in detail. The hybrids show a little effect on cell viability even at very high concentration (100 μg mL(-1)). Moreover, they possess intense red fluorescence signal under optical fluorescence microscopy and good fluorescence stability over 72-h exposure in living cell system.

Ni–Au core–shell nanowires: synthesis, microstructures, biofunctionalization, and the toxicological effects on pancreatic cancer cells

The nickel (Ni)–gold (Au) core–shell nanowires (CSNWs) were synthesized by a combination of electrodeposition and electroless-plating methods. This template based, electroless-plating approach can control the size and shape of nanostructures by adjusting the experimental conditions. The X-ray diffraction, transmission electron microscopy (TEM), and TEM line-scanning and elemental mapping analyses were applied to investigate the formation and microstructure of the core–shell nanostructure. Also using a focused ion beam lift-out technique provides an important route to prove the inner microstructural details of the CSNWs. The optical characterization showed the surface plasmon absorption shifting with electroless-plating time, whereas the magnetic measurements revealed the shape anisotropy and soft ferromagnetic properties of the NWs. Using the strong interaction between biotin and streptavidin, streptavidin–fluorescent dyes were successfully conjugated on the biotinylated CSNWs. This was then analyzed for the surface plasmon resonance effect and Stokes' shifting viaultraviolet-visible and photoluminescence spectroscopy measurements and imaged by confocal scanning laser microscopy. Proliferating cancer cells (Panc-1) have been used to study the toxicological effects of both Ni–Au CSNWs and Ni NWs in a living cell system: the cellular responses to nanowire effects were observed. Ni–Au CSNWs appeared to be tolerated more by this cell line at the dose tested than Ni NWs.

A novel 7‐azaisoindigo derivative‐induced cancer cell apoptosis and mitochondrial dysfunction mediated by oxidative stress

This research focused on a novel 7-azaisoindigo derivative [namely N(1)-(n-butyl)-7-azaisoindigo, 7-AI-b], and investigated its molecular antitumor mechanism by exploring the means of cell death and the effects on mitochondrial function. 7-AI-b inhibited cancer cell proliferation in a dose- and time-dependent way. The morphological and nuclei changes in H(2) B-GFP-labeled HeLa cells were observed using a live cell system. The results suggested that cell death induced by 7-AI-b is closely related to apoptosis. 7-AI-b induced release of cytochrome C from mitochondria to cytosol and activation of caspase-3, showing that the apoptosis is mediated by the mitochondrial pathway. Furthermore, our data indicated that 7-AI-b triggers apoptosis through reactive oxygen species (ROS): cellular ROS levels were increased after 3 h exposure of 7-AI-b, which was reversed by the ROS scavenger N-acetyl-L-cysteine. As a consequence, 7-AI-b-mediated cell death, mitochondrial transmembrane potential collapse and ATP level were partly blocked by N-acetyl-L-cysteine. Further study showed that 7-AI-b could induce mitochondrial dysfunction: collapse of the mitochondrial transmembrane potential and reduction of intracellular ATP level. In summary, the novel synthesized 7-AI-b was demonstrated to be effective in killing cancer cells via an ROS-promoted and mitochondria- and caspase-dependent apoptotic pathway.

Live imaging system for visualizing nuclear pore complex (NPC) formation during interphase in mammalian cells

Nuclear pore complexes (NPCs) are 'supramolecular complexes' on the nuclear envelope assembled from multiple copies of approximately 30 different proteins called nucleoporins (Nups) that provide aqueous channels for nucleocytoplasmic transport during interphase. Although the structural aspects of NPCs have been characterized in detail, NPC formation and its regulation, especially during interphase, are poorly understood. In this study, using the temperature-sensitive RCC1 mutant tsBN2, a baby hamster kidney 21 cell line, we found that a lack of RCC1 activity inhibited NPC formation during interphase, suggesting that RanGTP is required for NPC formation during interphase in mammalian cells. Utilizing the reversible RCC1 activity in tsBN2 cells, we established a live-cell system that allows for the inhibition or initiation of NPC formation by changes in temperature. Our system enables the examination of NPC formation during interphase in living cells. As a lack of RCC1 decreased some Nups containing unstructured phenylalanine-glycine repeats in the NPC structure, we propose that RCC1 is also involved in maintaining NPC integrity during interphase in mammalian cells.

Live Imaging of Chloroplast FtsZ1 Filaments, Rings, Spirals, and Motile Dot Structures in the AtMinE1 Mutant and Overexpressor of Arabidopsis thaliana

Chloroplast division involves the tubulin-related GTPase FtsZ that assembles into a ring structure (Z-ring) at the mid-chloroplast division site, which is where invagination and constriction of the envelope membranes occur. Z-ring assembly is usually confined to the mid-chloroplast site by a well balanced counteraction of the stromal proteins MinD and MinE. The in vivo mechanisms by which FtsZ nucleates at specific sites, polymerises into a protofilament and organizes a closed ring of filament bundles remain largely unknown. To clarify the dynamic aspects of FtsZ, we developed a living cell system for simultaneous visualisation of various FtsZ configurations, utilising the Arabidopsis thaliana overexpressor and mutant of the MinE (AtMinE1) gene, which were modified to weakly express green fluorescent protein (GFP) fused to AtFtsZ1-1. Time-lapse observation in the chloroplasts of both plants revealed disorderly movement of the dots and short filaments of FtsZ. The short filaments often appeared to emanate from the dots and to converge with a long filament, producing a thick cable. In the AtMinE1 overexpressor, we also observed spirals along the longitudinal axis of the organelle that often rolled the closed rings together. In the atminE1 mutant, we visualised the 'isolated' rings with a maximum diameter of approximately 2 mum that did not encircle the organelle periphery, but appeared to be suspended in the stroma. Our observations further demonstrated heterogeneity in chloroplast shapes and concurrently altered configurations of FtsZ in the mutant.

Physiological fluorescence lifetime imaging microscopy improves Förster resonance energy transfer detection in living cells

Accurate, unambiguous detection of molecular interactions in living cells via measurements of Forster (or fluorescence) resonance energy transfer (FRET) events is experimentally challenging. We develop and apply a physiological fluorescence lifetime imaging microscopy (physiological FLIM) system to significantly improve FRET detection in living cells. Multiple positive and negative cellular controls are implemented to validate the experimental method developed. FLIM measurement techniques were found to remove fluorescence intensity-based artifacts, resulting in a seven-fold improvement in fluorescence measurement precision. The addition of cellular environmental controls, including both temperature and CO(2) stabilization, for physiological FLIM eliminates nonspecific FRET in the live-cell system studied. Overall, only physiological FLIM results in statistically significant results that clearly indicated the presence of specific molecular interactions in the live-cell system. This approach can be applied generally to improve the accuracy and precision of FRET measurements in living cells.

Neuronal calcium sensor proteins are unable to modulate NFAT activation in mammalian cells

Calcium activated gene transcription through Nuclear Factor of Activated T-cells, (NFAT) proteins, is emerging as a ubiquitous mechanism for the control of important physiological processes. Of the five mammalian NFAT isoforms, transcriptional activities of NFATs 1-4 are stimulated by a calcium driven association between the ubiquitous phosphatase calcineurin and the calcium-sensing protein calmodulin. Published in vitro evidence has suggested that other members of the calmodulin super-family, in particular the neuronal calcium sensor (NCS) proteins, can similarly modulate calcineurin activity. In this study we have assessed the ability of NCS proteins to interact directly with calcineurin in vitro and report a specific if weak association between various NCS proteins and the phosphatase. In an extension to these analyses we have also examined the effects of over-expression of NCS-1 or NCS-1 mutants on calcineurin signalling in HeLa cells in experiments examining the dephosphorylation of an NFAT-GFP reporter construct as a readout of calcineurin activity. Results from these experiments indicate that NCS-1 was not able to detectably modulate calcineurin/NFAT signalling in a live mammalian cell system, findings that are consistent with the idea that calmodulin and not NCS-1 or other NCS family proteins is the physiologically relevant modulator of calcineurin activity.

Conceptual Modeling in Systems Biology Fosters Empirical Findings: The mRNA Lifecycle

One of the main obstacles to understanding complex biological systems is the extent and rapid evolution of information, way beyond the capacity individuals to manage and comprehend. Current modeling approaches and tools lack adequate capacity to model concurrently structure and behavior of biological systems. Here we propose Object-Process Methodology (OPM), a holistic conceptual modeling paradigm, as a means to model both diagrammatically and textually biological systems formally and intuitively at any desired number of levels of detail. OPM combines objects, e.g., proteins, and processes, e.g., transcription, in a way that is simple and easily comprehensible to researchers and scholars. As a case in point, we modeled the yeast mRNA lifecycle. The mRNA lifecycle involves mRNA synthesis in the nucleus, mRNA transport to the cytoplasm, and its subsequent translation and degradation therein. Recent studies have identified specific cytoplasmic foci, termed processing bodies that contain large complexes of mRNAs and decay factors. Our OPM model of this cellular subsystem, presented here, led to the discovery of a new constituent of these complexes, the translation termination factor eRF3. Association of eRF3 with processing bodies is observed after a long-term starvation period. We suggest that OPM can eventually serve as a comprehensive evolvable model of the entire living cell system. The model would serve as a research and communication platform, highlighting unknown and uncertain aspects that can be addressed empirically and updated consequently while maintaining consistency.