Use of computer vision for analysis of image datasets from high temperature plasma experiments.

Great strides have been made in improving the quality of x-ray radiographs in high energy density plasma experiments, enabled in part by innovations in engineering and manufacturing of integrated circuits and materials. As a consequence, the radiographs of today are filled with a great deal of detail, but few of these features are extracted in a systematic way. Analysis techniques familiar to plasma physicists tend toward brittle 1D lineout or Fourier transform type analyses. The techniques applied to process our data have not kept pace with improvements in the quality of our data. Fortunately, the field of computer vision has a wealth of tools to offer, which have been widely used in industrial imaging and, more recently, adopted in biological imaging. We demonstrate the application of computer vision techniques to the analysis of x-ray radiographs from high energy density plasma experiments, as well as give a brief tutorial on the computer vision techniques themselves. These tools robustly extract 2D contours of shocks, boundaries of inhomogeneities, and secondary flows, thereby allowing for increased automation of analysis, as well as direct and quantitative comparisons with simulations.

Observation of persistent species temperature separation in inertial confinement fusion mixtures.

The injection and mixing of contaminant mass into the fuel in inertial confinement fusion (ICF) implosions is a primary factor preventing ignition. ICF experiments have recently achieved an alpha-heating regime, in which fusion self-heating is the dominant source of yield, by reducing the susceptibility of implosions to instabilities that inject this mass. We report the results of unique separated reactants implosion experiments studying pre-mixed contaminant as well as detailed high-resolution three-dimensional simulations that are in good agreement with experiments. At conditions relevant to mixing regions in high-yield implosions, we observe persistent chunks of contaminant that do not achieve thermal equilibrium with the fuel throughout the burn phase. The assumption of thermal equilibrium is made in nearly all computational ICF modeling and methods used to infer levels of contaminant from experiments. We estimate that these methods may underestimate the amount of contaminant by a factor of two or more.

New Author Guidelines for Displaying Data and Reporting Data Analysis and Statistical Methods in Experimental Biology.

The American Society for Pharmacology and Experimental Therapeutics has revised the Instructions to Authors for Drug Metabolism and Disposition, Journal of Pharmacology and Experimental Therapeutics, and Molecular Pharmacology These revisions relate to data analysis (including statistical analysis) and reporting but do not tell investigators how to design and perform their experiments. Their overall focus is on greater granularity in the description of what has been done and found. Key recommendations include the need to differentiate between preplanned, hypothesis-testing, and exploratory experiments or studies; explanations of whether key elements of study design, such as sample size and choice of specific statistical tests, had been specified before any data were obtained or adapted thereafter; and explanation of whether any outliers (data points or entire experiments) were eliminated and when the rules for doing so had been defined. Variability should be described by S.D. or interquartile range, and precision should be described by confidence intervals; S.E. should not be used. P values should be used sparingly; in most cases, reporting differences or ratios (effect sizes) with their confidence intervals will be preferred. Depiction of data in figures should provide as much granularity as possible, e.g., by replacing bar graphs with scatter plots wherever feasible and violin or box-and-whisker plots when not. This editorial explains the revisions and the underlying scientific rationale. We believe that these revised guidelines will lead to a less biased and more transparent reporting of research findings.

New Author Guidelines for Displaying Data and Reporting Data Analysis and Statistical Methods in Experimental Biology.

The American Society for Pharmacology and Experimental Therapeutics has revised the Instructions to Authors for Drug Metabolism and Disposition, Journal of Pharmacology and Experimental Therapeutics, and Molecular Pharmacology These revisions relate to data analysis (including statistical analysis) and reporting but do not tell investigators how to design and perform their experiments. Their overall focus is on greater granularity in the description of what has been done and found. Key recommendations include the need to differentiate between preplanned, hypothesis-testing, and exploratory experiments or studies; explanations of whether key elements of study design, such as sample size and choice of specific statistical tests, had been specified before any data were obtained or adapted thereafter; and explanations of whether any outliers (data points or entire experiments) were eliminated and when the rules for doing so had been defined. Variability should be described by S.D. or interquartile range, and precision should be described by confidence intervals; S.E. should not be used. P values should be used sparingly; in most cases, reporting differences or ratios (effect sizes) with their confidence intervals will be preferred. Depiction of data in figures should provide as much granularity as possible, e.g., by replacing bar graphs with scatter plots wherever feasible and violin or box-and-whisker plots when not. This editorial explains the revisions and the underlying scientific rationale. We believe that these revised guidelines will lead to a less biased and more transparent reporting of research findings.

New Author Guidelines for Displaying Data and Reporting Data Analysis and Statistical Methods in Experimental Biology.

The American Society for Pharmacology and Experimental Therapeutics has revised the Instructions to Authors for Drug Metabolism and Disposition, Journal of Pharmacology and Experimental Therapeutics, and Molecular Pharmacology These revisions relate to data analysis (including statistical analysis) and reporting but do not tell investigators how to design and perform their experiments. Their overall focus is on greater granularity in the description of what has been done and found. Key recommendations include the need to differentiate between preplanned, hypothesis-testing, and exploratory experiments or studies; explanations of whether key elements of study design, such as sample size and choice of specific statistical tests, had been specified before any data were obtained or adapted thereafter; and explanations of whether any outliers (data points or entire experiments) were eliminated and when the rules for doing so had been defined. Variability should be described by S.D. or interquartile range, and precision should be described by confidence intervals; S.E. should not be used. P values should be used sparingly; in most cases, reporting differences or ratios (effect sizes) with their confidence intervals will be preferred. Depiction of data in figures should provide as much granularity as possible, e.g., by replacing bar graphs with scatter plots wherever feasible and violin or box-and-whisker plots when not. This editorial explains the revisions and the underlying scientific rationale. We believe that these revised guidelines will lead to a less biased and more transparent reporting of research findings.

Homeostatic Intrinsic Plasticity Is Functionally Altered in Fmr1 KO Cortical Neurons.

Cortical hyperexcitability is a hallmark of fragile X syndrome (FXS). In the Fmr1 knockout (KO) mouse model of FXS, cortical hyperexcitability is linked to sensory hypersensitivity and seizure susceptibility. It remains unclear why homeostatic mechanisms fail to prevent such activity. Homeostatic intrinsic plasticity (HIP) adjusts membrane excitability through regulation of ion channels to maintain activity levels following activity perturbation. Despite the critical role of HIP in the maturation of excitability, it has not been examined in FXS. Here, we demonstrate that HIP does not operate normally in a disease model, FXS. HIP was either lost or exaggerated in two distinct neuronal populations from Fmr1 KO cortical cultures. In addition, we have identified a mechanism for homeostatic intrinsic plasticity. Compromising HIP function during development could leave cortical neurons in the FXS nervous system vulnerable to hyperexcitability.

Systematic Fuel Cavity Asymmetries in Directly Driven Inertial Confinement Fusion Implosions.

We present narrow-band self-emission x-ray images from a titanium tracer layer placed at the fuel-shell interface in 60-laser-beam implosion experiments at the OMEGA facility. The images are acquired during deceleration with inferred convergences of ∼9-14. Novel here is that a systematically observed asymmetry of the emission is linked, using full sphere 3D implosion modeling, to performance-limiting low mode asymmetry of the drive.

Late-Time Mixing Sensitivity to Initial Broadband Surface Roughness in High-Energy-Density Shear Layers.

Using a large volume high-energy-density fluid shear experiment (8.5 cm^{3}) at the National Ignition Facility, we have demonstrated for the first time the ability to significantly alter the evolution of a supersonic sheared mixing layer by controlling the initial conditions of that layer. By altering the initial surface roughness of the tracer foil, we demonstrate the ability to transition the shear mixing layer from a highly ordered system of coherent structures to a randomly ordered system with a faster growing mix layer, indicative of strong mixing in the layer at a temperature of several tens of electron volts and at near solid density. Simulations using a turbulent-mix model show good agreement with the experimental results and poor agreement without turbulent mix.

Development of a Big Area BackLighter for high energy density experiments.

A very large area (7.5 mm(2)) laser-driven x-ray backlighter, termed the Big Area BackLighter (BABL) has been developed for the National Ignition Facility (NIF) to support high energy density experiments. The BABL provides an alternative to Pinhole-Apertured point-projection Backlighting (PABL) for a large field of view. This bypasses the challenges for PABL in the equatorial plane of the NIF target chamber where space is limited because of the unconverted laser light that threatens the diagnostic aperture, the backlighter foil, and the pinhole substrate. A transmission experiment using 132 kJ of NIF laser energy at a maximum intensity of 8.52 × 10(14) W/cm(2) illuminating the BABL demonstrated good conversion efficiency of >3.5% into K-shell emission producing ~4.6 kJ of high energy x rays, while yielding high contrast images with a highly uniform background that agree well with 2D simulated spectra and spatial profiles.

Implementation of a fluorescence-based screening assay identifies histamine H3 receptor antagonists clobenpropit and iodophenpropit as subunit-selective N-methyl-D-aspartate receptor antagonists.

N-Methyl-D-aspartate (NMDA) receptors are ligand-gated ion channels that mediate a slow, Ca(2+)-permeable component of excitatory synaptic transmission in the central nervous system and play a pivotal role in synaptic plasticity, neuronal development, and several neurological diseases. We describe a fluorescence-based assay that measures NMDA receptor-mediated changes in intracellular calcium in a BHK-21 cell line stably expressing NMDA receptor NR2D with NR1 under the control of a tetracycline-inducible promoter (Tet-On). The assay selectively identifies allosteric modulators by using supramaximal concentrations of glutamate and glycine to minimize detection of competitive antagonists. The assay is validated by successfully identifying known noncompetitive, but not competitive NMDA receptor antagonists among 1800 screened compounds from two small focused libraries, including the commercially available library of pharmacologically active compounds. Hits from the primary screen are validated through a secondary screen that used two-electrode voltage-clamp recordings on recombinant NMDA receptors expressed in Xenopus laevis oocytes. This strategy identified several novel modulators of NMDA receptor function, including the histamine H3 receptor antagonists clobenpropit and iodophenpropit, as well as the vanilloid receptor transient receptor potential cation channel, subfamily V, member 1 (TRPV1) antagonist capsazepine. These compounds are noncompetitive antagonists and the histamine H3 receptor ligand showed submicromolar potency at NR1/NR2B NMDA receptors, which raises the possibility that compounds can be developed that act with high potency on both glutamate and histamine receptor systems simultaneously. Furthermore, it is possible that some actions attributed to histamine H3 receptor inhibition in vivo may also involve NMDA receptor antagonism.

The mating response cascade does not modulate changes in the steady-state level of target mRNAs through control of mRNA stability.

Many extracellular signals trigger changes in gene expression by altering the steady-state level of target transcripts. This modulation of transcript levels is typically ascribed to changes in transcription of target genes; however, there are numerous examples of changes in mRNA processing and stability that contribute to the overall change in transcript levels following signalling pathway activation. The alpha-factor-stimulated mating pathway in Saccharomyces cerevisiae is a receptor-operated MAP kinase cascade that results in increased levels of a large number of target mRNA transcripts when stimulated acutely. A previous study identified many of the transcripts modulated in response to alpha-factor and argued, based on genetic studies, that the response occurred solely at the level of gene transcription (Roberts et al., 2000). We directly examined whether enhanced mRNA stability contributes to the increase in the steady-state level of alpha-factor target transcripts by exploiting a temperature-sensitive RNA Polymerase II mutant, a Ste12 transcription factor import mutant, and tet-regulated synthetic mating factor minigene reporters. Examination of a panel of alpha-factor-responsive transcripts reveals no change in mRNA stability in response to alpha-factor stimulation, providing direct evidence that this signal transduction pathway in S. cerevisiae does not function through modulating transcript stability.

Recognition of polyadenosine RNA by zinc finger proteins.

Messenger RNA transcripts are coated from cap to tail with a dynamic combination of RNA binding proteins that process, package, and ultimately regulate the fate of mature transcripts. One class of RNA binding proteins essential for multiple aspects of mRNA metabolism consists of the poly(A) binding proteins. Previous studies have concentrated on the canonical RNA recognition motif-containing poly(A) binding proteins as the sole family of poly(A)-specific RNA binding proteins. In this study, we present evidence for a previously uncharacterized poly(A) recognition motif consisting of tandem CCCH zinc fingers. We have probed the nucleic acid binding properties of a yeast protein, Nab2, that contains this zinc finger motif. Results of this study reveal that the seven tandem CCCH zinc fingers of Nab2 specifically bind to polyadenosine RNA with high affinity. Furthermore, we demonstrate that a human protein, ZC3H14, which contains CCCH zinc fingers homologous to those found in Nab2, also specifically binds polyadenosine RNA. Thus, we propose that these proteins are members of an evolutionarily conserved family of poly(A) RNA binding proteins that recognize poly(A) RNA through a fundamentally different mechanism than previously characterized RNA recognition motif-containing poly(A) binding proteins.

Differential effects of Gq alpha, G14 alpha, and G15 alpha on vascular smooth muscle cell survival and gene expression profiles.

Gqalpha family members (Gqalpha, G11alpha, G14alpha, and G15/16alpha) stimulate phospholipase Cbeta (PLCbeta) and inositol lipid signaling but differ markedly in amino acid sequence and tissue distribution predicting unappreciated functional diversity. To examine functional differences, we compared the signaling properties of Gqalpha, G14alpha, and G15alpha and their cellular responses in vascular smooth muscle cells (VSMC). Constitutively active forms of Gqalpha, G14alpha, or G15alpha elicit markedly different responses when introduced to VSMC. Whereas each Galpha stimulated PLCbeta to similar extents when expressed at equal protein levels, Gqalpha and G14alpha but not G15alpha initiated profound cell death within 48 h. This response was the result of activation of apoptotic pathways, because Gqalpha and G14alpha, but not G15alpha, stimulated caspase-3 activation and did not alter phospho-Akt, a regulator of cell survival pathways. Gqalpha and G14alpha stimulate nuclear factor of activated T cell (NFAT) activation in VSMC, but Galpha-induced cell death seems independent of PKC, InsP(3)/Ca(2+), and NFAT, in that pharmacological inhibitors of these pathways did not block cell death. Gene expression analysis indicates that Gqalpha, G14alpha, and G15alpha each elicit markedly different profiles of altered gene sets in VSMC after 24 h. Whereas all three Galpha stimulated changes (> or =2-fold) in 50 shared mRNA, Gqalpha and G14alpha (but not G15alpha) stimulated changes in 221 shared mRNA, many of which are reported to be pro-apoptotic and/or involved with TNF-alpha signaling. We were surprised to find that each Galpha also stimulated changes in nonoverlapping Galpha-specific gene sets. These findings demonstrate that Gqalpha family members activate both overlapping and distinct signaling pathways and are more functionally diverse than previously thought.

Ubiquitin-proteasome degradation of KLF5 transcription factor in cancer and untransformed epithelial cells.

Ubiquitin-mediated proteolysis plays a central role in controlling intracellular levels of essential regulatory molecules such as p53, cyclins, myc, BRCA1, HIF-1alpha, etc. The Kruppel-like factor 5 (KLF5) transcription factor regulates biological processes involved in carcinogenesis, angiogenesis, and smooth muscle cell differentiation. In carcinogenesis, KLF5's role has been indicated by frequent genetic deletion as well as functional studies. Here we show that KLF5 is an unstable protein with a short half-life. Destruction of KLF5 was prevented by each of the proteasome-specific inhibitors tested but not by an inhibitor for trypsin-like proteases and cysteine proteases or by a lysosome inhibitor in epithelial cells. Furthermore, KLF5 underwent ubiquitination, and deletion of a 56-amino-acid sequence adjacent to a known transactivation domain of KLF5 significantly reduced its ubiquitination and degradation. Interestingly, cancer cells appeared to be more active in KLF5 degradation than untransformed epithelial cells, yet their proteasome activity was not higher. These results suggest that KLF5 protein is degraded at least in part through ubiquitination-proteasome pathway, which may have become hyperactive for KLF5 in cancer cells.

Role of caspase activation in butyrate-induced terminal differentiation of HT29 colon carcinoma cells.

Colon epithelial cells have a defined life span and undergo terminal differentiation as they mature and migrate to the luminal surface. The differentiation process can be induced in cultured colon cancer cells by sodium butyrate, which induces expression of various differentiation markers followed subsequently by cell death. In the present study, HT29 colorectal carcinoma cells were shown to undergo butyrate-induced caspase activation that was mainly produced through a mitochondrial pathway. Inhibition of caspase activation, either by peptide pan caspase inhibitor Z-VAD-FMK, by caspase 9 inhibitor Z-LEHD-FMK, or by overexpression of Bcl-XL, also inhibited the expression of differentiation markers. These findings suggest (a) that terminal differentiation of HT29 colon carcinoma cells is tightly linked to caspase activation and (b) that increased expression of anti-apoptotic members of the Bcl-2 family of proteins, as well as other inhibitors of caspase activation, has the potential to inhibit terminal differentiation and thereby may contribute to the progression of colon cancer.

Common signaling pathways link activation of murine PAR-1, LPA, and S1P receptors to proliferation of astrocytes.

Receptors for the serine protease thrombin and for lysophospholipids are coupled to G proteins and control a wide range of cellular functions, including mitogenesis. Activators of these receptors are present in blood, and can enter the brain during central nervous system (CNS) injury. Reactive astrogliosis, a prominent component of CNS injury with potentially harmful consequences, may involve proliferation of astrocytes. In this study, we have examined the expression and activation of protease activated receptors (PARs), lysophosphatidic acid (LPA) receptors, and sphingosine-1-phosphate (S1P) receptors on murine astrocytes. We show that activation of these three receptor classes can lead to astrogliosis in vivo and proliferation of astrocytes in vitro. Cultured murine cortical astrocytes express mRNA for multiple receptor subtypes of PAR (PAR-1-4), LPA (LPA-1-3) and S1P (S1P-1, -3, -4, and -5) receptors. Comparison of the intracellular signaling pathways of glial PAR-1, LPA, and S1P receptors indicates that each receptor class activates multiple downstream signaling pathways, including Gq/11-directed inositol lipid/Ca2+ signaling, Gi/o activation of mitogen-activated protein kinases (MAPK) (extracellular signal-regulated kinase 1/2 and stress activated protein kinase/c-jun N-terminal kinase, but not p38), and activation of Rho pathways. Furthermore, activation of these different receptor classes can differentially regulate two transcription factor pathways, serum response element and nuclear factor of activated T cells. Blockade of Gi/o signaling with pertussis toxin, MAPK activation with 1,4-diamino-2,3-dicyano-1,4-bis(2-aminophynyltio)butadiene (U0126), or Rho kinase signaling with R-(+)-trans-N-(4-pyridyl)-4-(1-aminoethyl)-cyclohexane carboxamide (Y27632) can markedly reduce the proliferative response of glial cells to PAR-1, LPA, or S1P receptor activation, suggesting that each of these pathways is important in coupling of receptor activation to glial proliferation.

Expression of matrix metalloproteinase-9 in endothelial cells is differentially regulated by shear stress. Role of c-Myc.

Atherosclerotic plaques preferentially localize to areas of the vasculature with complex laminar or oscillatory blood flow. Prior data implicate matrix metalloproteinases (MMPs) in the initiation and progression of atherosclerotic lesions. In cultured endothelial cells, oscillatory but not unidirectional shear significantly increases MMP-9 mRNA as well as secretion of the MMP-9 protein (p < 0.05). In contrast, cell-associated protein levels of Tissue Inhibitor of MMP 1 (TIMP-1), an inhibitor of MMP-9, are insensitive to the shear regimen. To investigate transcriptional regulation of MMP-9 gene expression, we utilized retroviral-based reporter constructs containing different lengths of the human MMP-9 promoter. The activity of the full MMP-9 promoter is 3-fold higher (p < 0.05) in unidirectional shear compared with static conditions, and the activity is further increased approximately 10-fold by oscillatory shear (p < 0.01) over unidirectional flow. Our data identify a shear-sensitive binding site at -152 in the MMP-9 promoter. We show that the c-Myc transcription factor binds specifically to this site and that reporter constructs in which the c-Myc binding site was abolished lacked the shear responsiveness of native MMP-9 reporter constructs. Our results suggest that endothelial MMP-9 expression is flow-sensitive and is up-regulated by oscillatory flow via activation of c-Myc. This effect may contribute to the development and progression of atherosclerotic lesions in areas of vasculature that are subject to disturbed flow.

Transcription factor activation and mitogenic synergism in airway smooth muscle cells.

Simultaneous treatment of human airway smooth muscle (HASM) cells with lysophosphatidic acid (LPA) and epidermal growth factor (EGF) leads to strikingly synergistic stimulation of mitogenesis. The purpose of this study was to explore potential sites for signal integration mediating synergism, focusing on extracellular signal-regulated kinase (ERK) and transcription factors involved in proliferation and inflammation as likely candidates. Activation of ERK was analysed by immunoblotting. Transcription factor activation was assessed using HASM cells transduced with luciferase reporter gene constructs. LPA and EGF both activated ERK but had no synergistic effect when combined. LPA and EGF both activated activator protein (AP)-1, cyclic adenosine monophosphate response element-binding protein, nuclear factor of activated T-cells and the serum response element; however, only AP-1 activation exhibited synergism. Activation of the inhibitory guanine nucleotide-binding protein and of ERK signalling pathways were required for most transcription factor responses to LPA. In contrast, nuclear factor (NF)-kappaB was activated by LPA but not EGF and NF-kappaB activation was completely blocked only when Rho was inhibited. Rapid activation of Rho was observed in response to LPA but not to EGF. Importantly, inhibition of Rho selectively blocked synergism in both AP-1 activation and mitogenesis. In summary, extracellular signal-regulated kinase activation is required for many transcription factor responses to lysophosphatidic acid and epidermal growth factor, however it is not synergistic. Activation of activator protein-1 is synergistic, and Rho activation by lysophosphatidic acid is required for synergism in both activator protein-1 activation and mitogenesis.

Cell-type-dependent up-regulation of in vitro mineralization after overexpression of the osteoblast-specific transcription factor Runx2/Cbfal.

Functional expression of the transcriptional activator Runx2/Cbfal is essential for osteoblastic differentiation and bone formation and maintenance. Forced expression of Runx2 in nonosteoblastic cells induces expression of osteoblast-specific genes, but the effects of Runx2 overexpression on in vitro matrix mineralization have not been determined. To examine whether exogenous Runx2 expression is sufficient to direct in vitro mineralization, we investigated sustained expression of Runx2 in nonosteoblastic and osteoblast-like cell lines using retroviral gene delivery. As expected, forced expression of Runx2 induced several osteoblast-specific genes in NIH3T3 and C3H10T1/2 fibroblasts and up-regulated expression in MC3T3-E1 immature osteoblast-like cells. However, Runx2 expression enhanced matrix mineralization in a cell-type-dependent manner. NIH3T3 and IMR-90 fibroblasts overexpressing Runx2 did not produce a mineralized matrix, indicating that forced expression of Runx2 in these nonosteogenic cell lines is not sufficient to direct in vitro mineralization. Consistent with the pluripotent nature of the cell line, a fraction (25%) of Runx2-expressing C3H10T1/2 fibroblast cultures produced mineralized nodules in a viral supernatant-dependent manner. Notably, bone sialoprotein (BSP) gene expression was detected at significantly higher levels in mineralizing Runx2-infected C3H10T1/2 cells compared with Runx2-expressing cultures which did not mineralize. Treatment of Runx2-infected C3H10T1/2 cultures with dexamethasone enhanced osteoblastic phenotype expression, inducing low levels of mineralization independent of viral supernatant. Finally, Runx2 overexpression in immature osteoblast-like MC3T3-E1 cells resulted in acceleration and robust up-regulation of matrix mineralization compared with controls. These results suggest that, although functional Runx2 is essential to multiple osteoblast-specific activities, in vitro matrix mineralization requires additional tissue-specific cofactors, which supplement Runx2 activity.