WorldWideScience

Sample records for cell type-specific visualization

  1. Layer- and cell-type-specific subthreshold and suprathreshold effects of long-term monocular deprivation in rat visual cortex.

    Science.gov (United States)

    Medini, Paolo

    2011-11-23

    Connectivity and dendritic properties are determinants of plasticity that are layer and cell-type specific in the neocortex. However, the impact of experience-dependent plasticity at the level of synaptic inputs and spike outputs remains unclear along vertical cortical microcircuits. Here I compared subthreshold and suprathreshold sensitivity to prolonged monocular deprivation (MD) in rat binocular visual cortex in layer 4 and layer 2/3 pyramids (4Ps and 2/3Ps) and in thick-tufted and nontufted layer 5 pyramids (5TPs and 5NPs), which innervate different extracortical targets. In normal rats, 5TPs and 2/3Ps are the most binocular in terms of synaptic inputs, and 5NPs are the least. Spike responses of all 5TPs were highly binocular, whereas those of 2/3Ps were dominated by either the contralateral or ipsilateral eye. MD dramatically shifted the ocular preference of 2/3Ps and 4Ps, mostly by depressing deprived-eye inputs. Plasticity was profoundly different in layer 5. The subthreshold ocular preference shift was sevenfold smaller in 5TPs because of smaller depression of deprived inputs combined with a generalized loss of responsiveness, and was undetectable in 5NPs. Despite their modest ocular dominance change, spike responses of 5TPs consistently lost their typically high binocularity during MD. The comparison of MD effects on 2/3Ps and 5TPs, the main affected output cells of vertical microcircuits, indicated that subthreshold plasticity is not uniquely determined by the initial degree of input binocularity. The data raise the question of whether 5TPs are driven solely by 2/3Ps during MD. The different suprathreshold plasticity of the two cell populations could underlie distinct functional deficits in amblyopia. PMID:22114282

  2. Type-specific cell line models for type-specific ovarian cancer research.

    Directory of Open Access Journals (Sweden)

    Michael S Anglesio

    Full Text Available BACKGROUND: OVARIAN CARCINOMAS CONSIST OF AT LEAST FIVE DISTINCT DISEASES: high-grade serous, low-grade serous, clear cell, endometrioid, and mucinous. Biomarker and molecular characterization may represent a more biologically relevant basis for grouping and treating this family of tumors, rather than site of origin. Molecular characteristics have become the new standard for clinical pathology, however development of tailored type-specific therapies is hampered by a failure of basic research to recognize that model systems used to study these diseases must also be stratified. Unrelated model systems do offer value for study of biochemical processes but specific cellular context needs to be applied to assess relevant therapeutic strategies. METHODS: We have focused on the identification of clear cell carcinoma cell line models. A panel of 32 "ovarian cancer" cell lines has been classified into histotypes using a combination of mutation profiles, IHC mutation-surrogates, and a validated immunohistochemical model. All cell lines were identity verified using STR analysis. RESULTS: Many described ovarian clear cell lines have characteristic mutations (including ARID1A and PIK3CA and an overall molecular/immuno-profile typical of primary tumors. Mutations in TP53 were present in the majority of high-grade serous cell lines. Advanced genomic analysis of bona-fide clear cell carcinoma cell lines also support copy number changes in typical biomarkers such at MET and HNF1B and a lack of any recurrent expressed re-arrangements. CONCLUSIONS: As with primary ovarian tumors, mutation status of cancer genes like ARID1A and TP53 and a general immuno-profile serve well for establishing histotype of ovarian cancer cell We describe specific biomarkers and molecular features to re-classify generic "ovarian carcinoma" cell lines into type specific categories. Our data supports the use of prototype clear cell lines, such as TOV21G and JHOC-5, and questions the use of

  3. Cell type-specific transcriptome profiling in mammalian brains.

    Science.gov (United States)

    LoVerso, Peter R; Cui, Feng

    2016-01-01

    A mammalian brain contains numerous types of cells. Advances in neuroscience in the past decade allow us to identify and isolate neural cells of interest from mammalian brains. Recent developments in high-throughput technologies, such as microarrays and next-generation sequencing (NGS), provide detailed information on gene expression in pooled cells on a genomic scale. As a result, many novel genes have been found critical in cell type-specific transcriptional regulation. These differentially expressed genes can be used as molecular signatures, unique to a particular class of neural cells. Use of this gene expression-based approach can further differentiate neural cell types into subtypes, potentially linking some of them with neurological diseases. In this article, experimental techniques used to purify neural cells are described, followed by a review on recent microarray- or NGS-based transcriptomic studies of common neural cell types. The future prospects of cell type-specific research are also discussed. PMID:27100485

  4. Cell-type specific four-component hydrogel.

    Directory of Open Access Journals (Sweden)

    Timo Aberle

    Full Text Available In the field of regenerative medicine we aim to develop implant matrices for specific tissue needs. By combining two per se, cell-permissive gel systems with enzymatic crosslinkers (gelatin/transglutaminase and fibrinogen/thrombin to generate a blend (technical term: quattroGel, an unexpected cell-selectivity evolved. QuattroGels were porous and formed cavities in the cell diameter range, possessed gelation kinetics in the minute range, viscoelastic properties and a mechanical strength appropriate for general cell adhesion, and restricted diffusion. Cell proliferation of endothelial cells, chondrocytes and fibroblasts was essentially unaffected. In contrast, on quattroGels neither endothelial cells formed vascular tubes nor did primary neurons extend neurites in significant amounts. Only chondrocytes differentiated properly as judged by collagen isoform expression. The biophysical quattroGel characteristics appeared to leave distinct cell processes such as mitosis unaffected and favored differentiation of sessile cells, but hampered differentiation of migratory cells. This cell-type selectivity is of interest e.g. during articular cartilage or invertebral disc repair, where pathological innervation and angiogenesis represent adverse events in tissue engineering.

  5. Cell-type specific four-component hydrogel.

    Science.gov (United States)

    Aberle, Timo; Franke, Katrin; Rist, Elke; Benz, Karin; Schlosshauer, Burkhard

    2014-01-01

    In the field of regenerative medicine we aim to develop implant matrices for specific tissue needs. By combining two per se, cell-permissive gel systems with enzymatic crosslinkers (gelatin/transglutaminase and fibrinogen/thrombin) to generate a blend (technical term: quattroGel), an unexpected cell-selectivity evolved. QuattroGels were porous and formed cavities in the cell diameter range, possessed gelation kinetics in the minute range, viscoelastic properties and a mechanical strength appropriate for general cell adhesion, and restricted diffusion. Cell proliferation of endothelial cells, chondrocytes and fibroblasts was essentially unaffected. In contrast, on quattroGels neither endothelial cells formed vascular tubes nor did primary neurons extend neurites in significant amounts. Only chondrocytes differentiated properly as judged by collagen isoform expression. The biophysical quattroGel characteristics appeared to leave distinct cell processes such as mitosis unaffected and favored differentiation of sessile cells, but hampered differentiation of migratory cells. This cell-type selectivity is of interest e.g. during articular cartilage or invertebral disc repair, where pathological innervation and angiogenesis represent adverse events in tissue engineering. PMID:24475174

  6. Cell-Type Specific Four-Component Hydrogel

    OpenAIRE

    Timo Aberle; Katrin Franke; Elke Rist; Karin Benz; Burkhard Schlosshauer

    2014-01-01

    In the field of regenerative medicine we aim to develop implant matrices for specific tissue needs. By combining two per se, cell-permissive gel systems with enzymatic crosslinkers (gelatin/transglutaminase and fibrinogen/thrombin) to generate a blend (technical term: quattroGel), an unexpected cell-selectivity evolved. QuattroGels were porous and formed cavities in the cell diameter range, possessed gelation kinetics in the minute range, viscoelastic properties and a mechanical strength appr...

  7. Investigating Striatal Function through Cell-Type-Specific Manipulations

    OpenAIRE

    Kreitzer, Anatol C.; Berke, Joshua D.

    2011-01-01

    The striatum integrates convergent input from the cortex, thalamus, and midbrain, and has a powerful influence over motivated behavior via outputs to downstream basal ganglia nuclei. Although the anatomy and physiology of distinct classes of striatal neurons has been intensively studied, the specific functions of these cell subpopulations have been more difficult to address. Recently, application of new methodologies for perturbing activity and signaling in different cell types in vivo has be...

  8. Cell type-specific neuroprotective activity of untranslocated prion protein.

    Directory of Open Access Journals (Sweden)

    Elena Restelli

    Full Text Available BACKGROUND: A key pathogenic role in prion diseases was proposed for a cytosolic form of the prion protein (PrP. However, it is not clear how cytosolic PrP localization influences neuronal viability, with either cytotoxic or anti-apoptotic effects reported in different studies. The cellular mechanism by which PrP is delivered to the cytosol of neurons is also debated, and either retrograde transport from the endoplasmic reticulum or inefficient translocation during biosynthesis has been proposed. We investigated cytosolic PrP biogenesis and effect on cell viability in primary neuronal cultures from different mouse brain regions. PRINCIPAL FINDINGS: Mild proteasome inhibition induced accumulation of an untranslocated form of cytosolic PrP in cortical and hippocampal cells, but not in cerebellar granules. A cyclopeptolide that interferes with the correct insertion of the PrP signal sequence into the translocon increased the amount of untranslocated PrP in cortical and hippocampal cells, and induced its synthesis in cerebellar neurons. Untranslocated PrP boosted the resistance of cortical and hippocampal neurons to apoptotic insults but had no effect on cerebellar cells. SIGNIFICANCE: These results indicate cell type-dependent differences in the efficiency of PrP translocation, and argue that cytosolic PrP targeting might serve a physiological neuroprotective function.

  9. Cell-type specific light-mediated transcript regulation in the multicellular alga Volvox carteri

    OpenAIRE

    Kianianmomeni, Arash

    2014-01-01

    Background The multicellular green alga Volvox carteri makes use of none less than 13 photoreceptors, which are mostly expressed in a cell-type specific manner. This gives reason to believe that trasncriptome pattern of each cell type could change differentially in response to environmental light. Here, the cell-type specific changes of various transcripts from different pathways in response to blue, red and far-red light were analyzed. Results In response to different light qualities, distin...

  10. Sequence and chromatin determinants of cell-type-specific transcription factor binding.

    Science.gov (United States)

    Arvey, Aaron; Agius, Phaedra; Noble, William Stafford; Leslie, Christina

    2012-09-01

    Gene regulatory programs in distinct cell types are maintained in large part through the cell-type-specific binding of transcription factors (TFs). The determinants of TF binding include direct DNA sequence preferences, DNA sequence preferences of cofactors, and the local cell-dependent chromatin context. To explore the contribution of DNA sequence signal, histone modifications, and DNase accessibility to cell-type-specific binding, we analyzed 286 ChIP-seq experiments performed by the ENCODE Consortium. This analysis included experiments for 67 transcriptional regulators, 15 of which were profiled in both the GM12878 (lymphoblastoid) and K562 (erythroleukemic) human hematopoietic cell lines. To model TF-bound regions, we trained support vector machines (SVMs) that use flexible k-mer patterns to capture DNA sequence signals more accurately than traditional motif approaches. In addition, we trained SVM spatial chromatin signatures to model local histone modifications and DNase accessibility, obtaining significantly more accurate TF occupancy predictions than simpler approaches. Consistent with previous studies, we find that DNase accessibility can explain cell-line-specific binding for many factors. However, we also find that of the 10 factors with prominent cell-type-specific binding patterns, four display distinct cell-type-specific DNA sequence preferences according to our models. Moreover, for two factors we identify cell-specific binding sites that are accessible in both cell types but bound only in one. For these sites, cell-type-specific sequence models, rather than DNase accessibility, are better able to explain differential binding. Our results suggest that using a single motif for each TF and filtering for chromatin accessible loci is not always sufficient to accurately account for cell-type-specific binding profiles. PMID:22955984

  11. Cell-type specific roles for PTEN in establishing a functional retinal architecture.

    Directory of Open Access Journals (Sweden)

    Robert Cantrup

    Full Text Available BACKGROUND: The retina has a unique three-dimensional architecture, the precise organization of which allows for complete sampling of the visual field. Along the radial or apicobasal axis, retinal neurons and their dendritic and axonal arbors are segregated into layers, while perpendicular to this axis, in the tangential plane, four of the six neuronal types form patterned cellular arrays, or mosaics. Currently, the molecular cues that control retinal cell positioning are not well-understood, especially those that operate in the tangential plane. Here we investigated the role of the PTEN phosphatase in establishing a functional retinal architecture. METHODOLOGY/PRINCIPAL FINDINGS: In the developing retina, PTEN was localized preferentially to ganglion, amacrine and horizontal cells, whose somata are distributed in mosaic patterns in the tangential plane. Generation of a retina-specific Pten knock-out resulted in retinal ganglion, amacrine and horizontal cell hypertrophy, and expansion of the inner plexiform layer. The spacing of Pten mutant mosaic populations was also aberrant, as were the arborization and fasciculation patterns of their processes, displaying cell type-specific defects in the radial and tangential dimensions. Irregular oscillatory potentials were also observed in Pten mutant electroretinograms, indicative of asynchronous amacrine cell firing. Furthermore, while Pten mutant RGC axons targeted appropriate brain regions, optokinetic spatial acuity was reduced in Pten mutant animals. Finally, while some features of the Pten mutant retina appeared similar to those reported in Dscam-mutant mice, PTEN expression and activity were normal in the absence of Dscam. CONCLUSIONS/SIGNIFICANCE: We conclude that Pten regulates somal positioning and neurite arborization patterns of a subset of retinal cells that form mosaics, likely functioning independently of Dscam, at least during the embryonic period. Our findings thus reveal an unexpected

  12. Quantitative analysis of cell-type specific gene expression in the green alga Volvox carteri

    Directory of Open Access Journals (Sweden)

    Hallmann Armin

    2006-12-01

    Full Text Available Abstract Background The multicellular alga Volvox carteri possesses only two cell types: mortal, motile somatic cells and potentially immortal, immotile reproductive cells. It is therefore an attractive model system for studying how cell-autonomous cytodifferentiation is programmed within a genome. Moreover, there are ongoing genome projects both in Volvox carteri and in the closely related unicellular alga Chlamydomonas reinhardtii. However, gene sequencing is only the beginning. To identify cell-type specific expression and to determine relative expression rates, we evaluate the potential of real-time RT-PCR for quantifying gene transcript levels. Results Here we analyze a diversified pool of 39 target genes by real-time RT-PCR for each cell type. This gene pool contains previously known genes with unknown localization of cellular expression, 28 novel genes which are described in this study for the first time, and a few known, cell-type specific genes as a control. The respective gene products are, for instance, part of photosynthesis, cellular regulation, stress response, or transport processes. We provide expression data for all these genes. Conclusion The results show that quantitative real-time RT-PCR is a favorable approach to analyze cell-type specific gene expression in Volvox, which can be extended to a much larger number of genes or to developmental or metabolic mutants. Our expression data also provide a basis for a detailed analysis of individual, previously unknown, cell-type specifically expressed genes.

  13. Genetically-directed, cell type-specific sparse labeling for the analysis of neuronal morphology.

    Directory of Open Access Journals (Sweden)

    Thomas Rotolo

    Full Text Available BACKGROUND: In mammals, genetically-directed cell labeling technologies have not yet been applied to the morphologic analysis of neurons with very large and complex arbors, an application that requires extremely sparse labeling and that is only rendered practical by limiting the labeled population to one or a few predetermined neuronal subtypes. METHODS AND FINDINGS: In the present study we have addressed this application by using CreER technology to non-invasively label very small numbers of neurons so that their morphologies can be fully visualized. Four lines of IRES-CreER knock-in mice were constructed to permit labeling selectively in cholinergic or catecholaminergic neurons [choline acetyltransferase (ChAT-IRES-CreER or tyrosine hydroxylase (TH-IRES-CreER], predominantly in projection neurons [neurofilament light chain (NFL-IRES-CreER], or broadly in neurons and some glia [vesicle-associated membrane protein2 (VAMP2-IRES-CreER]. When crossed to the Z/AP reporter and exposed to 4-hydroxytamoxifen in the early postnatal period, the number of neurons expressing the human placental alkaline phosphatase reporter can be reproducibly lowered to fewer than 50 per brain. Sparse Cre-mediated recombination in ChAT-IRES-CreER;Z/AP mice shows the full axonal and dendritic arbors of individual forebrain cholinergic neurons, the first time that the complete morphologies of these very large neurons have been revealed in any species. CONCLUSIONS: Sparse genetically-directed, cell type-specific neuronal labeling with IRES-creER lines should prove useful for studying a wide variety of questions in neuronal development and disease.

  14. Interactive visual comparison of multimedia data through type-specific views

    Energy Technology Data Exchange (ETDEWEB)

    Burtner, Edwin R.; Bohn, Shawn J.; Payne, Deborah A.

    2013-02-05

    Analysts who work with collections of multimedia to perform information foraging understand how difficult it is to connect information across diverse sets of mixed media. The wealth of information from blogs, social media, and news sites often can provide actionable intelligence; however, many of the tools used on these sources of content are not capable of multimedia analysis because they only analyze a single media type. As such, analysts are taxed to keep a mental model of the relationships among each of the media types when generating the broader content picture. To address this need, we have developed Canopy, a novel visual analytic tool for analyzing multimedia. Canopy provides insight into the multimedia data relationships by exploiting the linkages found in text, images, and video co-occurring in the same document and across the collection. Canopy connects derived and explicit linkages and relationships through multiple connected visualizations to aid analysts in quickly summarizing, searching, and browsing collected information to explore relationships and align content. In this paper, we will discuss the features and capabilities of the Canopy system and walk through a scenario illustrating how this system might be used in an operational environment. Keywords: Multimedia (Image/Video/Music) Visualization.

  15. Common and cell type-specific responses of human cells to mitochondrial dysfunction

    International Nuclear Information System (INIS)

    In yeast, mitochondrial dysfunction activates a specific pathway, termed retrograde regulation, which alters the expression of specific nuclear genes and results in increased replicative life span. In mammalian cells, the specific nuclear genes induced in response to loss of mitochondrial function are less well defined. This study characterizes responses in nuclear gene expression to loss of mitochondrial DNA sequences in three different human cell types: T143B, an osteosarcoma-derived cell line; ARPE19, a retinal pigment epithelium cell line; and GMO6225, a fibroblast cell population from an individual with Kearns-Sayre syndrome (KSS). Quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR) was used to measure gene expression of a selection of glycolysis, TCA cycle, mitochondrial, peroxisomal, extracellular matrix, stress response, and regulatory genes. Gene expression changes that were common to all three cell types included up-regulation of GCK (glucokinase), CS (citrate synthase), HOX1 (heme oxygenase 1), CKMT2 (mitochondrial creatine kinase 2), MYC (v-myc myelocytomatosis viral oncogene homolog), and WRN (Werner syndrome helicase), and down-regulation of FBP1 (fructose-1, 6-bisphosphatase 1) and COL4A1 (collagen, type IV, alpha 1). RNA interference experiments show that induction of MYC is important in ρ0 cells for the up-regulation of glycolysis. In addition, a variety of cell type-specific gene changes was detected and most likely depended upon the differentiated functions of the individual cell types. These expression changes may help explain the response of different tissues to the loss of mitochondrial function due to aging or disease

  16. General and cell-type specific mechanisms target TRPP2/PKD-2 to cilia.

    Science.gov (United States)

    Bae, Young-Kyung; Qin, Hongmin; Knobel, Karla M; Hu, Jinghua; Rosenbaum, Joel L; Barr, Maureen M

    2006-10-01

    Ciliary localization of the transient receptor potential polycystin 2 channel (TRPP2/PKD-2) is evolutionarily conserved, but how TRPP2 is targeted to cilia is not known. In this study, we characterize the motility and localization of PKD-2, a TRPP2 homolog, in C. elegans sensory neurons. We demonstrate that GFP-tagged PKD-2 moves bidirectionally in the dendritic compartment. Furthermore, we show a requirement for different molecules in regulating the ciliary localization of PKD-2. PKD-2 is directed to moving dendritic particles by the UNC-101/adaptor protein 1 (AP-1) complex. When expressed in non-native neurons, PKD-2 remains in cell bodies and is not observed in dendrites or cilia, indicating that cell-type specific factors are required for directing PKD-2 to the dendrite. PKD-2 stabilization in cilia and cell bodies requires LOV-1, a functional partner and a TRPP1 homolog. In lov-1 mutants, PKD-2 is greatly reduced in cilia and forms abnormal aggregates in neuronal cell bodies. Intraflagellar transport (IFT) is not essential for PKD-2 dendritic motility or access to the cilium, but may regulate PKD-2 ciliary abundance. We propose that both general and cell-type-specific factors govern TRPP2/PKD-2 subcellular distribution by forming at least two steps involving somatodendritic and ciliary sorting decisions. PMID:16943275

  17. C/EBPβ Induces Chromatin Opening at a Cell-Type-Specific Enhancer▿

    OpenAIRE

    Plachetka, Annette; Chayka, Olesya; Wilczek, Carola; Melnik, Svitlana; Bonifer, Constanze; Klempnauer, Karl-Heinz

    2008-01-01

    We have used the chicken mim-1 gene as a model to study the mechanisms by which transcription factors gain initial access to their target sites in compacted chromatin. The expression of mim-1 is restricted to the myelomonocytic lineage of the hematopoietic system where it is regulated synergistically by the Myb and CCAAT/enhancer binding protein (C/EBP) factors. Myb and C/EBPβ cooperate at two distinct cis elements of mim-1, the promoter and a cell-type-specific enhancer, both of which are as...

  18. The roadmap for estimation of cell-type-specific neuronal activity from non-invasive measurements.

    Science.gov (United States)

    Uhlirova, Hana; Kılıç, Kıvılcım; Tian, Peifang; Sakadžić, Sava; Gagnon, Louis; Thunemann, Martin; Desjardins, Michèle; Saisan, Payam A; Nizar, Krystal; Yaseen, Mohammad A; Hagler, Donald J; Vandenberghe, Matthieu; Djurovic, Srdjan; Andreassen, Ole A; Silva, Gabriel A; Masliah, Eliezer; Kleinfeld, David; Vinogradov, Sergei; Buxton, Richard B; Einevoll, Gaute T; Boas, David A; Dale, Anders M; Devor, Anna

    2016-10-01

    The computational properties of the human brain arise from an intricate interplay between billions of neurons connected in complex networks. However, our ability to study these networks in healthy human brain is limited by the necessity to use non-invasive technologies. This is in contrast to animal models where a rich, detailed view of cellular-level brain function with cell-type-specific molecular identity has become available due to recent advances in microscopic optical imaging and genetics. Thus, a central challenge facing neuroscience today is leveraging these mechanistic insights from animal studies to accurately draw physiological inferences from non-invasive signals in humans. On the essential path towards this goal is the development of a detailed 'bottom-up' forward model bridging neuronal activity at the level of cell-type-specific populations to non-invasive imaging signals. The general idea is that specific neuronal cell types have identifiable signatures in the way they drive changes in cerebral blood flow, cerebral metabolic rate of O2 (measurable with quantitative functional Magnetic Resonance Imaging), and electrical currents/potentials (measurable with magneto/electroencephalography). This forward model would then provide the 'ground truth' for the development of new tools for tackling the inverse problem-estimation of neuronal activity from multimodal non-invasive imaging data.This article is part of the themed issue 'Interpreting BOLD: a dialogue between cognitive and cellular neuroscience'. PMID:27574309

  19. Towards identifying host cell-type specific response patterns to bacterial endosymbiosis

    DEFF Research Database (Denmark)

    Gavrilovic, Srdjan

    view, available techniques have relied heavily on whole organ analyses that disregard specificities of individual cell types. To address this issue we aimed to develop a technology for comparative global analysis of mature mRNA and small RNA populations at the cell type specific level in the model...... plant Lotus japonicus. A powerful approach referred to here as Defined Expression and RNA Affinity co-Purification (DERAP) was developed to study gene expression and small RNA populations in the host roots during early phases of signal exchange at the cell-type level. As a basis for DERAP analysis of......, namely epidermis with elongating root hairs, inner cortex, endodermis, phloem and xylem, were characterized in L. japonicus. In combination with tagged forms of a Ribosomal surface Protein (RP) and the viral small RNA binding protein P19, these promoters were introduced into L. japonicus ecotype Gifu...

  20. Glutamine synthetase is a genetic determinant of cell type-specific glutamine independence in breast epithelia.

    Directory of Open Access Journals (Sweden)

    Hsiu-Ni Kung

    2011-08-01

    Full Text Available Although significant variations in the metabolic profiles exist among different cells, little is understood in terms of genetic regulations of such cell type-specific metabolic phenotypes and nutrient requirements. While many cancer cells depend on exogenous glutamine for survival to justify the therapeutic targeting of glutamine metabolism, the mechanisms of glutamine dependence and likely response and resistance of such glutamine-targeting strategies among cancers are largely unknown. In this study, we have found a systematic variation in the glutamine dependence among breast tumor subtypes associated with mammary differentiation: basal- but not luminal-type breast cells are more glutamine-dependent and may be susceptible to glutamine-targeting therapeutics. Glutamine independence of luminal-type cells is associated mechanistically with lineage-specific expression of glutamine synthetase (GS. Luminal cells can also rescue basal cells in co-culture without glutamine, indicating a potential for glutamine symbiosis within breast ducts. The luminal-specific expression of GS is directly induced by GATA3 and represses glutaminase expression. Such distinct glutamine dependency and metabolic symbiosis is coupled with the acquisition of the GS and glutamine independence during the mammary differentiation program. Understanding the genetic circuitry governing distinct metabolic patterns is relevant to many symbiotic relationships among different cells and organisms. In addition, the ability of GS to predict patterns of glutamine metabolism and dependency among tumors is also crucial in the rational design and application of glutamine and other metabolic pathway targeted therapies.

  1. Transcription factor co-localization patterns affect human cell type-specific gene expression

    Directory of Open Access Journals (Sweden)

    Wang Dennis

    2012-06-01

    Full Text Available Abstract Background Cellular development requires the precise control of gene expression states. Transcription factors are involved in this regulatory process through their combinatorial binding with DNA. Information about transcription factor binding sites can help determine which combinations of factors work together to regulate a gene, but it is unclear how far the binding data from one cell type can inform about regulation in other cell types. Results By integrating data on co-localized transcription factor binding sites in the K562 cell line with expression data across 38 distinct hematopoietic cell types, we developed regression models to describe the relationship between the expression of target genes and the transcription factors that co-localize nearby. With K562 binding sites identifying the predictors, the proportion of expression explained by the models is statistically significant only for monocytic cells (p-valueFOS, TAF1 and YY1 to a sparsely studied gene LRIG2. We also find that the activity of a transcription factor may be different depending on the cell type and the identity of other co-localized factors. Conclusion Our approach shows that gene expression can be explained by a modest number of co-localized transcription factors, however, information on cell-type specific binding is crucial for understanding combinatorial gene regulation.

  2. Combinatorial topography and cell-type specific regulation of the ERK pathway by dopaminergic agonists in the mouse striatum.

    Science.gov (United States)

    Gangarossa, Giuseppe; Perroy, Julie; Valjent, Emmanuel

    2013-03-01

    Therapeutic agents and drugs of abuse regulate the extracellular signal-regulated kinase (ERK) cascade signaling in the medium-sized spiny neurons (MSNs) of the striatum. However, whether this regulation is associated with specific cortical and thalamic inputs has never been studied. We used Drd2-EGFP BAC-transgenic mice to undertake a topographical and cell-type specific analysis of ERK phosphorylation and two of its downstream targets histone H3 and ribosomal protein S6 (rS6) in the dorsal striatum following injection of SKF81297 (D1R-like agonist), quinpirole (D2R-like agonist) or apomorphine (non selective DA receptor agonist). In striatal areas receiving inputs from the cingulate/prelimbic, visual and auditory cortex, SKF81297 treatment increased phosphorylation of ERK, histone H3 and rS6 selectively in EGFP-negative MSNs of Drd2-EGFP mice. In contrast, no regulation was found in striatal region predominantly targeted by the sensorimotor and motor cortex. Apomorphine slightly enhanced ERK and rS6, but not histone H3 phosphorylation. This regulation occurred exclusively in EGFP-negative neurons mostly in striatal sectors receiving connections from the insular, visual and auditory cortex. Quinpirole administration inhibited basal ERK activation but did not change histone H3 and rS6 phosphorylation throughout the rostrocaudal axis of the dorsal striatum. This anatomo-functional study indicates that D1R and D2R agonists produce a unique topography and cell-type specific regulation of the ERK cascade signaling in the mouse striatum, and that those patterns are closely associated with particular cortical and thalamic inputs. This work evidences the need of a precise identification of the striatal areas under study to further understand striatal plasticity. PMID:22453353

  3. Protein conservation and variation suggest mechanisms of cell type-specific modulation of signaling pathways.

    Directory of Open Access Journals (Sweden)

    Martin H Schaefer

    2014-06-01

    Full Text Available Many proteins and signaling pathways are present in most cell types and tissues and yet perform specialized functions. To elucidate mechanisms by which these ubiquitous pathways are modulated, we overlaid information about cross-cell line protein abundance and variability, and evolutionary conservation onto functional pathway components and topological layers in the pathway hierarchy. We found that the input (receptors and the output (transcription factors layers evolve more rapidly than proteins in the intermediary transmission layer. In contrast, protein expression variability decreases from the input to the output layer. We observed that the differences in protein variability between the input and transmission layer can be attributed to both the network position and the tendency of variable proteins to physically interact with constitutively expressed proteins. Differences in protein expression variability and conservation are also accompanied by the tendency of conserved and constitutively expressed proteins to acquire somatic mutations, while germline mutations tend to occur in cell type-specific proteins. Thus, conserved core proteins in the transmission layer could perform a fundamental role in most cell types and are therefore less tolerant to germline mutations. In summary, we propose that the core signal transmission machinery is largely modulated by a variable input layer through physical protein interactions. We hypothesize that the bow-tie organization of cellular signaling on the level of protein abundance variability contributes to the specificity of the signal response in different cell types.

  4. Protein conservation and variation suggest mechanisms of cell type-specific modulation of signaling pathways.

    Science.gov (United States)

    Schaefer, Martin H; Yang, Jae-Seong; Serrano, Luis; Kiel, Christina

    2014-06-01

    Many proteins and signaling pathways are present in most cell types and tissues and yet perform specialized functions. To elucidate mechanisms by which these ubiquitous pathways are modulated, we overlaid information about cross-cell line protein abundance and variability, and evolutionary conservation onto functional pathway components and topological layers in the pathway hierarchy. We found that the input (receptors) and the output (transcription factors) layers evolve more rapidly than proteins in the intermediary transmission layer. In contrast, protein expression variability decreases from the input to the output layer. We observed that the differences in protein variability between the input and transmission layer can be attributed to both the network position and the tendency of variable proteins to physically interact with constitutively expressed proteins. Differences in protein expression variability and conservation are also accompanied by the tendency of conserved and constitutively expressed proteins to acquire somatic mutations, while germline mutations tend to occur in cell type-specific proteins. Thus, conserved core proteins in the transmission layer could perform a fundamental role in most cell types and are therefore less tolerant to germline mutations. In summary, we propose that the core signal transmission machinery is largely modulated by a variable input layer through physical protein interactions. We hypothesize that the bow-tie organization of cellular signaling on the level of protein abundance variability contributes to the specificity of the signal response in different cell types. PMID:24922536

  5. Dopamine D1 receptor expression is bipolar cell type-specific in the mouse retina.

    Science.gov (United States)

    Farshi, Pershang; Fyk-Kolodziej, Bozena; Krolewski, David M; Walker, Paul D; Ichinose, Tomomi

    2016-07-01

    In the retina, dopamine is a key molecule for daytime vision. Dopamine is released by retinal dopaminergic amacrine cells and transmits signaling either by conventional synaptic or by volume transmission. By means of volume transmission, dopamine modulates all layers of retinal neurons; however, it is not well understood how dopamine modulates visual signaling pathways in bipolar cells. Here we analyzed Drd1a-tdTomato BAC transgenic mice and found that the dopamine D1 receptor (D1R) is expressed in retinal bipolar cells in a type-dependent manner. Strong tdTomato fluorescence was detected in the inner nuclear layer and localized to type 1, 3b, and 4 OFF bipolar cells and type 5-2, XBC, 6, and 7 ON bipolar cells. In contrast, type 2, 3a, 5-1, 9, and rod bipolar cells did not express Drd1a-tdTomato. Other interneurons were also found to express tdTomato including horizontal cells and a subset (25%) of AII amacrine cells. Diverse visual processing pathways, such as color or motion-coded pathways, are thought to be initiated in retinal bipolar cells. Our results indicate that dopamine sculpts bipolar cell performance in a type-dependent manner to facilitate daytime vision. J. Comp. Neurol. 524:2059-2079, 2016. © 2015 Wiley Periodicals, Inc. PMID:26587737

  6. Epigenetic regulation of normal human mammary cell type-specific miRNAs

    Energy Technology Data Exchange (ETDEWEB)

    Vrba, Lukas [Univ. of Arizona, Tucson, AZ (United States). Arizona Cancer Center; Inst. of Plant Molecular Biology, Ceske Budejovice (Czech Republic). Biology Centre ASCR; Garbe, James C. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Life Sciences Center; Stampfer, Martha R. [Univ. of Arizona, Tucson, AZ (United States). Arizona Cancer Center; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Life Sciences Center; Futscher, Bernard W. [Univ. of Arizona, Tucson, AZ (United States). Arizona Cancer Center and Dept. of Pharmacology & Toxicology

    2011-08-26

    Epigenetic mechanisms are important regulators of cell type–specific genes, including miRNAs. In order to identify cell type-specific miRNAs regulated by epigenetic mechanisms, we undertook a global analysis of miRNA expression and epigenetic states in three isogenic pairs of human mammary epithelial cells (HMEC) and human mammary fibroblasts (HMF), which represent two differentiated cell types typically present within a given organ, each with a distinct phenotype and a distinct epigenotype. While miRNA expression and epigenetic states showed strong interindividual concordance within a given cell type, almost 10% of the expressed miRNA showed a cell type–specific pattern of expression that was linked to the epigenetic state of their promoter. The tissue-specific miRNA genes were epigenetically repressed in nonexpressing cells by DNA methylation (38%) and H3K27me3 (58%), with only a small set of miRNAs (21%) showing a dual epigenetic repression where both DNA methylation and H3K27me3 were present at their promoters, such as MIR10A and MIR10B. Individual miRNA clusters of closely related miRNA gene families can each display cell type–specific repression by the same or complementary epigenetic mechanisms, such as the MIR200 family, and MIR205, where fibroblasts repress MIR200C/141 by DNA methylation, MIR200A/200B/429 by H3K27me3, and MIR205 by both DNA methylation and H3K27me3. Since deregulation of many of the epigenetically regulated miRNAs that we identified have been linked to disease processes such as cancer, it is predicted that compromise of the epigenetic control mechanisms is important for this process. Overall, these results highlight the importance of epigenetic regulation in the control of normal cell type–specific miRNA expression.

  7. Cell Type-Specific Manipulation with GFP-Dependent Cre Recombinase

    OpenAIRE

    Tang, Jonathan C. Y.; Rudolph, Stephanie; Dhande, Onkar S.; Abraira, Victoria E.; Choi, Seungwon; Lapan, Sylvain; Drew, Iain R.; Drokhlyansky, Eugene; Huberman, Andrew D.; Regehr, Wade G.; Cepko, Constance L.

    2015-01-01

    Summary There are many transgenic GFP reporter lines that allow visualization of specific populations of cells. Using such lines for functional studies requires a method that transforms GFP into a molecule that enables genetic manipulation. Here we report the creation of a method that exploits GFP for gene manipulation, Cre Recombinase Dependent on GFP (CRE-DOG), a split component system that uses GFP and its derivatives to directly induce Cre/loxP recombination. Using plasmid electroporation...

  8. Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases

    Science.gov (United States)

    Gusev, Alexander; Lee, S. Hong; Trynka, Gosia; Finucane, Hilary; Vilhjálmsson, Bjarni J.; Xu, Han; Zang, Chongzhi; Ripke, Stephan; Bulik-Sullivan, Brendan; Stahl, Eli; Ripke, Stephan; Neale, Benjamin M.; Corvin, Aiden; Walters, James T.R.; Farh, Kai-How; Holmans, Peter A.; Lee, Phil; Bulik-Sullivan, Brendan; Collier, David A.; Huang, Hailiang; Pers, Tune H.; Agartz, Ingrid; Agerbo, Esben; Albus, Margot; Alexander, Madeline; Amin, Farooq; Bacanu, Silviu A.; Begemann, Martin; Belliveau, Richard A.; Bene, Judit; Bergen, Sarah E.; Bevilacqua, Elizabeth; Bigdeli, Tim B.; Black, Donald W.; Børglum, Anders D.; Bruggeman, Richard; Buccola, Nancy G.; Buckner, Randy L.; Byerley, William; Cahn, Wiepke; Cai, Guiqing; Campion, Dominique; Cantor, Rita M.; Carr, Vaughan J.; Carrera, Noa; Catts, Stanley V.; Chambert, Kimberly D.; Chan, Raymond C.K.; Chen, Ronald Y.L.; Chen, Eric Y.H.; Cheng, Wei; Cheung, Eric F.C.; Chong, Siow Ann; Cloninger, C. Robert; Cohen, David; Cohen, Nadine; Cormican, Paul; Craddock, Nick; Crowley, James J.; Curtis, David; Davidson, Michael; Davis, Kenneth L.; Degenhardt, Franziska; Del Favero, Jurgen; DeLisi, Lynn E.; Demontis, Ditte; Dikeos, Dimitris; Dinan, Timothy; Djurovic, Srdjan; Donohoe, Gary; Drapeau, Elodie; Duan, Jubao; Dudbridge, Frank; Durmishi, Naser; Eichhammer, Peter; Eriksson, Johan; Escott-Price, Valentina; Essioux, Laurent; Fanous, Ayman H.; Farrell, Martilias S.; Frank, Josef; Franke, Lude; Freedman, Robert; Freimer, Nelson B.; Friedl, Marion; Friedman, Joseph I.; Fromer, Menachem; Genovese, Giulio; Georgieva, Lyudmila; Gershon, Elliot S.; Giegling, Ina; Giusti-Rodrguez, Paola; Godard, Stephanie; Goldstein, Jacqueline I.; Golimbet, Vera; Gopal, Srihari; Gratten, Jacob; Grove, Jakob; de Haan, Lieuwe; Hammer, Christian; Hamshere, Marian L.; Hansen, Mark; Hansen, Thomas; Haroutunian, Vahram; Hartmann, Annette M.; Henskens, Frans A.; Herms, Stefan; Hirschhorn, Joel N.; Hoffmann, Per; Hofman, Andrea; Hollegaard, Mads V.; Hougaard, David M.; Ikeda, Masashi; Joa, Inge; Julià, Antonio; Kahn, René S.; Kalaydjieva, Luba; Karachanak-Yankova, Sena; Karjalainen, Juha; Kavanagh, David; Keller, Matthew C.; Kelly, Brian J.; Kennedy, James L.; Khrunin, Andrey; Kim, Yunjung; Klovins, Janis; Knowles, James A.; Konte, Bettina; Kucinskas, Vaidutis; Kucinskiene, Zita Ausrele; Kuzelova-Ptackova, Hana; Kähler, Anna K.; Laurent, Claudine; Keong, Jimmy Lee Chee; Lee, S. Hong; Legge, Sophie E.; Lerer, Bernard; Li, Miaoxin; Li, Tao; Liang, Kung-Yee; Lieberman, Jeffrey; Limborska, Svetlana; Loughland, Carmel M.; Lubinski, Jan; Lnnqvist, Jouko; Macek, Milan; Magnusson, Patrik K.E.; Maher, Brion S.; Maier, Wolfgang; Mallet, Jacques; Marsal, Sara; Mattheisen, Manuel; Mattingsdal, Morten; McCarley, Robert W.; McDonald, Colm; McIntosh, Andrew M.; Meier, Sandra; Meijer, Carin J.; Melegh, Bela; Melle, Ingrid; Mesholam-Gately, Raquelle I.; Metspalu, Andres; Michie, Patricia T.; Milani, Lili; Milanova, Vihra; Mokrab, Younes; Morris, Derek W.; Mors, Ole; Mortensen, Preben B.; Murphy, Kieran C.; Murray, Robin M.; Myin-Germeys, Inez; Mller-Myhsok, Bertram; Nelis, Mari; Nenadic, Igor; Nertney, Deborah A.; Nestadt, Gerald; Nicodemus, Kristin K.; Nikitina-Zake, Liene; Nisenbaum, Laura; Nordin, Annelie; O’Callaghan, Eadbhard; O’Dushlaine, Colm; O’Neill, F. Anthony; Oh, Sang-Yun; Olincy, Ann; Olsen, Line; Van Os, Jim; Pantelis, Christos; Papadimitriou, George N.; Papiol, Sergi; Parkhomenko, Elena; Pato, Michele T.; Paunio, Tiina; Pejovic-Milovancevic, Milica; Perkins, Diana O.; Pietilinen, Olli; Pimm, Jonathan; Pocklington, Andrew J.; Powell, John; Price, Alkes; Pulver, Ann E.; Purcell, Shaun M.; Quested, Digby; Rasmussen, Henrik B.; Reichenberg, Abraham; Reimers, Mark A.; Richards, Alexander L.; Roffman, Joshua L.; Roussos, Panos; Ruderfer, Douglas M.; Salomaa, Veikko; Sanders, Alan R.; Schall, Ulrich; Schubert, Christian R.; Schulze, Thomas G.; Schwab, Sibylle G.; Scolnick, Edward M.; Scott, Rodney J.; Seidman, Larry J.; Shi, Jianxin; Sigurdsson, Engilbert; Silagadze, Teimuraz; Silverman, Jeremy M.; Sim, Kang; Slominsky, Petr; Smoller, Jordan W.; So, Hon-Cheong; Spencer, Chris C.A.; Stahl, Eli A.; Stefansson, Hreinn; Steinberg, Stacy; Stogmann, Elisabeth; Straub, Richard E.; Strengman, Eric; Strohmaier, Jana; Stroup, T. Scott; Subramaniam, Mythily; Suvisaari, Jaana; Svrakic, Dragan M.; Szatkiewicz, Jin P.; Sderman, Erik; Thirumalai, Srinivas; Toncheva, Draga; Tooney, Paul A.; Tosato, Sarah; Veijola, Juha; Waddington, John; Walsh, Dermot; Wang, Dai; Wang, Qiang; Webb, Bradley T.; Weiser, Mark; Wildenauer, Dieter B.; Williams, Nigel M.; Williams, Stephanie; Witt, Stephanie H.; Wolen, Aaron R.; Wong, Emily H.M.; Wormley, Brandon K.; Wu, Jing Qin; Xi, Hualin Simon; Zai, Clement C.; Zheng, Xuebin; Zimprich, Fritz; Wray, Naomi R.; Stefansson, Kari; Visscher, Peter M.; Adolfsson, Rolf; Andreassen, Ole A.; Blackwood, Douglas H.R.; Bramon, Elvira; Buxbaum, Joseph D.; Brglum, Anders D.; Cichon, Sven; Darvasi, Ariel; Domenici, Enrico; Ehrenreich, Hannelore; Esko, Tõnu; Gejman, Pablo V.; Gill, Michael; Gurling, Hugh; Hultman, Christina M.; Iwata, Nakao; Jablensky, Assen V.; Jönsson, Erik G.; Kendler, Kenneth S.; Kirov, George; Knight, Jo; Lencz, Todd; Levinson, Douglas F.; Li, Qingqin S.; Liu, Jianjun; Malhotra, Anil K.; McCarroll, Steven A.; McQuillin, Andrew; Moran, Jennifer L.; Mortensen, Preben B.; Mowry, Bryan J.; Nthen, Markus M.; Ophoff, Roel A.; Owen, Michael J.; Palotie, Aarno; Pato, Carlos N.; Petryshen, Tracey L.; Posthuma, Danielle; Rietschel, Marcella; Riley, Brien P.; Rujescu, Dan; Sham, Pak C.; Sklar, Pamela; St. Clair, David; Weinberger, Daniel R.; Wendland, Jens R.; Werge, Thomas; Daly, Mark J.; Sullivan, Patrick F.; O’Donovan, Michael C.; Ripke, Stephan; O’Dushlaine, Colm; Chambert, Kimberly; Moran, Jennifer L.; Kähler, Anna K.; Akterin, Susanne; Bergen, Sarah; Magnusson, Patrik K.E.; Neale, Benjamin M.; Ruderfer, Douglas; Scolnick, Edward; Purcell, Shaun; McCarroll, Steve; Sklar, Pamela; Hultman, Christina M.; Sullivan, Patrick F.; Kähler, Anna K.; Hultman, Christina M.; Purcell, Shaun M.; McCarroll, Steven A.; Daly, Mark; Pasaniuc, Bogdan; Sullivan, Patrick F.; Neale, Benjamin M.; Wray, Naomi R.; Raychaudhuri, Soumya; Price, Alkes L.

    2014-01-01

    Regulatory and coding variants are known to be enriched with associations identified by genome-wide association studies (GWASs) of complex disease, but their contributions to trait heritability are currently unknown. We applied variance-component methods to imputed genotype data for 11 common diseases to partition the heritability explained by genotyped SNPs (hg2) across functional categories (while accounting for shared variance due to linkage disequilibrium). Extensive simulations showed that in contrast to current estimates from GWAS summary statistics, the variance-component approach partitions heritability accurately under a wide range of complex-disease architectures. Across the 11 diseases DNaseI hypersensitivity sites (DHSs) from 217 cell types spanned 16% of imputed SNPs (and 24% of genotyped SNPs) but explained an average of 79% (SE = 8%) of hg2 from imputed SNPs (5.1× enrichment; p = 3.7 × 10−17) and 38% (SE = 4%) of hg2 from genotyped SNPs (1.6× enrichment, p = 1.0 × 10−4). Further enrichment was observed at enhancer DHSs and cell-type-specific DHSs. In contrast, coding variants, which span 1% of the genome, explained <10% of hg2 despite having the highest enrichment. We replicated these findings but found no significant contribution from rare coding variants in independent schizophrenia cohorts genotyped on GWAS and exome chips. Our results highlight the value of analyzing components of heritability to unravel the functional architecture of common disease. PMID:25439723

  9. A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis.

    Science.gov (United States)

    Busser, Brian W; Taher, Leila; Kim, Yongsok; Tansey, Terese; Bloom, Molly J; Ovcharenko, Ivan; Michelson, Alan M

    2012-01-01

    coordinate cell type-specific developmental gene expression patterns. PMID:22412381

  10. Lim homeobox genes in the Ctenophore Mnemiopsis leidyi: the evolution of neural cell type specification

    Directory of Open Access Journals (Sweden)

    Simmons David K

    2012-01-01

    Full Text Available Abstract Background Nervous systems are thought to be important to the evolutionary success and diversification of metazoans, yet little is known about the origin of simple nervous systems at the base of the animal tree. Recent data suggest that ctenophores, a group of macroscopic pelagic marine invertebrates, are the most ancient group of animals that possess a definitive nervous system consisting of a distributed nerve net and an apical statocyst. This study reports on details of the evolution of the neural cell type specifying transcription factor family of LIM homeobox containing genes (Lhx, which have highly conserved functions in neural specification in bilaterian animals. Results Using next generation sequencing, the first draft of the genome of the ctenophore Mnemiopsis leidyi has been generated. The Lhx genes in all animals are represented by seven subfamilies (Lhx1/5, Lhx3/4, Lmx, Islet, Lhx2/9, Lhx6/8, and LMO of which four were found to be represented in the ctenophore lineage (Lhx1/5, Lhx3/4, Lmx, and Islet. Interestingly, the ctenophore Lhx gene complement is more similar to the sponge complement (sponges do not possess neurons than to either the cnidarian-bilaterian or placozoan Lhx complements. Using whole mount in situ hybridization, the Lhx gene expression patterns were examined and found to be expressed around the blastopore and in cells that give rise to the apical organ and putative neural sensory cells. Conclusion This research gives us a first look at neural cell type specification in the ctenophore M. leidyi. Within M. leidyi, Lhx genes are expressed in overlapping domains within proposed neural cellular and sensory cell territories. These data suggest that Lhx genes likely played a conserved role in the patterning of sensory cells in the ancestor of sponges and ctenophores, and may provide a link to the expression of Lhx orthologs in sponge larval photoreceptive cells. Lhx genes were later co-opted into patterning more

  11. Identification of Cell Type-Specific Differences in Erythropoietin Receptor Signaling in Primary Erythroid and Lung Cancer Cells

    Science.gov (United States)

    Salopiata, Florian; Depner, Sofia; Wäsch, Marvin; Böhm, Martin E.; Mücke, Oliver; Plass, Christoph; Lehmann, Wolf D.; Kreutz, Clemens; Timmer, Jens; Klingmüller, Ursula

    2016-01-01

    Lung cancer, with its most prevalent form non-small-cell lung carcinoma (NSCLC), is one of the leading causes of cancer-related deaths worldwide, and is commonly treated with chemotherapeutic drugs such as cisplatin. Lung cancer patients frequently suffer from chemotherapy-induced anemia, which can be treated with erythropoietin (EPO). However, studies have indicated that EPO not only promotes erythropoiesis in hematopoietic cells, but may also enhance survival of NSCLC cells. Here, we verified that the NSCLC cell line H838 expresses functional erythropoietin receptors (EPOR) and that treatment with EPO reduces cisplatin-induced apoptosis. To pinpoint differences in EPO-induced survival signaling in erythroid progenitor cells (CFU-E, colony forming unit-erythroid) and H838 cells, we combined mathematical modeling with a method for feature selection, the L1 regularization. Utilizing an example model and simulated data, we demonstrated that this approach enables the accurate identification and quantification of cell type-specific parameters. We applied our strategy to quantitative time-resolved data of EPO-induced JAK/STAT signaling generated by quantitative immunoblotting, mass spectrometry and quantitative real-time PCR (qRT-PCR) in CFU-E and H838 cells as well as H838 cells overexpressing human EPOR (H838-HA-hEPOR). The established parsimonious mathematical model was able to simultaneously describe the data sets of CFU-E, H838 and H838-HA-hEPOR cells. Seven cell type-specific parameters were identified that included for example parameters for nuclear translocation of STAT5 and target gene induction. Cell type-specific differences in target gene induction were experimentally validated by qRT-PCR experiments. The systematic identification of pathway differences and sensitivities of EPOR signaling in CFU-E and H838 cells revealed potential targets for intervention to selectively inhibit EPO-induced signaling in the tumor cells but leave the responses in erythroid

  12. Identification of Cell Type-Specific Differences in Erythropoietin Receptor Signaling in Primary Erythroid and Lung Cancer Cells.

    Science.gov (United States)

    Merkle, Ruth; Steiert, Bernhard; Salopiata, Florian; Depner, Sofia; Raue, Andreas; Iwamoto, Nao; Schelker, Max; Hass, Helge; Wäsch, Marvin; Böhm, Martin E; Mücke, Oliver; Lipka, Daniel B; Plass, Christoph; Lehmann, Wolf D; Kreutz, Clemens; Timmer, Jens; Schilling, Marcel; Klingmüller, Ursula

    2016-08-01

    Lung cancer, with its most prevalent form non-small-cell lung carcinoma (NSCLC), is one of the leading causes of cancer-related deaths worldwide, and is commonly treated with chemotherapeutic drugs such as cisplatin. Lung cancer patients frequently suffer from chemotherapy-induced anemia, which can be treated with erythropoietin (EPO). However, studies have indicated that EPO not only promotes erythropoiesis in hematopoietic cells, but may also enhance survival of NSCLC cells. Here, we verified that the NSCLC cell line H838 expresses functional erythropoietin receptors (EPOR) and that treatment with EPO reduces cisplatin-induced apoptosis. To pinpoint differences in EPO-induced survival signaling in erythroid progenitor cells (CFU-E, colony forming unit-erythroid) and H838 cells, we combined mathematical modeling with a method for feature selection, the L1 regularization. Utilizing an example model and simulated data, we demonstrated that this approach enables the accurate identification and quantification of cell type-specific parameters. We applied our strategy to quantitative time-resolved data of EPO-induced JAK/STAT signaling generated by quantitative immunoblotting, mass spectrometry and quantitative real-time PCR (qRT-PCR) in CFU-E and H838 cells as well as H838 cells overexpressing human EPOR (H838-HA-hEPOR). The established parsimonious mathematical model was able to simultaneously describe the data sets of CFU-E, H838 and H838-HA-hEPOR cells. Seven cell type-specific parameters were identified that included for example parameters for nuclear translocation of STAT5 and target gene induction. Cell type-specific differences in target gene induction were experimentally validated by qRT-PCR experiments. The systematic identification of pathway differences and sensitivities of EPOR signaling in CFU-E and H838 cells revealed potential targets for intervention to selectively inhibit EPO-induced signaling in the tumor cells but leave the responses in erythroid

  13. Cell-type specific regulation of cortical excitability through the allatostatin receptor system

    Directory of Open Access Journals (Sweden)

    Tomoko Velasquez

    2012-01-01

    Full Text Available Recent technical advances enable the regulation of neuronal circuit activity with high spatial and temporal resolution through genetic delivery of molecular activation or inactivation systems. Among them, the allatostatin receptor (AlstR/ligand system has been developed for selective and quickly reversible silencing of mammalian neurons. However, targeted AlstR-mediated inactivation of specific neuronal types, particularly diverse types of inhibitory interneurons, remains to be established. In the present study, we achieved Cre-directed expression of AlstRs to excitatory and inhibitory cell types in the cortex, and found that the AlstR-mediated inactivation was specific and robust at single cell and neuronal population levels. Bath application of the allatostatin peptide markedly reduced spiking activity of AlstR-expressing excitatory and inhibitory neurons in response to intrasomatic current injections and laser photostimulation via glutamate uncaging, but control neurons without AlstR expression were not affected. As for the cortical network activity, the peptide application constrained photostimulation-evoked excitatory activity propagation detected by fast voltage-sensitive dye (VSD imaging of the slices expressing AlstRs selectively in excitatory neurons, while it augmented excitatory activity in those slices with inhibitory neurons expressing AlstRs. In addition, AlstR-mediated inactivation effectively suppressed pharmacologically-induced seizure activity in the slices targeting AlstRs to excitatory neurons. Taken together, our work demonstrated that the genetic delivery of AlstRs can be used for regulation of cortical excitability in a cell-type specific manner, and suggested that the AlstR system can be potentially used for fast seizure control.

  14. Targeting the hemangioblast with a novel cell type-specific enhancer

    Directory of Open Access Journals (Sweden)

    Teixeira Vera

    2011-12-01

    Full Text Available Abstract Background Hemangioblasts are known as the common precursors for primitive hematopoietic and endothelial lineages. Their existence has been supported mainly by the observation that both cell types develop in close proximity and by in vitro differentiation and genetic studies. However, more compelling evidence will arise from tracking their cell fates using a lineage-specific marker. Results We report the identification of a hemangioblast-specific enhancer (Hb located in the cis-regulatory region of chick Cerberus gene (cCer that is able to direct the expression of enhanced green fluorescent protein (eGFP to the precursors of yolk sac blood and endothelial cells in electroporated chick embryos. Moreover, we present the Hb-eGFP reporter as a powerful live imaging tool for visualizing hemangioblast cell fate and blood island morphogenesis. Conclusions We hereby introduce the Hb enhancer as a valuable resource for genetically targeting the hemangioblast population as well as for studying the dynamics of vascular and blood cell development.

  15. Cell-Type Specific Inactivation of Hippocampal CA1 Disrupts Location-Dependent Object Recognition in the Mouse

    Science.gov (United States)

    Haettig, Jakob; Sun, Yanjun; Wood, Marcelo A.; Xu, Xiangmin

    2013-01-01

    The allatostatin receptor (AlstR)/ligand inactivation system enables potent regulation of neuronal circuit activity. To examine how different cell types participate in memory formation, we have used this system through Cre-directed, cell-type specific expression in mouse hippocampal CA1 in vivo and examined functional effects of inactivation of…

  16. Improved salinity tolerance of rice through cell type-specific expression of AtHKT1;1

    OpenAIRE

    Darren Plett; Gehan Safwat; Matthew Gilliham; Inge Skrumsager Møller; Stuart Roy; Neil Shirley; Andrew Jacobs; Alexander Johnson; Mark Tester

    2010-01-01

    Previously, cell type-specific expression of AtHKT1;1, a sodium transporter, improved sodium (Na(+)) exclusion and salinity tolerance in Arabidopsis. In the current work, AtHKT1;1, was expressed specifically in the root cortical and epidermal cells of an Arabidopsis GAL4-GFP enhancer trap line. These transgenic plants were found to have significantly improved Na(+) exclusion under conditions of salinity stress. The feasibility of a similar biotechnological approach in crop plants was explored...

  17. Cell type specificity of female lung cancer associated with sulfur dioxide from air pollutants in Taiwan: An ecological study

    OpenAIRE

    Tseng Ching-Yu; Huang Yi-Chia; Su Shih-Yung; Huang Jing-Yang; Lai Cheng-Hsiu; Lung Chia-Chi; Ho Chien-Chang; Liaw Yung-Po

    2012-01-01

    Abstract Background Many studies have examined the association between air pollutants (including sulfur dioxide [SO2], carbon monoxide [CO], nitrogen dioxide [NO2], nitric oxide [NO], ozone [O3], and particulate matter < 10 μm [PM10]) and lung cancer. However, data from previous studies on pathological cell types were limited, especially for SO2 exposure. We aimed to explore the association between SO2 exposure from outdoor air pollutants and female lung cancer incidence by cell type specific...

  18. Molecular Characterization of Arabidopsis GAL4/UAS Enhancer Trap Lines Identifies Novel Cell-Type-Specific Promoters.

    Science.gov (United States)

    Radoeva, Tatyana; Ten Hove, Colette A; Saiga, Shunsuke; Weijers, Dolf

    2016-06-01

    Cell-type-specific gene expression is essential to distinguish between the numerous cell types of multicellular organism. Therefore, cell-type-specific gene expression is tightly regulated and for most genes RNA transcription is the central point of control. Thus, transcriptional reporters are broadly used markers for cell identity. In Arabidopsis (Arabidopsis thaliana), a recognized standard for cell identities is a collection of GAL4/UAS enhancer trap lines. Yet, while greatly used, very few of them have been molecularly characterized. Here, we have selected a set of 21 frequently used GAL4/UAS enhancer trap lines for detailed characterization of expression pattern and genomic insertion position. We studied their embryonic and postembryonic expression domains and grouped them into three groups (early embryo development, late embryo development, and embryonic root apical meristem lines) based on their dominant expression. We show that some of the analyzed lines are expressed in a domain often broader than the one that is reported. Additionally, we present an overview of the location of the T-DNA inserts of all lines, with one exception. Finally, we demonstrate how the obtained information can be used for generating novel cell-type-specific marker lines and for genotyping enhancer trap lines. The knowledge could therefore support the extensive use of these valuable lines. PMID:27208300

  19. The evolutionary emergence of cell type-specific genes inferred from the gene expression analysis of Hydra

    Science.gov (United States)

    Hwang, Jung Shan; Ohyanagi, Hajime; Hayakawa, Shiho; Osato, Naoki; Nishimiya-Fujisawa, Chiemi; Ikeo, Kazuho; David, Charles N.; Fujisawa, Toshitaka; Gojobori, Takashi

    2007-01-01

    Cell lineages of cnidarians including Hydra represent the fundamental cell types of metazoans and provides us a unique opportunity to study the evolutionary diversification of cell type in the animal kingdom. Hydra contains epithelial cells as well as a multipotent interstitial cell (I-cell) that gives rise to nematocytes, nerve cells, gland cells, and germ-line cells. We used cDNA microarrays to identify cell type-specific genes by comparing gene expression in normal Hydra with animals lacking the I-cell lineage, so-called epithelial Hydra. We then performed in situ hybridization to localize expression to specific cell types. Eighty-six genes were shown to be expressed in specific cell types of the I-cell lineage. An additional 29 genes were expressed in epithelial cells and were down-regulated in epithelial animals lacking I-cells. Based on the above information, we constructed a database (http://hydra.lab.nig.ac.jp/hydra/), which describes the expression patterns of cell type-specific genes in Hydra. Most genes expressed specifically in either I-cells or epithelial cells have homologues in higher metazoans. By comparison, most nematocyte-specific genes and approximately half of the gland cell- and nerve cell-specific genes are unique to the cnidarian lineage. Because nematocytes, gland cells, and nerve cells appeared along with the emergence of cnidarians, this suggests that lineage-specific genes arose in cnidarians in conjunction with the evolution of new cell types required by the cnidarians. PMID:17766437

  20. CAST-ChIP Maps Cell-Type-Specific Chromatin States in the Drosophila Central Nervous System

    Directory of Open Access Journals (Sweden)

    Tamás Schauer

    2013-10-01

    Full Text Available Chromatin organization and gene activity are responsive to developmental and environmental cues. Although many genes are transcribed throughout development and across cell types, much of gene regulation is highly cell-type specific. To readily track chromatin features at the resolution of cell types within complex tissues, we developed and validated chromatin affinity purification from specific cell types by chromatin immunoprecipitation (CAST-ChIP, a broadly applicable biochemical procedure. RNA polymerase II (Pol II CAST-ChIP identifies ∼1,500 neuronal and glia-specific genes in differentiated cells within the adult Drosophila brain. In contrast, the histone H2A.Z is distributed similarly across cell types and throughout development, marking cell-type-invariant Pol II-bound regions. Our study identifies H2A.Z as an active chromatin signature that is refractory to changes across cell fates. Thus, CAST-ChIP powerfully identifies cell-type-specific as well as cell-type-invariant chromatin states, enabling the systematic dissection of chromatin structure and gene regulation within complex tissues such as the brain.

  1. Cell-type-specific control elements of the lymphotropic papovavirus enhancer.

    OpenAIRE

    Erselius, J R; Jostes, B; Hatzopoulos, A K; Mosthaf, L; Gruss, P

    1990-01-01

    Lymphotropic papovavirus (LPV) exhibits a highly restricted host range, in which only cells of primate B-lymphocyte origin are permissive for infection. Its enhancer element contributes to this tropism, since transcriptional potentiation is confined to cells of the hematopoietic lineage. Nuclear extracts from B and T cells, but not from HeLa cells, contain protein factors that interact specifically with the LPV 63-base-pair enhancer repeat, as demonstrated by DNase I footprinting and gel reta...

  2. Gene expression profiles of hepatic cell-type specific marker genes in progression of liver fibrosis

    Institute of Scientific and Technical Information of China (English)

    Yoshiyuki Takahara; Mitsuo Takahashi; Hiroki Wagatsuma; Fumihiko Yokoya; Qing-Wei Zhang; Mutsuyo Yamaguchi; Hiroyuki Aburatani; Norifumi Kawada

    2006-01-01

    AIM: To determine the gene expression profile data for the whole liver during development of dimethylnitrosamine (DMN)-induced hepatic fibrosis.METHODS: Marker genes were identified for different types of hepatic cells, including hepatic stellate cells (HSCs), Kupffer cells (including other inflammatory cells),and hepatocytes, using independent temporal DNA microarray data obtained from isolated hepatic cells.RESULTS: The cell-type analysis of gene expression gave several key results and led to formation of three hypotheses: (1) changes in the expression of HSCspecific marker genes during fibrosis were similar to gene expression data in in vitro cultured HSCs, suggesting a major role of the self-activating characteristics of HSCs in formation of fibrosis; (2) expression of mast cell-specific marker genes reached a peak during liver fibrosis,suggesting a possible role of mast cells in formation of fibrosis; and (3) abnormal expression of hepatocytespecific marker genes was found across several metabolic pathways during fibrosis, including sulfur-containing amino acid metabolism, fatty acid metabolism, and drug metabolism, suggesting a mechanistic relationship between these abnormalities and symptoms of liver fibrosis.CONCLUSION: Analysis of marker genes for specific hepatic cell types can identify the key aspects of fibrogenesis. Sequential activation of inflammatory cells and the self-supporting properties of HSCs play an important role in development of fibrosis.

  3. Defining cell-type specificity at the transcriptional level in human disease

    OpenAIRE

    Ju, Wenjun; Greene, Casey S; Eichinger, Felix; Nair, Viji; Hodgin, Jeffrey B.; Bitzer, Markus; Lee, Young-Suk; Zhu, Qian; Kehata, Masami; Li, Min; Jiang, Song; Rastaldi, Maria Pia; Cohen, Clemens D; Troyanskaya, Olga G.; Kretzler, Matthias

    2013-01-01

    Cell-lineage–specific transcripts are essential for differentiated tissue function, implicated in hereditary organ failure, and mediate acquired chronic diseases. However, experimental identification of cell-lineage–specific genes in a genome-scale manner is infeasible for most solid human tissues. We developed the first genome-scale method to identify genes with cell-lineage–specific expression, even in lineages not separable by experimental microdissection. Our machine-learning–based approa...

  4. Cell-type-specific neuroanatomy of cliques of autism-related genes in the mouse brain

    Directory of Open Access Journals (Sweden)

    Pascal eGrange

    2015-05-01

    Full Text Available Two cliques of genes identified computationally for their high co-expression in the mouse brain according to the Allen Brain Atlas, and for their enrichment in genes related to autism spectrum disorder, have recently been shown to be highly co-expressed in the cerebellar cortex, compared to what could be expected by chance. Moreover, the expression of these cliques of genes is not homogeneous across the cerebellar cortex, and it has been noted that their expression pattern seems to highlight the granular layer. However, this observation was only made by eye, and recent advances in computational neuroanatomy allow to rank cell types in the mouse brain (characterized by their transcriptome profiles according to the similarity between their spatial density profiles and the expression profiles of the cliques. We establish by Monte Carlo simulation that with probability at least 99%, the expression profiles of the two cliques are more similar to the density profile of granule cells than 99% of the expression of cliques containing the same number of genes (Purkinje cells also score above 99% in one of the cliques. Thresholding the expression profiles shows that the signal is more intense in the granular layer. Finally, we work out pairs of cell types whose combined expression profiles are more similar to the expression profiles of the cliquesthan any single cell type. These pairs predominantly consist of one cortical pyramidal cell and one cerebellar cell (whichcan be either a granule cell or a Purkinje cell.

  5. Cell-type-specific neuroanatomy of cliques of autism-related genes in the mouse brain.

    Science.gov (United States)

    Grange, Pascal; Menashe, Idan; Hawrylycz, Michael

    2015-01-01

    Two cliques of genes identified computationally for their high co-expression in the mouse brain according to the Allen Brain Atlas, and for their enrichment in genes related to autism spectrum disorder (ASD), have recently been shown to be highly co-expressed in the cerebellar cortex, compared to what could be expected by chance. Moreover, the expression of these cliques of genes is not homogeneous across the cerebellar cortex, and it has been noted that their expression pattern seems to highlight the granular layer. However, this observation was only made by eye, and recent advances in computational neuroanatomy allow to rank cell types in the mouse brain (characterized by their transcriptome profiles) according to the similarity between their spatial density profiles and the spatial expression profiles of the cliques. We establish by Monte Carlo simulation that with probability at least 99%, the expression profiles of the two cliques are more similar to the density profile of granule cells than 99% of the expression of cliques containing the same number of genes (Purkinje cells also score above 99% in one of the cliques). Thresholding the expression profiles shows that the signal is more intense in the granular layer. Finally, we work out pairs of cell types whose combined expression profiles are more similar to the expression profiles of the cliques than any single cell type. These pairs predominantly consist of one cortical pyramidal cell and one cerebellar cell (which can be either a granule cell or a Purkinje cell). PMID:26074809

  6. Assessment of Membrane Fluidity Fluctuations during Cellular Development Reveals Time and Cell Type Specificity.

    Science.gov (United States)

    Noutsi, Pakiza; Gratton, Enrico; Chaieb, Sahraoui

    2016-01-01

    Cell membrane is made up of a complex structure of lipids and proteins that diffuse laterally giving rise to what we call membrane fluidity. During cellular development, such as differentiation cell membranes undergo dramatic fluidity changes induced by proteins such as ARC and Cofilin among others. In this study we used the generalized polarization (GP) property of fluorescent probe Laurdan using two-photon microscopy to determine membrane fluidity as a function of time and for various cell lines. A low GP value corresponds to a higher fluidity and a higher GP value is associated with a more rigid membrane. Four different cell lines were monitored such as hN2, NIH3T3, HEK293 and L6 cells. Membrane fluidity was measured at 12h, 72h and 92 h. Our results show significant changes in membrane fluidity among all cell types at different time points. GP values tend to increase significantly within 92 h in hN2 cells and 72 h in NIH3T3 cells and only at 92 h in HEK293 cells. L6 showed a marked decrease in membrane fluidity at 72 h and starts to increase at 92 h. As expected, NIH3T3 cells have more rigid membrane at earlier time points. On the other hand, neurons tend to have the highest membrane fluidity at early time points emphasizing its correlation with plasticity and the need for this malleability during differentiation. This study sheds light on the involvement of membrane fluidity during neuronal differentiation and development of other cell lines. PMID:27362860

  7. Assessment of Membrane Fluidity Fluctuations during Cellular Development Reveals Time and Cell Type Specificity

    KAUST Repository

    Noutsi, Pakiza

    2016-06-30

    Cell membrane is made up of a complex structure of lipids and proteins that diffuse laterally giving rise to what we call membrane fluidity. During cellular development, such as differentiation cell membranes undergo dramatic fluidity changes induced by proteins such as ARC and Cofilin among others. In this study we used the generalized polarization (GP) property of fluorescent probe Laurdan using two-photon microscopy to determine membrane fluidity as a function of time and for various cell lines. A low GP value corresponds to a higher fluidity and a higher GP value is associated with a more rigid membrane. Four different cell lines were monitored such as hN2, NIH3T3, HEK293 and L6 cells. Membrane fluidity was measured at 12h, 72h and 92 h. Our results show significant changes in membrane fluidity among all cell types at different time points. GP values tend to increase significantly within 92 h in hN2 cells and 72 h in NIH3T3 cells and only at 92 h in HEK293 cells. L6 showed a marked decrease in membrane fluidity at 72 h and starts to increase at 92 h. As expected, NIH3T3 cells have more rigid membrane at earlier time points. On the other hand, neurons tend to have the highest membrane fluidity at early time points emphasizing its correlation with plasticity and the need for this malleability during differentiation. This study sheds light on the involvement of membrane fluidity during neuronal differentiation and development of other cell lines.

  8. Cell-Type Specific DNA Methylation Patterns Define Human Breast Cellular Identity

    Czech Academy of Sciences Publication Activity Database

    Novák, Petr; Stampfer, M.R.; Munoz-Rodriguez, J.L.; Garbe, J.C.; Ehrich, M.; Futscher, B. W.; Jensen, T.J.

    2012-01-01

    Roč. 7, č. 12 (2012), e52299. E-ISSN 1932-6203 Institutional research plan: CEZ:AV0Z50510513 Institutional support: RVO:60077344 Keywords : MAMMARY EPITHELIAL-CELLS * PLURIPOTENT STEM-CELLS * CPG ISLAND SHORES Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.730, year: 2012

  9. Gene Expression Programs in Response to Hypoxia: Cell Type Specificity and Prognostic Significance in Human Cancers.

    Directory of Open Access Journals (Sweden)

    2006-01-01

    Full Text Available BACKGROUND: Inadequate oxygen (hypoxia triggers a multifaceted cellular response that has important roles in normal physiology and in many human diseases. A transcription factor, hypoxia-inducible factor (HIF, plays a central role in the hypoxia response; its activity is regulated by the oxygen-dependent degradation of the HIF-1alpha protein. Despite the ubiquity and importance of hypoxia responses, little is known about the variation in the global transcriptional response to hypoxia among different cell types or how this variation might relate to tissue- and cell-specific diseases. METHODS AND FINDINGS: We analyzed the temporal changes in global transcript levels in response to hypoxia in primary renal proximal tubule epithelial cells, breast epithelial cells, smooth muscle cells, and endothelial cells with DNA microarrays. The extent of the transcriptional response to hypoxia was greatest in the renal tubule cells. This heightened response was associated with a uniquely high level of HIF-1alpha RNA in renal cells, and it could be diminished by reducing HIF-1alpha expression via RNA interference. A gene-expression signature of the hypoxia response, derived from our studies of cultured mammary and renal tubular epithelial cells, showed coordinated variation in several human cancers, and was a strong predictor of clinical outcomes in breast and ovarian cancers. In an analysis of a large, published gene-expression dataset from breast cancers, we found that the prognostic information in the hypoxia signature was virtually independent of that provided by the previously reported wound signature and more predictive of outcomes than any of the clinical parameters in current use. CONCLUSIONS: The transcriptional response to hypoxia varies among human cells. Some of this variation is traceable to variation in expression of the HIF1A gene. A gene-expression signature of the cellular response to hypoxia is associated with a significantly poorer prognosis

  10. Cell-type specific adhesive interactions of skeletal myoblasts with thrombospondin-1.

    OpenAIRE

    Adams, J. C.; Lawler, J

    1994-01-01

    Thrombospondin-1 (TSP-1) is an extracellular matrix glycoprotein that may play important roles in the morphogenesis and repair of skeletal muscle. To begin to explore the role of thrombospondin-1 in this tissue, we have examined the interactions of three rodent skeletal muscle cell lines, C2C12, G8, and H9c2, with platelet TSP-1. The cells secrete thrombospondin and incorporate it into the cell layer in a distribution distinct from that of fibronectin. Myoblasts attach and spread on fibronect...

  11. Cell type specificity and structural determinants of IRES activity from the 5' leaders of different HIV-1 transcripts.

    Science.gov (United States)

    Plank, Terra-Dawn M; Whitehurst, James T; Kieft, Jeffrey S

    2013-07-01

    Internal ribosome entry site (IRES) RNAs are important regulators of gene expression, but their diverse molecular mechanisms remain partially understood. The HIV-1 gag transcript leader contains an IRES that may be a good model for understanding the function of many other IRESs. We investigated the possibility that this IRES' function is linked to both the structure of the RNA and its cellular environment. We find that in the context of a bicistronic reporter construct, HIV-1 gag IRES' activity is cell type-specific, with higher activity in T-cell culture systems that model the natural target cells for HIV-1 infection. This finding underscores how an IRES may be fine tuned to function in certain cells, perhaps owing to cell type-specific protein factors. Using RNA probing and mutagenesis, we demonstrate that the HIV-1 gag IRES does not use pre-folded RNA structure to drive function, a finding that gives insight into how conformationally dynamic IRESs operate. Furthermore, we find that a common exon drives IRES activity in a diverse set of alternatively spliced transcripts. We propose a mechanism in which a structurally plastic RNA element confers the ability to initiate translation internally, and activity from this common element is modulated by 3' nucleotides added by alternative splicing. PMID:23661682

  12. Cell type specificity and structural determinants of IRES activity from the 5′ leaders of different HIV-1 transcripts

    Science.gov (United States)

    Plank, Terra-Dawn M.; Whitehurst, James T.; Kieft, Jeffrey S.

    2013-01-01

    Internal ribosome entry site (IRES) RNAs are important regulators of gene expression, but their diverse molecular mechanisms remain partially understood. The HIV-1 gag transcript leader contains an IRES that may be a good model for understanding the function of many other IRESs. We investigated the possibility that this IRES’ function is linked to both the structure of the RNA and its cellular environment. We find that in the context of a bicistronic reporter construct, HIV-1 gag IRES’ activity is cell type-specific, with higher activity in T-cell culture systems that model the natural target cells for HIV-1 infection. This finding underscores how an IRES may be fine tuned to function in certain cells, perhaps owing to cell type-specific protein factors. Using RNA probing and mutagenesis, we demonstrate that the HIV-1 gag IRES does not use pre-folded RNA structure to drive function, a finding that gives insight into how conformationally dynamic IRESs operate. Furthermore, we find that a common exon drives IRES activity in a diverse set of alternatively spliced transcripts. We propose a mechanism in which a structurally plastic RNA element confers the ability to initiate translation internally, and activity from this common element is modulated by 3′ nucleotides added by alternative splicing. PMID:23661682

  13. Targeting the hemangioblast with a novel cell type-specific enhancer

    OpenAIRE

    Teixeira Vera; Arede Natacha; Gardner Rui; Rodríguez-León Joaquín; Tavares Ana T

    2011-01-01

    Abstract Background Hemangioblasts are known as the common precursors for primitive hematopoietic and endothelial lineages. Their existence has been supported mainly by the observation that both cell types develop in close proximity and by in vitro differentiation and genetic studies. However, more compelling evidence will arise from tracking their cell fates using a lineage-specific marker. Results We report the identification of a hemangioblast-specific enhancer (Hb) located in the cis-regu...

  14. Cell type-specific interactions of transcription factors with a housekeeping promoter in vivo.

    OpenAIRE

    Stapleton, G; Somma, M P; Lavia, P

    1993-01-01

    Mammalian housekeeping promoters represent a class of regulatory elements different from those of tissues-specific genes, lacking a TATA box and associated with CG-rich DNA. We have compared the organization of the housekeeping Htf9 promoter in different cell types by genomic footprinting. The sites of in vivo occupancy clearly reflected local combinations of tissue-specific and ubiquitous binding factors. The flexibility of the Htf9 promoter in acting as the target of cell-specific combinati...

  15. Unique cell type-specific junctional complexes in vascular endothelium of human and rat liver sinusoids.

    Directory of Open Access Journals (Sweden)

    Cyrill Géraud

    Full Text Available Liver sinusoidal endothelium is strategically positioned to control access of fluids, macromolecules and cells to the liver parenchyma and to serve clearance functions upstream of the hepatocytes. While clearance of macromolecular debris from the peripheral blood is performed by liver sinusoidal endothelial cells (LSECs using a delicate endocytic receptor system featuring stabilin-1 and -2, the mannose receptor and CD32b, vascular permeability and cell trafficking are controlled by transcellular pores, i.e. the fenestrae, and by intercellular junctional complexes. In contrast to blood vascular and lymphatic endothelial cells in other organs, the junctional complexes of LSECs have not yet been consistently characterized in molecular terms. In a comprehensive analysis, we here show that LSECs express the typical proteins found in endothelial adherens junctions (AJ, i.e. VE-cadherin as well as α-, β-, p120-catenin and plakoglobin. Tight junction (TJ transmembrane proteins typical of endothelial cells, i.e. claudin-5 and occludin, were not expressed by rat LSECs while heterogenous immunreactivity for claudin-5 was detected in human LSECs. In contrast, junctional molecules preferentially associating with TJ such as JAM-A, B and C and zonula occludens proteins ZO-1 and ZO-2 were readily detected in LSECs. Remarkably, among the JAMs JAM-C was considerably over-expressed in LSECs as compared to lung microvascular endothelial cells. In conclusion, we show here that LSECs form a special kind of mixed-type intercellular junctions characterized by co-occurrence of endothelial AJ proteins, and of ZO-1 and -2, and JAMs. The distinct molecular architecture of the intercellular junctional complexes of LSECs corroborates previous ultrastructural findings and provides the molecular basis for further analyses of the endothelial barrier function of liver sinusoids under pathologic conditions ranging from hepatic inflammation to formation of liver metastasis.

  16. Analysis of cell-type-specific gene expression during mouse spermatogenesis

    DEFF Research Database (Denmark)

    Almstrup, Kristian; Nielsen, John E; Hansen, Martin Asser;

    2004-01-01

    In rodents, changes in gene expression during spermatogenesis can be monitored by sampling testis from each day during postnatal development. However, changes in gene expression at the tissue level can reflect changes in the concentration of an mRNA in a specific cell type, changes in volume of s...

  17. Strain Variation in Glycosaminoglycan Recognition Influences Cell-Type-Specific Binding by Lyme Disease Spirochetes

    OpenAIRE

    Parveen, Nikhat; Robbins, Douglas; Leong, John M.

    1999-01-01

    Lyme disease, a chronic multisystemic disorder that can affect the skin, heart, joints, and nervous system is caused by Borrelia burgdorferi sensu lato. Lyme disease spirochetes were previously shown to bind glycosaminoglycans (GAGs). In the current study, the GAG-binding properties of eight Lyme disease strains were determined. Binding by two high-passage HB19 derivatives to Vero cells could not be inhibited by enzymatic removal of GAGs or by the addition of exogenous GAG. The other six stra...

  18. Innate immune response to pulmonary contusion: Identification of cell-type specific inflammatory responses

    OpenAIRE

    Hoth, J. Jason; Wells, Jonathan D.; Yoza, Barbara K.; McCall, Charles E.

    2012-01-01

    Lung injury from pulmonary contusion is a common traumatic injury, predominantly seen after blunt chest trauma such as in vehicular accidents. The local and systemic inflammatory response to injury includes activation of innate immune receptors, elaboration of a variety inflammatory mediators, and recruitment of inflammatory cells to the injured lung. Using a mouse model of pulmonary contusion, we had previously shown that innate immune Toll like receptors 2 and 4 (TLR2 and TLR4) mediate the ...

  19. Cell-Type Specific Determinants of NRAMP1 Expression in Professional Phagocytes

    Directory of Open Access Journals (Sweden)

    Mathieu F. M. Cellier

    2013-01-01

    Full Text Available The Natural resistance-associated macrophage protein 1 (Nramp1 or Solute carrier 11 member 1, Slc11a1 transports divalent metals across the membrane of late endosomes and lysosomes in professional phagocytes. Nramp1 represents an ancient eukaryotic cell-autonomous defense whereas the gene duplication that yielded Nramp1 and Nramp2 predated the origin of Sarcopterygians (lobe-finned fishes and tetrapods. SLC11A1 genetic polymorphisms associated with human resistance to tuberculosis consist of potential regulatory variants. Herein, current knowledge of the regulation of SLC11A1 gene expression is reviewed and comprehensive analysis of ENCODE data available for hematopoietic cell-types suggests a hypothesis for the regulation of SLC11A1 expression during myeloid development and phagocyte functional polarization. SLC11A1 is part of a 34.6 kb CTCF-insulated locus scattered with predicted regulatory elements: a 3' enhancer, a large 5' enhancer domain and four elements spread around the transcription start site (TSS, including several C/EBP and PU.1 sites. SLC11A1 locus ends appear mobilized by ETS-related factors early during myelopoiesis; activation of both 5' and 3' enhancers in myelo-monocytic cells correlate with transcription factor binding at the TSS. Characterizing the corresponding cis/trans determinants functionally will establish the mechanisms involved and possibly reveal genetic variation that impacts susceptibility to infectious or immune diseases.

  20. Measuring cell-type specific differential methylation in human brain tissue.

    Science.gov (United States)

    Montaño, Carolina M; Irizarry, Rafael A; Kaufmann, Walter E; Talbot, Konrad; Gur, Raquel E; Feinberg, Andrew P; Taub, Margaret A

    2013-01-01

    The behavior of epigenetic mechanisms in the brain is obscured by tissue heterogeneity and disease-related histological changes. Not accounting for these confounders leads to biased results. We develop a statistical methodology that estimates and adjusts for celltype composition by decomposing neuronal and non-neuronal differential signal. This method provides a conceptual framework for deconvolving heterogeneous epigenetic data from postmortem brain studies. We apply it to find cell-specific differentially methylated regions between prefrontal cortex and hippocampus. We demonstrate the utility of the method on both Infinium 450k and CHARM data. PMID:24000956

  1. Cell-type specific mechanisms of D-serine uptake and release in the brain

    Directory of Open Access Journals (Sweden)

    Magalie eMartineau

    2014-05-01

    Full Text Available Accumulating evidence during the last decade established that D-serine is a key signaling molecule utilized by neurons and astroglia in the mammalian central nervous system. D-serine is increasingly appreciated as the main physiological endogenous coagonist for synaptic NMDA receptors at central excitatory synapses; it is mandatory for long-term changes in synaptic strength, memory, learning, and social interactions. Alterations in the extracellular levels of D-serine leading to disrupted cell-cell signaling are a trademark of many chronic or acute neurological (i.e. Alzheimer disease, epilepsy, stroke and psychiatric (i.e. schizophrenia disorders, and are associated with addictive behavior (i.e. cocaine addiction. Indeed, fine tuning of the extracellular levels of D-serine, achieved by various molecular machineries and signaling pathways, is necessary for maintenance of accurate NMDA receptor functions. Here, we review the experimental data supporting the notion that astroglia and neurons use different pathways to regulate levels of extracellular D-serine.

  2. Cell Type-Specific Control of Spike Timing by Gamma-Band Oscillatory Inhibition.

    Science.gov (United States)

    Hasenstaub, Andrea; Otte, Stephani; Callaway, Edward

    2016-02-01

    Many lines of theoretical and experimental investigation have suggested that gamma oscillations provide a temporal framework for cortical information processing, acting to either synchronize neuronal firing, restrict neuron's relative spike times, and/or provide a global reference signal to which neurons encode input strength. Each theory has been disputed and some believe that gamma is an epiphenomenon. We investigated the biophysical plausibility of these theories by performing in vitro whole-cell recordings from 6 cortical neuron subtypes and examining how gamma-band and slow fluctuations in injected input affect precision and phase of spike timing. We find that gamma is at least partially able to restrict the spike timing in all subtypes tested, but to varying degrees. Gamma exerts more precise control of spike timing in pyramidal neurons involved in cortico-cortical versus cortico-subcortical communication and in inhibitory neurons that target somatic versus dendritic compartments. We also find that relatively few subtypes are capable of phase-based information coding. Using simple neuron models and dynamic clamp, we determine which intrinsic differences lead to these variations in responsiveness and discuss both the flexibility and confounds of gamma-based spike-timing systems. PMID:25778344

  3. Cell-type specific oxytocin gene expression from AAV delivered promoter deletion constructs into the rat supraoptic nucleus in vivo.

    Directory of Open Access Journals (Sweden)

    Raymond L Fields

    Full Text Available The magnocellular neurons (MCNs in the hypothalamus selectively express either oxytocin (OXT or vasopressin (AVP neuropeptide genes, a property that defines their phenotypes. Here we examine the molecular basis of this selectivity in the OXT MCNs by stereotaxic microinjections of adeno-associated virus (AAV vectors that contain various OXT gene promoter deletion constructs using EGFP as the reporter into the rat supraoptic nucleus (SON. Two weeks following injection of the AAVs, immunohistochemical assays of EGFP expression from these constructs were done to determine whether the EGFP reporter co-localizes with either the OXT- or AVP-immunoreactivity in the MCNs. The results show that the key elements in the OT gene promoter that regulate the cell-type specific expression the SON are located -216 to -100 bp upstream of the transcription start site. We hypothesize that within this 116 bp domain a repressor exists that inhibits expression specifically in AVP MCNs, thereby leading to the cell-type specific expression of the OXT gene only in the OXT MCNs.

  4. A quantitative comparison of cell-type-specific microarray gene expression profiling methods in the mouse brain.

    Directory of Open Access Journals (Sweden)

    Benjamin W Okaty

    Full Text Available Expression profiling of restricted neural populations using microarrays can facilitate neuronal classification and provide insight into the molecular bases of cellular phenotypes. Due to the formidable heterogeneity of intermixed cell types that make up the brain, isolating cell types prior to microarray processing poses steep technical challenges that have been met in various ways. These methodological differences have the potential to distort cell-type-specific gene expression profiles insofar as they may insufficiently filter out contaminating mRNAs or induce aberrant cellular responses not normally present in vivo. Thus we have compared the repeatability, susceptibility to contamination from off-target cell-types, and evidence for stress-responsive gene expression of five different purification methods--Laser Capture Microdissection (LCM, Translating Ribosome Affinity Purification (TRAP, Immunopanning (PAN, Fluorescence Activated Cell Sorting (FACS, and manual sorting of fluorescently labeled cells (Manual. We found that all methods obtained comparably high levels of repeatability, however, data from LCM and TRAP showed significantly higher levels of contamination than the other methods. While PAN samples showed higher activation of apoptosis-related, stress-related and immediate early genes, samples from FACS and Manual studies, which also require dissociated cells, did not. Given that TRAP targets actively translated mRNAs, whereas other methods target all transcribed mRNAs, observed differences may also reflect translational regulation.

  5. Cell-Type-Specific Profiling of Gene Expression and Chromatin Binding without Cell Isolation: Assaying RNA Pol II Occupancy in Neural Stem Cells

    OpenAIRE

    Southall, Tony D.; Gold, Katrina S.; Egger, Boris; Davidson, Catherine M.; Caygill, Elizabeth E.; Marshall, Owen J.; Brand, Andrea H.

    2013-01-01

    Summary Cell-type-specific transcriptional profiling often requires the isolation of specific cell types from complex tissues. We have developed “TaDa,” a technique that enables cell-specific profiling without cell isolation. TaDa permits genome-wide profiling of DNA- or chromatin-binding proteins without cell sorting, fixation, or affinity purification. The method is simple, sensitive, highly reproducible, and transferable to any model system. We show that TaDa can be used to identify transc...

  6. Gamma-Retrovirus Integration Marks Cell Type-Specific Cancer Genes: A Novel Profiling Tool in Cancer Genomics

    Science.gov (United States)

    Gilroy, Kathryn L.; Terry, Anne; Naseer, Asif; de Ridder, Jeroen; Wang, Weiwei; Carpenter, Eric; Mason, Andrew; Wong, Gane K-S.; Kilbey, Anna; Neil, James C.

    2016-01-01

    Retroviruses have been foundational in cancer research since early studies identified proto-oncogenes as targets for insertional mutagenesis. Integration of murine gamma-retroviruses into the host genome favours promoters and enhancers and entails interaction of viral integrase with host BET/bromodomain factors. We report that this integration pattern is conserved in feline leukaemia virus (FeLV), a gamma-retrovirus that infects many human cell types. Analysis of FeLV insertion sites in the MCF-7 mammary carcinoma cell line revealed strong bias towards active chromatin marks with no evidence of significant post-integration growth selection. The most prominent FeLV integration targets had little overlap with the most abundantly expressed transcripts, but were strongly enriched for annotated cancer genes. A meta-analysis based on several gamma-retrovirus integration profiling (GRIP) studies in human cells (CD34+, K562, HepG2) revealed a similar cancer gene bias but also remarkable cell-type specificity, with prominent exceptions including a universal integration hotspot at the long non-coding RNA MALAT1. Comparison of GRIP targets with databases of super-enhancers from the same cell lines showed that these have only limited overlap and that GRIP provides unique insights into the upstream drivers of cell growth. These observations elucidate the oncogenic potency of the gamma-retroviruses and support the wider application of GRIP to identify the genes and growth regulatory circuits that drive distinct cancer types. PMID:27097319

  7. Gamma-Retrovirus Integration Marks Cell Type-Specific Cancer Genes: A Novel Profiling Tool in Cancer Genomics.

    Science.gov (United States)

    Gilroy, Kathryn L; Terry, Anne; Naseer, Asif; de Ridder, Jeroen; Allahyar, Amin; Wang, Weiwei; Carpenter, Eric; Mason, Andrew; Wong, Gane K-S; Cameron, Ewan R; Kilbey, Anna; Neil, James C

    2016-01-01

    Retroviruses have been foundational in cancer research since early studies identified proto-oncogenes as targets for insertional mutagenesis. Integration of murine gamma-retroviruses into the host genome favours promoters and enhancers and entails interaction of viral integrase with host BET/bromodomain factors. We report that this integration pattern is conserved in feline leukaemia virus (FeLV), a gamma-retrovirus that infects many human cell types. Analysis of FeLV insertion sites in the MCF-7 mammary carcinoma cell line revealed strong bias towards active chromatin marks with no evidence of significant post-integration growth selection. The most prominent FeLV integration targets had little overlap with the most abundantly expressed transcripts, but were strongly enriched for annotated cancer genes. A meta-analysis based on several gamma-retrovirus integration profiling (GRIP) studies in human cells (CD34+, K562, HepG2) revealed a similar cancer gene bias but also remarkable cell-type specificity, with prominent exceptions including a universal integration hotspot at the long non-coding RNA MALAT1. Comparison of GRIP targets with databases of super-enhancers from the same cell lines showed that these have only limited overlap and that GRIP provides unique insights into the upstream drivers of cell growth. These observations elucidate the oncogenic potency of the gamma-retroviruses and support the wider application of GRIP to identify the genes and growth regulatory circuits that drive distinct cancer types. PMID:27097319

  8. Cell-type-specific tuning of Cav1.3 Ca2+-channels by a C-terminal automodulatory domain

    Science.gov (United States)

    Scharinger, Anja; Eckrich, Stephanie; Vandael, David H.; Schönig, Kai; Koschak, Alexandra; Hecker, Dietmar; Kaur, Gurjot; Lee, Amy; Sah, Anupam; Bartsch, Dusan; Benedetti, Bruno; Lieb, Andreas; Schick, Bernhard; Singewald, Nicolas; Sinnegger-Brauns, Martina J.; Carbone, Emilio; Engel, Jutta; Striessnig, Jörg

    2015-01-01

    Cav1.3 L-type Ca2+-channel function is regulated by a C-terminal automodulatory domain (CTM). It affects channel binding of calmodulin and thereby tunes channel activity by interfering with Ca2+- and voltage-dependent gating. Alternative splicing generates short C-terminal channel variants lacking the CTM resulting in enhanced Ca2+-dependent inactivation and stronger voltage-sensitivity upon heterologous expression. However, the role of this modulatory domain for channel function in its native environment is unkown. To determine its functional significance in vivo, we interrupted the CTM with a hemagglutinin tag in mutant mice (Cav1.3DCRDHA/HA). Using these mice we provide biochemical evidence for the existence of long (CTM-containing) and short (CTM-deficient) Cav1.3 α1-subunits in brain. The long (HA-labeled) Cav1.3 isoform was present in all ribbon synapses of cochlear inner hair cells. CTM-elimination impaired Ca2+-dependent inactivation of Ca2+-currents in hair cells but increased it in chromaffin cells, resulting in hyperpolarized resting potentials and reduced pacemaking. CTM disruption did not affect hearing thresholds. We show that the modulatory function of the CTM is affected by its native environment in different cells and thus occurs in a cell-type specific manner in vivo. It stabilizes gating properties of Cav1.3 channels required for normal electrical excitability. PMID:26379493

  9. Cell-type-specific tuning of Cav1.3 Ca2+-channels by a C-terminal automodulatory domain

    Directory of Open Access Journals (Sweden)

    Anja eScharinger

    2015-08-01

    Full Text Available Cav1.3 L-type Ca2+-channel function is regulated by a C-terminal automodulatory domain (CTM. It affects channel binding of calmodulin and thereby tunes channel activity by interfering with Ca2+- and voltage-dependent gating. Alternative splicing generates short C-terminal channel variants lacking the CTM resulting in enhanced Ca2+-dependent inactivation and stronger voltage-sensitivity upon heterologous expression. However, the role of this modulatory domain for channel function in its native environment is unkown. To determine its functional significance in vivo, we interrupted the CTM with a hemagglutinin tag in mutant mice (Cav1.3DCRDHA/HA. Using these mice we provide biochemical evidence for the existence of long (CTM-containing and short (CTM-deficient Cav1.3 α1-subunits in brain. The long (HA-labeled Cav1.3 isoform was present in all ribbon synapses of cochlear inner hair cells. CTM-elimination impaired Ca2+-dependent inactivation of Ca2+-currents in hair cells but increased it in chromaffin cells, resulting in hyperpolarized resting potentials and reduced pacemaking. CTM disruption did not affect hearing thresholds. We show that the modulatory function of the CTM is affected by its native environment in different cells and thus occurs in a cell-type specific manner in vivo. It is required to stabilize gating properties of Cav1.3 channels required for normal electrical excitability.

  10. Dual-specificity anti-sigma factor reinforces control of cell-type specific gene expression in Bacillus subtilis.

    Science.gov (United States)

    Serrano, Mónica; Gao, JinXin; Bota, João; Bate, Ashley R; Meisner, Jeffrey; Eichenberger, Patrick; Moran, Charles P; Henriques, Adriano O

    2015-04-01

    Gene expression during spore development in Bacillus subtilis is controlled by cell type-specific RNA polymerase sigma factors. σFand σE control early stages of development in the forespore and the mother cell, respectively. When, at an intermediate stage in development, the mother cell engulfs the forespore, σF is replaced by σG and σE is replaced by σK. The anti-sigma factor CsfB is produced under the control of σF and binds to and inhibits the auto-regulatory σG, but not σF. A position in region 2.1, occupied by an asparagine in σG and by a glutamate in οF, is sufficient for CsfB discrimination of the two sigmas, and allows it to delay the early to late switch in forespore gene expression. We now show that following engulfment completion, csfB is switched on in the mother cell under the control of σK and that CsfB binds to and inhibits σE but not σK, possibly to facilitate the switch from early to late gene expression. We show that a position in region 2.3 occupied by a conserved asparagine in σE and by a conserved glutamate in σK suffices for discrimination by CsfB. We also show that CsfB prevents activation of σG in the mother cell and the premature σG-dependent activation of σK. Thus, CsfB establishes negative feedback loops that curtail the activity of σE and prevent the ectopic activation of σG in the mother cell. The capacity of CsfB to directly block σE activity may also explain how CsfB plays a role as one of the several mechanisms that prevent σE activation in the forespore. Thus the capacity of CsfB to differentiate between the highly similar σF/σG and σE/σK pairs allows it to rinforce the cell-type specificity of these sigma factors and the transition from early to late development in B. subtilis, and possibly in all sporeformers that encode a CsfB orthologue. PMID:25835496

  11. Balancing intestinal and systemic inflammation through cell type-specific expression of the aryl hydrocarbon receptor repressor.

    Science.gov (United States)

    Brandstätter, Olga; Schanz, Oliver; Vorac, Julia; König, Jessica; Mori, Tetsushi; Maruyama, Toru; Korkowski, Markus; Haarmann-Stemmann, Thomas; von Smolinski, Dorthe; Schultze, Joachim L; Abel, Josef; Esser, Charlotte; Takeyama, Haruko; Weighardt, Heike; Förster, Irmgard

    2016-01-01

    As a sensor of polyaromatic chemicals the aryl hydrocarbon receptor (AhR) exerts an important role in immune regulation besides its requirement for xenobiotic metabolism. Transcriptional activation of AhR target genes is counterregulated by the AhR repressor (AhRR) but the exact function of the AhRR in vivo is currently unknown. We here show that the AhRR is predominantly expressed in immune cells of the skin and intestine, different from other AhR target genes. Whereas AhRR antagonizes the anti-inflammatory function of the AhR in the context of systemic endotoxin shock, AhR and AhRR act in concert to dampen intestinal inflammation. Specifically, AhRR contributes to the maintenance of colonic intraepithelial lymphocytes and prevents excessive IL-1β production and Th17/Tc17 differentiation. In contrast, the AhRR enhances IFN-γ-production by effector T cells in the inflamed gut. Our findings highlight the physiologic importance of cell-type specific balancing of AhR/AhRR expression in response to microbial, nutritional and other environmental stimuli. PMID:27184933

  12. Induction of long-term potentiation and long-term depression is cell-type specific in the spinal cord.

    Science.gov (United States)

    Kim, Hee Young; Jun, Jaebeom; Wang, Jigong; Bittar, Alice; Chung, Kyungsoon; Chung, Jin Mo

    2015-04-01

    The underlying mechanism of chronic pain is believed to be changes in excitability in spinal dorsal horn (DH) neurons that respond abnormally to peripheral input. Increased excitability in pain transmission neurons, and depression of inhibitory neurons, are widely recognized in the spinal cord of animal models of chronic pain. The possible occurrence of 2 parallel but opposing forms of synaptic plasticity, long-term potentiation (LTP) and long-term depression (LTD) was tested in 2 types of identified DH neurons using whole-cell patch-clamp recordings in mouse spinal cord slices. The test stimulus was applied to the sensory fibers to evoke excitatory postsynaptic currents in identified spinothalamic tract neurons (STTn) and GABAergic neurons (GABAn). Afferent conditioning stimulation (ACS) applied to primary afferent fibers with various stimulation parameters induced LTP in STTn but LTD in GABAn, regardless of stimulation parameters. These opposite responses were further confirmed by simultaneous dual patch-clamp recordings of STTn and GABAn from a single spinal cord slice. Both the LTP in STTn and the LTD in GABAn were blocked by an NMDA receptor antagonist, AP5, or an intracellular Ca chelator, BAPTA. Both the pattern and magnitude of intracellular Ca after ACS were almost identical between STTn and GABAn based on live-cell calcium imaging. The results suggest that the intense sensory input induces an NMDA receptor-dependent intracellular Ca increase in both STTn and GABAn, but produces opposing synaptic plasticity. This study shows that there is cell type-specific synaptic plasticity in the spinal DH. PMID:25785524

  13. DETECTION OF E6, E7 AND CELL-TYPE SPECIFIC ENHANCER OF HUMAN PAPILLOMAVIRUS TYPE 16 IN BREAST CARCINOMA

    Institute of Scientific and Technical Information of China (English)

    HE Qian; CHU Yong-lie; JIA Xiao-li; ZHANG Shu-qun; LIU Wen-kang

    2008-01-01

    Objective To detect HPV16 E6, E7 genes and cell-type specific enhancer (CTSE) of long control region (LCR) in breast carcinoma (BC).Methods HPV16 E6,E7 genes and CTSE were detected in 40 BCs and 20 normal breast tissue (NBT) using polymerase chain reaction (PCR).Results The positive rates of HPV16 E6, E7genes and CTSE were 60% (24/40),55% (22/40) and 67.5%(27/40)respectively in BCs, whereas only 5% (1/20), 5%(1/20) and 15% (3/20) in NBTs (P<0.05). There exited significant correlation between E6 gene and CTSE in BCs (P<0.05), as well as E7 gene and CTSE. The infection of HPV16 E6, E7 and CTSE had no statistic relationship with pathological features.Conclusion There were HPV16 E6, E7 genes and CTSE together in BCs and CTSE may play an important role in pathogenesis of BC.

  14. Reversal of morphine-induced cell-type-specific synaptic plasticity in the nucleus accumbens shell blocks reinstatement.

    Science.gov (United States)

    Hearing, Matthew C; Jedynak, Jakub; Ebner, Stephanie R; Ingebretson, Anna; Asp, Anders J; Fischer, Rachel A; Schmidt, Clare; Larson, Erin B; Thomas, Mark John

    2016-01-19

    Drug-evoked plasticity at excitatory synapses on medium spiny neurons (MSNs) of the nucleus accumbens (NAc) drives behavioral adaptations in addiction. MSNs expressing dopamine D1 (D1R-MSN) vs. D2 receptors (D2R-MSN) can exert antagonistic effects in drug-related behaviors, and display distinct alterations in glutamate signaling following repeated exposure to psychostimulants; however, little is known of cell-type-specific plasticity induced by opiates. Here, we find that repeated morphine potentiates excitatory transmission and increases GluA2-lacking AMPA receptor expression in D1R-MSNs, while reducing signaling in D2-MSNs following 10-14 d of forced abstinence. In vivo reversal of this pathophysiology with optogenetic stimulation of infralimbic cortex-accumbens shell (ILC-NAc shell) inputs or treatment with the antibiotic, ceftriaxone, blocked reinstatement of morphine-evoked conditioned place preference. These findings confirm the presence of overlapping and distinct plasticity produced by classes of abused drugs within subpopulations of MSNs that may provide targetable molecular mechanisms for future pharmacotherapies. PMID:26739562

  15. Drug and cell type-specific regulation of genes with different classes of estrogen receptor beta-selective agonists.

    Directory of Open Access Journals (Sweden)

    Sreenivasan Paruthiyil

    Full Text Available Estrogens produce biological effects by interacting with two estrogen receptors, ERalpha and ERbeta. Drugs that selectively target ERalpha or ERbeta might be safer for conditions that have been traditionally treated with non-selective estrogens. Several synthetic and natural ERbeta-selective compounds have been identified. One class of ERbeta-selective agonists is represented by ERB-041 (WAY-202041 which binds to ERbeta much greater than ERalpha. A second class of ERbeta-selective agonists derived from plants include MF101, nyasol and liquiritigenin that bind similarly to both ERs, but only activate transcription with ERbeta. Diarylpropionitrile represents a third class of ERbeta-selective compounds because its selectivity is due to a combination of greater binding to ERbeta and transcriptional activity. However, it is unclear if these three classes of ERbeta-selective compounds produce similar biological activities. The goals of these studies were to determine the relative ERbeta selectivity and pattern of gene expression of these three classes of ERbeta-selective compounds compared to estradiol (E(2, which is a non-selective ER agonist. U2OS cells stably transfected with ERalpha or ERbeta were treated with E(2 or the ERbeta-selective compounds for 6 h. Microarray data demonstrated that ERB-041, MF101 and liquiritigenin were the most ERbeta-selective agonists compared to estradiol, followed by nyasol and then diarylpropionitrile. FRET analysis showed that all compounds induced a similar conformation of ERbeta, which is consistent with the finding that most genes regulated by the ERbeta-selective compounds were similar to each other and E(2. However, there were some classes of genes differentially regulated by the ERbeta agonists and E(2. Two ERbeta-selective compounds, MF101 and liquiritigenin had cell type-specific effects as they regulated different genes in HeLa, Caco-2 and Ishikawa cell lines expressing ERbeta. Our gene profiling studies

  16. Cell type specificity of female lung cancer associated with sulfur dioxide from air pollutants in Taiwan: An ecological study

    Directory of Open Access Journals (Sweden)

    Tseng Ching-Yu

    2012-01-01

    Full Text Available Abstract Background Many studies have examined the association between air pollutants (including sulfur dioxide [SO2], carbon monoxide [CO], nitrogen dioxide [NO2], nitric oxide [NO], ozone [O3], and particulate matter 10] and lung cancer. However, data from previous studies on pathological cell types were limited, especially for SO2 exposure. We aimed to explore the association between SO2 exposure from outdoor air pollutants and female lung cancer incidence by cell type specificity. Methods We conducted an ecological study and calculated annual average concentration of 6 air pollutants (SO2, CO, NO2, NO, O3, and PM10 using data from Taiwan Environmental Protection Administration air quality monitoring stations. The Poisson regression models were used to evaluate the association between SO2 and age-standardized incidence rate of female lung cancer by two major pathological types (adenocarcinoma [AC] and squamous cell carcinoma [SCC]. In order to understand whether there is a dose-response relationship between SO2 and two major pathological types, we analyzed 4 levels of exposure based on quartiles of concentration of SO2. Results The Poisson regression results showed that with the first quartile of SO2 concentration as the baseline, the relative risks for AC/SCC type cancer among females were 1.20 (95% confidence interval [CI], 1.04-1.37/1.39 (95% CI, 0.96-2.01 for the second, 1.22 (95% CI, 1.04-1.43/1.58 (95% CI, 1.06-2.37 for the third, and 1.27 (95% CI, 1.06-1.52/1.80 (95% CI, 1.15-2.84 for the fourth quartile of SO2 concentration. The tests for trend were statistically significant for both AC and SCC at P = 0.0272 and 0.0145, respectively. Conclusion The current study suggests that SO2 exposure as an air pollutant may increase female lung cancer incidence and the associations with female lung cancer is much stronger for SCC than for AC. The findings of this study warrant further investigation on the role of SO2 in the etiology of SCC.

  17. Curcumin as a double-edged sword for stem cells: dose, time and cell type-specific responses to curcumin

    OpenAIRE

    Attari, Fatemeh; Zahmatkesh, Maryam; Aligholi, Hadi; Mehr, Shahram Ejtemaei; Sharifzadeh, Mohammad; Gorji, Ali; Mokhtari, Tahmineh; Khaksarian, Mojtaba; Hassanzadeh, Gholamreza

    2015-01-01

    Background The beneficial effects of curcumin which includes its antioxidant, anti-inflammatory and cancer chemo-preventive properties have been identified. Little information is available regarding the optimal dose and treatment periods of curcumin on the proliferation rate of different sources of stem cells. Methods In this study, the effect of various concentrations of curcumin on the survival and proliferation of two types of outstanding stem cells which includes bone marrow stem cells (B...

  18. Coordinated cell type-specific epigenetic remodeling in prefrontal cortex begins before birth and continues into early adulthood.

    Directory of Open Access Journals (Sweden)

    Hennady P Shulha

    2013-04-01

    Full Text Available Development of prefrontal and other higher-order association cortices is associated with widespread changes in the cortical transcriptome, particularly during the transitions from prenatal to postnatal development, and from early infancy to later stages of childhood and early adulthood. However, the timing and longitudinal trajectories of neuronal gene expression programs during these periods remain unclear in part because of confounding effects of concomitantly occurring shifts in neuron-to-glia ratios. Here, we used cell type-specific chromatin sorting techniques for genome-wide profiling of a histone mark associated with transcriptional regulation--H3 with trimethylated lysine 4 (H3K4me3--in neuronal chromatin from 31 subjects from the late gestational period to 80 years of age. H3K4me3 landscapes of prefrontal neurons were developmentally regulated at 1,157 loci, including 768 loci that were proximal to transcription start sites. Multiple algorithms consistently revealed that the overwhelming majority and perhaps all of developmentally regulated H3K4me3 peaks were on a unidirectional trajectory defined by either rapid gain or loss of histone methylation during the late prenatal period and the first year after birth, followed by similar changes but with progressively slower kinetics during early and later childhood and only minimal changes later in life. Developmentally downregulated H3K4me3 peaks in prefrontal neurons were enriched for Paired box (Pax and multiple Signal Transducer and Activator of Transcription (STAT motifs, which are known to promote glial differentiation. In contrast, H3K4me3 peaks subject to a progressive increase in maturing prefrontal neurons were enriched for activating protein-1 (AP-1 recognition elements that are commonly associated with activity-dependent regulation of neuronal gene expression. We uncovered a developmental program governing the remodeling of neuronal histone methylation landscapes in the prefrontal

  19. Cell-type-specific profiling of protein-DNA interactions without cell isolation using targeted DamID with next-generation sequencing.

    Science.gov (United States)

    Marshall, Owen J; Southall, Tony D; Cheetham, Seth W; Brand, Andrea H

    2016-09-01

    This protocol is an extension to: Nat. Protoc. 2, 1467-1478 (2007); doi:10.1038/nprot.2007.148; published online 7 June 2007The ability to profile transcription and chromatin binding in a cell-type-specific manner is a powerful aid to understanding cell-fate specification and cellular function in multicellular organisms. We recently developed targeted DamID (TaDa) to enable genome-wide, cell-type-specific profiling of DNA- and chromatin-binding proteins in vivo without cell isolation. As a protocol extension, this article describes substantial modifications to an existing protocol, and it offers additional applications. TaDa builds upon DamID, a technique for detecting genome-wide DNA-binding profiles of proteins, by coupling it with the GAL4 system in Drosophila to enable both temporal and spatial resolution. TaDa ensures that Dam-fusion proteins are expressed at very low levels, thus avoiding toxicity and potential artifacts from overexpression. The modifications to the core DamID technique presented here also increase the speed of sample processing and throughput, and adapt the method to next-generation sequencing technology. TaDa is robust, reproducible and highly sensitive. Compared with other methods for cell-type-specific profiling, the technique requires no cell-sorting, cross-linking or antisera, and binding profiles can be generated from as few as 10,000 total induced cells. By profiling the genome-wide binding of RNA polymerase II (Pol II), TaDa can also identify transcribed genes in a cell-type-specific manner. Here we describe a detailed protocol for carrying out TaDa experiments and preparing the material for next-generation sequencing. Although we developed TaDa in Drosophila, it should be easily adapted to other organisms with an inducible expression system. Once transgenic animals are obtained, the entire experimental procedure-from collecting tissue samples to generating sequencing libraries-can be accomplished within 5 d. PMID:27490632

  20. Delta-9-tetrahydrocannabinol accumulation, metabolism and cell-type-specific adverse effects in aggregating brain cell cultures

    International Nuclear Information System (INIS)

    Despite the widespread use of Cannabis as recreational drug or as medicine, little is known about its toxicity. The accumulation, metabolism and toxicity of THC were analyzed 10 days after a single treatment, and after repeated exposures during 10 days. Mixed-cell aggregate cultures of fetal rat telencephalon were used as in vitro model, as well as aggregates enriched either in neurons or in glial cells. It was found that THC accumulated preferentially in neurons, and that glia-neuron interactions decreased THC accumulation. The quantification of 11-OH-THC and of THC-COOH showed that brain aggregates were capable of THC metabolism. No cell-type difference was found for the metabolite 11-OH-THC, whereas the THC-COOH content was higher in mixed-cell cultures. No cell death was found at THC concentrations of 2 μM in single treatment and of 1 μM and 2 μM in repeated treatments. Neurons, and particularly GABAergic neurons, were most sensitive to THC. Only the GABAergic marker was affected after the single treatment, whereas the GABAergic, cholinergic and astrocytic markers were decreased after the repeated treatments. JWH 015, a CB2 receptor agonist, showed effects similar to THC, whereas ACEA, a CB1 receptor agonist, had no effect. The expression of the cytokine IL-6 was upregulated 48 h after the single treatment with 5 μM of THC or JWH 015, whereas the expression of TNF-α remained unchanged. These results suggest that the adverse effects of THC were related either to THC accumulation or to cannabinoid receptor activation and associated with IL-6 upregulation

  1. Differential microRNA expression signatures and cell type-specific association with Taxol resistance in ovarian cancer cells

    Directory of Open Access Journals (Sweden)

    Kim YW

    2014-02-01

    Full Text Available Yong-Wan Kim,1 Eun Young Kim,1 Doin Jeon,1 Juinn-Lin Liu,2 Helena Suhyun Kim,3 Jin Woo Choi,4 Woong Shick Ahn5 1Cancer Research Institute of Medical Science, The Catholic University of Korea, Seoul, Republic of Korea; 2Brain Tumor Center, Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, TX, USA; 3Cancer Rehab Laboratory, RH Healthcare Systems Inc, TX, USA; 4Harvard Medical School and Wellman Center for Photomedicine, Cambridge, MA, USA; 5Department of Obstetrics and Gynecology, The Catholic University of Korea, Seoul, Republic of Korea Abstract: Paclitaxel (Taxol resistance remains a major obstacle for the successful treatment of ovarian cancer. MicroRNAs (miRNAs have oncogenic and tumor suppressor activity and are associated with poor prognosis phenotypes. miRNA screenings for this drug resistance are needed to estimate the prognosis of the disease and find better drug targets. miRNAs that were differentially expressed in Taxol-resistant ovarian cancer cells, compared with Taxol-sensitive cells, were screened by Illumina Human MicroRNA Expression BeadChips. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR was used to identify target genes of selected miRNAs. Kaplan–Meier survival analysis was applied to identify dysregulated miRNAs in ovarian cancer patients using data from The Cancer Genome Atlas. A total of 82 miRNAs were identified in ovarian carcinoma cells compared to normal ovarian cells. miR-141, miR-106a, miR-200c, miR-96, and miR-378 were overexpressed, and miR-411, miR-432, miR-494, miR-409-3p, and miR-655 were underexpressed in ovarian cancer cells. Seventeen miRNAs were overexpressed in Taxol-resistant cells, including miR-663, miR-622, and HS_188. Underexpressed miRNAs in Taxol-sensitive cells included miR-497, miR-187, miR-195, and miR-107. We further showed miR-663 and miR-622 as significant prognosis markers of the chemo-resistant patient group. In particular, the

  2. Characterisation of CD4 T cells in healthy and diseased koalas (Phascolarctos cinereus) using cell-type-specific monoclonal antibodies.

    Science.gov (United States)

    Mangar, Chandan; Armitage, Charles W; Timms, Peter; Corcoran, Lynn M; Beagley, Kenneth W

    2016-07-01

    The koala (Phascolarctos cinereus) is an arboreal herbivorous marsupial that is an Australian icon. Koalas in many parts of Australia are under multiple threats including habitat destruction, dog attacks, vehicular accidents, and infectious diseases such as Chlamydia spp. and the koala retrovirus (KoRV), which may contribute to the incidence of lymphoma and leukaemia in this species. Due to a lack of koala-specific immune reagents and assays there is currently no way to adequately analyse the immune response in healthy, diseased or vaccinated animals. This paper reports the production and characterisation of the first anti-koala CD4 monoclonal antibody (mAb). The koala CD4 gene was identified and used to develop recombinant proteins for mAb production. Fluorochrome-conjugated anti-CD4 mAb was used to measure the levels of CD4(+) lymphocytes collected from koala spleens (41.1%, range 20-45.1%) lymph nodes (36.3%, range 19-55.9%) and peripheral blood (23.8%, range 17.3-35%) by flow cytometry. Biotin-conjugated anti-CD4 mAb was used for western blot to determine an approximate size of 52 kDa for the koala CD4 molecule and used in immunohistochemistry to identify CD4(+) cells in the paracortical region and germinal centres of spleen and lymph nodes. Using the anti-CD4 mab we showed that CD4 cells from vaccinated, but not control, koalas proliferated following in vitro stimulation with UV-inactivated Chlamydia pecorum and recombinant chlamydial antigens. Since CD4(+) T cells have been shown to play a pivotal role in clearing chlamydial infection in both human and mouse infections, using this novel antibody will help determine the role CD4(+) T cells play in protection against chlamydial infection in koalas and also enhance our knowledge of how KoRV affects the koala immune system. PMID:26905635

  3. Cell Type-Specific Expression and Function of Toll-Like Receptors 2 and 4 in Human Placenta: Implications in Fetal Infection

    OpenAIRE

    Ma, Yuehong; Krikun, Graciela; Abrahams, Vikki M.; Mor, Gil; Guller, Seth

    2007-01-01

    Placental infection is associated with adverse fetal outcomes. Toll-like receptors (TLRs) are critical regulators of the innate immune response based on their ability to recognize and respond to pathogen-associated molecular patterns expressed by microbes. To date, cell-type specific expression and regulation of TLR function in human term placenta remains largely unelucidated. The goal of the current study was to examine the in vivo and in vitro patterns of TLR expression and function in majo...

  4. Microarray gene expression analysis to evaluate cell type specific expression of targets relevant for immunotherapy of hematological malignancies

    NARCIS (Netherlands)

    M.J. Pont (Margot); M.W. Honders; A.N. Kremer; C. van Kooten (Cees); C. Out; P.S. Hiemstra (Pieter); H.C. De Boer; M.J. Jager (Martine); E. Schmelzer; R.G.J. Vries (Robert); A.S. Al Hinai; W.G. Kroes (W.); R. Monajemi (Ramin); J.J. Goeman (Jelle); S. Böhringer (Stefan); W.A.F. Marijt; J.H.F. Falkenburg (Frederik); M. Griffioen

    2016-01-01

    textabstractCellular immunotherapy has proven to be effective in the treatment of hematological cancers by donor lymphocyte infusion after allogeneic hematopoietic stem cell transplantation and more recently by targeted therapy with chimeric antigen or T-cell receptor-engineered T cells. However, de

  5. Cell Type-Specific Activation of the Cytomegalovirus Promoter by Dimethylsulfoxide and 5-Aza-2′-deoxycytidine

    OpenAIRE

    Radhakrishnan, Prakash; Basma, Hesham; Klinkebiel, David; Christman, Judith; Cheng, Pi-Wan

    2008-01-01

    The cytomegalovirus promoter is a very potent promoter commonly used for driving the expression of transgenes, though it gradually becomes silenced in stably transfected cells. We examined the methylation status of the cytomegalovirus promoter in two different cell lines and characterized its mechanisms of activation by dimethylsulfoxide and 5-Aza-2′-deoxycytidine. The cytomegalovirus promoter stably transfected into Chinese hamster ovary cells is suppressed by DNA methylation-independent mec...

  6. Intrinsic properties of Tcf1 and Tcf4 splice variants determine cell-type-specific Wnt/β-catenin target gene expression

    OpenAIRE

    Wallmen, Britta; Schrempp, Monika; Hecht, Andreas

    2012-01-01

    T-cell factor (Tcf)/lymphoid-enhancer factor (Lef) proteins are a structurally diverse family of deoxyribonucleic acid-binding proteins that have essential nuclear functions in Wnt/β-catenin signalling. Expression of Wnt/β-catenin target genes is highly dependent on context, but the precise role of Tcf/Lef family members in the generation and maintenance of cell-type-specific Wnt/β-catenin responses is unknown. Herein, we show that induction of a subset of Wnt/β-catenin targets in embryonic s...

  7. Microarray Gene Expression Analysis to Evaluate Cell Type Specific Expression of Targets Relevant for Immunotherapy of Hematological Malignancies.

    Directory of Open Access Journals (Sweden)

    M J Pont

    Full Text Available Cellular immunotherapy has proven to be effective in the treatment of hematological cancers by donor lymphocyte infusion after allogeneic hematopoietic stem cell transplantation and more recently by targeted therapy with chimeric antigen or T-cell receptor-engineered T cells. However, dependent on the tissue distribution of the antigens that are targeted, anti-tumor responses can be accompanied by undesired side effects. Therefore, detailed tissue distribution analysis is essential to estimate potential efficacy and toxicity of candidate targets for immunotherapy of hematological malignancies. We performed microarray gene expression analysis of hematological malignancies of different origins, healthy hematopoietic cells and various non-hematopoietic cell types from organs that are often targeted in detrimental immune responses after allogeneic stem cell transplantation leading to graft-versus-host disease. Non-hematopoietic cells were also cultured in the presence of IFN-γ to analyze gene expression under inflammatory circumstances. Gene expression was investigated by Illumina HT12.0 microarrays and quality control analysis was performed to confirm the cell-type origin and exclude contamination of non-hematopoietic cell samples with peripheral blood cells. Microarray data were validated by quantitative RT-PCR showing strong correlations between both platforms. Detailed gene expression profiles were generated for various minor histocompatibility antigens and B-cell surface antigens to illustrate the value of the microarray dataset to estimate efficacy and toxicity of candidate targets for immunotherapy. In conclusion, our microarray database provides a relevant platform to analyze and select candidate antigens with hematopoietic (lineage-restricted expression as potential targets for immunotherapy of hematological cancers.

  8. Cell-Type-Specific Transcriptome Analysis in the Drosophila Mushroom Body Reveals Memory-Related Changes in Gene Expression.

    Science.gov (United States)

    Crocker, Amanda; Guan, Xiao-Juan; Murphy, Coleen T; Murthy, Mala

    2016-05-17

    Learning and memory formation in Drosophila rely on a network of neurons in the mushroom bodies (MBs). Whereas numerous studies have delineated roles for individual cell types within this network in aspects of learning or memory, whether or not these cells can also be distinguished by the genes they express remains unresolved. In addition, the changes in gene expression that accompany long-term memory formation within the MBs have not yet been studied by neuron type. Here, we address both issues by performing RNA sequencing on single cell types (harvested via patch pipets) within the MB. We discover that the expression of genes that encode cell surface receptors is sufficient to identify cell types and that a subset of these genes, required for sensory transduction in peripheral sensory neurons, is not only expressed within individual neurons of the MB in the central brain, but is also critical for memory formation. PMID:27160913

  9. Cell type-specific deficiency of c-kit gene expression in mutant mice of mi/mi genotype.

    OpenAIRE

    Isozaki, K; Tsujimura, T; Nomura, S; Morii, E; Koshimizu, U.; Nishimune, Y; Kitamura, Y.

    1994-01-01

    The mi locus of mice encodes a novel member of the basic-helix-loop-helix-leucine zipper protein family of transcription factors (hereafter called mi factor). In addition to microphthalmus, osteopetrosis, and lack of melanocytes, mice of mi/mi genotype are deficient in mast cells. Since the c-kit receptor tyrosine kinase plays an important role in the development of mast cells, and since the c-kit expression by cultured mast cells from mi/mi mice is deficient in both mRNA and protein levels, ...

  10. Fiber type specific response of skeletal muscle satellite cells to high-intensity resistance training in dialysis patients

    DEFF Research Database (Denmark)

    Molsted, Stig; Andersen, Jesper Løvind; Harrison, Adrian Paul;

    2015-01-01

    Introduction. The aim was to investigate the effect of high-intensity resistance training on satellite cell (SC) and myonuclear number in the muscle of patients undergoing dialysis. Methods. Patients (n=21) underwent a 16-week control period, followed by 16 weeks of resistance training thrice...... fibers of dialysis patients who perform resistance training suggests that satellite cell dysfunction is not the limiting factor for muscle growth. This article is protected by copyright. All rights reserved....

  11. Prolonged Exposure to NMDAR Antagonist Induces Cell-type Specific Changes of Glutamatergic Receptors in Rat Prefrontal Cortex

    OpenAIRE

    Wang, Huai-Xing; Gao, Wen-Jun

    2011-01-01

    N-methyl-D-aspartic acid (NMDA) receptors are critical for both normal brain functions and the pathogenesis of schizophrenia. We investigated the functional changes of glutamatergic receptors in the pyramidal cells and fast-spiking (FS) interneurons in the adolescent rat prefrontal cortex in MK-801 model of schizophrenia. We found that although both pyramidal cells and FS interneurons were affected by in vivo subchronic blockade of NMDA receptors, MK-801 induced distinct changes in αamino-3-h...

  12. A POP-1 repressor complex restricts inappropriate cell type-specific gene transcription during Caenorhabditis elegans embryogenesis

    OpenAIRE

    Calvo, Dominica; Victor, Martin; Gay, Frédérique; Sui, Guangchao; Luke, Margaret Po-Shan; Dufourcq, Pascale; Wen, Gengyun; Maduro, Morris; Rothman, Joel; Shi, Yang

    2001-01-01

    In Caenorhabditis elegans, histone acetyltransferase CBP-1 counteracts the repressive activity of the histone deacetylase HDA-1 to allow endoderm differentiation, which is specified by the E cell. In the sister MS cell, the endoderm fate is prevented by the action of an HMG box-containing protein, POP-1, through an unknown mechanism. In this study, we show that CBP-1, HDA-1 and POP-1 converge on end-1, an initial endoderm-determining gene. In the E lineage, an essential function of CBP-1 appe...

  13. High Intensity Training May Reverse the Fiber Type Specific Decline in Myogenic Stem Cells in Multiple Sclerosis Patients

    DEFF Research Database (Denmark)

    Farup, Jean; Dalgas, Ulrik; Keytsman, Charly;

    2016-01-01

    = 23) and age matched healthy controls (HC, n = 18). Furthermore, the effects of 12 weeks of high intensity training on SC and myonuclei content were explored in MS. Muscle biopsies were obtained from m. Vastus Lateralis at baseline (MS and HC) and following 12 weeks of training (MS only). Frozen...... increased by 165% (p < 0.05) and 135% (p < 0.05), respectively. Furthermore, the type II fiber MN content tended (p = 0.06) to be increased by 35% following training. In conclusion, the SC content is lower in type II compared to type I fibers in both MS and HC. Furthermore, high intensity training was......Multiple sclerosis (MS) is associated with loss of skeletal muscle mass and function. The myogenic stem cells (satellite cells-SCs) are instrumental to accretion of myonuclei, but remain to be investigated in MS. The present study aimed to compare the SC and myonuclei content between MS patients (n...

  14. Gamma-retrovirus integration marks cell type-specific cancer genes: a novel profiling tool in cancer genomics

    OpenAIRE

    Gilroy, Kathryn L.; Terry, Anne; Naseer, Asif; De Ridder, Jeroen; Allahyar, Amin; Wang, Weiwei; Carpenter, Eric; Mason, Andrew; Wong, Gane K-S; Cameron, Ewan R; Kilbey, Anna; Neil, James C.

    2016-01-01

    Retroviruses have been foundational in cancer research since early studies identified proto-oncogenes as targets for insertional mutagenesis. Integration of murine gamma-retroviruses into the host genome favours promoters and enhancers and entails interaction of viral integrase with host BET/bromodomain factors. We report that this integration pattern is conserved in feline leukaemia virus (FeLV), a gamma-retrovirus that infects many human cell types. Analysis of FeLV insertion sites in the M...

  15. Cell-type-specific repression by methyl-CpG-binding protein 2 is biased toward long genes.

    Science.gov (United States)

    Sugino, Ken; Hempel, Chris M; Okaty, Benjamin W; Arnson, Hannah A; Kato, Saori; Dani, Vardhan S; Nelson, Sacha B

    2014-09-17

    Mutations in methyl-CpG-binding protein 2 (MeCP2) cause Rett syndrome and related autism spectrum disorders (Amir et al., 1999). MeCP2 is believed to be required for proper regulation of brain gene expression, but prior microarray studies in Mecp2 knock-out mice using brain tissue homogenates have revealed only subtle changes in gene expression (Tudor et al., 2002; Nuber et al., 2005; Jordan et al., 2007; Chahrour et al., 2008). Here, by profiling discrete subtypes of neurons we uncovered more dramatic effects of MeCP2 on gene expression, overcoming the "dilution problem" associated with assaying homogenates of complex tissues. The results reveal misregulation of genes involved in neuronal connectivity and communication. Importantly, genes upregulated following loss of MeCP2 are biased toward longer genes but this is not true for downregulated genes, suggesting MeCP2 may selectively repress long genes. Because genes involved in neuronal connectivity and communication, such as cell adhesion and cell-cell signaling genes, are enriched among longer genes, their misregulation following loss of MeCP2 suggests a possible etiology for altered circuit function in Rett syndrome. PMID:25232122

  16. LaeA control of velvet family regulatory proteins for light-dependent development and fungal cell-type specificity.

    Directory of Open Access Journals (Sweden)

    Ozlem Sarikaya Bayram

    Full Text Available VeA is the founding member of the velvet superfamily of fungal regulatory proteins. This protein is involved in light response and coordinates sexual reproduction and secondary metabolism in Aspergillus nidulans. In the dark, VeA bridges VelB and LaeA to form the VelB-VeA-LaeA (velvet complex. The VeA-like protein VelB is another developmental regulator, and LaeA has been known as global regulator of secondary metabolism. In this study, we show that VelB forms a second light-regulated developmental complex together with VosA, another member of the velvet family, which represses asexual development. LaeA plays a key role, not only in secondary metabolism, but also in directing formation of the VelB-VosA and VelB-VeA-LaeA complexes. LaeA controls VeA modification and protein levels and possesses additional developmental functions. The laeA null mutant results in constitutive sexual differentiation, indicating that LaeA plays a pivotal role in inhibiting sexual development in response to light. Moreover, the absence of LaeA results in the formation of significantly smaller fruiting bodies. This is due to the lack of a specific globose cell type (Hülle cells, which nurse the young fruiting body during development. This suggests that LaeA controls Hülle cells. In summary, LaeA plays a dynamic role in fungal morphological and chemical development, and it controls expression, interactions, and modification of the velvet regulators.

  17. Balancing intestinal and systemic inflammation through cell type-specific expression of the aryl hydrocarbon receptor repressor

    OpenAIRE

    Olga Brandstätter; Oliver Schanz; Julia Vorac; Jessica König; Tetsushi Mori; Toru Maruyama; Markus Korkowski; Thomas Haarmann-Stemmann; Dorthe von Smolinski; Schultze, Joachim L.; Josef Abel; Charlotte Esser; Haruko Takeyama; Heike Weighardt; Irmgard Förster

    2016-01-01

    As a sensor of polyaromatic chemicals the aryl hydrocarbon receptor (AhR) exerts an important role in immune regulation besides its requirement for xenobiotic metabolism. Transcriptional activation of AhR target genes is counterregulated by the AhR repressor (AhRR) but the exact function of the AhRR in vivo is currently unknown. We here show that the AhRR is predominantly expressed in immune cells of the skin and intestine, different from other AhR target genes. Whereas AhRR antagonizes the a...

  18. Cell-Type-Specific Circuit Connectivity of Hippocampal CA1 Revealed through Cre-Dependent Rabies Tracing

    Directory of Open Access Journals (Sweden)

    Yanjun Sun

    2014-04-01

    Full Text Available We developed and applied a Cre-dependent, genetically modified rabies-based tracing system to map direct synaptic connections to specific CA1 neuron types in the mouse hippocampus. We found common inputs to excitatory and inhibitory CA1 neurons from CA3, CA2, the entorhinal cortex (EC, the medial septum (MS, and, unexpectedly, the subiculum. Excitatory CA1 neurons receive inputs from both cholinergic and GABAergic MS neurons, whereas inhibitory neurons receive a great majority of inputs from GABAergic MS neurons. Both cell types also receive weaker input from glutamatergic MS neurons. Comparisons of inputs to CA1 PV+ interneurons versus SOM+ interneurons showed similar strengths of input from the subiculum, but PV+ interneurons received much stronger input than SOM+ neurons from CA3, the EC, and the MS. Thus, rabies tracing identifies hippocampal circuit connections and maps how the different input sources to CA1 are distributed with different strengths on each of its constituent cell types.

  19. Correlation of mRNA and protein levels: Cell type-specific gene expression of cluster designation antigens in the prostate

    Directory of Open Access Journals (Sweden)

    Deutsch Eric W

    2008-05-01

    Full Text Available Abstract Background: Expression levels of mRNA and protein by cell types exhibit a range of correlations for different genes. In this study, we compared levels of mRNA abundance for several cluster designation (CD genes determined by gene arrays using magnetic sorted and laser-capture microdissected human prostate cells with levels of expression of the respective CD proteins determined by immunohistochemical staining in the major cell types of the prostate – basal epithelial, luminal epithelial, stromal fibromuscular, and endothelial – and for prostate precursor/stem cells and prostate carcinoma cells. Immunohistochemical stains of prostate tissues from more than 50 patients were scored for informative CD antigen expression and compared with cell-type specific transcriptomes. Results: Concordance between gene and protein expression findings based on 'present' vs. 'absent' calls ranged from 46 to 68%. Correlation of expression levels was poor to moderate (Pearson correlations ranged from 0 to 0.63. Divergence between the two data types was most frequently seen for genes whose array signals exceeded background (> 50 but lacked immunoreactivity by immunostaining. This could be due to multiple factors, e.g. low levels of protein expression, technological sensitivities, sample processing, probe set definition or anatomical origin of tissue and actual biological differences between transcript and protein abundance. Conclusion: Agreement between these two very different methodologies has great implications for their respective use in both molecular studies and clinical trials employing molecular biomarkers.

  20. Regional and cell-type-specific effects of DAMGO on striatal D1 and D2 dopamine receptor-expressing medium-sized spiny neurons

    Directory of Open Access Journals (Sweden)

    Christopher J Evans

    2012-03-01

    Full Text Available The striatum can be divided into the DLS (dorsolateral striatum and the VMS (ventromedial striatum, which includes NAcC (nucleus accumbens core and NAcS (nucleus accumbens shell. Here, we examined differences in electrophysiological properties of MSSNs (medium-sized spiny neurons based on their location, expression of DA (dopamine D1/D2 receptors and responses to the μ-opioid receptor agonist, DAMGO {[D-Ala2-MePhe4-Gly(ol5]enkephalin}. The main differences in morphological and biophysical membrane properties occurred among striatal sub-regions. MSSNs in the DLS were larger, had higher membrane capacitances and lower Rin (input resistances compared with cells in the VMS. RMPs (resting membrane potentials were similar among regions except for D2 cells in the NAcC, which displayed a significantly more depolarized RMP. In contrast, differences in frequency of spontaneous excitatory synaptic inputs were more prominent between cell types, with D2 cells receiving significantly more excitatory inputs than D1 cells, particularly in the VMS. Inhibitory inputs were not different between D1 and D2 cells. However, MSSNs in the VMS received more inhibitory inputs than those in the DLS. Acute application of DAMGO reduced the frequency of spontaneous excitatory and inhibitory postsynaptic currents, but the effect was greater in the VMS, in particular in the NAcS, where excitatory currents from D2 cells and inhibitory currents from D1 cells were inhibited by the largest amount. DAMGO also increased cellular excitability in the VMS, as shown by reduced threshold for evoking APs (action potentials. Together the present findings help elucidate the regional and cell-type-specific substrate of opioid actions in the striatum and point to the VMS as a critical mediator of DAMGO effects.

  1. Tissue-specific regulatory network extractor (TS-REX): a database and software resource for the tissue and cell type-specific investigation of transcription factor-gene networks.

    Science.gov (United States)

    Colecchia, Federico; Kottwitz, Denise; Wagner, Mandy; Pfenninger, Cosima V; Thiel, Gerald; Tamm, Ingo; Peterson, Carsten; Nuber, Ulrike A

    2009-06-01

    The prediction of transcription factor binding sites in genomic sequences is in principle very useful to identify upstream regulatory factors. However, when applying this concept to genomes of multicellular organisms such as mammals, one has to deal with a large number of false positive predictions since many transcription factor genes are only expressed in specific tissues or cell types. We developed TS-REX, a database/software system that supports the analysis of tissue and cell type-specific transcription factor-gene networks based on expressed sequence tag abundance of transcription factor-encoding genes in UniGene EST libraries. The use of expression levels of transcription factor-encoding genes according to hierarchical anatomical classifications covering different tissues and cell types makes it possible to filter out irrelevant binding site predictions and to identify candidates of potential functional importance for further experimental testing. TS-REX covers ESTs from H. sapiens and M. musculus, and allows the characterization of both presence and specificity of transcription factors in user-specified tissues or cell types. The software allows users to interactively visualize transcription factor-gene networks, as well as to export data for further processing. TS-REX was applied to predict regulators of Polycomb group genes in six human tumor tissues and in human embryonic stem cells. PMID:19443447

  2. In Vivo Zonal Variation and Liver Cell-Type Specific NF-κB Localization after Chronic Adaptation to Ethanol and following Partial Hepatectomy.

    Directory of Open Access Journals (Sweden)

    Harshavardhan Nilakantan

    Full Text Available NF-κB is a major inflammatory response mediator in the liver, playing a key role in the pathogenesis of alcoholic liver injury. We investigated zonal as well as liver cell type-specific distribution of NF-κB activation across the liver acinus following adaptation to chronic ethanol intake and 70% partial hepatectomy (PHx. We employed immunofluorescence staining, digital image analysis and statistical distributional analysis to quantify subcellular localization of NF-κB in hepatocytes and hepatic stellate cells (HSCs. We detected significant spatial heterogeneity of NF-κB expression and cellular localization between cytoplasm and nucleus across liver tissue. Our main aims involved investigating the zonal bias in NF-κB localization and determining to what extent chronic ethanol intake affects this zonal bias with in hepatocytes at baseline and post-PHx. Hepatocytes in the periportal area showed higher NF-κB expression than in the pericentral region in the carbohydrate-fed controls, but not in the ethanol group. However, the distribution of NF-κB nuclear localization in hepatocytes was shifted towards higher levels in pericentral region than in periportal area, across all treatment conditions. Chronic ethanol intake shifted the NF-κB distribution towards higher nuclear fraction in hepatocytes as compared to the pair-fed control group. Ethanol also stimulated higher NF-κB expression in a subpopulation of HSCs. In the control group, PHx elicited a shift towards higher NF-κB nuclear fraction in hepatocytes. However, this distribution remained unchanged in the ethanol group post-PHx. HSCs showed a lower NF-κB expression following PHx in both ethanol and control groups. We conclude that adaptation to chronic ethanol intake attenuates the liver zonal variation in NF-κB expression and limits the PHx-induced NF-κB activation in hepatocytes, but does not alter the NF-κB expression changes in HSCs in response to PHx. Our findings provide new

  3. Global mapping of cell type-specific open chromatin by FAIRE-seq reveals the regulatory role of the NFI family in adipocyte differentiation.

    Directory of Open Access Journals (Sweden)

    Hironori Waki

    2011-10-01

    Full Text Available Identification of regulatory elements within the genome is crucial for understanding the mechanisms that govern cell type-specific gene expression. We generated genome-wide maps of open chromatin sites in 3T3-L1 adipocytes (on day 0 and day 8 of differentiation and NIH-3T3 fibroblasts using formaldehyde-assisted isolation of regulatory elements coupled with high-throughput sequencing (FAIRE-seq. FAIRE peaks at the promoter were associated with active transcription and histone modifications of H3K4me3 and H3K27ac. Non-promoter FAIRE peaks were characterized by H3K4me1+/me3-, the signature of enhancers, and were largely located in distal regions. The non-promoter FAIRE peaks showed dynamic change during differentiation, while the promoter FAIRE peaks were relatively constant. Functionally, the adipocyte- and preadipocyte-specific non-promoter FAIRE peaks were, respectively, associated with genes up-regulated and down-regulated by differentiation. Genes highly up-regulated during differentiation were associated with multiple clustered adipocyte-specific FAIRE peaks. Among the adipocyte-specific FAIRE peaks, 45.3% and 11.7% overlapped binding sites for, respectively, PPARγ and C/EBPα, the master regulators of adipocyte differentiation. Computational motif analyses of the adipocyte-specific FAIRE peaks revealed enrichment of a binding motif for nuclear family I (NFI transcription factors. Indeed, ChIP assay showed that NFI occupy the adipocyte-specific FAIRE peaks and/or the PPARγ binding sites near PPARγ, C/EBPα, and aP2 genes. Overexpression of NFIA in 3T3-L1 cells resulted in robust induction of these genes and lipid droplet formation without differentiation stimulus. Overexpression of dominant-negative NFIA or siRNA-mediated knockdown of NFIA or NFIB significantly suppressed both induction of genes and lipid accumulation during differentiation, suggesting a physiological function of these factors in the adipogenic program. Together, our

  4. Gene expression relationship between prostate cancer cells of Gleason 3, 4 and normal epithelial cells as revealed by cell type-specific transcriptomes

    International Nuclear Information System (INIS)

    Prostate cancer cells in primary tumors have been typed CD10-/CD13-/CD24hi/CD26+/CD38lo/CD44-/CD104-. This CD phenotype suggests a lineage relationship between cancer cells and luminal cells. The Gleason grade of tumors is a descriptive of tumor glandular differentiation. Higher Gleason scores are associated with treatment failure. CD26+ cancer cells were isolated from Gleason 3+3 (G3) and Gleason 4+4 (G4) tumors by cell sorting, and their gene expression or transcriptome was determined by Affymetrix DNA array analysis. Dataset analysis was used to determine gene expression similarities and differences between G3 and G4 as well as to prostate cancer cell lines and histologically normal prostate luminal cells. The G3 and G4 transcriptomes were compared to those of prostatic cell types of non-cancer, which included luminal, basal, stromal fibromuscular, and endothelial. A principal components analysis of the various transcriptome datasets indicated a closer relationship between luminal and G3 than luminal and G4. Dataset comparison also showed that the cancer transcriptomes differed substantially from those of prostate cancer cell lines. Genes differentially expressed in cancer are potential biomarkers for cancer detection, and those differentially expressed between G3 and G4 are potential biomarkers for disease stratification given that G4 cancer is associated with poor outcomes. Differentially expressed genes likely contribute to the prostate cancer phenotype and constitute the signatures of these particular cancer cell types

  5. Gene expression relationship between prostate cancer cells of Gleason 3, 4 and normal epithelial cells as revealed by cell type-specific transcriptomes

    Directory of Open Access Journals (Sweden)

    Page Laura S

    2009-12-01

    Full Text Available Abstract Background Prostate cancer cells in primary tumors have been typed CD10-/CD13-/CD24hi/CD26+/CD38lo/CD44-/CD104-. This CD phenotype suggests a lineage relationship between cancer cells and luminal cells. The Gleason grade of tumors is a descriptive of tumor glandular differentiation. Higher Gleason scores are associated with treatment failure. Methods CD26+ cancer cells were isolated from Gleason 3+3 (G3 and Gleason 4+4 (G4 tumors by cell sorting, and their gene expression or transcriptome was determined by Affymetrix DNA array analysis. Dataset analysis was used to determine gene expression similarities and differences between G3 and G4 as well as to prostate cancer cell lines and histologically normal prostate luminal cells. Results The G3 and G4 transcriptomes were compared to those of prostatic cell types of non-cancer, which included luminal, basal, stromal fibromuscular, and endothelial. A principal components analysis of the various transcriptome datasets indicated a closer relationship between luminal and G3 than luminal and G4. Dataset comparison also showed that the cancer transcriptomes differed substantially from those of prostate cancer cell lines. Conclusions Genes differentially expressed in cancer are potential biomarkers for cancer detection, and those differentially expressed between G3 and G4 are potential biomarkers for disease stratification given that G4 cancer is associated with poor outcomes. Differentially expressed genes likely contribute to the prostate cancer phenotype and constitute the signatures of these particular cancer cell types.

  6. Cell type-specific conditional regulation of the c-myc proto-oncogene by combining Cre/loxP recombination and tamoxifen-mediated activation.

    Science.gov (United States)

    Jäger, Richard; Maurer, Jochen; Jacob, Andrea; Schorle, Hubert

    2004-03-01

    Development of inducible genetic switches for in vivo use with transgenic mice has revolutionized many areas in modern molecular biology. Combining two techniques, Cre/loxP-based genetic recombination and ligand-dependent activation of a chimeric protein, we generated transgenic mice which allow for the spatiotemporal control of expression and of activity of the proto-oncogene c-myc. To these ends, the gene encoding the tamoxifen-inducible c-mycER(T) fusion protein (mycER(T)) was inserted in the ubiquitously active ROSA 26 gene locus by gene targeting. In the resulting ROSAMER allele, generalized transcription of the mycER(T) gene is prevented by a preceding transcriptional stop sequence which is flanked by loxP sites. Crosses of ROSAMER transgenic mice with Mox2 cre transgenic mice revealed tight control of mycER(T) transcription in various tissues unless the transcriptional stop sequence was removed by cre-mediated excision. Furthermore, we were able to demonstrate tamoxifen-dependent activation of the MycER(T) protein in embryonic fibroblasts derived from such mice. As a proof of principle, we demonstrate that primary neural crest cultures established from ROSAMER mice maintain their proliferative capacity in a 4-OHT-dependent manner. Furthermore, we demonstrate that such neural crest cells retain their differentiation potential as shown by expression of NF 160, a marker of neuronal differentiation upon 4-OHT withdrawal. The transgenic mice produced may thus be valuable tools for studying the cell type-specific effects of c-myc activity in development and disease. PMID:15048812

  7. A multi-omics approach identifies key hubs associated with cell type-specific responses of airway epithelial cells to staphylococcal alpha-toxin.

    Directory of Open Access Journals (Sweden)

    Erik Richter

    Full Text Available Responsiveness of cells to alpha-toxin (Hla from Staphylococcus aureus appears to occur in a cell-type dependent manner. Here, we compare two human bronchial epithelial cell lines, i.e. Hla-susceptible 16HBE14o- and Hla-resistant S9 cells, by a quantitative multi-omics strategy for a better understanding of Hla-induced cellular programs. Phosphoproteomics revealed a substantial impact on phosphorylation-dependent signaling in both cell models and highlights alterations in signaling pathways associated with cell-cell and cell-matrix contacts as well as the actin cytoskeleton as key features of early rHla-induced effects. Along comparable changes in down-stream activity of major protein kinases significant differences between both models were found upon rHla-treatment including activation of the epidermal growth factor receptor EGFR and mitogen-activated protein kinases MAPK1/3 signaling in S9 and repression in 16HBE14o- cells. System-wide transcript and protein expression profiling indicate induction of an immediate early response in either model. In addition, EGFR and MAPK1/3-mediated changes in gene expression suggest cellular recovery and survival in S9 cells but cell death in 16HBE14o- cells. Strikingly, inhibition of the EGFR sensitized S9 cells to Hla indicating that the cellular capacity of activation of the EGFR is a major protective determinant against Hla-mediated cytotoxic effects.

  8. Antibody-based screening of cell wall matrix glycans in ferns reveals taxon, tissue and cell-type specific distribution patterns

    DEFF Research Database (Denmark)

    Leroux, Olivier; Sørensen, Iben; Marcus, Susan E.;

    2015-01-01

    Background: While it is kno3wn that complex tissues with specialized functions emerged during land plant evolution, it is not clear how cell wall polymers and their structural variants are associated with specific tissues or cell types. Moreover, due to the economic importance of many flowering...... plants, ferns have been largely neglected in cell wall comparative studies. Results: To explore fern cell wall diversity sets of monoclonal antibodies directed to matrix glycans of angiosperm cell walls have been used in glycan microarray and in situ analyses with 76 fern species and four species of...... across the ferns and specifically associated with phloem cell walls and similarly the LM11 xylan epitope was associated with xylem cell walls. The LM5 galactan and LM6 arabinan epitopes, linked to pectic supramolecules in angiosperms, were associated with vascular structures with only limited detection...

  9. Single-cell RNA-seq reveals cell type-specific transcriptional signatures at the maternal–foetal interface during pregnancy

    Science.gov (United States)

    Nelson, Andrew C.; Mould, Arne W.; Bikoff, Elizabeth K.; Robertson, Elizabeth J.

    2016-01-01

    Growth and survival of the mammalian embryo within the uterine environment depends on the placenta, a highly complex vascularized organ comprised of both maternal and foetal tissues. Recent experiments demonstrate that the zinc finger transcriptional repressor Prdm1/Blimp1 is essential for specification of spiral artery trophoblast giant cells (SpA-TGCs) that invade and remodel maternal blood vessels. To learn more about functional contributions made by Blimp1+ cell lineages here we perform the first single-cell RNA-seq analysis of the placenta. Cell types of both foetal and maternal origin are profiled. Comparisons with microarray datasets from mutant placenta and in vitro differentiated trophoblast stem cells allow us to identify Blimp1-dependent transcripts enriched in SpA-TGCs. Our experiments provide new insights into the functionally distinct cell types present at the maternal–foetal interface and advance our knowledge of dynamic gene expression patterns controlling placental morphogenesis and vascular mimicry. PMID:27108815

  10. RAG-mediated DNA double-strand breaks activate a cell type-specific checkpoint to inhibit pre-B cell receptor signals.

    Science.gov (United States)

    Bednarski, Jeffrey J; Pandey, Ruchi; Schulte, Emily; White, Lynn S; Chen, Bo-Ruei; Sandoval, Gabriel J; Kohyama, Masako; Haldar, Malay; Nickless, Andrew; Trott, Amanda; Cheng, Genhong; Murphy, Kenneth M; Bassing, Craig H; Payton, Jacqueline E; Sleckman, Barry P

    2016-02-01

    DNA double-strand breaks (DSBs) activate a canonical DNA damage response, including highly conserved cell cycle checkpoint pathways that prevent cells with DSBs from progressing through the cell cycle. In developing B cells, pre-B cell receptor (pre-BCR) signals initiate immunoglobulin light (Igl) chain gene assembly, leading to RAG-mediated DNA DSBs. The pre-BCR also promotes cell cycle entry, which could cause aberrant DSB repair and genome instability in pre-B cells. Here, we show that RAG DSBs inhibit pre-BCR signals through the ATM- and NF-κB2-dependent induction of SPIC, a hematopoietic-specific transcriptional repressor. SPIC inhibits expression of the SYK tyrosine kinase and BLNK adaptor, resulting in suppression of pre-BCR signaling. This regulatory circuit prevents the pre-BCR from inducing additional Igl chain gene rearrangements and driving pre-B cells with RAG DSBs into cycle. We propose that pre-B cells toggle between pre-BCR signals and a RAG DSB-dependent checkpoint to maintain genome stability while iteratively assembling Igl chain genes. PMID:26834154

  11. Vectorial secretion of CTGF as a cell-type specific response to LPA and TGF-β in human tubular epithelial cells

    Directory of Open Access Journals (Sweden)

    Zuehlke Jonathan

    2012-09-01

    Full Text Available Abstract Background Increased expression of the pro-fibrotic protein connective tissue growth factor (CTGF has been detected in injured kidneys and elevated urinary levels of CTGF are discussed as prognostic marker of chronic kidney disease. There is evidence that epithelial cells lining the renal tubular system contribute to uptake and secretion of CTGF. However, the role of different types of tubular epithelial cells in these processes so far has not been addressed in primary cultures of human cells. Results Tubular epithelial cells of proximal and distal origin were isolated from human kidneys and cultured as polarized cells in insert wells. The pro-fibrotic stimuli lysophosphatidic acid (LPA and transforming growth factor β (TGF-β were used to induce CTGF secretion. LPA activated CTGF secretion in proximal tubular cells when applied from either the apical or the basolateral side as shown by immunocytochemistry. CTGF was secreted exclusively to the apical side. Signaling pathways activated by LPA included MAP kinase and Rho kinase signaling. TGF-β applied from either side also stimulated CTGF secretion primarily to the apical side with little basolateral release. Interestingly, TGF-β activation induced different signaling pathways depending on the side of TGF-β application. Smad signaling was almost exclusively activated from the basolateral side most prominently in cells of distal origin. Only part of these cells also synthesized CTGF indicating that Smad activation alone was not sufficient for CTGF induction. MAP kinases were involved in apical TGF-β-mediated activation of CTGF synthesis in proximal cells and a subset of epithelial cells of distal origin. This subpopulation of distal tubular cells was also able to internalize recombinant apical CTGF, in addition to proximal cells which were the main cells to take up exogenous CTGF. Conclusions Analysis of polarized human primary renal epithelial cells in a transwell system shows that

  12. The multifunctional FUS, EWS and TAF15 proto-oncoproteins show cell type-specific expression patterns and involvement in cell spreading and stress response

    Directory of Open Access Journals (Sweden)

    Stenman Göran

    2008-07-01

    Full Text Available Abstract Background FUS, EWS and TAF15 are structurally similar multifunctional proteins that were first discovered upon characterization of fusion oncogenes in human sarcomas and leukemias. The proteins belong to the FET (previously TET family of RNA-binding proteins and are implicated in central cellular processes such as regulation of gene expression, maintenance of genomic integrity and mRNA/microRNA processing. In the present study, we investigated the expression and cellular localization of FET proteins in multiple human tissues and cell types. Results FUS, EWS and TAF15 were expressed in both distinct and overlapping patterns in human tissues. The three proteins showed almost ubiquitous nuclear expression and FUS and TAF15 were in addition present in the cytoplasm of most cell types. Cytoplasmic EWS was more rarely detected and seen mainly in secretory cell types. Furthermore, FET expression was downregulated in differentiating human embryonic stem cells, during induced differentiation of neuroblastoma cells and absent in terminally differentiated melanocytes and cardiac muscle cells. The FET proteins were targeted to stress granules induced by heat shock and oxidative stress and FUS required its RNA-binding domain for this translocation. Furthermore, FUS and TAF15 were detected in spreading initiation centers of adhering cells. Conclusion Our results point to cell-specific expression patterns and functions of the FET proteins rather than the housekeeping roles inferred from earlier studies. The localization of FET proteins to stress granules suggests activities in translational regulation during stress conditions. Roles in central processes such as stress response, translational control and adhesion may explain the FET proteins frequent involvement in human cancer.

  13. Triiodothyronine regulates angiogenic growth factor and cytokine secretion by isolated human decidual cells in a cell-type specific and gestational age-dependent manner

    OpenAIRE

    Vasilopoulou, E.; Loubière, L.S.; Lash, G.E.; Ohizua, O.; McCabe, C.J.; Franklyn, J A; Kilby, M. D.; Chan, S Y

    2014-01-01

    STUDY QUESTION Does triiodothyronine (T3) regulate the secretion of angiogenic growth factors and cytokines by human decidual cells isolated from early pregnancy? SUMMARY ANSWER T3 modulates the secretion of specific angiogenic growth factors and cytokines, with different regulatory patterns observed amongst various isolated subpopulations of human decidual cells and with a distinct change between the first and second trimesters of pregnancy. WHAT IS KNOWN ALREADY Maternal thyroid dysfunction...

  14. Enhanced detection with spectral imaging fluorescence microscopy reveals tissue- and cell-type-specific compartmentalization of surface-modified polystyrene nanoparticles

    OpenAIRE

    Kenesei, Kata; Murali, Kumarasamy; Czéh, Árpád; Piella, Jordi; Puntes, Victor; Madarász, Emília

    2016-01-01

    Background Precisely targeted nanoparticle delivery is critically important for therapeutic applications. However, our knowledge on how the distinct physical and chemical properties of nanoparticles determine tissue penetration through physiological barriers, accumulation in specific cells and tissues, and clearance from selected organs has remained rather limited. In the recent study, spectral imaging fluorescence microscopy was exploited for precise and rapid monitoring of tissue- and cell-...

  15. Specific residues of the GDP/GTP exchange factor Bud5p are involved in establishment of the cell type-specific budding pattern in yeast.

    Science.gov (United States)

    Kang, Pil Jung; Lee, Bongyong; Park, Hay-Oak

    2004-07-01

    Cells of the budding yeast undergo oriented cell division by choosing a specific site for growth depending on their cell type. Haploid a and alpha cells bud in an axial pattern whereas diploid a/alpha cells bud in a bipolar pattern. The Ras-like GTPase Rsr1p/Bud1p, its GDP-GTP exchange factor Bud5p, and its GTPase-activating protein Bud2p are essential for selecting the proper site for polarized growth in all cell types. Here we showed that specific residues at the N terminus and the C terminus of Bud5p were important for bipolar budding, while some residues were involved in both axial and bipolar budding. These bipolar-specific mutations of BUD5 disrupted proper localization of Bud5p in diploid a/alpha cells without affecting Bud5p localization in haploid alpha cells. In contrast, Bud5p expressed in the bud5 mutants defective in both budding patterns failed to localize in all cell types. Thus, these results identify specific residues of Bud5p that are likely to be involved in direct interaction with spatial landmarks, which recruit Bud5p to the proper bud site. Finally, we found a new start codon of BUD5, which extends the open reading frame to 210 bp upstream of the previously estimated start site, thus encoding a polypeptide of 608 amino acid residues. Bud5p with these additional N-terminal residues interacted with Bud8p, a potential bipolar landmark, suggesting that the N-terminal region is necessary for recognition of the spatial cues. PMID:15136576

  16. Cell-type specific photoreceptors and light signaling pathways in the multicellular green alga volvox carteri and their potential role in cellular differentiation

    OpenAIRE

    Kianianmomeni, Arash

    2015-01-01

    The formation of multicellular organisms requires genetically predefined signaling pathways in various cell types. Besides differences in size, energy balance and life time, cell types should be enable to modulate appropriate developmental and adaptive responses in ever-changing surrounding environment. One of the most important environmental cues is light which regulates a variety of physiological and cellular processes. During evolution, diverse light-sensitive proteins, so-called photorece...

  17. Cell-type-specific Jumonji histone demethylase gene expression in the healthy rat CNS: detection by a novel flow cytometry method

    Directory of Open Access Journals (Sweden)

    Stephanie M.C. Smith

    2014-05-01

    Full Text Available Our understanding of how histone demethylation contributes to the regulation of basal gene expression in the brain is largely unknown in any injury model, and especially in the healthy adult brain. Although Jumonji genes are often regulated transcriptionally, cell-specific gene expression of Jumonji histone demethylases in the brain remains poorly understood. Thus, in the present study we profiled the mRNA levels of 26 Jumonji genes in microglia (CD11b+, neurons (NeuN+ and astrocytes (GFAP+ from the healthy adult rat brain. We optimized a method combining a mZBF (modified zinc-based fixative and FCM (flow cytometry to simultaneously sort cells from non-transgenic animals. We evaluated cell-surface, intracellular and nuclear proteins, including histones, as well as messenger- and micro-RNAs in different cell types simultaneously from a single-sorted sample. We found that 12 Jumonji genes were differentially expressed between adult microglia, neurons and astrocytes. While JMJD2D was neuron-restricted, PHF8 and JMJD1C were expressed in all three cell types although the expression was highest in neurons. JMJD3 and JMJD5 were expressed in all cell types, but were highly enriched in microglia; astrocytes had the lowest expression of UTX and JHDM1D. Levels of global H3K27 (H3 lysine 27 methylation varied among cell types and appeared to be lowest in microglia, indicating that differences in basal gene expression of specific Jumonji histone demethylases may contribute to cell-specific gene expression in the CNS (central nervous system. This multiparametric technique will be valuable for simultaneously assaying chromatin modifications and gene regulation in the adult CNS.

  18. Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3

    OpenAIRE

    Frietze, Seth; Wang, Rui; Yao, Lijing; Tak, Yu Gyoung; Ye, Zhenqing; Gaddis, Malaina; Witt, Heather; Farnham, Peggy J.; Jin, Victor X.

    2012-01-01

    Background The TCF7L2 transcription factor is linked to a variety of human diseases, including type 2 diabetes and cancer. One mechanism by which TCF7L2 could influence expression of genes involved in diverse diseases is by binding to distinct regulatory regions in different tissues. To test this hypothesis, we performed ChIP-seq for TCF7L2 in six human cell lines. Results We identified 116,000 non-redundant TCF7L2 binding sites, with only 1,864 sites common to the six cell lines. Using ChIP-...

  19. Two Golgi integral membrane proteins (GIMPS) exhibit region- and cell type-specific distribution in the epididymis of the adult rat.

    Science.gov (United States)

    Suarez-Quian, C A; Jelesoff, N

    1994-12-15

    The epididymis participates in the post-testicular maturation and storage of spermatozoa by secreting proteins into the tubule lumen in a region-specific fashion. The underlying molecular mechanisms leading to biogenesis of these region-specific differences, however, are not known, although components of the Golgi complex membrane container must undoubtedly be intimately involved. Two monoclonal antibodies raised against Golgi integral membrane proteins, recognizing either the cis (GIMPc) or trans Golgi (GIMPt) cisternae, were used as molecular probes of these regions to begin the characterization of the Golgi complex of in vivo and in vitro epididymal cells. Immunolocalization of GIMPs was performed on frozen sections and in cultured cells using biotin-streptavidin-peroxidase immunocytochemistry. In tissue sections, immunostaining of GIMPt was extremely robust in the supranuclear cytoplasm throughout the epididymis. In contrast, no GIMPc immunostaining was detected in the initial segment or in clear cells of the distal caput, corpus, and cauda. Immunodetection of GIMPc and GIMPt in epididymal cells in vitro revealed a reticular, perinuclear pattern, and NH4Cl treatment preferentially disrupted the GIMPt immunolocalization. These results characterizing the molecular components of the Golgi complex will form the basis of additional studies to gain further insight into mechanisms leading to generation of regional differences in epididymal function. PMID:7873795

  20. Using laser micro-dissection and qRT-PCR to analyze cell type-specific gene expression in Norway spruce phloem

    Directory of Open Access Journals (Sweden)

    Nina E. Nagy

    2014-04-01

    Full Text Available The tangentially oriented polyphenolic parenchyma (PP and radially organized ray parenchyma in the phloem are central in the defense of conifer stems against insects and pathogens. Laser micro-dissection enables examination of cell-specific defense responses. To examine induced defense responses in Norway spruce stems inoculated with the necrotrophic blue-stain fungus Ceratocystis polonica, RNA extracted from laser micro-dissected phloem parenchyma and vascular cambium was analyzed using real-time RT-PCR (qRT-PCR to profile transcript levels of selected resistance marker genes. The monitored transcripts included three pathogenesis-related proteins (class IV chitinase (CHI4, defensin (SPI1, peroxidase (PX3, two terpene synthesis related proteins (DXPS and LAS, one ethylene biosynthesis related protein (ACS, and a phenylalanine ammonia-lyase (PAL. Three days following inoculation, four genes (CHI4, PAL, PX3, SPI1 were differentially induced in individual cell and tissue types, both close to the inoculation site (5 mm above and, to a lesser degree, further away (10 mm above. These resistance marker genes were all highly induced in ray parenchyma, supporting the important role of the rays in spruce defense propagation. CHI4 and PAL were also induced in PP cells and in conducting secondary phloem tissues. Our data suggests that different cell types in the secondary phloem of Norway spruce have overlapping but not fully redundant roles in active host defense. Furthermore, the study demonstrates the usefulness of laser micro-dissection coupled with qRT-PCR to characterize gene expression in different cell types of conifer bark.

  1. Cell type-specific control of protein synthesis and proliferation by FGF-dependent signaling to the translation repressor 4E-BP.

    Science.gov (United States)

    Ruoff, Rachel; Katsara, Olga; Kolupaeva, Victoria

    2016-07-01

    Regulation of protein synthesis plays a vital role in posttranscriptional modulation of gene expression. Translational control most commonly targets the initiation of protein synthesis: loading 40S ribosome complexes onto mRNA and AUG start codon recognition. This step is initiated by eukaryotic initiation factor 4E (eIF4E) (the m7GTP cap-binding protein), whose binding to eIF4G (a scaffolding subunit) and eIF4A (an ATP-dependent RNA helicase) leads to assembly of active eIF4F complex. The ability of eIF4E to recognize the cap is prevented by its binding to eIF4E binding protein (4E-BP), which thereby inhibits cap-dependent translation by sequestering eIF4E. The 4E-BP activity is, in turn, inhibited by mTORC1 [mTOR (the mechanistic target of rapamycin) complex 1] mediated phosphorylation. Here, we define a previously unidentified mechanism of mTOR-independent 4E-BP1 regulation that is used by chondrocytes upon FGF signaling. Chondrocytes are responsible for the formation of the skeleton long bones. Unlike the majority of cell types where FGF signaling triggers proliferation, chondrocytes respond to FGF with inhibition. We establish that FGF specifically suppresses protein synthesis in chondrocytes, but not in any other cells of mesenchymal origin. Furthermore, 4E-BP1 repressor activity is necessary not only for suppression of protein synthesis, but also for FGF-induced cell-cycle arrest. Importantly, FGF-induced changes in the 4E-BP1 activity observed in cell culture are likewise detected in vivo and reflect the action of FGF signaling on downstream targets during bone development. Thus, our findings demonstrate that FGF signaling differentially impacts protein synthesis through either stimulation or repression, in a cell-type-dependent manner, with 4E-BP1 being a key player. PMID:27313212

  2. Analysis of the c-myc IRES; a potential role for cell-type specific trans-acting factors and the nuclear compartment

    OpenAIRE

    Stoneley, Mark; Subkhankulova, Tatyana; Le Quesne, John P.C.; Coldwell, Mark J; Jopling, Catherine L; Belsham, Graham J.; Willis, Anne E.

    2000-01-01

    The 5′ UTR of c-myc mRNA contains an internal ribosome entry segment (IRES) and consequently, c-myc mRNAs can be translated by the alternative mechanism of internal ribosome entry. However, there is also some evidence suggesting that c-myc mRNA translation can occur via the conventional cap-dependent scanning mechanism. Using both bicistronic and monocistronic mRNAs containing the c-myc 5′ UTR, we demonstrate that both mechanisms can contribute to c-myc protein synthesis. A wide range of cell...

  3. Characterization of the Dictyostelium homolog of chromatin binding protein DET1 suggests a conserved pathway regulating cell type specification and developmental plasticity.

    Science.gov (United States)

    Dubin, Manu J; Kasten, Sonja; Nellen, Wolfgang

    2011-03-01

    DET1 (De-etiolated 1) is a chromatin binding protein involved in developmental regulation in both plants and animals. DET1 is largely restricted to multicellular eukaryotes, and here we report the characterization of a DET1 homolog from the social amoeba Dictyostelium discoideum. As in other species, Dictyostelium DET1 is nuclear localized. In contrast to other species, where it is an essential protein, loss of DET1 is nonlethal in Dictyostelium, although viability is significantly reduced. The phenotype of the det1(-) mutant is highly pleiotropic and results in a large degree of heterogeneity in developmental parameters. Loss of DET1 results in delayed and abnormal development with enlarged aggregation territories. Mutant slugs displayed cell type patterning with a bias toward the prestalk pathway. A number of DET1-interacting proteins are conserved in Dictyostelium, and the apparently conserved role of DET1 in regulatory pathways involving the bZIP transcription factors DimB, c-Jun, and HY5 suggests a highly conserved mechanism regulating development in multicellular eukaryotes. While the mechanism by which DET1 functions is unclear, it appears that it has a key role in regulation of developmental plasticity and integration of information on environmental conditions into the developmental program of an organism. PMID:21193547

  4. Time- and cell-type specific changes in iron, ferritin, and transferrin in the gerbil hippocampal CA1 region after transient forebrain ischemia

    Science.gov (United States)

    Yoo, Dae Young; Yoo, Ki-Yeon; Park, Joon Ha; Kwon, Hyun Jung; Jung, Hyo Young; Kim, Jong Whi; Choi, Goang-Min; Moon, Seung Myung; Kim, Dae Won; Yoon, Yeo Sung; Won, Moo-Ho; Hwang, In Koo

    2016-01-01

    In the present study, we used immunohistochemistry and western blot analysis to examine changes in the levels and cellular localization of iron, heavy chain ferritin (ferritin-H), and transferrin in the gerbil hippocampal CA1 region from 30 minutes to 7 days following transient forebrain ischemia. Relative to sham controls, iron reactivity increased significantly in the stratum pyramidale and stratum oriens at 12 hours following ischemic insult, transiently decreased at 1–2 days and then increased once again within the CA1 region at 4–7 days after ischemia. One day after ischemia, ferritin-H immunoreactivity increased significantly in the stratum pyramidale and decreased at 2 days. At 4–7 days after ischemia, ferritin-H immunoreactivity in the glial components in the CA1 region was significantly increased. Transferrin immunoreactivity was increased significantly in the stratum pyramidale at 12 hours, peaked at 1 day, and then decreased significantly at 2 days after ischemia. Seven days after ischemia, Transferrin immunoreactivity in the glial cells of the stratum oriens and radiatum was significantly increased. Western blot analyses supported these results, demonstrating that compared to sham controls, ferritin H and transferrin protein levels in hippocampal homogenates significantly increased at 1 day after ischemia, peaked at 4 days and then decreased. These results suggest that iron overload-induced oxidative stress is most prominent at 12 hours after ischemia in the stratum pyramidale, suggesting that this time window may be the optimal period for therapeutic intervention to protect neurons from ischemia-induced death.

  5. The complex becomes more complex: protein-protein interactions of SnRK1 with DUF581 family proteins provide a framework for cell- and stimulus type-specific SnRK1 signaling in plants

    Directory of Open Access Journals (Sweden)

    Madlen eNietzsche

    2014-02-01

    Full Text Available In plants, SNF1-related kinase (SnRK1 responds to the availability of carbohydrates as well as to environmental stresses by down-regulating ATP consuming biosynthetic processes, while stimulating energy-generating catabolic reactions through gene expression and post-transcriptional regulation. The functional SnRK1 complex is a heterotrimer where the catalytic alpha subunit associates with a regulatory beta subunit and an activating gamma subunit. Several different metabolites as well as the hormone abscisic acid (ABA have been shown to modulate SnRK1 activity in a cell- and stimulus-type specific manner. It has been proposed that tissue- or stimulus-specific expression of adapter proteins mediating SnRK1 regulation can at least partly explain the differences observed in SnRK1 signaling. By using yeast two-hybrid and in planta bi-molecular fluorescence complementation assays we were able to demonstrate that proteins containing the domain of unknown function (DUF 581 could interact with both isoforms of the SnRK1 alpha subunit (AKIN10/11 of Arabidopsis. A structure/function analysis suggests that the DUF581 is a generic SnRK1 interaction module and co-expression with DUF581 proteins in plant cells leads to reallocation of the kinase to specific regions within the nucleus. Yeast two-hybrid analyses suggest that SnRK1 and DUF581 proteins can share common interaction partners inside the nucleus. The analysis of available microarray data implies that expression of the 19 members of the DUF581 encoding gene family in Arabidopsis is differentially regulated by hormones and environmental cues, indicating specialized functions of individual family members. We hypothesize that DUF581 proteins could act as mediators conferring tissue- and stimulus-type specific differences in SnRK1 regulation.

  6. Visualizing cell state transition using Raman spectroscopy.

    Directory of Open Access Journals (Sweden)

    Taro Ichimura

    Full Text Available System level understanding of the cell requires detailed description of the cell state, which is often characterized by the expression levels of proteins. However, understanding the cell state requires comprehensive information of the cell, which is usually obtained from a large number of cells and their disruption. In this study, we used Raman spectroscopy, which can report changes in the cell state without introducing any label, as a non-invasive method with single cell capability. Significant differences in Raman spectra were observed at the levels of both the cytosol and nucleus in different cell-lines from mouse, indicating that Raman spectra reflect differences in the cell state. Difference in cell state was observed before and after the induction of differentiation in neuroblastoma and adipocytes, showing that Raman spectra can detect subtle changes in the cell state. Cell state transitions during embryonic stem cell (ESC differentiation were visualized when Raman spectroscopy was coupled with principal component analysis (PCA, which showed gradual transition in the cell states during differentiation. Detailed analysis showed that the diversity between cells are large in undifferentiated ESC and in mesenchymal stem cells compared with terminally differentiated cells, implying that the cell state in stem cells stochastically fluctuates during the self-renewal process. The present study strongly indicates that Raman spectral morphology, in combination with PCA, can be used to establish cells' fingerprints, which can be useful for distinguishing and identifying different cellular states.

  7. Visualization of DNA damage in individual cells

    International Nuclear Information System (INIS)

    A simple technique of micro-agarose gel electrophoresis has been developed to permit an evaluation of DNA damage in individual cells. Cells are embeded in agarose gel on microscope slides, lysed by detergents and then electrophoresed for a short time. In damaged cells, DNA migrated from the nuclei toward the anode, displaying 'comets' visualized by staining with a DNA-specific fluorochrome, acridine orange. The technique was applicable to quantifying DNA damage in individual cells exposed to Gy level of reactor radiation. (author)

  8. Seeing Cells: Teaching the Visual/Verbal Rhetoric of Biology

    Science.gov (United States)

    Dinolfo, John; Heifferon, Barbara; Temesvari, Lesly A.

    2007-01-01

    This pilot study obtained baseline information on verbal and visual rhetorics to teach microscopy techniques to college biology majors. We presented cell images to students in cell biology and biology writing classes and then asked them to identify textual, verbal, and visual cues that support microscopy learning. Survey responses suggest that…

  9. Visualizing Without Vision at the Microscale: Students With Visual Impairments Explore Cells With Touch

    Science.gov (United States)

    Jones, M. Gail; Minogue, James; Oppewal, Tom; Cook, Michelle P.; Broadwell, Bethany

    2006-12-01

    Science instruction is typically highly dependent on visual representations of scientific concepts that are communicated through textbooks, teacher presentations, and computer-based multimedia materials. Little is known about how students with visual impairments access and interpret these types of visually-dependent instructional materials. This study explored the efficacy of new haptic (simulated tactile feedback and kinesthetics) instructional technology for teaching cell morphology and function to middle and high school students with visual impairments. The study examined students' prior experiences learning about the cell and cell functions in classroom instruction, as well as how haptic feedback technology impacted students' awareness of the 3-D nature of an animal cell, the morphology and function of cell organelles, and students' interest in the haptic technology as an instructional tool. Twenty-one students with visual impairment participated in the study. Students explored a tactile model of the cell with a haptic point probe that allowed them to feel the cell and its organelles. Results showed that students made significant gains in their ability to identify cell organelles and found the technology to be highly interesting as an instructional tool. The need for additional adaptive technology for students with visual impairments is discussed.

  10. Visualization of RNA-Quadruplexes in Live Cells.

    Science.gov (United States)

    Laguerre, Aurélien; Hukezalie, Kyle; Winckler, Pascale; Katranji, Fares; Chanteloup, Gaëtan; Pirrotta, Marc; Perrier-Cornet, Jean-Marie; Wong, Judy M Y; Monchaud, David

    2015-07-01

    Visualization of DNA and RNA quadruplex formation in human cells was demonstrated recently with different quadruplex-specific antibodies. Despite the significant interest in these immunodetection approaches, dynamic detection of quadruplex in live cells remains elusive. Here, we report on NaphthoTASQ (N-TASQ), a next-generation quadruplex ligand that acts as a multiphoton turn-on fluorescent probe. Single-step incubation of human and mouse cells with N-TASQ enables the direct detection of RNA-quadruplexes in untreated cells (no fixation, permeabilization or mounting steps), thus offering a unique, unbiased visualization of quadruplexes in live cells. PMID:26056849

  11. Atypical visual loss in giant cell arteritis

    DEFF Research Database (Denmark)

    Thystrup, Jan Deichmann; Knudsen, G M; Mogensen, A M;

    1994-01-01

    terminal stage of his disease due to bilateral occipital cortex infarctions, verified by CT-scan. Autopsy revealed involvement of several intracranial arteries. In case No. 2 there was severe unilateral visual loss and cotton-wool exudates in both eyes. Central vision recovered after corticosteroid therapy...

  12. The role of cell adhesion molecules in visual circuit formation: from neurite outgrowth to maps and synaptic specificity.

    Science.gov (United States)

    Missaire, Mégane; Hindges, Robert

    2015-06-01

    The formation of visual circuitry is a multistep process that involves cell-cell interactions based on a range of molecular mechanisms. The correct implementation of individual events, including axon outgrowth and guidance, the formation of the topographic map, or the synaptic targeting of specific cellular subtypes, are prerequisites for a fully functional visual system that is able to appropriately process the information captured by the eyes. Cell adhesion molecules (CAMs) with their adhesive properties and their high functional diversity have been identified as key actors in several of these fundamental processes. Because of their growth-promoting properties, CAMs play an important role in neuritogenesis. Furthermore, they are necessary to control additional neurite development, regulating dendritic spacing and axon pathfinding. Finally, trans-synaptic interactions of CAMs ensure cell type-specific connectivity as a basis for the establishment of circuits processing distinct visual features. Recent discoveries implicating CAMs in novel mechanisms have led to a better general understanding of neural circuit formation, but also revealed an increasing complexity of their function. This review aims at describing the different levels of action for CAMs to shape neural connectivity, with a special focus on the visual system. PMID:25649254

  13. The cell-type specific uptake of polymer-coated or micelle-embedded QDs and SPIOs does not provoke an acute pro-inflammatory response in the liver

    Directory of Open Access Journals (Sweden)

    Markus Heine

    2014-09-01

    Full Text Available Semiconductor quantum dots (QD and superparamagnetic iron oxide nanocrystals (SPIO have exceptional physical properties that are well suited for biomedical applications in vitro and in vivo. For future applications, the direct injection of nanocrystals for imaging and therapy represents an important entry route into the human body. Therefore, it is crucial to investigate biological responses of the body to nanocrystals to avoid harmful side effects. In recent years, we established a system to embed nanocrystals with a hydrophobic oleic acid shell either by lipid micelles or by the amphiphilic polymer poly(maleic anhydride-alt-1-octadecene (PMAOD. The goal of the current study is to investigate the uptake processes as well as pro-inflammatory responses in the liver after the injection of these encapsulated nanocrystals. By immunofluorescence and electron microscopy studies using wild type mice, we show that 30 min after injection polymer-coated nanocrystals are primarily taken up by liver sinusoidal endothelial cells. In contrast, by using wild type, Ldlr-/- as well as Apoe-/- mice we show that nanocrystals embedded within lipid micelles are internalized by Kupffer cells and, in a process that is dependent on the LDL receptor and apolipoprotein E, by hepatocytes. Gene expression analysis of pro-inflammatory markers such as tumor necrosis factor alpha (TNFα or chemokine (C-X-C motif ligand 10 (Cxcl10 indicated that 48 h after injection internalized nanocrystals did not provoke pro-inflammatory pathways. In conclusion, internalized nanocrystals at least in mouse liver cells, namely endothelial cells, Kupffer cells and hepatocytes are at least not acutely associated with potential adverse side effects, underlining their potential for biomedical applications.

  14. Type I interferon production during herpes simplex virus infection is controlled by cell-type-specific viral recognition through Toll-like receptor 9, the mitochondrial antiviral signaling protein pathway, and novel recognition systems

    DEFF Research Database (Denmark)

    Rasmussen, Simon Brandtoft; Sørensen, Louise Nørgaard; Malmgaard, Lene; Ank, Nina; Baines, JD; Chen, ZJ; Paludan, Søren Riis

    2007-01-01

    Recognition of viruses by germ line-encoded pattern recognition receptors of the innate immune system is essential for rapid production of type I interferon (IFN) and early antiviral defense. We investigated the mechanisms of viral recognition governing production of type I IFN during herpes...... fibroblasts, where the virus was able to replicate, HSV-induced IFN-alpha/beta production was dependent on both viral entry and replication, and ablated in cells unable to signal through the mitochondrial antiviral signaling protein pathway. Thus, during an HSV infection in vivo, multiple mechanisms of...

  15. Phase sensitivity of complex cells in primary visual cortex.

    Science.gov (United States)

    Hietanen, M A; Cloherty, S L; van Kleef, J P; Wang, C; Dreher, B; Ibbotson, M R

    2013-05-01

    Neurons in the primary visual cortex are often classified as either simple or complex based on the linearity (or otherwise) of their response to spatial luminance contrast. In practice, classification is typically based on Fourier analysis of a cell's response to an optimal drifting sine-wave grating. Simple cells are generally considered to be linear and produce responses modulated at the fundamental frequency of the stimulus grating. In contrast, complex cells exhibit significant nonlinearities that reduce the response at the fundamental frequency. Cells can therefore be easily and objectively classified based on the relative modulation of their responses - the ratio of the phase-sensitive response at the fundamental frequency of the stimulus (F₁) to the phase-invariant sustained response (F₀). Cells are classified as simple if F₁/F₀>1 and complex if F₁/F₀<1. This classification is broadly consistent with criteria based on the spatial organisation of cells' receptive fields and is accordingly presumed to reflect disparate functional roles of simple and complex cells in coding visual information. However, Fourier analysis of spiking responses is sensitive to the number of spikes available - F₁/F₀ increases as the number of spikes is reduced, even for phase-invariant complex cells. Moreover, many complex cells encountered in the laboratory exhibit some phase sensitivity, evident as modulation of their responses at the fundamental frequency. There currently exists no objective quantitative means of assessing the significance or otherwise of these modulations. Here we derive a statistical basis for objectively assessing whether the modulation of neuronal responses is reliable, thereby adding a level of statistical certainty to measures of phase sensitivity. We apply our statistical analysis to neuronal responses to moving sine-wave gratings recorded from 367 cells in cat primary visual cortex. We find that approximately 60% of complex cells exhibit

  16. Glial cell development and function in the Drosophila visual system

    OpenAIRE

    CHOTARD, CAROLE; Salecker, Iris

    2007-01-01

    In the developing nervous system, building a functional neuronal network relies on coordinating the formation, specification and survival to diverse neuronal and glial cell subtypes. The establishment of neuronal connections further depends on sequential neuron–neuron and neuron–glia interactions that regulate cell-migration patterns and axon guidance. The visual system of Drosophila has a highly regular, retinotopic organization into reiterated interconnected synaptic circuits. It is therefo...

  17. Robust Type-specific Hemisynapses Induced by Artificial Dendrites

    Science.gov (United States)

    Kim, Eun Joong; Jeon, Chang Su; Lee, Soo Youn; Hwang, Inseong; Chung, Taek Dong

    2016-04-01

    Type-specificity of synapses, excitatory and inhibitory, regulates information process in neural networks via chemical neurotransmitters. To lay a foundation of synapse-based neural interfaces, artificial dendrites are generated by covering abiotic substrata with ectodomains of type-specific synaptogenic proteins that are C-terminally tagged with biotinylated fluorescent proteins. The excitatory artificial synapses displaying engineered ectodomains of postsynaptic neuroligin-1 (NL1) induce the formation of excitatory presynapses with mixed culture of neurons in various developmental stages, while the inhibitory artificial dendrites displaying engineered NL2 and Slitrk3 induce inhibitory presynapses only with mature neurons. By contrast, if the artificial dendrites are applied to the axonal components of micropatterned neurons, correctly-matched synaptic specificity emerges regardless of the neuronal developmental stages. The hemisynapses retain their initially established type-specificity during neuronal development and maintain their synaptic strength provided live neurons, implying the possibility of durable synapse-based biointerfaces.

  18. Visualization and targeted disruption of protein interactions in living cells

    OpenAIRE

    Herce, Henry D.; Deng, Wen; Helma, Jonas; Leonhardt, Heinrich; Cardoso, M. Cristina

    2013-01-01

    Protein–protein interactions are the basis of all processes in living cells, but most studies of these interactions rely on biochemical in vitro assays. Here we present a simple and versatile fluorescent-three-hybrid (F3H) strategy to visualize and target protein–protein interactions. A high-affinity nanobody anchors a GFP-fusion protein of interest at a defined cellular structure and the enrichment of red-labelled interacting proteins is measured at these sites. With this approach, we visual...

  19. Developmental changes in cytosolic coupling between epidermis cells as visualized by photoactivation of fluorescein

    DEFF Research Database (Denmark)

    Liu, Xiangdong; Martens, Helle; Schulz, Alexander

    Developmental changes in cytosolic coupling between epidermis cells as visualized by photoactivation of fluorescein.......Developmental changes in cytosolic coupling between epidermis cells as visualized by photoactivation of fluorescein....

  20. Effect of Contrast on Visual Spatial Summation in Different Cell Categories in Cat Primary Visual Cortex.

    Directory of Open Access Journals (Sweden)

    Ke Chen

    Full Text Available Multiple cell classes have been found in the primary visual cortex, but the relationship between cell types and spatial summation has seldom been studied. Parvalbumin-expressing inhibitory interneurons can be distinguished from pyramidal neurons based on their briefer action potential durations. In this study, we classified V1 cells into fast-spiking units (FSUs and regular-spiking units (RSUs and then examined spatial summation at high and low contrast. Our results revealed that the excitatory classical receptive field and the suppressive non-classical receptive field expanded at low contrast for both FSUs and RSUs, but the expansion was more marked for the RSUs than for the FSUs. For most V1 neurons, surround suppression varied as the contrast changed from high to low. However, FSUs exhibited no significant difference in the strength of suppression between high and low contrast, although the overall suppression decreased significantly at low contrast for the RSUs. Our results suggest that the modulation of spatial summation by stimulus contrast differs across populations of neurons in the cat primary visual cortex.

  1. Visualization and targeted disruption of protein interactions in living cells.

    Science.gov (United States)

    Herce, Henry D; Deng, Wen; Helma, Jonas; Leonhardt, Heinrich; Cardoso, M Cristina

    2013-01-01

    Protein-protein interactions are the basis of all processes in living cells, but most studies of these interactions rely on biochemical in vitro assays. Here we present a simple and versatile fluorescent-three-hybrid (F3H) strategy to visualize and target protein-protein interactions. A high-affinity nanobody anchors a GFP-fusion protein of interest at a defined cellular structure and the enrichment of red-labelled interacting proteins is measured at these sites. With this approach, we visualize the p53-HDM2 interaction in living cells and directly monitor the disruption of this interaction by Nutlin 3, a drug developed to boost p53 activity in cancer therapy. We further use this approach to develop a cell-permeable vector that releases a highly specific peptide disrupting the p53 and HDM2 interaction. The availability of multiple anchor sites and the simple optical readout of this nanobody-based capture assay enable systematic and versatile analyses of protein-protein interactions in practically any cell type and species. PMID:24154492

  2. Visualization of Carbon Nanoparticles Within Cells and Implications for Toxicity

    Science.gov (United States)

    Porter, Alexandra; Gass, Mhairi

    Carbon nanostructures (CNS), such as C60, single-walled nanotubes (SWNTs) exhibit extraordinary properties and are one of the most commercially relevant class of NS. CNS have already found uses in high-performance sports equipment (nanotubes) and face cream (C60), whilst potential applications include optical and electronic materials and superconductors. Following the huge growth in these nanotechnology-related industries, significant concerns have arisen about their potential toxicity and impact on the environment. A lack in understanding of the interaction of such small structures with cellular material has resulted in concerns over their impact on human health. The potential toxicity of CNS and safety to human health requires an understanding of their interaction with cells and this in turn relies on the measurement of the pathways by which they enter the cell, their spatial distribution within and whether the CNS are transformed by the action of the cell; visualization of intracellular CNS is therefore imperative. However visualizing unlabelled CNS within cells is demanding because it is difficult to distinguish CNS from carbon-rich organelles given their similarity in composition and dimensions. In particular, the challenge lies in translating analytical imaging tools developed for inorganic systems to organic systems. This chapter describes how the state-of-the-art transmission electron microscopy (TEM) techniques, such as low-loss energy-filtered TEM (EFTEM) can be employed to differentiate between unlabelled C60, SWNTs and the cell. Further, we demonstrate how these techniques can be used to trace the uptake of CNS into the cell and to assess their localized effects on cell structure.

  3. Visual Servoed Three-Dimensional Cell Rotation System.

    Science.gov (United States)

    Wang, Zenan; Latt, Win Tun; Tan, Steven Yih Min; Ang, Wei Tech

    2015-10-01

    Three-dimensional (3-D) positioning and orientation of embryos/oocytes is necessary to facilitate micromanipulation tasks such as cell injection and cellular structural biopsy commonly performed under a microscope. Conventional cell orientation is performed manually by using a vacuum equipped micropipette to aspirate and release the cell, which is a trial-and-error approach. The conventional method relies heavily on the skill of the operator; it also suffers from low precision, low success rate and low controllability. These drawbacks illustrate the need for a systematic 3-D cell rotational system to automate the cell orientation process. In this paper, we present a noninvasive single cell rotation system that can automatically orientate a zebrafish embryo to a desired position when both the cytoplasm and the yolk are in the focal plane. A three-point-contact model for cell rotation that involves a custom-designed rotational stage is introduced to provide precise rotational position control. A vision recognition algorithm is also proposed to enable the visual servoing function of the system. Experimental results show that the proposed system can achieve high success rates of 92.5% (x-axis rotation with 40 trails) and 97.5% (about the z-axis with 80 trails). The system can also successfully complete 3-D cell orientation at an average speed of 31 s/cell with a high in-plane rotation accuracy of 0.3 (°) . As a high precise, high controllable and deterministic cell manipulating system, it provides a starting point for automated cell manipulation for intracytoplasmic sperm injection and embryo biopsy for preimplantation genetic diagnosis. PMID:25993702

  4. From grid cells and visual place cells to multimodal place cell: a new robotic architecture.

    Science.gov (United States)

    Jauffret, Adrien; Cuperlier, Nicolas; Gaussier, Philippe

    2015-01-01

    In the present study, a new architecture for the generation of grid cells (GC) was implemented on a real robot. In order to test this model a simple place cell (PC) model merging visual PC activity and GC was developed. GC were first built from a simple "several to one" projection (similar to a modulo operation) performed on a neural field coding for path integration (PI). Robotics experiments raised several practical and theoretical issues. To limit the important angular drift of PI, head direction information was introduced in addition to the robot proprioceptive signal coming from the wheel rotation. Next, a simple associative learning between visual place cells and the neural field coding for the PI has been used to recalibrate the PI and to limit its drift. Finally, the parameters controlling the shape of the PC built from the GC have been studied. Increasing the number of GC obviously improves the shape of the resulting place field. Yet, other parameters such as the discretization factor of PI or the lateral interactions between GC can have an important impact on the place field quality and avoid the need of a very large number of GC. In conclusion, our results show our GC model based on the compression of PI is congruent with neurobiological studies made on rodent. GC firing patterns can be the result of a modulo transformation of PI information. We argue that such a transformation may be a general property of the connectivity from the cortex to the entorhinal cortex. Our model predicts that the effect of similar transformations on other kinds of sensory information (visual, tactile, auditory, etc…) in the entorhinal cortex should be observed. Consequently, a given EC cell should react to non-contiguous input configurations in non-spatial conditions according to the projection from its different inputs. PMID:25904862

  5. Direct Visualization of De novo Lipogenesis in Single Living Cells

    Science.gov (United States)

    Li, Junjie; Cheng, Ji-Xin

    2014-10-01

    Increased de novo lipogenesis is being increasingly recognized as a hallmark of cancer. Despite recent advances in fluorescence microscopy, autoradiography and mass spectrometry, direct observation of de novo lipogenesis in living systems remains to be challenging. Here, by coupling stimulated Raman scattering (SRS) microscopy with isotope labeled glucose, we were able to trace the dynamic metabolism of glucose in single living cells with high spatial-temporal resolution. As the first direct visualization, we observed that glucose was largely utilized for lipid synthesis in pancreatic cancer cells, which occurs at a much lower rate in immortalized normal pancreatic epithelial cells. By inhibition of glycolysis and fatty acid synthase (FAS), the key enzyme for fatty acid synthesis, we confirmed the deuterium labeled lipids in cancer cells were from de novo lipid synthesis. Interestingly, we also found that prostate cancer cells exhibit relatively lower level of de novo lipogenesis, but higher fatty acid uptake compared to pancreatic cancer cells. Together, our results demonstrate a valuable tool to study dynamic lipid metabolism in cancer and other disorders.

  6. Development of an autonomous biological cell manipulator with single-cell electroporation and visual servoing capabilities.

    Science.gov (United States)

    Sakaki, Kelly; Dechev, Nikolai; Burke, Robert D; Park, Edward J

    2009-08-01

    Studies of single cells via microscopy and microinjection are a key component in research on gene functions, cancer, stem cells, and reproductive technology. As biomedical experiments become more complex, there is an urgent need to use robotic systems to improve cell manipulation and microinjection processes. Automation of these tasks using machine vision and visual servoing creates significant benefits for biomedical laboratories, including repeatability of experiments, higher throughput, and improved cell viability. This paper presents the development of a new 5-DOF robotic manipulator, designed for manipulating and microinjecting single cells. This biological cell manipulator (BCM) is capable of autonomous scanning of a cell culture followed by autonomous injection of cells using single-cell electroporation (SCE). SCE does not require piercing the cell membrane, thereby keeping the cell membrane fully intact. The BCM features high-precision 3-DOF translational and 2-DOF rotational motion, and a second z-axis allowing top-down placement of a micropipette tip onto the cell membrane for SCE. As a technical demonstration, the autonomous visual servoing and microinjection capabilities of the single-cell manipulator are experimentally shown using sea urchin eggs. PMID:19605307

  7. Visualizing dopamine released from living cells using a nanoplasmonic probe

    Science.gov (United States)

    Qin, W. W.; Wang, S. P.; Li, J.; Peng, T. H.; Xu, Y.; Wang, K.; Shi, J. Y.; Fan, C. H.; Li, D.

    2015-09-01

    We report the development of an ultrasensitive nanoplasmonic probe for discriminative detection and imaging of dopamine released from living cells. The sensing mechanism is based on the dopamine-induced seeded-growth of Au nanoparticles (Au NPs) that leads to the shift of the plasmon band. This platform allows for the detection of dopamine with a detection limit down to 0.25 pM within 1 min. This nanoplasmonic assay is further applied to visualize the release of dopamine from living rat pheochromocytoma (PC12) cells under ATP-stimulation with dark-field microscopy (DFM). The DFM results together with real time fluorescence imaging of PC12 cells stained with the Fluo calcium indicator, suggested that ATP stimulated-release of dopamine is concomitant with the Ca2+ influx, and the influx of Ca2+ is through ATP-activated channels instead of the voltage-gated Ca2+ channel (VGC).We report the development of an ultrasensitive nanoplasmonic probe for discriminative detection and imaging of dopamine released from living cells. The sensing mechanism is based on the dopamine-induced seeded-growth of Au nanoparticles (Au NPs) that leads to the shift of the plasmon band. This platform allows for the detection of dopamine with a detection limit down to 0.25 pM within 1 min. This nanoplasmonic assay is further applied to visualize the release of dopamine from living rat pheochromocytoma (PC12) cells under ATP-stimulation with dark-field microscopy (DFM). The DFM results together with real time fluorescence imaging of PC12 cells stained with the Fluo calcium indicator, suggested that ATP stimulated-release of dopamine is concomitant with the Ca2+ influx, and the influx of Ca2+ is through ATP-activated channels instead of the voltage-gated Ca2+ channel (VGC). Electronic supplementary information (ESI) available: Fig. S1-S4 and Table S1. See DOI: 10.1039/c5nr04433b

  8. A Robot-Assisted Cell Manipulation System with an Adaptive Visual Servoing Method

    OpenAIRE

    Yu Xie; Feng Zeng; Wenming Xi; Yunlei Zhou; Houde Liu; Mingliang Chen

    2016-01-01

    Robot-assisted cell manipulation is gaining attention for its ability in providing high throughput and high precision cell manipulation for the biological industry. This paper presents a visual servo microrobotic system for cell microinjection. We investigated the automatic cell autofocus method that reduced the complexity of the system. Then, we produced an adaptive visual processing algorithm to detect the location of the cell and micropipette toward the uneven illumination problem. Fourtee...

  9. Visual cells remember earlier applied target: plasticity of orientation selectivity.

    Directory of Open Access Journals (Sweden)

    Narcis Ghisovan

    Full Text Available BACKGROUND: A canonical proposition states that, in mature brain, neurons responsive to sensory stimuli are tuned to specific properties installed shortly after birth. It is amply demonstrated that that neurons in adult visual cortex of cats are orientation-selective that is they respond with the highest firing rates to preferred oriented stimuli. METHODOLOGY/PRINCIPAL FINDINGS: In anesthetized cats, prepared in a conventional fashion for single cell recordings, the present investigation shows that presenting a stimulus uninterruptedly at a non-preferred orientation for twelve minutes induces changes in orientation preference. Across all conditions orientation tuning curves were investigated using a trial by trial method. Contrary to what has been previously reported with shorter adaptation duration, twelve minutes of adaptation induces mostly attractive shifts, i.e. toward the adapter. After a recovery period allowing neurons to restore their original orientation tuning curves, we carried out a second adaptation which produced three major results: (1 more frequent attractive shifts, (2 an increase of their magnitude, and (3 an additional enhancement of responses at the new or acquired preferred orientation. Additionally, we also show that the direction of shifts depends on the duration of the adaptation: shorter adaptation in most cases produces repulsive shifts, whereas adaptation exceeding nine minutes results in attractive shifts, in the same unit. Consequently, shifts in preferred orientation depend on the duration of adaptation. CONCLUSION/SIGNIFICANCE: The supplementary response improvements indicate that neurons in area 17 keep a memory trace of the previous stimulus properties, thereby upgrading cellular performance. It also highlights the dynamic nature of basic neuronal properties in adult cortex since repeated adaptations modified both the orientation tuning selectivity and the response strength to the preferred orientation. These

  10. Endothelial cell-initiated extravasation of cancer cells visualized in zebrafish

    Directory of Open Access Journals (Sweden)

    Masamitsu Kanada

    2014-12-01

    Full Text Available The extravasation of cancer cells, a key step for distant metastasis, is thought to be initiated by disruption of the endothelial barrier by malignant cancer cells. An endothelial covering-type extravasation of cancer cells in addition to conventional cancer cell invasion-type extravasation was dynamically visualized in a zebrafish hematogenous metastasis model. The inhibition of VEGF-signaling impaired the invasion-type extravasation via inhibition of cancer cell polarization and motility. Paradoxically, the anti-angiogenic treatment showed the promotion, rather than the inhibition, of the endothelial covering-type extravasation of cancer cells, with structural changes in the endothelial walls. These findings may be a set of clues to the full understanding of the metastatic process as well as the metastatic acceleration by anti-angiogenic reagents observed in preclinical studies.

  11. A Robot-Assisted Cell Manipulation System with an Adaptive Visual Servoing Method

    Directory of Open Access Journals (Sweden)

    Yu Xie

    2016-06-01

    Full Text Available Robot-assisted cell manipulation is gaining attention for its ability in providing high throughput and high precision cell manipulation for the biological industry. This paper presents a visual servo microrobotic system for cell microinjection. We investigated the automatic cell autofocus method that reduced the complexity of the system. Then, we produced an adaptive visual processing algorithm to detect the location of the cell and micropipette toward the uneven illumination problem. Fourteen microinjection experiments were conducted with zebrafish embryos. A 100% success rate was achieved either in autofocus or embryo detection, which verified the robustness of the proposed automatic cell manipulation system.

  12. Experience of in-cell visual inspection using CCD camera in hot cell of Reprocessing Plant

    International Nuclear Information System (INIS)

    This paper describes the selection, customization and operating experience of the visual inspection system for the hot cell of a Reprocessing Plant. For process equipment such as fuel chopping machine, dissolver, centrifuge, centrifugal extractors etc., viewing of operations and maintenance using manipulators is required. For this, the service of in-cell camera is essential. The ambience of the hot cell of Compact facility for Reprocessing of Advanced fuels in Lead cell (CORAL) for the reprocessing of fast reactor spent fuel has high gamma radiation and acidic vapors. Black and white Charge Coupled Device (CCD) camera has been used in CORAL incorporating in-house modifications to suit the operating ambient conditions, thereby extending the operating life of the camera. (author)

  13. Birth time/order-dependent neuron type specification

    OpenAIRE

    Kao, Chih-Fei; Lee, Tzumin

    2009-01-01

    Neurons derived from the same progenitor may acquire different fates according to their birth timing/order. To reveal temporally guided cell fates, we must determine neuron types as well as their lineage relationships and times of birth. Recent advances in genetic lineage analysis and fate mapping are facilitating such studies. For example, high-resolution lineage analysis can identify each sequentially derived neuron of a lineage and has revealed abrupt temporal identity changes in diverse D...

  14. Vascular Cell Induction Culture System Using Arabidopsis Leaves (VISUAL) Reveals the Sequential Differentiation of Sieve Element-Like Cells.

    Science.gov (United States)

    Kondo, Yuki; Nurani, Alif Meem; Saito, Chieko; Ichihashi, Yasunori; Saito, Masato; Yamazaki, Kyoko; Mitsuda, Nobutaka; Ohme-Takagi, Masaru; Fukuda, Hiroo

    2016-06-01

    Cell differentiation is a complex process involving multiple steps, from initial cell fate specification to final differentiation. Procambial/cambial cells, which act as vascular stem cells, differentiate into both xylem and phloem cells during vascular development. Recent studies have identified regulatory cascades for xylem differentiation. However, the molecular mechanism underlying phloem differentiation is largely unexplored due to technical challenges. Here, we established an ectopic induction system for phloem differentiation named Vascular Cell Induction Culture System Using Arabidopsis Leaves (VISUAL). Our results verified similarities between VISUAL-induced Arabidopsis thaliana phloem cells and in vivo sieve elements. We performed network analysis using transcriptome data with VISUAL to dissect the processes underlying phloem differentiation, eventually identifying a factor involved in the regulation of the master transcription factor gene APL Thus, our culture system opens up new avenues not only for genetic studies of phloem differentiation, but also for future investigations of multidirectional differentiation from vascular stem cells. PMID:27194709

  15. Ctip2-, Satb2-, Prox1-, and GAD65-Expressing Neurons in Rat Cultures: Preponderance of Single- and Double-Positive Cells, and Cell Type-Specific Expression of Neuron-Specific Gene Family Members, Nsg-1 (NEEP21 and Nsg-2 (P19.

    Directory of Open Access Journals (Sweden)

    Laura Digilio

    Full Text Available The brain consists of many distinct neuronal cell types, but which cell types are present in widely used primary cultures of embryonic rodent brain is often not known. We characterized how abundantly four cell type markers (Ctip2, Satb2, Prox1, GAD65 were represented in cultured rat neurons, how easily neurons expressing different markers can be transfected with commonly used plasmids, and whether neuronal-enriched endosomal proteins Nsg-1 (NEEP21 and Nsg-2 (P19 are ubiquitously expressed in all types of cultured neurons. We found that cultured neurons stably maintain cell type identities that are reflective of cell types in vivo. This includes neurons maintaining simultaneous expression of two transcription factors, such as Ctip2+/Satb2+ or Prox1+/Ctip2+ double-positive cells, which have also been described in vivo. Secondly, we established the superior efficiency of CAG promoters for both Lipofectamine-mediated transfection as well as for electroporation. Thirdly, we discovered that Nsg-1 and Nsg-2 were not expressed equally in all neurons: whereas high levels of both Nsg-1 and Nsg-2 were found in Satb2-, Ctip2-, and GAD65-positive neurons, Prox1-positive neurons in hippocampal cultures expressed low levels of both. Our findings thus highlight the importance of identifying neuronal cell types for doing cell biology in cultured neurons: Keeping track of neuronal cell type might uncover effects in assays that might otherwise be masked by the mixture of responsive and non-responsive neurons in the dish.

  16. Circadian plasticity in photoreceptor cells controls visual coding efficiency in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Martin Barth

    Full Text Available In the fly Drosophila melanogaster, neuronal plasticity of synaptic terminals in the first optic neuropil, or lamina, depends on early visual experience within a critical period after eclosion. The current study revealed two additional and parallel mechanisms involved in this type of synaptic terminal plasticity. First, an endogenous circadian rhythm causes daily oscillations in the volume of photoreceptor cell terminals. Second, daily visual experience precisely modulates the circadian time course and amplitude of the volume oscillations that the photoreceptor-cell terminals undergo. Both mechanisms are separable in their molecular basis. We suggest that the described neuronal plasticity in Drosophila ensures continuous optimal performance of the visual system over the course of a 24 h-day. Moreover, the sensory system of Drosophila cannot only account for predictable, but also for acute, environmental changes. The volumetric changes in the synaptic terminals of photoreceptor cells are accompanied by circadian and light-induced changes of presynaptic ribbons as well as extensions of epithelial glial cells into the photoreceptor terminals, suggesting that the architecture of the lamina is altered by both visual exposure and the circadian clock. Clock-mutant analysis and the rescue of PER protein rhythmicity exclusively in all R1-6 cells revealed that photoreceptor-cell plasticity is autonomous and sufficient to control visual behavior. The strength of a visually guided behavior, the optomotor turning response, co-varies with synaptic-terminal volume oscillations of photoreceptor cells when elicited at low light levels. Our results show that behaviorally relevant adaptive processing of visual information is performed, in part, at the level of visual input level.

  17. Visualization and orchestration of the dynamic molecular society in cells

    Institute of Scientific and Technical Information of China (English)

    Xuebiao Yao; Guowei Fang

    2009-01-01

    @@ Visualization of specific molecules and their interactions in real space and time is essential to delineate how cellular plasticity and dynamics are achieved and orchestrated as perturbation of cellular plasticity and dynamics is detrimental to health. Elucidation of cellular dynamics requires molecular imaging at nanometer scale at millisecond resolution. The 1st International Conference on Cellular Dynamics and Chemical Biology held in Hefei, China (from 12 September to 15 September,2008) launched the quest by bringing synergism among photonics, chemistry and biology.

  18. Pineal photoreceptor cells are required for maintaining the circadian rhythms of behavioral visual sensitivity in zebrafish.

    Directory of Open Access Journals (Sweden)

    Xinle Li

    Full Text Available In non-mammalian vertebrates, the pineal gland functions as the central pacemaker that regulates the circadian rhythms of animal behavior and physiology. We generated a transgenic zebrafish line [Tg(Gnat2:gal4-VP16/UAS:nfsB-mCherry] in which the E. coli nitroreductase is expressed in pineal photoreceptor cells. In developing embryos and young adults, the transgene is expressed in both retinal and pineal photoreceptor cells. During aging, the expression of the transgene in retinal photoreceptor cells gradually diminishes. By 8 months of age, the Gnat2 promoter-driven nitroreductase is no longer expressed in retinal photoreceptor cells, but its expression in pineal photoreceptor cells persists. This provides a tool for selective ablation of pineal photoreceptor cells, i.e., by treatments with metronidazole. In the absence of pineal photoreceptor cells, the behavioral visual sensitivity of the fish remains unchanged; however, the circadian rhythms of rod and cone sensitivity are diminished. Brief light exposures restore the circadian rhythms of behavioral visual sensitivity. Together, the data suggest that retinal photoreceptor cells respond to environmental cues and are capable of entraining the circadian rhythms of visual sensitivity; however, they are insufficient for maintaining the rhythms. Cellular signals from the pineal photoreceptor cells may be required for maintaining the circadian rhythms of visual sensitivity.

  19. Visualizing and quantifying cell phenotype using soft X-ray tomography

    OpenAIRE

    McDermott, Gerry; Fox, Douglas M.; Epperly, Lindsay; Wetzler, Modi; Barron, Annelise E.; Le Gros, Mark A.; Larabell, Carolyn A.

    2012-01-01

    Soft X-ray tomography (SXT) is an imaging technique capable of characterizing and quantifying the structural phenotype of cells. In particular, SXT is used to visualize the internal architecture of fully hydrated, intact eukaryotic and prokaryotic cells at high spatial resolution (50 nm or better). Image contrast in SXT is derived from the biochemical composition of the cell, and obtained without the need to use potentially damaging contrast-enhancing agents, such as heavy metals. The cells a...

  20. Xenopus laevis retinal ganglion cell dendritic arbors develop independently of visual stimulation

    OpenAIRE

    Barbara Lom; Rebecca L. Rigel

    2004-01-01

    Newly formed neurons must locate their appropriate target cells and then form synaptic connections with these targets in order to establish a functional nervous system. In the vertebrate retina, retinal ganglion cell (RGC) dendrites extend from the cell body and form synapses with nearby amacrine and bipolar cells. RGC axons, however, exit the retina and synapse with the dendrites of midbrain neurons in the optic tectum. We examined how visual stimulation influenced Xenopus RGC dendritic arbo...

  1. A dedicated circuit linking direction selective retinal ganglion cells to primary visual cortex

    OpenAIRE

    Cruz-Martín, Alberto; El-Danaf, Rana N.; Osakada, Fumitaka; Sriram, Balaji; Dhande, Onkar S.; Nguyen, Phong L.; Callaway, Edward M.; Ghosh, Anirvan; Huberman, Andrew D.

    2014-01-01

    How specific features in the environment are represented within the brain is an important unanswered question in neuroscience. A subset of retinal neurons, called direction selective ganglion cells (DSGCs) are specialized for detecting motion along specific axes of the visual field 1 . Despite extensive study of the retinal circuitry that endows DSGCs with their unique tuning properties 2,3 , their downstream circuitry in the brain and thus their contribution to visual processing has remained...

  2. Visualization of multivalent histone modification in a single cell reveals highly concerted epigenetic changes on differentiation of embryonic stem cells

    DEFF Research Database (Denmark)

    Hattori, Naoko; Niwa, Tohru; Kimura, Kana;

    2013-01-01

    Combinations of histone modifications have significant biological roles, such as maintenance of pluripotency and cancer development, but cannot be analyzed at the single cell level. Here, we visualized a combination of histone modifications by applying the in situ proximity ligation assay, which....... Bivalent modification was clearly visualized by iChmo in wild-type embryonic stem cells (ESCs) known to have it, whereas rarely in Suz12 knockout ESCs and mouse embryonic fibroblasts known to have little of it. iChmo was applied to analysis of epigenetic and phenotypic changes of heterogeneous cell...

  3. 3D-dynamic visualization of complex molecular cell biology processes : 1-year university students' understanding of visualizations of signal transduction

    OpenAIRE

    Jacobsson, Johan Lars Henrik

    2008-01-01

    This study deals with the use of 3D-dynamic visualizations for teaching complex molecular cell biology concepts. The focus is on signal transduction, which is a concept that constitutes an important part of biological systems. 3D-dynamic visualizations (animations) were produced and shown for a total of 24 students attending a course in molecular cell biology at Karlstad University, Sweden. Data were collected by questionnaires and interviews which were structured around the understandability...

  4. Immunohistochemical visualization of neurons and specific glial cells for stereological application in the porcine neocortex

    DEFF Research Database (Denmark)

    Lyck, Lise; Jelsing, Jacob; Jensen, Pia Søndergaard;

    2006-01-01

    The pig is becoming an increasingly used non-primate model in basic experimental studies of human neurological diseases. In spite of the widespread use of immunohistochemistry and cell type specific markers, the application of immunohistochemistry in the pig brain has not been systematically...... described. Therefore, to facilitate future stereological studies of the neuronal and glial cell populations in experimental neurological diseases in the pig, we established a battery of immunohistochemical protocols for staining of perfusion fixed porcine brain tissue processed as free floating cryostat......-, vibratome- or paraffin sections. Antibodies against NeuN, GFAP, S100-protein, MBP, CNPase, CD11b, CD68 (KP1), CD45 and Ki67 were evaluated, and all except CD68 and CD45 resulted in staining of high quality in either type of tissue. Each staining was evaluated with respect to specificity and sensitivity in...

  5. Generation of Rho Zero Cells: Visualization and Quantification of the mtDNA Depletion Process

    OpenAIRE

    Susanna Schubert; Sandra Heller; Birgit Löffler; Ingo Schäfer; Martina Seibel; Gaetano Villani; Peter Seibel

    2015-01-01

    Human mitochondrial DNA (mtDNA) is located in discrete DNA-protein complexes, so called nucleoids. These structures can be easily visualized in living cells by utilizing the fluorescent stain PicoGreen®. In contrary, cells devoid of endogenous mitochondrial genomes (ρ0 cells) display no mitochondrial staining in the cytoplasm. A modified restriction enzyme can be targeted to mitochondria to cleave the mtDNA molecules in more than two fragments, thereby activating endogenous nucleases. By a...

  6. cellPACK: A Virtual Mesoscope to Model and Visualize Structural Systems Biology

    OpenAIRE

    Johnson, Graham T; Autin, Ludovic; Al-Alusi, Mostafa; Goodsell, David S.; Sanner, Michel F.; Olson, Arthur J.

    2014-01-01

    cellPACK assembles computational models of the biological mesoscale, an intermediate scale (10−7–10−8m) between molecular and cellular biology. cellPACK’s modular architecture unites existing and novel packing algorithms to generate, visualize and analyze comprehensive 3D models of complex biological environments that integrate data from multiple experimental systems biology and structural biology sources. cellPACK is currently available as open source code, with tools for validation of model...

  7. Visualization of mRNA translation in living cells

    OpenAIRE

    RODRIGUEZ, ALEXIS J.; Shenoy, Shailesh M; Singer, Robert H.; Condeelis, John

    2006-01-01

    The role of mRNA localization is presumably to effect cell asymmetry by synthesizing proteins in specific cellular compartments. However, protein synthesis has never been directly demonstrated at the sites of mRNA localization. To address this, we developed a live cell method for imaging translation of β-actin mRNA. Constructs coding for β-actin, containing tetracysteine motifs, were transfected into C2C12 cells, and sites of nascent polypeptide chains were detected using the biarsenial dyes ...

  8. Common transcriptional mechanisms for visual photoreceptor cell differentiation among Pancrustaceans.

    Directory of Open Access Journals (Sweden)

    Simpla Mahato

    2014-07-01

    Full Text Available A hallmark of visual rhabdomeric photoreceptors is the expression of a rhabdomeric opsin and uniquely associated phototransduction molecules, which are incorporated into a specialized expanded apical membrane, the rhabdomere. Given the extensive utilization of rhabdomeric photoreceptors in the eyes of protostomes, here we address whether a common transcriptional mechanism exists for the differentiation of rhabdomeric photoreceptors. In Drosophila, the transcription factors Pph13 and Orthodenticle (Otd direct both aspects of differentiation: rhabdomeric opsin transcription and rhabdomere morphogenesis. We demonstrate that the orthologs of both proteins are expressed in the visual systems of the distantly related arthropod species Tribolium castaneum and Daphnia magna and that their functional roles are similar in these species. In particular, we establish that the Pph13 homologs have the ability to bind a subset of Rhodopsin core sequence I sites and that these sites are present in key phototransduction genes of both Tribolium and Daphnia. Furthermore, Pph13 and Otd orthologs are capable of executing deeply conserved functions of photoreceptor differentiation as evidenced by the ability to rescue their respective Drosophila mutant phenotypes. Pph13 homologs are equivalent in their ability to direct both rhabdomere morphogenesis and opsin expression within Drosophila, whereas Otd paralogs demonstrate differential abilities to regulate photoreceptor differentiation. Finally, loss-of-function analyses in Tribolium confirm the conserved requirement of Pph13 and Otd in regulating both rhabdomeric opsin transcription and rhabdomere morphogenesis. Taken together, our data identify components of a regulatory framework for rhabdomeric photoreceptor differentiation in Pancrustaceans, providing a foundation for defining ancestral regulatory modules of rhabdomeric photoreceptor differentiation.

  9. A Model of Generating Visual Place Cells Based on Environment Perception and Similar Measure

    Science.gov (United States)

    2016-01-01

    It is an important content to generate visual place cells (VPCs) in the field of bioinspired navigation. By analyzing the firing characteristic of biological place cells and the existing methods for generating VPCs, a model of generating visual place cells based on environment perception and similar measure is abstracted in this paper. VPCs' generation process is divided into three phases, including environment perception, similar measure, and recruiting of a new place cell. According to this process, a specific method for generating VPCs is presented. External reference landmarks are obtained based on local invariant characteristics of image and a similar measure function is designed based on Euclidean distance and Gaussian function. Simulation validates the proposed method is available. The firing characteristic of the generated VPCs is similar to that of biological place cells, and VPCs' firing fields can be adjusted flexibly by changing the adjustment factor of firing field (AFFF) and firing rate's threshold (FRT). PMID:27597859

  10. A Model of Generating Visual Place Cells Based on Environment Perception and Similar Measure.

    Science.gov (United States)

    Zhou, Yang; Wu, Dewei

    2016-01-01

    It is an important content to generate visual place cells (VPCs) in the field of bioinspired navigation. By analyzing the firing characteristic of biological place cells and the existing methods for generating VPCs, a model of generating visual place cells based on environment perception and similar measure is abstracted in this paper. VPCs' generation process is divided into three phases, including environment perception, similar measure, and recruiting of a new place cell. According to this process, a specific method for generating VPCs is presented. External reference landmarks are obtained based on local invariant characteristics of image and a similar measure function is designed based on Euclidean distance and Gaussian function. Simulation validates the proposed method is available. The firing characteristic of the generated VPCs is similar to that of biological place cells, and VPCs' firing fields can be adjusted flexibly by changing the adjustment factor of firing field (AFFF) and firing rate's threshold (FRT). PMID:27597859

  11. The cell type-specific effect of TAp73 isoforms on the cell cycle and apoptosis

    Czech Academy of Sciences Publication Activity Database

    Holčáková, J.; Češková, P.; Hrstka, R.; Muller, P.; Dubská, L.; Coates, P.J.; Paleček, Emil; Vojtěšek, B.

    2008-01-01

    Roč. 13, č. 3 (2008), s. 404-420. ISSN 1425-8153 R&D Projects: GA ČR(CZ) GA301/05/0416; GA AV ČR(CZ) IAA500040513 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : p53 * TAp73 * DNA binding Subject RIV: BO - Biophysics Impact factor: 1.454, year: 2008

  12. Automated type specific ELISA probe detection of amplified NS3 gene products of dengue viruses.

    OpenAIRE

    Chow, V T; Yong, R Y; Ngoh, B L; Chan, Y. C.

    1997-01-01

    AIM: To apply an automated system of nucleic acid hybridisation coupled with the enzyme linked immunosorbent assay (ELISA) for the type specific detection of amplification products of dengue viruses. METHODS: Non-structural 3 (NS3) gene targets of reference strains of all four dengue and other flaviviruses, as well as dengue patient viraemic sera, were subjected to reverse transcription and polymerase chain reaction using consensus and dengue type specific primers and digoxigenin-11-dUTP labe...

  13. Human muscle fibre type-specific regulation of AMPK and downstream targets by exercise

    DEFF Research Database (Denmark)

    Kristensen, Dorte Enggaard; Albers, Peter Hjorth; Prats, Clara;

    2015-01-01

    ) ). Exercise-induced glycogen degradation in type I vs. II fibres was similar (CON) or lower (INT). In conclusion, a differentiated response to exercise of metabolic signalling/effector proteins in human type I and II fibres was evident during interval exercise. This could be important for exercise......-type specific adaptations, i.e. insulin sensitivity and mitochondrial density, and highlights the potential for new discoveries when investigating fibre type-specific signalling. This article is protected by copyright. All rights reserved....

  14. Xenopus laevis retinal ganglion cell dendritic arbors develop independently of visual stimulation

    Directory of Open Access Journals (Sweden)

    Rebecca L. Rigel

    2004-06-01

    Full Text Available Newly formed neurons must locate their appropriate target cells and then form synaptic connections with these targets in order to establish a functional nervous system. In the vertebrate retina, retinal ganglion cell (RGC dendrites extend from the cell body and form synapses with nearby amacrine and bipolar cells. RGC axons, however, exit the retina and synapse with the dendrites of midbrain neurons in the optic tectum. We examined how visual stimulation influenced Xenopus RGC dendritic arborization. Neuronal activity is known to be an important factor in shaping dendritic and axonal arborization. Thus, we reared tadpoles in dark and light environments then used rhodamine dextran retrograde labeling to identify RGCs in the retina. When we compared RGC dendritic arbors from tadpoles reared in dark and light environments, we found no morphological differences, suggesting that physiological visual activity did not contribute to the morphological development of Xenopus RGC dendritic arbors.

  15. Xenopus laevis Retinal Ganglion Cell Dendritic Arbors Develop Independently of Visual Stimulation

    Directory of Open Access Journals (Sweden)

    Barbara Lom

    2004-01-01

    Full Text Available Newly formed neurons must locate their appropriate target cells and then form synaptic connections with these targets in order to establish a functional nervous system. In the vertebrate retina, retinal ganglion cell (RGC dendrites extend from the cell body and form synapses with nearby amacrine and bipolar cells. RGC axons, however, exit the retina and synapse with the dendrites of midbrain neurons in the optic tectum. We examined how visual stimulation influenced Xenopus RGC dendritic arborization. Neuronal activity is known to be an important factor in shaping dendritic and axonal arborization. Thus, we reared tadpoles in dark and light environments then used rhodamine dextran retrograde labeling to identify RGCs in the retina. When we compared RGC dendritic arbors from tadpoles reared in dark and light environments, we found no morphological differences, suggesting that physiological visual activity did not contribute to the morphological development of Xenopus RGC dendritic arbors.

  16. Drivers' Visual Behavior When Using Hand-Held and Hands-Free Cell Phones

    OpenAIRE

    Fitch, Gregory M.; Guo, Feng; Hanowski, Richard J.; Perez, M. P.

    2014-01-01

    This study investigated driver distraction and how the use of handheld (HH), portable hands-free (PHF), and integrated hands-free (IHF) cell phones affected the visual behavior of motor vehicle drivers. Method A naturalistic driving study recorded 204 participating drivers using video cameras and vehicle sensors for an average of 31 days. A total of 1564 cell phone calls made and 844 text messages sent while driving were sampled and underwent a video review. Baselines were established by reco...

  17. Teneurin-3 Specifies Morphological and Functional Connectivity of Retinal Ganglion Cells in the Vertebrate Visual System

    OpenAIRE

    Paride Antinucci; Nikolas Nikolaou; Martin P. Meyer; Robert Hindges

    2013-01-01

    Summary A striking feature of the CNS is the precise wiring of its neuronal connections. During vertebrate visual system development, different subtypes of retinal ganglion cells (RGCs) form specific connections with their corresponding synaptic partners. However, the underlying molecular mechanisms remain to be fully elucidated. Here, we report that the cell-adhesive transmembrane protein Teneurin-3 (Tenm3) is required by zebrafish RGCs for acquisition of their correct morphological and func...

  18. Both visual and idiothetic cues contribute to head direction cell stability during navigation along complex routes

    OpenAIRE

    Yoder, Ryan M.; Clark, Benjamin J.; Brown, Joel E.; Lamia, Mignon V.; Valerio, Stephane; Shinder, Michael E.; Taube, Jeffrey S.

    2011-01-01

    Successful navigation requires a constantly updated neural representation of directional heading, which is conveyed by head direction (HD) cells. The HD signal is predominantly controlled by visual landmarks, but when familiar landmarks are unavailable, self-motion cues are able to control the HD signal via path integration. Previous studies of the relationship between HD cell activity and path integration have been limited to two or more arenas located in the same room, a drawback for interp...

  19. NaviCell Web Service for network-based data visualization.

    Science.gov (United States)

    Bonnet, Eric; Viara, Eric; Kuperstein, Inna; Calzone, Laurence; Cohen, David P A; Barillot, Emmanuel; Zinovyev, Andrei

    2015-07-01

    Data visualization is an essential element of biological research, required for obtaining insights and formulating new hypotheses on mechanisms of health and disease. NaviCell Web Service is a tool for network-based visualization of 'omics' data which implements several data visual representation methods and utilities for combining them together. NaviCell Web Service uses Google Maps and semantic zooming to browse large biological network maps, represented in various formats, together with different types of the molecular data mapped on top of them. For achieving this, the tool provides standard heatmaps, barplots and glyphs as well as the novel map staining technique for grasping large-scale trends in numerical values (such as whole transcriptome) projected onto a pathway map. The web service provides a server mode, which allows automating visualization tasks and retrieving data from maps via RESTful (standard HTTP) calls. Bindings to different programming languages are provided (Python and R). We illustrate the purpose of the tool with several case studies using pathway maps created by different research groups, in which data visualization provides new insights into molecular mechanisms involved in systemic diseases such as cancer and neurodegenerative diseases. PMID:25958393

  20. A dedicated circuit links direction-selective retinal ganglion cells to the primary visual cortex

    Science.gov (United States)

    Cruz-Martín, Alberto; El-Danaf, Rana N.; Osakada, Fumitaka; Sriram, Balaji; Dhande, Onkar S.; Nguyen, Phong L.; Callaway, Edward M.; Ghosh, Anirvan; Huberman, Andrew D.

    2014-03-01

    How specific features in the environment are represented within the brain is an important unanswered question in neuroscience. A subset of retinal neurons, called direction-selective ganglion cells (DSGCs), are specialized for detecting motion along specific axes of the visual field. Despite extensive study of the retinal circuitry that endows DSGCs with their unique tuning properties, their downstream circuitry in the brain and thus their contribution to visual processing has remained unclear. In mice, several different types of DSGCs connect to the dorsal lateral geniculate nucleus (dLGN), the visual thalamic structure that harbours cortical relay neurons. Whether direction-selective information computed at the level of the retina is routed to cortical circuits and integrated with other visual channels, however, is unknown. Here we show that there is a di-synaptic circuit linking DSGCs with the superficial layers of the primary visual cortex (V1) by using viral trans-synaptic circuit mapping and functional imaging of visually driven calcium signals in thalamocortical axons. This circuit pools information from several types of DSGCs, converges in a specialized subdivision of the dLGN, and delivers direction-tuned and orientation-tuned signals to superficial V1. Notably, this circuit is anatomically segregated from the retino-geniculo-cortical pathway carrying non-direction-tuned visual information to deeper layers of V1, such as layer 4. Thus, the mouse harbours several functionally specialized, parallel retino-geniculo-cortical pathways, one of which originates with retinal DSGCs and delivers direction- and orientation-tuned information specifically to the superficial layers of the primary visual cortex. These data provide evidence that direction and orientation selectivity of some V1 neurons may be influenced by the activation of DSGCs.

  1. Effects of deuterium oxide and galvanic vestibular stimulation on visual cortical cell function

    International Nuclear Information System (INIS)

    The spontaneous and evoked unit activities of complex visual cortical cells were recorded from Brodmann's area 18 in immobilized, unanesthetized cats before, during, and after stimulation of the vestibular system. The vestibular system was stimulated by intravenous injection of deuterium oxide (D2O)--a noted nystagmogenic agent--or by direct galvanic stimulation of the labyrinth. Measures of the receptive-field areas, poststimulus time histograms, directional preferences, and the optimal speed of the light bar stimulating the cell were obtained before and after the application of D2O. Directional preferences were determined in a novel manner, using a method derived from a hierarchical clustering technique. Data were collected and analyzed from a) visual cortical cells in cats with intact labyrinths, b) visual cortical cells in cats following bilateral labrinthectomies, and c) nonvisual cortical cells in cats with intact labyrinths. The other cellular characteristics were also altered by the D2O. Galvanic stimulation of the labyrinth resembles, in its effects, the injection of D2O. In labyrinth-intact cats, the time course of area 18 spontaneous activity dramatically increased 30 min or more after D2O was administered. It peaked 2-3 h later and still had not returned to preinjection levels even 7 h after the D2O administration. In bilaterally labyrinthectomized cats, the spontaneous activity of the visual cells did not change following D2O administration. In nonvisual cells from labyrinth-intact cats, the spontaneous activity demonstrated a slight but significant decrease over time after D2O injection. In pilot studies, the cats were injected with D2O. Within 8-10 min afterward, signs of positional nystagmus commenced; and within 30 min, problems in maintaining balance were noted. This continued for 7-8 h before disappearing. In the labyrinthectomized animals, such effects were not observed

  2. Effects of deuterium oxide and galvanic vestibular stimulation on visual cortical cell function

    Energy Technology Data Exchange (ETDEWEB)

    Reinis, S.; Landolt, J.P.; Weiss, D.S.; Money, K.E.

    1984-03-01

    The spontaneous and evoked unit activities of complex visual cortical cells were recorded from Brodmann's area 18 in immobilized, unanesthetized cats before, during, and after stimulation of the vestibular system. The vestibular system was stimulated by intravenous injection of deuterium oxide (D2O)--a noted nystagmogenic agent--or by direct galvanic stimulation of the labyrinth. Measures of the receptive-field areas, poststimulus time histograms, directional preferences, and the optimal speed of the light bar stimulating the cell were obtained before and after the application of D2O. Directional preferences were determined in a novel manner, using a method derived from a hierarchical clustering technique. Data were collected and analyzed from a) visual cortical cells in cats with intact labyrinths, b) visual cortical cells in cats following bilateral labrinthectomies, and c) nonvisual cortical cells in cats with intact labyrinths. The other cellular characteristics were also altered by the D2O. Galvanic stimulation of the labyrinth resembles, in its effects, the injection of D2O. In labyrinth-intact cats, the time course of area 18 spontaneous activity dramatically increased 30 min or more after D2O was administered. It peaked 2-3 h later and still had not returned to preinjection levels even 7 h after the D2O administration. In bilaterally labyrinthectomized cats, the spontaneous activity of the visual cells did not change following D2O administration. In nonvisual cells from labyrinth-intact cats, the spontaneous activity demonstrated a slight but significant decrease over time after D2O injection. In pilot studies, the cats were injected with D2O. Within 8-10 min afterward, signs of positional nystagmus commenced; and within 30 min, problems in maintaining balance were noted. This continued for 7-8 h before disappearing. In the labyrinthectomized animals, such effects were not observed.

  3. Visualization and cellular hierarchy inference of single-cell data using SPADE.

    Science.gov (United States)

    Anchang, Benedict; Hart, Tom D P; Bendall, Sean C; Qiu, Peng; Bjornson, Zach; Linderman, Michael; Nolan, Garry P; Plevritis, Sylvia K

    2016-07-01

    High-throughput single-cell technologies provide an unprecedented view into cellular heterogeneity, yet they pose new challenges in data analysis and interpretation. In this protocol, we describe the use of Spanning-tree Progression Analysis of Density-normalized Events (SPADE), a density-based algorithm for visualizing single-cell data and enabling cellular hierarchy inference among subpopulations of similar cells. It was initially developed for flow and mass cytometry single-cell data. We describe SPADE's implementation and application using an open-source R package that runs on Mac OS X, Linux and Windows systems. A typical SPADE analysis on a 2.27-GHz processor laptop takes ∼5 min. We demonstrate the applicability of SPADE to single-cell RNA-seq data. We compare SPADE with recently developed single-cell visualization approaches based on the t-distribution stochastic neighborhood embedding (t-SNE) algorithm. We contrast the implementation and outputs of these methods for normal and malignant hematopoietic cells analyzed by mass cytometry and provide recommendations for appropriate use. Finally, we provide an integrative strategy that combines the strengths of t-SNE and SPADE to infer cellular hierarchy from high-dimensional single-cell data. PMID:27310265

  4. High-definition optical coherence tomography enables visualization of individual cells in healthy skin

    DEFF Research Database (Denmark)

    Boone, Marc; Jemec, Gregor B E; Del Marmol, Véronique

    2012-01-01

    HD-OCT could be confirmed by the phantom analysis. The identification of cells in the epidermis can be made by both techniques. RCM offers the best lateral resolution, and HD-OCT has the best penetration depth, providing images of individual cells deeper within the dermis. Eccrine ducts and hair...... shafts with pilosebaceous units can be observed depending on skin site. HD-OCT provides morphological imaging with sufficient resolution and penetration depth to permit visualization of individual cells at up to 570 μm in depth offering the possibility of additional structural information complementary...

  5. Bonafide, type-specific human papillomavirus persistence among HIV-positive pregnant women: predictive value for cytological abnormalities, a longitudinal cohort study

    Directory of Open Access Journals (Sweden)

    Angela RI Meyrelles

    2016-02-01

    Full Text Available This study investigated the rate of human papillomavirus (HPV persistence, associated risk factors, and predictors of cytological alteration outcomes in a cohort of human immunodeficiency virus-infected pregnant women over an 18-month period. HPV was typed through L1 gene sequencing in cervical smears collected during gestation and at 12 months after delivery. Outcomes were defined as nonpersistence (clearance of the HPV in the 2nd sample, re-infection (detection of different types of HPV in the 2 samples, and type-specific HPV persistence (the same HPV type found in both samples. An unfavourable cytological outcome was considered when the second exam showed progression to squamous intraepithelial lesion or high squamous intraepithelial lesion. Ninety patients were studied. HPV DNA persistence occurred in 50% of the cases composed of type-specific persistence (30% or re-infection (20%. A low CD4+T-cell count at entry was a risk factor for type-specific, re-infection, or HPV DNA persistence. The odds ratio (OR was almost three times higher in the type-specific group when compared with the re-infection group (OR = 2.8; 95% confidence interval: 0.43-22.79. Our findings show that bonafide (type-specific HPV persistence is a stronger predictor for the development of cytological abnormalities, highlighting the need for HPV typing as opposed to HPV DNA testing in the clinical setting.

  6. Bonafide, type-specific human papillomavirus persistence among HIV-positive pregnant women: predictive value for cytological abnormalities, a longitudinal cohort study

    Science.gov (United States)

    Meyrelles, Angela RI; Siqueira, Juliana D; dos Santos, Pâmela P; Hofer, Cristina B; Luiz, Ronir R; Seuánez, Héctor N; Almeida, Gutemberg; Soares, Marcelo A; Soares, Esmeralda A; Machado, Elizabeth S

    2016-01-01

    This study investigated the rate of human papillomavirus (HPV) persistence, associated risk factors, and predictors of cytological alteration outcomes in a cohort of human immunodeficiency virus-infected pregnant women over an 18-month period. HPV was typed through L1 gene sequencing in cervical smears collected during gestation and at 12 months after delivery. Outcomes were defined as nonpersistence (clearance of the HPV in the 2nd sample), re-infection (detection of different types of HPV in the 2 samples), and type-specific HPV persistence (the same HPV type found in both samples). An unfavourable cytological outcome was considered when the second exam showed progression to squamous intraepithelial lesion or high squamous intraepithelial lesion. Ninety patients were studied. HPV DNA persistence occurred in 50% of the cases composed of type-specific persistence (30%) or re-infection (20%). A low CD4+T-cell count at entry was a risk factor for type-specific, re-infection, or HPV DNA persistence. The odds ratio (OR) was almost three times higher in the type-specific group when compared with the re-infection group (OR = 2.8; 95% confidence interval: 0.43-22.79). Our findings show that bonafide (type-specific) HPV persistence is a stronger predictor for the development of cytological abnormalities, highlighting the need for HPV typing as opposed to HPV DNA testing in the clinical setting. PMID:26872340

  7. Calcium dynamics in root cells of Arabidopsis thaliana visualized with selective plane illumination microscopy.

    Directory of Open Access Journals (Sweden)

    Alex Costa

    Full Text Available Selective Plane Illumination Microscopy (SPIM is an imaging technique particularly suited for long term in-vivo analysis of transparent specimens, able to visualize small organs or entire organisms, at cellular and eventually even subcellular resolution. Here we report the application of SPIM in Calcium imaging based on Förster Resonance Energy Transfer (FRET. Transgenic Arabidopsis plants expressing the genetically encoded-FRET-based Ca(2+ probe Cameleon, in the cytosol or nucleus, were used to demonstrate that SPIM enables ratiometric fluorescence imaging at high spatial and temporal resolution, both at tissue and single cell level. The SPIM-FRET technique enabled us to follow nuclear and cytosolic Ca(2+ dynamics in Arabidopsis root tip cells, deep inside the organ, in response to different stimuli. A relevant physiological phenomenon, namely Ca(2+ signal percolation, predicted in previous studies, has been directly visualized.

  8. The Emergence of Contrast-Invariant Orientation Tuning in Simple Cells of Cat Visual Cortex

    OpenAIRE

    Finn, Ian M.; Priebe, Nicholas J.; Ferster, David

    2007-01-01

    Simple cells in primary visual cortex exhibit contrast-invariant orientation tuning, in seeming contradiction to feed-forward models relying on lateral geniculate nucleus (LGN) input alone. Contrast invariance has therefore been thought to depend on the presence of intracortical lateral inhibition. In vivo intracellular recordings instead suggest that contrast invariance can be explained by three properties of the excitatory pathway. 1) Depolarizations evoked by orthogonal stimuli are determi...

  9. Quantitative o perando visualization of the energy band depth profile in solar cells

    OpenAIRE

    Chen, Qi; Mao, Lin; LI, YAOWEN; Kong, Tao; Wu, Na; Ma, Changqi; Bai, Sai; Jin, Yizheng; Wu, Dan; Lu, Wei; Wang, Bing; Chen, Liwei

    2015-01-01

    The energy band alignment in solar cell devices is critically important because it largely governs elementary photovoltaic processes, such as the generation, separation, transport, recombination and collection of charge carriers. Despite the expenditure of considerable effort, the measurement of energy band depth profiles across multiple layers has been extremely challenging, especially for operando devices. Here we present direct visualization of the surface potential depth profile over the ...

  10. Machine-Part cell formation through visual decipherable clustering of Self Organizing Map

    CERN Document Server

    Chattopadhyay, Manojit; Dan, Pranab K; 10.1007/s00170-010-2802-4

    2011-01-01

    Machine-part cell formation is used in cellular manufacturing in order to process a large variety, quality, lower work in process levels, reducing manufacturing lead-time and customer response time while retaining flexibility for new products. This paper presents a new and novel approach for obtaining machine cells and part families. In the cellular manufacturing the fundamental problem is the formation of part families and machine cells. The present paper deals with the Self Organising Map (SOM) method an unsupervised learning algorithm in Artificial Intelligence, and has been used as a visually decipherable clustering tool of machine-part cell formation. The objective of the paper is to cluster the binary machine-part matrix through visually decipherable cluster of SOM color-coding and labelling via the SOM map nodes in such a way that the part families are processed in that machine cells. The Umatrix, component plane, principal component projection, scatter plot and histogram of SOM have been reported in t...

  11. A two- and three-dimensional approach for visualizing human embryonic stem cell differentiation

    DEFF Research Database (Denmark)

    Brøchner, Christian Beltoft; Vestentoft, Peter S; Lynnerup, Niels;

    2010-01-01

    Undifferentiated human embryonic stem cells are characterized by expression of specific cell markers like the transcription factors OCT4, SOX2, and NANOG, the stage-specific embryonic antigen SSEA4, and the tumor-related antigens TRA-1-60 and TRA-1-81 and by their ability to differentiate under...... accomplished. An extended version of this technique even allows for a high-magnification 3D-reconstruction of an area of interest (AOI), e.g., the developing hepatic stem cells. These techniques allow both a 2D and a 3D visualization of hESC colonies and lead to new insights into and information about the...... interaction of stem cells....

  12. The role of cell adhesion molecules in visual circuit formation: From neurite outgrowth to maps and synaptic specificity

    OpenAIRE

    Missaire, Mégane; Hindges, Robert

    2015-01-01

    ABSTRACT The formation of visual circuitry is a multistep process that involves cell–cell interactions based on a range of molecular mechanisms. The correct implementation of individual events, including axon outgrowth and guidance, the formation of the topographic map, or the synaptic targeting of specific cellular subtypes, are prerequisites for a fully functional visual system that is able to appropriately process the information captured by the eyes. Cell adhesion molecules (CAMs) with th...

  13. Differential cell type-specific transcriptional regulation of the CYP1A1 gene

    OpenAIRE

    Adamska, Magdalena

    2005-01-01

    Cytochrome P450 1A1 (CYP1A1) monooxygenase plays an important role in the metabolism of environmental pollutants such as polycyclic aromatic hydrocarbons (PAHs) and halogenated polycyclic aromatic hydrocarbons (HAHs). Oxidation of these compounds converts them to the metabolites that subsequently can be conjugated to hydrophilic endogenous entities e.g. glutathione. Derivates generated in this way are water soluble and can be excreted in bile or urine, which is a defense mechanism. Besides de...

  14. State-dependent and cell type-specific temporal processing in auditory thalamocortical circuit

    OpenAIRE

    Shuzo Sakata

    2016-01-01

    Ongoing spontaneous activity in cortical circuits defines cortical states, but it still remains unclear how cortical states shape sensory processing across cortical laminae and what type of response properties emerge in the cortex. Recording neural activity from the auditory cortex (AC) and medial geniculate body (MGB) simultaneously with electrical stimulations of the basal forebrain (BF) in urethane-anesthetized rats, we investigated state-dependent spontaneous and auditory-evoked activitie...

  15. Cell type-specific termination of transcription by transposable element sequences

    OpenAIRE

    Conley Andrew B; Jordan I

    2012-01-01

    Abstract Background Transposable elements (TEs) encode sequences necessary for their own transposition, including signals required for the termination of transcription. TE sequences within the introns of human genes show an antisense orientation bias, which has been proposed to reflect selection against TE sequences in the sense orientation owing to their ability to terminate the transcription of host gene transcripts. While there is evidence in support of this model for some elements, the ex...

  16. Epigenetic regulation of normal human mammary cell type-specific miRNAs

    Czech Academy of Sciences Publication Activity Database

    Vrba, Lukáš; Garbe, J.; Stampfer, M.R.; Futscher, B. W.

    2011-01-01

    Roč. 21, č. 12 (2011), s. 2026-2037. ISSN 1088-9051 Institutional research plan: CEZ:AV0Z50510513 Institutional support: RVO:60077344 Keywords : DNA metylation * gene expression * transcription Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 13.608, year: 2011

  17. Cell type-specific delivery of short interfering RNAs by dye-functionalised theranostic nanoparticles

    Science.gov (United States)

    Press, Adrian T.; Traeger, Anja; Pietsch, Christian; Mosig, Alexander; Wagner, Michael; Clemens, Mark G.; Jbeily, Nayla; Koch, Nicole; Gottschaldt, Michael; Bézière, Nicolas; Ermolayev, Volodymyr; Ntziachristos, Vasilis; Popp, Jürgen; Kessels, Michael M.; Qualmann, Britta; Schubert, Ulrich S.; Bauer, Michael

    2014-12-01

    Efficient delivery of short interfering RNAs reflects a prerequisite for the development of RNA interference therapeutics. Here, we describe highly specific nanoparticles, based on near infrared fluorescent polymethine dye-derived targeting moieties coupled to biodegradable polymers. The fluorescent dye, even when coupled to a nanoparticle, mimics a ligand for hepatic parenchymal uptake transporters resulting in hepatobiliary clearance of approximately 95% of the dye within 45 min. Body distribution, hepatocyte uptake and excretion into bile of the dye itself, or dye-coupled nanoparticles can be tracked by intravital microscopy or even non-invasively by multispectral optoacoustic tomography. Efficacy of delivery is demonstrated in vivo using 3-hydroxy-3-methyl-glutaryl-CoA reductase siRNA as an active payload resulting in a reduction of plasma cholesterol levels if siRNA was formulated into dye-functionalised nanoparticles. This suggests that organ-selective uptake of a near infrared dye can be efficiently transferred to theranostic nanoparticles allowing novel possibilities for personalised silencing of disease-associated genes.

  18. Posttranscriptional Control Mediates Cell Type-Specific Localization of Catalase A during Aspergillus nidulans Development

    OpenAIRE

    Navarro, Rosa E.; Aguirre, Jesús

    1998-01-01

    Two differentially regulated catalase genes have been identified in the fungus Aspergillus nidulans. The catA gene belongs to a class whose transcripts are specifically induced during asexual sporulation (conidiation) and encodes a catalase accumulated in conidia. Using a developmental mutant affected in the brlA gene, which is unable to form conidia but capable of producing sexual spores (ascospores), we demonstrated that the catA mRNA accumulated during induction of conidiation but did not ...

  19. Ligation-free ribosome profiling of cell type-specific translation in the brain

    OpenAIRE

    Hornstein, Nicholas; Torres, Daniela; Das Sharma, Sohani; Tang, Guomei; Canoll, Peter; Sims, Peter A

    2016-01-01

    Ribosome profiling has emerged as a powerful tool for genome-wide measurements of translation, but library construction requires multiple ligation steps and remains cumbersome relative to more conventional deep-sequencing experiments. We report a new, ligation-free approach to ribosome profiling that does not require ligation. Library construction for ligation-free ribosome profiling can be completed in one day with as little as 1 ng of purified RNA footprints. We apply ligation-free ribosome...

  20. Cell-Type-Specific Cytokinin Distribution within the Arabidopsis Primary Root Apex

    Czech Academy of Sciences Publication Activity Database

    Antoniadi, I.; Plačková, Lenka; Simonovik, B.; Doležal, Karel; Turnbull, C.; Ljung, K.; Novák, Ondřej

    2015-01-01

    Roč. 27, č. 7 (2015), s. 1955-1967. ISSN 1040-4651 R&D Projects: GA ČR GA14-34792S; GA MŠk(CZ) LO1204; GA MŠk LK21306 Institutional support: RVO:61389030 Keywords : SOLID-PHASE EXTRACTION * ENDOPLASMIC-RETICULUM * MERISTEM ACTIVITY Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 9.338, year: 2014

  1. Cell-type Specific Development of NMDA Receptors in the Interneurons of Rat Prefrontal Cortex

    OpenAIRE

    Wang, Huai-Xing; Gao, Wen-Jun

    2009-01-01

    In the prefrontal cortex, N-methyl-D-aspartic acid (NMDA) receptors are critical not only for normal prefrontal functions but also for the pathological processes of schizophrenia. Little is known, however, about the developmental properties of NMDA receptors in the functionally diverse subpopulations of interneurons. We investigated the developmental changes of NMDA receptors in rat prefrontal interneurons using patch clamp recording in cortical slices. We found that fast-spiking (FS) interne...

  2. oca2 Regulation of chromatophore differentiation and number is cell type specific in zebrafish.

    Science.gov (United States)

    Beirl, Alisha J; Linbo, Tor H; Cobb, Marea J; Cooper, Cynthia D

    2014-03-01

    We characterized a zebrafish mutant that displays defects in melanin synthesis and in the differentiation of melanophores and iridophores of the skin and retinal pigment epithelium. Positional cloning and candidate gene sequencing link this mutation to a 410-kb region on chromosome 6, containing the oculocutaneous albinism 2 (oca2) gene. Quantification of oca2 mutant melanophores shows a reduction in the number of differentiated melanophores compared with wildtype siblings. Consistent with the analysis of mouse Oca2-deficient melanocytes, zebrafish mutant melanophores have immature melanosomes which are partially rescued following treatment with vacuolar-type ATPase inhibitor/cytoplasmic pH modifier, bafilomycin A1. Melanophore-specific gene expression is detected at the correct time and in anticipated locations. While oca2 zebrafish display unpigmented gaps on the head region of mutants 3 days post-fertilization, melanoblast quantification indicates that oca2 mutants have the correct number of melanoblasts, suggesting a differentiation defect explains the reduced melanophore number. Unlike melanophores, which are reduced in number in oca2 mutants, differentiated iridophores are present at significantly higher numbers. These data suggest distinct mechanisms for oca2 in establishing differentiated chromatophore number in developing zebrafish. PMID:24330346

  3. Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases

    DEFF Research Database (Denmark)

    Gusev, Alexander; Lee, S Hong; Trynka, Gosia;

    2014-01-01

    diseases to partition the heritability explained by genotyped SNPs (hg(2)) across functional categories (while accounting for shared variance due to linkage disequilibrium). Extensive simulations showed that in contrast to current estimates from GWAS summary statistics, the variance-component approach...

  4. Indirect micro-immunofluorescence test for detecting type-specific antibodies to herpes simplex virus.

    OpenAIRE

    Forsey, T; Darougar, S

    1980-01-01

    A rapid indirect micro-immunofluorescence test capable of detecting and differentiating type-specific antibodies to herpes simplex virus is described. The test proved highly sensitive and, in 80 patients with active herpes ocular infection, antibody was detected in 94%. No anti-herpes antibody was detected in a control group of 20 patients with adenovirus infections. Testing of animal sera prepared against herpes simplex virus types 1 and 2 and of human sera from cases of ocular and genital h...

  5. HDAC4 Regulates Muscle Fiber Type-Specific Gene Expression Programs

    OpenAIRE

    Cohen, Todd J.; Choi, Moon-Chang; Kapur, Meghan; Lira, Vitor A.; Yan, Zhen; Yao, Tso-Pang

    2015-01-01

    Fiber type-specific programs controlled by the transcription factor MEF2 dictate muscle functionality. Here, we show that HDAC4, a potent MEF2 inhibitor, is predominantly localized to the nuclei in fast/glycolytic fibers in contrast to the sarcoplasm in slow/oxidative fibers. The cytoplasmic localization is associated with HDAC4 hyper-phosphorylation in slow/oxidative-fibers. Genetic reprogramming of fast/glycolytic fibers to oxidative fibers by active CaMKII or calcineurin leads to increased...

  6. Teneurin-3 Specifies Morphological and Functional Connectivity of Retinal Ganglion Cells in the Vertebrate Visual System

    Directory of Open Access Journals (Sweden)

    Paride Antinucci

    2013-11-01

    Full Text Available A striking feature of the CNS is the precise wiring of its neuronal connections. During vertebrate visual system development, different subtypes of retinal ganglion cells (RGCs form specific connections with their corresponding synaptic partners. However, the underlying molecular mechanisms remain to be fully elucidated. Here, we report that the cell-adhesive transmembrane protein Teneurin-3 (Tenm3 is required by zebrafish RGCs for acquisition of their correct morphological and functional connectivity in vivo. Teneurin-3 is expressed by RGCs and their presynaptic amacrine and postsynaptic tectal cell targets. Knockdown of Teneurin-3 leads to RGC dendrite stratification defects within the inner plexiform layer, as well as mistargeting of dendritic processes into outer portions of the retina. Moreover, a subset of RGC axons exhibits tectal laminar arborization errors. Finally, functional analysis of RGCs targeting the tectum reveals a selective deficit in the development of orientation selectivity after Teneurin-3 knockdown. These results suggest that Teneurin-3 plays an instructive role in the functional wiring of the vertebrate visual system.

  7. Visual appearance and CMT score of foremilk of individual quarters in relation to cell count of cows milked automatically.

    Science.gov (United States)

    Rasmussen, Morten D; Bjerring, Martin; Skjøth, Flemming

    2005-02-01

    The objectives of the study were: to evaluate the interaction between visual appearance and California mastitis test (CMT) score of the foremilk in relation to the cell count of the milk; to evaluate the consequences of sorting milk according to these criteria; and to explore whether visual appearance and CMT score of foremilk depended on the time interval between milkings. Measuring somatic cell count (SCC) in composite milk only and discarding milk above certain thresholds will not ensure that milk from all cows with visually abnormal foremilk is withheld from delivery. Low thresholds of SCC will reduce the frequency of cows with abnormal milk but increase the discarding of milk from cows with visually normal foremilk. CMT score of foremilk differentiated better between cows with high and low SCC in composite milk than visual inspection of foremilk. CMT scores of foremilk decreased with increasing interval between milkings within cow, whereas the visual appearance was independent of the interval. We propose that visual appearance of the foremilk should be kept as a criterion for sorting milk at time of milking. For test purposes, the use of visual appearance of foremilk for differentiation between normal and abnormal milk has to be done on multiple milkings. Additionally, CMT scoring of foremilk improves correct classification of normal and abnormal quarters and especially when including data from the previous milking. PMID:15747731

  8. Demonstration of a visual cell-based assay for screening glucose transporter 4 translocation modulators in real time

    Indian Academy of Sciences (India)

    Maleppillil Vavachan Vijayakumar; Amrendra Kumar Ajay; Manoj Kumar Bhat

    2010-12-01

    Insulin-stimulated translocation of glucose transporter 4 (GLUT4) to cell membrane leading to glucose uptake is the rate-limiting step in diabetes. It is also a defined target of antidiabetic drug research. Existing GLUT4 translocation assays are based on time-consuming immunoassays and are hampered by assay variability and low sensitivity. We describe a real-time, visual, cell-based qualitative GLUT4 translocation assay using CHO-HIRc-myc-GLUT4eGFP cells that stably express myc- and eGFP-tagged GLUT4 in addition to human insulin receptor (HIRc). GLUT4 translocation is visualized by live cell imaging based on GFP fluorescence by employing a cooled charge-coupled device camera attached to a fluorescent microscope. This video imaging method and further quantitative analysis of GLUT4 on the cell membrane provide rapid and foolproof visual evidence that this method is suitable for screening GLUT4 translocation modulators.

  9. Inverting adherent cells for visualizing ECM interactions at the basal cell side

    International Nuclear Information System (INIS)

    Interactions with the extracellular matrix (ECM) govern a wide range of cellular functions, including survival, migration and invasion. However, in adherent cells these interactions occur primarily on the basal cell side, making them inaccessible to high-resolution, surface-scanning imaging techniques such as atomic force microscopy (AFM) or scanning electron microscopy (SEM). Here we describe a fast and reliable method for inverting adherent cells, exposing the basal cell membrane for direct analysis by AFM or SEM in combination with fluorescence microscopy. Cells including their matrix adhesion sites remain intact during the inversion process and are transferred together with the complete array of basally associated ECM proteins. Molecular features of ECM proteins, such as the characteristic 67 nm collagen D-periodicity, are well preserved after inversion. To demonstrate the versatility of the method, we compared basal interactions of fibroblasts with fibrillar collagen I and fibronectin matrices. While fibroblasts remodel the fibronectin layer exclusively from above, they actively invade even thin collagen layers by contacting individual collagen nanofibrils both basally and apically through a network of cellular extensions. Cell–matrix entanglement coincides with enhanced cell spreading and flattening, indicating that nanoscale ECM interactions govern macroscopic changes in cell morphology. The presented cell inversion technique can thus provide novel insight into nanoscale cell–matrix interactions at the basal cell side. - Highlights: ► We present a novel method for inverting adherent cells to expose the basal cell side. ► Basal cell sides can be imaged at high resolution by AFM and SEM. ► Cells can be inverted together with the underlying extracellular matrix. ► AFM images of inverted cells provide a nanoscale look at basal cell–ECM interactions

  10. A system and methodology for high-content visual screening of individual intact living cells in suspension

    Science.gov (United States)

    Renaud, Olivier; Heintzmann, Rainer; Sáez-Cirión, Asier; Schnelle, Thomas; Mueller, Torsten; Shorte, Spencer

    2007-02-01

    Three dimensional imaging provides high-content information from living intact biology, and can serve as a visual screening cue. In the case of single cell imaging the current state of the art uses so-called "axial through-stacking". However, three-dimensional axial through-stacking requires that the object (i.e. a living cell) be adherently stabilized on an optically transparent surface, usually glass; evidently precluding use of cells in suspension. Aiming to overcome this limitation we present here the utility of dielectric field trapping of single cells in three-dimensional electrode cages. Our approach allows gentle and precise spatial orientation and vectored rotation of living, non-adherent cells in fluid suspension. Using various modes of widefield, and confocal microscope imaging we show how so-called "microrotation" can provide a unique and powerful method for multiple point-of-view (three-dimensional) interrogation of intact living biological micro-objects (e.g. single-cells, cell aggregates, and embryos). Further, we show how visual screening by micro-rotation imaging can be combined with micro-fluidic sorting, allowing selection of rare phenotype targets from small populations of cells in suspension, and subsequent one-step single cell cloning (with high-viability). Our methodology combining high-content 3D visual screening with one-step single cell cloning, will impact diverse paradigms, for example cytological and cytogenetic analysis on haematopoietic stem cells, blood cells including lymphocytes, and cancer cells.

  11. Visualization of N-acylhomoserine lactone-mediated cell-cell communication between bacteria colonizing the tomato rhizosphere

    DEFF Research Database (Denmark)

    Steidle, A.; Sigl, K.; Schuhegger, R.;

    2001-01-01

    developed and characterized novel Gfp-based monitor strains that allow in situ visualization of AHL-mediated communication between individual cells in the plant rhizosphere. For this purpose, three Gfp-based AHL sensor plasmids that respond to different spectra of AHL molecules were transferred into AHL...... into the chromosome of AHL-negative P. putida strain F117 an AHL sensor cassette that responds to the presence of long-chain AHLs with the expression of Gfp. This monitor strain was used to demonstrate that the indigenous bacterial community colonizing the roots of tomato plants growing in nonsterile soil produces...

  12. Specific visualization of glioma cells in living low-grade tumor tissue.

    Directory of Open Access Journals (Sweden)

    Sven R Kantelhardt

    Full Text Available BACKGROUND: The current therapy of malignant gliomas is based on surgical resection, radio-chemotherapy and chemotherapy. Recent retrospective case-series have highlighted the significance of the extent of resection as a prognostic factor predicting the course of the disease. Complete resection in low-grade gliomas that show no MRI-enhanced images are especially difficult. The aim in this study was to develop a robust, specific, new fluorescent probe for glioma cells that is easy to apply to live tumor biopsies and could identify tumor cells from normal brain cells at all levels of magnification. METHODOLOGY/PRINCIPAL FINDINGS: In this investigation we employed brightly fluorescent, photostable quantum dots (QDs to specifically target epidermal growth factor receptor (EGFR that is upregulated in many gliomas. Living glioma and normal cells or tissue biopsies were incubated with QDs coupled to EGF and/or monoclonal antibodies against EGFR for 30 minutes, washed and imaged. The data include results from cell-culture, animal model and ex vivo human tumor biopsies of both low-grade and high-grade gliomas and show high probe specificity. Tumor cells could be visualized from the macroscopic to single cell level with contrast ratios as high as 1000: 1 compared to normal brain tissue. CONCLUSIONS/SIGNIFICANCE: The ability of the targeted probes to clearly distinguish tumor cells in low-grade tumor biopsies, where no enhanced MRI image was obtained, demonstrates the great potential of the method. We propose that future application of specifically targeted fluorescent particles during surgery could allow intraoperative guidance for the removal of residual tumor cells from the resection cavity and thus increase patient survival.

  13. Comparison of HPV genotyping by type-specific PCR and sequencing

    OpenAIRE

    Nara de Oliveira Carvalho; Dora Méndez del Castillo; Carlos Perone; José Nélio Januário; Victor Hugo de Melo; Geraldo Brasileiro Filho

    2010-01-01

    Human papillomavirus (HPV) infection is the most common sexually transmitted disease worldwide and there is a strong link between certain high-risk viral types and cervical carcinogenesis. Although there are several typing methods, it is still unclear which test is the best. This study compared the effectiveness of type-specific PCR (TS-PCR) and sequencing, with a focus on their clinical application. A total of 260 cervical samples from HPV-positive patients were tested for types 6, 11, 16, 1...

  14. Live-cell visualization of excitation energy dynamics in chloroplast thylakoid structures.

    Science.gov (United States)

    Iwai, Masakazu; Yokono, Makio; Kurokawa, Kazuo; Ichihara, Akira; Nakano, Akihiko

    2016-01-01

    The intricate molecular processes underlying photosynthesis have long been studied using various analytic approaches. However, the three-dimensional (3D) dynamics of such photosynthetic processes remain unexplored due to technological limitations related to investigating intraorganellar mechanisms in vivo. By developing a system for high-speed 3D laser scanning confocal microscopy combined with high-sensitivity multiple-channel detection, we visualized excitation energy dynamics in thylakoid structures within chloroplasts of live Physcomitrella patens cells. Two distinct thylakoid structures in the chloroplast, namely the grana and stroma lamellae, were visualized three-dimensionally in live cells. The simultaneous detection of the shorter (than ~670 nm) and longer (than ~680 nm) wavelength regions of chlorophyll (Chl) fluorescence reveals different spatial characteristics-irregular and vertical structures, respectively. Spectroscopic analyses showed that the shorter and longer wavelength regions of Chl fluorescence are affected more by free light-harvesting antenna proteins and photosystem II supercomplexes, respectively. The high-speed 3D time-lapse imaging of the shorter and longer wavelength regions also reveals different structural dynamics-rapid and slow movements within 1.5 seconds, respectively. Such structural dynamics of the two wavelength regions of Chl fluorescence would indicate excitation energy dynamics between light-harvesting antenna proteins and photosystems, reflecting the energetically active nature of photosynthetic proteins in thylakoid membranes. PMID:27416900

  15. Postnatal development of layer III pyramidal cells in the primary visual, inferior temporal, and prefrontal cortices of the marmoset

    OpenAIRE

    Hirosato eAoi; Tomofumi eOga; Tetsuya eSasaki; Ichiro eFujita; Noritaka eIchinohe

    2013-01-01

    Abnormalities in the processes of the generation and/or pruning of dendritic spines have been implicated in several mental disorders including autism and schizophrenia. We have chosen to examine the common marmoset (Callithrix jacchus) as a primate model to explore the processes. As a first step, we studied the postnatal development of basal dendritic trees and spines of layer-III pyramidal cells in the primary visual sensory cortex (V1), a visual association cortex (inferior temporal area, T...

  16. Comparison of HPV genotyping by type-specific PCR and sequencing

    Directory of Open Access Journals (Sweden)

    Nara de Oliveira Carvalho

    2010-02-01

    Full Text Available Human papillomavirus (HPV infection is the most common sexually transmitted disease worldwide and there is a strong link between certain high-risk viral types and cervical carcinogenesis. Although there are several typing methods, it is still unclear which test is the best. This study compared the effectiveness of type-specific PCR (TS-PCR and sequencing, with a focus on their clinical application. A total of 260 cervical samples from HPV-positive patients were tested for types 6, 11, 16, 18, 31, 33 and 35 using TS-PCR and sequencing. The genotype was identified in 36% of cases by TS-PCR and in 75% by sequencing. Sequencing was four times more likely to identify the viral type in positive samples than TS-PCR (p = 0.00. Despite being more effective for virus genotyping, sequencing was unable to identify viral types in multiple infections. Combining both techniques resulted in highly sensitive detection (87% of cases, showing that they are complementary methods. HPV genotyping is an important step in HPV management, helping to identify patients with a higher risk of developing cervical cancer and contributing to the development of type-specific vaccines.

  17. Visualization of the Nucleolus in Living Cells with Cell-Penetrating Fluorescent Peptides.

    Science.gov (United States)

    Martin, Robert M; Herce, Henry D; Ludwig, Anne K; Cardoso, M Cristina

    2016-01-01

    The nucleolus is the hallmark of nuclear compartmentalization and has been shown to exert multiple roles in cellular metabolism besides its main function as the place of ribosomal RNA synthesis and assembly of ribosomes. The nucleolus plays also a major role in nuclear organization as the largest compartment within the nucleus. The prominent structure of the nucleolus can be detected using contrast light microscopy providing an approximate localization of the nucleolus, but this approach does not allow to determine accurately the three-dimensional structure of the nucleolus in cells and tissues. Immunofluorescence staining with antibodies specific to nucleolar proteins albeit very useful is time consuming, normally antibodies recognize their epitopes only within a small range of species and is applicable only in fixed cells. Here, we present a simple method to selectively and accurately label this ubiquitous subnuclear compartment in living cells of a large range of species using a fluorescently labeled cell-penetrating peptide. PMID:27576711

  18. Can retinal ganglion cell dipoles seed iso-orientation domains in the visual cortex?

    Directory of Open Access Journals (Sweden)

    Manuel Schottdorf

    Full Text Available It has been argued that the emergence of roughly periodic orientation preference maps (OPMs in the primary visual cortex (V1 of carnivores and primates can be explained by a so-called statistical connectivity model. This model assumes that input to V1 neurons is dominated by feed-forward projections originating from a small set of retinal ganglion cells (RGCs. The typical spacing between adjacent cortical orientation columns preferring the same orientation then arises via Moiré-Interference between hexagonal ON/OFF RGC mosaics. While this Moiré-Interference critically depends on long-range hexagonal order within the RGC mosaics, a recent statistical analysis of RGC receptive field positions found no evidence for such long-range positional order. Hexagonal order may be only one of several ways to obtain spatially repetitive OPMs in the statistical connectivity model. Here, we investigate a more general requirement on the spatial structure of RGC mosaics that can seed the emergence of spatially repetitive cortical OPMs, namely that angular correlations between so-called RGC dipoles exhibit a spatial structure similar to that of OPM autocorrelation functions. Both in cat beta cell mosaics as well as primate parasol receptive field mosaics we find that RGC dipole angles are spatially uncorrelated. To help assess the level of these correlations, we introduce a novel point process that generates mosaics with realistic nearest neighbor statistics and a tunable degree of spatial correlations of dipole angles. Using this process, we show that given the size of available data sets, the presence of even weak angular correlations in the data is very unlikely. We conclude that the layout of ON/OFF ganglion cell mosaics lacks the spatial structure necessary to seed iso-orientation domains in the primary visual cortex.

  19. Fluorescently labeled collagen binding proteins allow specific visualization of collagen in tissues and live cell culture.

    Science.gov (United States)

    Krahn, Katy Nash; Bouten, Carlijn V C; van Tuijl, Sjoerd; van Zandvoort, Marc A M J; Merkx, Maarten

    2006-03-15

    Visualization of the formation and orientation of collagen fibers in tissue engineering experiments is crucial for understanding the factors that determine the mechanical properties of tissues. In this study, collagen-specific fluorescent probes were developed using a new approach that takes advantage of the inherent specificity of collagen binding protein domains present in bacterial adhesion proteins (CNA35) and integrins (GST-alpha1I). Both collagen binding domains were obtained as fusion proteins from an Escherichia coli expression system and fluorescently labeled using either amine-reactive succinimide (CNA35) or cysteine-reactive maleimide (GST-alpha1I) dyes. Solid-phase binding assays showed that both protein-based probes are much more specific than dichlorotriazinyl aminofluorescein (DTAF), a fluorescent dye that is currently used to track collagen formation in tissue engineering experiments. The CNA35 probe showed a higher affinity for human collagen type I than did the GST-alpha1I probe (apparent K(d) values of 0.5 and 50 microM, respectively) and showed very little cross-reactivity with noncollagenous extracellular matrix proteins. The CNA35 probe was also superior to both GST-alpha1I and DTAF in visualizing the formation of collagen fibers around live human venous saphena cells. Immunohistological experiments on rat tissue showed colocalization of the CNA35 probe with collagen type I and type III antibodies. The fluorescent probes described here have important advantages over existing methods for visualization of collagen, in particular for monitoring the formation of collagen in live tissue cultures over prolonged time periods. PMID:16476406

  20. Visualization of Polarized Membrane Type 1 Matrix Metalloproteinase Activity in Live Cells by Fluorescence Resonance Energy Transfer Imaging*S⃞

    OpenAIRE

    Ouyang, Mingxing; Lu, Shaoying; Li, Xiao-Yan; Xu, Jing; Seong, Jihye; Giepmans, Ben N. G.; Shyy, John Y.-J.; Weiss, Stephen J.; Wang, Yingxiao

    2008-01-01

    Membrane type 1 matrix metalloproteinase (MT1-MMP) plays a critical role in cancer cell biology by proteolytically remodeling the extracellular matrix. Utilizing fluorescence resonance energy transfer (FRET) imaging, we have developed a novel biosensor, with its sensing element anchoring at the extracellular surface of cell membrane, to visualize MT1-MMP activity dynamically in live cells with subcellular resolution. Epidermal growth factor (EGF) induced significant FR...

  1. Super-resolution imaging with Pontamine Fast Scarlet 4BS enables direct visualization of cellulose orientation and cell connection architecture in onion epidermis cells

    OpenAIRE

    Liesche, Johannes; Ziomkiewicz, Iwona; Schulz, Alexander

    2013-01-01

    BackgroundIn plants, a complex cell wall protects cells and defines their shape. Cellulose fibrils form a multilayered network inside the cell-wall matrix that plays a direct role in controlling cell expansion. Resolving the structure of this network will allow us to comprehend the relationship of cellulose fibril orientation and growth.The fluorescent dye Pontamine Fast Scarlet 4BS (PFS) was shown to stain cellulose with high specificity and could be used to visualize cellulose bundles in ce...

  2. Comparison of digital image analysis versus visual assessment to assess survivin expression as an independent predictor of survival for patients with clear cell renal cell carcinoma✩

    OpenAIRE

    Parker, Alexander S.; Lohse, Christine M.; Leibovich, Bradley C.; Cheville, John C; Sheinin, Yuri M.; Kwon, Eugene D.

    2008-01-01

    We previously used quantitative digital image analysis to report that high immunohistochemical tumor expression levels of survivin independently predict poor outcome among patients with clear cell renal cell carcinoma. However, given the cumbersome and costly nature of digital image analysis, we evaluated simple visual assessment as an alternative to digital image analysis for assessing survivin as a predictor of clear cell renal cell carcinoma patient outcomes. We identified 310 patients tre...

  3. Isolation of a nucleocapsid polypeptide of herpes simplex virus types 1 and 2 possessing immunologically type-specific and cross-reactive determinants.

    Science.gov (United States)

    Heilman, C J; Zweig, M; Stephenson, J R; Hampar, B

    1979-01-01

    A polypeptide (p40) of approximately 40,000 molecular weight was isolated from herpes simplex virus type 1 and 2 nucleocapsids by gel filtration and ion exchange chromatography. This protein appears to be the same as protein 22a described previously (Gibson and Roizman, J. Virol. 10:1044--1052, 1972). Competition immunoassays were developed by using purified p40 and antisera prepared in guinea pigs. The assays indicated that the p40's from herpes simplex virus types 1 and 2 possess both type-specific and cross-reactive antigenic determinants. Antibodies to the p40 cross-reactive determinant reacted with antigens in simian herpes virus SA8-infected cells, but not with antigens induced by pseudorabies virus. Preliminary results indicated that a radioimmunoprecipitation test can be used to detect type-specific herpes simplex virus p40 antibodies in human sera. PMID:85720

  4. Retinal ganglion cell projections to the hamster suprachiasmatic nucleus, intergeniculate leaflet, and visual midbrain: bifurcation and melanopsin immunoreactivity

    Science.gov (United States)

    Morin, Lawrence P.; Blanchard, Jane H.; Provencio, Ignacio

    2003-01-01

    The circadian clock in the suprachiasmatic nucleus (SCN) receives direct retinal input via the retinohypothalamic tract (RHT), and the retinal ganglion cells contributing to this projection may be specialized with respect to direct regulation of the circadian clock. However, some ganglion cells forming the RHT bifurcate, sending axon collaterals to the intergeniculate leaflet (IGL) through which light has secondary access to the circadian clock. The present studies provide a more extensive examination of ganglion cell bifurcation and evaluate whether ganglion cells projecting to several subcortical visual nuclei contain melanopsin, a putative ganglion cell photopigment. The results showed that retinal ganglion cells projecting to the SCN send collaterals to the IGL, olivary pretectal nucleus, and superior colliculus, among other places. Melanopsin-immunoreactive (IR) ganglion cells are present in the hamster retina, and some of these cells project to the SCN, IGL, olivary pretectal nucleus, or superior colliculus. Triple-label analysis showed that melanopsin-IR cells bifurcate and project bilaterally to each SCN, but not to the other visual nuclei evaluated. The melanopsin-IR cells have photoreceptive characteristics optimal for circadian rhythm regulation. However, the presence of moderately widespread bifurcation among ganglion cells projecting to the SCN, and projection by melanopsin-IR cells to locations distinct from the SCN and without known rhythm function, suggest that this ganglion cell type is generalized, rather than specialized, with respect to the conveyance of photic information to the brain. Copyright 2003 Wiley-Liss, Inc.

  5. Quantitative operando visualization of the energy band depth profile in solar cells.

    Science.gov (United States)

    Chen, Qi; Mao, Lin; Li, Yaowen; Kong, Tao; Wu, Na; Ma, Changqi; Bai, Sai; Jin, Yizheng; Wu, Dan; Lu, Wei; Wang, Bing; Chen, Liwei

    2015-01-01

    The energy band alignment in solar cell devices is critically important because it largely governs elementary photovoltaic processes, such as the generation, separation, transport, recombination and collection of charge carriers. Despite the expenditure of considerable effort, the measurement of energy band depth profiles across multiple layers has been extremely challenging, especially for operando devices. Here we present direct visualization of the surface potential depth profile over the cross-sections of operando organic photovoltaic devices using scanning Kelvin probe microscopy. The convolution effect due to finite tip size and cantilever beam crosstalk has previously prohibited quantitative interpretation of scanning Kelvin probe microscopy-measured surface potential depth profiles. We develop a bias voltage-compensation method to address this critical problem and obtain quantitatively accurate measurements of the open-circuit voltage, built-in potential and electrode potential difference. PMID:26166580

  6. Quantitative operando visualization of the energy band depth profile in solar cells

    Science.gov (United States)

    Chen, Qi; Mao, Lin; Li, Yaowen; Kong, Tao; Wu, Na; Ma, Changqi; Bai, Sai; Jin, Yizheng; Wu, Dan; Lu, Wei; Wang, Bing; Chen, Liwei

    2015-07-01

    The energy band alignment in solar cell devices is critically important because it largely governs elementary photovoltaic processes, such as the generation, separation, transport, recombination and collection of charge carriers. Despite the expenditure of considerable effort, the measurement of energy band depth profiles across multiple layers has been extremely challenging, especially for operando devices. Here we present direct visualization of the surface potential depth profile over the cross-sections of operando organic photovoltaic devices using scanning Kelvin probe microscopy. The convolution effect due to finite tip size and cantilever beam crosstalk has previously prohibited quantitative interpretation of scanning Kelvin probe microscopy-measured surface potential depth profiles. We develop a bias voltage-compensation method to address this critical problem and obtain quantitatively accurate measurements of the open-circuit voltage, built-in potential and electrode potential difference.

  7. Visualization of the Activity of Rac1 Small GTPase in a Cell

    International Nuclear Information System (INIS)

    Rho family G proteins including Rac regulate a variety of cellular functions, such as morphology, motility, and gene expression. Here we developed a fluorescence resonance energy transfer-based analysis in which we could monitor the activity of Rac1. To detect fluorescence resonance energy transfer, yellow fluorescent protein fused Rac1 and cyan fluorescent protein fused Cdc42-Rac1-interaction-binding domain of Pak1 protein were used as intermolecular probes of FRET. The fluorophores were separated with linear unmixing method. The fluorescence resonance energy transfer efficiency was measured by acceptor photobleaching assisted assay. With these methods, the Rac1 activity was visualized in a cell. The present findings indicate that this approach is sensitive enough to achieve results similar to those from ratiometric fluorescence resonance energy transfer analysis

  8. Visualization of Assembly Intermediates and Budding Vacuoles of Singapore Grouper Iridovirus in Grouper Embryonic Cells

    Science.gov (United States)

    Liu, Yang; Tran, Bich Ngoc; Wang, Fan; Ounjai, Puey; Wu, Jinlu; Hew, Choy L.

    2016-01-01

    Iridovirid infection is associated with the catastrophic loss in aquaculture industry and the population decline of wild amphibians and reptiles, but none of the iridovirid life cycles have been well explored. Here, we report the detailed visualization of the life cycle of Singapore grouper iridovirus (SGIV) in grouper cells by cryo-electron microscopy (cryoEM) and tomography (ET). EM imaging revealed that SGIV viral particles have an outer capsid layer, and the interaction of this layer with cellular plasma membrane initiates viral entry. Subsequent viral replication leads to formation of a viral assembly site (VAS), where membranous structures emerge as precursors to recruit capsid proteins to form an intermediate, double-shell, crescent-shaped structure, which curves to form icosahedral capsids. Knockdown of the major capsid protein eliminates the formation of viral capsids. As capsid formation progresses, electron-dense materials known to be involved in DNA encapsidation accumulate within the capsid until it is fully occupied. Besides the well-known budding mechanism through the cell periphery, we demonstrate a novel budding process in which viral particles bud into a tubular-like structure within vacuoles. This budding process may denote a new strategy used by SGIV to disseminate viral particles into neighbor cells while evading host immune response. PMID:26727547

  9. Visualizing Stable Features in Live Cell Nucleus for Evaluation of the Cell Global Motion Compensation

    Czech Academy of Sciences Publication Activity Database

    Sorokin, D.V.; Suchánková, Jana; Bártová, Eva; Matula, P.

    2014-01-01

    Roč. 60, č. 1 (2014), s. 45-49. ISSN 0015-5500 R&D Projects: GA ČR GBP302/12/G157; GA MŠk(CZ) EE2.3.30.0030 Institutional support: RVO:68081707 Keywords : cell global motion compensation * UV laser bleaching * image registration Subject RIV: BO - Biophysics Impact factor: 1.000, year: 2014

  10. Rapid, sensitive, type specific PCR detection of the E7 region of human papillomavirus type 16 and 18 from paraffin embedded sections of cervical carcinoma

    DEFF Research Database (Denmark)

    Lesnikova, Iana; Lidang, Marianne; Hamilton-Dutoit, Steven; Koch, Jørn

    2010-01-01

    ABSTRACT: Human papillomavirus (HPV) infection, and in particularly infection with HPVs 16 and 18, is a central carcinogenic factor in the uterine cervix. We established and optimized a PCR assay for the detection and discrimination of HPV types 16 and 18 in archival formaldehyde fixed and paraffin...... embedded (FFPE) sections of cervical cancer.Tissue blocks from 35 cases of in situ or invasive cervical squamous cell carcinoma and surrogate FFPE sections containing the cell lines HeLa and SiHa were tested for HPV 16 and HPV18 by conventional PCR using type specific primers, and for the housekeeping gene...

  11. Restoration of visual function by expression of a light-gated mammalian ion channel in retinal ganglion cells or ON-bipolar cells

    OpenAIRE

    Gaub, Benjamin M.; Berry, Michael H.; Holt, Amy E.; Reiner, Andreas; Kienzler, Michael A; Dolgova, Natalia; Nikonov, Sergei; Aguirre, Gustavo D.; Beltran, William A.; Flannery, John G.; Isacoff, Ehud Y.

    2014-01-01

    We restored visual function to animal models of human blindness using a chemical compound that photosensitizes a mammalian ion channel. Virus-mediated expression of this light sensor in surviving retinal cells of blind mice restored light responses in vitro, reanimated innate light avoidance, and enabled learned visually guided behavior. The treatment also restored light responses to the retina of blind dogs. Patients that might benefit from this treatment would need to have intact ganglion c...

  12. Three counting methods agree on cell and neuron number in chimpanzee primary visual cortex

    Directory of Open Access Journals (Sweden)

    Daniel James Miller

    2014-05-01

    Full Text Available Determining the cellular composition of specific brain regions is crucial to our understanding of the function of neurobiological systems. It is therefore useful to identify the extent to which different methods agree when estimating the same properties of brain circuitry. In this study, we estimated the number of neuronal and non-neuronal cells in the primary visual cortex (area 17 or V1 of both hemispheres from a single chimpanzee. Specifically, we processed samples distributed across V1 of the right hemisphere after cortex was flattened into a sheet using two variations of the isotropic fractionator cell and neuron counting method. We processed the left hemisphere as serial brain slices for stereological investigation. The goal of this study was to evaluate the agreement between these methods in the most direct manner possible by comparing estimates of cell density across one brain region of interest in a single individual. In our hands, these methods produced similar estimates of the total cellular population (approximately 1 billion as well as the number of neurons (approximately 675 million in chimpanzee V1, providing evidence that both techniques estimate the same parameters of interest. In addition, our results indicate the strengths of each distinct tissue preparation procedure, highlighting the importance of attention to anatomical detail. In summary, we found that the isotropic fractionator and the stereological optical fractionator produced concordant estimates of the cellular composition of V1, and that this result supports the conclusion that chimpanzees conform to the primate pattern of exceptionally high packing density in V1. Ultimately, our data suggest that investigators can optimize their experimental approach by using any of these counting methods to obtain reliable cell and neuron counts.

  13. Visualizing Nanoscale Distribution of Corrosion Cells by Open-Loop Electric Potential Microscopy.

    Science.gov (United States)

    Honbo, Kyoko; Ogata, Shoichiro; Kitagawa, Takuya; Okamoto, Takahiro; Kobayashi, Naritaka; Sugimoto, Itto; Shima, Shohei; Fukunaga, Akira; Takatoh, Chikako; Fukuma, Takeshi

    2016-02-23

    Corrosion is a traditional problem but still one of the most serious problems in industry. To reduce the huge economic loss caused by corrosion, tremendous effort has been made to understand, predict and prevent it. Corrosion phenomena are generally explained by the formation of corrosion cells at a metal-electrolyte interface. However, experimental verification of their nanoscale distribution has been a major challenge owing to the lack of a method able to visualize the local potential distribution in an electrolytic solution. In this study, we have investigated the nanoscale corrosion behavior of Cu fine wires and a duplex stainless steel by in situ imaging of local corrosion cells by open-loop electric potential microscopy (OL-EPM). For both materials, potential images obtained by OL-EPM show nanoscale contrasts, where areas of higher and lower potential correspond to anodic areas (i.e., corrosion sites) and cathodic areas, respectively. This imaging capability allows us to investigate the real-time transition of local corrosion sites even when surface structures show little change. This is particularly useful for investigating reactions under surface oxide layers or highly corrosion-resistant materials as demonstrated here. The proposed technique should be applicable to the study of other redox reactions on a battery electrode or a catalytic material. The results presented here open up such future applications of OL-EPM in nanoscale electrochemistry. PMID:26811989

  14. Visualization of NRAS RNA G-Quadruplex Structures in Cells with an Engineered Fluorogenic Hybridization Probe.

    Science.gov (United States)

    Chen, Shuo-Bin; Hu, Ming-Hao; Liu, Guo-Cai; Wang, Jin; Ou, Tian-Miao; Gu, Lian-Quan; Huang, Zhi-Shu; Tan, Jia-Heng

    2016-08-24

    The RNA G-quadruplex is an important secondary structure formed by guanine-rich RNA sequences. However, its folding studies have mainly been studied in vitro. Accurate identification of RNA G-quadruplex formation within a sequence of interest remains difficult in cells. Herein, and based on the guanine-rich sequence in the 5'-UTR of NRAS mRNA, we designed and synthesized the first G-quadruplex-triggered fluorogenic hybridization (GTFH) probe, ISCH-nras1, for the unique visualization of the G-quadruplexes that form in this region. ISCH-nras1 is made up of two parts: The first is a fluorescent light-up moiety specific to G-quadruplex structures, and the second is a DNA molecule that can hybridize with a sequence that is adjacent to the guanine-rich sequence in the NRAS mRNA 5'-UTR. Further evaluation studies indicated that ISCH-nras1 could directly and precisely detect the targeted NRAS RNA G-quadruplex structures, both in vitro and in cells. Thus, this GTFH probe was a useful tool for directly investigating the folding of G-quadruplex structures within an RNA of interest and represents a new direction for the design of smart RNA G-quadruplex probes. PMID:27508892

  15. A "turn-on" silver nanocluster based fluorescent sensor for folate receptor detection and cancer cell imaging under visual analysis.

    Science.gov (United States)

    Jiang, Hong; Xu, Gang; Sun, Yimin; Zheng, Weiwei; Zhu, Xiangxiang; Wang, Baojuan; Zhang, Xiaojun; Wang, Guangfeng

    2015-07-28

    A novel terminal protection based label-free and "turn-on" fluorescent sensor for detection of folate receptors (FRs) and HeLa cells is developed by fluorescence resonance energy transfer (FRET) between single-walled carbon nanotubes (SWCNTs) and silver nanoclusters (AgNCs). Multilevel visual analysis (m(2)VA) was firstly proposed and applied in optimizing the experimental parameters. PMID:26108636

  16. Visualizing viral protein structures in cells using genetic probes for correlated light and electron microscopy.

    Science.gov (United States)

    Ou, Horng D; Deerinck, Thomas J; Bushong, Eric; Ellisman, Mark H; O'Shea, Clodagh C

    2015-11-15

    Structural studies of viral proteins most often use high-resolution techniques such as X-ray crystallography, nuclear magnetic resonance, single particle negative stain, or cryo-electron microscopy (EM) to reveal atomic interactions of soluble, homogeneous viral proteins or viral protein complexes. Once viral proteins or complexes are separated from their host's cellular environment, their natural in situ structure and details of how they interact with other cellular components may be lost. EM has been an invaluable tool in virology since its introduction in the late 1940's and subsequent application to cells in the 1950's. EM studies have expanded our knowledge of viral entry, viral replication, alteration of cellular components, and viral lysis. Most of these early studies were focused on conspicuous morphological cellular changes, because classic EM metal stains were designed to highlight classes of cellular structures rather than specific molecular structures. Much later, to identify viral proteins inducing specific structural configurations at the cellular level, immunostaining with a primary antibody followed by colloidal gold secondary antibody was employed to mark the location of specific viral proteins. This technique can suffer from artifacts in cellular ultrastructure due to compromises required to provide access to the immuno-reagents. Immunolocalization methods also require the generation of highly specific antibodies, which may not be available for every viral protein. Here we discuss new methods to visualize viral proteins and structures at high resolutions in situ using correlated light and electron microscopy (CLEM). We discuss the use of genetically encoded protein fusions that oxidize diaminobenzidine (DAB) into an osmiophilic polymer that can be visualized by EM. Detailed protocols for applying the genetically encoded photo-oxidizing protein MiniSOG to a viral protein, photo-oxidation of the fusion protein to yield DAB polymer staining, and

  17. Neuron-type specific cannabinoid-mediated G protein signalling in mouse hippocampus.

    Science.gov (United States)

    Steindel, Frauke; Lerner, Raissa; Häring, Martin; Ruehle, Sabine; Marsicano, Giovanni; Lutz, Beat; Monory, Krisztina

    2013-03-01

    Type 1 cannabinoid receptor (CB1) is expressed in different neuronal populations in the mammalian brain. In particular, CB1 on GABAergic or glutamatergic neurons exerts different functions and display different pharmacological properties in vivo. This suggests the existence of neuron-type specific signalling pathways activated by different subpopulations of CB1. In this study, we analysed CB1 expression, binding and signalling in the hippocampus of conditional mutant mice, bearing CB1 deletion in GABAergic (GABA-CB1-KO mice) or cortical glutamatergic neurons (Glu-CB1-KO mice). Compared to their wild-type littermates, Glu-CB1-KO displayed a small decrease of CB1 mRNA amount, immunoreactivity and [³H]CP55,940 binding. Conversely, GABA-CB1-KO mice showed a drastic reduction of these parameters, confirming that CB1 is present at much higher density on hippocampal GABAergic interneurons than glutamatergic neurons. Surprisingly, however, saturation analysis of HU210-stimulated [(35) S]GTPγS binding demonstrated that 'glutamatergic' CB1 is more efficiently coupled to G protein signalling than 'GABAergic' CB1. Thus, the minority of CB1 on glutamatergic neurons is paradoxically several fold more strongly coupled to G protein signalling than 'GABAergic' CB1. This selective signalling mechanism raises the possibility of designing novel cannabinoid ligands that differentially activate only a subset of physiological effects of CB1 stimulation, thereby optimizing therapeutic action. PMID:23289830

  18. Assessing the role of cell-surface molecules in central synaptogenesis in the Drosophila visual system.

    Directory of Open Access Journals (Sweden)

    Sandra Berger-Müller

    Full Text Available A hallmark of the central nervous system is its spatial and functional organization in synaptic layers. During neuronal development, axons form transient contacts with potential post-synaptic elements and establish synapses with appropriate partners at specific layers. These processes are regulated by synaptic cell-adhesion molecules. In the Drosophila visual system, R7 and R8 photoreceptor subtypes target distinct layers and form en passant pre-synaptic terminals at stereotypic loci of the axonal shaft. A leucine-rich repeat transmembrane protein, Capricious (Caps, is known to be selectively expressed in R8 axons and their recipient layer, which led to the attractive hypothesis that Caps mediates R8 synaptic specificity by homophilic adhesion. Contradicting this assumption, our results indicate that Caps does not have a prominent role in synaptic-layer targeting and synapse formation in Drosophila photoreceptors, and that the specific recognition of the R8 target layer does not involve Caps homophilic axon-target interactions. We generated flies that express a tagged synaptic marker to evaluate the presence and localization of synapses in R7 and R8 photoreceptors. These genetic tools were used to assess how the synaptic profile is affected when axons are forced to target abnormal layers by expressing axon guidance molecules. When R7 axons were mistargeted to the R8-recipient layer, R7s either maintained an R7-like synaptic profile or acquired a similar profile to r8s depending on the overexpressed protein. When R7 axons were redirected to a more superficial medulla layer, the number of presynaptic terminals was reduced. These results indicate that cell-surface molecules are able to dictate synapse loci by changing the axon terminal identity in a partially cell-autonomous manner, but that presynapse formation at specific sites also requires complex interactions between pre- and post-synaptic elements.

  19. Visualization of Photoexcited Carrier Responses in a Solar Cell Using Optical Pump—Terahertz Emission Probe Technique

    Science.gov (United States)

    Nakanishi, Hidetoshi; Ito, Akira; Takayama, Kazuhisa; Kawayama, Iwao; Murakami, Hironaru; Tonouchi, Masayoshi

    2016-05-01

    We observed photoexcited carrier responses in solar cells excited by femtosecond laser pulses with spatial and temporal resolution using an optical pump-terahertz emission probe technique. We visualized the ultrafast local variation of the intensity of terahertz emission from a polycrystalline silicon solar cell using this technique and clearly observed the change in signals between a grain boundary and the inside of a grain in the solar cell. Further, the time evolution of the pump-probe signals of the polycrystalline and monocrystalline silicon solar cells was observed, and the relaxation times of photoexcited carriers in the emitter layers of crystalline silicon solar cells were estimated using this technique. The estimated relaxation time was consistent with the lifetime of the Auger recombination process that was dominant in heavily doped silicon used as an emitter layer for the silicon solar cells, which is difficult to obtain with photoluminescence method commonly used for the evaluation of solar cells.

  20. Parasol cell mosaics are unlikely to drive the formation of structured orientation maps in primary visual cortex.

    Science.gov (United States)

    Hore, Victoria R A; Troy, John B; Eglen, Stephen J

    2012-11-01

    The receptive fields of on- and off-center parasol cell mosaics independently tile the retina to ensure efficient sampling of visual space. A recent theoretical model represented the on- and off-center mosaics by noisy hexagonal lattices of slightly different density. When the two lattices are overlaid, long-range Moiré interference patterns are generated. These Moiré interference patterns have been suggested to drive the formation of highly structured orientation maps in visual cortex. Here, we show that noisy hexagonal lattices do not capture the spatial statistics of parasol cell mosaics. An alternative model based upon local exclusion zones, termed as the pairwise interaction point process (PIPP) model, generates patterns that are statistically indistinguishable from parasol cell mosaics. A key difference between the PIPP model and the hexagonal lattice model is that the PIPP model does not generate Moiré interference patterns, and hence stimulated orientation maps do not show any hexagonal structure. Finally, we estimate the spatial extent of spatial correlations in parasol cell mosaics to be only 200-350 μm, far less than that required to generate Moiré interference. We conclude that parasol cell mosaics are too disordered to drive the formation of highly structured orientation maps in visual cortex. PMID:23110776

  1. Aminomethylenediphosphonate: A Potent Type-Specific Inhibitor of Both Plant and Phototrophic Bacterial H+-Pyrophosphatases.

    Science.gov (United States)

    Zhen, R. G.; Baykov, A. A.; Bakuleva, N. P.; Rea, P. A.

    1994-01-01

    The suitability of different pyrophosphate (PPi) analogs as inhibitors of the vacuolar H+-translocating inorganic pyrophosphatase (V-PPase; EC 3.6.1.1) of tonoplast vesicles isolated from etiolated hypocotyls of Vigna radiata was investigated. Five 1,1-diphosphonates and imidodiphosphate were tested for their effects on substrate hydrolysis by the V-PPase at a substrate concentration corresponding to the Km of the enzyme. The order of inhibitory potency (apparent inhibition constants, Kiapp values, [mu]M, in parentheses) of the compounds examined was aminomethylenediphosphonate (1.8) > hydroxymethylenediphosphonate (5.7) [almost equal to] ethane-1-hydroxy-1,1-diphosphonate (6.5) > imidodiphosphate (12) > methylenediphosphonate (68) > dichloromethylenediphosphonate (>500). The specificity of three of these compounds, aminomethylenediphosphonate, imidodiphosphate, and methylenediphosphonate, was determined by comparing their effects on the V-PPase and vacuolar H+-ATPase from Vigna, plasma membrane H+-ATPase from Beta vulgaris, H+-PPi synthase of chromatophores prepared from Rhodospirillum rubrum, soluble PPase from Saccharomyces cerevisiae, alkaline phosphatase from bovine intestinal mucosa, and nonspecific monophosphoesterase from Vigna at a PPi concentration equivalent to 10 times the Km of the V-PPase. Although all three PPi analogs inhibited the plant V-PPase and bacterial H+-PPi synthase with qualitatively similar kinetics, whether substrate hydrolysis or PPi-dependent H+-translocation was measured, neither the vacuolar H+-ATPase nor plasma membrane H+-ATPase nor any of the non-V-PPase-related PPi hydrolases were markedly inhibited under these conditions. It is concluded that 1, 1-diphosphonates, in general, and aminomethylenediphosphonate, in particular, are potent type-specific inhibitors of the V-PPase and its putative bacterial homolog, the H+-PPi synthase of Rhodospirillum. PMID:12232069

  2. Muscle-Type Specific Autophosphorylation of CaMKII Isoforms after Paced Contractions

    Directory of Open Access Journals (Sweden)

    Wouter Eilers

    2014-01-01

    Full Text Available We explored to what extent isoforms of the regulator of excitation-contraction and excitation-transcription coupling, calcium/calmodulin protein kinase II (CaMKII contribute to the specificity of myocellular calcium sensing between muscle types and whether concentration transients in its autophosphorylation can be simulated. CaMKII autophosphorylation at Thr287 was assessed in three muscle compartments of the rat after slow or fast motor unit-type stimulation and was compared against a computational model (CaMuZclE coupling myocellular calcium dynamics with CaMKII Thr287 phosphorylation. Qualitative differences existed between fast- (gastrocnemius medialis and slow-type muscle (soleus for the expression pattern of CaMKII isoforms. Phospho-Thr287 content of δA CaMKII, associated with nuclear functions, demonstrated a transient and compartment-specific increase after excitation, which contrasted to the delayed autophosphorylation of the sarcoplasmic reticulum-associated βM CaMKII. In soleus muscle, excitation-induced δA CaMKII autophosphorylation demonstrated frequency dependence (P = 0.02. In the glycolytic compartment of gastrocnemius medialis, CaMKII autophosphorylation after excitation was blunted. In silico assessment emphasized the importance of mitochondrial calcium buffer capacity for excitation-induced CaMKII autophosphorylation but did not predict its isoform specificity. The findings expose that CaMKII autophosphorylation with paced contractions is regulated in an isoform and muscle type-specific fashion and highlight properties emerging for phenotype-specific regulation of CaMKII.

  3. World Health Organization Guidelines for Containment of Poliovirus Following Type-Specific Polio Eradication - Worldwide, 2015.

    Science.gov (United States)

    Previsani, Nicoletta; Tangermann, Rudolph H; Tallis, Graham; Jafari, Hamid S

    2015-08-28

    In 1988, the World Health Assembly of the World Health Organization (WHO) resolved to eradicate polio worldwide. Among the three wild poliovirus (WPV) types (type 1, type 2, and type 3), WPV type 2 (WPV2) has been eliminated in the wild since 1999, and WPV type 3 (WPV3) has not been reported since 2012. In 2015, only Afghanistan and Pakistan have reported WPV transmission. On May 25, 2015, all WHO Member States endorsed World Health Assembly resolution 68.3 on full implementation of the Polio Eradication and Endgame Strategic Plan 2013-2018 (the Endgame Plan), and with it, the third Global Action Plan to minimize poliovirus facility-associated risk (GAPIII). All WHO Member States have committed to implementing appropriate containment of WPV2 in essential laboratory and vaccine production facilities* by the end of 2015 and of type 2 oral poliovirus vaccine (OPV2) within 3 months of global withdrawal of OPV2, which is planned for April 2016. This report summarizes critical steps for essential laboratory and vaccine production facilities that intend to retain materials confirmed to contain or potentially containing type-specific WPV, vaccine-derived poliovirus (VDPV), or OPV/Sabin viruses, and steps for nonessential facilities† that process specimens that contain or might contain polioviruses. National authorities will need to certify that the essential facilities they host meet the containment requirements described in GAPIII. After certification of WPV eradication, the use of all OPV will cease; final containment of all polioviruses after polio eradication and OPV cessation will minimize the risk for reintroduction of poliovirus into a polio-free world. PMID:26313474

  4. Software tools for simultaneous data visualization and T cell epitopes and disorder prediction in proteins.

    Science.gov (United States)

    Jandrlić, Davorka R; Lazić, Goran M; Mitić, Nenad S; Pavlović, Mirjana D

    2016-04-01

    We have developed EpDis and MassPred, extendable open source software tools that support bioinformatic research and enable parallel use of different methods for the prediction of T cell epitopes, disorder and disordered binding regions and hydropathy calculation. These tools offer a semi-automated installation of chosen sets of external predictors and an interface allowing for easy application of the prediction methods, which can be applied either to individual proteins or to datasets of a large number of proteins. In addition to access to prediction methods, the tools also provide visualization of the obtained results, calculation of consensus from results of different methods, as well as import of experimental data and their comparison with results obtained with different predictors. The tools also offer a graphical user interface and the possibility to store data and the results obtained using all of the integrated methods in the relational database or flat file for further analysis. The MassPred part enables a massive parallel application of all integrated predictors to the set of proteins. Both tools can be downloaded from http://bioinfo.matf.bg.ac.rs/home/downloads.wafl?cat=Software. Appendix A includes the technical description of the created tools and a list of supported predictors. PMID:26851400

  5. Kinetics of linear rouleaux formation studied by visual monitoring of red cell dynamic organization.

    Science.gov (United States)

    Barshtein, G; Wajnblum, D; Yedgar, S

    2000-05-01

    Red blood cells (RBCs) in the presence of plasma proteins or other macromolecules may form aggregates, normally in rouleaux formations, which are dispersed with increasing blood flow. Experimental observations have suggested that the spontaneous aggregation process involves the formation of linear rouleaux (FLR) followed by formation of branched rouleaux networks. Theoretical models for the spontaneous rouleaux formation were formulated, taking into consideration that FLR may involve both "polymerization," i.e., interaction between two single RBCs (e + e) and the addition of a single RBC to the end of an existing rouleau (e + r), as well as "condensation" between two rouleaux by end-to-end addition (r + r). The present study was undertaken to experimentally examine the theoretical models and their assumptions, by visual monitoring of the spontaneous FLR (from singly dispersed RBC) in plasma, in a narrow gap flow chamber. The results validate the theoretical model, showing that FLR involves both polymerization and condensation, and that the kinetic constants for the above three types of intercellular interactions are the same, i.e., k(ee) = k(er) = k(rr) = k, and for all tested hematocrits (0.625-6%) k < 0.13 +/- 0.03 s(-1). PMID:10777743

  6. Treatment of one case of cerebral palsy combined with posterior visual pathway injury using autologous bone marrow mesenchymal stem cells

    Directory of Open Access Journals (Sweden)

    Li Min

    2012-05-01

    Full Text Available Abstract Background Cerebral palsy is currently one of the major diseases that cause severe paralysis of the nervous system in children; approximately 9–30% of cerebral palsy patients are also visually impaired, for which no effective treatment is available. Bone marrow mesenchymal stem cells (BMSCs have very strong self-renewal, proliferation, and pluripotent differentiation potentials. Therefore, autologous BMSC transplantation has become a novel method for treating cerebral palsy. Methods An 11-year-old boy had a clear history of dystocia and asphyxia after birth; at the age of 6 months, the family members observed that his gaze roamed and noted that he displayed a lack of attention. A brain MRI examination at the age of 7 years showed that the child had cerebral palsy with visual impairment (i.e., posterior visual pathway injury. The patient was hospitalized for 20 days and was given four infusions of intravenous autologous BMSCs. Before transplantation and 1, 6, and 12 months after transplantation, a visual evoked potential test, an electrocardiogram, routine blood tests, and liver and kidney function tests were performed. Results The patient did not have any adverse reactions during hospitalization or postoperative follow-up. After discharge, the patient could walk more smoothly than he could before transplantation; furthermore, his vision significantly improved 6 months after transplantation, which was also supported by the electrophysiological examinations. Conclusions The clinical application of BMSCs is effective for improving vision in a patient with cerebral palsy combined with visual impairment.

  7. Visualization of radiation-induced cell cycle-associated events in tumor cells expressing the fusion protein of Azami Green and the destruction box of human Geminin

    International Nuclear Information System (INIS)

    Ionizing radiation (IR) influences cell cycle-associated events in tumor cells. We expressed the fusion protein of Azami Green (AG) and the destruction box plus nuclear localization signal of human Geminin, an inhibitor of DNA replication licensing factor, in oral tumor cells. This approach allowed us to visualize G2 arrest in living cells following irradiation. The combination of time-lapse imaging analysis allowed us to observe the nuclear envelope break down (NEBD) at early M phase, and disappearance of fluorescence (DF) at the end of M phase. The duration from NEBD to DF was not much affected in irradiated cells; however, most of daughter cells harbored double-strand breaks. Complete DF was also observed in cells exhibiting abnormal mitosis or cytokinesis. We conclude that the fluorescent Geminin probe could function as a stable cell cycle indicator irrespective of genome integrity.

  8. Novel technique for visualizing primordial germ cells in sturgeons (Acipenser ruthenus, A. gueldenstaedtii, A. baerii, and Huso huso).

    Science.gov (United States)

    Saito, Taiju; Psenicka, Martin

    2015-10-01

    Primordial germ cells (PGCs) are the origin of all germ cells in developing embryos. In the sturgeon embryo, PGCs develop from the vegetal hemisphere, which mainly acts as an extraembryonic source of nutrition. Current methods for studying sturgeon PGCs require either killing the fish or using costly and time-consuming histological procedures. Here, we demonstrate that visualization of sterlet (Acipenser ruthenus>) PGCs in vivo is feasible by simply labeling the vegetal hemisphere with fluorescein isothiocyanate (FITC)-dextran. We injected FITC-dextrans, with molecular weights varying between 10 000 and 2 000 000, into the vegetal pole of 1- to 4-cell stage embryos. At the neurula to tail-bud developmental stages, FITC-positive PGC-like cells appeared ventrally around the developing tail bud in the experimental group that received a high-molecular-weight FITC-dextran. The highest average number of FITC-positive PGC-like cells was observed in embryos injected with FITC-dextran having a molecular weight of 500 000 (FD-500). The pattern of migration of the labeled cells was identical to that of PGCs, clearly indicating that the FITC-positive PGC-like cells were PGCs. Labeled vegetal cells, except for the PGCs, were digested and excreted before the embryos starting feeding. FITC-labeled PGCs were observed in the developing gonads of fish for at least 3 mo after injection. We also found that FD-500 could be used to visualize PGCs in other sturgeon species. To the best of our knowledge, this report is the first to demonstrate in any animal species that PGCs can be visualized in vivo for a long period by the injection of a simple reagent. PMID:26134864

  9. Comparison between numerical simulation and visualization experiment on water behavior in single straight flow channel polymer electrolyte fuel cells

    Science.gov (United States)

    Masuda, Hiromitsu; Ito, Kohei; Oshima, Toshihiro; Sasaki, Kazunari

    A relationship between a flooding and a cell voltage drop for polymer electrolyte fuel cell was investigated experimentally and numerically. A visualization cell, which has single straight gas flow channel (GFC) and observation window, was fabricated to visualize the flooding in GFC. We ran the cell with changing operation condition, and measured the time evolution of cell voltage and took the images of cathode GFC. Considering the operation condition, we executed a developed numerical simulation, which is based on multiphase mixture model with a formulation on water transport through the surface of polymer electrolyte membrane and the interface of gas diffusion layer/GFC. As a result in experiment, we found that the cell voltage decreased with time and this decrease was accelerated by larger current and smaller air flow rate. Our simulation succeeded to demonstrate this trend of cell voltage. In experiment, we also found that the water flushing in GFC caused an immediate voltage change, resulting in voltage recovery or electricity generation stop. Although our simulation could not replicate this immediate voltage change, the supersaturated area obtained by our simulation well corresponded to fogging area appeared on the window surface in the GFC.

  10. Accurate assessment of Congo basin forest carbon stocks requires forest type specific assessments

    Science.gov (United States)

    Moonen, Pieter C. J.; Van Ballaert, Siege; Verbist, Bruno; Boyemba, Faustin; Muys, Bart

    2014-05-01

    Due to a limited number of field-based studies estimations of carbon stocks in the Central Congo Basin remain highly uncertain. In particular, more information is needed about the variation in stocks between forest types and on the factors explaining these differences. This study presents results from biomass and soil carbon inventories in 46 0.25ha old-growth forest plots located in three study sites in Tshopo District, Democratic Republic of Congo. Four forest community types were identified using cluster and indicator species analysis based on the plots' large tree (>30cm DBH) species composition. Carbon stocks were calculated using newly established forest type specific tree height-diameter relationships to prevent errors related to the use of inappropriate regional relationships from literature. Using the Akaike criterion it became clear that for one site and a few forest types separate tree height-diameter relationships gave a robust and significant better fit, showing that there was a clear and significant interaction effect between sites and forest type. Mean above-ground carbon stocks were estimated at 165 ±44 Mg ha-1. Significant differences were found between forest types, but not between sites for a given forest type. Largest stocks were found in monodominant Gilbertiodendron dewevrei forests (187 ± 37 Mg C ha-1), which occurred in all sites. Smallest stocks (91 ± 14 Mg C ha-1) were found in the Margaritaria discoidea mixed forest type, which occurred only in one site, while two other mixed forest types showed intermediate stocks (148 ± 28 Mg C ha-1 and 160 ± 36 Mg C ha-1 respectively). The observed differences in aboveground stocks between forest types could be explained by forest structure related variables including number of large trees (DBH>70cm), average wood density and dominant height. When comparing the G. dewevrei monodominant type with mixed forest types within each study site, the former showed equal basal area and sometimes higher

  11. Visualization and quantitative analysis of extrachromosomal telomere-repeat DNA in individual human cells by Halo-FISH.

    Science.gov (United States)

    Komosa, Martin; Root, Heather; Meyn, M Stephen

    2015-02-27

    Current methods for characterizing extrachromosomal nuclear DNA in mammalian cells do not permit single-cell analysis, are often semi-quantitative and frequently biased toward the detection of circular species. To overcome these limitations, we developed Halo-FISH to visualize and quantitatively analyze extrachromosomal DNA in single cells. We demonstrate Halo-FISH by using it to analyze extrachromosomal telomere-repeat (ECTR) in human cells that use the Alternative Lengthening of Telomeres (ALT) pathway(s) to maintain telomere lengths. We find that GM847 and VA13 ALT cells average ∼80 detectable G/C-strand ECTR DNA molecules/nucleus, while U2OS ALT cells average ∼18 molecules/nucleus. In comparison, human primary and telomerase-positive cells contain 300), range widely in length (200 kb) and are composed of primarily G- or C-strand telomere-repeat DNA. Halo-FISH enables, for the first time, the simultaneous analysis of ECTR DNA and chromosomal telomeres in a single cell. We find that ECTR DNA comprises ∼15% of telomere-repeat DNA in GM847 and VA13 cells, but <4% in U2OS cells. In addition to its use in ALT cell analysis, Halo-FISH can facilitate the study of a wide variety of extrachromosomal DNA in mammalian cells. PMID:25662602

  12. Alpha-bungarotoxin binding to target cell in a developing visual system by carboxylated nanodiamond

    Science.gov (United States)

    Liu, Kuang-Kai; Chen, Mei-Fang; Chen, Po-Yi; Lee, Tony J. F.; Cheng, Chia-Liang; Chang, Chia-Ching; Ho, Yen-Peng; Chao, Jui-I.

    2008-05-01

    Biological molecules conjugating with nanoparticles are valuable for applications including bio-imaging, bio-detection, and bio-sensing. Nanometer-sized diamond particles have excellent electronic and chemical properties for bio-conjugation. In this study, we manipulated the carboxyl group produced on the surface of nanodiamond (carboxylated nanodiamond, cND) for conjugating with alpha-bungarotoxin (α-BTX), a neurotoxin derived from Bungarus multicinctus with specific blockade of alpha7-nicotinic acetylcholine receptor (α7-nAChR). The electrostatic binding of cND-α-BTX was mediated by the negative charge of the cND and the positive charge of the α-BTX in physiological pH conditions. Sodium dodecyl sulfate-polyacrylamide gel analysis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI/TOF-MS) spectra displayed that α-BTX proteins were conjugated with cND particles via non-covalent bindings. The green fluorescence of the cND particles combining with the red fluorescence of tetramethylrhodamine-labeled α-BTX presented a yellow color at the same location, which indicated that α-BTX proteins were conjugated with cND particles. Xenopus laevis's oocytes expressed the human α7-nAChR proteins by microinjection with α7-nAChR mRNA. The cND-α-BTX complexes were bound to α7-nAChR locating on the cell membrane of oocytes and human lung A549 cancer cells analyzed by laser scanning confocal microscopy. The choline-evoked α7-nAChR-mediated inward currents of the oocytes were blocked by cND-α-BTX complexes in a concentration-dependent manner using two-electrode voltage-clamp recording. Furthermore, the fluorescence intensity of cND-α-BTX binding on A549 cells could be quantified by flow cytometry. These results indicate that cND-conjugated α-BTX still preserves its biological activity in blocking the function of α7-nAChR, and provide a visual system showing the binding of α-BTX to α7-nAChR.

  13. Alpha-bungarotoxin binding to target cell in a developing visual system by carboxylated nanodiamond

    International Nuclear Information System (INIS)

    Biological molecules conjugating with nanoparticles are valuable for applications including bio-imaging, bio-detection, and bio-sensing. Nanometer-sized diamond particles have excellent electronic and chemical properties for bio-conjugation. In this study, we manipulated the carboxyl group produced on the surface of nanodiamond (carboxylated nanodiamond, cND) for conjugating with alpha-bungarotoxin (α-BTX), a neurotoxin derived from Bungarus multicinctus with specific blockade of alpha7-nicotinic acetylcholine receptor (α7-nAChR). The electrostatic binding of cND-α-BTX was mediated by the negative charge of the cND and the positive charge of the α-BTX in physiological pH conditions. Sodium dodecyl sulfate-polyacrylamide gel analysis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI/TOF-MS) spectra displayed that α-BTX proteins were conjugated with cND particles via non-covalent bindings. The green fluorescence of the cND particles combining with the red fluorescence of tetramethylrhodamine-labeled α-BTX presented a yellow color at the same location, which indicated that α-BTX proteins were conjugated with cND particles. Xenopus laevis's oocytes expressed the human α7-nAChR proteins by microinjection with α7-nAChR mRNA. The cND-α-BTX complexes were bound to α7-nAChR locating on the cell membrane of oocytes and human lung A549 cancer cells analyzed by laser scanning confocal microscopy. The choline-evoked α7-nAChR-mediated inward currents of the oocytes were blocked by cND-α-BTX complexes in a concentration-dependent manner using two-electrode voltage-clamp recording. Furthermore, the fluorescence intensity of cND-α-BTX binding on A549 cells could be quantified by flow cytometry. These results indicate that cND-conjugated α-BTX still preserves its biological activity in blocking the function of α7-nAChR, and provide a visual system showing the binding of α-BTX to α7-nAChR

  14. Behavior of a metabolic cycling population at the single cell level as visualized by fluorescent gene expression reporters.

    Directory of Open Access Journals (Sweden)

    Sunil Laxman

    Full Text Available BACKGROUND: During continuous growth in specific chemostat cultures, budding yeast undergo robust oscillations in oxygen consumption that are accompanied by highly periodic changes in transcript abundance of a majority of genes, in a phenomenon called the Yeast Metabolic Cycle (YMC. This study uses fluorescent reporters of genes specific to different YMC phases in order to visualize this phenomenon and understand the temporal regulation of gene expression at the level of individual cells within the cycling population. METHODOLOGY: Fluorescent gene expression reporters for different phases of the YMC were constructed and stably integrated into the yeast genome. Subsequently, these reporter-expressing yeast were used to visualize YMC dynamics at the individual cell level in cultures grown in a chemostat or in a microfluidics platform under varying glucose concentrations, using fluorescence microscopy and quantitative Western blots. CONCLUSIONS: The behavior of single cells within a metabolic cycling population was visualized using phase-specific fluorescent reporters. The reporters largely recapitulated genome-specified mRNA expression profiles. A significant fraction of the cell population appeared to exhibit basal expression of the reporters, supporting the hypothesis that there are at least two distinct subpopulations of cells within the cycling population. Although approximately half of the cycling population initiated cell division in each permissive window of the YMC, metabolic synchrony of the population was maintained. Using a microfluidics platform we observed that low glucose concentrations appear to be necessary for metabolic cycling. Lastly, we propose that there is a temporal window in the oxidative growth phase of the YMC where the cycling population segregates into at least two subpopulations, one which will enter the cell cycle and one which does not.

  15. Myelin repair by Schwann cells in the regenerating goldfish visual pathway: regional patterns revealed by X-irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Nona, S.N.; Stafford, C.A.; Cronly-Dillon, J.R. (Manchester Univ. (United Kingdom). Inst. of Science and Technology); Duncan, A. (Guy' s Hospital, London (United Kingdom). Dept. of Anatomy); Scholes, J. (University Coll., London (United Kingdom))

    1994-07-01

    In the regenerating goldfish optic nerves, Schwann cells of unknown origin reliably infiltrate the lesion site forming a band of peripheral-type myelinating tissue by 1-2 months, sharply demarcated form the adjacent new CNS myelin. To investigate this effect, we have interfered with cell proliferation by locally X-irradiating the fish visual pathway 24 h after the lesion. As assayed by immunohistochemistry and EM, irradiation retards until 6 months formation of new myelin by Schwann cells at the lesion site, and virtually abolishes oligodendrocyte myelination distally, but has little or no effect on nerve fibre regrowth. Optic nerve astrocyte processes normally fail to re-infiltrate the lesion, but re-occupy it after irradiation, suggesting that they are normally excluded by early cell proliferation at this site. Moreover, scattered myelinating Schwann cells also appear in the oligodendrocyte-depleted distal optic nerve after irradiation, although only as far as the optic tract. (Author).

  16. Treatment of one case of cerebral palsy combined with posterior visual pathway injury using autologous bone marrow mesenchymal stem cells

    OpenAIRE

    Li Min; Yu Aixue; Zhang Fangfang; Dai GuangHui; Cheng Hongbin; Wang Xiaodong; An Yihua

    2012-01-01

    Abstract Background Cerebral palsy is currently one of the major diseases that cause severe paralysis of the nervous system in children; approximately 9–30% of cerebral palsy patients are also visually impaired, for which no effective treatment is available. Bone marrow mesenchymal stem cells (BMSCs) have very strong self-renewal, proliferation, and pluripotent differentiation potentials. Therefore, autologous BMSC transplantation has become a novel method for treating cerebral palsy. Methods...

  17. Visualization study of motion and deformation of red blood cells in a microchannel with straight, divergent and convergent sections

    OpenAIRE

    Chen, Bin; Guo, Fang; Xiang, Hao

    2011-01-01

    The size of red blood cells (RBC) is on the same order as the diameter of microvascular vessels. Therefore, blood should be regarded as a two-phase flow system of RBCs suspended in plasma rather than a continuous medium of microcirculation. It is of great physiological and pathological significance to investigate the effects of deformation and aggregation of RBCs on microcirculation. In this study, a visualization experiment was conducted to study the microcirculatory behavior of RBCs in susp...

  18. Visualization of Fuel Cell Water Transport and Performance Characterization under Freezing Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Kandlikar, S.G.; Lu, Z.; Rao, N.; Sergi, J.; Rath, C.; Dade, C.; Trabold, T.; Owejan, J.; Gagliardo, J.; Allen, J.; Yassar, R.S.; Medici, E.; Herescu, A.

    2010-05-30

    mechanism. The breakdown and redevelopment of the water paths in GDLs lead to an intermittent water drainage behavior, which is characterized by dynamic capillary pressure and changing of breakthrough location. MPL was found to not only limit the number of water entry locations into the GDL (thus drastically reducing water saturation), but also stabilizes the water paths (or morphology). • Simultaneously visualized the water transport on cathode and anode channels of an operating fuel cell. It was found that under relatively dry hydrogen/air conditions at lower temperatures, the cathode channels display a similar flow pattern map to the ex-situ experiments under similar conditions. Liquid water on the anode side is more likely formed via condensation of water vapor which is transported through the anode GDL. • Investigated the water percolation through the GDL with pseudo-Hele-Shaw experiments and simulated the capillary-driven two-phase flow inside gas diffusion media, with the pore size distributions being modeled by using Weibull distribution functions. The effect of the inclusion of the microporous layer in the fuel cell assembly was explored numerically. • Developed and validated a simple, reliable computational tool for predicting liquid water transport in GDLs. • Developed a new method of determining the pore size distribution in GDL using scanning electron microscope (SEM) image processing, which allows for separate characterization of GDL wetting properties and pore size distribution. • Determined the effect of surface wettability and channel cross section and bend dihedral on liquid holdup in fuel cell flow channels. A major thrust of this research program has been the development of an optimal combination of materials, design features and cell operating conditions that achieve a water management strategy which facilitates fuel cell operation under freezing conditions. Based on our various findings, we have made the final recommendation relative to GDL

  19. Visualization of the solubilization process of the plasma membrane of a living cell by waveguide evanescent field fluorescence microscopy

    Science.gov (United States)

    Hassanzadeh, Abdollah; Ma, Heun Kan; Dixon, S. Jeffrey; Mittler, Silvia

    2012-07-01

    Waveguide evanescent field fluorescence microscopy (WEFF) is a novel microscopy technology that allows imaging of a cell's plasma membrane in the vicinity of a glass substrate with high axial resolution, low background and little photobleaching. Time-lapse imaging can be performed to investigate changes in cell morphology in the presence or absence of chemical agents. WEFF microscopy provides a method to investigate plasma membranes of living cells and allows a comparison to simplified model membranes immobilized on planar substrates. The interaction of the nonionic detergent Triton X-100 with plasma membranes of osteoblasts in an aqueous environment was investigated. Solubilization of the membranes very close to the waveguide surface was visualized and related to the three-stage solubilisation model proposed for liposomes and supported lipid bilayers. Findings for the plasma membranes of cells are in excellent agreement with results reported for these artificial model systems.

  20. Human Embryonic and Hepatic Stem Cell Differentiation Visualized in Two and Three Dimensions Based on Serial Sections

    DEFF Research Database (Denmark)

    Vestentoft, Peter S.; Brøchner, Christian B; Lynnerup, Niels;

    2016-01-01

    Pluripotent human embryonic stem cells (hESCs) are characterized by two defining properties, self-renewal and differentiation. Self-renewing hESCs express transcription factors OCT4, SOX2, and NANOG, and surface markers SSEA-4 and TRA-1-60 and TRA-1-81 and their ability to differentiate into...... an entire colony is accomplished using 3D image processing software such as Mimics(®) or Amira(®). An extended version of this technique even allows for a high-magnification 3D-reconstruction of, e.g., hepatic stem cells in developing liver. These techniques combined allow for both a 2- and a 3......-dimensional visualization of hESC colonies and stem cells in organs, which leads to new insights into and information about the interaction of stem cells with their surroundings....

  1. Super-resolution imaging with Pontamine Fast Scarlet 4BS enables direct visualization of cellulose orientation and cell connection architecture in onion epidermis cells

    DEFF Research Database (Denmark)

    Liesche, Johannes; Ziomkiewicz, Iwona; Schulz, Alexander

    2013-01-01

    microscopy of some 200 nm in xy and 550 nm in z for green light, restricts the direct visualization of cellulose to relatively large bundles, whereas the structure of cellulose microfibrils with their diameter below 10 nm remains unresolved. Over the last decade, several so-called super-resolution microscopy...... approaches have been developed; in this paper we explore the potential of such approaches for the direct visualization of cellulose. Results To ensure optimal imaging we determined the spectral properties of PFS-stained tissue. PFS was found not to affect cell viability in the onion bulb scale epidermis. We...... confocal microscopy and the approach could be used to demonstrate differences in fibril orientation in different layers of the cell wall as well as particular cellulose fortifications around plasmodesmata. Conclusions Super-resolution light microscopy of PFS-stained cellulose fibrils is possible...

  2. Effects of the concomitant activation of ON and OFF retinal ganglion cells on the visual thalamus: evidence for an enhanced recruitment of GABAergic cells

    Directory of Open Access Journals (Sweden)

    Giovanni Montesano

    2015-11-01

    Full Text Available A fundamental question in vision neuroscience is how parallel processing of Retinal Ganglion Cell (RGC signals is integrated at the level of the visual thalamus. It is well known that parallel ON-OFF pathways generate output signals from the retina that are conveyed to the dorsal lateral geniculate nucleus (dLGN. However, it is unclear how these signals distribute onto thalamic cells and how these two pathways interact. Here, by electrophysiological recordings and c-Fos expression analysis, we characterized the effects of pharmacological manipulations of the retinal circuit aimed at inducing either a selective activation of a single pathway, OFF RGCs (intravitreal L-(+-2-Amino-4-phosphonobutyric, L-AP4 or an unregulated activity of all classes of retinal ganglion cells (intravitreal 4-Aminopyridine, 4-AP. In in vivo experiments, the analysis of c-Fos expression in the dLGN showed that these two manipulations recruited active cells from the same area, the lateral edge of the dLGN. Despite this similarity, the unregulated co-activation of both ON and OFF pathways by 4-AP yielded a much stronger recruitment of GABAergic interneurons in the dLGN when compared to L-AP4 pure OFF activation. The increased activation of an inhibitory thalamic network by a high level of unregulated discharge of ON and OFF RGCs might suggest that cross-inhibitory pathways between opposing visual channels are presumably replicated at multiple levels in the visual pathway, thus increasing the filtering ability for non-informative or noisy visual signals.

  3. Optimized labeling of bone marrow mesenchymal cells with superparamagnetic iron oxide nanoparticles and in vivo visualization by magnetic resonance imaging

    Directory of Open Access Journals (Sweden)

    Spray David C

    2011-02-01

    Full Text Available Abstract Background Stem cell therapy has emerged as a promising addition to traditional treatments for a number of diseases. However, harnessing the therapeutic potential of stem cells requires an understanding of their fate in vivo. Non-invasive cell tracking can provide knowledge about mechanisms responsible for functional improvement of host tissue. Superparamagnetic iron oxide nanoparticles (SPIONs have been used to label and visualize various cell types with magnetic resonance imaging (MRI. In this study we performed experiments designed to investigate the biological properties, including proliferation, viability and differentiation capacity of mesenchymal cells (MSCs labeled with clinically approved SPIONs. Results Rat and mouse MSCs were isolated, cultured, and incubated with dextran-covered SPIONs (ferumoxide alone or with poly-L-lysine (PLL or protamine chlorhydrate for 4 or 24 hrs. Labeling efficiency was evaluated by dextran immunocytochemistry and MRI. Cell proliferation and viability were evaluated in vitro with Ki67 immunocytochemistry and live/dead assays. Ferumoxide-labeled MSCs could be induced to differentiate to adipocytes, osteocytes and chondrocytes. We analyzed ferumoxide retention in MSCs with or without mitomycin C pretreatment. Approximately 95% MSCs were labeled when incubated with ferumoxide for 4 or 24 hrs in the presence of PLL or protamine, whereas labeling of MSCs incubated with ferumoxide alone was poor. Proliferative capacity was maintained in MSCs incubated with ferumoxide and PLL for 4 hrs, however, after 24 hrs it was reduced. MSCs incubated with ferumoxide and protamine were efficiently visualized by MRI; they maintained proliferation and viability for up to 7 days and remained competent to differentiate. After 21 days MSCs pretreated with mitomycin C still showed a large number of ferumoxide-labeled cells. Conclusions The efficient and long lasting uptake and retention of SPIONs by MSCs using a protocol

  4. Serial type-specific human papillomavirus (HPV) load measurement allows differentiation between regressing cervical lesions and serial virion productive transient infections

    International Nuclear Information System (INIS)

    Persistent high-risk human papillomavirus (HPV) infection is strongly associated with the development of high-grade cervical intraepithelial neoplasia (CIN) or cancer. Not all persistent infections lead to cancer. Viral load measured at a single time-point is a poor predictor of the natural history of HPV infections. However the profile of viral load evolution over time could distinguish nonprogressive from progressive (carcinogenic) infections. A retrospective natural history study was set up using a Belgian laboratory database including more than 800,000 liquid cytology specimens. All samples were submitted to qPCR identifying E6/E7 genes of 18 HPV types. Viral load changes over time were assessed by the linear regression slope. Database search identified 261 untreated women with persistent type-specific HPV DNA detected (270 infections) in at least three of the last smears for a average period of 3.2 years. Using the coefficient of determination (R²) infections could be subdivided in a latency group (n = 143; R² < 0.85) and a regressing group (n = 127; R² ≥ 0.85). In (≥3) serial viral load measurements, serial transient infections with latency is characterized by a nonlinear limited difference in decrease or increase of type-specific viral load (R² < 0.85 and slopes between 2 measurements 0.0010 and −0.0010 HPV copies/cell per day) over a longer period of time (1553 days), whereas regression of a clonal cell population is characterized by a linear (R² ≥ 0.85) decrease (−0.0033 HPV copies/cell per day) over a shorter period of time (708 days; P < 0.001). Using serial HPV type-specific viral load measurements we could for the first time identify regressing CIN2 and CIN3 lesions. Evolution of the viral load is an objective measurable indicator of the natural history of HPV infections and could be used for future triage in HPV-based cervical screening programs

  5. A Virus-type Specific Serological Diagnosis of Flavivirus Infection Using Virus-like Particles

    Institute of Scientific and Technical Information of China (English)

    Min QING; Zhi-ming YUAN; Pei-Yong Shi

    2009-01-01

    Many flaviviruses are emerging and reemerging pathogens, such as West Nile virus (WNV), dengue virus (DENV), yellow fever virus (YFV), and Japanese encephalitis virus. Serological assay is the dominant method for diagnosis of flavivirus infections in human. Because antibodies generated during flavivirus infections cross-react with other flavivirus members, plaque reduction neutralization test (PRNT) is the only available assay to determine the infecting flavivirus type.Since PRNT requires culturing raw viruses, it must be performed in biosafety level-3 or level-4 containment for many flaviviruses, and takes more than ten days to complete. To overcome these problems, we have developed flavivirus viral-like particles (VLPs) that could be used to replace raw viruses in the neutralization assay. The VLPs were prepared by trans packaging a luciferase-reporting replicon with viral structural proteins. This novel assay involves three simple steps: (ⅰ) VLPs from a panel of flaviviruses are incubated with flavivirus-infected sera at 37℃ for 1 h; (ⅱ)the neutralized VLPs are used to infect Vero cells; and (ⅲ) the infected cells are measured for luciferase activities at 22 h post-infection. The virus type whose VLP is most efficiently neutralized by the serum specimen (as quantified by the luciferase activities) is the etiologic agent. As a proof-of-concept, we show that a WNV-infected mouse serum neutralized the WNV VLP more efficiently and selectively than the DENV and YFV VLPs. Our results demonstrate that the VLP neutralization assay maintains the "gold standard" of the classic PRNT; importantly, it shortens the assay time from >10 days to <1 day, and can be performed in biosafety level-2 facility.

  6. Adult stem cells in mice : visualization and characterization using genetic mouse models

    NARCIS (Netherlands)

    Snippert, H.J.G.

    2011-01-01

    The onset of each living organism starts with pluripotent stem cells that have the ability to differentiate into all the different cell types of an organism. However, during the earliest stages of development, the pluripotent stem cells will stepwise lose their developmental potential. The cells tha

  7. A dual-mode turn-on fluorescent BODIPY-based probe for visualization of mercury ions in living cells.

    Science.gov (United States)

    Wang, Yue; Pan, Fuchao; Zhang, Yuanlin; Peng, Fangfang; Huang, Zhentao; Zhang, Weijuan; Zhao, Weili

    2016-08-01

    A novel turn-on fluorescent 8-amino BODIPY-based probe carrying a thiourea unit as the mercury ion recognition unit has been developed. Due to the cascade reaction processes, consecutive color changes reflecting the electronic absorption and emission responses were observed upon addition of increased concentrations of mercury(ii) ions. The likely sensing mechanism was proposed as mercury ion-promoted cyclization and subsequent hydrolysis. The probe displayed a selective response to mercury ions over other metal ions. Additionally, experiments with living Human Hepatoma SMMC-7721 cells to visualize intracellular mercury ions in biological systems were carried out with the probe. PMID:27251011

  8. Oral human papillomavirus type-specific infection in HIV-infected men: a prospective cohort study among men who have sex with men and heterosexual men.

    Science.gov (United States)

    Darwich, L; Cañadas, M P; Videla, S; Coll, J; Molina-López, R A; Cobarsi, P; Sirera, G; Clotet, B

    2014-09-01

    The natural history of type-specific oral infection of human papillomavirus (HPV) was assessed in a cohort of HIV-infected men (538 men who have sex with men (MSM); 195 heterosexuals). Risk factors associated with oral HPV infections were examined. The overall prevalence of HPV was 16%: HPV-16 was the most prevalent type (3.7% MSM; 7.8% heterosexuals). The prevalence of HPV-16 in heterosexuals was associated with CD4 nadir counts <200 cells/μL (ORadjusted = 3.0, 95% CI, 1.4-6.3). The overall incidence of HPV was similar between groups (11%), but the incidence of HPV-16 was higher in heterosexuals (ORadjusted = 3.2, 95% CI, 1.1-9.5). Not only MSM but also HIV-infected heterosexual men are at risk of HPV infection. Regular and careful oral inspection is needed. PMID:24382308

  9. Muscle fiber type specific induction of slow myosin heavy chain 2 gene expression by electrical stimulation

    Energy Technology Data Exchange (ETDEWEB)

    Crew, Jennifer R.; Falzari, Kanakeshwari [Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064 (United States); DiMario, Joseph X., E-mail: joseph.dimario@rosalindfranklin.edu [Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064 (United States)

    2010-04-01

    Vertebrate skeletal muscle fiber types are defined by a broad array of differentially expressed contractile and metabolic protein genes. The mechanisms that establish and maintain these different fiber types vary throughout development and with changing functional demand. Chicken skeletal muscle fibers can be generally categorized as fast and fast/slow based on expression of the slow myosin heavy chain 2 (MyHC2) gene in fast/slow muscle fibers. To investigate the cellular and molecular mechanisms that control fiber type formation in secondary or fetal muscle fibers, myoblasts from the fast pectoralis major (PM) and fast/slow medial adductor (MA) muscles were isolated, allowed to differentiate in vitro, and electrically stimulated. MA muscle fibers were induced to express the slow MyHC2 gene by electrical stimulation, whereas PM muscle fibers did not express the slow MyHC2 gene under identical stimulation conditions. However, PM muscle fibers did express the slow MyHC2 gene when electrical stimulation was combined with inhibition of inositol triphosphate receptor (IP3R) activity. Electrical stimulation was sufficient to increase nuclear localization of expressed nuclear-factor-of-activated-T-cells (NFAT), NFAT-mediated transcription, and slow MyHC2 promoter activity in MA muscle fibers. In contrast, both electrical stimulation and inhibitors of IP3R activity were required for these effects in PM muscle fibers. Electrical stimulation also increased levels of peroxisome-proliferator-activated receptor-{gamma} co-activator-1 (PGC-1{alpha}) protein in PM and MA muscle fibers. These results indicate that MA muscle fibers can be induced by electrical stimulation to express the slow MyHC2 gene and that fast PM muscle fibers are refractory to stimulation-induced slow MyHC2 gene expression due to fast PM muscle fiber specific cellular mechanisms involving IP3R activity.

  10. Muscle fiber type specific induction of slow myosin heavy chain 2 gene expression by electrical stimulation

    International Nuclear Information System (INIS)

    Vertebrate skeletal muscle fiber types are defined by a broad array of differentially expressed contractile and metabolic protein genes. The mechanisms that establish and maintain these different fiber types vary throughout development and with changing functional demand. Chicken skeletal muscle fibers can be generally categorized as fast and fast/slow based on expression of the slow myosin heavy chain 2 (MyHC2) gene in fast/slow muscle fibers. To investigate the cellular and molecular mechanisms that control fiber type formation in secondary or fetal muscle fibers, myoblasts from the fast pectoralis major (PM) and fast/slow medial adductor (MA) muscles were isolated, allowed to differentiate in vitro, and electrically stimulated. MA muscle fibers were induced to express the slow MyHC2 gene by electrical stimulation, whereas PM muscle fibers did not express the slow MyHC2 gene under identical stimulation conditions. However, PM muscle fibers did express the slow MyHC2 gene when electrical stimulation was combined with inhibition of inositol triphosphate receptor (IP3R) activity. Electrical stimulation was sufficient to increase nuclear localization of expressed nuclear-factor-of-activated-T-cells (NFAT), NFAT-mediated transcription, and slow MyHC2 promoter activity in MA muscle fibers. In contrast, both electrical stimulation and inhibitors of IP3R activity were required for these effects in PM muscle fibers. Electrical stimulation also increased levels of peroxisome-proliferator-activated receptor-γ co-activator-1 (PGC-1α) protein in PM and MA muscle fibers. These results indicate that MA muscle fibers can be induced by electrical stimulation to express the slow MyHC2 gene and that fast PM muscle fibers are refractory to stimulation-induced slow MyHC2 gene expression due to fast PM muscle fiber specific cellular mechanisms involving IP3R activity.

  11. Visual bone marrow mesenchymal stem cell transplantation in the repair of spinal cord injury

    OpenAIRE

    Rui-ping Zhang; Cheng Xu; Yin Liu; Jian-ding Li; Jun Xie

    2015-01-01

    An important factor in improving functional recovery from spinal cord injury using stem cells is maximizing the number of transplanted cells at the lesion site. Here, we established a contusion model of spinal cord injury by dropping a weight onto the spinal cord at T 7-8 . Superparamagnetic iron oxide-labeled bone marrow mesenchymal stem cells were transplanted into the injured spinal cord via the subarachnoid space. An outer magnetic field was used to successfully guide the labeled cells to...

  12. Real-time visualization of oxygen partial pressures in straight channels of running polymer electrolyte fuel cell with water plugging

    Science.gov (United States)

    Nagase, Katsuya; Suga, Takeo; Nagumo, Yuzo; Uchida, Makoto; Inukai, Junji; Nishide, Hiroyuki; Watanabe, Masahiro

    2015-01-01

    Visualization inside polymer electrolyte fuel cells (PEFCs) for elucidating the reaction distributions is expected to improve the performance, durability, and stability. An oxygen-sensitive film of a luminescent porphyrin was used to visualize the oxygen partial pressures in five straight gas-flow channels of a running PEFC with liquid-water blockages formed at the end of the channels. The blockage greatly lowered and unstabilized the cell voltage. The oxygen partial pressure decreased nearly to 0 kPa in the blocked channel. With a water blockage in a channel, the oxygen partial pressures in the adjacent channels were lowered due to an extra demand of oxygen consumption. When the number of the blocked channels increased, the oxygen partial pressure in the unblocked channels became much lowered. When the water blockages disappeared, the oxygen partial pressures quickly returned to the values before plugging. The influence of the cross flows of air through the gas diffusion layers in straight channels was much smaller than that in serpentine flow channels.

  13. Ocular morphology, topography of ganglion cell distribution and visual resolution of the pilot whale (Globicephala melas)

    OpenAIRE

    Mengual Molina, Rosa María; García Irles, Magdalena; Segovia Huertas, Yolanda; Pertusa, José Francisco

    2015-01-01

    The ocular morphology, morphological characteristics and topography of ganglion cell distribution were studied in four eyes of Globicephala melas to estimate the retinal resolution. The ganglion cell layer was composed of a single row of ganglion cells with a primarily round shape and a cell size which varied from 10 to 75 µm (mean 33.5 µm) in diameter. The typical feature was that 65 % of ganglion cells had a diameter larger than 25 µm, with a similar average size in all regions of the retin...

  14. Visualization of cell death in mice with focal cerebral ischemia using fluorescent annexin A5, propidium iodide, and TUNEL staining.

    Science.gov (United States)

    Bahmani, Peyman; Schellenberger, Eyk; Klohs, Jan; Steinbrink, Jens; Cordell, Ryan; Zille, Marietta; Müller, Jochen; Harhausen, Denise; Hofstra, Leo; Reutelingsperger, Chris; Farr, Tracy Deanne; Dirnagl, Ulrich; Wunder, Andreas

    2011-05-01

    To monitor stroke-induced brain damage and assess neuroprotective therapies, specific imaging of cell death after cerebral ischemia in a noninvasive manner is highly desirable. Annexin A5 has been suggested as a marker for imaging cell death under various disease conditions including stroke. In this study, C57BL6/N mice received middle cerebral artery occlusion (MCAO) and were injected intravenously with either active or inactive Cy5.5-annexin A5 48 hours after reperfusion. Some mice also received propidium iodide (PI), a cell integrity marker. Only in mice receiving active Cy5.5-annexin A5 were fluorescence intensities significantly higher over the hemisphere ipsilateral to MCAO than on the contralateral side. This was detected noninvasively and ex vivo 4 and 8 hours after injection. The majority of cells positive for fluorescent annexin A5 were also positive for PI and fragmented DNA as detected by terminal deoxynucleotidyl transferase-mediated 2'-deoxyuridine 5'-triphosphate-biotin nick end labeling (TUNEL) staining. This study demonstrates the high specificity of annexin A5 for visualization of cell death in a mouse model of stroke. To our knowledge, this is the first study to compare the distribution of injected active and inactive annexin A5, PI, and TUNEL staining. It provides important information on the experimental and potential clinical applications of annexin A5-based imaging agents in stroke. PMID:21245871

  15. A visual cell for measuring the solubility of prograde soluble salts in water at high temperatures and pressures

    Energy Technology Data Exchange (ETDEWEB)

    Moore, R.C.; Simonson, J.M.; Mesmer, R.E.

    1994-10-01

    An apparatus has been constructed for measuring the solubility of prograde soluble salts in water at high temperatures and pressures. The apparatus consists of a visually accessible cell thermostated in a rocking furnace. The apparatus allows for rapid, accurate solubility measurements for temperatures over 650 K and pressures up to 170 bars. The cell was constructed of platinum with sapphire windows and gold seals for corrosion resistance. A 3x telescope is used to observe the phase change in the cell. A key feature of the cell is the ability to control the system pressure. A section of small bore platinum tubing is used to connect the cell to an external pressure source. The tubing can remain open to the pressure source or be sealed off during a measurement. To minimize equilibration times, the entire apparatus was mounted to a rocking frame which can operate in the horizontal or vertical position. The apparatus was tested by measuring the solubility of NaCl in water at temperatures between 345 and 516 K at saturation pressure. Results are in good agreement with existing literature values.

  16. Cell-type-specific and hypoxia-inducible expression of the human erythropoietin gene in transgenic mice.

    OpenAIRE

    Semenza, G L; Koury, S. T.; Nejfelt, M K; Gearhart, J D; Antonarakis, S E

    1991-01-01

    Synthesis of erythropoietin, the primary humoral regulator of erythropoiesis, in liver and kidney is inducible by anemia or hypoxia. Analysis of human erythropoietin gene expression in transgenic mice revealed that sequences located 6-14 kilobases 5' to the gene direct expression to the kidney, whereas sequences within the immediate 3'-flanking region control hepatocyte-specific expression. Human erythropoietin transcription initiation sites were differentially utilized in liver and kidney. I...

  17. A 350 bp region of the proximal promoter of Rds drives cell-type specific gene expression

    OpenAIRE

    Cai, Xue; Conley, Shannon M.; Cheng, Tong; Al-Ubaidi, Muayyad R.; Naash, Muna I.

    2010-01-01

    RDS (retinal degeneration slow) is a photoreceptor-specific tetraspanin protein required for the biogenesis and maintenance of rod and cone outer segments. Mutations in the Rds gene are associated with multiple forms of rod- and cone-dominant retinal degeneration. To gain more insight into the mechanisms underlying the regulation of this gene the identification of regulatory sequences within the promoter of Rds was undertaken. A 3.5kb fragment of the 5′ flanking region of the mouse Rds gene w...

  18. Development of Cell-type specific anti-HIV gp120 aptamers for siRNA delivery

    OpenAIRE

    Zhou, Jiehua; Li, Haitang; Zhang, Jane; Piotr, Swiderski; Rossi, John

    2011-01-01

    The global epidemic of infection by HIV has created an urgent need for new classes of antiretroviral agents. The potent ability of small interfering (si)RNAs to inhibit the expression of complementary RNA transcripts is being exploited as a new class of therapeutics for a variety of diseases including HIV. Many previous reports have shown that novel RNAi-based anti-HIV/AIDS therapeutic strategies have considerable promise; however, a key obstacle to the successful therapeutic application and ...

  19. Induction of long-term potentiation and long-term depression is cell-type specific in the spinal cord

    OpenAIRE

    Kim, Hee Young; Jun, Jaebeom; Wang, Jigong; Bittar, Alice; Chung, Kyungsoon; Chung, Jin Mo

    2015-01-01

    Abstract The underlying mechanism of chronic pain is believed to be changes in excitability in spinal dorsal horn (DH) neurons that respond abnormally to peripheral input. Increased excitability in pain transmission neurons, and depression of inhibitory neurons, are widely recognized in the spinal cord of animal models of chronic pain. The possible occurrence of 2 parallel but opposing forms of synaptic plasticity, long-term potentiation (LTP) and long-term depression (LTD) was tested in 2 ty...

  20. Nr2e3-directed transcriptional regulation of genes involved in photoreceptor development and cell-type specific phototransduction.

    Science.gov (United States)

    Haider, Neena B; Mollema, Nissa; Gaule, Meghan; Yuan, Yang; Sachs, Andrew J; Nystuen, Arne M; Naggert, Jürgen K; Nishina, Patsy M

    2009-09-01

    The retinal transcription factor Nr2e3 plays a key role in photoreceptor development and function. In this study we examine gene expression in the retina of Nr2e3(rd7/rd7) mutants with respect to wild-type control mice, to identify genes that are misregulated and hence potentially function in the Nr2e3 transcriptional network. Quantitative candidate gene real time PCR and subtractive hybridization approaches were used to identify transcripts that were misregulated in Nr2e3(rd7/rd7) mice. Chromatin immunoprecipitation assays were then used to determine which of the misregulated transcripts were direct targets of NR2E3. We identified 24 potential targets of NR2E3. In the developing retina, NR2E3 targets transcription factors such as Ror1, Rorg, and the nuclear hormone receptors Nr1d1 and Nr2c1. In the mature retina NR2E3 targets several genes including the rod specific gene Gnb1 and cone specific genes blue opsin, and two of the cone transducin subunits, Gnat2 and Gnb3. In addition, we identified 5 novel transcripts that are targeted by NR2E3. While mislocalization of proteins between rods and cones was not observed, we did observe diminished concentration of GNB1 protein in adult Nr2e3(rd7/rd7) retinas. These studies identified novel transcriptional pathways that are potentially targeted by Nr2e3 in the retina and specifically demonstrate a novel role for NR2E3 in regulating genes involved in phototransduction. PMID:19379737

  1. Cell type-specific modulation of lipid mediator's formation in murine adipose tissue by omega-3 fatty acids

    Czech Academy of Sciences Publication Activity Database

    Kuda, Ondřej; Rombaldová, Martina; Janovská, Petra; Flachs, Pavel; Kopecký, Jan

    2016-01-01

    Roč. 469, č. 3 (2016), s. 731-736. ISSN 0006-291X R&D Projects: GA ČR(CZ) GP13-04449P; GA ČR(CZ) GA13-00871S; GA MŠk(CZ) LH14040 Institutional support: RVO:67985823 Keywords : adipose tissue macrophages * omega-3 PUFA * protectin D1 * lipid mediators * lipidomics Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.297, year: 2014

  2. Translaminar Inhibitory Cells Recruited by Layer 6 Cortico-Thalamic Neurons Suppress Visual Cortex

    OpenAIRE

    Bortone, Dante S.; Olsen, Shawn R.; Scanziani, Massimo

    2014-01-01

    In layer 6 (L6), a principal output layer of the mammalian cerebral cortex, a population of excitatory neurons defined by the NTSR1-Cre mouse line inhibit cortical responses to visual stimuli. Here we show that of the two major types of excitatory neurons existing in L6, the NTSR1-Cre line selectively targets those whose axon innervate both cortex and thalamus and not those whose axons remain within the cortex. These cortico-thalamic neurons mediate widespread inhibition across all cortical l...

  3. Machine-Part cell formation through visual decipherable clustering of Self Organizing Map

    OpenAIRE

    Chattopadhyay, Manojit; Chattopadhyay, Surajit; Dan, Pranab K

    2011-01-01

    Machine-part cell formation is used in cellular manufacturing in order to process a large variety, quality, lower work in process levels, reducing manufacturing lead-time and customer response time while retaining flexibility for new products. This paper presents a new and novel approach for obtaining machine cells and part families. In the cellular manufacturing the fundamental problem is the formation of part families and machine cells. The present paper deals with the Self Organising Map (...

  4. Visualization of immediate immune responses to pioneer metastatic cells in the lung.

    Science.gov (United States)

    Headley, Mark B; Bins, Adriaan; Nip, Alyssa; Roberts, Edward W; Looney, Mark R; Gerard, Audrey; Krummel, Matthew F

    2016-03-24

    Lung metastasis is the lethal determinant in many cancers and a number of lines of evidence point to monocytes and macrophages having key roles in its development. Yet little is known about the immediate fate of incoming tumour cells as they colonize this tissue, and even less known about how they make first contact with the immune system. Primary tumours liberate circulating tumour cells (CTCs) into the blood and we have developed a stable intravital two-photon lung imaging model in mice for direct observation of the arrival of CTCs and subsequent host interaction. Here we show dynamic generation of tumour microparticles in shear flow in the capillaries within minutes of CTC entry. Rather than dispersing under flow, many of these microparticles remain attached to the lung vasculature or independently migrate along the inner walls of vessels. Using fluorescent lineage reporters and flow cytometry, we observed 'waves' of distinct myeloid cell subsets that load differentially and sequentially with this CTC-derived material. Many of these tumour-ingesting myeloid cells collectively accumulated in the lung interstitium along with the successful metastatic cells and, as previously understood, promote the development of successful metastases from surviving tumour cells. Although the numbers of these cells rise globally in the lung with metastatic exposure and ingesting myeloid cells undergo phenotypic changes associated with microparticle ingestion, a consistently sparse population of resident conventional dendritic cells, among the last cells to interact with CTCs, confer anti-metastatic protection. This work reveals that CTC fragmentation generates immune-interacting intermediates, and defines a competitive relationship between phagocyte populations for tumour loading during metastatic cell seeding. PMID:26982733

  5. visual bone marrow mesenchymal stem cell transplantation in the repair of spinal cord injury

    Institute of Scientific and Technical Information of China (English)

    Rui-ping Zhang; Cheng Xu; Yin Liu; Jian-ding Li; Jun Xie

    2015-01-01

    An important factor in improving functional recovery from spinal cord injury using stem cells is maximizing the number of transplanted cells at the lesion site. Here, we established a contusion model of spinal cord injury by dropping a weight onto the spinal cord at T7–8. Superparamagnet-ic iron oxide-labeled bone marrow mesenchymal stem cells were transplanted into the injured spinal cordvia the subarachnoid space. An outer magnetic ifeld was used to successfully guide the labeled cells to the lesion site. Prussian blue staining showed that more bone marrow mesen-chymal stem cells reached the lesion site in these rats than in those without magnetic guidance or superparamagnetic iron oxide labeling, and immunolfuorescence revealed a greater number of complete axons at the lesion site. Moreover, the Basso, Beattie and Bresnahan (BBB) locomotor rating scale scores were the highest in rats with superparamagnetic labeling and magnetic guid-ance. Our data conifrm that superparamagnetic iron oxide nanoparticles effectively label bone marrow mesenchymal stem cells and impart sufficient magnetism to respond to the external magnetic ifeld guides. More importantly, superparamagnetic iron oxide-labeled bone marrow mesenchymal stem cells can be dynamically and non-invasively trackedin vivo using magnetic resonance imaging. Superparamagnetic iron oxide labeling of bone marrow mesenchymal stem cells coupled with magnetic guidance offers a promising avenue for the clinical treatment of spinal cord injury.

  6. Fabrication of gold nanodot arrays on a transparent substrate as a nanobioplatform for label-free visualization of living cells

    International Nuclear Information System (INIS)

    Two-dimensional gold (Au) nanodot arrays on a transparent substrate were fabricated for imaging of living cells. A nanoporous alumina mask with large-area coverage capability was prepared by a two-step chemical wet etching process after a second anodization. Highly ordered Au nanodot arrays were formed on indium-tin-oxide (ITO) glass using very thin nanoporous alumina of approximately 200 nm thickness as an evaporation mask. The large-area Au nanodot arrays on ITO glass were modified with RGD peptide (arginine; glycine; aspartic acid) containing a cysteine (Cys) residue and then used to immobilize human cancer HeLa cells, the morphology of which was observed by confocal microscopy. The confocal micrographs of living HeLa cells on Au nanodot arrays revealed enhanced contrast and resolution, which enabled discernment of cytoplasmic organelles more clearly. These results suggest that two-dimensional Au nanodot arrays modified with RGD peptide on ITO glass have potential as a biocompatible nanobioplatform for the label-free visualization and adhesion of living cells.

  7. Visualizing early splenic memory CD8+ T cells reactivation against intracellular bacteria in the mouse.

    Directory of Open Access Journals (Sweden)

    Marc Bajénoff

    Full Text Available Memory CD8(+ T cells represent an important effector arm of the immune response in maintaining long-lived protective immunity against viruses and some intracellular bacteria such as Listeria monocytogenes (L.m. Memory CD8(+ T cells are endowed with enhanced antimicrobial effector functions that perfectly tail them to rapidly eradicate invading pathogens. It is largely accepted that these functions are sufficient to explain how memory CD8(+ T cells can mediate rapid protection. However, it is important to point out that such improved functional features would be useless if memory cells were unable to rapidly find the pathogen loaded/infected cells within the infected organ. Growing evidences suggest that the anatomy of secondary lymphoid organs (SLOs fosters the cellular interactions required to initiate naive adaptive immune responses. However, very little is known on how the SLOs structures regulate memory immune responses. Using Listeria monocytogenes (L.m as a murine infection model and imaging techniques, we have investigated if and how the architecture of the spleen plays a role in the reactivation of memory CD8(+ T cells and the subsequent control of L.m growth. We observed that in the mouse, memory CD8(+ T cells start to control L.m burden 6 hours after the challenge infection. At this very early time point, L.m-specific and non-specific memory CD8(+ T cells localize in the splenic red pulp and form clusters around L.m infected cells while naïve CD8(+ T cells remain in the white pulp. Within these clusters that only last few hours, memory CD8(+ T produce inflammatory cytokines such as IFN-gamma and CCL3 nearby infected myeloid cells known to be crucial for L.m killing. Altogether, we describe how memory CD8(+ T cells trafficking properties and the splenic micro-anatomy conjugate to create a spatio-temporal window during which memory CD8(+ T cells provide a local response by secreting effector molecules around infected cells.

  8. Interactions of multiwalled carbon nanotubes with algal cells: quantification of association, visualization of uptake, and measurement of alterations in the composition of cells.

    Science.gov (United States)

    Rhiem, Stefan; Riding, Matthew J; Baumgartner, Werner; Martin, Francis L; Semple, Kirk T; Jones, Kevin C; Schäffer, Andreas; Maes, Hanna M

    2015-01-01

    Carbon nanotubes (CNTs) are considered promising materials in nanotechnology. We quantified CNT accumulation by the alga Desmodesmus subspicatus. Cells were exposed to radiolabeled CNTs ((14)C-CNTs;1 mg/L) to determine uptake and association, as well as elimination and dissociation in clear media.Attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR) was used to detect effects of CNTs on algae. CNT-cell interactions were visualized by electron microscopy and related to alterations in their cell composition. A concentration factor of 5000 L/kg dry weight was calculated. Most of the material agglomerated around the cells, but single tubes were detected in the cytoplasm. Computational analyses of the ATR-FTIR data showed that CNT treated algae differed from controls at all sampling times.CNT exposure changed the biochemical composition of cells. The fact that CNTs are bioavailable for algae and that they influence the cell composition is important with regard to environmental risk assessment of this nanomaterial. PMID:25467692

  9. Characterization of HPV16 L1 loop domains in the formation of a type-specific, conformational epitope

    Directory of Open Access Journals (Sweden)

    Schlegel Richard

    2004-07-01

    Full Text Available Abstract Background Virus-like particles (VLPs formed by the human papillomavirus (HPV L1 capsid protein are currently being tested in clinical trials as prophylactic vaccines against genital warts and cervical cancer. The efficacy of these vaccines is critically dependent upon L1 type-specific conformational epitopes. To investigate the molecular determinants of the HPV16 L1 conformational epitope recognized by monoclonal antibody 16A, we utilized a domain-swapping approach to generate a series of L1 proteins composed of a canine oral papillomavirus (COPV L1 backbone containing different regions of HPV16 L1. Results Gross domain swaps, which did not alter the ability of L1 to assemble into VLPs, demonstrated that the L1 N-terminus encodes at least a component of the 16A antigenic determinant. Finer epitope mapping, using GST-L1 fusion proteins, mapped the 16A epitope to the L1 variable regions I and possibly II within the N-terminus. Conclusions These results suggest that non-contiguous loop regions of L1 display critical components of a type-specific, conformational epitope.

  10. VISUALIZATION OF LIP AND BASAL-CELL SKIN CANCER IN HIGH-FREQUENCY ELECTRICAL FIELD

    OpenAIRE

    Zabunyan G. A.; Ovsiyenko P. G.

    2015-01-01

    In patients, there has been registered luminescence of skin sites affected by basal cell skin cancer at stage III in high-frequency electric field. The diagnosis was confirmed by histological analysis of excised cancer sites

  11. Fluorescent Lipids: Functional Parts of Fusogenic Liposomes and Tools for Cell Membrane Labeling and Visualization

    OpenAIRE

    Christian Kleusch; Bernd Hoffmann; Nils Hersch; Agnes Csiszár; Rudolf Merkel

    2012-01-01

    In this paper a rapid and highly efficient method for controlled incorporation of fluorescent lipids into living mammalian cells is introduced. Here, the fluorescent molecules have two consecutive functions: First, they trigger rapid membrane fusion between cellular plasma membranes and the lipid bilayers of their carrier particles, so called fusogenic liposomes, and second, after insertion into cellular membranes these molecules enable fluorescence imaging of cell membranes and membrane traf...

  12. Visualization and measurement of ATP levels in living cells replicating hepatitis C virus genome RNA.

    Directory of Open Access Journals (Sweden)

    Tomomi Ando

    Full Text Available Adenosine 5'-triphosphate (ATP is the primary energy currency of all living organisms and participates in a variety of cellular processes. Although ATP requirements during viral lifecycles have been examined in a number of studies, a method by which ATP production can be monitored in real-time, and by which ATP can be quantified in individual cells and subcellular compartments, is lacking, thereby hindering studies aimed at elucidating the precise mechanisms by which viral replication energized by ATP is controlled. In this study, we investigated the fluctuation and distribution of ATP in cells during RNA replication of the hepatitis C virus (HCV, a member of the Flaviviridae family. We demonstrated that cells involved in viral RNA replication actively consumed ATP, thereby reducing cytoplasmic ATP levels. Subsequently, a method to measure ATP levels at putative subcellular sites of HCV RNA replication in living cells was developed by introducing a recently-established Förster resonance energy transfer (FRET-based ATP indicator, called ATeam, into the NS5A coding region of the HCV replicon. Using this method, we were able to observe the formation of ATP-enriched dot-like structures, which co-localize with non-structural viral proteins, within the cytoplasm of HCV-replicating cells but not in non-replicating cells. The obtained FRET signals allowed us to estimate ATP concentrations within HCV replicating cells as ∼5 mM at possible replicating sites and ∼1 mM at peripheral sites that did not appear to be involved in HCV replication. In contrast, cytoplasmic ATP levels in non-replicating Huh-7 cells were estimated as ∼2 mM. To our knowledge, this is the first study to demonstrate changes in ATP concentration within cells during replication of the HCV genome and increased ATP levels at distinct sites within replicating cells. ATeam may be a powerful tool for the study of energy metabolism during replication of the viral genome.

  13. Visualization of the gas flow in fuel cell bipolar plates using molecular flow seeding and micro-particle image velocimetry

    Energy Technology Data Exchange (ETDEWEB)

    Hecht, Christian; Wlokas, Irenaeus; Schulz, Christof [University of Duisburg-Essen, IVG and CeNIDE, Duisburg (Germany); Schoot, Nadine van der; Lindken, Ralph [Center for Fuel Cell Technology ZBT GmbH, Duisburg (Germany); Kronemayer, Helmut [University of Duisburg-Essen, IVG and CeNIDE, Duisburg (Germany); BASF SE, Ludwigshafen (Germany)

    2012-03-15

    Main components of proton exchange membrane fuel cells are bipolar plates that electrically connect the electrodes and provide a gas flow to the membrane. We investigate the flow in the channel structures of bipolar plates. Flow seeding is used to visualize the propagating and mixing gas stream. It is shown that a part of the gas is transported perpendicularly to the channel structure. An analysis of the diffusion compared with the convection shows different transport behavior for both flow directions. Additionally, the convective flow field is investigated in detail near the channel wall using Micro-PIV in a Reynolds-number-scaled liquid fluid system. For a more exact comparison of the experimental setups, flow seeding in both gas and liquid systems is performed. (orig.)

  14. A water framework directive (WFD) compliant determination of eologically acceptable flows in alpine rivers - a river type specific approach

    Science.gov (United States)

    Jäger, Paul; Zitek, Andreas

    2010-05-01

    Currently the EU-Water Framework Directive (WFD) represents the driving force behind the assessment for rehabilitation and conservation of aquatic resources throughout Europe. Hydropower production, often considered as "green energy", in the past has put significant pressures on river systems like fragmentation by weirs, impoundment, hydropeaking and water abstraction. Due to the limited availability of data for determining ecologically acceptable flow for rivers at water abstraction sites, a special monitoring program was conducted in the federal state of Salzburg in Austria from 2006 to 2009. Water abstraction sites at 19 hydropower plants, mostly within the trout region of the River Salzach catchment, were assessed in detail with regard to the effect of water abstraction on fish and macrozoobenthos. Based on a detailed assessment of the specific local hydro-morphological and biological situations, the validity of natural low flow criteria (Absolute Minimum Flow - AMF, the lowest daily average flow ever measured and Mean Annual Daily Low Flow - MADLF) as starting points for the determination of an ecologically acceptable flow was tested. It was assessed, if a good ecological status in accordance with the EU-WFD can be maintained at natural AMF. Additionally it was tested, if important habitat parameters describing connectivity, river type specific flow variability and river type specific habitats are maintained at this discharge. Habitat modelling was applied in some situations. Hydraulic results showed that at AMF the highest flow velocity classes were lost in most situations. When AMF was significantly undercut, flow velocities between 0,0 - 0,4 m/s became dominant, describing the loss of the river type specific flow character, leading to a loss of river type specific flow variability and habitats and increased sedimentation of fines. Furthermore limits for parameters describing connectivity for fish like maximum depth at the pessimum profile and minimum flow

  15. NADPH-diaphorase activity in area 17 of the squirrel monkey visual cortex: neuropil pattern, cell morphology and laminar distribution

    Directory of Open Access Journals (Sweden)

    Franca J.G.

    1997-01-01

    Full Text Available We studied the distribution of NADPH-diaphorase activity in the visual cortex of normal adult New World monkeys (Saimiri sciureus using the malic enzyme "indirect" method. NADPH-diaphorase neuropil activity had a heterogeneous distribution. In coronal sections, it had a clear laminar pattern that was coincident with Nissl-stained layers. In tangential sections, we observed blobs in supragranular layers of V1 and stripes throughout the entire V2. We quantified and compared the tangential distribution of NADPH-diaphorase and cytochrome oxidase blobs in adjacent sections of the supragranular layers of V1. Although their spatial distributions were rather similar, the two enzymes did not always overlap. The histochemical reaction also revealed two different types of stained cells: a slightly stained subpopulation and a subgroup of deeply stained neurons resembling a Golgi impregnation. These neurons were sparsely spined non-pyramidal cells. Their dendritic arbors were very well stained but their axons were not always evident. In the gray matter, heavily stained neurons showed different dendritic arbor morphologies. However, most of the strongly reactive cells lay in the subjacent white matter, where they presented a more homogenous morphology. Our results demonstrate that the pattern of NADPH-diaphorase activity is similar to that previously described in Old World monkeys

  16. Iron labeling and pre-clinical MRI visualization of therapeutic human neural stem cells in a murine glioma model.

    Directory of Open Access Journals (Sweden)

    Mya S Thu

    Full Text Available BACKGROUND: Treatment strategies for the highly invasive brain tumor, glioblastoma multiforme, require that cells which have invaded into the surrounding brain be specifically targeted. The inherent tumor-tropism of neural stem cells (NSCs to primary and invasive tumor foci can be exploited to deliver therapeutics to invasive brain tumor cells in humans. Use of the strategy of converting prodrug to drug via therapeutic transgenes delivered by immortalized therapeutic NSC lines have shown efficacy in animal models. Thus therapeutic NSCs are being proposed for use in human brain tumor clinical trials. In the context of NSC-based therapies, MRI can be used both to non-invasively follow dynamic spatio-temporal patterns of the NSC tumor targeting allowing for the optimization of treatment strategies and to assess efficacy of the therapy. Iron-labeling of cells allows their presence to be visualized and tracked by MRI. Thus we aimed to iron-label therapeutic NSCs without affecting their cellular physiology using a method likely to gain United States Federal Drug Administration (FDA approval. METHODOLOGY: For human use, the characteristics of therapeutic Neural Stem Cells must be clearly defined with any pertubation to the cell including iron labeling requiring reanalysis of cellular physiology. Here, we studied the effect of iron-loading of the therapeutic NSCs, with ferumoxide-protamine sulfate complex (FE-Pro on viability, proliferation, migratory properties and transgene expression, when compared to non-labeled cells. FE-Pro labeled NSCs were imaged by MRI at tumor sites, after intracranial administration into the hemisphere contralateral to the tumor, in an orthotopic human glioma xenograft mouse model. CONCLUSION: FE-Pro labeled NSCs retain their proliferative status, tumor tropism, and maintain stem cell character, while allowing in vivo cellular MRI tracking at 7 Tesla, to monitor their real-time migration and distribution at brain tumor sites

  17. Visualization of the chromosome scaffold and intermediates of loop domain compaction in extracted mitotic cells.

    Science.gov (United States)

    Sheval, Eugene V; Polyakov, Vladimir Y

    2006-12-01

    A novel extraction protocol for cells cultured on coverslips is described. Observations of the extraction process in a perfusion chamber reveal that cells of all mitotic stages are not detached from coverslips during extraction, and all stages can be recognized using phase contrast images. We studied the extracted cell morphology and distribution of a major scaffold component - topoisomerase IIalpha, in extracted metaphase and anaphase cells. An extraction using 2M NaCl leads to destruction of chromosomes at the light microscope level. Immunogold studies demonstrate that the only residual structure observed is an axial chromosome scaffold that contains topoisomerase IIalpha. In contrast, mitotic chromosomes are swelled only partially after an extraction using dextran sulphate and heparin, and it appears that this treatment does not lead to total destruction of loop domains. In this case, the chromosome scaffold and numerous structures resembling small rosettes are revealed inside extracted cells. The rosettes observed condense after addition of Mg2+-ions and do not contain topoisomerase IIalpha suggesting that these structures correspond to intermediates of loop domain compaction. We propose a model of chromosome structure in which the loop domains are condensed into highly regular structures with rosette organization. PMID:17029868

  18. Fluorescent Lipids: Functional Parts of Fusogenic Liposomes and Tools for Cell Membrane Labeling and Visualization

    Directory of Open Access Journals (Sweden)

    Christian Kleusch

    2012-01-01

    Full Text Available In this paper a rapid and highly efficient method for controlled incorporation of fluorescent lipids into living mammalian cells is introduced. Here, the fluorescent molecules have two consecutive functions: First, they trigger rapid membrane fusion between cellular plasma membranes and the lipid bilayers of their carrier particles, so called fusogenic liposomes, and second, after insertion into cellular membranes these molecules enable fluorescence imaging of cell membranes and membrane traffic processes. We tested the fluorescent derivatives of the following essential membrane lipids for membrane fusion: Ceramide, sphingomyelin, phosphocholine, phosphatidylinositol-bisphosphate, ganglioside, cholesterol, and cholesteryl ester. Our results show that all probed lipids could more efficiently be incorporated into the plasma membrane of living cells than by using other methods. Moreover, labeling occurred in a gentle manner under classical cell culture conditions reducing cellular stress responses. Staining procedures were monitored by fluorescence microscopy and it was observed that sphingolipids and cholesterol containing free hydroxyl groups exhibit a decreased distribution velocity as well as a longer persistence in the plasma membrane compared to lipids without hydroxyl groups like phospholipids or other artificial lipid analogs. After membrane staining, the fluorescent molecules were sorted into membranes of cell organelles according to their chemical properties and biological functions without any influence of the delivery system.

  19. Real-time visualization of prion transport in single live cells using quantum dots

    International Nuclear Information System (INIS)

    Prion diseases are fatal neurodegenerative disorders resulting from structural conversion of the cellular isoform of PrPC to the infectious scrapie isoform PrPSc. It is believed that such structural alteration may occur within the internalization pathway. However, there is no direct evidence to support this hypothesis. Employing quantum dots (QDs) as a probe, we have recorded a real-time movie demonstrating the process of prion internalization in a living cell for the first time. The entire internalization process can be divided into four discrete but connected stages. In addition, using methyl-beta-cyclodextrin to disrupt cell membrane cholesterol, we show that lipid rafts play an important role in locating cellular PrPC to the cell membrane and in initiating PrPC endocytosis.

  20. Visualization of Water Accumulation Process in Polymer Electrolyte Fuel Cell Using Neutron Radiography

    Science.gov (United States)

    Murakawa, Hideki; Sugimoto, Katsumi; Kitamura, Nobuki; Sawada, Masataka; Asano, Hitoshi; Takenaka, Nobuyuki; Saito, Yasushi

    In order to clarify the water-accumulation phenomena in an operating polymer electrolyte fuel cell (PEFC), the water distribution in a small fuel cell was measured in the through-plane direction by using neutron radiography. The fuel cell had nine parallel channels for classifying the water-accumulation process in the gas diffusion layer (GDL) under the lands and channels. The experimental results were compared with numerical results. The water accumulation in the GDL under the lands was larger than that under the channels during the period of early PEFC operation. The difference of the water accumulation in the GDL under the land and channel was related to the water vapor. Because of the land, the vapor fraction in the GDL under the land was also higher than that under the channel. As a result, condensation was easy to occur in the GDL under the land.

  1. Real-time visualization of prion transport in single live cells using quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Kan [State Key Laboratory of Virology and Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072 (China); Li, Shu [AIDS Research Centre, Institute of Pathogen Biology, Chinese Academy of Medical Science, Beijing 100730 (China); Xie, Min [College of Chemistry and Molecular Science, Wuhan University, Wuhan 430072 (China); Wu, Di; Wang, WenXi; Chen, Rui; Huang, Liqin; Huang, Tao [State Key Laboratory of Virology and Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072 (China); Pang, Daiwen, E-mail: dwpang@whu.edu.cn [College of Chemistry and Molecular Science, Wuhan University, Wuhan 430072 (China); Xiao, Gengfu, E-mail: xiaogf@wh.iov.cn [State Key Laboratory of Virology and Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072 (China); Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071 (China)

    2010-04-09

    Prion diseases are fatal neurodegenerative disorders resulting from structural conversion of the cellular isoform of PrP{sup C} to the infectious scrapie isoform PrP{sup Sc}. It is believed that such structural alteration may occur within the internalization pathway. However, there is no direct evidence to support this hypothesis. Employing quantum dots (QDs) as a probe, we have recorded a real-time movie demonstrating the process of prion internalization in a living cell for the first time. The entire internalization process can be divided into four discrete but connected stages. In addition, using methyl-beta-cyclodextrin to disrupt cell membrane cholesterol, we show that lipid rafts play an important role in locating cellular PrP{sup C} to the cell membrane and in initiating PrP{sup C} endocytosis.

  2. VISUALIZATION OF DYNAMIC ORGANIZATION OF CYTOSKELETON GELS IN LIVING CELLS BY HYBRID-SPM

    Institute of Scientific and Technical Information of China (English)

    K.Kawabata; Y.Sado; M.Nagayama; T.Nitta; K.Nemoto; Y.Koyama; H.Haga

    2003-01-01

    We succeeded in performing of hybrid Scanning Probe Microscopy (hybrid-SPM) in which mechanical-SPM and fluorescence microscopy are combined. This technique is able to measure simultaneously mechanical properties and distribution of cytoskeletons of living cells by using green fluorescent protein. We measured evolution of both local elasticity and distributions of actin stress fibers in an identical fibroblast living in physiological conditions. The SPM experiments revealed that stiffer lines develop in living cells, which correspond to actin stress fibers. The elasticity of the actin stress fibers is as high as 100 kPa. We discuss mechanical effects on the development of actin filament networks.

  3. Cllmodulin in tip-growing plant cells, visualized by fluorescing calmodulin-binding phenothiazines.

    Science.gov (United States)

    Haußer, I; Herth, W; Reiss, H D

    1984-09-01

    Calmodulin (CaM) was visualized light-microscopically by the fluorescent CaM inhibitors fluphenazine and chlorpromazine, both phenothiazines, during polar tip growth of pollen tubes of Lilium longiflorum, root hairs of Lepidium sativum, moss caulonema of Funaria hygrometrica, fungal hyphae of Achlya spec. and in the alga Acetabularia mediterranea, as well as during multipolar tip growth in Micrasterias denticulata. Young pollen tubes and root hairs showed tip fluorescence; at later stages and in the growing parts of the other subjects the fluorescence was almost uniform. After treatment with cytochalasin B, punctuate fluorescence occurred in the clear zone adjacent to the tip of pollen tubes. The observations indicate that there is CaM in all our tested systems detectable with this method. It may play a key role in starting polar growth. As in pollen tubes, CaM might be in part associated with the microfilament network at the tip, and thus regulate vesicle transport and cytoplasmic streaming. PMID:24253945

  4. IDENTIFICATION OF THE MINUS MATING-TYPE SPECIFIC GENE MTD1 FROM GONIUM PECTORALE (VOLVOCALES, CHLOROPHYTA)(1).

    Science.gov (United States)

    Hamaji, Takashi; Ferris, Patrick J; Nishii, Ichiro; Nozaki, Hisayoshi

    2009-12-01

    Gonium pectorale O. F. Müll. (Volvocales, Chlorophyta), a colonial 8- or 16-cellular alga, is phylogenetically important as an intermediate form between isogametic unicellular Chlamydomonas and oogamous Volvox. We identified the mating-type specific gene GpMTD1, from G. pectorale, the first homologue of Chlamydomonas reinhardtii MTD1 (CrMTD1). The GpMTD1 gene was found to be present only in the minus mating-type locus and was expressed specifically in the gametic phase as is the case for CrMTD1, suggested to participate in development of the minus gametes. This gene is useful as a probe in analyzing the bacterial artificial chromosome (BAC) library for resolving genomic structures of the mating-type loci in isogamous and oogamous colonial volvocaleans. PMID:27032588

  5. Fluorescent Probes for Nucleic Acid Visualization in Fixed and Live Cells

    Directory of Open Access Journals (Sweden)

    Alexandre S. Boutorine

    2013-12-01

    Full Text Available This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i sequence-specific peptides and proteins; (ii triplex-forming oligonucleotides and (iii polyamide oligo(N-methylpyrrole/N-methylimidazole minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.

  6. Visualizing the molecular sociology at the HeLa cell nuclear periphery

    NARCIS (Netherlands)

    Mahamid, Julia; Pfeffer, Stefan; Schaffer, Miroslava; Villa, Elizabeth; Danev, Radostin; Cuellar, Luis Kuhn; Förster, Friedrich; Hyman, Anthony A; Plitzko, Jürgen M; Baumeister, Wolfgang

    2016-01-01

    The molecular organization of eukaryotic nuclear volumes remains largely unexplored. Here we combined recent developments in cryo-electron tomography (cryo-ET) to produce three-dimensional snapshots of the HeLa cell nuclear periphery. Subtomogram averaging and classification of ribosomes revealed th

  7. Visualizing pancreatic {beta}-cell mass with [{sup 11}C]DTBZ

    Energy Technology Data Exchange (ETDEWEB)

    Simpson, Norman Ray [Department of Radiology, Columbia University Medical School, New York, NY 10032 (United States); Souza, Fabiola [Department of Surgery, Columbia University Medical School, New York, NY 10032 (United States); Witkowski, Piotr [Department of Medicine, Columbia University Medical School, New York, NY 10032 (United States); Maffei, Antonella [Institute of Genetics and Biophysics ' Adriano Buzzati-Traverso' , CNR, Naples 80131 (Italy); Raffo, Anthony [Department of Surgery, Columbia University Medical School, New York, NY 10032 (United States); Herron, Alan [Center for Comparative Medicine and The Department of Pathology, Baylor College of Medicine, Houston, TX 77030 (United States); Kilbourn, Michael [Department of Radiology, University of Michigan, Ann Arbor, MI 48109-0638 (United States); Jurewicz, Agata [Department of Radiology, Columbia University Medical School, New York, NY 10032 (United States); Herold, Kevan [Department of Surgery, Columbia University Medical School, New York, NY 10032 (United States); Liu, Eric [Diabetes Branch, NIDDK, National Institutes of Health, Bethesda, MD 20854 (United States); Hardy, Mark Adam [Department of Medicine, Columbia University Medical School, New York, NY 10032 (United States); Van Heertum, Ronald [Department of Radiology, Columbia University Medical School, New York, NY 10032 (United States); Harris, Paul Emerson [Department of Surgery, Columbia University Medical School, New York, NY 10032 (United States)]. E-mail: peh1@columbia.edu

    2006-10-15

    {beta}-Cell mass (BCM) influences the total amount of insulin secreted, varies by individual and by the degree of insulin resistance, and is affected by physiologic and pathologic conditions. The islets of Langerhans, however, appear to have a reserve capacity of insulin secretion and, overall, assessments of insulin and blood glucose levels remain poor measures of BCM, {beta}-cell function and progression of diabetes. Thus, novel noninvasive determinations of BCM are needed to provide a quantitative endpoint for novel therapies of diabetes, islet regeneration and transplantation. Built on previous gene expression studies, we tested the hypothesis that the targeting of vesicular monoamine transporter 2 (VMAT2), which is expressed by {beta} cells, with [{sup 11}C]dihydrotetrabenazine ([{sup 11}C]DTBZ), a radioligand specific for VMAT2, and the use of positron emission tomography (PET) can provide a measure of BCM. In this report, we demonstrate decreased radioligand uptake within the pancreas of Lewis rats with streptozotocin-induced diabetes relative to their euglycemic historical controls. These studies suggest that quantitation of VMAT2 expression in {beta} cells with the use of [{sup 11}C]DTBZ and PET represents a method for noninvasive longitudinal estimates of changes in BCM that may be useful in the study and treatment of diabetes.

  8. Visualizing Single Cell Biology: Nanosims Studies of Carbon and Nitrogen Metabolism in Diazotrophic Cyanobacteria

    Science.gov (United States)

    Pett-Ridge, J.; Finzi, J. A.; Capone, D. G.; Popa, R.; Nealson, K. H.; Ng, W.; Spormann, A. M.; Hutcheon, I. D.; Weber, P. K.

    2007-12-01

    Filamentous nitrogen fixing (diazotrophic) cyanobacteria are key players in global nutrient cycling, but the relationship between CO2- and N2-fixation and intercellular exchange of these elements remains poorly understood in many genera. These bacteria are faced with the challenge of isolating regions of N-fixation (O2 inhibited) and photosynthetic (O2 producing) activity. We used isotope labeling in conjunction with a high-resolution isotope and elemental mapping technique (NanoSIMS) to quantitatively describe 13C and 15N uptake and transport in two aquatic cyanobacteria grown on NaH13CO3 and 15N2. The technical challenges of tracing isotopes within individual bacteria can be overcome with high resolution Secondary Ion Mass Spectrometry (NanoSIMS). In NanoSIMS analysis, samples are sputtered with an energetic primary beam (Cs+, O-) liberating secondary ions that are separated by the mass spectrometer and detected in a suite of electron multipliers. Five isotopic species may be analyzed concurrently with spatial resolution as fine as 50nm. A high sensitivity isotope ratio 'map' can then be generated for the analyzed area. Using sequentially harvested cyanobacteria in conjunction with enriched H13CO3 and 15N2 incubations, we measured temporal enrichment patterns that evolve over the course of a day's growth and suggest tightly regulated changes in fixation kinetics. With a combination of TEM, SEM and NanoSIMS analyses, we also mapped the distribution of C, N and Mo (a critical nitrogenase co-factor) isotopes in intact cells. Our results suggest that NanoSIMS mapping of metal enzyme co-factors may be a powerful method of identifying physiological and morphological characteristics within individual bacterial cells, and could be used to provide a 3-dimensional context for more traditional analyses such as immunogold labeling. Finally, we resolved patterns of isotope enrichment at multiple spatial scales: sub-cellular variation, cell-cell differences along filaments

  9. Visualization of Fuel Cell Water Transport and Performance Characterization under Freezing Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Kandlikar, Satish G. [Rochester Inst. of Technology, Rochester, NY (United States); Lu, Zijie [Rochester Inst. of Technology, Rochester, NY (United States); Rao, Navalgund [Rochester Inst. of Technology, Rochester, NY (United States); Sergi, Jacqueline [Rochester Inst. of Technology, Rochester, NY (United States); Rath, Cody [Rochester Inst. of Technology, Rochester, NY (United States); McDade, Christopher [Rochester Inst. of Technology, Rochester, NY (United States); Trabold, Thomas [General Motors, Honeoye Falls, NY (United States); Owejan, Jon [General Motors, Honeoye Falls, NY (United States); Gagliardo, Jeffrey [General Motors, Honeoye Falls, NY (United States); Allen, Jeffrey [Michigan Technological Univ., Houghton, MI (United States); Yassar, Reza S. [Michigan Technological Univ., Houghton, MI (United States); Medici, Ezequiel [Michigan Technological Univ., Houghton, MI (United States); Herescu, Alexandru [Michigan Technological Univ., Houghton, MI (United States)

    2010-05-30

    In this program, Rochester Institute of Technology (RIT), General Motors (GM) and Michigan Technological University (MTU) have focused on fundamental studies that address water transport, accumulation and mitigation processes in the gas diffusion layer and flow field channels of the bipolar plate. These studies have been conducted with a particular emphasis on understanding the key transport phenomena which control fuel cell operation under freezing conditions.

  10. Kinetics of linear rouleaux formation studied by visual monitoring of red cell dynamic organization.

    OpenAIRE

    Barshtein, G; Wajnblum, D; Yedgar, S

    2000-01-01

    Red blood cells (RBCs) in the presence of plasma proteins or other macromolecules may form aggregates, normally in rouleaux formations, which are dispersed with increasing blood flow. Experimental observations have suggested that the spontaneous aggregation process involves the formation of linear rouleaux (FLR) followed by formation of branched rouleaux networks. Theoretical models for the spontaneous rouleaux formation were formulated, taking into consideration that FLR may involve both "po...

  11. Dynamic visualization of dendritic cell-antigen interactions in the skin following transcutaneous immunization.

    Directory of Open Access Journals (Sweden)

    Teerawan Rattanapak

    Full Text Available Delivery of vaccines into the skin provides many advantages over traditional parenteral vaccination and is a promising approach due to the abundance of antigen presenting cells (APC residing in the skin including Langerhans cells (LC and dermal dendritic cells (DDC. However, the main obstacle for transcutaneous immunization (TCI is the effective delivery of the vaccine through the stratum corneum (SC barrier to the APC in the deeper skin layers. This study therefore utilized microneedles (MN and a lipid-based colloidal delivery system (cubosomes as a synergistic approach for the delivery of vaccines to APC in the skin. The process of vaccine uptake and recruitment by specific types of skin APC was investigated in real-time over 4 hours in B6.Cg-Tg (Itgax-EYFP 1 Mnz/J mice by two-photon microscopy. Incorporation of the vaccine into a particulate delivery system and the use of MN preferentially increased vaccine antigen uptake by a highly motile subpopulation of skin APC known as CD207⁺ DC. No uptake of antigen or any response to immunisation by LC could be detected.

  12. Organelle interactions and possible degradation pathways visualized in high-pressure frozen algal cells.

    Science.gov (United States)

    Aichinger, N; Lütz-Meindl, U

    2005-08-01

    Summary Organelle interactions, although essential for both anabolic and catabolic pathways in plant cells have not been examined in detail so far. In the present study the structure of different organelle-organelle, organelle-vesicle and organelle-membrane interactions were investigated in growing and nongrowing cells of the green alga Micrasterias denticulata by use of high pressure freeze fixation and energy filtering transmission electron microscopy. It became clear that contacts between mitochondria always occur by formation of a cone-shaped protuberance of one of the mitochondria which penetrates into its fusion partner. In the same way, structural interactions between mitochondria and mucilage vesicles and between microbodies and mucilage vesicles are achieved. Lytic compartments contact mitochondria or mucilage vesicles again by forming protuberances and by extending their contents into the respective compartment. Detached portions of mitochondria are found inside lytic compartments as a consequence of such interactions. Mitochondria found in contact with the plasma membrane reveal structural disintegration. Our study shows that interactions of organelles and vesicles are frequent events in Micrasterias cells of different ages. The interactive contacts between lytic compartments and organelles or vesicles suggest a degradation pathway different from autophagy processes described in the literature. Both the interactions between vesicles and organelles and the degradation pathways occur independently from cytoskeleton function as demonstrated by use of cytochalasin D and the microtubule inhibitor amiprophos-methyl. PMID:16159344

  13. FLIM-FRET microscopy to visualize transcription factor interactions in the nucleus of the living cell

    Science.gov (United States)

    Day, Richard N.; Demarco, Ignacio A.; Voss, Ty C.; Chen, Ye; Periasamy, Ammasi

    2004-06-01

    Wide-field fluorescence microscopy was used to monitor the co-localization of the homeodomain (HD) transcription factor Pit-1 and the basic-leucine zipper protein CCAAT/enhancer binding protein alpha (C/EBPa), each labeled with fluorescent proteins (FP) in the living cell nucleus. Fluorescence resonance energy transfer (FRET) microscopy was used to resolve the angstrom-scale spatial relationships of these expressed proteins, and the effect of a Pit-1 point mutation on the interaction with C/EBPa was characterized. Two-photon excitation fluorescence lifetime imaging microscopy (2p-FLIM) was then used as an independent method to detect these protein interactions. The excited-state lifetime for the cyan FP (CFP) labeling C/EBPa was determined, and the measurements were repeated in cells co-expressing yellow FP (YFP) labeled-proteins. The CFP lifetime was decreased in the presence of the YFP acceptor, which is consistent with donor quenching by FRET. This was verified by acceptor photobleaching, which caused a shift in the donor lifetime to that similar to the donor alone. However, a significant limitation of this technique was demonstrated by the observation that high-energy 2p-excitation resulted in CFP photobleaching and a parallel decrease in its excited-state lifetime. The key question is whether the sensitivity of this imaging approach will be sufficient to acquire significant data from living cells expressing physiological levels of the labeled proteins.

  14. On the chemical identification and visualization of uranium species in biofilms and Euglena mutabilis cells

    International Nuclear Information System (INIS)

    For risk assessment of anthropogenic uranium contaminations in the environment a detailed knowledge of the migration and immobilization behavior is required to prevent health hazards for humans and animals caused by an uncontrolled discharge of uranium. Hence, comprehensive studies on the interactions of uranium with the environment are required. Besides the influences of the geological materials, there is a huge effect of the biosphere, especially the interactions with microorganisms and biofilms, on the properties of uranium in the environment. The aim of this study was to investigate and to describe naturally occurring biofilms from real uranium contaminated areas and their influence on the uranium migration. The investigations in this study on the localization and the speciation of the uranium in the biosystems were primarily done with a coupled system of laser scanning microscopy (CLSM) and laser induced fluorescence spectroscopy (LIFS). Natural biofilms collected from two uranium contaminated acid mine drainage (AMD) environments, the former uranium mine in Koenigstein (Saxony, Germany) and the former Gessenheap near Ronneburg (Thuringia,Germany), were investigated in this study. The chosen samples represent typical biofilm communities living in AMD water and are exemplary for potentially occurring scenarios of contaminated mining water both in the underground and on the surface. The investigation on the interactions between uranium and Euglena mutabilis, which is a typical unicellular microorganism that can be found in acidic, uranium and other heavy metal containing waters, was another important part of this study. Bioaccumulation experiments of uranium on living Euglena mutabilis cells depending on the pH (pH 3 - 6) and on the background media in sodium perchlorate (9 g/l) or sodium sulfate (3.48 g/l) solution containing 0.01 mM uranium show an effective immobilization of uranium. At the acidic pH-values (pH 3 - 4) over 90 % of the added uranium was

  15. A TP-FRET-based two-photon fluorescent probe for ratiometric visualization of endogenous sulfur dioxide derivatives in mitochondria of living cells and tissues.

    Science.gov (United States)

    Yang, Xiaoguang; Zhou, Yibo; Zhang, Xiufang; Yang, Sheng; Chen, Yun; Guo, Jingru; Li, Xiaoxuan; Qing, Zhihe; Yang, Ronghua

    2016-08-11

    A ratiometric two-photon fluorescent probe for SO2 derivatives was first proposed based on acedan-merocyanine dyads via a TP-FRET strategy. It was successfully applied to visualization of the fluctuations of enzymatically generated SO2 derivatives in the mitochondria of HepG2 cells and rat liver tissues using two-photon fluorescence microscopy imaging. PMID:27469474

  16. Neuron analysis of visual perception

    Science.gov (United States)

    Chow, K. L.

    1980-01-01

    The receptive fields of single cells in the visual system of cat and squirrel monkey were studied investigating the vestibular input affecting the cells, and the cell's responses during visual discrimination learning process. The receptive field characteristics of the rabbit visual system, its normal development, its abnormal development following visual deprivation, and on the structural and functional re-organization of the visual system following neo-natal and prenatal surgery were also studied. The results of each individual part of each investigation are detailed.

  17. Visual agnosia.

    Science.gov (United States)

    Álvarez, R; Masjuan, J

    2016-03-01

    Visual agnosia is defined as an impairment of object recognition, in the absence of visual acuity or cognitive dysfunction that would explain this impairment. This condition is caused by lesions in the visual association cortex, sparing primary visual cortex. There are 2 main pathways that process visual information: the ventral stream, tasked with object recognition, and the dorsal stream, in charge of locating objects in space. Visual agnosia can therefore be divided into 2 major groups depending on which of the two streams is damaged. The aim of this article is to conduct a narrative review of the various visual agnosia syndromes, including recent developments in a number of these syndromes. PMID:26358494

  18. The acceptability of the introduction of a type specific herpes antibody screening test into a genitourinary medicine clinic in the United Kingdom

    OpenAIRE

    Mullan, H; Munday, P.

    2003-01-01

    Objective: To determine the uptake of a type specific herpes simplex antibody test if it were offered as part of routine screening in a genitourinary medicine clinic in a district general hospital in the United Kingdom.

  19. Visualization and quantification of archaeal and bacterial metabolically active cells in soil using fluorescence in situ hybridization method

    Science.gov (United States)

    Semenov, Mikhail; Manucharova, Natalia; Stepanov, Alexey

    2015-04-01

    The method of in situ hybridization using fluorescent labeled 16S rRNA-targeted oligonucleotide probes (FISH - fluorescence in situ hybridization) combines identification and quantification of groups of microorganisms at different phylogenetic levels, from domain to species. The FISH method enables to study the soil microbial community in situ, avoiding plating on nutrient media, and allows to identify and quantify living, metabolically active cells of Bacteria and Archaea. The full procedure consists of the following steps: desorption of the cells from the soil particles, fixation of cells, coating a fixed sample on the glass slide, hybridization with the specific probes and, finally, microscopic observation and cell counting. For the FISH analysis of Bacteria and Archaea, the paraformaldehyde-fixed samples were hybridized with Cy3-labeled Archaea-specific probe(Arc915) and 6-carboxyfluorescein (FAM)-labeled Bacteria-specific probe(EUB338). When a molecular probe is incorporated into a cell, it can hybridize solely with a complementary rRNA sequence. The hybridization can be visualized under the fluorescent microscope and counted. The application of FISH will be demonstrated by the abundance of metabolically active cells of Archaea and Bacteria depending on soil properties, depth and land use. The research was carried out at field and natural ecosystems of European part of Russia. Samples were collected within the soil profiles (3-6 horizons) of Chernozem and Kastanozem with distinct land use. Quantification of metabolically active cells in virgin and arable Chernozem revealed that the abundance of Archaea in topsoil of virgin Chernozem was doubled as compared with arable soil, but it leveled off in the deeper horizons. Plowing of Chernozem decreased an amount of archaeal and bacterial active cells simultaneously, however, Bacteria were more resistant to agrogenic impact than Archaea. In Kastanozem, a significant change in the abundance of metabolically active

  20. Clustered Regularly Interspaced Short Palindromic Repeats Are emm Type-Specific in Highly Prevalent Group A Streptococci.

    Directory of Open Access Journals (Sweden)

    Po-Xing Zheng

    Full Text Available Clustered regularly interspaced short palindromic repeats (CRISPR are the bacterial adaptive immune system against foreign nucleic acids. Given the variable nature of CRISPR, it could be a good marker for molecular epidemiology. Group A streptococcus is one of the major human pathogens. It has two CRISPR loci, including CRISPR01 and CRISPR02. The aim of this study was to analyze the distribution of CRISPR-associated gene cassettes (cas and CRISPR arrays in highly prevalent emm types. The cas cassette and CRISPR array in two CRISPR loci were analyzed in a total of 332 strains, including emm1, emm3, emm4, emm12, and emm28 strains. The CRISPR type was defined by the spacer content of each CRISPR array. All strains had at least one cas cassette or CRISPR array. More than 90% of the spacers were found in one emm type, specifically. Comparing the consistency between emm and CRISPR types by Simpson's index of diversity and the adjusted Wallace coefficient, CRISPR01 type was concordant to emm type, and CRISPR02 showed unidirectional congruence to emm type, suggesting that at least for the majority of isolates causing infection in high income countries, the emm type can be inferred from CRISPR analysis, which can further discriminate isolates sharing the same emm type.

  1. Dynamics of bacterial communities in two unpolluted soils after spiking with phenanthrene: soil type specific and common responders

    Directory of Open Access Journals (Sweden)

    Guo-Chun eDing

    2012-08-01

    Full Text Available Considering their key role for ecosystem processes, it is important to understand the response of microbial communities in unpolluted soils to pollution with polycyclic aromatic hydrocarbons (PAH. Phenanthrene, a model compound for PAH, was spiked to a Cambisol and a Luvisol soil. Total community DNA from phenanthrene-spiked and control soils collected on days 0, 21 and 63 were analyzed based on PCR-amplified 16S rRNA genefragments. Denaturing gradient gel electrophoresis (DGGE fingerprints of bacterial communities increasingly deviated with time between spiked and control soils. In taxon specific DGGE, significant responses of Alphaproteobacteria and Actinobacteria became only detectable after 63 days, while significant effects on Betaproteobacteria were detectable in both soils after 21 days. Comparison of the taxonomic distribution of bacteria in spiked and control soils on day 63 as revealed by pyrosequencing indicated soil type specific negative effects of phenanthrene on several taxa, many of them belonging to the Gamma-, Beta- or Deltaproteobacteria. Bacterial richness and evenness decreased in spiked soils. Despite the significant differences in the bacterial community structure between both soils on day 0, similar genera increased in relative abundance after PAH spiking, especially Sphingomonas and Polaromonas. However, this did not result in an increased overall similarity of the bacterial communities in both soils.

  2. Comprehensive analysis of ultrasonic vocalizations in a mouse model of fragile X syndrome reveals limited, call type specific deficits.

    Directory of Open Access Journals (Sweden)

    Snigdha Roy

    Full Text Available Fragile X syndrome (FXS is a well-recognized form of inherited mental retardation, caused by a mutation in the fragile X mental retardation 1 (Fmr1 gene. The gene is located on the long arm of the X chromosome and encodes fragile X mental retardation protein (FMRP. Absence of FMRP in fragile X patients as well as in Fmr1 knockout (KO mice results, among other changes, in abnormal dendritic spine formation and altered synaptic plasticity in the neocortex and hippocampus. Clinical features of FXS include cognitive impairment, anxiety, abnormal social interaction, mental retardation, motor coordination and speech articulation deficits. Mouse pups generate ultrasonic vocalizations (USVs when isolated from their mothers. Whether those social ultrasonic vocalizations are deficient in mouse models of FXS is unknown. Here we compared isolation-induced USVs generated by pups of Fmr1-KO mice with those of their wild type (WT littermates. Though the total number of calls was not significantly different between genotypes, a detailed analysis of 10 different categories of calls revealed that loss of Fmr1 expression in mice causes limited and call-type specific deficits in ultrasonic vocalization: the carrier frequency of flat calls was higher, the percentage of downward calls was lower and that the frequency range of complex calls was wider in Fmr1-KO mice compared to their WT littermates.

  3. Visualization of transverse diffusion paths across fiber cells of the ocular lens by small animal MRI

    International Nuclear Information System (INIS)

    The sense of vision requires that light penetrate through the ocular lens. Experiments, performed and published by many research groups, have suggested that the lens, which has no blood vessels, relies on internally directed ion and water fluxes for its circulation, survival and transparency. We investigated the internal diffusive pathways of the lens in order to better understand the constraints that may be operating on directional lens fluxes. Small animal magnetic resonance imaging, including T2-weighted and diffusion tensor imaging, was used to measure tissue properties and diffusivity throughout cultured bovine lenses. A range of concentric regions of signal intensity was distinguished inside the lens, by both T2-weighted signal and mean diffusivity. Diffusivity mapping of the lens revealed novel anisotropic polar and equatorial zones of pronounced diffusivity directed transverse to the fiber cells. In contrast, an inner zone including the lens nucleus showed isotropic and weak diffusivity. Our results lend support to models of internally directed lens micro-circulation, by placing non-structural diffusive constraints on global patterns of fluid circulation

  4. Direct visualization of vaults within intact cells by electron cryo-tomography.

    Science.gov (United States)

    Woodward, Cora L; Mendonça, Luiza M; Jensen, Grant J

    2015-09-01

    The vault complex is the largest cellular ribonucleoprotein complex ever characterized and is present across diverse Eukarya. Despite significant information regarding the structure, composition and evolutionary conservation of the vault, little is know about the complex's actual biological function. To determine if intracellular vaults are morphologically similar to previously studied purified and recombinant vaults, we have used electron cryo-tomography to characterize the vault complexes found in the thin edges of primary human cells growing in tissue culture. Our studies confirm that intracellular vaults are similar in overall size and shape to purified and recombinant vaults previously analyzed. Results from subtomogram averaging indicate that densities within the vault lumen are not ordered, but randomly distributed. We also observe that vaults located in the extreme periphery of the cytoplasm predominately associate with granule-like structures and actin. Our ultrastructure studies augment existing biochemical, structural and genetic information on the vault, and provide important intracellular context for the ongoing efforts to understand the biological function of the native cytoplasmic vault. PMID:25864047

  5. Germanium-doped carbon dots as a new type of fluorescent probe for visualizing the dynamic invasions of mercury(ii) ions into cancer cells

    Science.gov (United States)

    Yuan, Yun Huan; Li, Rong Sheng; Wang, Qiang; Wu, Zhu Lian; Wang, Jian; Liu, Hui; Huang, Cheng Zhi

    2015-10-01

    Carbon dots doped with germanium (GeCDs) were firstly prepared by a new simple 15 min carbonation synthesis route, exhibiting excitation-independent photoluminescence (PL), which could avoid autofluorescence in bioimaging applications. The as-prepared GeCDs have low cell toxicity, good biocompatibility, high intracellular delivery efficiency, stability and could be applied for detection of mercury(ii) ions with excellent selectivity in complicated medium. It is to be noted that the as-prepared GeCDs used as a new type of probe for visualization of dynamic invasions of mercury(ii) ions into Hep-2 cells display greatly different properties from most of the previously reported CDs which are regularly responsive to iron ions. All the results suggest that the GeCDs can be employed for visualization and monitoring of the significant physiological changes of living cells induced by Hg2+.Carbon dots doped with germanium (GeCDs) were firstly prepared by a new simple 15 min carbonation synthesis route, exhibiting excitation-independent photoluminescence (PL), which could avoid autofluorescence in bioimaging applications. The as-prepared GeCDs have low cell toxicity, good biocompatibility, high intracellular delivery efficiency, stability and could be applied for detection of mercury(ii) ions with excellent selectivity in complicated medium. It is to be noted that the as-prepared GeCDs used as a new type of probe for visualization of dynamic invasions of mercury(ii) ions into Hep-2 cells display greatly different properties from most of the previously reported CDs which are regularly responsive to iron ions. All the results suggest that the GeCDs can be employed for visualization and monitoring of the significant physiological changes of living cells induced by Hg2+. Electronic supplementary information (ESI) available: Experimental section and additional figures (Fig. S1-15). See DOI: 10.1039/c5nr05326a

  6. Micro-PIV (micro particle image velocimetry) visualization of red blood cells (RBCs) sucked by a female mosquito

    International Nuclear Information System (INIS)

    A mosquito's pump is a highly effective system in the small suction domain. To understand a mosquito's blood suction mechanism, we analysed the characteristics of red blood cells (RBCs) in human blood during and after suction by a female mosquito. Focussing on the flow patterns of the RBCs in human blood being sucked by a mosquito, we visualized blood flow by using a micro-particle image velocimetry (μ-PIV) system, which combines an optical microscope and a PIV method. In an ex vivo experiment, a female mosquito was supplied diluted blood at the tip of the proboscis. We examined the blood flow around the tip of the proboscis and observed that RBCs were periodically sucked towards a hole around the tip. The sucked RBCs then homogeneously flowed parallel to the inner surface of the proboscis without adhering to the wall. Furthermore, using a bioelectric recording system, we directly measured electrical signals generated during suction by the pump muscles located in the mosquito's head. We found that the electrical signal power was synchronized with the acceleration of the RBCs in the sucking phase. A histological stain method was adapted for the observation of the form and internal structure of RBCs in the mosquito. Although the blood flow analysis revealed that the RBCs underwent shear stress during suction, RBCs in the mosquito's stomach maintained their original shape

  7. Visualization study of motion and deformation of red blood cells in a microchannel with straight, divergent and convergent sections.

    Science.gov (United States)

    Chen, Bin; Guo, Fang; Xiang, Hao

    2011-09-01

    The size of red blood cells (RBC) is on the same order as the diameter of microvascular vessels. Therefore, blood should be regarded as a two-phase flow system of RBCs suspended in plasma rather than a continuous medium of microcirculation. It is of great physiological and pathological significance to investigate the effects of deformation and aggregation of RBCs on microcirculation. In this study, a visualization experiment was conducted to study the microcirculatory behavior of RBCs in suspension. Motion and deformation of RBCs in a microfluidic chip with straight, divergent, and convergent microchannel sections have been captured by microscope and high-speed camera. Meanwhile, deformation and movement of RBCs were investigated under different viscosity, hematocrit, and flow rate in this system. For low velocity and viscosity, RBCs behaved in their normal biconcave disc shape and their motion was found as a flipping motion: they not only deformed their shapes along the flow direction, but also rolled and rotated themselves. RBCs were also found to aggregate, forming rouleaux at very low flow rate and viscosity. However, for high velocity and viscosity, RBCs deformed obviously under the shear stress. They elongated along the flow direction and performed a tank-treading motion. PMID:22942486

  8. Flow visualization

    CERN Document Server

    Merzkirch, Wolfgang

    1974-01-01

    Flow Visualization describes the most widely used methods for visualizing flows. Flow visualization evaluates certain properties of a flow field directly accessible to visual perception. Organized into five chapters, this book first presents the methods that create a visible flow pattern that could be investigated by visual inspection, such as simple dye and density-sensitive visualization methods. It then deals with the application of electron beams and streaming birefringence. Optical methods for compressible flows, hydraulic analogy, and high-speed photography are discussed in other cha

  9. TRAIL protein localization in human primary T cells by 3D microscopy using 3D interactive surface plot: a new method to visualize plasma membrane.

    Science.gov (United States)

    Gras, Christophe; Smith, Nikaïa; Sengmanivong, Lucie; Gandini, Mariana; Kubelka, Claire Fernandes; Herbeuval, Jean-Philippe

    2013-01-31

    The apoptotic ligand TNF-related apoptosis ligand (TRAIL) is expressed on the membrane of immune cells during HIV infection. The intracellular stockade of TRAIL in human primary CD4(+) T cells is not known. Here we investigated whether primary CD4(+) T cells expressed TRAIL in their intracellular compartment and whether TRAIL is relocalized on the plasma membrane under HIV activation. We found that TRAIL protein was stocked in intracellular compartment in non activated CD4(+) T cells and that the total level of TRAIL protein was not increased under HIV-1 stimulation. However, TRAIL was massively relocalized on plasma membrane when cells were cultured with HIV. Using three dimensional (3D) microscopy we localized TRAIL protein in human T cells and developed a new method to visualize plasma membrane without the need of a membrane marker. This method used the 3D interactive surface plot and bright light acquired images. PMID:23085529

  10. Roles of Treg/Th17 Cell Imbalance and Neuronal Damage in the Visual Dysfunction Observed in Experimental Autoimmune Optic Neuritis Chronologically.

    Science.gov (United States)

    Liu, Yuanyuan; You, Caiyun; Zhang, Zhuhong; Zhang, Jingkai; Yan, Hua

    2015-12-01

    Optic neuritis associated with multiple sclerosis and its animal model, experimental autoimmune optic neuritis (EAON), is characterized by inflammation, T cell activation, demyelination, and neuronal damage, which might induce permanent vision loss. Elucidating the chronological relationship among the features is critical for treatment of demyelinating optic neuritis. EAON was induced in C57BL/6 mice immunized with myelin oligodendrocyte glycoprotein subcutaneously, and visual function was assessed by flash-visual evoked potential (F-VEP) at days 7, 11, 14, 19, 23, 28 post-immunization. Retinal ganglion cell (RGC) apoptosis was measured by terminal-deoxynucleotidyl transferase-mediated nick-end labeling. Demyelination and axonal damage were verified with myelin basic protein (MBP) and β-amyloid precursor protein staining, respectively. Real-time polymerase chain reaction quantified IL-17, IL-1β, TGF-β, FoxP3, IL-6, and IL-10 mRNA expression in the optic nerve, as well as FoxP3 and IL-17 staining. Systemic changes of Th17 and Treg cells were tested by flow cytometry in spleen. F-VEP latency was prolonged at 11 days and peaked at 23 days commensurate with demyelination. However, F-VEP amplitude was reduced at 11 days, preceding axon damage, and was exacerbated at 23 days when a peak in RGC apoptosis was detected. Th17 cells up-regulated as early as 7 days and peaked at 11 days, while Treg cells down-regulated inversely compared to Th17 cells change as verified by IL-17 and FoxP3 expression; spleen cell samples were slightly different, demonstrating marked changed at 14 days. Treg/Th17 cell imbalance in the optic nerve precedes and may initiate neuronal damage of axons and RGCs. These changes are commensurate with the appearances of visual dysfunction reflected in F-VEP and hence may offer a novel therapeutic avenue for vision preservation. PMID:26318182

  11. Visualization of the African swine fever virus infection in living cells by incorporation into the virus particle of green fluorescent protein-p54 membrane protein chimera

    International Nuclear Information System (INIS)

    Many stages of African swine fever virus infection have not yet been studied in detail. To track the behavior of African swine fever virus (ASFV) in the infected cells in real time, we produced an infectious recombinant ASFV (B54GFP-2) that expresses and incorporates into the virus particle a chimera of the p54 envelope protein fused to the enhanced green fluorescent protein (EGFP). The incorporation of the fusion protein into the virus particle was confirmed immunologically and it was determined that p54-EGFP was fully functional by confirmation that the recombinant virus made normal-sized plaques and presented similar growth curves to the wild-type virus. The tagged virus was visualized as individual fluorescent particles during the first stages of infection and allowed to visualize the infection progression in living cells through the viral life cycle by confocal microscopy. In this work, diverse potential applications of B54GFP-2 to study different aspects of ASFV infection are shown. By using this recombinant virus it was possible to determine the trajectory and speed of intracellular virus movement. Additionally, we have been able to visualize for first time the ASFV factory formation dynamics and the cytophatic effect of the virus in live infected cells. Finally, we have analyzed virus progression along the infection cycle and infected cell death as time-lapse animations

  12. Restoration of visual function by expression of a light-gated mammalian ion channel in retinal ganglion cells or ON-bipolar cells.

    Science.gov (United States)

    Gaub, Benjamin M; Berry, Michael H; Holt, Amy E; Reiner, Andreas; Kienzler, Michael A; Dolgova, Natalia; Nikonov, Sergei; Aguirre, Gustavo D; Beltran, William A; Flannery, John G; Isacoff, Ehud Y

    2014-12-23

    Most inherited forms of blindness are caused by mutations that lead to photoreceptor cell death but spare second- and third-order retinal neurons. Expression of the light-gated excitatory mammalian ion channel light-gated ionotropic glutamate receptor (LiGluR) in retinal ganglion cells (RGCs) of the retina degeneration (rd1) mouse model of blindness was previously shown to restore some visual functions when stimulated by UV light. Here, we report restored retinal function in visible light in rodent and canine models of blindness through the use of a second-generation photoswitch for LiGluR, maleimide-azobenzene-glutamate 0 with peak efficiency at 460 nm (MAG0(460)). In the blind rd1 mouse, multielectrode array recordings of retinal explants revealed robust and uniform light-evoked firing when LiGluR-MAG0(460) was targeted to RGCs and robust but diverse activity patterns in RGCs when LiGluR-MAG0(460) was targeted to ON-bipolar cells (ON-BCs). LiGluR-MAG0(460) in either RGCs or ON-BCs of the rd1 mouse reinstated innate light-avoidance behavior and enabled mice to distinguish between different temporal patterns of light in an associative learning task. In the rod-cone dystrophy dog model of blindness, LiGluR-MAG0(460) in RGCs restored robust light responses to retinal explants and intravitreal delivery of LiGluR and MAG0(460) was well tolerated in vivo. The results in both large and small animal models of photoreceptor degeneration provide a path to clinical translation. PMID:25489083

  13. Data visualization

    CERN Document Server

    Azzam, Tarek

    2013-01-01

    Do you communicate data and information to stakeholders? In Part 1, we introduce recent developments in the quantitative and qualitative data visualization field and provide a historical perspective on data visualization, its potential role in evaluation practice, and future directions. Part 2 delivers concrete suggestions for optimally using data visualization in evaluation, as well as suggestions for best practices in data visualization design. It focuses on specific quantitative and qualitative data visualization approaches that include data dashboards, graphic recording, and geographic information systems (GIS). Readers will get a step-by-step process for designing an effective data dashboard system for programs and organizations, and various suggestions to improve their utility.

  14. Visual imagery without visual perception?

    OpenAIRE

    Helder Bértolo

    2005-01-01

    The question regarding visual imagery and visual perception remain an open issue. Many studies have tried to understand if the two processes share the same mechanisms or if they are independent, using different neural substrates. Most research has been directed towards the need of activation of primary visual areas during imagery. Here we review some of the works providing evidence for both claims. It seems that studying visual imagery in blind subjects can be us...

  15. Visual Language in Visual Communication

    OpenAIRE

    Jia Wang

    2009-01-01

    In visual communication the design information is mainly communicated by visual language, the correct use of which is the standard of evaluation of a graphic design composition. Therefore it is necessary to understand and percept visual language properly. It will be helpful for viewers to percept the desired information from the designer as well as the significance within the work.

  16. A neural network model on self-organizing emergence of simple-cell receptive field with orientation selectivity in visual cortex

    Institute of Scientific and Technical Information of China (English)

    YANG; Qian(

    2001-01-01

    [1]Hubel, D. H.. Wiesel. T. N., Receptive fields of single neuron in the cat striate cortex, Journal of Physiology, 1959, 148:574-591.[2]Hubel. D. H.. Wiesel, T. N., Functional architecture macaque monkey visual cortexm, Proc. Roy. Soc. B, 1977, 198: 1-59.[3]Shou. T. D., Brain Mechanisms of Visual Information Processing (in Chinese), Shanghai: Shanghai Science-Technology and Education Press, 1997, 188-197.[4]Ferster, D., Chung, S., Wheat, H., Orientation selectivity of thalamic input to simple cells of cat visual cortex, Nature,1996, 380: 249-252.[5]Vidyasagar. T. R., Pei, X., Volgushev, M., Multiple mechanisms underlying the orientation selectivity of visual cortical neurons. TINS, 1996, 19: 272-277.[6]Artun, O. B., Shouval, H. Z., Cooper, L. N., The effect of dynamic synapses on spatiotemporal receptive fields in visual cortex, Proc. Natl. Acad. Sci. USA, 1998, 95:11999-12003.[7]Rolls, E. T.. Tovee, M. J., Sparseness of the neuronal representation of stimuli in the primate temporal visual cortex, J.Neurophysiology, 1995,73: 713-726.[8]Olshausen. B. A.. Field, D. J., Sparse coding with an overcomplete basis set: A strategy employed by V 1 ? Vision Research,1997.37: 3311-3325.[9]Bell. A. J., Sejnoswski, T. J., The "Independent components" of natural scenes are edge filters, Vision Research, 1997, 37:3327-3338.[10]Dan, Y., Atick, J. J., Reid, R. C., Efficient coding of natural scenes in the lateral geniculate nucleus: experimental test of a computational theory, Journal of Neuroscience, 1996, 16:3351-3362.[11]Field. D. J., Relations between the statistics of natural images and the response properties of cortical cells, Journal of the Optical Society of America A, 1987, 4: 2379-2394.[12]DeAngelis, G. C., Ohzawa, I., Freeman, R. D., Receptive filed dynamics in the central visual pathway, TINS, 1995,18:451-458.[13]Wang, Y. J., Qi, X. L., Chen, Y. Z., Simulations of receptive fields dynamics, TINS, 1996, 19: 385-386.

  17. BINDING TO AND RETENTION BY MUCOSAL CELLS OF THE TAMARINDUS INDICA SEED POLYSACCHARIDE: VISUAL EVALUATION BY MEANS OF INORGANIC AND ORGANIC MARKERS

    Directory of Open Access Journals (Sweden)

    P.C. Braga*, M. Dal Sasso, M. Culici

    2012-06-01

    Full Text Available The aim of this study was to investigate the possibility of using inorganic and organic markers to visualize the ability of the transparent polysaccharide (TSP polymer isolated from the endosperm of the seed kernel of Tamarindus indica, a tree that mainly grows in India and South-East Asia, to bind to human mucosal cells. A layer of human buccal cells was prepared on slides and overlaid by 0.2 ml of 0.6, 0.3, 0.15 and 0.075 % TSP solutions in phosphate buffer and then colloidal carbon black particles were deposited on the slides. The unbound colloidal carbon black particles were cleared by thoroughly washing the slides. The slides were then examined by means of Nomarski interference contrast microscopy in order to visualize the degree of surface retention of the black particles by the buccal cells. The same procedure was followed using Escherichia coli as organic markers. The clearly visible binding of black carbon particles to the cells treated with polymer revealed the presence of a thin layer of TSP covering the cells (untreated cells had no black carbon particles binding. The presence of the TSP has also been confirmed by a significant reduction in bacterial adhesiveness. Both markers made it possible to visualize the binding of the thin transparent layer of TSP and its retention, which was proportional to the degree of dilution. Using Escherichia coli it has been observed the possibility of counteracting the lock-and-key mechanism of micro-organism adhesion using the bioadhesive properties of this polymer to prevent possible contact between microorganism adhesins and complementary receptors.

  18. Visual imagery without visual perception?

    Directory of Open Access Journals (Sweden)

    Helder Bértolo

    2005-01-01

    Full Text Available The question regarding visual imagery and visual perception remain an open issue. Many studies have tried to understand if the two processes share the same mechanisms or if they are independent, using different neural substrates. Most research has been directed towards the need of activation of primary visual areas during imagery. Here we review some of the works providing evidence for both claims. It seems that studying visual imagery in blind subjects can be used as a way of answering some of those questions, namely if it is possible to have visual imagery without visual perception. We present results from the work of our group using visual activation in dreams and its relation with EEG’s spectral components, showing that congenitally blind have visual contents in their dreams and are able to draw them; furthermore their Visual Activation Index is negatively correlated with EEG alpha power. This study supports the hypothesis that it is possible to have visual imagery without visual experience.

  19. Mining and visualization of microarray and metabolomic data reveal extensive cell wall remodeling during winter hardening in Sitka spruce (Picea sitchensis

    Directory of Open Access Journals (Sweden)

    Ruth eGrene

    2012-10-01

    Full Text Available Microarray gene expression profiling is a powerful technique to understand complex developmental processes, but making biologically meaningful inferences from such studies has always been challenging. We previously reported a microarray study of the freezing acclimation period in Sitka spruce (Picea sitchensis in which a large number of candidate genes for climatic adaptation were identified. In the current paper, we apply additional systems biology tools to these data to further probe changes in the levels of genes and metabolites and activities of associated pathways that regulate this complex developmental transition. One aspect of this adaptive process that is not well understood is the role of the cell wall. Our data suggest coordinated metabolic and signaling responses leading to cell wall remodeling. Co-expression of genes encoding proteins associated with biosynthesis of structural and non-structural cell wall carbohydrates was observed, which may be regulated by ethylene signaling components. At the same time, numerous genes, whose products are putatively localized to the endomembrane system and involved in both the synthesis and trafficking of cell wall carbohydrates, were up-regulated. Taken together, these results suggest a link between ethylene signaling and biosynthesis, and targeting of cell wall related gene products during the period of winter hardening. ALPINE, an in-house plugin for the Cytoscape visualization environment that utilizes the existing GeneMANIA and Mosaic plugins, together with the use of visualization tools, provided images of proposed signaling processes that became active over the time course of winter hardening, particularly at later time points in the process. The resulting visualizations have the potential to reveal novel, hypothesis-generating, gene association patterns in the context of targeted subcellular location.

  20. Mining and visualization of microarray and metabolomic data reveal extensive cell wall remodeling during winter hardening in Sitka spruce (Picea sitchensis).

    Science.gov (United States)

    Grene, Ruth; Klumas, Curtis; Suren, Haktan; Yang, Kuan; Collakova, Eva; Myers, Elijah; Heath, Lenwood S; Holliday, Jason A

    2012-01-01

    Microarray gene expression profiling is a powerful technique to understand complex developmental processes, but making biologically meaningful inferences from such studies has always been challenging. We previously reported a microarray study of the freezing acclimation period in Sitka spruce (Picea sitchensis) in which a large number of candidate genes for climatic adaptation were identified. In the current paper, we apply additional systems biology tools to these data to further probe changes in the levels of genes and metabolites and activities of associated pathways that regulate this complex developmental transition. One aspect of this adaptive process that is not well understood is the role of the cell wall. Our data suggest coordinated metabolic and signaling responses leading to cell wall remodeling. Co-expression of genes encoding proteins associated with biosynthesis of structural and non-structural cell wall carbohydrates was observed, which may be regulated by ethylene signaling components. At the same time, numerous genes, whose products are putatively localized to the endomembrane system and involved in both the synthesis and trafficking of cell wall carbohydrates, were up-regulated. Taken together, these results suggest a link between ethylene signaling and biosynthesis, and targeting of cell wall related gene products during the period of winter hardening. Automated Layout Pipeline for Inferred NEtworks (ALPINE), an in-house plugin for the Cytoscape visualization environment that utilizes the existing GeneMANIA and Mosaic plugins, together with the use of visualization tools, provided images of proposed signaling processes that became active over the time course of winter hardening, particularly at later time points in the process. The resulting visualizations have the potential to reveal novel, hypothesis-generating, gene association patterns in the context of targeted subcellular location. PMID:23112803

  1. A neural network model on self-organizing emergence of simple-cell receptive field with orientation selectivity in visual cortex

    Institute of Scientific and Technical Information of China (English)

    杨谦; 齐翔林; 汪云九

    2001-01-01

    In order to probe into the self-organizing emergence of simple cell orientation selectivity,we tried to construct a neural network model that consists of LGN neurons and simple cells in visual cortex and obeys the Hebbian learning rule. We investigated the neural coding and representation of simple cells to a natural image by means of this model. The results show that the structures of their receptive fields are determined by the preferred orientation selectivity of simple cells.However, they are also decided by the emergence of self-organization in the unsupervision learning process. This kind of orientation selectivity results from dynamic self-organization based on the interactions between LGN and cortex.

  2. Visualization Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Evaluates and improves the operational effectiveness of existing and emerging electronic warfare systems. By analyzing and visualizing simulation results...

  3. Traffic Visualization

    DEFF Research Database (Denmark)

    Picozzi, Matteo; Verdezoto, Nervo; Pouke, Matti;

    2013-01-01

    In this paper, we present a space-time visualization to provide city's decision-makers the ability to analyse and uncover important "city events" in an understandable manner for city planning activities. An interactive Web mashup visualization is presented that integrates several visualization...... techniques to give a rapid overview of traffic data. We illustrate our approach as a case study for traffic visualization systems, using datasets from the city of Oulu that can be extended to other city planning activities. We also report the feedback of real users (traffic management employees, traffic police...

  4. Immunohistochemical visualization of insulin receptors in formalin-fixed bovine ovaries post mortem and in granulosa cells collected in vivo.

    Science.gov (United States)

    Bossaert, P; De Cock, H; Leroy, J L M R; De Campeneere, S; Bols, P E J; Filliers, M; Opsomer, G

    2010-06-01

    Insulin is crucial for granulosa cell (GC) function, follicle growth and ovulation in cows; low insulin levels increase the risk for anoestrus. Apart from insulin concentration, alterations in the insulin receptor (IR) density on GC may affect follicular growth and steroidogenesis. Data about the IR protein distribution in the bovine follicle are scarce. Therefore, we aimed to develop a quantifiable staining method for IR protein on histological sections of bovine follicles in different developmental stages, and to apply this technique on GC obtained in living cows. In a first experiment, bovine ovaries were collected post mortem, formalin fixed, routinely processed, and stained with monoclonal murine IR-antibodies, peroxidase-labeled goat anti-mouse antibodies, and substrate chromogen. Based on their diameter, follicles were morphologically classified as small antral (SAF; n = 141), dominant (DF; n=28) or subordinate (SF; n=8); DF and SF were further classified as healthy or atretic based on the ratio of estrogen and progesterone concentrations in their follicular fluid. Using specialized software, the proportion of pixels displaying a positive staining signal was computed as a measure for IR density in three selected follicular regions: GC, theca (T) and stroma (STR). Results were analyzed in an ANOVA model with follicle type, region and health status as fixed factors. In SAF, DF, and SF, IR density was notably higher in GC than T or STR; the latter two displayed very low or no IR presence. The IR density in SAF was stronger than in DF and tended to be stronger than in SF. Staining intensity was not altered in atretic compared to healthy follicles. In corpus luteum, cumulus-oocyte complexes and pre-antral follicles, no IR could be detected. In a second experiment, GC samples were collected from 20 live cows on 30 and 70 d post partum by transvaginal follicular fluid aspiration, projected on glass slides, and stained using the protocol described above. Most

  5. Visual art and visual perception

    OpenAIRE

    Koenderink, Jan J.

    2015-01-01

    Visual art and visual perception ‘Visual art’ has become a minor cul-de-sac orthogonal to THE ART of the museum directors and billionaire collectors. THE ART is conceptual, instead of visual. Among its cherished items are the tins of artist’s shit (Piero Manzoni, 1961, Merda d’Artista) “worth their weight in gold”. I perceive a metabletic (van den Berg, 1956) parallel to philosophy transforming itself into speculative logic games, and psychology going cognitive by freeing itself from phenomen...

  6. Nanoscale Relationship Between CD4 and CD25 of T Cells Visualized with NSOM/QD-Based Dual-Color Imaging System

    Science.gov (United States)

    Fan, Jinping; Lu, Xiaoxu; Liu, Shengde; Zhong, Liyun

    2015-10-01

    In this study, by using of near-field scanning optical microscopy (NSOM)/immune-labeling quantum dot (QD)-based dual-color imaging system, we achieved the direct visualization of nanoscale profiles for distribution and organization of CD4 and CD25 molecules in T cells. A novel and interesting finding was that though CD25 clustering as nanodomains were observed on the surface of CD4+CD25high regulatory T cells, these CD25 nanodomains were not co-localized with CD4 nanodomains. This result presented that the formation of these CD25 nanodomains on the surface of CD4+CD25high T cells were not associated with the response of T cell receptor (TCR)/CD3-dependent signal transduction. In contrast, on the surface of CD4+CD25low T cells, CD25 molecules distributed randomly without forming nanodomains while CD4 clustering as nanodomains can be observed; on the surface of CD8+CD25+ T cells, CD25 clustering as nanodomains and co-localization with CD8 nanodomains were observed. Collectively, above these results exhibited that TCR/CD3-based microdomains were indeed required for TCR/CD3-mediated T cells activation and enhanced the immune activity of CD4+CD25low T cells or CD8+CD25+ T cells. In particular, it was found that the formation of CD25 nanodomains and their segregation from TCR/CD3 microdomains were the intrinsic capability of CD4+CD25high T cells, suggesting this specific imaging feature of CD25 should be greatly associated with the regulatory activity of CD4+CD25high T cells. Importantly, this novel NSOM/QD-based dual-color imaging system will provide a useful tool for the research of distribution-function relationship of cell-surface molecules.

  7. Visual Education

    DEFF Research Database (Denmark)

    Buhl, Mie; Flensborg, Ingelise

    2010-01-01

    The intrinsic breadth of various types of images creates new possibilities and challenges for visual education. The digital media have moved the boundaries between images and other kinds of modalities (e.g. writing, speech and sound) and have augmented the possibilities for integrating...... the learning potential of images and visuality from two perspectives: 1) The perspective of digital media which are assumed to form an increasing part of experience and communication from the use of internet, tv and mobile devices. 2) The perspective of culture where images and visualisations are assumed...... to emerge in the interlocutory space of a global visual repertoire and diverse local interpretations. The two perspectives represent challenges for future visual education which require visual competences, not only within the arts but also within the subjects of natural sciences, social sciences, languages...

  8. Principles of visual attention

    DEFF Research Database (Denmark)

    Bundesen, Claus; Habekost, Thomas

    The nature of attention is one of the oldest and most central problems in psychology. A huge amount of research has been produced on this subject in the last half century, especially on attention in the visual modality, but a general explanation has remained elusive. Many still view attention...... mechanisms are described in a set of simple equations, which allow TVA to mathematically model a large number of classical results in the attention literature. The theory explains psychological and neuroscientific findings by the same equations; TVA is a complete theory of visual attention, linking mind and...... brain. Aimed at advanced students and professional researchers, Principles of Visual Attention contains a detailed review of the most important research done on attention in vision, spanning cognitive psychology, brain imaging, patient studies, and recordings from single cells in the visual cortex. The...

  9. Identification of three new type-specific antigen epitopes in the capsid protein of porcine circovirus type 1.

    Science.gov (United States)

    Huang, Liping; Lu, Yuehua; Wei, Yanwu; Guo, Longjun; Liu, Changming

    2012-07-01

    Porcine circovirus type 1 (PCV1) has been identified as a contaminant of porcine kidney cell line (PK-15). Serological evidence and genetic studies have suggested that PCV1 is widespread in domestic pigs. In this study, monoclonal antibodies (mAbs) and polyclonal antibodies (pAbs) were generated against a recombinant PCV1 Cap protein (PCV1-Cap), which was expressed using the baculovirus system. PEPSCAN analysis was used to identify epitopes on the PCV1-Cap with mAbs and pAbs. Three linear B-cell epitopes, including residues (85)GGTNPLP(91), (162)FTPKPELDKTIDWFHPNNK(180) and (219)YVQFREFILKDPLNK(233), specific for PCV1-Cap, were finely defined. These results will facilitate future investigations into antigenic differences and differential diagnosis between PCV1 and PCV2. PMID:22437253

  10. A cell type-specific allele of the POU gene Oct-6 reveals Schwann cell autonomous function in nerve development and regeneration

    NARCIS (Netherlands)

    M. Ghazvini (Mehrnaz); W.J. Mandemakers (Wim); M.M. Jaegle (Martine); M. Piirsoo (Marko); M. Koutsourakis (Manousos); X. Smit (Xander); D.N. Meijer (Dies); M.J.F. Driegen (Siska); F.G. Grosveld (Frank)

    2002-01-01

    textabstractWhile an important role for the POU domain transcription factor Oct-6 in the developing peripheral nerve has been well established, studies into its exact role in nerve development and regeneration have been hampered by the high mortality rate of newborn Oct-6 mutant an

  11. A cell type-specific allele of the POU gene Oct-6 reveals Schwann cell autonomous function in nerve development and regeneration.

    NARCIS (Netherlands)

    M. Ghazvini (Mehrnaz); W.J. Mandemakers (Wim); M.M. Jaegle (Martine); M. Piirsoo (Marko); M. Koutsourakis (Manousos); X. Smit (Xander); F.G. Grosveld (Frank); D.N. Meijer (Dies); M.J.F. Driegen (Siska)

    2002-01-01

    textabstractWhile an important role for the POU domain transcription factor Oct-6 in the developing peripheral nerve has been well established, studies into its exact role in nerve development and regeneration have been hampered by the high mortality rate of newborn Oct-6 mutant animals. In this stu

  12. Visualization and analysis of active dopant distribution in a p-i-n structured amorphous silicon solar cell using scanning nonlinear dielectric microscopy

    OpenAIRE

    Hirose, K.; N. Chinone; Cho, Y.

    2015-01-01

    Scanning nonlinear dielectric microscopy (SNDM) and super-higher-order (SHO-) SNDM were used for dopant profiling analysis of a cross-section of the p-i-n structure of an amorphous silicon solar cell. The p-i-n and zigzag structures of each layer boundary were visualized as carrier polarity and density images on 10-20 nm scale through a SNDM measurement. A capacitance-voltage curve was obtained at each pixel in the scan area through a SHO-SNDM measurement. The obtained SNDM and SHO-SNDM data ...

  13. Visual Impairment

    Science.gov (United States)

    ... poorly lit spaces, and colors that seem faded. Diabetic retinopathy (pronounced: reh-ton-AH-pa-thee) occurs when ... that is likely to cause visual impairment, many treatments are available. Options may include eyeglasses, contact lenses, ...

  14. Oral human papillomavirus type-specific infection in HIV-infected men: a prospective cohort study among men who have sex with men and heterosexual men.

    OpenAIRE

    Darwich, L.; Cañadas, M.P.; Videla, S; Coll, J.; Molina-López, R. A.; Cobarsi, P.; Sirera, G.; Clotet, Bonaventura

    2014-01-01

    The natural history of type-specific oral infection of human papillomavirus (HPV) was assessed in a cohort of HIV-infected men (538 men who have sex with men (MSM); 195 heterosexuals). Risk factors associated with oral HPV infections were examined. The overall prevalence of HPV was 16%: HPV-16 was the most prevalent type (3.7% MSM; 7.8% heterosexuals). The prevalence of HPV-16 in heterosexuals was associated with CD4 nadir counts

  15. Type-specific PCR assays for Babesia bovis msa-1 genotypes in Asia: Revisiting the genetic diversity in Sri Lanka, Mongolia, and Vietnam.

    Science.gov (United States)

    Liyanagunawardena, Nilukshi; Sivakumar, Thillaiampalam; Kothalawala, Hemal; Silva, Seekkuge Susil Priyantha; Battsetseg, Badgar; Lan, Dinh Thi Bich; Inoue, Noboru; Igarashi, Ikuo; Yokoyama, Naoaki

    2016-01-01

    Babesia bovis is the most virulent Babesia organism, resulting in a high mortality rate in cattle. The genetic diversity of B. bovis merozoite surface antigens (MSAs), such as MSA-1, MSA-2b, and MSA-2c, might be linked to altered immune profiles in the host animals. The present study aimed to develop type-specific PCR assays for Asian msa-1 genotypes, thereby re-analyzing the genetic diversity of msa-1 in Sri Lanka, Mongolia, and Vietnam. Specific primers were designed for nine Asian msa-1 genotypes, which had been detected based on the phylogeny constructed using msa-1 gene sequences retrieved from the GenBank database. Specificity of the type-specific PCR assays was confirmed using plasmids containing the inserts of msa-1 gene fragments that represent Asian genotypes. Furthermore, no amplicons were observed by these PCR assays when DNA samples of Babesia bigemina, Babesia ovata, Theileria annulata, Theileria orientalis, Trypanosoma evansi, Trypanosoma theileri, Anaplasma marginale, and Anaplasma bovis, and non-infected bovine blood were analyzed. In total, 109 B. bovis-positive blood DNA samples sourced from Sri Lanka (44 cattle), Mongolia (26 cattle), and Vietnam (23 cattle and 16 water buffaloes) were then screened by the type-specific PCR assays. The sequences derived from all of the PCR amplicons were phylogenetically analyzed. Out of 109 DNA samples, 23 (20 from cattle and 3 from water buffaloes) were positive for at least one genotype. In agreement with previous studies, five and four different genotypes were detected among the DNA samples from Sri Lanka and Vietnam, respectively. In contrast, four genotypes, including three novel genotypes, were detected from Mongolia. Five DNA samples were found to be co-infected with multiple genotypes. The sequences of the PCR amplicons clustered phylogenetically within the corresponding clades. These findings indicated that the type-specific PCR assays described herein are useful for the determination of genotypic

  16. Visual cognition

    Energy Technology Data Exchange (ETDEWEB)

    Pinker, S.

    1985-01-01

    This book consists of essays covering issues in visual cognition presenting experimental techniques from cognitive psychology, methods of modeling cognitive processes on computers from artificial intelligence, and methods of studying brain organization from neuropsychology. Topics considered include: parts of recognition; visual routines; upward direction; mental rotation, and discrimination of left and right turns in maps; individual differences in mental imagery, computational analysis and the neurological basis of mental imagery: componental analysis.

  17. Visual detection of cancer cells by colorimetric aptasensor based on aggregation of gold nanoparticles induced by DNA hybridization.

    Science.gov (United States)

    Borghei, Yasaman-Sadat; Hosseini, Morteza; Dadmehr, Mehdi; Hosseinkhani, Saman; Ganjali, Mohammad Reza; Sheikhnejad, Reza

    2016-01-21

    A simple but highly sensitive colorimetric method was developed to detect cancer cells based on aptamer-cell interaction. Cancer cells were able to capture nucleolin aptamers (AS 1411) through affinity interaction between AS 1411 and nucleolin receptors that are over expressed in cancer cells, The specific binding of AS 1411 to the target cells triggered the removal of aptamers from the solution. Therefore no aptamer remained in the solution to hybridize with complementary ssDNA-AuNP probes as a result the solution color is red. In the absence of target cells or the presence of normal cells, ssDNA-AuNP probes and aptamers were coexisted in solution and the aptamers assembled DNA-AuNPs, produced a purple solution. UV-vis spectrometry demonstrated that this hybridization-based method exhibited selective colorimetric responses to the presence or absence of target cells, which is detectable with naked eye. The linear response for MCF-7 cells in a concentration range from 10 to 10(5) cells was obtained with a detection limit of 10 cells. The proposed method could be extended to detect other cells and showed potential applications in cancer cell detection and early cancer diagnosis. PMID:26724767

  18. Analysis of Multiple HPV E6 PDZ Interactions Defines Type-Specific PDZ Fingerprints That Predict Oncogenic Potential

    Science.gov (United States)

    Thomas, Miranda; Myers, Michael P.; Guarnaccia, Corrado; Banks, Lawrence

    2016-01-01

    The high-risk Human Papillomavirus (HPV) E6 oncoproteins are characterised by the presence of a class I PDZ-binding motif (PBM) on their extreme carboxy termini. The PBM is present on the E6 proteins derived from all cancer-causing HPV types, but can also be found on some related non-cancer-causing E6 proteins. We have therefore been interested in investigating the potential functional differences between these different E6 PBMs. Using an unbiased proteomic approach in keratinocytes, we have directly compared the interaction profiles of these different PBMs. This has allowed us to identify the potential PDZ target fingerprints of the E6 PBMs from 7 different cancer-causing HPV types, from 3 HPV types with weak cancer association, and from one benign HPV type that possesses an ancestral PBM. We demonstrate a striking increase in the number of potential PDZ targets bound by each E6 PBM as cancer-causing potential increases, and show that the HPV-16 and HPV-18 PBMs have the most flexibility in their PDZ target selection. Furthermore, the specific interaction with hScrib correlates directly with increased oncogenic potential. In contrast, hDlg is bound equally well by all the HPV E6 PBMs analysed, indicating that this is an evolutionarily conserved interaction, and was most likely one of the original E6 PBM target proteins that was important for the occupation of a potential new niche. Finally, we present evidence that the cell junction components ZO-2 and β-2 syntrophin are novel PDZ domain–containing targets of a subset of high-risk HPV types. PMID:27483446

  19. Visual comparison for information visualization

    KAUST Repository

    Gleicher, M.

    2011-09-07

    Data analysis often involves the comparison of complex objects. With the ever increasing amounts and complexity of data, the demand for systems to help with these comparisons is also growing. Increasingly, information visualization tools support such comparisons explicitly, beyond simply allowing a viewer to examine each object individually. In this paper, we argue that the design of information visualizations of complex objects can, and should, be studied in general, that is independently of what those objects are. As a first step in developing this general understanding of comparison, we propose a general taxonomy of visual designs for comparison that groups designs into three basic categories, which can be combined. To clarify the taxonomy and validate its completeness, we provide a survey of work in information visualization related to comparison. Although we find a great diversity of systems and approaches, we see that all designs are assembled from the building blocks of juxtaposition, superposition and explicit encodings. This initial exploration shows the power of our model, and suggests future challenges in developing a general understanding of comparative visualization and facilitating the development of more comparative visualization tools. © The Author(s) 2011.

  20. Compass Cells in the Brain of an Insect Are Sensitive to Novel Events in the Visual World.

    Science.gov (United States)

    Bockhorst, Tobias; Homberg, Uwe

    2015-01-01

    The central complex of the insect brain comprises a group of neuropils involved in spatial orientation and memory. In fruit flies it mediates place learning based on visual landmarks and houses neurons that encode the orientation for goal-directed locomotion, based on landmarks and self-motion cues for angular path-integration. In desert locusts, the central complex holds a compass-like representation of head directions, based on the polarization pattern of skylight. Through intracellular recordings from immobilized locusts, we investigated whether sky compass neurons of the central complex also represent the position or any salient feature of possible landmarks, in analogy to the observations in flies. Neurons showed strongest responses to the novel appearance of a small moving square, but we found no evidence for a topographic representation of object positions. Responses to an individual square were independent of direction of motion and trajectory, but showed rapid adaptation to successive stimulation, unaffected by changing the direction of motion. Responses reappeared, however, if the moving object changed its trajectory or if it suddenly reversed moving direction against the movement of similar objects that make up a coherent background-flow as induced by ego-motion. Response amplitudes co-varied with the precedent state of dynamic background activity, a phenomenon that has been related to attention-dependent saliency coding in neurons of the mammalian primary visual cortex. The data show that neurons of the central complex of the locust brain are visually bimodal, signaling sky compass direction and the novelty character of moving objects. These response properties might serve to attune compass-aided locomotor control to unexpected events in the environment. The difference to data obtained in fruit flies might relate to differences in the lifestyle of landmark learners (fly) and compass navigators (locust), point to the existence of parallel networks for

  1. Visualizing Cell Architecture and Molecular Location Using Soft X-Ray Tomography and Correlated Cryo-Light Microscopy

    Science.gov (United States)

    McDermott, Gerry; Le Gros, Mark A.; Larabell, Carolyn A.

    2012-05-01

    Living cells are structured to create a range of microenvironments that support specific chemical reactions and processes. Understanding how cells function therefore requires detailed knowledge of both the subcellular architecture and the location of specific molecules within this framework. Here we review the development of two correlated cellular imaging techniques that fulfill this need. Cells are first imaged using cryogenic fluorescence microscopy to determine the location of molecules of interest that have been labeled with fluorescent tags. The same specimen is then imaged using soft X-ray tomography to generate a high-contrast, 3D reconstruction of the cells. Data from the two modalities are then combined to produce a composite, information-rich view of the cell. This correlated imaging approach can be applied across the spectrum of problems encountered in cell biology, from basic research to biotechnological and biomedical applications such as the optimization of biofuels and the development of new pharmaceuticals.

  2. Visualizing Cell Architecture and Molecular Location Using Soft X-Ray Tomography and Correlated Cryo-Light Microscopy

    OpenAIRE

    McDermott, Gerry; Le Gros, Mark A.; Larabell, Carolyn A.

    2012-01-01

    Living cells are structured to create a range of microenvironments that support specific chemical reactions and processes. Understanding how cells function therefore requires detailed knowledge of both the subcellular architecture and the location of specific molecules within this framework. Here we review the development of two correlated cellular imaging techniques that fulfill this need. Cells are first imaged using cryogenic fluorescence microscopy to determine the location of molecules o...

  3. Canine mesenchymal stem cells are effectively labeled with silica nanoparticles and unambiguously visualized in highly autofluorescent tissues

    OpenAIRE

    Han Sei-Myoung; Lee Hee-Woo; Bhang Dong-Ha; Seo Kyoung-Won; Youn Hwa-Young

    2012-01-01

    Abstract Background Development of a method for long-term labeling of cells is critical to elucidate transplanted cell fate and migration as well as the contribution to tissue regeneration. Silica nanoparticles have been recently developed and demonstrated to be biocompatible with a high labeling capacity. Thus, our study was designed to assess the suitability of silica nanoparticles for labeling canine mesenchymal stem cells (MSCs) and the fluorescence afficiency in highly autofluorescent ti...

  4. Optimization of the magnetic labeling of human neural stem cells and MRI visualization in the hemiparkinsonian rat brain

    OpenAIRE

    Ramos-Gómez, Milagros; Seiz, Emma G; Martínez-Serrano, Alberto

    2015-01-01

    Background Magnetic resonance imaging is the ideal modality for non-invasive in vivo cell tracking allowing for longitudinal studies over time. Cells labeled with superparamagnetic iron oxide nanoparticles have been shown to induce sufficient contrast for in vivo magnetic resonance imaging enabling the in vivo analysis of the final location of the transplanted cells. For magnetic nanoparticles to be useful, a high internalization efficiency of the particles is required without compromising ce...

  5. Visual cognition

    Energy Technology Data Exchange (ETDEWEB)

    Pinker, S.

    1985-01-01

    This collection of research papers on visual cognition first appeared as a special issue of Cognition: International Journal of Cognitive Science. The study of visual cognition has seen enormous progress in the past decade, bringing important advances in our understanding of shape perception, visual imagery, and mental maps. Many of these discoveries are the result of converging investigations in different areas, such as cognitive and perceptual psychology, artificial intelligence, and neuropsychology. This volume is intended to highlight a sample of work at the cutting edge of this research area for the benefit of students and researchers in a variety of disciplines. The tutorial introduction that begins the volume is designed to help the nonspecialist reader bridge the gap between the contemporary research reported here and earlier textbook introductions or literature reviews.

  6. Visualizing Transformation

    DEFF Research Database (Denmark)

    Pedersen, Pia

    2012-01-01

    Transformation, defined as the step of extracting, arranging and simplifying data into visual form (M. Neurath, 1974), was developed in connection with ISOTYPE (International System Of TYpographic Picture Education) and might well be the most important legacy of Isotype to the field of graphic...... design. Recently transformation has attracted renewed interest because of the book ‘The Transformer’ written by Robin Kinross and Marie Neurath. My on-going research project, summarized in this paper, identifies and depicts the essential principles of data visualization underlying the process of...... transformation with reference to Marie Neurath’s sketches on the Bilston Project. The material has been collected at the Otto and Marie Neurath Collection housed at the University of Reading, UK. By using data visualization as a research method to look directly into the process of transformation the project...

  7. Co-visualization of DNA damage and ion traversals in live mammalian cells using a fluorescent nuclear track detector

    International Nuclear Information System (INIS)

    The geometric locations of ion traversals in mammalian cells constitute important information in the study of heavy ion-induced biological effect. Single ion traversal through a cellular nucleus produces complex and massive DNA damage at a nanometer level, leading to cell inactivation, mutations and transformation. We present a novel approach that uses a fluorescent nuclear track detector (FNTD) for the simultaneous detection of the geometrical images of ion traversals and DNA damage in single cells using confocal microscopy. HT1080 or HT1080–53BP1-GFP cells were cultured on the surface of a FNTD and exposed to 5.1-MeV/n neon ions. The positions of the ion traversals were obtained as fluorescent images of a FNTD. Localized DNA damage in cells was identified as fluorescent spots of γ-H2AX or 53BP1-GFP. These track images and images of damaged DNA were obtained in a short time using a confocal laser scanning microscope. The geometrical distribution of DNA damage indicated by fluorescent γ-H2AX spots in fixed cells or fluorescent 53BP1-GFP spots in living cells was found to correlate well with the distribution of the ion traversals. This method will be useful for evaluating the number of ion hits on individual cells, not only for micro-beam but also for random-beam experiments. (author)

  8. Adipogenic placenta-derived mesenchymal stem cells are not lineage restricted by withdrawing extrinsic factors: developing a novel visual angle in stem cell biology.

    Science.gov (United States)

    Hu, C; Cao, H; Pan, X; Li, J; He, J; Pan, Q; Xin, J; Yu, X; Li, J; Wang, Y; Zhu, D; Li, L

    2016-01-01

    Current evidence implies that differentiated bone marrow mesenchymal stem cells (BMMSCs) can act as progenitor cells and transdifferentiate across lineage boundaries. However, whether this unrestricted lineage has specificities depending on the stem cell type is unknown. Placental-derived mesenchymal stem cells (PDMSCs), an easily accessible and less invasive source, are extremely useful materials in current stem cell therapies. No studies have comprehensively analyzed the transition in morphology, surface antigens, metabolism and multilineage potency of differentiated PDMSCs after their dedifferentiation. In this study, we showed that after withdrawing extrinsic factors, adipogenic PDMSCs reverted to a primitive cell population and retained stem cell characteristics. The mitochondrial network during differentiation and dedifferentiation may serve as a marker of absent or acquired pluripotency in various stem cell models. The new population proliferated faster than unmanipulated PDMSCs and could be differentiated into adipocytes, osteocytes and hepatocytes. The cell adhesion molecules (CAMs) signaling pathway and extracellular matrix (ECM) components modulate cell behavior and enable the cells to proliferate or differentiate during the differentiation, dedifferentiation and redifferentiation processes in our study. These observations indicate that the dedifferentiated PDMSCs are distinguishable from the original PDMSCs and may serve as a novel source in stem cell biology and cell-based therapeutic strategies. Furthermore, whether PDMSCs differentiated into other lineages can be dedifferentiated to a primitive cell population needs to be investigated. PMID:26986509

  9. Visual detection of glial cell line-derived neurotrophic factor based on a molecular translator and isothermal strand-displacement polymerization reaction

    Directory of Open Access Journals (Sweden)

    Zhang LY

    2015-03-01

    Full Text Available Li-Yong Zhang,1,* Tao Xing,1,* Li-Xin Du,1,* Qing-Min Li,2 Wei-Dong Liu,1 Ji-Yue Wang,1 Jing Cai31Department of neurosurgery, Liaocheng People’s Hospital, Liaocheng, Shandong, People’s Republic of China; 2Department of Neurosurgery, Tai’an Central Hospital, Tai’an, Shandong, People’s Republic of China; 3Department of Neurosurgery, LinYi People Hospital, LinYi, Shandong, People’s Republic of China*These authors contributed equally to this workBackground: Glial cell line-derived neurotrophic factor (GDNF is a small protein that potently promotes the survival of many types of neurons. Detection of GDNF is vital to monitoring the survival of sympathetic and sensory neurons. However, the specific method for GDNF detection is also un-discovered. The purpose of this study is to explore the method for protein detection of GDNF.Methods: A novel visual detection method based on a molecular translator and isothermal strand-displacement polymerization reaction (ISDPR has been proposed for the detection of GDNF. In this study, a molecular translator was employed to convert the input protein to output deoxyribonucleic acid signal, which was further amplified by ISDPR. The product of ISDPR was detected by a lateral flow biosensor within 30 minutes.Results: This novel visual detection method based on a molecular translator and ISDPR has very high sensitivity and selectivity, with a dynamic response ranging from 1 pg/mL to 10 ng/mL, and the detection limit was 1 pg/mL of GDNF.Conclusion: This novel visual detection method exhibits high sensitivity and selectivity, which is very simple and universal for GDNF detection to help disease therapy in clinical practice.Keywords: lateral flow biosensor, molecular translator, isothermal strand-displacement polymerization reaction

  10. Type-specific interaction between human papillomavirus type 58 E2 protein and E7 protein inhibits E7-mediated oncogenicity

    OpenAIRE

    Wang, Xin; Qi, Mei; Yu, Xiuping; Yuan, Yan; Zhao, Weiming

    2012-01-01

    Human papillomavirus type 58 (HPV-58) is a very common HPV type in eastern Asia. Little is known about its biology and tumorigenesis. In this study, HPV-58 E2 protein (58E2) was found to interact with E7 protein (58E7), and the hinge domain of 58E2 was shown to be responsible for binding to the 58E7 protein. Interestingly, the E2–E7 interaction appears to be HPV type-specific, as we found that the HPV-16 E2 could not bind to the 58E7 protein, and neither did 58E2 interact with HPV-16 E7. The ...

  11. Cross-neutralizing antibodies elicited by the Cervarix® human papillomavirus vaccine display a range of Alpha-9 inter-type specificities

    OpenAIRE

    Bissett, Sara L; Draper, Eve; Myers, Richard E.; Godi, Anna; Beddows, Simon

    2014-01-01

    The highly efficacious human papillomavirus (HPV) vaccines contain virus-like particles (VLP) representing genotypes HPV16 and HPV18, which together account for approximately 70% of cervical cancer cases. Vaccine-type protection is thought to be mediated by high titer, type-specific neutralizing antibodies. The vaccines also confer a degree of cross-protection against some genetically-related types from the Alpha-9 (HPV16-like: HPV31, HPV33, HPV35, HPV52, HPV58) and Alpha-7 (HPV18-like: HPV39...

  12. HPV type-specific risks of high-grade CIN during 4 years of follow-up: A population-based prospective study

    OpenAIRE

    Naucler, P; Ryd, W; Törnberg, S; A. Strand; Wadell, G; Hansson, B. G.; Rylander, E; Dillner, J

    2007-01-01

    We followed a population-based cohort of 5696 women, 32–38 years of age, by registry linkage with cytology and pathology registries during a mean follow-up time of 4.1 years to assess the importance for CIN2+ development of type-specific HPV DNA positivity at baseline. HPV 16, 31 and 33 conveyed the highest risks and were responsible for 33.1, 18.3 and 7.7% of CIN2+ cases, respectively. Women infected with HPV 18, 35, 39, 45, 51, 52, 56, 58, 59 and 66 had significantly lower risks of CIN2+ th...

  13. Motion as a phenotype: the use of live-cell imaging and machine visual screening to characterize transcription-dependent chromosome dynamics

    Directory of Open Access Journals (Sweden)

    Silver Pamela A

    2006-04-01

    Full Text Available Abstract Background Gene transcriptional activity is well correlated with intra-nuclear position, especially relative to the nuclear periphery, which is a region classically associated with gene silencing. Recently however, actively transcribed genes have also been found localized to the nuclear periphery in the yeast Saccharomyces cerevisiae. When genes are activated, they become associated with the nuclear pore complex (NPC at the nuclear envelope. Furthermore, chromosomes are not static structures, but exhibit constrained diffusion in real-time, live-cell studies of particular loci. The relationship of chromosome motion with transcriptional activation and active-gene recruitment to the nuclear periphery has not yet been investigated. Results We have generated a yeast strain that enables us to observe the motion of the galactose-inducible GAL gene locus relative to the nuclear periphery in real-time under transcriptionally active and repressed conditions. Using segmented geometric particle tracking, we show that the repressed GAL locus undergoes constrained diffusive movement, and that transcriptional induction with galactose is associated with an enrichment in cells with GAL loci that are both associated with the nuclear periphery and much more constrained in their movement. Furthermore, we report that the mRNA export factor Sac3 is involved in this galactose-induced enrichment of GAL loci at the nuclear periphery. In parallel, using a novel machine visual screening technique, we find that the motion of constrained GAL loci correlates with the motion of the cognate nuclei in galactose-induced cells. Conclusion Transcriptional activation of the GAL genes is associated with their tethering and motion constraint at the nuclear periphery. We describe a model of gene recruitment to the nuclear periphery involving gene diffusion and the mRNA export factor Sac3 that can be used as a framework for further experimentation. In addition, we applied to

  14. Canine mesenchymal stem cells are effectively labeled with silica nanoparticles and unambiguously visualized in highly autofluorescent tissues

    Directory of Open Access Journals (Sweden)

    Han Sei-Myoung

    2012-08-01

    Full Text Available Abstract Background Development of a method for long-term labeling of cells is critical to elucidate transplanted cell fate and migration as well as the contribution to tissue regeneration. Silica nanoparticles have been recently developed and demonstrated to be biocompatible with a high labeling capacity. Thus, our study was designed to assess the suitability of silica nanoparticles for labeling canine mesenchymal stem cells (MSCs and the fluorescence afficiency in highly autofluorescent tissue. Results We examined the effect of silica nanoparticle labeling on stem cell morphology, viability and differentiation as compared with those of unlabeled control cells. After 4 h of incubation with silica nanoparticles, they were internalized by canine MSCs without a change in the morphology of cells compared with that of control cells. The viability and proliferation of MSCs labeled with silica nanoparticles were evaluated by a WST-1 assay and trypan blue exclusion. No effects on cell viability were observed, and the proliferation of canine MSCs was not inhibited during culture with silica nanoparticles. Furthermore, adipogenic and osteogenic differentiation of silica nanoparticle-labeled canine MSCs was at a similar level compared with that of unlabeled cells, indicating that silica nanoparticle labeling did not alter the differentiation capacity of canine MSCs. Silica nanoparticle-labeled canine MSCs were injected into the kidneys of BALB/c mice after celiotomy, and then the mice were sacrificed after 2 or 3 weeks. The localization of injected MSCs was closely examined in highly autofluorescent renal tissues. Histologically, canine MSCs were uniformly and completely labeled with silica nanoparticles, and were unambiguously imaged in histological sections. Conclusions The results of the current study showed that silica nanoparticles are useful as an effective labeling marker for MSCs, which can elucidate the distribution and fate of transplanted

  15. NSOM/QD-Based Visualization of GM1 Serving as Platforms for TCR/CD3 Mediated T-Cell Activation

    Directory of Open Access Journals (Sweden)

    Liyun Zhong

    2013-01-01

    Full Text Available Direct molecular imaging of nanoscale relationship between T-cell receptor complexes (TCR/CD3 and gangliosidosis GM1 before and after T-cell activation has not been reported. In this study, we made use of our expertise of near-field scanning optical microscopy(NSOM/immune-labeling quantum dots- (QD-based dual-color imaging system to visualize nanoscale profiles for distribution and organization of TCR/CD3, GM1, as well as their nanospatial relationship and their correlation with PKCθ signaling cascade during T-cell activation. Interestingly, after anti-CD3/anti-CD28 Ab co-stimulation, both TCR/CD3 and GM1 were clustered to form nanodomains; moreover, all of TCR/CD3 nanodomains were colocalized with GM1 nanodomains, indicating that the formation of GM1 nanodomains was greatly correlated with TCR/CD3 mediated signaling. Specially, while T-cells were pretreated with PKCθ signaling inhibitor rottlerin to suppress IL-2 cytokine production, no visible TCR/CD3 nanodomains appeared while a lot of GM1 nanodomains were still observed. However, while T-cells are pretreated with PKCαβ signaling inhibitor GÖ6976 to suppress calcium-dependent manner, all of TCR/CD3 nanodomains were still colocalized with GM1 nanodomains. These findings possibly support the notion that the formation of GM1 nanodomains indeed serves as platforms for the recruitment of TCR/CD3 nanodomains, and TCR/CD3 nanodomains are required for PKCθ signaling cascades and T-cell activation

  16. Aged human bone marrow stromal cells maintaining bone forming capacity in vivo evaluated using an improved method of visualization

    DEFF Research Database (Denmark)

    Stenderup, Karin; Rosada, Cecilia; Justesen, J;

    2004-01-01

    weeks, the implants were removed and embedded un-decalcified in methyl methacrylate (MMA). Sections were stained histochemically with Goldner's Trichrome stain and immuno-histochemically using human-specific antibodies against known osteogenic markers. Implanted human marrow stromal cells (hMSC) were...... able to form bone in vivo. The donor origin of bone was verified using several human-specific antibodies. Dose-response experiments demonstrated that 5 x 10(5) hMSC per implant gave the maximal bone formation after 8 weeks. No difference in BFC was observed between cells obtained from young (24...... vivo assay for quantifying the bone forming capacity (BFC) and we compared the BFC of osteoblastic cells obtained from young and old donors. Osteoblasts were obtained from human bone marrow stromal cell cultures and implanted subcutaneously in immuno-deficient mice (NOD/LtSz- Prkdc(scid)). After 8...

  17. OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data

    OpenAIRE

    Leng, Ning; Choi, Jeea; Chu, Li-Fang; Thomson, James A.; Kendziorski, Christina; Stewart, Ron

    2016-01-01

    Summary: A recent article identified an artifact in multiple single-cell RNA-seq (scRNA-seq) datasets generated by the Fluidigm C1 platform. Specifically, Leng et al. showed significantly increased gene expression in cells captured from sites with small or large plate output IDs. We refer to this artifact as an ordering effect (OE). Including OE genes in downstream analyses could lead to biased results. To address this problem, we developed a statistical method and software called OEFinder to...

  18. Pericellular Hyaluronan Coat Visualized in Live Cells With a Fluorescent Probe Is Scaffolded by Plasma Membrane Protrusions

    OpenAIRE

    Rilla, Kirsi; Tiihonen, Riikka; Kultti, Anne; Tammi, Markku; Tammi, Raija

    2008-01-01

    Many cell types wear up to 20-μm-wide hyaluronidase-sensitive surface coats, detected by exclusion of sedimenting particles like fixed erythrocytes. The structure of the coat is enigmatic, being apparently too thick to be accounted by random coils or even extended chains of just hyaluronan attached to cell surface. We have shown that hyaluronan synthesis enforced by green fluorescent protein–hyaluronan synthase transfection creates microvillous protrusions. The idea that the plasma membrane p...

  19. Visualization and analysis of active dopant distribution in a p-i-n structured amorphous silicon solar cell using scanning nonlinear dielectric microscopy

    Directory of Open Access Journals (Sweden)

    K. Hirose

    2015-09-01

    Full Text Available Scanning nonlinear dielectric microscopy (SNDM and super-higher-order (SHO- SNDM were used for dopant profiling analysis of a cross-section of the p-i-n structure of an amorphous silicon solar cell. The p-i-n and zigzag structures of each layer boundary were visualized as carrier polarity and density images on 10-20 nm scale through a SNDM measurement. A capacitance-voltage curve was obtained at each pixel in the scan area through a SHO-SNDM measurement. The obtained SNDM and SHO-SNDM data suggest that the i-layer was not completely intrinsic, but was very-low-density p-type.

  20. Mouse Skeletal Muscle Fiber-Type-Specific Macroautophagy and Muscle Wasting Are Regulated by a Fyn/STAT3/Vps34 Signaling Pathway

    Directory of Open Access Journals (Sweden)

    Eijiro Yamada

    2012-05-01

    Full Text Available Skeletal muscle atrophy induced by aging (sarcopenia, inactivity, and prolonged fasting states (starvation is predominantly restricted to glycolytic type II muscle fibers and typical spares oxidative type I fibers. However, the mechanisms accounting for muscle fiber-type specificity of atrophy have remained enigmatic. In the current study, although the Fyn tyrosine kinase activated the mTORC1 signaling complex, it also induced marked atrophy of glycolytic fibers with relatively less effect on oxidative muscle fibers. This was due to inhibition of macroautophagy via an mTORC1-independent but STAT3-dependent reduction in Vps34 protein levels and decreased Vps34/p150/Beclin1/Atg14 complex 1. Physiologically, in the fed state endogenous Fyn kinase activity was increased in glycolytic but not oxidative skeletal muscle. In parallel, Y705-STAT3 phosphorylation increased with decreased Vps34 protein levels. Moreover, fed/starved regulation of Y705-STAT3 phosphorylation and Vps34 protein levels was prevented in skeletal muscle of Fyn null mice. These data demonstrate a Fyn/STAT3/Vps34 pathway that is responsible for fiber-type-specific regulation of macroautophagy and skeletal muscle atrophy.

  1. Classifying the motion of visual stimuli from the spike response of a population of retinal ganglion cells.

    Science.gov (United States)

    Cerquera, Alexander; Greschner, Martin; Freund, Jan A

    2008-01-01

    We present an analysis of the spike response of a retinal ganglion cell ensemble. The retina of a turtle was stimulated in vitro by moving light patterns. Its non-steady motion was specified by two features: changes of direction and changes of speed. The spike response of a ganglion cell population was recorded extracellularly with a multielectrode array and responding neurons were identified through spike sorting. Restricting further analysis to a time window of greatest firing activity, we selected a subset of cells with reliable firing patterns, excluding cells that were not selective to the stimulus. The reliability of a firing pattern was assessed on the single cell level in terms of two measures: temporal precision (jitter) of the first spike and the fraction of trials in which a spike was generated. We then condensed the spike response of the extracted group by merging the multivariate spike trains into a single spike train. Finally, we compared different coding hypotheses that are based on the timing of the first and the second spike of the population or the spike count in the preselected time window. We found that the second spike of the population significantly increases the classification efficiency beyond that of the first spike. Moreover, the combination of first plus second spike is comparably efficient as the combination of the first spike plus the spike count but allows for a classification that is much faster. PMID:19163609

  2. Visualization of cell death in mice with focal cerebral ischemia using fluorescent annexin A5, propidium iodide, and TUNEL staining

    OpenAIRE

    Bahmani, Peyman; Schellenberger, Eyk; Klohs, Jan; Steinbrink, Jens; Cordell, Ryan; Zille, Marietta; Müller, Jochen; Harhausen, Denise; Hofstra, Leo; Reutelingsperger, Chris; Farr, Tracy Deanne; Dirnagl, Ulrich; Wunder, Andreas

    2011-01-01

    To monitor stroke-induced brain damage and assess neuroprotective therapies, specific imaging of cell death after cerebral ischemia in a noninvasive manner is highly desirable. Annexin A5 has been suggested as a marker for imaging cell death under various disease conditions including stroke. In this study, C57BL6/N mice received middle cerebral artery occlusion (MCAO) and were injected intravenously with either active or inactive Cy5.5-annexin A5 48 hours after reperfusion. Some mice also rec...

  3. Proposal of the visual inspection of the integrity of the storage cells of spent fuel from the nuclear power plant of Laguna Verde

    International Nuclear Information System (INIS)

    As part of the evaluation of the structural integrity of the components of nuclear plants, particularly those applying for life extension is necessary to carry out inspections and nondestructive testing to determine the state meet. In many cases these activities are carried out in areas with high levels of radiation and contamination difficult to access, so that are required to use equipment or robotic systems operated remotely. Among others, the frames and cells of the storage pools for spent fuel are structures subject to a program of tests and inspections, and become relevant because the nuclear power plant of Laguna Verde (NPP-LV) is processing the license to extend the operational life of its reactors. Of non-destructive testing can be used to verify the physical condition of the frames and storage cells, is the remote visual inspection which is a test that allows determine the physical integrity of the components by one or more video cameras designed to applications in underwater environments with radiation, and are used to identify and locate adverse conditions such as ampoules, protuberances, pitting, cracks, stains or buckling, which could affect the three main functions for which the store components are designed: to maintain the physical integrity of spent fuels, store them properly guaranteeing their free insertion and removal, and ensure that the store as a whole meets the criticality criteria that keff is less than 0.95 throughout the life of the plant. This paper describes a proposal to carry out the visual inspection of the storage cells of spent fuel from the NPP-LV using a probe including one or more video cameras along with your recorder, and its corresponding control program. It is noted that due to the obtained results, the nuclear power plant personnel can make decisions regarding remedial actions or applying complementary methods to verify that the cells and frames have not lost their physical integrity, or in particular that the cover plates

  4. Chronic cellular imaging of mouse visual cortex during operant behavior and passive viewing

    Directory of Open Access Journals (Sweden)

    Mark L Andermann

    2010-03-01

    Full Text Available Nearby neurons in mammalian neocortex demonstrate a great diversity of cell types and connectivity patterns. The importance of this diversity for computation is not understood. While extracellular recording studies in visual cortex have provided a particularly rich description of behavioral modulation of neural activity, new methods are needed to dissect the contribution of specific circuit elements in guiding visual perception. Here, we describe a method for three-dimensional cellular imaging of neural activity in the awake mouse visual cortex during active discrimination and passive viewing of visual stimuli. Head-fixed mice demonstrated robust discrimination for many hundred trials per day after initial task acquisition. To record from multiple neurons during operant behavior with single-trial resolution and minimal artifacts, we built a sensitive microscope for two-photon calcium imaging, capable of rapid tracking of neurons in three dimensions. We demonstrate stable recordings of cellular calcium activity during discrimination behavior across hours, days, and weeks, using both synthetic and genetically-encoded calcium indicators. When combined with molecular and genetic technologies in mice (e.g., cell-type specific transgenic labeling, this approach allows the identification of neuronal classes in vivo. Physiological measurements from distinct classes of neighboring neurons will enrich our understanding of the coordinated roles of diverse elements of cortical microcircuits in guiding sensory perception and perceptual learning. Further, our method provides a high-throughput, chronic in vivo assay of behavioral influences on cellular activity that is applicable to a wide range of mouse models of neurologic disease.

  5. Cell-Type Specific Insertion of GluA2-Lacking AMPARs with Cocaine Exposure Leading to Sensitization, Cue-Induced Seeking, and Incubation of Craving.

    Science.gov (United States)

    Terrier, Jean; Lüscher, Christian; Pascoli, Vincent

    2016-06-01

    Addiction is a behavioral disease, of which core components can be modeled in rodents. Much evidence implicates drug-evoked synaptic plasticity in cocaine-evoked locomotor sensitization, cue-induced cocaine seeking, and incubation of cocaine craving. However, the type of plasticity evoked by different modalities of cocaine administration (eg contingent vs non-contingent) and its role in reshaping circuit function remains largely elusive. Here we exposed mice to various regimens of cocaine and recorded excitatory transmission onto identified medium-sized spiny neurons (MSN, expressing fluorescent proteins under the control of either D1R or D2R dopamine receptor promotor) in the nucleus accumbens at time points when behavioral adaptations are observed. In D1-MSN, we found the presence of GluA2-lacking α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) after single or chronic non-contingent exposure to cocaine as well as after cocaine self-administration (SA). We also report an increase in the AMPA/NMDA ratio (A/N) in D1-MSN, which was observed only after repeated passive injections associated with locomotor sensitization as well as in a condition of SA leading to seeking behavior. Remarkably, insertion of GluA2-lacking AMPARs was also detected in D2-MSN after SA of a high dose of cocaine but not regular dose (1.5 vs 0.75 mg/kg), which was the only condition where incubation of cocaine craving was observed in this study. Moreover, synapses containing GluA2-lacking AMPARs belonged to amygdala inputs in D2-MSN and to medial prefrontal cortex inputs in D1-MSN. Taken together this study allows for a refinement of a circuit model of addiction based on specific synaptic changes induced by cocaine. PMID:26585289

  6. Antiestrogenic activity of flavnoid phytochemicals mediated via c-Jun N-terminal protein kinase pathway. Cell-type specific regulation of estrogen receptor alpha

    Science.gov (United States)

    Flavonoid phytochemicals act as both agonists and antagonists of the human estrogen receptors (ERs). While a number of these compounds act by directly binding to the ER, certain phytochemicals, such as the flavonoid compounds chalcone and flavone, elicit antagonistic effects on estrogen signaling in...

  7. Cell-type specific recognition of human Metapneumoviruses by RIG-I and TLR7 and viral interference of RIG-I ligand recognition by HMPVB1 Phosphoprotein

    OpenAIRE

    Goutagny, Nadege; Jiang, Zhaozhao; Tian, Jane; Parroche, Peggy; Schlicki, Jeanne; Monks, Brian G; Ulbrandt, Nancy; Ji, Hong; Kiener, Peter; Coyle, Anthony J.; Fitzgerald, Katherine A.

    2009-01-01

    Human Metapneumoviruses (HMPV) are recently identified Paramyxoviridae that contribute to respiratory tract infections in children. No effective treatments or vaccines are available. Successful defense against virus infection relies on early detection by germline encoded pattern recognition receptors and activation of cytokine and type I interferon genes. Recently, the RNA helicase Retinoic acid inducible gene (RIG-I) has been shown to sense HMPV. In this study, we investigated the ability of...

  8. Expression of the Ly-6 family proteins Lynx1 and Ly6H in the rat brain is compartmentalized, cell-type specific, and developmentally regulated

    DEFF Research Database (Denmark)

    Thomsen, Morten Skøtt; Cinar, Betül; Jensen, Majbrit Myrup;

    2014-01-01

    The Ly-6 superfamily of proteins, which affects diverse processes in the immune system, has attracted renewed attention due to the ability of some Ly-6 proteins to bind to and modulate the function of neuronal nicotinic acetylcholine receptors (nAChRs). However, there is a scarcity of knowledge r...

  9. Live-Cell Imaging Visualizes Frequent Mitotic Skipping During Senescence-Like Growth Arrest in Mammary Carcinoma Cells Exposed to Ionizing Radiation

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki, Masatoshi, E-mail: msuzuki@nagasaki-u.ac.jp [Department of Radiation Medical Sciences, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki (Japan); Yamauchi, Motohiro; Oka, Yasuyoshi; Suzuki, Keiji; Yamashita, Shunichi [Department of Radiation Medical Sciences, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki (Japan)

    2012-06-01

    Purpose: Senescence-like growth arrest in human solid carcinomas is now recognized as the major outcome of radiotherapy. This study was designed to analyze cell cycle during the process of senescence-like growth arrest in mammary carcinoma cells exposed to X-rays. Methods and Materials: Fluorescent ubiquitination-based cell cycle indicators were introduced into the human mammary carcinoma cell line MCF-7. Cell cycle was sequentially monitored by live-cell imaging for up to 5 days after exposure to 10 Gy of X-rays. Results: Live-cell imaging revealed that cell cycle transition from G2 to G1 phase without mitosis, so-called mitotic skipping, was observed in 17.1% and 69.8% of G1- and G2-irradiated cells, respectively. Entry to G1 phase was confirmed by the nuclear accumulation of mKO{sub 2}-hCdt1 as well as cyclin E, which was inversely correlated to the accumulation of G2-specific markers such as mAG-hGeminin and CENP-F. More than 90% of cells skipping mitosis were persistently arrested in G1 phase and showed positive staining for the senescent biochemical marker, which is senescence-associated ss-galactosidase, indicating induction of senescence-like growth arrest accompanied by mitotic skipping. While G2 irradiation with higher doses of X-rays induced mitotic skipping in approximately 80% of cells, transduction of short hairpin RNA (shRNA) for p53 significantly suppressed mitotic skipping, suggesting that ionizing radiation-induced mitotic skipping is associated with p53 function. Conclusions: The present study found the pathway of senescence-like growth arrest in G1 phase without mitotic entry following G2-irradiation.

  10. Live-Cell Imaging Visualizes Frequent Mitotic Skipping During Senescence-Like Growth Arrest in Mammary Carcinoma Cells Exposed to Ionizing Radiation

    International Nuclear Information System (INIS)

    Purpose: Senescence-like growth arrest in human solid carcinomas is now recognized as the major outcome of radiotherapy. This study was designed to analyze cell cycle during the process of senescence-like growth arrest in mammary carcinoma cells exposed to X-rays. Methods and Materials: Fluorescent ubiquitination-based cell cycle indicators were introduced into the human mammary carcinoma cell line MCF-7. Cell cycle was sequentially monitored by live-cell imaging for up to 5 days after exposure to 10 Gy of X-rays. Results: Live-cell imaging revealed that cell cycle transition from G2 to G1 phase without mitosis, so-called mitotic skipping, was observed in 17.1% and 69.8% of G1- and G2-irradiated cells, respectively. Entry to G1 phase was confirmed by the nuclear accumulation of mKO2-hCdt1 as well as cyclin E, which was inversely correlated to the accumulation of G2-specific markers such as mAG-hGeminin and CENP-F. More than 90% of cells skipping mitosis were persistently arrested in G1 phase and showed positive staining for the senescent biochemical marker, which is senescence-associated ß-galactosidase, indicating induction of senescence-like growth arrest accompanied by mitotic skipping. While G2 irradiation with higher doses of X-rays induced mitotic skipping in approximately 80% of cells, transduction of short hairpin RNA (shRNA) for p53 significantly suppressed mitotic skipping, suggesting that ionizing radiation-induced mitotic skipping is associated with p53 function. Conclusions: The present study found the pathway of senescence-like growth arrest in G1 phase without mitotic entry following G2-irradiation.

  11. Variation in assessment of oxidatively damaged DNA in mononuclear blood cells by the comet assay with visual scoring

    DEFF Research Database (Denmark)

    Forchhammer, Lykke; Bräuner, Elvira Vaclavik; Folkmann, Janne Kjaersgaard;

    2008-01-01

    The comet assay is popular for assessments of genotoxicity, but the comparison of results between studies is challenging because of differences in experimental procedures and reports of DNA damage in different units. We investigated the variation of DNA damage in mononuclear blood cells (MNBCs......) measured by the comet assay with focus on the variation related to alkaline unwinding and electrophoresis time, number of cells scored, as well as the putative benefits of transforming the primary end points to common units by the use of reference standards and calibration curves. Eight experienced...... conclusion, our results indicate that inter-investigator difference in scoring is a strong determinant of DNA damage levels measured by the comet assay....

  12. From primordial germ cells to primordial follicles: a review and visual representation of early ovarian development in mice

    OpenAIRE

    Wear, Hannah M.; McPike, Matthew J; Watanabe, Karen H.

    2016-01-01

    Background Normal development of reproductive organs is crucial for successful reproduction. In mice the early ovarian developmental process occurs during the embryonic and postnatal period and is regulated through a series of molecular signaling events. Early ovarian development in mice is a seventeen-day process that begins with the rise of six primordial germ cells on embryonic day five (E5) and ends with the formation of primordial follicles on postnatal day two (P2). Results We reviewed ...

  13. Quantification and visualization of glutathione S-transferase omega 1 in cells using inductively coupled plasma mass spectrometry (ICP-MS) and fluorescence microscopy.

    Science.gov (United States)

    Liang, Yong; Jiang, Xin; Tang, Nannan; Yang, Limin; Chen, Haifeng; Wang, Qiuquan

    2015-03-01

    We report a novel activity-based and Cu-free click chemistry (CC) mediated methodology for glutathione S-transferase omega 1 (GSTO1) quantification using species-unspecific isotope dilution inductively coupled plasma mass spectrometry (SUID ICP-MS), in which dibenzylcyclooctyne-modified 2-chloroacetamide (DBCO-ChAcA) was designed and synthesized, meanwhile, as a navigator towards GSTO1 for subsequent N3-DOTA-Eu-tagging via Cu-free CC. Using (153)Eu-SUID ICP-MS coupled with size exclusion chromatography (SEC), the LOD (3σ) of GSTO1 reached 6.9 fmol with an RSD of 2.4% at the 0.1 μM level (n = 5) considering the recovery of GSTO1 on the SEC was 96.5 ± 2.4%. The GSTO1 contents in the cells of human hepatocellular carcinoma C7721 and breast carcinoma MCF-7 as well as normal hepatic C7701 without or with cis-platin administration were quantified to be from 1.2 μg/10,000 cells (n = 3, RSD = 4.5%) corresponding to 1.2 × 10(-2) ng per cell to 4.76 μg/10,000 cells (n = 3, RSD = 2.9%) corresponding to 4.76 × 10(-2) ng per cell. For a comparative study, DBCO-ChAcA-fluor 488-based fluorescence microscopy could not alone visualize GSTO1 in the cells but could together with those from the small SH-containing molecules such as GSH and that from extra N3-fluor 488 in the cells. This activity-based CC-mediated tagging/labeling strategy provided an opportunity for ICP-MS-based targeted protein quantification, and is very much expected to find its applications in biological mechanism study and the subsequent drug design. PMID:25410639

  14. Characterization of an antigenic site that contains a dominant, type-specific neutralization determinant on the envelope protein domain III (ED3) of dengue 2 virus

    International Nuclear Information System (INIS)

    The surface of the mature dengue virus (DENV) particle consists of 90 envelope (E) protein dimers that mediate both receptor binding and fusion. The E protein ectodomain can be divided into three structural domains designated ED1, ED2, and ED3, of which ED3 contains the critical and dominant virus-specific neutralization sites. In this study the ED3 epitopes recognized by seven, murine, IgG1 DENV-2 type-specific, monoclonal antibodies (MAbs) were determined using site-directed mutagenesis of a recombinant DENV-2 ED3 (rED3) protein. A total of 41 single amino acid substitutions were introduced into the rED3 at 30 different surface accessible residues. The affinity of each MAb with the mutant rED3s was assessed by indirect ELISA and the results indicate that all seven MAbs recognize overlapping epitopes with residues K305 and P384 critical for binding. These residues are conserved among DENV-2 strains and cluster together on the upper lateral face of ED3. A linear relationship was observed between relative occupancy of ED3 on the virion by MAb and neutralization of the majority of virus infectivity (∼ 90%) for all seven MAbs. Depending on the MAb, it is predicted that between 10% and 50% relative occupancy of ED3 on the virion is necessary for virus neutralization and for all seven MAbs occupancy levels approaching saturation were required for 100% neutralization of virus infectivity. Overall, the conserved antigenic site recognized by all seven MAbs is likely to be a dominant DENV-2 type-specific, neutralization determinant

  15. Reproducibility of 'Intelligent' Contouring of Gross Tumor Volume in Non-Small-Cell Lung Cancer on PET/CT Images Using a Standardized Visual Method

    International Nuclear Information System (INIS)

    Purpose: Positron emission tomography/computed tomography (PET/CT) is increasingly used for delineating gross tumor volume (GTV) in non-small-cell lung cancer (NSCLC). The methodology for contouring tumor margins remains controversial. We developed a rigorous visual protocol for contouring GTV that uses all available clinical information and studied its reproducibility in patients from a prospective PET/CT planning trial. Methods and Materials: Planning PET/CT scans from 6 consecutive patients were selected. Six 'observers' (two radiation oncologists, two nuclear medicine physicians, and two radiologists) contoured GTVs for each patient using a predefined protocol and subsequently recontoured 2 patients. For the estimated GTVs and axial distances, least-squares means for each observer and for each case were calculated and compared, using the F test and pairwise t-tests. In five cases, tumor margins were also autocontoured using standardized uptake value (SUV) cutoffs of 2.5 and 3.5 and 40% SUVmax. Results: The magnitude of variation between observers was small relative to the mean (coefficient of variation [CV] = 3%), and the total variation (intraclass correlation coefficient [ICC] = 3%). For estimation of superior/inferior (SI), left/right (LR), and anterior/posterior (AP) borders of the GTV, differences between observers were also small (AP, CV = 2%, ICC = 0.4%; LR, CV = 6%, ICC = 2%; SI, CV 4%, ICC = 2%). GTVs autocontoured generated using SUV 2.5, 3.5, and 40% SUVmax differed widely in each case. An SUV contour of 2.5 was most closely correlated with the mean GTV defined by the human observers. Conclusions: Observer variation contributed little to total variation in the GTV and axial distances. A visual contouring protocol gave reproducible results for contouring GTV in NSCLC.

  16. High-recovery visual identification and single-cell retrieval of circulating tumor cells for genomic analysis using a dual-technology platform integrated with automated immunofluorescence staining

    International Nuclear Information System (INIS)

    Circulating tumor cells (CTCs) are malignant cells that have migrated from solid cancers into the blood, where they are typically present in rare numbers. There is great interest in using CTCs to monitor response to therapies, to identify clinically actionable biomarkers, and to provide a non-invasive window on the molecular state of a tumor. Here we characterize the performance of the AccuCyte® – CyteFinder® system, a comprehensive, reproducible and highly sensitive platform for collecting, identifying and retrieving individual CTCs from microscopic slides for molecular analysis after automated immunofluorescence staining for epithelial markers. All experiments employed a density-based cell separation apparatus (AccuCyte) to separate nucleated cells from the blood and transfer them to microscopic slides. After staining, the slides were imaged using a digital scanning microscope (CyteFinder). Precisely counted model CTCs (mCTCs) from four cancer cell lines were spiked into whole blood to determine recovery rates. Individual mCTCs were removed from slides using a single-cell retrieval device (CytePicker™) for whole genome amplification and subsequent analysis by PCR and Sanger sequencing, whole exome sequencing, or array-based comparative genomic hybridization. Clinical CTCs were evaluated in blood samples from patients with different cancers in comparison with the CellSearch® system. AccuCyte – CyteFinder presented high-resolution images that allowed identification of mCTCs by morphologic and phenotypic features. Spike-in mCTC recoveries were between 90 and 91%. More than 80% of single-digit spike-in mCTCs were identified and even a single cell in 7.5 mL could be found. Analysis of single SKBR3 mCTCs identified presence of a known TP53 mutation by both PCR and whole exome sequencing, and confirmed the reported karyotype of this cell line. Patient sample CTC counts matched or exceeded CellSearch CTC counts in a small feasibility cohort. The AccuCyte

  17. Live-cell imaging of phosphatidic acid dynamics in pollen tubes visualized by Spo20p-derived biosensor

    Czech Academy of Sciences Publication Activity Database

    Potocký, Martin; Pleskot, Roman; Pejchar, Přemysl; Vitale, N.; Kost, B.; Žárský, Viktor

    2014-01-01

    Roč. 203, č. 2 (2014), s. 483-494. ISSN 0028-646X R&D Projects: GA ČR GA13-19073S Institutional support: RVO:61389030 Keywords : live-cell microscopy * Nicotiana tabacum (tobacco) * phosphatidic acid (PA) Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 7.672, year: 2014 http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=CCC&DestLinkType=FullRecord&UT=000337639800015

  18. Glow in the Dark: Fluorescent Proteins as Cell and Tissue-Specific Markers in Plants

    Institute of Scientific and Technical Information of China (English)

    Wenzislava Ckurshumova; Adriana E. Caragea; Rochelle S. Goldstein; Thomas Berleth

    2011-01-01

    Since the hallmark discovery of Aequorea victoria's Green Fluorescent Protein (GFP) and its adaptation for efficient use in plants,fluorescent protein tags marking expression profiles or genuine proteins of interest have been used to recognize plant tissues and cell types,to monitor dynamic cell fate selection processes,and to obtain cell type-specific transcriptomes.Fluorescent tagging enabled visualization in living tissues and the precise recordings of dynamic expression pattern changes.The resulting accurate recording of cell fate acquisition kinetics in space and time has strongly stimulated mathematical modeling of self-organizing feedback mechanisms.In developmental studies,the use of fluorescent proteins has become critical,where morphological markers of tissues,cell types,or differentiation stages are either not known or not easily recognizable.In this review,we focus on the use of fluorescent markers to identify and illuminate otherwise invisible cell states in plant development.

  19. Visualization of the Epiblast and Visceral Endodermal Cells Using Fgf5-P2A-Venus BAC Transgenic Mice and Epiblast Stem Cells

    Science.gov (United States)

    Tsukiyama, Tomoyuki; Matsushita, Jun; Tsukiyama-Fujii, Setsuko; Takahashi, Satoru; Ema, Masatsugu

    2016-01-01

    Fibroblast growth factor 5 (Fgf5) has been widely used as a marker for the epiblast in the postimplantation embryo and epiblast stem cells (mEpiSCs) in the mouse, making it valuable for study of differentiation of various tissues and epiblast cells in vivo and in vitro. Here, we report for the first time the generation of Fgf5-P2A-Venus BAC transgenic (Tg) mice and show that the BAC Tg can recapitulate endogenous Fgf5 expression in epiblast and visceral endodermal cells of E6.5 and 7.5 embryos. We also show that Fgf5-P2A-Venus BAC Tg mEpiSCs in the undifferentiated state expressed abundant Venus, and upon reprogramming into naïve state, Venus was suppressed. Furthermore, while most Tg mEpiSCs expressed Venus abundantly, surprisingly the Tg mEpiSCs contained a minor subpopulation of Venus-negative cells that were capable of conversion to Venus-positive cells, indicating that even Fgf5 expression shows dynamic heterogeneity in mEpiSCs. Taken together, Fgf5-P2A-Venus BAC Tg mice and mEpiSCs generated in this study will be useful for developmental biology as well as stem cell biology research. PMID:27409080

  20. Bimolecular Complementation to Visualize Filovirus VP40-Host Complexes in Live Mammalian Cells: Toward the Identification of Budding Inhibitors

    Directory of Open Access Journals (Sweden)

    Yuliang Liu

    2011-01-01

    Full Text Available Virus-host interactions play key roles in promoting efficient egress of many RNA viruses, including Ebola virus (EBOV or “e” and Marburg virus (MARV or “m”. Late- (L- domains conserved in viral matrix proteins recruit specific host proteins, such as Tsg101 and Nedd4, to facilitate the budding process. These interactions serve as attractive targets for the development of broad-spectrum budding inhibitors. A major gap still exists in our understanding of the mechanism of filovirus budding due to the difficulty in detecting virus-host complexes and mapping their trafficking patterns in the natural environment of the cell. To address this gap, we used a bimolecular complementation (BiMC approach to detect, localize, and follow the trafficking patterns of eVP40-Tsg101 complexes in live mammalian cells. In addition, we used the BiMC approach along with a VLP budding assay to test small molecule inhibitors identified by in silico screening for their ability to block eVP40 PTAP-mediated interactions with Tsg101 and subsequent budding of eVP40 VLPs. We demonstrated the potential broad spectrum activity of a lead candidate inhibitor by demonstrating its ability to block PTAP-dependent binding of HIV-1 Gag to Tsg101 and subsequent egress of HIV-1 Gag VLPs.

  1. A pyrene-benzthiazolium conjugate portraying aggregation induced emission, a ratiometric detection and live cell visualization of HSO3(.).

    Science.gov (United States)

    Diwan, Uzra; Kumar, Virendra; Mishra, Rakesh K; Rana, Nishant Kumar; Koch, Biplob; Singh, Manish Kumar; Upadhyay, K K

    2016-07-27

    The present study deals with the photophysical property of a pyrene-benzthiazolium conjugate R1, as a strong intramolecular charge transfer (ICT) probe exhibiting long wavelength emission in the red region. Unlike traditional planar polyaromatic hydrocarbons whose aggregation generally quenches the light emission, the pyrene based R1 was found to display aggregation-induced emission (AIE) property along with simultaneous increase in its quantum yield upon increasing the water content of the medium. The R1 exhibits high specificity towards HSO3(-)/SO3(2-) by interrupting its own ICT producing there upon a large ratiometric blue shift of ∼220 nm in its emission spectrum. The lowest detection limit for the above measurement was found to be 8.90 × 10(-8) M. The fluorescent detection of HSO3(-) was also demonstrated excellently by test paper strip and silica coated TLC plate incorporating R1. The live cell imaging of HSO3(─) through R1 in HeLa cells was studied using fluorescence microscopic studies. The particle size and morphological features of R1 and R1-HSO3(-) aggregates in aqueous solution were characterized by DLS along with SEM analysis. PMID:27251947

  2. Visualization rhetoric: framing effects in narrative visualization.

    Science.gov (United States)

    Hullman, Jessica; Diakopoulos, Nicholas

    2011-12-01

    Narrative visualizations combine conventions of communicative and exploratory information visualization to convey an intended story. We demonstrate visualization rhetoric as an analytical framework for understanding how design techniques that prioritize particular interpretations in visualizations that "tell a story" can significantly affect end-user interpretation. We draw a parallel between narrative visualization interpretation and evidence from framing studies in political messaging, decision-making, and literary studies. Devices for understanding the rhetorical nature of narrative information visualizations are presented, informed by the rigorous application of concepts from critical theory, semiotics, journalism, and political theory. We draw attention to how design tactics represent additions or omissions of information at various levels-the data, visual representation, textual annotations, and interactivity-and how visualizations denote and connote phenomena with reference to unstated viewing conventions and codes. Classes of rhetorical techniques identified via a systematic analysis of recent narrative visualizations are presented, and characterized according to their rhetorical contribution to the visualization. We describe how designers and researchers can benefit from the potentially positive aspects of visualization rhetoric in designing engaging, layered narrative visualizations and how our framework can shed light on how a visualization design prioritizes specific interpretations. We identify areas where future inquiry into visualization rhetoric can improve understanding of visualization interpretation. PMID:22034342

  3. Assessment of brain cell function using 123I-IMP SPECT of cerebral blood flow and visual evoked potential by photic stimulation in normal and demented elderly subjects

    International Nuclear Information System (INIS)

    Cerebral blood flow was quantitatively measured using 123I-IMP SPECT by photic stimulation and visual evoked potential (VEPs) in normal and dementia subjects: 8 with Alzheimer-type dementia, 9 with cerebrovascular dementia and 7 normal elderly subjects were divided into the three groups based on the Clinical Dementia Rating (CDR) grade: Group I (CDR 0), Group II (CDR 0.5-1), Group III (CDR 2-3). The 123I-IMP SPECT measurement was conducted at rest with the eyes closed and also during photic stimulation. VEPs were measured simultaneously. The results reveal prolongation of the P2 latency of the VEPs prolonged in accordance with the increasing severity of the dementia, and quantitative cerebral blood flow was lower in Group II and Group III than in Group I at rest, while during photic stimulation it significantly increased in Group I and II, but showed no change in Group III. The results suggest that quantitative measurement of cerebral blood flow using 123I-IMP SPECT by photic stimulation may enable more detailed assessment of brain cell function. (author)

  4. Long-term high-fat-diet feeding induces skeletal muscle mitochondrial biogenesis in rats in a sex-dependent and muscle-type specific manner

    Directory of Open Access Journals (Sweden)

    Gómez-Pérez Yolanda

    2012-02-01

    Full Text Available Abstract Background Mitochondrial dysfunction is thought to play a crucial role in the etiology of insulin resistance, in which skeletal muscle is the main tissue contributor. Sex differences in skeletal muscle insulin and antioxidant responses to high-fat-diet (HFD feeding have been described. The aim of this study was to elucidate whether there is a sex dimorphism in the effects of HFD feeding on skeletal muscle mitochondrial biogenesis and on the adiponectin signaling pathway, as well as the influence of the muscle type (oxidative or glycolytic. Methods Gastrocnemius and soleus muscles of male and female Wistar rats of 2 months of age fed with a high-fat-diet (HFD or a low fat diet for 26 weeks were used. Mitochondrial biogenesis and oxidative damage markers, oxidative capacity and antioxidant defences were analyzed. Serum insulin sensitivity parameters and the levels of proteins involved in adiponectin signaling pathway were also determined. Results HFD feeding induced mitochondrial biogenesis in both sexes, but to a higher degree in male rats. Although HFD female rats showed greater antioxidant protection and maintained a better insulin sensitivity profile than their male counterparts, both sexes showed an impaired response to adiponectin, which was more evident in gastrocnemius muscle. Conclusions We conclude that HFD rats may induce skeletal muscle mitochondrial biogenesis as an attempt to compensate the deleterious consequences of adiponectin and insulin resistance on oxidative metabolism, and that the effects of HFD feeding are sex-dependent and muscle-type specific.

  5. Why Teach Visual Culture?

    Science.gov (United States)

    Passmore, Kaye

    2007-01-01

    Visual culture is a hot topic in art education right now as some teachers are dedicated to teaching it and others are adamant that it has no place in a traditional art class. Visual culture, the author asserts, can include just about anything that is visually represented. Although people often think of visual culture as contemporary visuals such…

  6. Visualizing Gene Expression In Situ

    Energy Technology Data Exchange (ETDEWEB)

    Burlage, R.S.

    1998-11-02

    Visualizing bacterial cells and describing their responses to the environment are difficult tasks. Their small size is the chief reason for the difficulty, which means that we must often use many millions of cells in a sample in order to determine what the average response of the bacteria is. However, an average response can sometimes mask important events in bacterial physiology, which means that our understanding of these organisms will suffer. We have used a variety of instruments to visualize bacterial cells, all of which tell us something different about the sample. We use a fluorescence activated cell sorter to sort cells based on the fluorescence provided by bioreporter genes, and these can be used to select for particular genetic mutations. Cells can be visualized by epifluorescent microscopy, and sensitive photodetectors can be added that allow us to find a single bacterial cell that is fluorescent or bioluminescent. We have also used standard photomultipliers to examine cell aggregates as field bioreporter microorganisms. Examples of each of these instruments show how our understanding of bacterial physiology has changed with the technology.

  7. Data Visualization and Infographics

    OpenAIRE

    Prepared by Mathematica Policy Research

    2014-01-01

    Data visualization translates complex ideas and concepts into a simple visual context. Patterns, trends, and relationships that might go undetected in text are conveyed at a glance in effective data visualization.

  8. Learning Visualizations by Analogy: Promoting Visual Literacy through Visualization Morphing.

    Science.gov (United States)

    Ruchikachorn, Puripant; Mueller, Klaus

    2015-09-01

    We propose the concept of teaching (and learning) unfamiliar visualizations by analogy, that is, demonstrating an unfamiliar visualization method by linking it to another more familiar one, where the in-betweens are designed to bridge the gap of these two visualizations and explain the difference in a gradual manner. As opposed to a textual description, our morphing explains an unfamiliar visualization through purely visual means. We demonstrate our idea by ways of four visualization pair examples: data table and parallel coordinates, scatterplot matrix and hyperbox, linear chart and spiral chart, and hierarchical pie chart and treemap. The analogy is commutative i.e. any member of the pair can be the unfamiliar visualization. A series of studies showed that this new paradigm can be an effective teaching tool. The participants could understand the unfamiliar visualization methods in all of the four pairs either fully or at least significantly better after they observed or interacted with the transitions from the familiar counterpart. The four examples suggest how helpful visualization pairings be identified and they will hopefully inspire other visualization morphings and associated transition strategies to be identified. PMID:26357285

  9. Anti-proliferative and anti-tumour effects of lymphocyte-derived microparticles are neither species- nor tumour-type specific

    Directory of Open Access Journals (Sweden)

    Chun Yang

    2014-05-01

    Full Text Available Background: Unregulated cell proliferation or growth is a prominent characteristic of cancer. We have previously demonstrated that LMPs (cell membrane microparticles derived from apoptotic human CEM T lymphoma cells stimulated with actinomycin D strongly suppress the proliferation of not only human endothelial cells but also mouse Lewis lung carcinoma cells. Methods: LMPs were generated either from CEM T cells using different stimuli or from 3 different types of lymphocytes. The effects of LMPs on cancer cell proliferation were examined using cell lines from different species and tissues. The cell cycle kinetics was evaluated by FACS and the expression of cell cycle-related genes was determined using quantitative RT-PCR. The in vivo anti-tumor effect of LMPs was investigated using xenografts and allografts. Results: LMPs at doses far above physiological levels dramatically suppressed the proliferation of cancer cells in a non species-specific manner. LMPs selectively target high proliferating cells and their anti-proliferative effect is not dependent on parental cell origin or stimuli. The anti-proliferative effect of LMPs was due to induction of cell-cycle arrest in G0/G1, with associated increases in expression of the cyclin-dependent kinase inhibitors p15INK4b, p16INK4a, and p21Cip1. In vivo, LMPs significantly suppressed tumor growth in animal tumor models. Conclusion: These results highlight the potential role of LMPs in modulating the growth of high proliferating cells. Given that cell-based therapies are considered less toxic than pharmacologic approaches and have the potential to target multiple pathways in a synergistic manner, LMPs may serve as a veritable option for cancer treatment.

  10. Summer depth distribution profiles of dissolved CO2 and O2 in shallow temperate lakes reveal trophic state and lake type specific differences.

    Science.gov (United States)

    Laas, Alo; Cremona, Fabien; Meinson, Pille; Rõõm, Eva-Ingrid; Nõges, Tiina; Nõges, Peeter

    2016-10-01

    Knowledge about dissolved oxygen (DO) and carbon dioxide (CO2) distribution in lakes has increased considerably over the last decades. However, studies about high resolution dynamics of dissolved CO2 in different types of lakes over daily or weekly time scales are still very scarce. We measured summertime vertical DO and CO2 profiles at sub-hourly intervals during one week in eight Estonian lakes representing different lake types according to European Water Framework Directive. The lakes showed considerable differences in thermal stratification and vertical distribution of dissolved oxygen and CO2 as well as different diurnal dynamics over the measurement period. We observed a continuous CO2 supersaturation in the upper mixed layer of the alkalitrophic (calcareous groundwater-fed) lake and the dark soft-water lake showing them as CO2 emitting "chimneys" although with different underlying mechanisms. In three lake types strong undersaturation with CO2 occurred in the surface layer characterising them as CO2 sinks for the measurement period while in another three types the surface layer CO2 was mostly in equilibrium with the atmosphere. Factor analysis showed that DO% in the surface layer and the strength of its relationship with CO2% were positively related to alkalinity and negatively to trophic state and DOC gradients, whereas deeper lakes were characterised by higher surface concentration but smaller spatial and temporal variability of CO2. Multiple regression analysis revealed lake area, maximum depth and the light attenuation coefficient as variables affecting the largest number of gas regime indicators. We conclude that the trophic status of lakes in combination with type specific features such as morphometry, alkalinity and colour (DOC) determines the distribution and dynamics of dissolved CO2 and DO, which therefore may indicate functional differences in carbon cycling among lakes. PMID:27213672

  11. Neocortical Rebound Depolarization Enhances Visual Perception.

    Science.gov (United States)

    Funayama, Kenta; Minamisawa, Genki; Matsumoto, Nobuyoshi; Ban, Hiroshi; Chan, Allen W; Matsuki, Norio; Murphy, Timothy H; Ikegaya, Yuji

    2015-08-01

    Animals are constantly exposed to the time-varying visual world. Because visual perception is modulated by immediately prior visual experience, visual cortical neurons may register recent visual history into a specific form of offline activity and link it to later visual input. To examine how preceding visual inputs interact with upcoming information at the single neuron level, we designed a simple stimulation protocol in which a brief, orientated flashing stimulus was subsequently coupled to visual stimuli with identical or different features. Using in vivo whole-cell patch-clamp recording and functional two-photon calcium imaging from the primary visual cortex (V1) of awake mice, we discovered that a flash of sinusoidal grating per se induces an early, transient activation as well as a long-delayed reactivation in V1 neurons. This late response, which started hundreds of milliseconds after the flash and persisted for approximately 2 s, was also observed in human V1 electroencephalogram. When another drifting grating stimulus arrived during the late response, the V1 neurons exhibited a sublinear, but apparently increased response, especially to the same grating orientation. In behavioral tests of mice and humans, the flashing stimulation enhanced the detection power of the identically orientated visual stimulation only when the second stimulation was presented during the time window of the late response. Therefore, V1 late responses likely provide a neural basis for admixing temporally separated stimuli and extracting identical features in time-varying visual environments. PMID:26274866

  12. Snowflake Visualization

    Science.gov (United States)

    Bliven, L. F.; Kucera, P. A.; Rodriguez, P.

    2010-12-01

    NASA Snowflake Video Imagers (SVIs) enable snowflake visualization at diverse field sites. The natural variability of frozen precipitation is a complicating factor for remote sensing retrievals in high latitude regions. Particle classification is important for understanding snow/ice physics, remote sensing polarimetry, bulk radiative properties, surface emissivity, and ultimately, precipitation rates and accumulations. Yet intermittent storms, low temperatures, high winds, remote locations and complex terrain can impede us from observing falling snow in situ. SVI hardware and software have some special features. The standard camera and optics yield 8-bit gray-scale images with resolution of 0.05 x 0.1 mm, at 60 frames per second. Gray-scale images are highly desirable because they display contrast that aids particle classification. Black and white (1-bit) systems display no contrast, so there is less information to recognize particle types, which is particularly burdensome for aggregates. Data are analyzed at one-minute intervals using NASA's Precipitation Link Software that produces (a) Particle Catalogs and (b) Particle Size Distributions (PSDs). SVIs can operate nearly continuously for long periods (e.g., an entire winter season), so natural variability can be documented. Let’s summarize results from field studies this past winter and review some recent SVI enhancements. During the winter of 2009-2010, SVIs were deployed at two sites. One SVI supported weather observations during the 2010 Winter Olympics and Paralympics. It was located close to the summit (Roundhouse) of Whistler Mountain, near the town of Whistler, British Columbia, Canada. In addition, two SVIs were located at the King City Weather Radar Station (WKR) near Toronto, Ontario, Canada. Access was prohibited to the SVI on Whistler Mountain during the Olympics due to security concerns. So to meet the schedule for daily data products, we operated the SVI by remote control. We also upgraded the

  13. VISUAL LANDSCAPE PERCEPTION

    OpenAIRE

    ASLAN, Fürüzan; Aslan, Edanur; Atik, Atilla

    2015-01-01

    Landscape, the way that people perceive, is described as areas the characteristics of which are made up as a result of the interaction and activity of natural and/or human factors. The composition which is formed as a result of this interaction of natural and cultural components sets forth the visual landscape conception.In the scope of study landscape, perception, visual landscape concepts, visual design factors and visual design principles in support of related descriptions and the visuals ...

  14. Visual thinking & digital imagery

    OpenAIRE

    Blevis, Eli; Churchill, Elizabeth; Odom, William; Pierre, James; Roedl, David; Wakkary, Ron

    2012-01-01

    This workshop focuses on exploring the centrality of visual literacy and visual thinking to HCI. Drawing on emerging critical perspectives, the workshop will address visual literacy and visual thinking from an interdisciplinary and transdisciplinary design-orientation [2, 8], foregrounding the notion that imagery is a primary form of visual thinking. Imagery—which subsumes digital imagery—goes well beyond sketching and beyond storyboards, screenshots and wireframes. We will address how a broa...

  15. Qualitative visual trichotomous assessment improves the value of fluorine-18 fluorodeoxyglucose positron emission tomography/computed tomography in predicting the prognosis of diffuse large B-cell lymphoma

    Institute of Scientific and Technical Information of China (English)

    Xu Zhang; Wei Fan; Ying-Ying Hu; Zhi-Ming Li; Zhong-Jun Xia; Xiao-Ping Lin; Ya-Rui Zhang; Pei-Yan Liang; Yuan-Hua Li

    2015-01-01

    Introduction:Fluorine-18 fluorodeoxyglucose (18 F-FDG) positron emission tomography/computed tomography (PET/CT) is a powerful tool for monitoring the response of diffuse large B-cell lymphoma (DLBCL) to therapy, but the criteria to interpret PET/CT results remain under debate. We investigated the value of post-treatment PET/CT in predicting the prognosis of DLBCL patients when interpreted according to qualitative visual trichotomous assessment (QVTA) criteria compared with the Deauvil e criteria. Methods:In this retrospective study, final PET/CT scans of DLBCL patients treated with rituximab-based regimens between October 2005 and November 2010 were interpreted using the Deauvil e and QVTA criteria. Survival curves were estimated using Kaplan-Meier analysis and compared using the log-rank test. Results:A total of 253 patients were enrol ed. The interpretation according to the Deauvil e criteria revealed that 181 patients had negative PET/CT scan results and 72 had positive results. The 3 year overal survival (OS) rate was significantly higher in patients with negative scan results than in those with positive results (91.6%vs. 57.5%, P<0.001). The 72 patients with positive scan results according to the Deauville criteria were divided into two groups by the interpretation according to the QVTA criteria:29 had indeterminate results, and 43 had positive results. The 3 year OS rate was significantly higher in patients with indeterminate scan results than in those with positive results (91.2%vs. 33.5%, P<0.001) but was similar between patients with negative and indeterminate scan results (91.6%vs. 91.2%, P=0.921). Conclusions:Compared with the Deauvil e criteria, using the QVTA criteria for interpreting post-treatment PET/CT scans of DLBCL patients is likely to reduce the number of false positive results. The QVTA criteria are feasible for therapeutic outcome evaluation and can be used to guide risk-adapted therapy.

  16. A neural theory of visual attention

    DEFF Research Database (Denmark)

    Bundesen, Claus; Habekost, Thomas; Kyllingsbæk, Søren

    2005-01-01

    A neural theory of visual attention (NTVA) is presented. NTVA is a neural interpretation of C. Bundesen's (1990) theory of visual attention (TVA). In NTVA, visual processing capacity is distributed across stimuli by dynamic remapping of receptive fields of cortical cells such that more processing...... resources (cells) are devoted to behaviorally important objects than to less important ones. By use of the same basic equations used in TVA, NTVA accounts for a wide range of known attentional effects in human performance (reaction times and error rates) and a wide range of effects observed in firing rates...

  17. Visualization analysis and design

    CERN Document Server

    Munzner, Tamara

    2015-01-01

    Visualization Analysis and Design provides a systematic, comprehensive framework for thinking about visualization in terms of principles and design choices. The book features a unified approach encompassing information visualization techniques for abstract data, scientific visualization techniques for spatial data, and visual analytics techniques for interweaving data transformation and analysis with interactive visual exploration. It emphasizes the careful validation of effectiveness and the consideration of function before form. The book breaks down visualization design according to three questions: what data users need to see, why users need to carry out their tasks, and how the visual representations proposed can be constructed and manipulated. It walks readers through the use of space and color to visually encode data in a view, the trade-offs between changing a single view and using multiple linked views, and the ways to reduce the amount of data shown in each view. The book concludes with six case stu...

  18. Universal visualization platform

    Science.gov (United States)

    Gee, Alexander G.; Li, Hongli; Yu, Min; Smrtic, Mary Beth; Cvek, Urska; Goodell, Howie; Gupta, Vivek; Lawrence, Christine; Zhou, Jainping; Chiang, Chih-Hung; Grinstein, Georges G.

    2005-03-01

    Although there are a number of visualization systems to choose from when analyzing data, only a few of these allow for the integration of other visualization and analysis techniques. There are even fewer visualization toolkits and frameworks from which one can develop ones own visualization applications. Even within the research community, scientists either use what they can from the available tools or start from scratch to define a program in which they are able to develop new or modified visualization techniques and analysis algorithms. Presented here is a new general-purpose platform for constructing numerous visualization and analysis applications. The focus of this system is the design and experimentation of new techniques, and where the sharing of and integration with other tools becomes second nature. Moreover, this platform supports multiple large data sets, and the recording and visualizing of user sessions. Here we introduce the Universal Visualization Platform (UVP) as a modern data visualization and analysis system.

  19. Interaction for visualization

    CERN Document Server

    Tominski, Christian

    2015-01-01

    Visualization has become a valuable means for data exploration and analysis. Interactive visualization combines expressive graphical representations and effective user interaction. Although interaction is an important component of visualization approaches, much of the visualization literature tends to pay more attention to the graphical representation than to interaction.The goal of this work is to strengthen the interaction side of visualization. Based on a brief review of general aspects of interaction, we develop an interaction-oriented view on visualization. This view comprises five key as

  20. Improved visualization of lung metastases at single cell resolution in mice by combined in-situ perfusion of lung tissue and X-Gal staining of lacZ-tagged tumor cells.

    Science.gov (United States)

    Arlt, Matthias J E; Born, Walter; Fuchs, Bruno

    2012-01-01

    Metastasis is the main cause of death in the majority of cancer types and consequently a main focus in cancer research. However, the detection of micrometastases by radiologic imaging and the success in their therapeutic eradication remain limited. While animal models have proven to be invaluable tools for cancer research, the monitoring/visualization of micrometastases remains a challenge and inaccurate evaluation of metastatic spread in preclinical studies potentially leads to disappointing results in clinical trials. Consequently, there is great interest in refining the methods to finally allow reproducible and reliable detection of metastases down to the single cell level in normal tissue. The main focus therefore is on techniques, which allow the detection of tumor cells in vivo, like micro-computer tomography (micro-CT), positron emission tomography (PET), bioluminescence or fluorescence imaging. We are currently optimizing these techniques for in vivo monitoring of primary tumor growth and metastasis in different osteosarcoma models. Some of these techniques can also be used for ex vivo analysis of metastasis beside classical methods like qPCR, FACS or different types of histological staining. As a benchmark, we have established in the present study the stable transfection or transduction of tumor cells with the lacZ gene encoding the bacterial enzyme β-galactosidase that metabolizes the chromogenic substrate 5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside (X-Gal) to an insoluble indigo blue dye and allows highly sensitive and selective histochemical blue staining of tumor cells in mouse tissue ex vivo down to the single cell level as shown here. This is a low-cost and not equipment-intensive tool, which allows precise validation of metastasis in studies assessing new anticancer therapies. A limiting factor of X-gal staining is the low contrast to e.g. blood-related red staining of well vascularized tissues. In lung tissue this problem can be solved by

  1. Visualization of Social Networks

    NARCIS (Netherlands)

    Boertjes, E.M.; Kotterink, B.; Jager, E.J.

    2011-01-01

    Current visualizations of social networks are mostly some form of node-link diagram. Depending on the type of social network, this can be some treevisualization with a strict hierarchical structure or a more generic network visualization.

  2. Visualizing Knowledge Domains.

    Science.gov (United States)

    Borner, Katy; Chen, Chaomei; Boyack, Kevin W.

    2003-01-01

    Reviews visualization techniques for scientific disciplines and information retrieval and classification. Highlights include historical background of scientometrics, bibliometrics, and citation analysis; map generation; process flow of visualizing knowledge domains; measures and similarity calculations; vector space model; factor analysis;…

  3. Constructing visual representations

    DEFF Research Database (Denmark)

    Huron, Samuel; Jansen, Yvonne; Carpendale, Sheelagh

    2014-01-01

    tangible building blocks. We learned that all participants, most of whom had little experience in visualization authoring, were readily able to create and talk about their own visualizations. Based on our observations, we discuss participants’ actions during the development of their visual representations......The accessibility of infovis authoring tools to a wide audience has been identified as a major research challenge. A key task in the authoring process is the development of visual mappings. While the infovis community has long been deeply interested in finding effective visual mappings......, comparatively little attention has been placed on how people construct visual mappings. In this paper, we present the results of a study designed to shed light on how people transform data into visual representations. We asked people to create, update and explain their own information visualizations using only...

  4. Topological Methods for Visualization

    Energy Technology Data Exchange (ETDEWEB)

    Berres, Anne Sabine [Los Alamos National Lab. (LANL), Los Alamos, NM (United Stat

    2016-04-07

    This slide presentation describes basic topological concepts, including topological spaces, homeomorphisms, homotopy, betti numbers. Scalar field topology explores finding topological features and scalar field visualization, and vector field topology explores finding topological features and vector field visualization.

  5. Visual experience and blindsight

    DEFF Research Database (Denmark)

    Overgaard, Morten

    2011-01-01

    Blindsight is classically defined as residual visual capacity, e.g., to detect and identify visual stimuli, in the total absence of perceptual awareness following lesions to V1. However, whereas most experiments have investigated what blindsight patients can and cannot do, the literature contains...... several, often contradictory, remarks about remaining visual experience. This review examines closer these remarks as well as experiments that directly approach the nature of possibly spared visual experiences in blindsight....

  6. Visual Data Mining Techniques

    OpenAIRE

    Keim, Daniel A.; Ward, Matthew O.

    2002-01-01

    Never before in history has data been generated at such high volumes as it is today. Exploring and analyzing the vast volumes of data has become increasingly difficult. Information visualization and visual data mining can help to deal with the flood of information. The advantage of visual data exploration is that the user is directly involved in the data mining process. There are a large number of information visualization techniques that have been developed over the last two decades to suppo...

  7. Visual explorer facilitator's guide

    CERN Document Server

    Palus, Charles J

    2010-01-01

    Grounded in research and practice, the Visual Explorer™ Facilitator's Guide provides a method for supporting collaborative, creative conversations about complex issues through the power of images. The guide is available as a component in the Visual Explorer Facilitator's Letter-sized Set, Visual Explorer Facilitator's Post card-sized Set, Visual Explorer Playing Card-sized Set, and is also available as a stand-alone title for purchase to assist multiple tool users in an organization.

  8. Tools for software visualization

    OpenAIRE

    Stojanova, Aleksandra; Stojkovic, Natasa; Bikov, Dusan

    2015-01-01

    Software visualization is a kind of computer art, and in the same time is a science for generating visual representations of different software aspects and of software development process. There are many tools that allow software visualization but we are focusing on some of them. In this paper will be examined in details just four tools: Jeliot 3, SRec, jGrasp and DDD. Visualizations that they produce will be reviewed and analyzed and will be mentioned possible places for their application. A...

  9. Acquisition of new infection and clearance of type-specific human papillomavirus infections in female students in Busan, South Korea: a follow-up study

    OpenAIRE

    Quint Wim; Franceschi Silvia; Ju Young-Hee; Oh Jin-Kyoung; Shin Hai-Rim

    2008-01-01

    Abstract Background Little is known about the natural history of human papillomavirus (HPV) infection in Asian women. Methods A follow-up study was conducted, with exfoliated cervicovaginal cells self-collected from, and questionnaires administered to 197 female students, aged 17–26 years, who had been already examined one and half years before. The presence of 25 HPV types was evaluated by a polymerase chain reaction-based assay. Results The acquisition of new infection for any HPV type amon...

  10. Professional Visual Studio 2010

    CERN Document Server

    Randolph, Nick; Anderson, Chris

    2010-01-01

    A must-have guide that covers all the new features of Visual Studio 2010. Visual Studio allows you to create and manage programming projects for the Windows platform, and the new 2010 version has undergone a major overhaul comprised of significant changes. Written by an author team of veteran programmers and developers, Professional Visual Studio 2010 gets you quickly up to speed on what you can expect from the newest version of Visual Studio. This book's first section is dedicated to familiarizing you with the core aspects of Visual Studio 2010. Everything you need is contained in the first f

  11. Python data visualization cookbook

    CERN Document Server

    Milovanovic, Igor

    2013-01-01

    This book is written in a Cookbook style targeted towards an advanced audience. It covers the advanced topics of data visualization in Python.Python Data Visualization Cookbook is for developers that already know about Python programming in general. If you have heard about data visualization but you don't know where to start, then this book will guide you from the start and help you understand data, data formats, data visualization, and how to use Python to visualize data.You will need to know some general programming concepts, and any kind of programming experience will be helpful, but the co

  12. Visualization system on ITBL

    International Nuclear Information System (INIS)

    Visualization systems PATRAS/ITBL and AVS/ITBL, which are based on visualization software PATRAS and AVS/Express respectively, have been developed on a global, heterogeneous computing environment, Information Technology Based Laboratory (ITBL). PATRAS/ITBL allows for real-time visualization of the numerical results acquired from coupled multi-physics numerical simulations, executed on different hosts situated in remote locations. AVS/ITBL allow for post processing visualization. The scientific data located in remote sites may be selected and visualized on a web browser installed in a user terminal. The global structure and main functions of these systems are presented. (author)

  13. Beginning Visual Basic 2010

    CERN Document Server

    Willis, Thearon

    2010-01-01

    A focused, step-by-step approach to Visual Basic for new programmers. What better way to get started with Visual Basic than with this essential Wrox beginner's guide? Beginning Microsoft Visual Basic 2010 not only shows you how to write Windows applications, Web applications with ASP.NET, and Windows mobile and embedded CE apps with Visual Basic 2010, but you'll also get a thorough grounding in the basic nuts-and-bolts of writing good code. You'll be exposed to the very latest VB tools and techniques with coverage of both the Visual Studio 2010 and .NET 4 releases. Plus, the book walks you ste

  14. Visual perception and visual cognition in healthy and pathological ageing

    OpenAIRE

    MarkW.Greenlee; AllisonB.Sekuler

    2014-01-01

    Our understanding of visual perception and visual cognition has advanced considerably over the last decades. The effects of ageing on visual perception and visual cognition are less well understood. This Research Topic features state-of-the-art approaches to determining the effects of ageing on visual perception, visual attention, visual memory and visually guided behaviour. Studies using methods that incorporate psychophysics, eye movements, electrophysiology, structural and functional neuro...

  15. Rapid, sensitive, type specific PCR detection of the E7 region of human papillomavirus type 16 and 18 from paraffin embedded sections of cervical carcinoma

    DEFF Research Database (Denmark)

    Lesnikova, Iana; Lidang, Marianne; Hamilton-Dutoit, Stephen Jacques; Koch, Jørn

    2010-01-01

    ABSTRACT: Human papillomavirus (HPV) infection, and in particularly infection with HPVs 16 and 18 is a central carcinogenic factor in the uterine cervix. We established and optimized a PCR assay for the detection and discrimination of HPV types 16 and 18 in archival formaldehyde fixed and paraffin...... embedded (FFPE) sections of cervical cancer. Tissue blocks from 35 cases of in situ or invasive cervical squamouscell carcinoma and surrogate FFPE sections containing the cell lines HeLa and SiHa were tested for HPV 16 and HPV18 and for the housekeeping gene beta-actin by conventional PCR using type...

  16. Visualization Learning for Visually Impaired People

    OpenAIRE

    Salamin, Patrick; Thalmann, Daniel; Vexo,Frederic

    2007-01-01

    Virtual Environments (VE) are mainly visual experiments that exclude visually impaired people. In this paper we present an application that should allow almost everybody to ``see'' or at least to perceive 3D shapes. We will first describe the mandatory aspects of such an application, the tests we made and finally conclude by the results we obtained with geometrically basic shapes that are very promising.

  17. A combined method of small-angle neutron scattering and neutron radiography to visualize water in an operating fuel cell over a wide length scale from nano to millimeter

    International Nuclear Information System (INIS)

    In order to visualize water generated in an operating polymer electrolyte fuel cell (PEFC), a neutron radiography (NR) apparatus, composed of a scintillator, optical mirrors and a CCD camera, was installed at a sample position of the focusing and polarized neutron small-angle scattering (SANS) spectrometer (SANS-J-II) at research reactor JRR-3 at Japan Atomic Energy Agency, Tokai, Japan. By combining SANS and NR, we aim to cover a wide length scale from nanometer to millimeter. The new method succeeded in detecting a spatial distribution of the water generated in individual cell elements; NR detected the water in a gas diffusion layer and a flow field, whereas SANS quantitatively determines the water content in a membrane electrode assembly (MEA).

  18. Acquisition of new infection and clearance of type-specific human papillomavirus infections in female students in Busan, South Korea: a follow-up study

    Directory of Open Access Journals (Sweden)

    Quint Wim

    2008-01-01

    Full Text Available Abstract Background Little is known about the natural history of human papillomavirus (HPV infection in Asian women. Methods A follow-up study was conducted, with exfoliated cervicovaginal cells self-collected from, and questionnaires administered to 197 female students, aged 17–26 years, who had been already examined one and half years before. The presence of 25 HPV types was evaluated by a polymerase chain reaction-based assay. Results The acquisition of new infection for any HPV type among 171 female students at risk who were negative at baseline, 60% of whom had remained as virgins, was 17.5% (95% confidence interval [CI]: 11.8–23.2. Among individual types, HPV16, 18 and 35 showed the highest rate of new infection. Women who had had first sexual intercourse (OR = 2.9; 95% CI: 1.0–8.8, or had changed sexual partners (OR = 2.9; 95% CI: 0.9–9.3 during the follow-up period showed a higher risk of new HPV infection than women who had remained virgins since baseline. The rate of new infection also tended to be higher in those who started, or continued smoking during the follow-up period, than in nonsmokers. Clearance of HPV infections since baseline examination was 80.6% (95% CI: 67.6–93.5, and did not differ between high-risk and low-risk HPV types or between single- and multiple-type infections. Conclusion This study shows that the acquisition of new HPV infection among young women in the Republic of Korea is high and also the clearance is frequent. Self-collection of cervicovaginal cells is applicable to follow-up studies that include virgins.

  19. Fast Wavelet-Based Visual Classification

    OpenAIRE

    Yu, Guoshen; Slotine, Jean-Jacques

    2008-01-01

    We investigate a biologically motivated approach to fast visual classification, directly inspired by the recent work of Serre et al. Specifically, trading-off biological accuracy for computational efficiency, we explore using wavelet and grouplet-like transforms to parallel the tuning of visual cortex V1 and V2 cells, alternated with max operations to achieve scale and translation invariance. A feature selection procedure is applied during learning to accelerate recognition. We introduce a si...

  20. Detection of FMD virus type specific IgG1, IgG2 and IgA antibodies in milk and serum of buffaloes vaccinated with oil adjuvanted polyvalent FMD vaccine

    Directory of Open Access Journals (Sweden)

    R. Sharma

    2010-02-01

    Full Text Available The present investigation was carried out on 15 randomly selected milch buffaloes divided into three groups on the basis of lactation at an organized farm, to study the foot and mouth disease virus type specific antibodies in milk and serum following FMD vaccination. Milk and serum samples collected before vaccination i.e. 0 day and on 7, 14, 28, 42 and 56 days post vaccination, were analyzed for the detection of FMD virus specific IgG1, IgG2 and IgA antibody response by indirect double antibody sandwich ELISA. Significant FMD virus type specific antibody titres (IgG1, IgG2 and IgA were detected in milk and serum of buffaloes on different days post vaccination, though the levels of antibodies were lower in milk as compared to serum. FMD virus type specific IgG1 was found to be the predominant subclass as compared to IgG2 and IgA both in milk and serum of vaccinated buffaloes. Milk and serum IgG1, IgG2 and IgA antibody titres were positively correlated with values of regression coefficient (R as 0.506, 0.434 and 0.396, respectively.

  1. Evaluation of Visualization Software

    Science.gov (United States)

    Globus, Al; Uselton, Sam

    1995-01-01

    Visualization software is widely used in scientific and engineering research. But computed visualizations can be very misleading, and the errors are easy to miss. We feel that the software producing the visualizations must be thoroughly evaluated and the evaluation process as well as the results must be made available. Testing and evaluation of visualization software is not a trivial problem. Several methods used in testing other software are helpful, but these methods are (apparently) often not used. When they are used, the description and results are generally not available to the end user. Additional evaluation methods specific to visualization must also be developed. We present several useful approaches to evaluation, ranging from numerical analysis of mathematical portions of algorithms to measurement of human performance while using visualization systems. Along with this brief survey, we present arguments for the importance of evaluations and discussions of appropriate use of some methods.

  2. [Migraine with visual aura].

    Science.gov (United States)

    Bidot, S; Biotti, D

    2016-06-01

    Migraine with visual aura is marked by recurrent episodes of transient visual disturbance, often followed by headaches. Its pathophysiology has not been fully understood, but visual auras might be related to a self-propagating wave of cortical depolarization called "cortical spreading depression", triggering a trigemino-vascular "storm" ultimately leading to headaches. The most specific visual symptom is the "fortification spectrum" consisting of glimmering jagged lines spreading from the center to the periphery, and leaving a transient scotoma in its wake. Other visual symptoms are numerous, ranging from elementary positive or negative visual phenomena to complex and elaborate hallucinations. The diagnosis can be made according to the International Classification of Headache Disorders revised in 2013. The main goal of the treatment is to relieve the patient's pain quickly and to decrease the frequency of the episodes. PMID:27324232

  3. Exploring the Visual Landscape

    OpenAIRE

    Nijhuis, S.; Van Lammeren, R.; van Der Hoeven, F

    2011-01-01

    Exploring the Visual Landscape is about the combination of landscape research and planning, visual perception and Geographic Information Science. It showcases possible ways of getting a grip on themes like: landscape openness, cluttering of the rural landscape, high-rise buildings in relation to cityscape, historic landscapes and motorway panoramas. It offers clues for visual landscape assessment of spaces in cities, parks and rural areas. In that respect, it extends the long tradition in the...

  4. Data Visualization in Sociology

    OpenAIRE

    Healy, Kieran; Moody, James

    2014-01-01

    Visualizing data is central to social scientific work. Despite a promising early beginning, sociology has lagged in the use of visual tools. We review the history and current state of visualization in sociology. Using examples throughout, we discuss recent developments in ways of seeing raw data and presenting the results of statistical modeling. We make a general distinction between those methods and tools designed to help explore datasets, and those designed to help present results to other...

  5. WLAN visual sensor networking

    Science.gov (United States)

    Kostrzewski, Andrew A.; Wang, Wenjian; Jannson, Tomasz P.

    2002-12-01

    This paper presents a discussion on constructing a wireless ad hoc network using unattended ground visual sensors. The IEEE 802.11 WLAN standard is used to implement a single-hop ad hoc network because of its simplicity. The bandwidth allocation and traffic control between visual sensors is coordinated by the Medium Access Control (MAC) protocol. A ground visual sensor tower is designed for the networking purpose with specially designed video compression, power management, and network module to achieve maximum thoroughput

  6. Intelligent Visual Analytics Queries

    OpenAIRE

    Hao, Ming C.; Dayal, Umeshwar; Keim, Daniel A.; Morent, Dominik; Schneidewind, Jörn

    2007-01-01

    Visualizations of large multi-dimensional data sets, occurring in scientific and commercial applications, often reveal interesting local patterns. Analysts want to identify the causes and impacts of these interesting areas, and they also want to search for similar patterns occurring elsewhere in the data set. In this paper we introduce the Intelligent Visual Analytics Query (IVQuery) concept that combines visual interaction with automated analytical methods to support analysts in discovering ...

  7. Sickle Cell Information Center

    Science.gov (United States)

    ... Word Visual Art Historical Perspectives General Information Research Articles Books Primary Documents Images Sickle Cell on Instagram Sickle Cell Organizations State National International Newsletter NIH Report on Evidence- ...

  8. Visual computing scientific visualization and imaging systems

    CERN Document Server

    2014-01-01

    This volume aims to stimulate discussions on research involving the use of data and digital images as an understanding approach for analysis and visualization of phenomena and experiments. The emphasis is put not only on graphically representing data as a way of increasing its visual analysis, but also on the imaging systems which contribute greatly to the comprehension of real cases. Scientific Visualization and Imaging Systems encompass multidisciplinary areas, with applications in many knowledge fields such as Engineering, Medicine, Material Science, Physics, Geology, Geographic Information Systems, among others. This book is a selection of 13 revised and extended research papers presented in the International Conference on Advanced Computational Engineering and Experimenting -ACE-X conferences 2010 (Paris), 2011 (Algarve), 2012 (Istanbul) and 2013 (Madrid). The examples were particularly chosen from materials research, medical applications, general concepts applied in simulations and image analysis and ot...

  9. Spatio-temporal visualization

    International Nuclear Information System (INIS)

    We propose a spatio-temporal visualization technique. The spatio-temporal visualization technique, which is created by spatio-temporal information mapping, is an information visualization technique useful for specifying the feature area from simulation and measurement results. In the map, the change of a physical quantity is allocated in two-dimensional space with spatial and temporal information in each dimension. By applying the spatio-temporal visualization technique to the three-dimensional virtual vibration simulator, we confirmed that the technique was helpful to detect the region of interest. (author)

  10. Visualization in modern cartography

    CERN Document Server

    MacEachren, AM

    1994-01-01

    Visualization in Modern Cartography explores links between the centuries-old discipline of cartography and today's revolutionary developments in scientific visualization. The book has three main goals: (1) to pass on design and symbolization expertise to the scientific visualization community - information that comes from centuries of pre-computer visualization by cartographers, and their more recent experiences with computerizing the discipline; (2) to help cartographers cope with the dramatic shift from print cartography to a dynamic virtual cartography for which their role is changing from

  11. Sound visualization and manipulation

    CERN Document Server

    Kim, Yang-Hann

    2013-01-01

    Unique in addressing two different problems - sound visualization and manipulation - in a unified way Advances in signal processing technology are enabling ever more accurate visualization of existing sound fields and precisely defined sound field production. The idea of explaining both the problem of sound visualization and the problem of the manipulation of sound within one book supports this inter-related area of study.  With rapid development of array technologies, it is possible to do much in terms of visualization and manipulation, among other technologies involved with the spatial dis

  12. Visual languages and applications

    CERN Document Server

    Zhang, Kang

    2010-01-01

    Visual languages have long been a pursuit of effective communication between human and machine. With rapid advances of the Internet and Web technology, human-human communication through the Web or electronic mobile devices is becoming more and more prevalent. Visual Languages and Applications is a comprehensive introduction to diagrammatical visual languages. This book discusses what visual programming languages are, and how such languages and their underlying foundations can be usefully applied to other fields in computer science. It also covers a broad range of contents from the underlying t

  13. MOVES’ Visualization Capabilities

    OpenAIRE

    Johnson, Erik

    2012-01-01

    MOVES Research & Education Systems Seminar: Presentation; Session 7: Computer Gaming and Web-Delivered Simulation; Moderator: Perry McDowell; MOVES’ Visualization Capabilities; speaker: Erik Johnson

  14. Visual Literacy in Educational Practice

    OpenAIRE

    Duchak Oksana

    2014-01-01

    In the 21stcentury the ability to interpret digital, visual and audio media is a form of literacy which is as basic as reading and writing skills. Visual literacy is required of us as much as textual literacy. Visual literacy gives educators a chance to increase the quality of their teaching and to connect with learners in more interesting way. The article elucidates the definition of visual literacy, types of visual assessment, challenges of visual literacy, and proves that visual literacy i...

  15. Proposal of the visual inspection of the integrity of the storage cells of spent fuel from the nuclear power plant of Laguna Verde; Propuesta para la inspeccion visual de la integridad de las celdas de almacenamiento de combustible gastado de la Central Laguna Verde (CLV)

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez M, J. L.; Rivero G, T.; Merino C, F. J. [ININ, Carretera Mexico-Toluca s/n, 52750 Ocoyoacac, Estado de Mexico (Mexico); Santander C, L. E., E-mail: francisco.merino@inin.gob.mx [Comision Federal de Electricidad, Central Nucleoelectrica Laguna Verde, Carretera Veracruz-Medellin Km 7.5, Col. Dos Bocas, 94271 Medellin, Veracruz (Mexico)

    2015-09-15

    As part of the evaluation of the structural integrity of the components of nuclear plants, particularly those applying for life extension is necessary to carry out inspections and nondestructive testing to determine the state meet. In many cases these activities are carried out in areas with high levels of radiation and contamination difficult to access, so that are required to use equipment or robotic systems operated remotely. Among others, the frames and cells of the storage pools for spent fuel are structures subject to a program of tests and inspections, and become relevant because the nuclear power plant of Laguna Verde (NPP-LV) is processing the license to extend the operational life of its reactors. Of non-destructive testing can be used to verify the physical condition of the frames and storage cells, is the remote visual inspection which is a test that allows determine the physical integrity of the components by one or more video cameras designed to applications in underwater environments with radiation, and are used to identify and locate adverse conditions such as ampoules, protuberances, pitting, cracks, stains or buckling, which could affect the three main functions for which the store components are designed: to maintain the physical integrity of spent fuels, store them properly guaranteeing their free insertion and removal, and ensure that the store as a whole meets the criticality criteria that k{sub eff} is less than 0.95 throughout the life of the plant. This paper describes a proposal to carry out the visual inspection of the storage cells of spent fuel from the NPP-LV using a probe including one or more video cameras along with your recorder, and its corresponding control program. It is noted that due to the obtained results, the nuclear power plant personnel can make decisions regarding remedial actions or applying complementary methods to verify that the cells and frames have not lost their physical integrity, or in particular that the cover

  16. A global look into human T cell subsets before and after cryopreservation using multiparametric flow cytometry and two-dimensional visualization analysis.

    Science.gov (United States)

    Lemieux, Jennifer; Jobin, Christine; Simard, Carl; Néron, Sonia

    2016-07-01

    The cryopreservation of human lymphocytes is an essential step for the achievement of several cellular therapies. Besides, T cells are considered as promising actors in cancer therapy for their cytotoxic and regulatory properties. Consequently, the development of tools to monitor the impact of freezing and thawing processes on their fine distribution may be an asset to achieve quality control in cellular therapy. In this study, the phenotypes of freshly isolated human mononuclear cells were compared to those observed following one cycle of cryopreservation and rest periods 0h, 1h and 24h after thawing but before staining. T cells were scrutinized for their distribution according to naive, memory effector, regulatory and helper subsets. Flow cytometry analyses were done using eight-color antibody panels as proposed by the Human Immunophenotyping Consortium. Data were further analyzed by using conventional directed gating and clustering software, namely SPADE and viSNE. Overall, SPADE and viSNE tools were very efficient to monitor the outcome of PBMC populations and T cell subsets. T cells were more sensitive to cryopreservation than other cells. Our results indicated that submitting the thawed cells to a 1h rest period improved the detection of some cell markers when compared to fresh samples. In contrast, cells submitted to a 24h rest period, or to none, were less representative of fresh sample distribution. The heterogeneity of PBMC, as well as the effects of freeze-thaw cycle on their distribution, can be easily monitored by using SPADE and viSNE. PMID:27129808

  17. Extended visual regions among the deaf

    International Nuclear Information System (INIS)

    Whatever is the source of the deafness (genetic or acquired in the childhood) it leads to a partial re-arrangement of brain. It has been shown at animals that nerve cells of the auditive cortex acquire some characteristics of the visual nerve cells. At men, the NMR imaging confirms it: it seems that a part of the visual cortex appropriates some cortex zones which are normally intended to audition. It has been verified too that the deaf language solicit more the right hemisphere than the spoken language. (O.M.)

  18. Complex Digital Visual Systems

    Science.gov (United States)

    Sweeny, Robert W.

    2013-01-01

    This article identifies possibilities for data visualization as art educational research practice. The author presents an analysis of the relationship between works of art and digital visual culture, employing aspects of network analysis drawn from the work of Barabási, Newman, and Watts (2006) and Castells (1994). Describing complex network…

  19. Visualizing Dynamic Memory Allocations

    NARCIS (Netherlands)

    Moreta, Sergio; Telea, Alexandru

    2007-01-01

    We present a visualization tool for dynamic memory allocation information obtained from instrumenting the runtime allocator used by C programs. The goal of the presented visualization techniques is to convey insight in the dynamic behavior of the allocator. The purpose is to help the allocator desig

  20. Mathematica data visualization

    CERN Document Server

    Saquib, Nazmus

    2014-01-01

    If you are planning to create data analysis and visualization tools in the context of science, engineering, economics, or social science, then this book is for you. With this book, you will become a visualization expert, in a short time, using Mathematica.

  1. Sizing Up Visualizations

    DEFF Research Database (Denmark)

    Jakobsen, Mikkel Rønne; Hornbæk, Kasper Anders Søren

    2011-01-01

    Whereas the literature is clear on the benefits of large displays and visualizations, little is known about their combination, that is, how display size affect the usability of visualizations. We describe a controlled experiment where 19 participants used focus+context, overview+detail, and zoomi...

  2. Visual Impairment, Including Blindness

    Science.gov (United States)

    ... top Adapting the Environment Making adaptations to the environment where a child with a visual impairment lives, works, or plays ... can consult, depending on your role in the child’s life, are: Family Connect ... to the Physical Environment: Setting up a Classroom for Students with Visual ...

  3. Visual Complexity: A Review

    Science.gov (United States)

    Donderi, Don C.

    2006-01-01

    The idea of visual complexity, the history of its measurement, and its implications for behavior are reviewed, starting with structuralism and Gestalt psychology at the beginning of the 20th century and ending with visual complexity theory, perceptual learning theory, and neural circuit theory at the beginning of the 21st. Evidence is drawn from…

  4. Visual Arts Research, 1994.

    Science.gov (United States)

    Gardner, Nancy C., Ed.; Thompson, Christine, Ed.

    1994-01-01

    This document consists of the two issues of the journal "Visual Arts in Research" published in 1994. This journal focuses on the theory and practice of visual arts education from educational, historical, philosophical, and psychological perspectives. Number 1 of this volume includes the following contributions: (1) "Zooming in on the Qualitative…

  5. Visual attention capacity

    DEFF Research Database (Denmark)

    Habekost, Thomas; Starrfelt, Randi

    2009-01-01

    Psychophysical studies have identified two distinct limitations of visual attention capacity: processing speed and apprehension span. Using a simple test, these cognitive factors can be analyzed by Bundesen's Theory of Visual Attention (TVA). The method has strong specificity and sensitivity, and...

  6. Visual Signs of Ageing

    Directory of Open Access Journals (Sweden)

    Helle Rexbye

    2007-07-01

    Full Text Available Consumer culture has placed the ageing body in a dilemma of representation. Physical appearance has become increasingly important as a symbol of identity, and at the same time society idealizes youth. This study explores visual ageing empirically. By using photographs of older persons (70+ as starting point, it is explored how visual age is assessed and interpreted. It is shown that informants read age in a spread of stages and categories. Main age indicators are biological markers: skin, eyes, and hair colour, but supplemented by vigour, style, and grooming. Furthermore, in-depth interviews indicate that visual age is mainly interpreted into categories and moral regulations rooted in early modernity. Subsequently the question of a postmodern perspective of visual ageing is discussed in this article. The empirical findings in the study question a postmodern fluidity of visual signs – at least when the concern is signs of ageing.

  7. Visualization of JPEG Metadata

    Science.gov (United States)

    Malik Mohamad, Kamaruddin; Deris, Mustafa Mat

    There are a lot of information embedded in JPEG image than just graphics. Visualization of its metadata would benefit digital forensic investigator to view embedded data including corrupted image where no graphics can be displayed in order to assist in evidence collection for cases such as child pornography or steganography. There are already available tools such as metadata readers, editors and extraction tools but mostly focusing on visualizing attribute information of JPEG Exif. However, none have been done to visualize metadata by consolidating markers summary, header structure, Huffman table and quantization table in a single program. In this paper, metadata visualization is done by developing a program that able to summarize all existing markers, header structure, Huffman table and quantization table in JPEG. The result shows that visualization of metadata helps viewing the hidden information within JPEG more easily.

  8. Visualization and mathematics III

    CERN Document Server

    Polthier, Konrad

    2003-01-01

    This research book on Mathematical Visualization contains state of the art presentations on visualization problems in mathematics, on fundamental mathematical research in computer graphics, and on software frameworks for the application of visualization to real-world problems. All contributions were written by leading experts in the field and peer-refereed by an international editorial team. The book grew out of the third international workshop "Visualization and Mathematics", which was held from May 22-25, 2002 in Berlin. The themes of the book cover important recent developments on - Geometry and Combinatorics of Meshes - Discrete Vector Fields and Topology - Geometric Modelling - Image Based Visualization - Software Environments and Applications - Education and Communication The variety of topics makes the book a suitable resource for researchers, lecturers, and practitioners; http://www-sfb288.math.tu-berlin.de/vismath/

  9. Visualization of Social Networks

    Science.gov (United States)

    Chen, Ing-Xiang; Yang, Cheng-Zen

    With the ubiquitous characteristic of the Internet, today many online social environments are provided to connect people. Various social relationships are thus created, connected, and migrated from our real lives to the Internet environment from different social groups. Many social communities and relationships are also quickly constructed and connected via instant personal messengers, blogs, Twitter, Facebook, and a great variety of online social services. Since social network visualizations can structure the complex relationships between different groups of individuals or organizations, they are helpful to analyze the social activities and relationships of actors, particularly over a large number of nodes. Therefore, many studies and visualization tools have been investigated to present social networks with graph representations. In this chapter, we will first review the background of social network analysis and visualization methods, and then introduce various novel visualization applications for social networks. Finally, the challenges and the future development of visualizing online social networks are discussed.

  10. Visualizing Data Streams

    Energy Technology Data Exchange (ETDEWEB)

    Wong, Pak C.; Foote, Harlan P.; Adams, Daniel R.; Cowley, Wendy E.; Leung, Lai R.; Thomas, James J.

    2004-12-01

    We introduce two dynamic visualization techniques using multi-dimensional scaling to analyze transient data streams such as newswires and remote sensing imagery. While the time-sensitive nature of these data streams requires immediate attention in many applications, the unpredictable and unbounded characteristics of this information can potentially overwhelm many scaling algorithms that require a full re-computation for every update. We present an adaptive visualization technique based on data stratification to ingest stream information adaptively when influx rate exceeds processing rate. We also describe an incremental visualization technique based on data fusion to project new information directly onto a visualization subspace spanned by the singular vectors of the previously processed neighboring data. The ultimate goal is to leverage the value of legacy and new information and minimize re-processing of the entire dataset in full resolution. We demonstrate these dynamic visualization results using a newswire corpus and a remote sensing imagery sequence.

  11. Quantitation and visualization of tumor-specific T cells in the secondary lymphoid organs during and after tumor elimination by PET

    Energy Technology Data Exchange (ETDEWEB)

    Matsui, Ken; Wang Zheng; McCarthy, Timothy J.; Allen, Paul M.; Reichert, David E. E-mail: ReichertD@wustl.edu

    2004-11-01

    Increased understanding in the area of trafficking behavior of adoptively transferred tumor-specific T cells could help develop better therapeutic protocols. We utilized the DUC18/CMS5 tumor model system in conjunction with a microPET scanner to study the DUC18 T cell distribution pattern in spleens and lymph nodes in live mice. Anti-Thy1.2 antibodies conjugated to 1,4,7,10-tetraazacyclododecane-N,N',N'',N''-tetraacetic acid (DOTA) and radiolabeled with {sup 64}Cu were administered to three groups of BALB-Thy1.1 mice on days 4, 7, or 14 post-DUC18 T cell transfer. We were able to detect the transferred cells in all the major lymph nodes, spleens, and in tumors. Our findings suggest that tumor-specific T cells do not all preferentially localize to the tumors but they also home to all the major lymphoid organs; additionally the number of DUC18 T cells remains relatively constant during and after tumor elimination within each lymphoid organ.

  12. Detection of FMD virus type specific IgG1, IgG2 and IgA antibodies in milk and serum of buffaloes vaccinated with oil adjuvanted polyvalent FMD vaccine

    OpenAIRE

    Sharma, R.; Sharma, A.; Yadav, V.

    2010-01-01

    The present investigation was carried out on 15 randomly selected milch buffaloes divided into three groups on the basis of lactation at an organized farm, to study the foot and mouth disease virus type specific antibodies in milk and serum following FMD vaccination. Milk and serum samples collected before vaccination i.e. 0 day and on 7, 14, 28, 42 and 56 days post vaccination, were analyzed for the detection of FMD virus specific IgG1, IgG2 and IgA antibody response by indirect double antib...

  13. Designing Visual Earth: Multimedia Geographic Visualization for the Classroom.

    Science.gov (United States)

    McWilliams, Harold

    1998-01-01

    Provides information on computer software using Geographic Information Systems (GIS) and visualization technologies and Visual Earth, a series of integrated classroom solutions for a variety of science topics. Describes some uses of GIS and Visual Earth in science classrooms. (ASK)

  14. Visual sensing technology

    International Nuclear Information System (INIS)

    Recently the spread of arc welding robots is conspicuous, and as the sensors for the robots, wire touch sensor and arc sensor have been put to practical use. However, when the welding of high quality is required, the objects which are welded complately automatically in unmanned state are limited. Mitsubishi Heavy Industries, Ltd. has advanced the research on unmanned welding, and in particular, on the visual sensor which can detect plural objects during welding. In this report, the outline of visual sensors, the example of their development in Mitsubishi, and the limit of visual sensing are mentioned. As the light sensors for arc welding, there are point sensor, linear sensor and area sensor, and the linear and area sensors are called visual sensor. The visual sensors have been utilized for the profile control of welding lines, the adaptive control of welding conditions, the profile control and adaptive control of welding lines and the monitoring of welding. As the examples of applying visual sensors, the applications to GMA multi-layer welding, GMA narrow groove welding and orbital TIG welding are reported. As nthe limit of visual sensors, in the linear sensor, the grasp of melting phenomena, the effect of surface roughness and color, and the problem of sensing position, and in the area sensor, the problem of the blooming and smear phenomena of cameras are discussed. (K.I.)

  15. Scientific visualization and radiology

    International Nuclear Information System (INIS)

    Scientific visualization is the visual presentation of numerical data. The National Center for Supercomputing Applications (NCSA) has developed methods for visualizing computerbased simulations of digital imaging data. The applicability of these various tools for unique and potentially medical beneficial display of MR images is investigated. Raw data are obtained from MR images of the brain, neck, spine, and brachial plexus obtained on a 1.5-T imager with multiple pulse sequences. A supercomputer and other mainframe resources run a variety of graphic and imaging programs using this data. An interdisciplinary team of imaging scientists, computer graphic programmers, an physicians works together to achieve useful information

  16. Master VISUALLY Excel 2010

    CERN Document Server

    Marmel, Elaine

    2010-01-01

    The complete visual reference on Excel basics. Aimed at visual learners who are seeking an all-in-one reference that provides in-depth coveage of Excel from a visual viewpoint, this resource delves into all the newest features of Excel 2010. You'll explore Excel with helpful step-by-step instructions that show you, rather than tell you, how to navigate Excel, work with PivotTables and PivotCharts, use macros to streamline work, and collaborate with other users in one document.: This two-color guide features screen shots with specific, numbered instructions so you can learn the actions you need

  17. VISUAL VOCABULARY IN BRANDING

    OpenAIRE

    Adriana Vintean; Ovidiu Matiu

    2011-01-01

    Visual vocabulary or visual language is a set of symbols used to describe a system or a process; it refers to all graphical representations that supplement a brand image, a logo, and build a brand identity that is bound to remain invariable even when the sign undergoes fundamental changes. The article is a presentation of the concept of visual vocabulary/language and of its relevance to branding and marketing. We argue that these symbols are culturally dependent and a key element in brand des...

  18. Visual responses in adult cat visual cortex depend on N-methyl-D-aspartate receptors.

    OpenAIRE

    Miller, K. D.; Chapman, B; Stryker, M.P.

    1989-01-01

    We have investigated the role of the N-methyl-D-aspartate (NMDA) receptor, a subtype of glutamate receptor, in the responses of cells in adult cat visual cortex. After intracortical infusion of the NMDA receptor antagonist DL-2-amino-5-phosphonovalerate (DL-APV) for one day, iontophoretic responses to NMDA, to kainate, and to quisqualate revealed a receptor blockade specific to NMDA receptors and extending several millimeters from the cannula. In this region, neuronal responses to visual stim...

  19. A Critical Discussion of the Efficacy of Using Visual Learning Aids from the Internet to Promote Understanding, Illustrated with Examples Explaining the Daniell Voltaic Cell

    Science.gov (United States)

    Eilks, Ingo; Witteck, Torsten; Pietzner, Verena

    2009-01-01

    This paper discusses what chemistry students might see while working with animations found on the Internet and how these electronic illustrations can potentially interact to reinforce rather than resolve misconceptions about chemical principles that a student may possess. The Daniell voltaic cell serves as an example to illustrate the ways in…

  20. Clock and clock-controlled genes are differently expressed in the retina, lamina and in selected cells of the visual system of Drosophila melanogaster

    Directory of Open Access Journals (Sweden)

    Milena eDamulewicz

    2015-09-01

    Full Text Available The retina and the first optic neuropil (lamina of Drosophila show circadian rhythms in various processes. To learn about the regulation of circadian rhythms in the retina and lamina and in two cell types, glial and the lamina L2 interneurons, we examined expression of the following clock genes; per, tim, clk, and cry and clock-controlled genes; Atp, nrv2, brp, Pdfr. We found that the expression of gene studied is specific for the retina and lamina. The rhythms of per and tim expression in the retina and glial cells are similar to that observed in the whole head and in clock neurons, while they differ in the lamina and L2 cells. In both the retina and lamina, CRY seems to be a repressor of clk expression. In L2 interneurons per expression is not cyclic indicating the other function of PER in those cells than in the circadian molecular clock. In contrast to per and tim, the pattern of clk and cry expression is similar in both the retina and lamina. The retina holds the autonomous oscillators but the expression of cry and clock-controlled genes, Atp and nrv2, is also regulated by inputs from the pacemaker transmitted by PDF and ITP neuropeptides.

  1. Focal damage to macaque photoreceptors produces persistent visual loss

    OpenAIRE

    Strazzeri, Jennifer M.; Hunter, Jennifer J.; Masella, Benjamin D.; Yin, Lu; Fischer, William S.; DiLoreto, David A.; Libby, Richard T.; Williams, David R.; Merigan, William H.

    2013-01-01

    Insertion of light-gated channels into inner retina neurons restores neural light responses, light evoked potentials, visual optomotor responses and visually-guided maze behavior in mice blinded by retinal degeneration. This method of vision restoration bypasses damaged outer retina, providing stimulation directly to retinal ganglion cells in inner retina. The approach is similar to that of electronic visual protheses, but may offer some advantages, such as avoidance of complex surgery and di...

  2. Role of emergent neural activity in visual map development

    OpenAIRE

    Ackman, James B.; Crair, Michael C.

    2013-01-01

    The initial structural and functional development of visual circuits in reptiles, birds, and mammals happens independent of sensory experience. After eye opening, visual experience further refines and elaborates circuits that are critical for normal visual function. Innate genetic programs that code for gradients of molecules provide gross positional information for developing nerve cells, yet much of the cytoarchitectural complexity and synaptogenesis of neurons depends on calcium influx, ne...

  3. NSOM/QD-based direct visualization of CD3-induced and CD28-enhanced nanospatial coclustering of TCR and coreceptor in nanodomains in T cell activation.

    Science.gov (United States)

    Zhong, Liyun; Zeng, Gucheng; Lu, Xiaoxu; Wang, Richard C; Gong, Guangming; Yan, Lin; Huang, Dan; Chen, Zheng W

    2009-01-01

    Direct molecular imaging of nano-spatial relationship between T cell receptor (TCR)/CD3 and CD4 or CD8 co-receptor before and after activation of a primary T cell has not been reported. We have recently innovated application of near-field scanning optical microscopy (NSOM) and immune-labeling quantum dots (QD) to image Ag-specific TCR response during in vivo clonal expansion, and now up-graded the NSOM/QD-based nanotechnology through dipole-polarization and dual-color imaging. Using this imaging system scanning cell-membrane molecules at a best-optical lateral resolution, we demonstrated that CD3, CD4 or CD8 molecules were distinctly distributed as single QD-bound molecules or nano-clusters equivalent to 2-4 QD fluorescence-intensity/size on cell-membrane of un-stimulated primary T cells, and approximately 6-10% of CD3 were co-clustering with CD4 or CD8 as 70-110 nm nano-clusters without forming nano-domains. The ligation of TCR/CD3 on CD4 or CD8 T cells led to CD3 nanoscale co-clustering or interaction with CD4 or CD8 co-receptors forming 200-500 nm nano-domains or >500 nm micro-domains. Such nano-spatial co-clustering of CD3 and CD4 or CD3 and CD8 appeared to be an intrinsic event of TCR/CD3 ligation, not purely limited to MHC engagement, and be driven by Lck phosphorylation. Importantly, CD28 co-stimulation remarkably enhanced TCR/CD3 nanoscale co-clustering or interaction with CD4 co-receptor within nano- or micro-domains on the membrane. In contrast, CD28 co-stimulation did not enhance CD8 clustering or CD3-CD8 co-clustering in nano-domains although it increased molecular number and density of CD3 clustering in the enlarged nano-domains. These nanoscale findings provide new insights into TCR/CD3 interaction with CD4 or CD8 co-receptor in T-cell activation. PMID:19536289

  4. NSOM/QD-based direct visualization of CD3-induced and CD28-enhanced nanospatial coclustering of TCR and coreceptor in nanodomains in T cell activation.

    Directory of Open Access Journals (Sweden)

    Liyun Zhong

    Full Text Available Direct molecular imaging of nano-spatial relationship between T cell receptor (TCR/CD3 and CD4 or CD8 co-receptor before and after activation of a primary T cell has not been reported. We have recently innovated application of near-field scanning optical microscopy (NSOM and immune-labeling quantum dots (QD to image Ag-specific TCR response during in vivo clonal expansion, and now up-graded the NSOM/QD-based nanotechnology through dipole-polarization and dual-color imaging. Using this imaging system scanning cell-membrane molecules at a best-optical lateral resolution, we demonstrated that CD3, CD4 or CD8 molecules were distinctly distributed as single QD-bound molecules or nano-clusters equivalent to 2-4 QD fluorescence-intensity/size on cell-membrane of un-stimulated primary T cells, and approximately 6-10% of CD3 were co-clustering with CD4 or CD8 as 70-110 nm nano-clusters without forming nano-domains. The ligation of TCR/CD3 on CD4 or CD8 T cells led to CD3 nanoscale co-clustering or interaction with CD4 or CD8 co-receptors forming 200-500 nm nano-domains or >500 nm micro-domains. Such nano-spatial co-clustering of CD3 and CD4 or CD3 and CD8 appeared to be an intrinsic event of TCR/CD3 ligation, not purely limited to MHC engagement, and be driven by Lck phosphorylation. Importantly, CD28 co-stimulation remarkably enhanced TCR/CD3 nanoscale co-clustering or interaction with CD4 co-receptor within nano- or micro-domains on the membrane. In contrast, CD28 co-stimulation did not enhance CD8 clustering or CD3-CD8 co-clustering in nano-domains although it increased molecular number and density of CD3 clustering in the enlarged nano-domains. These nanoscale findings provide new insights into TCR/CD3 interaction with CD4 or CD8 co-receptor in T-cell activation.

  5. COMPARISON OF VISUAL CRYPTOGRAPHIC SCHEMES

    OpenAIRE

    M.Amarnath Reddy,; P.Shanthi Bala,; Aghila, G.

    2011-01-01

    Visual cryptography technique allows the visual information to be encrypted in such a way that their decryption can be performed by human visual system. This technique used to encrypt a image into shares such that stacking a sufficient number of shares reveals the secret images. In visual cryptography there are different technique like sub pixel, error diffusion, Boolean operation etc. Visual cryptography can be applied for copyright for images, access control to user images, Visual authentic...

  6. Visual imagery without visual perception: lessons from blind subjects

    Science.gov (United States)

    Bértolo, Helder

    2014-08-01

    The question regarding visual imagery and visual perception remain an open issue. Many studies have tried to understand if the two processes share the same mechanisms or if they are independent, using different neural substrates. Most research has been directed towards the need of activation of primary visual areas during imagery. Here we review some of the works providing evidence for both claims. It seems that studying visual imagery in blind subjects can be used as a way of answering some of those questions, namely if it is possible to have visual imagery without visual perception. We present results from the work of our group using visual activation in dreams and its relation with EEG's spectral components, showing that congenitally blind have visual contents in their dreams and are able to draw them; furthermore their Visual Activation Index is negatively correlated with EEG alpha power. This study supports the hypothesis that it is possible to have visual imagery without visual experience.

  7. Scientific visualization uncertainty, multifield, biomedical, and scalable visualization

    CERN Document Server

    Chen, Min; Johnson, Christopher; Kaufman, Arie; Hagen, Hans

    2014-01-01

    Based on the seminar that took place in Dagstuhl, Germany in June 2011, this contributed volume studies the four important topics within the scientific visualization field: uncertainty visualization, multifield visualization, biomedical visualization and scalable visualization. • Uncertainty visualization deals with uncertain data from simulations or sampled data, uncertainty due to the mathematical processes operating on the data, and uncertainty in the visual representation, • Multifield visualization addresses the need to depict multiple data at individual locations and the combination of multiple datasets, • Biomedical is a vast field with select subtopics addressed from scanning methodologies to structural applications to biological applications, • Scalability in scientific visualization is critical as data grows and computational devices range from hand-held mobile devices to exascale computational platforms. Scientific Visualization will be useful to practitioners of scientific visualization, ...

  8. Improved Visualization of Lung Metastases at Single Cell Resolution in Mice by Combined In-situ Perfusion of Lung Tissue and X-Gal Staining of lacZ-Tagged Tumor Cells

    OpenAIRE

    Matthias J E Arlt; Born, Walter; Fuchs, Bruno

    2012-01-01

    Metastasis is the main cause of death in the majority of cancer types and consequently a main focus in cancer research. However, the detection of micrometastases by radiologic imaging and the success in their therapeutic eradication remain limited. While animal models have proven to be invaluable tools for cancer research1, the monitoring/visualization of micrometastases remains a challenge and inaccurate evaluation of metastatic spread in preclinical studies potentially leads to disappointin...

  9. Aids for visual impairment.

    OpenAIRE

    Dudley, N. J.

    1990-01-01

    This article provides only a flavour of the type and range of aids available to the visually impaired person. Many other aids for leisure, learning, and daily living are illustrated in the RNIB equipment and games catalogue.

  10. Introduction to information visualization

    CERN Document Server

    Mazza, Riccardo

    2009-01-01

    Accessible and easy to readCovers techniques specific for the Web and (unlike existing books) techniques for evaluating visualisationsFocuses on the human aspects of the process of visualization rather than the algoritmic or graphic design aspects

  11. Adaptive semantics visualization

    CERN Document Server

    Nazemi, Kawa

    2016-01-01

    This book introduces a novel approach for intelligent visualizations that adapts the different visual variables and data processing to human’s behavior and given tasks. Thereby a number of new algorithms and methods are introduced to satisfy the human need of information and knowledge and enable a usable and attractive way of information acquisition. Each method and algorithm is illustrated in a replicable way to enable the reproduction of the entire “SemaVis” system or parts of it. The introduced evaluation is scientifically well-designed and performed with more than enough participants to validate the benefits of the methods. Beside the introduced new approaches and algorithms, readers may find a sophisticated literature review in Information Visualization and Visual Analytics, Semantics and information extraction, and intelligent and adaptive systems. This book is based on an awarded and distinguished doctoral thesis in computer science.

  12. Visualizations as Projection Devices

    DEFF Research Database (Denmark)

    Harty, Chris; Holm Jacobsen, Peter; Tryggestad, Kjell

    The aim of this paper is to inquire into the role of project visualizations in shaping healthcare spaces and practices. The study draws upon an ethnographic field study from a large on-going hospital construction project in Denmark, and focuses on the early phases of on-boarding the design team...... into the project organization. During the on-boarding visualizations multiplies in form, content and purpose, ranging from paper and digitally based projections of clinical work spaces and practices for the future hospital building in use, to paper and digitally based projections of the cost budget and time...... visualizations plays an active role in developing novel conceptions of space and how these are mobilized in the process of on-boarding, in terms of; design space, physical space, organizational space and economic space. Our findings show the visualizations of different spaces and how they are dynamically...

  13. Visualization Design Environment

    Energy Technology Data Exchange (ETDEWEB)

    Pomplun, A.R.; Templet, G.J.; Jortner, J.N.; Friesen, J.A.; Schwegel, J.; Hughes, K.R.

    1999-02-01

    Improvements in the performance and capabilities of computer software and hardware system, combined with advances in Internet technologies, have spurred innovative developments in the area of modeling, simulation and visualization. These developments combine to make it possible to create an environment where engineers can design, prototype, analyze, and visualize components in virtual space, saving the time and expenses incurred during numerous design and prototyping iterations. The Visualization Design Centers located at Sandia National Laboratories are facilities built specifically to promote the ''design by team'' concept. This report focuses on designing, developing and deploying this environment by detailing the design of the facility, software infrastructure and hardware systems that comprise this new visualization design environment and describes case studies that document successful application of this environment.

  14. Infant Visual Habituation

    OpenAIRE

    Colombo, John; Mitchell, D. Wayne

    2008-01-01

    The use of visual habituation in the study of infant cognition and learning is reviewed. This article traces the history of the technique, underlying theory, and procedural variation in its measurement. In addition, we review empirical findings with respect to the cognitive processes that presumably contribute to habituation, studies of developmental course and long-term prediction, as well as recent attempts to address or explain the phenomenon of visual habituation through the use of mathem...

  15. Uncalibrated visual servoing

    OpenAIRE

    Spratling, M. W.; Cipolla, R.

    1996-01-01

    Visual servoing is a process to enable a robot to position a camera with respect to known landmarks using the visual data obtained by the camera itself to guide camera motion. A solution is described which requires very little a priori information freeing it from being specific to a particular configuration of robot and camera. The solution is based on closed loop control together with deliberate perturbations of the trajectory to provide calibration movements for refining t...

  16. Visualizing Risk Prediction Models

    OpenAIRE

    Vanya Van Belle; Ben Van Calster

    2015-01-01

    Objective Risk prediction models can assist clinicians in making decisions. To boost the uptake of these models in clinical practice, it is important that end-users understand how the model works and can efficiently communicate its results. We introduce novel methods for interpretable model visualization. Methods The proposed visualization techniques are applied to two prediction models from the Framingham Heart Study for the prediction of intermittent claudication and stroke after atrial fib...

  17. Visualizing the human connectome

    OpenAIRE

    Margulies, D.; Böttger, J; Watanabe, A; Gorgolewski, K.

    2013-01-01

    Innovations in data visualization punctuate the landmark advances in human connectome research since its beginnings. From tensor glyphs for diffusion-weighted imaging, to advanced rendering of anatomical tracts, to more recent graph-based representations of functional connectivity data, many of the ways we have come to understand the human connectome are through the intuitive insight these visualizations enable. Nonetheless, several unresolved problems persist. For example, probabilistic trac...

  18. Visualization of particle complexes in the plasma membrane of Micrasterias denticulata associated with the formation of cellulose fibrils in primary and secondary cell walls

    OpenAIRE

    1980-01-01

    Highly ordered arrays of intramembrane particles are observed in freeze- fractured plasma membranes of the green alga Micrasterias denticulata during the synthesis of the secondary cell wall. The observable architecture of the complex consists primarily of a precise hexagonal array of from 3 to 175 rosettes, consisting of 6 particles each, which fracture with the P-face. The complexes are observed at the ends of impressions of cellulose fibrils. The distance between rows of rosettes is equal ...

  19. Visualization of Content Release from Cell Surface-Attached Single HIV-1 Particles Carrying an Extra-Viral Fluorescent pH-Sensor.

    Directory of Open Access Journals (Sweden)

    Chetan Sood

    Full Text Available HIV-1 fusion leading to productive entry has long been thought to occur at the plasma membrane. However, our previous single virus imaging data imply that, after Env engagement of CD4 and coreceptors at the cell surface, the virus enters into and fuses with intracellular compartments. We were unable to reliably detect viral fusion at the plasma membrane. Here, we implement a novel virus labeling strategy that biases towards detection of virus fusion that occurs in a pH-neutral environment-at the plasma membrane or, possibly, in early pH-neutral vesicles. Virus particles are co-labeled with an intra-viral content marker, which is released upon fusion, and an extra-viral pH sensor consisting of ecliptic pHluorin fused to the transmembrane domain of ICAM-1. This sensor fully quenches upon virus trafficking to a mildly acidic compartment, thus precluding subsequent detection of viral content release. As an interesting secondary observation, the incorporation of the pH-sensor revealed that HIV-1 particles occasionally shuttle between neutral and acidic compartments in target cells expressing CD4, suggesting a small fraction of viral particles is recycled to the plasma membrane and re-internalized. By imaging viruses bound to living cells, we found that HIV-1 content release in neutral-pH environment was a rare event (~0.4% particles. Surprisingly, viral content release was not significantly reduced by fusion inhibitors, implying that content release was due to spontaneous formation of viral membrane defects occurring at the cell surface. We did not measure a significant occurrence of HIV-1 fusion at neutral pH above this defect-mediated background loss of content, suggesting that the pH sensor may destabilize the membrane of the HIV-1 pseudovirus and, thus, preclude reliable detection of single virus fusion events at neutral pH.

  20. Visualization of Content Release from Cell Surface-Attached Single HIV-1 Particles Carrying an Extra-Viral Fluorescent pH-Sensor.

    Science.gov (United States)

    Sood, Chetan; Marin, Mariana; Mason, Caleb S; Melikyan, Gregory B

    2016-01-01

    HIV-1 fusion leading to productive entry has long been thought to occur at the plasma membrane. However, our previous single virus imaging data imply that, after Env engagement of CD4 and coreceptors at the cell surface, the virus enters into and fuses with intracellular compartments. We were unable to reliably detect viral fusion at the plasma membrane. Here, we implement a novel virus labeling strategy that biases towards detection of virus fusion that occurs in a pH-neutral environment-at the plasma membrane or, possibly, in early pH-neutral vesicles. Virus particles are co-labeled with an intra-viral content marker, which is released upon fusion, and an extra-viral pH sensor consisting of ecliptic pHluorin fused to the transmembrane domain of ICAM-1. This sensor fully quenches upon virus trafficking to a mildly acidic compartment, thus precluding subsequent detection of viral content release. As an interesting secondary observation, the incorporation of the pH-sensor revealed that HIV-1 particles occasionally shuttle between neutral and acidic compartments in target cells expressing CD4, suggesting a small fraction of viral particles is recycled to the plasma membrane and re-internalized. By imaging viruses bound to living cells, we found that HIV-1 content release in neutral-pH environment was a rare event (~0.4% particles). Surprisingly, viral content release was not significantly reduced by fusion inhibitors, implying that content release was due to spontaneous formation of viral membrane defects occurring at the cell surface. We did not measure a significant occurrence of HIV-1 fusion at neutral pH above this defect-mediated background loss of content, suggesting that the pH sensor may destabilize the membrane of the HIV-1 pseudovirus and, thus, preclude reliable detection of single virus fusion events at neutral pH. PMID:26863211