Advancing haematopoietic stem and progenitor cell biology through single-cell profiling.

PubMed

Hamey, Fiona K; Nestorowa, Sonia; Wilson, Nicola K; Göttgens, Berthold

2016-11-01

Haematopoietic stem and progenitor cells (HSPCs) sit at the top of the haematopoietic hierarchy, and their fate choices need to be carefully controlled to ensure balanced production of all mature blood cell types. As cell fate decisions are made at the level of the individual cells, recent technological advances in measuring gene and protein expression in increasingly large numbers of single cells have been rapidly adopted to study both normal and pathological HSPC function. In this review we emphasise the importance of combining the correct computational models with single-cell experimental techniques, and illustrate how such integrated approaches have been used to resolve heterogeneities in populations, reconstruct lineage differentiation, identify regulatory relationships and link molecular profiling to cellular function. © 2016 Federation of European Biochemical Societies.

Single-Cell and Single-Molecule Analysis of Gene Expression Regulation.

PubMed

Vera, Maria; Biswas, Jeetayu; Senecal, Adrien; Singer, Robert H; Park, Hye Yoon

2016-11-23

Recent advancements in single-cell and single-molecule imaging technologies have resolved biological processes in time and space that are fundamental to understanding the regulation of gene expression. Observations of single-molecule events in their cellular context have revealed highly dynamic aspects of transcriptional and post-transcriptional control in eukaryotic cells. This approach can relate transcription with mRNA abundance and lifetimes. Another key aspect of single-cell analysis is the cell-to-cell variability among populations of cells. Definition of heterogeneity has revealed stochastic processes, determined characteristics of under-represented cell types or transitional states, and integrated cellular behaviors in the context of multicellular organisms. In this review, we discuss novel aspects of gene expression of eukaryotic cells and multicellular organisms revealed by the latest advances in single-cell and single-molecule imaging technology.

Lights, Camera, Action! Antimicrobial Peptide Mechanisms Imaged in Space and Time

PubMed Central

Choi, Heejun; Rangarajan, Nambirajan; Weisshaar, James C.

2015-01-01

Deeper understanding of the bacteriostatic and bactericidal mechanisms of antimicrobial peptides (AMPs) should help in the design of new antibacterial agents. Over several decades, a variety of biochemical assays have been applied to bulk bacterial cultures. While some of these bulk assays provide time resolution on the order of 1 min, they do not capture faster mechanistic events. Nor can they provide subcellular spatial information or discern cell-to-cell heterogeneity within the bacterial population. Single-cell, time-resolved imaging assays bring a completely new spatiotemporal dimension to AMP mechanistic studies. We review recent work that provides new insights into the timing, sequence, and spatial distribution of AMP-induced effects on bacterial cells. PMID:26691950

Cellular autofluorescence imaging for early diagnosis of cancers

NASA Astrophysics Data System (ADS)

Steenkeste, Karine; Deniset, Ariane; Lecart, Sandrine; Leveque-Fort, Sandrine; Fontaine-Aupart, Marie-Pierre; Ferlicot, Sophie; Eschwege, Pascal

2005-08-01

Urinary cytology is employed in diagnostic guidelines of bladder cancer in anatomo-pathological laboratories mostly for its ability to diagnose non detectable cancers using cystoscopy, but also because it is a non-invasive and non-constraining technique for a regular follow-up of the more exposed populations. The impossibility to detect such cancers is mainly due to their localization either in the bladder or in the upper urinary tract and the prostate. However, urinary cytology lacks sensitivity, especially for the detection of low grade low stage tumors due to inherent limitation of morphological criteria to distinguish low grade tumor cells from normal urothelial cells. For this purpose, we developed, in addition to urinary cytology, an original screening of these cytological slides by using spectrally-resolved and time-resolved fluorescence as a contrast factor, without changing any parameters in the cytological slide preparation. This method takes advantage of a femtosecond Ti:sapphire laser, continuously tunable in the spectral range 700-950 nm allowing the observation of most endogenous cellular chromophores by biphotonic excitation. A commercial confocal microscope was also used in the measurements allowing an excitation of the samples between 458 nm and 633 nm. We observed that the fluorescence emission is differentially distributed in normal and pathological urothelial cells. Spectral- and time-resolved measurements attested this difference over about one hundred cases which have been tested to confirm the high accuracy of this non-invasive technique.

DAFi: A directed recursive data filtering and clustering approach for improving and interpreting data clustering identification of cell populations from polychromatic flow cytometry data.

PubMed

Lee, Alexandra J; Chang, Ivan; Burel, Julie G; Lindestam Arlehamn, Cecilia S; Mandava, Aishwarya; Weiskopf, Daniela; Peters, Bjoern; Sette, Alessandro; Scheuermann, Richard H; Qian, Yu

2018-04-17

Computational methods for identification of cell populations from polychromatic flow cytometry data are changing the paradigm of cytometry bioinformatics. Data clustering is the most common computational approach to unsupervised identification of cell populations from multidimensional cytometry data. However, interpretation of the identified data clusters is labor-intensive. Certain types of user-defined cell populations are also difficult to identify by fully automated data clustering analysis. Both are roadblocks before a cytometry lab can adopt the data clustering approach for cell population identification in routine use. We found that combining recursive data filtering and clustering with constraints converted from the user manual gating strategy can effectively address these two issues. We named this new approach DAFi: Directed Automated Filtering and Identification of cell populations. Design of DAFi preserves the data-driven characteristics of unsupervised clustering for identifying novel cell subsets, but also makes the results interpretable to experimental scientists through mapping and merging the multidimensional data clusters into the user-defined two-dimensional gating hierarchy. The recursive data filtering process in DAFi helped identify small data clusters which are otherwise difficult to resolve by a single run of the data clustering method due to the statistical interference of the irrelevant major clusters. Our experiment results showed that the proportions of the cell populations identified by DAFi, while being consistent with those by expert centralized manual gating, have smaller technical variances across samples than those from individual manual gating analysis and the nonrecursive data clustering analysis. Compared with manual gating segregation, DAFi-identified cell populations avoided the abrupt cut-offs on the boundaries. DAFi has been implemented to be used with multiple data clustering methods including K-means, FLOCK, FlowSOM, and the ClusterR package. For cell population identification, DAFi supports multiple options including clustering, bisecting, slope-based gating, and reversed filtering to meet various autogating needs from different scientific use cases. © 2018 International Society for Advancement of Cytometry. © 2018 International Society for Advancement of Cytometry.

Simulating Heterogeneous Tumor Cell Populations

PubMed Central

Bar-Sagi, Dafna; Mishra, Bud

2016-01-01

Certain tumor phenomena, like metabolic heterogeneity and local stable regions of chronic hypoxia, signify a tumor’s resistance to therapy. Although recent research has shed light on the intracellular mechanisms of cancer metabolic reprogramming, little is known about how tumors become metabolically heterogeneous or chronically hypoxic, namely the initial conditions and spatiotemporal dynamics that drive these cell population conditions. To study these aspects, we developed a minimal, spatially-resolved simulation framework for modeling tissue-scale mixed populations of cells based on diffusible particles the cells consume and release, the concentrations of which determine their behavior in arbitrarily complex ways, and on stochastic reproduction. We simulate cell populations that self-sort to facilitate metabolic symbiosis, that grow according to tumor-stroma signaling patterns, and that give rise to stable local regions of chronic hypoxia near blood vessels. We raise two novel questions in the context of these results: (1) How will two metabolically symbiotic cell subpopulations self-sort in the presence of glucose, oxygen, and lactate gradients? We observe a robust pattern of alternating striations. (2) What is the proper time scale to observe stable local regions of chronic hypoxia? We observe the stability is a function of the balance of three factors related to O2—diffusion rate, local vessel release rate, and viable and hypoxic tumor cell consumption rate. We anticipate our simulation framework will help researchers design better experiments and generate novel hypotheses to better understand dynamic, emergent whole-tumor behavior. PMID:28030620

Population Distribution Analyses Reveal a Hierarchy of Molecular Players Underlying Parallel Endocytic Pathways

PubMed Central

Gupta, Gagan D.; Howes, Mark T.; Chandran, Ruma; Das, Anupam; Menon, Sindhu; Parton, Robert G.; Sowdhamini, R.; Thattai, Mukund; Mayor, Satyajit

2014-01-01

Single-cell-resolved measurements reveal heterogeneous distributions of clathrin-dependent (CD) and -independent (CLIC/GEEC: CG) endocytic activity in Drosophila cell populations. dsRNA-mediated knockdown of core versus peripheral endocytic machinery induces strong changes in the mean, or subtle changes in the shapes of these distributions, respectively. By quantifying these subtle shape changes for 27 single-cell features which report on endocytic activity and cell morphology, we organize 1072 Drosophila genes into a tree-like hierarchy. We find that tree nodes contain gene sets enriched in functional classes and protein complexes, providing a portrait of core and peripheral control of CD and CG endocytosis. For 470 genes we obtain additional features from separate assays and classify them into early- or late-acting genes of the endocytic pathways. Detailed analyses of specific genes at intermediate levels of the tree suggest that Vacuolar ATPase and lysosomal genes involved in vacuolar biogenesis play an evolutionarily conserved role in CG endocytosis. PMID:24971745

Unresolved versus resolved: testing the validity of young simple stellar population models with VLT/MUSE observations of NGC 3603

NASA Astrophysics Data System (ADS)

Kuncarayakti, H.; Galbany, L.; Anderson, J. P.; Krühler, T.; Hamuy, M.

2016-09-01

Context. Stellar populations are the building blocks of galaxies, including the Milky Way. The majority, if not all, extragalactic studies are entangled with the use of stellar population models given the unresolved nature of their observation. Extragalactic systems contain multiple stellar populations with complex star formation histories. However, studies of these systems are mainly based upon the principles of simple stellar populations (SSP). Hence, it is critical to examine the validity of SSP models. Aims: This work aims to empirically test the validity of SSP models. This is done by comparing SSP models against observations of spatially resolved young stellar population in the determination of its physical properties, that is, age and metallicity. Methods: Integral field spectroscopy of a young stellar cluster in the Milky Way, NGC 3603, was used to study the properties of the cluster as both a resolved and unresolved stellar population. The unresolved stellar population was analysed using the Hα equivalent width as an age indicator and the ratio of strong emission lines to infer metallicity. In addition, spectral energy distribution (SED) fitting using STARLIGHT was used to infer these properties from the integrated spectrum. Independently, the resolved stellar population was analysed using the colour-magnitude diagram (CMD) to determine age and metallicity. As the SSP model represents the unresolved stellar population, the derived age and metallicity were tested to determine whether they agree with those derived from resolved stars. Results: The age and metallicity estimate of NGC 3603 derived from integrated spectroscopy are confirmed to be within the range of those derived from the CMD of the resolved stellar population, including other estimates found in the literature. The result from this pilot study supports the reliability of SSP models for studying unresolved young stellar populations. Based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programme 60.A-9344.

Cryptic deletions and inversions of chromosome 21 in a phenotypically normal infant with transient abnormal myelopoiesis: a molecular cytogenetic study.

PubMed

Kempski, H M; Craze, J L; Chessells, J M; Reeves, B R

1998-11-01

A case of transient abnormal myelopoiesis in a normal newborn without features of Down syndrome is described. The majority of bone marrow cells analysed belonged to a chromosomally abnormal clone with trisomy for chromosomes 18 and 21. Complex intrachromosomal rearrangements of one chromosome 21, demonstrated by fluorescence in situ hybridization using locus-specific probes, were found in a minor population of the clonal cells. These rearrangements involved loci previously shown to be rearranged in the leukaemic cells from patients with Down syndrome and leukaemia. However, the child's myeloproliferation resolved rapidly, with disappearance of the abnormal clone, and 3.5 years later she remains well.

Nondestructive nanostraw intracellular sampling for longitudinal cell monitoring

PubMed Central

Cao, Yuhong; Chen, Haodong; Birey, Fikri; Leal-Ortiz, Sergio A.; Han, Crystal M.; Santiago, Juan G.; Paşca, Sergiu P.; Wu, Joseph C.; Melosh, Nicholas A.

2017-01-01

Here, we report a method for time-resolved, longitudinal extraction and quantitative measurement of intracellular proteins and mRNA from a variety of cell types. Cytosolic contents were repeatedly sampled from the same cell or population of cells for more than 5 d through a cell-culture substrate, incorporating hollow 150-nm-diameter nanostraws (NS) within a defined sampling region. Once extracted, the cellular contents were analyzed with conventional methods, including fluorescence, enzymatic assays (ELISA), and quantitative real-time PCR. This process was nondestructive with >95% cell viability after sampling, enabling long-term analysis. It is important to note that the measured quantities from the cell extract were found to constitute a statistically significant representation of the actual contents within the cells. Of 48 mRNA sequences analyzed from a population of cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs), 41 were accurately quantified. The NS platform samples from a select subpopulation of cells within a larger culture, allowing native cell-to-cell contact and communication even during vigorous activity such as cardiomyocyte beating. This platform was applied both to cell lines and to primary cells, including CHO cells, hiPSC-CMs, and human astrocytes derived in 3D cortical spheroids. By tracking the same cell or group of cells over time, this method offers an avenue to understand dynamic cell behavior, including processes such as induced pluripotency and differentiation. PMID:28223521

Complexities and sequence similarities of mRNA populations of cholinergic (NS20-Y) and adrenergic (N1E-115) murine neuroblastoma cell lines.

PubMed

Strauss, W L

1990-07-01

The clonal murine neuroblastoma cell lines NS20-Y and N1E-115 have been proposed as models for examining the commitment of neural crest cells to either the cholinergic or adrenergic phenotype, respectively. The validity of this model depends in part on the extent to which these two cell lines have diverged as a result of their transformed, rather than neuronal properties. In order to quantitate differences in gene expression between NS20-Y and N1E-115 cells, the mRNA complexity of each cell type was determined. An analysis of the kinetics of hybridization of NS20-Y cell mRNA with cDNA prepared from NS20-Y cell mRNA demonstrated the presence of approximately 11,700 mRNA species assuming an average length of 1900 nucleotides. A similar analysis using mRNA isolated from N1E-115 cells and cDNA prepared from N1E-115 cell mRNA demonstrated that the adrenergic cell line expressed approximately 11,600 mRNA species. The species of mRNA expressed by each cell line were resolved into high, intermediate, and low abundance populations. In order to determine whether mRNAs were expressed by the cholinergic, but not by the adrenergic cell line, NS20-Y cDNA was hybridized to an excess of N1E-115 cell mRNA. An analysis of the solution hybridization kinetics from this procedure demonstrated that the two cell lines do not differ significantly in the nucleotide complexity of their mRNA populations. The extensive similarity between the two mRNA populations suggests that only a small number of genes are expressed differentially between the two cell lines and supports their use as models for the differentiation of cholinergic and adrenergic neurons.

Are neural correlates of visual consciousness retinotopic?

PubMed

ffytche, Dominic H; Pins, Delphine

2003-11-14

Some visual neurons code what we see, their defining characteristic being a response profile which mirrors conscious percepts rather than veridical sensory attributes. One issue yet to be resolved is whether, within a given cortical area, conscious visual perception relates to diffuse activity across the entire population of such cells or focal activity within the sub-population mapping the location of the perceived stimulus. Here we investigate the issue in the human brain with fMRI, using a threshold stimulation technique to dissociate perceptual from non-perceptual activity. Our results point to a retinotopic organisation of perceptual activity in early visual areas, with independent perceptual activations for different regions of visual space.

Evaluation of suppressive and pro-resolving effects of EPA and DHA in human primary monocytes and T-helper cells[S

PubMed Central

Jaudszus, Anke; Gruen, Michael; Watzl, Bernhard; Ness, Christina; Roth, Alexander; Lochner, Alfred; Barz, Dagmar; Gabriel, Holger; Rothe, Michael; Jahreis, Gerhard

2013-01-01

Despite their beneficial anti-inflammatory properties, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) may increase the infection risk at high doses, likely by generating an immune-depressed state. To assess the contribution of different immune cell populations to the immunomodulatory fatty acid effect, we comparatively investigated several aspects of inflammation in human T-helper (Th) cells and monocytes. Both fatty acids, but DHA to a lesser extent compared with EPA, selectively and dose-dependently reduced the percentage of cytokine-expressing Th cells in a peroxisome proliferator-activated receptor (PPAR)γ-dependent fashion, whereas the expression of the cell surface marker CD69 was unaltered on activated T cells. In monocytes, both EPA and DHA increased interleukin (IL)-10 without affecting tumor necrosis factor (TNF)-α and IL-6. Cellular incorporation of EPA and DHA occurred mainly at the expense of arachidonic acid. Concomitantly, thromboxane B (TXB)2 and leukotriene B (LTB)4 in supernatants decreased, while levels of TXB3 and LTB5 increased. This increase was independent of activation and in accordance with cyclooxygenase expression patterns in monocytes. Moreover, EPA and DHA gave rise to a variety of mono- and trihydroxy derivatives of highly anti-inflammatory potential, such as resolvins and their precursors. Our results suggest that EPA and DHA do not generally affect immune cell functions in an inhibitory manner but rather promote pro-resolving responses. PMID:23349208

Vaccination with Dendritic Cell Myeloma Fusions in Conjunction with Stem Cell Transplantation and PD-1 Blockade

DTIC Science & Technology

2014-05-01

UNRELATED DEFINITE NONE RESOLVED PM34 Injection site reaction 9/5/2013 1 UNRELATED DEFINITE (GM-CSF) NONE RESOLVED PM35 Neutropenia 10/8/2013 3 PROBABLE...PROBABLE NONE RESOLVED PM35 Neutropenia 10/11/2013 4 PROBABLE PROBABLE NONE RESOLVED PM35 Neutropenia 10/15/2013 3 PROBABLE PROBABLE NONE RESOLVED...presented to clinic for week 2 follow-up after his second infusion of CT-011 with grade 4 neutropenia (expected, probably related to CT-011 and

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carreon-Rodriguez, A.; Belkind-Gerson, J.; Serrano-Luna, G.

Availability of adult stem cells from several organs like bone marrow, umbilical cord blood or peripheral blood has become a powerful therapeutic tool for many chronic diseases. Potential of adult stem cells for regeneration extents to other tissues among them the nervous system. However two obstacles should be resolved before such cells could be currently applied in clinical practice: a) slow growth rate and b) ability to form enough dense colonies in order to populate a specific injury or cellular deficiency. Many approaches have been explored as genetic differentiation programs, growth factors, and supplemented culture media, among others. Electromagnetic fieldmore » stimulation of differentiation, proliferation, migration, and particularly on neurogenesis is little known. Since the biological effects of ELF-EMF are well documented, we hypothesize ELF-EMF could affect growth and maturation of stem cells derived of enteric tissue.« less

Characterizing the heterogeneity of tumor tissues from spatially resolved molecular measures

PubMed Central

Zavodszky, Maria I.

2017-01-01

Background Tumor heterogeneity can manifest itself by sub-populations of cells having distinct phenotypic profiles expressed as diverse molecular, morphological and spatial distributions. This inherent heterogeneity poses challenges in terms of diagnosis, prognosis and efficient treatment. Consequently, tools and techniques are being developed to properly characterize and quantify tumor heterogeneity. Multiplexed immunofluorescence (MxIF) is one such technology that offers molecular insight into both inter-individual and intratumor heterogeneity. It enables the quantification of both the concentration and spatial distribution of 60+ proteins across a tissue section. Upon bioimage processing, protein expression data can be generated for each cell from a tissue field of view. Results The Multi-Omics Heterogeneity Analysis (MOHA) tool was developed to compute tissue heterogeneity metrics from MxIF spatially resolved tissue imaging data. This technique computes the molecular state of each cell in a sample based on a pathway or gene set. Spatial states are then computed based on the spatial arrangements of the cells as distinguished by their respective molecular states. MOHA computes tissue heterogeneity metrics from the distributions of these molecular and spatially defined states. A colorectal cancer cohort of approximately 700 subjects with MxIF data is presented to demonstrate the MOHA methodology. Within this dataset, statistically significant correlations were found between the intratumor AKT pathway state diversity and cancer stage and histological tumor grade. Furthermore, intratumor spatial diversity metrics were found to correlate with cancer recurrence. Conclusions MOHA provides a simple and robust approach to characterize molecular and spatial heterogeneity of tissues. Research projects that generate spatially resolved tissue imaging data can take full advantage of this useful technique. The MOHA algorithm is implemented as a freely available R script (see supplementary information). PMID:29190747

Identification of a role for the nuclear receptor EAR-2 in the maintenance of clonogenic status within the leukemia cell hierarchy

PubMed Central

Ichim, CV; Atkins, HL; Iscove, NN; Wells, RA

2016-01-01

Identification of genes that regulate clonogenicity of acute myelogenous leukemia (AML) cells is hindered by the difficulty of isolating pure populations of cells with defined proliferative abilities. By analyzing the growth of clonal siblings in low passage cultures of the cell line OCI/AML4 we resolved this heterogeneous population into strata of distinct clonogenic potential, permitting analysis of the transcriptional signature of single cells with defined proliferative abilities. By microarray analysis we showed that the expression of the orphan nuclear receptor EAR-2 (NR2F6) is greater in leukemia cells with extensive proliferative capacity than in those that have lost proliferative ability. EAR-2 is expressed highly in long-term hematopoietic stem cells, relative to short-term hematopoietic stem and progenitor cells, and is downregulated in AML cells after induction of differentiation. Exogenous expression of EAR-2 increased the growth of U937 cells and prevented the proliferative arrest associated with terminal differentiation, and blocked differentiation of U937 and 32Dcl3 cells. Conversely, silencing of EAR-2 by short-hairpin RNA initiated terminal differentiation of these cell lines. These data identify EAR-2 as an important factor in the regulation of clonogenicity and differentiation, and establish that analysis of clonal siblings allows the elucidation of differences in gene expression within the AML hierarchy. PMID:21637284

The Andromeda Optical and Infrared Disk Survey

NASA Astrophysics Data System (ADS)

Sick, Jonathan

The spectral energy distributions of galaxies inform us about a galaxy's stellar populations and interstellar medium, revealing stories of galaxy formation and evolution. How we interpret this light depends in part on our proximity to the galaxy. For nearby galaxies, detailed star formation histories can be extracted from the resolved stellar populations, while more distant galaxies feature the contributions of entire stellar populations within their integrated spectral energy distribution (SED). This thesis aims to resolve whether the techniques used to investigate stellar populations in distant galaxies are consistent with those available for nearby galaxies. As the nearest spiral galaxy, the Andromeda Galaxy (M31) is the ideal testbed for the joint study of resolved stellar populations and panchromatic SEDs. We present the Andromeda Optical and Infrared Disk Survey (ANDROIDS), which adds new near-UV to near-IR (u*g'r'i'JKs) imaging using the MegaCam and WIRCam cameras at the Canada-France-Hawaii telescope to the available M31 panchromatic dataset. To accurately subtract photometric background from our extremely wide-field (14 square degree) mosaics, we present observing and data reduction techniques with sky-target nodding, optimization of image-to-image surface brightness, and a novel hierarchical Bayesian model to trace the background signal while modelling the astrophysical SED. We model the spectral energy distributions of M31 pixels with MAGPHYS (da Cunha et al. 2008) and compare those results to resolved stellar population models of the same pixels from the Panchromatic Hubble Andromeda Treasury (PHAT) survey (Williams et al. 2017). We find substantial (0.3 dex) differences in stellar mass estimates despite a common use of the Chabrier (2003) initial mass function. Stellar mass estimated from the resolved stellar population is larger than any mass estimate from SED models or colour-M/L relations (CMLRs). There is also considerable diversity among CMLR estimators, largely driven by differences in the star formation history prior distribution. We find broad consistency between the star formation history estimated by integrated spectral energy distributions and resolved stars. Generally, spectral energy distribution models yield a stronger inside-out radial metallicity gradient and bias towards younger mean ages than resolved stellar population models.

Drug-induced pseudo-Sezary syndrome: a case report and literature review.

PubMed

Reeder, Margo J; Wood, Gary S

2015-01-01

Pseudo-Sezary syndrome is a benign lymphoproliferative disorder, which clinically and pathologically mimics true Sezary syndrome. In this article, a case of pseudo-Sezary syndrome and review the literature has been reported. The patient was a 51-year-old man who developed erythroderma and palmoplantar keratoderma. The patient's medication history included fosinopril and combination metoprolol/hydrochlorothiazide. Flow cytometry showed a population of 2500 "Sezary-like" CD4726 T cells per microliter in the peripheral blood. Skin biopsy showed numerous atypical lymphocytes with epidermotropism, and there was matching dominant T-cell clonality in the skin and peripheral blood. After stopping all antihypertensive medications, the eruption resolved in its entirety.

Effects of Electromagnetic Stimulation on Cell Density and Neural Markers in Murine Enteric Cell Cultures

NASA Astrophysics Data System (ADS)

Carreón-Rodríguez, A.; Belkind-Gerson, J.; Serrano-Luna, G.; Cañedo-Dorantes, L.

2008-08-01

Availability of adult stem cells from several organs like bone marrow, umbilical cord blood or peripheral blood has become a powerful therapeutic tool for many chronic diseases. Potential of adult stem cells for regeneration extents to other tissues among them the nervous system. However two obstacles should be resolved before such cells could be currently applied in clinical practice: a) slow growth rate and b) ability to form enough dense colonies in order to populate a specific injury or cellular deficiency. Many approaches have been explored as genetic differentiation programs, growth factors, and supplemented culture media, among others. Electromagnetic field stimulation of differentiation, proliferation, migration, and particularly on neurogenesis is little known. Since the biological effects of ELF-EMF are well documented, we hypothesize ELF-EMF could affect growth and maturation of stem cells derived of enteric tissue.

Application of phasor plot and autofluorescence correction for study of heterogeneous cell population

PubMed Central

Szmacinski, Henryk; Toshchakov, Vladimir; Lakowicz, Joseph R.

2014-01-01

Abstract. Protein-protein interactions in cells are often studied using fluorescence resonance energy transfer (FRET) phenomenon by fluorescence lifetime imaging microscopy (FLIM). Here, we demonstrate approaches to the quantitative analysis of FRET in cell population in a case complicated by a highly heterogeneous donor expression, multiexponential donor lifetime, large contribution of cell autofluorescence, and significant presence of unquenched donor molecules that do not interact with the acceptor due to low affinity of donor-acceptor binding. We applied a multifrequency phasor plot to visualize FRET FLIM data, developed a method for lifetime background correction, and performed a detailed time-resolved analysis using a biexponential model. These approaches were applied to study the interaction between the Toll Interleukin-1 receptor (TIR) domain of Toll-like receptor 4 (TLR4) and the decoy peptide 4BB. TLR4 was fused to Cerulean fluorescent protein (Cer) and 4BB peptide was labeled with Bodipy TMRX (BTX). Phasor displays for multifrequency FLIM data are presented. The analytical procedure for lifetime background correction is described and the effect of correction on FLIM data is demonstrated. The absolute FRET efficiency was determined based on the phasor plot display and multifrequency FLIM data analysis. The binding affinity between TLR4-Cer (donor) and decoy peptide 4BB-BTX (acceptor) was estimated in a heterogeneous HeLa cell population. PMID:24770662

In vitro antigen-specific induction of IL-22 in human subjects that resolved HCV infection

PubMed Central

Cusick, Matthew F; Libbey, Jane E; Fujinami, Robert S; Eckels, David D

2012-01-01

Aims To determine if in vitro production of IL-22 and IL-17 correlated with resolution of HCV infection. Materials & methods Human peripheral blood cells isolated from a well-defined cohort of resolved and chronic HCV-infected subjects were used to measure HCV-, influenza- and mitogen-activated T-cell proliferation. In addition, IL-22 and IL-17 production was measured via ELISAs and flow cytometry. Results Resolved HCV subjects had a significantly higher T-cell proliferative response to recombinant NS3 protein compared with chronic HCV subjects. Resolved subjects had a dose-dependent IL-22 response to recombinant NS3 compared with chronic HCV subjects. Conclusion IL-22 production is associated with antigen-specific induction of CD4 + T cells in individuals that resolved HCV infection, suggesting a potential role for IL-22 in HCV clearance. PMID:23185211

High-resolution Myogenic Lineage Mapping by Single-Cell Mass Cytometry

PubMed Central

Porpiglia, Ermelinda; Samusik, Nikolay; Ho, Andrew Tri Van; Cosgrove, Benjamin D.; Mai, Thach; Davis, Kara L.; Jager, Astraea; Nolan, Garry P.; Bendall, Sean C.; Fantl, Wendy J.; Blau, Helen M.

2017-01-01

Muscle regeneration is a dynamic process during which cell state and identity change over time. A major roadblock has been a lack of tools to resolve a myogenic progression in vivo. Here we capitalize on a transformative technology, single-cell mass cytometry (CyTOF), to identify in vivo skeletal muscle stem cell and previously unrecognized progenitor populations that precede differentiation. We discovered two cell surface markers, CD9 and CD104, whose combined expression enabled in vivo identification and prospective isolation of stem and progenitor cells. Data analysis using the X-shift algorithm paired with single-cell force directed layout visualization, defined a molecular signature of the activated stem cell state (CD44+/CD98+/MyoD+) and delineated a myogenic trajectory during recovery from acute muscle injury. Our studies uncover the dynamics of skeletal muscle regeneration in vivo and pave the way for the elucidation of the regulatory networks that underlie cell-state transitions in muscle diseases and aging. PMID:28414312

Microchip-Based Single-Cell Functional Proteomics for Biomedical Applications

PubMed Central

Lu, Yao; Yang, Liu; Wei, Wei; Shi, Qihui

2017-01-01

Cellular heterogeneity has been widely recognized but only recently have single cell tools become available that allow characterizing heterogeneity at the genomic and proteomic levels. We review the technological advances in microchip-based toolkits for single-cell functional proteomics. Each of these tools has distinct advantages and limitations, and a few have advanced toward being applied to address biological or clinical problems that fail to be addressed by traditional population-based methods. High-throughput single-cell proteomic assays generate high-dimensional data sets that contain new information and thus require developing new analytical framework to extract new biology. In this review article, we highlight a few biological and clinical applications in which the microchip-based single-cell proteomic tools provide unique advantages. The examples include resolving functional heterogeneity and dynamics of immune cells, dissecting cell-cell interaction by creating well-contolled on-chip microenvironment, capturing high-resolution snapshots of immune system functions in patients for better immunotherapy and elucidating phosphoprotein signaling networks in cancer cells for guiding effective molecularly targeted therapies. PMID:28280819

Measurements of population densities of metastable and resonant levels of argon using laser induced fluorescence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nikolić, M.; Newton, J.; Sukenik, C. I.

2015-01-14

We present a new approach to measure population densities of Ar I metastable and resonant excited states in low temperature Ar plasmas at pressures higher than 1 Torr. This approach combines the time resolved laser induced fluorescence technique with the kinetic model of Ar. The kinetic model of Ar is based on calculating the population rates of metastable and resonant levels by including contributions from the processes that affect population densities of Ar I excited states. In particular, we included collisional quenching processes between atoms in the ground state and excited states, since we are investigating plasma at higher pressures. Wemore » also determined time resolved population densities of Ar I 2 p excited states by employing optical emission spectroscopy technique. Time resolved Ar I excited state populations are presented for the case of the post-discharge of the supersonic flowing microwave discharge at pressures of 1.7 and 2.3 Torr. The experimental set-up consists of a pulsed tunable dye laser operating in the near infrared region and a cylindrical resonance cavity operating in TE{sub 111} mode at 2.45 GHz. Results show that time resolved population densities of Ar I metastable and resonant states oscillate with twice the frequency of the discharge.« less

General statistics of stochastic process of gene expression in eukaryotic cells.

PubMed Central

Kuznetsov, V A; Knott, G D; Bonner, R F

2002-01-01

Thousands of genes are expressed at such very low levels (< or =1 copy per cell) that global gene expression analysis of rarer transcripts remains problematic. Ambiguity in identification of rarer transcripts creates considerable uncertainty in fundamental questions such as the total number of genes expressed in an organism and the biological significance of rarer transcripts. Knowing the distribution of the true number of genes expressed at each level and the corresponding gene expression level probability function (GELPF) could help resolve these uncertainties. We found that all observed large-scale gene expression data sets in yeast, mouse, and human cells follow a Pareto-like distribution model skewed by many low-abundance transcripts. A novel stochastic model of the gene expression process predicts the universality of the GELPF both across different cell types within a multicellular organism and across different organisms. This model allows us to predict the frequency distribution of all gene expression levels within a single cell and to estimate the number of expressed genes in a single cell and in a population of cells. A random "basal" transcription mechanism for protein-coding genes in all or almost all eukaryotic cell types is predicted. This fundamental mechanism might enhance the expression of rarely expressed genes and, thus, provide a basic level of phenotypic diversity, adaptability, and random monoallelic expression in cell populations. PMID:12136033

The Resolved Stellar Populations Early Release Science Program

NASA Astrophysics Data System (ADS)

Weisz, Daniel; Anderson, J.; Boyer, M.; Cole, A.; Dolphin, A.; Geha, M.; Kalirai, J.; Kallivayalil, N.; McQuinn, K.; Sandstrom, K.; Williams, B.

2017-11-01

We propose to obtain deep multi-band NIRCam and NIRISS imaging of three resolved stellar systems within 1 Mpc (NOI 104). We will use this broad science program to optimize observational setups and to develop data reduction techniques that will be common to JWST studies of resolved stellar populations. We will combine our expertise in HST resolved star studies with these observations to design, test, and release point spread function (PSF) fitting software specific to JWST. PSF photometry is at the heart of resolved stellar populations studies, but is not part of the standard JWST reduction pipeline. Our program will establish JWST-optimized methodologies in six scientific areas: star formation histories, measurement of the sub-Solar mass stellar IMF, extinction maps, evolved stars, proper motions, and globular clusters, all of which will be common pursuits for JWST in the local Universe. Our observations of globular cluster M92, ultra-faint dwarf Draco II, and star-forming dwarf WLM, will be of high archival value for other science such as calibrating stellar evolution models, measuring properties of variable stars, and searching for metal-poor stars. We will release the results of our program, including PSF fitting software, matched HST and JWST catalogs, clear documentation, and step-by-step tutorials (e.g., Jupyter notebooks) for data reduction and science application, to the community prior to the Cycle 2 Call for Proposals. We will host a workshop to help community members plan their Cycle 2 observations of resolved stars. Our program will provide blueprints for the community to efficiently reduce and analyze JWST observations of resolved stellar populations.

Mature B-cell neoplasms in Chernobyl clean-up workers of 1986-1987: summary of cytomorphological and immunocytochemical study in 25 years after Chernobyl accident.

PubMed

Gluzman, D F; Sklyarenko, L M; Nadgornaya, V A; Zavelevich, M P

2011-03-01

The data on the verified cases of mature B-cell neoplasms (chronic lymphocytic leukemia - CLL, B-prolymphocytic leukemia, non-Hodgkin's lymphoma in leukemization phase and multiple myeloma - MM; 146 cases in total) in the consecutive group of Ukrainian clean-up workers within 10-25 years after Chernobyl accident are summarized. B-cell neoplasms represent the most prevalent group among all diagnosed neoplasms of hematopoietic and lymphoid tissues in clean-up worker patients under study (49.4%). MM percentage in the patients of Chernobyl clean-up worker group turned out to be significantly higher than in the patients of the general populations studied at the same period. While the percentage of B-CLL is similar in clean-up worker patients and patients of general population, the trend towards younger age of patients with mature B-cell neoplasms in clean-up worker group is evident. The current concepts on the possible association between mature B-cell neoplasms (mainly B-CLL) and radiation exposure are briefly outlined. Only the precise diagnosis of hematopoietic malignancies combining with large-scale analytical epidemiological studies with careful dose assessment and long-term follow-up may represent the basis for resolving the question whether mature B-cell neoplasms may be radiogenic.

Neutrophils confer T cell resistance to myeloid-derived suppressor cell-mediated suppression to promote chronic inflammation.

PubMed

Ryan, Sean O; Johnson, Jenny L; Cobb, Brian A

2013-05-15

Low-grade chronic inflammation can persist in aging humans unnoticed for years or even decades, inflicting continuous damage that can culminate later in life as organ dysfunction, physical frailty, and some of the most prominent debilitating and deadly age-associated diseases, including rheumatoid arthritis, diabetes, heart disease, and cancer. Despite the near universal acceptance of these associations, the mechanisms underlying unresolved inflammation remain poorly understood. In this study, we describe a novel inducible method to examine systemic chronic inflammation using susceptible animal models. Induced inflammation results in unresolved innate cellular responses and persistence of the same serum proinflammatory molecules used as diagnostic biomarkers and therapeutic targets for chronic inflammation in humans. Surprisingly, we found long-term persistence of an inflammation-associated neutrophil cell population constitutively producing the proinflammatory IFN-γ cytokine, which until now has only been detected transiently in acute inflammatory responses. Interestingly, these cells appear to confer T cell resistance to the otherwise potent anti-inflammatory function of myeloid-derived suppressor cells, revealing a novel mechanism for the maintenance of chronic inflammatory responses over time. This discovery represents an attractive target to resolve inflammation and prevent the inflammation-induced pathologies that are of critical concern for the well-being of the aging population.

Vaccination with Dendritic Cell Myeloma Fusions in Conjuction with Stem Cell Transplantation and PD-1 Blockade

DTIC Science & Technology

2015-07-01

Definite (GM- CSF) None Resolved PM35 Neutropenia 10/8/2013 3 Probable Probable None Resolved PM35 Neutropenia 10/11/2013 4 Probable Probable None...Resolved PM35 Neutropenia 10/15/2013 3 Probable Probable None Resolved 13 Subject ID AE Start Date CTC Grade Relationship to CT-011...participant PM35 presented to clinic for week 2 follow-up after his second infusion of CT-011 with grade 4 neutropenia (expected, probably related

Polypeptide profiles of human oocytes and preimplantation embryos.

PubMed

Capmany, G; Bolton, V N

1993-11-01

The polypeptides that direct fertilization and early development until activation of the embryonic genome occurs, at the 4-8 cell stage in the human, are exclusively maternal in origin, and are either synthesized during oogenesis or translated later from maternal mRNA. Using sodium dodecyl sulphate-polyacrylamide gel electrophoresis and silver stain, we have visualized and compared the polypeptides present in different populations of human oocytes and cleavage stage embryos obtained after superovulation and insemination in vitro. Two polypeptide patterns were resolved, differing in the region of mol. wt 69 kDa. The distribution of these patterns showed no correlation with the ability of individual oocytes to achieve fertilization and develop normally to the 8-cell stage.

Functional classification of memory CD8(+) T cells by CX3CR1 expression.

PubMed

Böttcher, Jan P; Beyer, Marc; Meissner, Felix; Abdullah, Zeinab; Sander, Jil; Höchst, Bastian; Eickhoff, Sarah; Rieckmann, Jan C; Russo, Caroline; Bauer, Tanja; Flecken, Tobias; Giesen, Dominik; Engel, Daniel; Jung, Steffen; Busch, Dirk H; Protzer, Ulrike; Thimme, Robert; Mann, Matthias; Kurts, Christian; Schultze, Joachim L; Kastenmüller, Wolfgang; Knolle, Percy A

2015-09-25

Localization of memory CD8(+) T cells to lymphoid or peripheral tissues is believed to correlate with proliferative capacity or effector function. Here we demonstrate that the fractalkine-receptor/CX3CR1 distinguishes memory CD8(+) T cells with cytotoxic effector function from those with proliferative capacity, independent of tissue-homing properties. CX3CR1-based transcriptome and proteome-profiling defines a core signature of memory CD8(+) T cells with effector function. We find CD62L(hi)CX3CR1(+) memory T cells that reside within lymph nodes. This population shows distinct migration patterns and positioning in proximity to pathogen entry sites. Virus-specific CX3CR1(+) memory CD8(+) T cells are scarce during chronic infection in humans and mice but increase when infection is controlled spontaneously or by therapeutic intervention. This CX3CR1-based functional classification will help to resolve the principles of protective CD8(+) T-cell memory.

Primary Intracranial Sarcoma Presenting as Chronic Subdural Fluid Collections in a Child.

PubMed

Glenn, Chad A; Fung, Kar-Ming; Tullos, Hurtis J; McNall-Knapp, Rene Y; Gunda, Divya; Mapstone, Timothy B

2016-02-01

Chronic subdural hematoma in the pediatric population often results from trauma. Asymptomatic and benign-appearing subdural collections are generally managed conservatively without operative intervention. Primary intracranial sarcomas are uncommon entities. Diagnosis of sarcoma can be difficult because these lesions often manifest as apparent hematoma. Presented is the case of a primary intracranial mucoid spindle cell sarcoma that arose in a child with a history of benign-appearing bilateral subdural fluid collections in the setting of nonaccidental trauma. The patient was initially managed conservatively because her neurological examination result was normal and her subdural collections decreased in size on repeated imaging. The collections did not resolve completely. Years later, she exhibited weakness, seizure, and an increase in the size of her subdural fluid collection. Subdural drainage was attempted without significant effect. Cytologic assessment of fluid was negative for malignant cells. Magnetic resonance imaging revealed multiple enhancing masses along the subdural collection. The patient eventually underwent craniotomy in which a diagnosis of sarcoma was obtained. Pathological and radiographic findings as well as oncological management are reviewed. The authors also review the natural history and treatment of primary intracranial sarcoma in the pediatric population. Early contrasted magnetic resonance imaging should be obtained in patients with subdural fluid collections that appear asymmetric or do not resolve in the expected time course, despite having a normal neurologic examination result. Negative cytologic assessment does not exclude sarcoma diagnosis. Copyright © 2016 Elsevier Inc. All rights reserved.

Single-cell RNA sequencing reveals developmental heterogeneity among early lymphoid progenitors.

PubMed

Alberti-Servera, Llucia; von Muenchow, Lilly; Tsapogas, Panagiotis; Capoferri, Giuseppina; Eschbach, Katja; Beisel, Christian; Ceredig, Rhodri; Ivanek, Robert; Rolink, Antonius

2017-12-15

Single-cell RNA sequencing is a powerful technology for assessing heterogeneity within defined cell populations. Here, we describe the heterogeneity of a B220 + CD117 int CD19 - NK1.1 - uncommitted hematopoietic progenitor having combined lymphoid and myeloid potential. Phenotypic and functional assays revealed four subpopulations within the progenitor with distinct lineage developmental potentials. Among them, the Ly6D + SiglecH - CD11c - fraction was lymphoid-restricted exhibiting strong B-cell potential, whereas the Ly6D - SiglecH - CD11c - fraction showed mixed lympho-myeloid potential. Single-cell RNA sequencing of these subsets revealed that the latter population comprised a mixture of cells with distinct lymphoid and myeloid transcriptional signatures and identified a subgroup as the potential precursor of Ly6D + SiglecH - CD11c - Subsequent functional assays confirmed that B220 + CD117 int CD19 - NK1.1 - single cells are, with rare exceptions, not bipotent for lymphoid and myeloid lineages. A B-cell priming gradient was observed within the Ly6D + SiglecH - CD11c - subset and we propose a herein newly identified subgroup as the direct precursor of the first B-cell committed stage. Therefore, the apparent multipotency of B220 + CD117 int CD19 - NK1.1 - progenitors results from underlying heterogeneity at the single-cell level and highlights the validity of single-cell transcriptomics for resolving cellular heterogeneity and developmental relationships among hematopoietic progenitors. © 2017 The Authors.

Lymphosarcoma associated with Heterobilharzia americana infection in a dog.

PubMed

Stone, Richard H; Frontera-Acevedo, Karelma; Saba, Corey F; Ambrose, Dana; Moorhead, Andrew R; Brown, Cathy A

2011-09-01

Hepatic T-cell lymphosarcoma with involvement of regional lymph nodes and concurrent schistosomiasis were diagnosed in an 11-year-old male neutered mixed-breed dog with a history of chronic weight loss, inappetence, vomiting, and diarrhea. Trematode ova present in the hepatic parenchyma and mesenteric node were surrounded by sheets of neoplastic lymphocytes while those in the intestinal wall were surrounded by large numbers of non-neoplastic lymphocytes. Immunohistochemistry revealed that both the neoplastic and hyperplastic populations were T lymphocytes. The ova were identified by fecal saline sedimentation as Heterobilharzia spp., and fecal ova shedding resolved after praziquantel anthelmintic treatment. The lymphoma progressed despite chemotherapy, and the dog was euthanized after developing neurologic signs and a necropsy was performed. A monomorphic population of neoplastic T cells expanded and replaced normal architecture in the liver and spleen, surrounded nerve roots within the cauda equina, and infiltrated the meninges of the brain. The presence of schistosome ova embedded within neoplastic T-cell infiltrates suggests that, as previously reported in human schistosomiasis, heterobilharziasis may be associated with neoplasia.

Endorsing cellular competitiveness in aberrant epithelium of oral submucous fibrosis progression: neighbourhood analysis of immunohistochemical attributes.

PubMed

Anura, Anji; Kazi, Anees; Pal, Mousumi; Paul, Ranjan Rashmi; Sengupta, Sanghamitra; Chatterjee, Jyotirmoy

2018-04-23

Epithelial abnormality during the transformation of oral submucous fibrosis (OSF) into oral squamous cell carcinoma has been well studied and documented. However, the differential contribution of atrophy and hyperplasia for malignant potentiality of OSF is yet to be resolved. Existing diagnostic conjectures lack precise diagnostic attributes which may be effectively resolved by substantiation of specific molecular pathology signatures. Present study elucidates existence of cellular competitiveness in OSF conditions using computer-assisted neighbourhood analysis in quantitative immunohistochemistry (IHC) framework. The concept of field cancerization was contributory in finding correspondence among neighbouring cells of epithelial layers with reference to differential expression of cardinal cancer-related genes [c-Myc (oncogene), p53 (tumour suppressor), and HIF-1α (hypoxia regulator)] which are known to be important sensors in recognizing cellular competitive interface. Our analyses indicate that different states of OSF condition may be associated with different forms of competitiveness within epithelial neighbouring cells which might be responsible to shape the present and future of the pre-malignant condition. Analytical findings indicated association of atrophic epithelium with stress-driven competitive environment having low c-Myc, high-p53, and stable HIF-1α (the looser cells) which undergo apoptosis. Whereas, the cells with high c-Myc + (winner cells) give rise to hyperplastic epithelium via possible mutation in p53. The epithelial dysplasia plausibly occurs due to clonal expansion of c-Myc and p53 positive supercompetitor cells. Present study proposes quantitative IHC along with neighbourhood analysis which might help us to dig deeper on to the interaction among epithelial cell population to provide a better understanding of field cancerization and malignant transformation of pre-malignancy.

Mechanistic characterization of chloride interferences in electrothermal atomization systems

USGS Publications Warehouse

Shekiro, J.M.; Skogerboe, R.K.; Taylor, Howard E.

1988-01-01

A computer-controlled spectrometer with a photodiode array detector has been used for wavelength and temperature resolved characterization of the vapor produced by an electrothermal atomizer. The system has been used to study the chloride matrix interference on the atomic absorption spectrometric determination of manganese and copper. The suppression of manganese and copper atom populations by matrix chlorides such as those of calcium and magnesium is due to the gas-phase formation of an analyte chloride species followed by the diffusion of significant fractions of these species from the atom cell prior to completion of the atomization process. The analyte chloride species cannot be formed when matrix chlorides with metal-chloride bond dissociation energies above those of the analyte chlorides are the principal entitles present. The results indicate that multiple wavelength spectrometry used to obtain temperature-resolved spectra is a viable tool in the mechanistic characterization of interference effects observed with electrothermal atomization systems. ?? 1988 American Chemical Society.

Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells.

PubMed

Zhu, Ying; Piehowski, Paul D; Zhao, Rui; Chen, Jing; Shen, Yufeng; Moore, Ronald J; Shukla, Anil K; Petyuk, Vladislav A; Campbell-Thompson, Martha; Mathews, Clayton E; Smith, Richard D; Qian, Wei-Jun; Kelly, Ryan T

2018-02-28

Nanoscale or single-cell technologies are critical for biomedical applications. However, current mass spectrometry (MS)-based proteomic approaches require samples comprising a minimum of thousands of cells to provide in-depth profiling. Here, we report the development of a nanoPOTS (nanodroplet processing in one pot for trace samples) platform for small cell population proteomics analysis. NanoPOTS enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive liquid chromatography-MS, nanoPOTS allows identification of ~1500 to ~3000 proteins from ~10 to ~140 cells, respectively. By incorporating the Match Between Runs algorithm of MaxQuant, >3000 proteins are consistently identified from as few as 10 cells. Furthermore, we demonstrate quantification of ~2400 proteins from single human pancreatic islet thin sections from type 1 diabetic and control donors, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues.

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Ying; Piehowski, Paul D.; Zhao, Rui

Nanoscale or single-cell technologies are critical for biomedical applications. However, current mass spectrometry (MS)-based proteomic approaches require samples comprising a minimum of thousands of cells to provide in-depth profiling. Here in this paper, we report the development of a nanoPOTS (nanodroplet processing in one pot for trace samples) platform for small cell population proteomics analysis. NanoPOTS enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive liquid chromatography-MS, nanoPOTS allows identification of ~1500 to ~3000 proteins from ~10 to ~140 cells, respectively. By incorporating the Match Betweenmore » Runs algorithm of MaxQuant, >3000 proteins are consistently identified from as few as 10 cells. Furthermore, we demonstrate quantification of ~2400 proteins from single human pancreatic islet thin sections from type 1 diabetic and control donors, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues.« less

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells

DOE PAGES

Zhu, Ying; Piehowski, Paul D.; Zhao, Rui; ...

2018-02-28

Nanoscale or single-cell technologies are critical for biomedical applications. However, current mass spectrometry (MS)-based proteomic approaches require samples comprising a minimum of thousands of cells to provide in-depth profiling. Here in this paper, we report the development of a nanoPOTS (nanodroplet processing in one pot for trace samples) platform for small cell population proteomics analysis. NanoPOTS enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive liquid chromatography-MS, nanoPOTS allows identification of ~1500 to ~3000 proteins from ~10 to ~140 cells, respectively. By incorporating the Match Betweenmore » Runs algorithm of MaxQuant, >3000 proteins are consistently identified from as few as 10 cells. Furthermore, we demonstrate quantification of ~2400 proteins from single human pancreatic islet thin sections from type 1 diabetic and control donors, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues.« less

Rationale for the potential use of mesenchymal stromal cells in liver transplantation

PubMed Central

Vandermeulen, Morgan; Grégoire, Céline; Briquet, Alexandra; Lechanteur, Chantal; Beguin, Yves; Detry, Olivier

2014-01-01

Mesenchymal stromal cells (MSCs) are multipotent and self-renewing cells that reside essentially in the bone marrow as a non-hematopoietic cell population, but may also be isolated from the connective tissues of most organs. MSCs represent a heterogeneous population of adult, fibroblast-like cells characterized by their ability to differentiate into tissues of mesodermal lineages including adipocytes, chondrocytes and osteocytes. For several years now, MSCs have been evaluated for their in vivo and in vitro immunomodulatory and ‘tissue reconstruction’ properties, which could make them interesting in various clinical settings, and particularly in organ transplantation. This paper aims to review current knowledge on the properties of MSCs and their use in pre-clinical and clinical studies in solid organ transplantation, and particularly in the field of liver transplantation. The first available clinical data seem to show that MSCs are safe to use, at least in the medium-term, but more time is needed to evaluate the potential adverse effects of long-term use. Many issues must be resolved on the correct use of MSCs. Intensive in vitro and pre-clinical research are the keys to a better understanding of the way that MSCs act, and to eventually lead to clinical success. PMID:25469010

Evaluation of Sanofi Diagnostics Pasteur Chlamydia Microplate EIA shortened assay and comparison with cell culture and Syva Chlamydia MicroTrak II EIA in high- and low-risk populations.

PubMed

Chan, E L; Brandt, K; Horsman, G

1995-11-01

Seven hundred thirty-two female urogenital samples were collected for Chlamydia trachomatis testing by both the Sanofi Diagnostics Pasteur (Chaska, Minn.) Chlamydia Microplate EIA by the shortened protocol and the Syva (San Jose, Calif.) MicroTrak II EIA, and the results were compared with those obtained by cell culture. For the analysis of samples from female patients, the patients were divided into high- and low-risk categories. An additional 121 male urethral samples were collected and tested by the Sanofi Microplate EIA and cell culture; for the analysis of samples from male patients, the patients were divided into asymptomatic and symptomatic categories. All specimens positive by enzyme immunoassay (EIA) were confirmed by a blocking assay following the respective manufacturer's instructions. Specimens negative by EIA that fell within a gray zone 30% below the cutoff and negative cultures with one or more corresponding positive EIA results were tested further by cytocentrifugation and direct immunofluorescent assay. The overall sensitivity, specificity, positive predictive value, and negative predictive value for Syva versus culture were 94, 98.8, 85.5 and 99.6%, respectively. After resolution, the results were 94.5, 99.6, 94.5, and 99.6%, respectively. The parallel results for the Sanofi Microplate EIA versus culture were 94.0, 98.7, and 83.9, and 99.6%, respectively, and after being resolved, the results were 94.9, 100, 100, and 99.6%, respectively. In the small male population tested, the resolved results of the Sanofi Microplate EIA versus culture demonstrated sensitivity, specificity, positive predictive value, and negative predictive value of 100, 100, 100, and 100%, respectively. The present study demonstrated that the Sanofi Microplate EIA shortened protocol is highly sensitive and specific in comparison with cell culture and the Syva MicroTrak II EIA.

Resolving stem and progenitor cells in the adult mouse incisor through gene co-expression analysis

PubMed Central

Seidel, Kerstin; Marangoni, Pauline; Tang, Cynthia; Houshmand, Bahar; Du, Wen; Maas, Richard L; Murray, Steven; Oldham, Michael C; Klein, Ophir D

2017-01-01

Investigations into stem cell-fueled renewal of an organ benefit from an inventory of cell type-specific markers and a deep understanding of the cellular diversity within stem cell niches. Using the adult mouse incisor as a model for a continuously renewing organ, we performed an unbiased analysis of gene co-expression relationships to identify modules of co-expressed genes that represent differentiated cells, transit-amplifying cells, and residents of stem cell niches. Through in vivo lineage tracing, we demonstrated the power of this approach by showing that co-expression module members Lrig1 and Igfbp5 define populations of incisor epithelial and mesenchymal stem cells. We further discovered that two adjacent mesenchymal tissues, the periodontium and dental pulp, are maintained by distinct pools of stem cells. These findings reveal novel mechanisms of incisor renewal and illustrate how gene co-expression analysis of intact biological systems can provide insights into the transcriptional basis of cellular identity. DOI: http://dx.doi.org/10.7554/eLife.24712.001 PMID:28475038

The Resolved Stellar Populations Early Release Science Program

NASA Astrophysics Data System (ADS)

Gilbert, Karoline; Weisz, Daniel; Resolved Stellar Populations ERS Program Team

2018-06-01

The Resolved Stellar Populations Early Release Science Program (PI D. Weisz) will observe Local Group targets covering a range of stellar density and star formation histories, including a globular cluster, and ultra-faint dwarf galaxy, and a star-forming dwarf galaxy. Using observations of these diverse targets we will explore a broad science program: we will measure star formation histories, the sub-solar stellar initial mass function, and proper motions, perform studies of evolved stars, and map extinction in the target fields. Our observations will be of high archival value for other science such as calibrating stellar evolution models, studying variable stars, and searching for metal-poor stars. We will determine optimal observational setups and develop data reduction techniques that will be common to JWST studies of resolved stellar populations. We will also design, test, and release point spread function (PSF) fitting software specific to NIRCam and NIRISS, required for the crowded stellar regime. Prior to the Cycle 2 Call for Proposals, we will release PSF fitting software, matched HST and JWST catalogs, and clear documentation and step-by-step tutorials (such as Jupyter notebooks) for reducing crowded stellar field data and producing resolved stellar photometry catalogs, as well as for specific resolved stellar photometry science applications.

Examination of laser microbeam cell lysis in a PDMS microfluidic channel using time-resolved imaging

PubMed Central

Quinto-Su, Pedro A.; Lai, Hsuan-Hong; Yoon, Helen H.; Sims, Christopher E.; Allbritton, Nancy L.; Venugopalan, Vasan

2008-01-01

We use time-resolved imaging to examine the lysis dynamics of non-adherent BAF-3 cells within a microfluidic channel produced by the delivery of single highly-focused 540 ps duration laser pulses at λ = 532 nm. Time-resolved bright-field images reveal that the delivery of the pulsed laser microbeam results in the formation of a laser-induced plasma followed by shock wave emission and cavitation bubble formation. The confinement offered by the microfluidic channel constrains substantially the cavitation bubble expansion and results in significant deformation of the PDMS channel walls. To examine the cell lysis and dispersal of the cellular contents, we acquire time-resolved fluorescence images of the process in which the cells were loaded with a fluorescent dye. These fluorescence images reveal cell lysis to occur on the nanosecond to microsecond time scale by the plasma formation and cavitation bubble dynamics. Moreover, the time-resolved fluorescence images show that while the cellular contents are dispersed by the expansion of the laser-induced cavitation bubble, the flow associated with the bubble collapse subsequently re-localizes the cellular contents to a small region. This capacity of pulsed laser microbeam irradiation to achieve rapid cell lysis in microfluidic channels with minimal dilution of the cellular contents has important implications for their use in lab-on-a-chip applications. PMID:18305858

From Supercomputer Modeling to Highest Mass Resolution in FT-ICR.

PubMed

N Nikolaev, Evgene; N Vladimirov, Gleb; Jertz, Roland; Baykut, Gökhan

2013-01-01

Understanding of behavior of ion ensembles inside FT-ICR cell based on the computer simulation of ion motion gives rise to the new ideas of cell designs. The recently introduced novel FT-ICR cell based on a Penning ion trap with specially shaped excitation and detection electrodes prevents distortion of ion cyclotron motion phases (normally caused by non-ideal electric trapping fields) by averaging the trapping DC electric field during the ion motion in the ICR cell. Detection times of 5 min resulting in resolving power close to 40,000,000 have been reached for reserpine at m/z 609 at a magnetic field of only 7 Tesla. Fine structures of resolved 13Cn isotopic cluster groups could be measured for molecular masses up to 5.7 kDa (insulin) with resolving power of 4,000,000 at 7 Tesla. Based on resolved fine structure patterns atomic compositions can be directly determined using a new developed algorithm for fine structure processing. Mass spectra of proteins and multimers of proteins reaching masses up to 186 kDa (enolase tetramer) could be measured with isotopic resolution. For instance, at 7 Tesla resolving power of 800,000 was achieved for enolase dimer (96 kDa) and 500,000 for molecular masses above 100 kDa. Experimental data indicate that there is practically no limit for the resolving power of this ICR cell except by collisional damping in the ultrahigh vacuum chamber.

Autofluorescence imaging captures heterogeneous drug response differences between 2D and 3D breast cancer cultures

PubMed Central

Cannon, T. M.; Shah, A. T.; Skala, M. C.

2017-01-01

Two-photon microscopy of cellular autofluorescence intensity and lifetime (optical metabolic imaging, or OMI) is a promising tool for preclinical drug development. OMI, which exploits the endogenous fluorescence from the metabolic coenzymes NAD(P)H and FAD, is sensitive to changes in cell metabolism produced by drug treatment. Previous studies have shown that drug response, genetic expression, cell-cell communication, and cell signaling in 3D culture match those of the original in vivo tumor, but not those of 2D culture. The goal of this study is to use OMI to quantify dynamic cell-level metabolic differences in drug response in 2D cell lines vs. 3D organoids generated from xenograft tumors of the same cell origin. BT474 cells and Herceptin-resistant BT474 (HR6) cells were tested. Cells were treated with vehicle control, Herceptin, XL147 (PI3K inhibitor), and the combination. The OMI index was used to quantify response, and is a linear combination of the redox ratio (intensity of NAD(P)H divided by FAD), mean NADH lifetime, and mean FAD lifetime. The results confirm that the OMI index resolves significant differences (p<0.05) in drug response for 2D vs. 3D cultures, specifically for BT474 cells 24 hours after Herceptin treatment, for HR6 cells 24 and 72 hours after combination treatment, and for HR6 cells 72 hours after XL147 treatment. Cell-level analysis of the OMI index also reveals differences in the number of cell sub-populations in 2D vs. 3D culture at 24, 48, and 72 hours post-treatment in control and treated groups. Finally, significant increases (p<0.05) in the mean lifetime of NADH and FAD were measured in 2D vs. 3D for both cell lines at 72 hours post-treatment in control and all treatment groups. These whole-population differences in the mean NADH and FAD lifetimes are supported by differences in the number of cell sub-populations in 2D vs. 3D. Overall, these studies confirm that OMI is sensitive to differences in drug response in 2D vs. 3D, and provides further information on dynamic changes in the relative abundance of metabolic cell sub-populations that contribute to this difference. PMID:28663873

Viability and Isolation of Marine Bacteria by Dilution Culture: Theory, Procedures, and Initial Results

PubMed Central

Button, D. K.; Schut, Frits; Quang, Pham; Martin, Ravonna; Robertson, Betsy R.

1993-01-01

Dilution culture, a method for growing the typical small bacteria from natural aquatic assemblages, has been developed. Each of 11 experimental trials of the technique was successful. Populations are measured, diluted to a small and known number of cells, inoculated into unamended sterilized seawater, and examined three times for the presence of 104 or more cells per ml over a 9-week interval. Mean viability for assemblage members is obtained from the frequency of growth, and many of the cultures produced are pure. Statistical formulations for determining viability and the frequency of pure culture production are derived. Formulations for associated errors are derived as well. Computer simulations of experiments agreed with computed values within the expected error, which verified the formulations. These led to strategies for optimizing viability determinations and pure culture production. Viabilities were usually between 2 and 60% and decreased with >5 mg of amino acids per liter as carbon. In view of difficulties in growing marine oligobacteria, these high values are noteworthy. Significant differences in population characteristics during growth, observed by high-resolution flow cytometry, suggested substantial population diversity. Growth of total populations as well as of cytometry-resolved subpopulations sometimes were truncated at levels of near 104 cells per ml, showing that viable cells could escape detection. Viability is therefore defined as the ability to grow to that population; true viabilities could be even higher. Doubling times, based on whole populations as well as individual subpopulations, were in the 1-day to 1-week range. Data were examined for changes in viability with dilution suggesting cell-cell interactions, but none could be confirmed. The frequency of pure culture production can be adjusted by inoculum size if the viability is known. These apparently pure cultures produced retained the size and apparent DNA-content characteristic of the bulk of the organisms in the parent seawater. Three cultures are now available, two of which have been carried for 3 years. The method is thus seen as a useful step for improving our understanding of typical aquatic organisms. PMID:16348896

Impedance spectroscopy of micro-Droplets reveals activation of Bacterial Mechanosensitive Channels in Hypotonic Solutions

NASA Astrophysics Data System (ADS)

Ebrahimi, Aida; Alam, Muhammad A.

Rapid detection of bacterial pathogens is of great importance in healthcare, food safety, environmental monitoring, and homeland security. Most bacterial detection platforms rely on binary fission (i.e. cell growth) to reach a threshold cell population that can be resolved by the sensing method. Since cell division depends on the bacteria type, the detection time of such methods can vary from hours to days. In contrast, in this work, we show that bacteria cells can be detected within minutes by relying on activation of specific protein channels, i.e. mechanosensitive channels (MS channels). When cells are exposed to hypotonic solutions, MS channels allow efflux of solutes to the external solution which leads to release the excessive membrane tension. Release of the cytoplasmic solutes, in turn, results in increase of the electrical conductance measured by droplet-based impedance sensing. The approach can be an effective technique for fast, pre-screening of bacterial contamination at ultra-low concentration.

One-Cell Doubling Evaluation by Living Arrays of Yeast, ODELAY!

DOE PAGES

Herricks, Thurston; Dilworth, David J.; Mast, Fred D.; ...

2016-11-16

Cell growth is a complex phenotype widely used in systems biology to gauge the impact of genetic and environmental perturbations. Due to the magnitude of genome-wide studies, resolution is often sacrificed in favor of throughput, creating a demand for scalable, time-resolved, quantitative methods of growth assessment. We present ODELAY (One-cell Doubling Evaluation by Living Arrays of Yeast), an automated and scalable growth analysis platform. High measurement density and single-cell resolution provide a powerful tool for large-scale multiparameter growth analysis based on the modeling of microcolony expansion on solid media. Pioneered in yeast but applicable to other colony forming organisms, ODELAYmore » extracts the three key growth parameters (lag time, doubling time, and carrying capacity) that define microcolony expansion from single cells, simultaneously permitting the assessment of population heterogeneity. The utility of ODELAY is illustrated using yeast mutants, revealing a spectrum of phenotypes arising from single and combinatorial growth parameter perturbations.« less

One-Cell Doubling Evaluation by Living Arrays of Yeast, ODELAY!

DOE Office of Scientific and Technical Information (OSTI.GOV)

Herricks, Thurston; Dilworth, David J.; Mast, Fred D.

Cell growth is a complex phenotype widely used in systems biology to gauge the impact of genetic and environmental perturbations. Due to the magnitude of genome-wide studies, resolution is often sacrificed in favor of throughput, creating a demand for scalable, time-resolved, quantitative methods of growth assessment. We present ODELAY (One-cell Doubling Evaluation by Living Arrays of Yeast), an automated and scalable growth analysis platform. High measurement density and single-cell resolution provide a powerful tool for large-scale multiparameter growth analysis based on the modeling of microcolony expansion on solid media. Pioneered in yeast but applicable to other colony forming organisms, ODELAYmore » extracts the three key growth parameters (lag time, doubling time, and carrying capacity) that define microcolony expansion from single cells, simultaneously permitting the assessment of population heterogeneity. The utility of ODELAY is illustrated using yeast mutants, revealing a spectrum of phenotypes arising from single and combinatorial growth parameter perturbations.« less

Identification and super-resolution imaging of ligand-activated receptor dimers in live cells

NASA Astrophysics Data System (ADS)

Winckler, Pascale; Lartigue, Lydia; Giannone, Gregory; de Giorgi, Francesca; Ichas, François; Sibarita, Jean-Baptiste; Lounis, Brahim; Cognet, Laurent

2013-08-01

Molecular interactions are key to many chemical and biological processes like protein function. In many signaling processes they occur in sub-cellular areas displaying nanoscale organizations and involving molecular assemblies. The nanometric dimensions and the dynamic nature of the interactions make their investigations complex in live cells. While super-resolution fluorescence microscopies offer live-cell molecular imaging with sub-wavelength resolutions, they lack specificity for distinguishing interacting molecule populations. Here we combine super-resolution microscopy and single-molecule Förster Resonance Energy Transfer (FRET) to identify dimers of receptors induced by ligand binding and provide super-resolved images of their membrane distribution in live cells. By developing a two-color universal-Point-Accumulation-In-the-Nanoscale-Topography (uPAINT) method, dimers of epidermal growth factor receptors (EGFR) activated by EGF are studied at ultra-high densities, revealing preferential cell-edge sub-localization. This methodology which is specifically devoted to the study of molecules in interaction, may find other applications in biological systems where understanding of molecular organization is crucial.

Redundant function of DNA ligase 1 and 3 in alternative end-joining during immunoglobulin class switch recombination.

PubMed

Masani, Shahnaz; Han, Li; Meek, Katheryn; Yu, Kefei

2016-02-02

Nonhomologous end-joining (NHEJ) is the major DNA double-strand break (DSB) repair pathway in mammals and resolves the DSBs generated during both V(D)J recombination in developing lymphocytes and class switch recombination (CSR) in antigen-stimulated B cells. In contrast to the absolute requirement for NHEJ to resolve DSBs associated with V(D)J recombination, DSBs associated with CSR can be resolved in NHEJ-deficient cells (albeit at a reduced level) by a poorly defined alternative end-joining (A-EJ) pathway. Deletion of DNA ligase IV (Lig4), a core component of the NHEJ pathway, reduces CSR efficiency in a mouse B-cell line capable of robust cytokine-stimulated CSR in cell culture. Here, we report that CSR levels are not further reduced by deletion of either of the two remaining DNA ligases (Lig1 and nuclear Lig3) in Lig4(-/-) cells. We conclude that in the absence of Lig4, Lig1, and Lig3 function in a redundant manner in resolving switch region DSBs during CSR.

Differential dynamics of spatial attention, position, and color coding within the parietofrontal network.

PubMed

Astrand, Elaine; Ibos, Guilhem; Duhamel, Jean-René; Ben Hamed, Suliann

2015-02-18

Despite an ever growing knowledge on how parietal and prefrontal neurons encode low-level spatial and color information or higher-level information, such as spatial attention, an understanding of how these cortical regions process neuronal information at the population level is still missing. A simple assumption would be that the function and temporal response profiles of these neuronal populations match that of its constituting individual cells. However, several recent studies suggest that this is not necessarily the case and that the single-cell approach overlooks dynamic changes in how information is distributed over the neuronal population. Here, we use a time-resolved population pattern analysis to explore how spatial position, spatial attention and color information are differentially encoded and maintained in the macaque monkey prefrontal (frontal eye fields) and parietal cortex (lateral intraparietal area). Overall, our work brings about three novel observations. First, we show that parietal and prefrontal populations operate in two distinct population regimens for the encoding of sensory and cognitive information: a stationary mode and a dynamic mode. Second, we show that the temporal dynamics of a heterogeneous neuronal population brings about complementary information to that of its functional subpopulations. Thus, both need to be investigated in parallel. Last, we show that identifying the neuronal configuration in which a neuronal population encodes given information can serve to reveal this same information in a different context. All together, this work challenges common views on neural coding in the parietofrontal network. Copyright © 2015 the authors 0270-6474/15/353174-16$15.00/0.

HOXB4 overexpression mediates very rapid stem cell regeneration and competitive hematopoietic repopulation.

PubMed

Antonchuk, J; Sauvageau, G; Humphries, R K

2001-09-01

Hox transcription factors have emerged as important regulators of hematopoiesis. In particular, we have shown that overexpression of HOXB4 in mouse bone marrow can greatly enhance the level of hematopoietic stem cell (HSC) regeneration achieved at late times (> 4 months) posttransplantation. The objective of this study was to resolve if HOXB4 increases the rate and/or duration of HSC regeneration, and also to see if this enhancement was associated with impaired production of end cells or would lead to competitive reconstitution of all compartments. Retroviral vectors were generated with the GFP reporter gene +/- HOXB4 to enable the isolation and direct tracking of transduced cells in culture or following transplantation. Stem cell recovery was measured by limit dilution assay for long-term competitive repopulating cells (CRU). HOXB4-overexpressing cells have enhanced growth in vitro, as demonstrated by their rapid dominance in mixed cultures and their shortened population doubling time. Furthermore, HOXB4-transduced cells have a marked competitive repopulating advantage in vivo in both primitive and mature compartments. CRU recovery in HOXB4 recipients was extremely rapid, reaching 25% of normal by 14 days posttransplant or some 80-fold greater than control transplant recipients, and attaining normal numbers by 12 weeks. Mice transplanted with even higher numbers of HOXB4-transduced CRU regenerated up to but not beyond the normal CRU levels. HOXB4 is a potent enhancer of primitive hematopoietic cell growth, likely by increasing self-renewal probability but without impairing homeostatic control of HSC population size or the rate of production and maintenance of mature end cells.

Time- and spectrally resolved characteristics of flavin fluorescence in U87MG cancer cells in culture

NASA Astrophysics Data System (ADS)

Horilova, Julia; Cunderlikova, Beata; Marcek Chorvatova, Alzbeta

2015-05-01

Early detection of cancer is crucial for the successful diagnostics of its presence and its subsequent treatment. To improve cancer detection, we tested the progressive multimodal optical imaging of U87MG cells in culture. A combination of steady-state spectroscopic methods with the time-resolved approach provides a new insight into the native metabolism when focused on endogenous tissue fluorescence. In this contribution, we evaluated the metabolic state of living U87MG cancer cells in culture by means of endogenous flavin fluorescence. Confocal microscopy and time-resolved fluorescence imaging were employed to gather spectrally and time-resolved images of the flavin fluorescence. We observed that flavin fluorescence in U87MG cells was predominantly localized outside the cell nucleus in mitochondria, while exhibiting a spectral maximum under 500 nm and fluorescence lifetimes under 1.4 ns, suggesting the presence of bound flavins. In some cells, flavin fluorescence was also detected inside the cell nuclei in the nucleoli, exhibiting longer fluorescence lifetimes and a red-shifted spectral maximum, pointing to the presence of free flavin. Extra-nuclear flavin fluorescence was diminished by 2-deoxyglucose, but failed to increase with 2,4-dinitrophenol, the uncoupler of oxidative phosphorylation, indicating that the cells use glycolysis, rather than oxidative phosphorylation for functioning. These gathered data are the first step toward monitoring the metabolic state of U87MG cancer cells.

gC1qR expression in chimpanzees with resolved and chronic infection: Potential role of HCV core/gC1qR-mediated T cell suppression in the outcome of HCV infection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yao Zhiqang; Shata, Mohamed Tarek; Tricoche, Nancy

2006-03-15

Chimpanzee is a unique animal model for HCV infection, in which about 50% of infections resolve spontaneously. It has been reported that the magnitude of T cell responses to HCV core in recovered chimpanzees is greater than that in chronically infected ones. However, the mechanism(s) by which the chimpanzees with resolved infection overcome core-mediated immunosuppression remains unknown. In this study, we examined the effect of HCV core on T cell responsiveness in chimpanzees with resolved and chronic HCV infection. We found that core protein strongly inhibited T cell activation and proliferation in chimpanzees with chronic infection, while this inhibition wasmore » limited in chimpanzees with resolved infection. Notably, the level of gC1qR, as well as the binding of core protein, on the surface of T cells was lower in recovered chimpanzees when compared to chimpanzees with chronic HCV infection. Intriguingly, the observed differences in gC1qR expression levels and susceptibility to core-induced suppression amongst HCV-chronically infected and recovered chimpanzees were observed prior to HCV challenge, suggesting a possible genetic determination of the outcome of infection. These findings suggest that gC1qR expression on the surface of T cells is crucial for HCV core-mediated T cell suppression and viral clearance, and that represents a novel mechanism by which a virus usurps host machinery for persistence.« less

Detection of Sickle Cell Hemoglobin in Haiti by Genotyping and Hemoglobin Solubility Tests

PubMed Central

Carter, Tamar E.; von Fricken, Michael; Romain, Jean R.; Memnon, Gladys; St. Victor, Yves; Schick, Laura; Okech, Bernard A.; Mulligan, Connie J.

2014-01-01

Sickle cell disease is a growing global health concern because infants born with the disorder in developing countries are now surviving longer with little access to diagnostic and management options. In Haiti, the current state of sickle cell disease/trait in the population is unclear. To inform future screening efforts in Haiti, we assayed sickle hemoglobin mutations using traditional hemoglobin solubility tests (HST) and add-on techniques, which incorporated spectrophotometry and insoluble hemoglobin separation. We also generated genotype data as a metric for HST performance. We found 19 of 202 individuals screened with HST were positive for sickle hemoglobin, five of whom did not carry the HbS allele. We show that spectrophotometry and insoluble hemoglobin separation add-on techniques could resolve false positives associated with the traditional HST approach, with some limitations. We also discuss the incorporation of insoluble hemoglobin separation observation with HST in suboptimal screening settings like Haiti. PMID:24957539

Modeling the winter-to-summer transition of prokaryotic and viral abundance in the Arctic Ocean.

PubMed

Winter, Christian; Payet, Jérôme P; Suttle, Curtis A

2012-01-01

One of the challenges in oceanography is to understand the influence of environmental factors on the abundances of prokaryotes and viruses. Generally, conventional statistical methods resolve trends well, but more complex relationships are difficult to explore. In such cases, Artificial Neural Networks (ANNs) offer an alternative way for data analysis. Here, we developed ANN-based models of prokaryotic and viral abundances in the Arctic Ocean. The models were used to identify the best predictors for prokaryotic and viral abundances including cytometrically-distinguishable populations of prokaryotes (high and low nucleic acid cells) and viruses (high- and low-fluorescent viruses) among salinity, temperature, depth, day length, and the concentration of Chlorophyll-a. The best performing ANNs to model the abundances of high and low nucleic acid cells used temperature and Chl-a as input parameters, while the abundances of high- and low-fluorescent viruses used depth, Chl-a, and day length as input parameters. Decreasing viral abundance with increasing depth and decreasing system productivity was captured well by the ANNs. Despite identifying the same predictors for the two populations of prokaryotes and viruses, respectively, the structure of the best performing ANNs differed between high and low nucleic acid cells and between high- and low-fluorescent viruses. Also, the two prokaryotic and viral groups responded differently to changes in the predictor parameters; hence, the cytometric distinction between these populations is ecologically relevant. The models imply that temperature is the main factor explaining most of the variation in the abundances of high nucleic acid cells and total prokaryotes and that the mechanisms governing the reaction to changes in the environment are distinctly different among the prokaryotic and viral populations.

Modeling the Winter–to–Summer Transition of Prokaryotic and Viral Abundance in the Arctic Ocean

PubMed Central

Winter, Christian; Payet, Jérôme P.; Suttle, Curtis A.

2012-01-01

One of the challenges in oceanography is to understand the influence of environmental factors on the abundances of prokaryotes and viruses. Generally, conventional statistical methods resolve trends well, but more complex relationships are difficult to explore. In such cases, Artificial Neural Networks (ANNs) offer an alternative way for data analysis. Here, we developed ANN-based models of prokaryotic and viral abundances in the Arctic Ocean. The models were used to identify the best predictors for prokaryotic and viral abundances including cytometrically-distinguishable populations of prokaryotes (high and low nucleic acid cells) and viruses (high- and low-fluorescent viruses) among salinity, temperature, depth, day length, and the concentration of Chlorophyll-a. The best performing ANNs to model the abundances of high and low nucleic acid cells used temperature and Chl-a as input parameters, while the abundances of high- and low-fluorescent viruses used depth, Chl-a, and day length as input parameters. Decreasing viral abundance with increasing depth and decreasing system productivity was captured well by the ANNs. Despite identifying the same predictors for the two populations of prokaryotes and viruses, respectively, the structure of the best performing ANNs differed between high and low nucleic acid cells and between high- and low-fluorescent viruses. Also, the two prokaryotic and viral groups responded differently to changes in the predictor parameters; hence, the cytometric distinction between these populations is ecologically relevant. The models imply that temperature is the main factor explaining most of the variation in the abundances of high nucleic acid cells and total prokaryotes and that the mechanisms governing the reaction to changes in the environment are distinctly different among the prokaryotic and viral populations. PMID:23285186

Combining animal personalities with transcriptomics resolves individual variation within a wild-type zebrafish population and identifies underpinning molecular differences in brain function.

PubMed

Rey, S; Boltana, S; Vargas, R; Roher, N; Mackenzie, S

2013-12-01

Resolving phenotype variation within a population in response to environmental perturbation is central to understanding biological adaptation. Relating meaningful adaptive changes at the level of the transcriptome requires the identification of processes that have a functional significance for the individual. This remains a major objective towards understanding the complex interactions between environmental demand and an individual's capacity to respond to such demands. The interpretation of such interactions and the significance of biological variation between individuals from the same or different populations remain a difficult and under-addressed question. Here, we provide evidence that variation in gene expression between individuals in a zebrafish population can be partially resolved by a priori screening for animal personality and accounts for >9% of observed variation in the brain transcriptome. Proactive and reactive individuals within a wild-type population exhibit consistent behavioural responses over time and context that relates to underlying differences in regulated gene networks and predicted protein-protein interactions. These differences can be mapped to distinct regions of the brain and provide a foundation towards understanding the coordination of underpinning adaptive molecular events within populations. © 2013 John Wiley & Sons Ltd.

Science with Synthetic Stellar Surveys

NASA Astrophysics Data System (ADS)

Sanderson, Robyn Ellyn

2018-04-01

A new generation of observational projects is poised to revolutionize our understanding of the resolved stellar populations of Milky-Way-like galaxies at an unprecedented level of detail, ushering in an era of precision studies of galaxy formation. In the Milky Way itself, astrometric, spectroscopic and photometric surveys will measure three-dimensional positions and velocities and numerous chemical abundances for stars from the disk to the halo, as well as for many satellite dwarf galaxies. In the Local Group and beyond, HST, JWST and eventually WFIRST will deliver pristine views of resolved stars. The groundbreaking scale and dimensionality of this new view of resolved stellar populations in galaxies challenge us to develop new theoretical tools to robustly compare these surveys to simulated galaxies, in order to take full advantage of our new ability to make detailed predictions for stellar populations within a cosmological context. I will describe a framework for generating realistic synthetic star catalogs and mock surveys from state-of-the-art cosmological-hydrodynamical simulations, and present several early scientific results from, and predictions for, resolved stellar surveys of our Galaxy and its neighbors.

Magnetic nanoparticles to recover cellular organelles and study the time resolved nanoparticle-cell interactome throughout uptake.

PubMed

Bertoli, Filippo; Davies, Gemma-Louise; Monopoli, Marco P; Moloney, Micheal; Gun'ko, Yurii K; Salvati, Anna; Dawson, Kenneth A

2014-08-27

Nanoparticles in contact with cells and living organisms generate quite novel interactions at the interface between the nanoparticle surface and the surrounding biological environment. However, a detailed time resolved molecular level description of the evolving interactions as nanoparticles are internalized and trafficked within the cellular environment is still missing and will certainly be required for the emerging arena of nanoparticle-cell interactions to mature. In this paper promising methodologies to map out the time resolved nanoparticle-cell interactome for nanoparticle uptake are discussed. Thus silica coated magnetite nanoparticles are presented to cells and their magnetic properties used to isolate, in a time resolved manner, the organelles containing the nanoparticles. Characterization of the recovered fractions shows that different cell compartments are isolated at different times, in agreement with imaging results on nanoparticle intracellular location. Subsequently the internalized nanoparticles can be further isolated from the recovered organelles, allowing the study of the most tightly nanoparticle-bound biomolecules, analogous to the 'hard corona' that so far has mostly been characterized in extracellular environments. Preliminary data on the recovered nanoparticles suggest that significant portion of the original corona (derived from the serum in which particles are presented to the cells) is preserved as nanoparticles are trafficked through the cells. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Velocity landscape correlation resolves multiple flowing protein populations from fluorescence image time series.

PubMed

Pandžić, Elvis; Abu-Arish, Asmahan; Whan, Renee M; Hanrahan, John W; Wiseman, Paul W

2018-02-16

Molecular, vesicular and organellar flows are of fundamental importance for the delivery of nutrients and essential components used in cellular functions such as motility and division. With recent advances in fluorescence/super-resolution microscopy modalities we can resolve the movements of these objects at higher spatio-temporal resolutions and with better sensitivity. Previously, spatio-temporal image correlation spectroscopy has been applied to map molecular flows by correlation analysis of fluorescence fluctuations in image series. However, an underlying assumption of this approach is that the sampled time windows contain one dominant flowing component. Although this was true for most of the cases analyzed earlier, in some situations two or more different flowing populations can be present in the same spatio-temporal window. We introduce an approach, termed velocity landscape correlation (VLC), which detects and extracts multiple flow components present in a sampled image region via an extension of the correlation analysis of fluorescence intensity fluctuations. First we demonstrate theoretically how this approach works, test the performance of the method with a range of computer simulated image series with varying flow dynamics. Finally we apply VLC to study variable fluxing of STIM1 proteins on microtubules connected to the plasma membrane of Cystic Fibrosis Bronchial Epithelial (CFBE) cells. Copyright © 2018 Elsevier Inc. All rights reserved.

Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria

PubMed Central

Lönnberg, Tapio; Svensson, Valentine; James, Kylie R.; Fernandez-Ruiz, Daniel; Sebina, Ismail; Montandon, Ruddy; Soon, Megan S. F.; Fogg, Lily G.; Nair, Arya Sheela; Liligeto, Urijah; Stubbington, Michael J. T.; Ly, Lam-Ha; Bagger, Frederik Otzen; Zwiessele, Max; Lawrence, Neil D.; Souza-Fonseca-Guimaraes, Fernando; Bunn, Patrick T.; Engwerda, Christian R.; Heath, William R.; Billker, Oliver; Stegle, Oliver; Haque, Ashraful; Teichmann, Sarah A.

2017-01-01

Differentiation of naïve CD4+ T cells into functionally distinct T helper subsets is crucial for the orchestration of immune responses. Due to extensive heterogeneity and multiple overlapping transcriptional programs in differentiating T cell populations, this process has remained a challenge for systematic dissection in vivo. By using single-cell transcriptomics and computational analysis using a temporal mixtures of Gaussian processes model, termed GPfates, we reconstructed the developmental trajectories of Th1 and Tfh cells during blood-stage Plasmodium infection in mice. By tracking clonality using endogenous TCR sequences, we first demonstrated that Th1/Tfh bifurcation had occurred at both population and single-clone levels. Next, we identified genes whose expression was associated with Th1 or Tfh fates, and demonstrated a T-cell intrinsic role for Galectin-1 in supporting a Th1 differentiation. We also revealed the close molecular relationship between Th1 and IL-10-producing Tr1 cells in this infection. Th1 and Tfh fates emerged from a highly proliferative precursor that upregulated aerobic glycolysis and accelerated cell cycling as cytokine expression began. Dynamic gene expression of chemokine receptors around bifurcation predicted roles for cell-cell in driving Th1/Tfh fates. In particular, we found that precursor Th cells were coached towards a Th1 but not a Tfh fate by inflammatory monocytes. Thus, by integrating genomic and computational approaches, our study has provided two unique resources, a database www.PlasmoTH.org, which facilitates discovery of novel factors controlling Th1/Tfh fate commitment, and more generally, GPfates, a modelling framework for characterizing cell differentiation towards multiple fates. PMID:28345074

Fuel cells and the city of the future — a Japanese view

NASA Astrophysics Data System (ADS)

Satomi, Tomohide

The development and practical application of fuel cells have been promoted aggressively in Japan, and the on-site phosphoric acid fuel cell (PAFC) has been attained with the prospect for practical market enery in commercial buildings by the middle of the 1990s. Fuel cells have features of less environmental impact and high energy efficiency which meet the requirements of the utility system for the future city. In Japan, the recent concentration of social functions and population to the city have begun to cause many serious problems. To resolve these environmental and resource related problems and to move towards developing and constructing a new city, one answer offered is the concept of CAN (community amenity network). CAN is a sophisticated utility system which integrates fuel cells as well as a system for effective use of unused energy and recycling of waste disposal and water. For solving the housing shortage problem in the next century, the concept of skyscraper building cities is currently proposed. Fuel cell systems can also be applied to these cities as a major element of the integrated zone energy supply network facility.

Anti-angiogenesis effect of the novel anti-inflammatory and pro-resolving lipid mediators.

PubMed

Jin, Yiping; Arita, Makoto; Zhang, Qiang; Saban, Daniel R; Chauhan, Sunil K; Chiang, Nan; Serhan, Charles N; Dana, Reza

2009-10-01

Resolvins and lipoxins are lipid mediators generated from essential polyunsaturated fatty acids that are the first dual anti-inflammatory and pro-resolving signals identified in the resolution phase of inflammation. Here the authors investigated the potential of aspirin-triggered lipoxin (LX) A4 analog (ATLa), resolving (Rv) D1, and RvE1, in regulating angiogenesis in a murine model. ATLa and RvE1 receptor expression was tested in different corneal cell populations by RT-PCR. Corneal neovascularization (CNV) was induced by suture or micropellet (IL-1 beta, VEGF-A) placement. Mice were then treated with ATLa, RvD1, RvE1, or vehicle, subconjunctivally at 48-hour intervals. Infiltration of neutrophils and macrophages was quantified after immunofluorescence staining. The mRNA expression levels of inflammatory cytokines, VEGFs, and VEGFRs were analyzed by real-time PCR. CNV was evaluated intravitally and morphometrically. The receptors for LXA4, ALX/Fpr-rs-2 and for RvE1, ChemR23 were each expressed by epithelium, stromal keratocytes, and infiltrated CD11b(+) cells in corneas. Compared to the vehicle-treated eye, ATLa-, RvD1-, and RvE1-treated eyes had reduced numbers of infiltrating neutrophils and macrophages and reduced mRNA expression levels of TNF-alpha, IL-1 alpha, IL-1 beta, VEGF-A, VEGF-C, and VEGFR2. Animals treated with these mediators had significantly suppressed suture-induced or IL-1 beta-induced hemangiogenesis (HA) but not lymphangiogenesis. Interestingly, only the application of ATLa significantly suppressed VEGF-A-induced HA. ATLa, RvE1, and RvD1 all reduce inflammatory corneal HA by early regulation of resolution mechanisms in innate immune responses. In addition, ATLa directly inhibits VEGF-A-mediated angiogenesis and is the most potent inhibitor of NV among this new genus of dual anti-inflammatory and pro-resolving lipid mediators.

Review: the role of neural crest cells in the endocrine system.

PubMed

Adams, Meghan Sara; Bronner-Fraser, Marianne

2009-01-01

The neural crest is a pluripotent population of cells that arises at the junction of the neural tube and the dorsal ectoderm. These highly migratory cells form diverse derivatives including neurons and glia of the sensory, sympathetic, and enteric nervous systems, melanocytes, and the bones, cartilage, and connective tissues of the face. The neural crest has long been associated with the endocrine system, although not always correctly. According to current understanding, neural crest cells give rise to the chromaffin cells of the adrenal medulla, chief cells of the extra-adrenal paraganglia, and thyroid C cells. The endocrine tumors that correspond to these cell types are pheochromocytomas, extra-adrenal paragangliomas, and medullary thyroid carcinomas. Although controversies concerning embryological origin appear to have mostly been resolved, questions persist concerning the pathobiology of each tumor type and its basis in neural crest embryology. Here we present a brief history of the work on neural crest development, both in general and in application to the endocrine system. In particular, we present findings related to the plasticity and pluripotency of neural crest cells as well as a discussion of several different neural crest tumors in the endocrine system.

PHAT+MaNGA: Using resolved stellar populations to improve the recovery of star formation histories from galaxy spectra

NASA Astrophysics Data System (ADS)

Byler, Nell

2017-08-01

Stellar Population Synthesis (SPS) models are routinely used to interpret extragalactic observations at all redshifts. Currently, the dominant source of uncertainty in SPS modeling lies in the degeneracies associated with synthesizing and fitting complex stellar populations to observed galaxy spectra. To remedy this, we propose an empirical calibration of SPS models using resolved stellar population observations from Hubble Space Telescope (HST) to constrain the stellar masses, ages, and star formation histories (SFHs) in regions matched to 2D spectroscopic observations from MaNGA. We will take advantage of the state of the art observations from the Panchromatic Hubble Andromeda Treasury (PHAT), which maps the dust content, history of chemical enrichment, and history of star formation across the disk of M31 in exquisite detail. Recently, we have coupled these observations with an unprecedented, spatially-resolved suite of IFU observations from MaNGA. With these two comprehensive data sets we can use the true underlying stellar properties from PHAT to properly interpret the aperture-matched integrated spectra from MaNGA. Our MaNGA observations target 20 regions within the PHAT footprint that fully sample the available range in metallicity, SFR, dust content, and stellar density. This transformative dataset will establish a comprehensive link between resolved stellar populations and the inferred properties of unresolved stellar populations across astrophysically important environments. The net data product will be a library of galaxy spectra matched to the true underlying stellar properties, a comparison set that has lasting legacy value for the extragalactic community.

Time-resolved optical spectroscopic quantification of red blood cell damage caused by cardiovascular devices

NASA Astrophysics Data System (ADS)

Sakota, D.; Sakamoto, R.; Sobajima, H.; Yokoyama, N.; Yokoyama, Y.; Waguri, S.; Ohuchi, K.; Takatani, S.

2008-02-01

Cardiovascular devices such as heart-lung machine generate un-physiological level of shear stress to damage red blood cells, leading to hemolysis. The diagnostic techniques of cell damages, however, have not yet been established. In this study, the time-resolved optical spectroscopy was applied to quantify red blood cell (RBC) damages caused by the extracorporeal circulation system. Experimentally, the fresh porcine blood was subjected to varying degrees of shear stress in the rotary blood pump, followed with measurement of the time-resolved transmission characteristics using the pico-second pulses at 651 nm. The propagated optical energy through the blood specimen was detected using a streak camera. The data were analyzed in terms of the mean cell volume (MCV) and mean cell hemoglobin concentration (MCHC) measured separately versus the energy and propagation time of the light pulses. The results showed that as the circulation time increased, the MCV increased with decrease in MCHC. It was speculated that the older RBCs with smaller size and fragile membrane properties had been selectively destroyed by the shear stress. The time-resolved optical spectroscopy is a useful technique in quantifying the RBCs' damages by measuring the energy and propagation time of the ultra-short light pulses through the blood.

Retinal ganglion cell distribution and spatial resolving power in elasmobranchs.

PubMed

Lisney, Thomas J; Collin, Shaun P

2008-01-01

The total number, distribution and peak density of presumed retinal ganglion cells was assessed in 10 species of elasmobranch (nine species of shark and one species of batoid) using counts of Nissl-stained cells in retinal wholemounts. The species sampled include a number of active, predatory benthopelagic and pelagic sharks that are found in a variety of coastal and oceanic habitats and represent elasmobranch groups for which information of this nature is currently lacking. The topographic distribution of cells was heterogeneous in all species. Two benthic species, the shark Chiloscyllium punctatum and the batoid Taeniura lymma, have a dorsal or dorso-central horizontal streak of increased cell density, whereas the majority of the benthopelagic and pelagic sharks examined exhibit a more concentric pattern of increasing cell density, culminating in a central area centralis of higher cell density located close to the optic nerve head. The exception is the shark Alopias superciliosus, which possesses a ventral horizontal streak. Variation in retinal ganglion cell topography appears to be related to the visual demands of different habitats and lifestyles, as well as the positioning of the eyes in the head. The upper limits of spatial resolving power were calculated for all 10 species, using peak ganglion cell densities and estimates of focal length taken from cryo-sectioned eyes in combination with information from the literature. Spatial resolving power ranged from 2.02 to 10.56 cycles deg(-1), which is in accordance with previous studies. Species with a lower spatial resolving power tend to be benthic and/or coastal species that feed on benthic invertebrates and fishes. Active, benthopelagic and pelagic species from more oceanic habitats which feed on larger, more active prey, possess a higher resolving power. Additionally, ganglion cells in a juvenile of C. punctatum, were retrogradely-labeled from the optic nerve with biotinylated dextran amine (BDA). A comparison of the BDA- labeled material and tissue stained for Nissl substance indicates that 76% of the cells in the retinal ganglion cell and inner plexiform layers of the central retina in this species are non-ganglion cells. Copyright 2008 S. Karger AG, Basel.

A portable low-cost long-term live-cell imaging platform for biomedical research and education.

PubMed

Walzik, Maria P; Vollmar, Verena; Lachnit, Theresa; Dietz, Helmut; Haug, Susanne; Bachmann, Holger; Fath, Moritz; Aschenbrenner, Daniel; Abolpour Mofrad, Sepideh; Friedrich, Oliver; Gilbert, Daniel F

2015-02-15

Time-resolved visualization and analysis of slow dynamic processes in living cells has revolutionized many aspects of in vitro cellular studies. However, existing technology applied to time-resolved live-cell microscopy is often immobile, costly and requires a high level of skill to use and maintain. These factors limit its utility to field research and educational purposes. The recent availability of rapid prototyping technology makes it possible to quickly and easily engineer purpose-built alternatives to conventional research infrastructure which are low-cost and user-friendly. In this paper we describe the prototype of a fully automated low-cost, portable live-cell imaging system for time-resolved label-free visualization of dynamic processes in living cells. The device is light-weight (3.6 kg), small (22 × 22 × 22 cm) and extremely low-cost (<€1250). We demonstrate its potential for biomedical use by long-term imaging of recombinant HEK293 cells at varying culture conditions and validate its ability to generate time-resolved data of high quality allowing for analysis of time-dependent processes in living cells. While this work focuses on long-term imaging of mammalian cells, the presented technology could also be adapted for use with other biological specimen and provides a general example of rapidly prototyped low-cost biosensor technology for application in life sciences and education. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Femtosecond Fluorescence Upconversion Study of a Naphthalimide-Bithiophene-Triphenylamine Push-Pull Dye in Solution.

PubMed

Maffeis, Valentin; Brisse, Romain; Labet, Vanessa; Jousselme, Bruno; Gustavsson, Thomas

2018-06-13

There is a high interest in the development of new push-pull dyes for the use in dye sensitized solar cells. The pronounced charge transfer character of the directly photoexcited state is in principle favorable for a charge injection. Here, we report a time-resolved fluorescence study of a triphenylamine-bithiophene-naphthalimide dye in four solvents of varying polarity using fluorescence upconversion. The recording of femtosecond time-resolved fluorescence spectra corrected for the group velocity dispersion allows for a detailed analysis discriminating between spectral shifts and total intensity decays. After photoexcitation, the directly populated state (S 1 /FC) evolves toward a relaxed charge transfer state (S 1 /CT). This S 1 /CT state is characterized by a lower radiative transition moment and a higher nonradiative quenching. The fast dynamic shift of the fluorescence band is well described by solvation dynamics in polar solvents, but less so in nonpolar solvents, hinting that the excited-state relaxation process occurs on a free energy surface whose topology is strongly governed by the solvent polarity. This study underlines the influence of the environment on the intramolecular charge transfer (ICT) process, and the necessity to analyze time-resolved data in detail when solvation and ICT occur simultaneously.

Spectrally resolved fluorescence lifetime imaging to investigate cell metabolism in malignant and nonmalignant oral mucosa cells

NASA Astrophysics Data System (ADS)

Rück, Angelika; Hauser, Carmen; Mosch, Simone; Kalinina, Sviatlana

2014-09-01

Fluorescence-guided diagnosis of tumor tissue is in many cases insufficient, because false positive results interfere with the outcome. Improvement through observation of cell metabolism might offer the solution, but needs a detailed understanding of the origin of autofluorescence. With respect to this, spectrally resolved multiphoton fluorescence lifetime imaging was investigated to analyze cell metabolism in metabolic phenotypes of malignant and nonmalignant oral mucosa cells. The time-resolved fluorescence characteristics of NADH were measured in cells of different origins. The fluorescence lifetime of bound and free NADH was calculated from biexponential fitting of the fluorescence intensity decay within different spectral regions. The mean lifetime was increased from nonmalignant oral mucosa cells to different squamous carcinoma cells, where the most aggressive cells showed the longest lifetime. In correlation with reports in the literature, the total amount of NADH seemed to be less for the carcinoma cells and the ratio of free/bound NADH was decreased from nonmalignant to squamous carcinoma cells. Moreover for squamous carcinoma cells a high concentration of bound NADH was found in cytoplasmic organelles (mainly mitochondria). This all together indicates that oxidative phosphorylation and a high redox potential play an important role in the energy metabolism of these cells.

Airborne detection of oceanic turbidity cell structure using depth-resolved laser-induced water Raman backscatter

NASA Technical Reports Server (NTRS)

Hoge, F. E.; Swift, R. N.

1983-01-01

Airborne laser-induced, depth-resolved water Raman backscatter is useful in the detection and mapping of water optical transmission variations. This test, together with other field experiments, has identified the need for additional field experiments to resolve the degree of the contribution to the depth-resolved, Raman-backscattered signal waveform that is due to (1) sea surface height or elevation probability density; (2) off-nadir laser beam angle relative to the mean sea surface; and (3) the Gelbstoff fluorescence background, and the analytical techniques required to remove it. When converted to along-track profiles, the waveforms obtained reveal cells of a decreased Raman backscatter superimposed on an overall trend of monotonically decreasing water column optical transmission.

Dynamics of monochromatically generated nonequilibrium phonons in LaF3:Pr3+

NASA Astrophysics Data System (ADS)

Tolbert, W. A.; Dennis, W. M.; Yen, W. M.

1990-07-01

The temporal evolution of nonequilibrium phonon populations in LaF3:Pr3+ is investigated at low temperatures (1.8 K) utilizing pulsed, tunable, monochromatic generation and time-resolved, tunable, narrow-band detection. High occupation number, narrow-band phonon populations are generated via far-infrared pumping of defect-induced one-phonon absorption. Time-resolved, frequency-selective detection is provided by optical sideband absorption. Nonequilibrium phonon decay times are measured and attributed to anharmonic decay.

WFIRST: Resolving the Milky Way Galaxy

NASA Astrophysics Data System (ADS)

Kalirai, Jason; Conroy, Charlie; Dressler, Alan; Geha, Marla; Levesque, Emily; Lu, Jessica; Tumlinson, Jason

2018-01-01

WFIRST will yield a transformative impact in measuring and characterizing resolved stellar populations in the Milky Way. The proximity and level of detail that such populations need to be studied at directly map to all three pillars of WFIRST capabilities - sensitivity from a 2.4 meter space based telescope, resolution from 0.1" pixels, and large 0.3 degree field of view from multiple detectors. In this poster, we describe the activities of the WFIRST Science Investigation Team (SIT), "Resolving the Milky Way with WFIRST". Notional programs guiding our analysis include targeting sightlines to establish the first well-resolved large scale maps of the Galactic bulge aand central region, pockets of star formation in the disk, benchmark star clusters, and halo substructure and ultra faint dwarf satellites. As an output of this study, our team is building optimized strategies and tools to maximize stellar population science with WFIRST. This will include: new grids of IR-optimized stellar evolution and synthetic spectroscopic models; pipelines and algorithms for optimal data reduction at the WFIRST sensitivity and pixel scale; wide field simulations of Milky Way environments including new astrometric studies; and strategies and automated algorithms to find substructure and dwarf galaxies in the Milky Way through the WFIRST High Latitude Survey.

Communication—indentation of Li-ion pouch cell: Effect of material homogenization on prediction of internal short circuit

DOE PAGES

Kumar, A.; Kalnaus, Sergiy; Simunovic, Srdjan; ...

2016-09-12

We performed finite element simulations of spherical indentation of Li-ion pouch cells. Our model fully resolves different layers in the cell. The results of the layer resolved models were compared to the models available in the literature that treat the cell as an equivalent homogenized continuum material. Simulations were carried out for different sizes of the spherical indenter. Here, we show that calibration of a failure criterion for the cell in the homogenized model depends on the indenter size, whereas in the layer-resoled model, such dependency is greatly diminished.

Automatic detection and analysis of cell motility in phase-contrast time-lapse images using a combination of maximally stable extremal regions and Kalman filter approaches.

PubMed

Kaakinen, M; Huttunen, S; Paavolainen, L; Marjomäki, V; Heikkilä, J; Eklund, L

2014-01-01

Phase-contrast illumination is simple and most commonly used microscopic method to observe nonstained living cells. Automatic cell segmentation and motion analysis provide tools to analyze single cell motility in large cell populations. However, the challenge is to find a sophisticated method that is sufficiently accurate to generate reliable results, robust to function under the wide range of illumination conditions encountered in phase-contrast microscopy, and also computationally light for efficient analysis of large number of cells and image frames. To develop better automatic tools for analysis of low magnification phase-contrast images in time-lapse cell migration movies, we investigated the performance of cell segmentation method that is based on the intrinsic properties of maximally stable extremal regions (MSER). MSER was found to be reliable and effective in a wide range of experimental conditions. When compared to the commonly used segmentation approaches, MSER required negligible preoptimization steps thus dramatically reducing the computation time. To analyze cell migration characteristics in time-lapse movies, the MSER-based automatic cell detection was accompanied by a Kalman filter multiobject tracker that efficiently tracked individual cells even in confluent cell populations. This allowed quantitative cell motion analysis resulting in accurate measurements of the migration magnitude and direction of individual cells, as well as characteristics of collective migration of cell groups. Our results demonstrate that MSER accompanied by temporal data association is a powerful tool for accurate and reliable analysis of the dynamic behaviour of cells in phase-contrast image sequences. These techniques tolerate varying and nonoptimal imaging conditions and due to their relatively light computational requirements they should help to resolve problems in computationally demanding and often time-consuming large-scale dynamical analysis of cultured cells. © 2013 The Authors Journal of Microscopy © 2013 Royal Microscopical Society.

The Usefulness of Readout-Segmented Echo-Planar Imaging (RESOLVE) for Bio-phantom Imaging Using 3-Tesla Clinical MRI.

PubMed

Yoshimura, Yuuki; Kuroda, Masahiro; Sugiantoc, Irfan; Bamgbosec, Babatunde O; Miyahara, Kanae; Ohmura, Yuichi; Kurozumi, Akira; Matsushita, Toshi; Ohno, Seiichiro; Kanazawa, Susumu; Asaumi, Junichi

2018-02-01

Readout-segmented echo-planar imaging (RESOLVE) is a multi-shot echo-planar imaging (EPI) modality with k-space segmented in the readout direction. We investigated whether RESOLVE decreases the distortion and artifact in the phase direction and increases the signal-to-noise ratio (SNR) in phantoms image taken with 3-tesla (3T) MRI versus conventional EPI. We used a physiological saline phantom and subtraction mapping and observed that RESOLVE's SNR was higher than EPI's. Using RESOLVE, the combination of a special-purpose coil and a large-loop coil had a higher SNR compared to using only a head/neck coil. RESOLVE's image distortioas less than EPI's. We used a 120 mM polyethylene glycol phantom to examine the phase direction artifact.vThe range where the artifact appeared in the apparent diffusion coefficient (ADC) image was shorter with RESOLVE compared to EPI. We used RESOLVE to take images of a Jurkat cell bio-phantom: the cell-region ADC was 856×10-6mm2/sec and the surrounding physiological saline-region ADC was 2,951×10-6mm2/sec. The combination of RESOLVE and the 3T clinical MRI device reduced image distortion and improved SNR and the identification of accurate ADC values due to the phase direction artifact reduction. This combination is useful for obtaining accurate ADC values of bio-phantoms.

Stochastic 2-D galaxy disk evolution models. Resolved stellar populations in the galaxy M33

NASA Astrophysics Data System (ADS)

Mineikis, T.; Vansevičius, V.

We improved the stochastic 2-D galaxy disk models (Mineikis & Vansevičius 2014a) by introducing enriched gas outflows from galaxies and synthetic color-magnitude diagrams of stellar populations. To test the models, we use the HST/ACS stellar photometry data in four fields located along the major axis of the galaxy M33 (Williams et al. 2009) and demonstrate the potential of the models to derive 2-D star formation histories in the resolved disk galaxies.

In vivo detection of macrophages in a rabbit atherosclerotic model by time-resolved laser-induced fluorescence spectroscopy

PubMed Central

Marcu, Laura; Fang, Qiyin; Jo, Javier A.; Papaioannou, Thanassis; Dorafshar, Amir; Reil, Todd; Qiao, Jian-Hua; Baker, J. Dennis; Freischlag, Julie A.; Fishbein, Michael C.

2007-01-01

Accumulation of numerous macrophages in the fibrous cap is a key identifying feature of plaque inflammation and vulnerability. This study investigates the use of time-resolved laser-induced fluorescence spectroscopy (TR-LIFS) as a potential tool for detection of macrophage foam cells in the intima of atherosclerotic plaques. Experiments were conducted in vivo on 14 New Zealand rabbits (6 control, 8 hypercholesterolemic) following aortotomy to expose the intimal luminal surface of the aorta. Tissue autofluorescence was induced with a nitrogen pulse laser (337 nm, 1 ns). Lesions were histologically classified by the percent of collagen or macrophage foam cells as well as thickness of the intima. Using parameters derived from the time-resolved fluorescence emission of plaques, we determined that intima rich in macrophage foam cells can be distinguished from intima rich in collagen with high sensitivity (>85%) and specificity (>95%). This study demonstrates, for the first time, that a time-resolved fluorescence-based technique can differentiate and demark macrophage content versus collagen content in vivo. Our results suggest that TR-LIFS technique can be used in clinical applications for identification of inflammatory cells important in plaque formation and rupture. PMID:16039283

In vivo detection of macrophages in a rabbit atherosclerotic model by time-resolved laser-induced fluorescence spectroscopy.

PubMed

Marcu, Laura; Fang, Qiyin; Jo, Javier A; Papaioannou, Thanassis; Dorafshar, Amir; Reil, Todd; Qiao, Jian-Hua; Baker, J Dennis; Freischlag, Julie A; Fishbein, Michael C

2005-08-01

Accumulation of numerous macrophages in the fibrous cap is a key identifying feature of plaque inflammation and vulnerability. This study investigates the use of time-resolved laser-induced fluorescence spectroscopy (TR-LIFS) as a potential tool for detection of macrophage foam cells in the intima of atherosclerotic plaques. Experiments were conducted in vivo on 14 New Zealand rabbits (6 control, 8 hypercholesterolemic) following aortotomy to expose the intimal luminal surface of the aorta. Tissue autofluorescence was induced with a nitrogen pulse laser (337 nm, 1 ns). Lesions were histologically classified by the percent of collagen or macrophage foam cells as well as thickness of the intima. Using parameters derived from the time-resolved fluorescence emission of plaques, we determined that intima rich in macrophage foam cells can be distinguished from intima rich in collagen with high sensitivity (>85%) and specificity (>95%). This study demonstrates, for the first time, that a time-resolved fluorescence-based technique can differentiate and demark macrophage content versus collagen content in vivo. Our results suggest that TR-LIFS technique can be used in clinical applications for identification of inflammatory cells important in plaque formation and rupture.

MFSD2A Promotes Endothelial Generation of Inflammation-Resolving Lipid Mediators and Reduces Colitis in Mice.

PubMed

Ungaro, Federica; Tacconi, Carlotta; Massimino, Luca; Corsetto, Paola Antonia; Correale, Carmen; Fonteyne, Philippe; Piontini, Andrea; Garzarelli, Valeria; Calcaterra, Francesca; Della Bella, Silvia; Spinelli, Antonino; Carvello, Michele; Rizzo, Angela Maria; Vetrano, Stefania; Petti, Luciana; Fiorino, Gionata; Furfaro, Federica; Mavilio, Domenico; Maddipati, Krishna Rao; Malesci, Alberto; Peyrin-Biroulet, Laurent; D'Alessio, Silvia; Danese, Silvio

2017-11-01

Alterations in signaling pathways that regulate resolution of inflammation (resolving pathways) contribute to pathogenesis of ulcerative colitis (UC). The resolution process is regulated by lipid mediators, such as those derived from the ω-3 docosahexaenoic acid (DHA), whose esterified form is transported by the major facilitator superfamily domain containing 2A (MFSD2A) through the endothelium of brain, retina, and placenta. We investigated if and how MFSD2A regulates lipid metabolism of gut endothelial cells to promote resolution of intestinal inflammation. We performed lipidomic and functional analyses of MFSD2A in mucosal biopsies and primary human intestinal microvascular endothelial cells (HIMECs) isolated from surgical specimens from patients with active, resolving UC and healthy individuals without UC (controls). MFSD2A was knocked down in HIMECs with small hairpin RNAs or overexpressed from a lentiviral vector. Human circulating endothelial progenitor cells that overexpress MFSD2A were transferred to CD1 nude mice with dextran sodium sulfate-induced colitis, with or without oral administration of DHA. Colonic biopsies from patients with UC had reduced levels of inflammation-resolving DHA-derived epoxy metabolites compared to healthy colon tissues or tissues with resolution of inflammation. Production of these metabolites by HIMECs required MFSD2A, which is required for DHA retention and metabolism in the gut vasculature. In mice with colitis, transplanted endothelial progenitor cells that overexpressed MFSD2A not only localized to the inflamed mucosa but also restored the ability of the endothelium to resolve intestinal inflammation, compared with mice with colitis that did not receive MFSD2A-overexpressing endothelial progenitors. Levels of DHA-derived epoxides are lower in colon tissues from patients with UC than healthy and resolving mucosa. Production of these metabolites by gut endothelium requires MFSD2A; endothelial progenitor cells that overexpress MFSD2A reduce colitis in mice. This pathway might be induced to resolve intestinal inflammation in patients with colitis. Copyright © 2017 AGA Institute. Published by Elsevier Inc. All rights reserved.

A radially accessible tubular in situ X-ray cell for spatially resolved operando scattering and spectroscopic studies of electrochemical energy storage devices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Hao; Allan, Phoebe K.; Borkiewicz, Olaf J.

2016-09-16

A tubularoperandoelectrochemical cell has been developed to allow spatially resolved X-ray scattering and spectroscopic measurements of individual cell components, or regions thereof, during device operation. These measurements are enabled by the tubular cell geometry, wherein the X-ray-transparent tube walls allow radial access for the incident and scattered/transmitted X-ray beam; by probing different depths within the electrode stack, the transformation of different components or regions can be resolved. The cell is compatible with a variety of synchrotron-based scattering, absorption and imaging methodologies. The reliability of the electrochemical cell and the quality of the resulting X-ray scattering and spectroscopic data are demonstratedmore » for two types of energy storage: the evolution of the distribution of the state of charge of an Li-ion battery electrode during cycling is documented using X-ray powder diffraction, and the redistribution of ions between two porous carbon electrodes in an electrochemical double-layer capacitor is documented using X-ray absorption near-edge spectroscopy.« less

Novel Electron-Phonon Relaxation Pathway in Graphite Revealed by Time-Resolved Raman Scattering and Angle-Resolved Photoemission Spectroscopy.

PubMed

Yang, Jhih-An; Parham, Stephen; Dessau, Daniel; Reznik, Dmitry

2017-01-19

Time dynamics of photoexcited electron-hole pairs is important for a number of technologies, in particular solar cells. We combined ultrafast pump-probe Raman scattering and photoemission to directly follow electron-hole excitations as well as the G-phonon in graphite after an excitation by an intense laser pulse. This phonon is known to couple relatively strongly to electrons. Cross-correlating effective electronic and phonon temperatures places new constraints on model-based fits. The accepted two-temperature model predicts that G-phonon population should start to increase as soon as excited electron-hole pairs are created and that the rate of increase should not depend strongly on the pump fluence. Instead we found that the increase of the G-phonon population occurs with a delay of ~65 fs. This time-delay is also evidenced by the absence of the so-called self-pumping for G phonons. It decreases with increased pump fluence. We show that these observations imply a new relaxation pathway: Instead of hot carriers transferring energy to G-phonons directly, the energy is first transferred to optical phonons near the zone boundary K-points, which then decay into G-phonons via phonon-phonon scattering. Our work demonstrates that phonon-phonon interactions must be included in any calculations of hot carrier relaxation in optical absorbers even when only short timescales are considered.

Polarization of fluorescein fluorescence in single cells.

PubMed

Udkoff, R; Norman, A

1979-01-01

Measurement of fluorescence polarization (P) gives information about the immediate environment of the fluorescent molecule. We used a flow polarimeter to investigate the factors influencing P of fluorescein in mammalian cells to determine whether such measurements are useful for characterizing heterogeneous cell populations. Fluorescein was introduced into cells by incubation with FDA. Measurements of the intensity of fluorescence (TI) and polarization (P) revealed an unexpected dependence: P decreased with increasing intensity of fluorescence. This may be accounted for by the classical model of the binding of small molecules to protein in which P is dependent on the ratio bound to unbound molecules. We have been able to estimate the quenching due to binding and construct a Scatchard plot. We estimated a wavelength shift from in vitro data consistent with the dependence of P on wavelength seen in our cell work. Generally, the distributions of P are symmetrical. Photon statistics broadens the P distribution of dim cells. However, structure does develop in the P distribution when the cells are deprived of calcium or incubated in the cold. This appears as a shoulder on the P distribution or resolves into two peaks. Calcium deprivation may differentially affect a subpopulation of cells whose significance remains to be explored in various cell types.

Recording High Resolution 3D Lagrangian Motions In Marine Dinoflagellates using Digital Holographic Microscopic Cinematography

NASA Astrophysics Data System (ADS)

Sheng, J.; Malkiel, E.; Katz, J.; Place, A. R.; Belas, R.

2006-11-01

Detailed data on swimming behavior and locomotion for dense population of dinoflagellates constitutes a key component to understanding cell migration, cell-cell interactions and predator-prey dynamics, all of which affect algae bloom dynamics. Due to the multi-dimensional nature of flagellated cell motions, spatial-temporal Lagrangian measurements of multiple cells in high concentration are very limited. Here we present detailed data on 3D Lagrangian motions for three marine dinoflagellates: Oxyrrhis marina, Karlodinium veneficum, and Pfiesteria piscicida, using digital holographic microscopic cinematography. The measurements are performed in a 5x5x25mm cuvette with cell densities varying from 50,000 ˜ 90,000 cells/ml. Approximately 200-500 cells are tracked simultaneously for 12s at 60fps in a sample volume of 1x1x5 mm at a spatial resolution of 0.4x0.4x2 μm. We fully resolve the longitudinal flagella (˜200nm) along with the Lagrangian trajectory of each organism. Species dependent swimming behavior are identified and categorized quantitatively by velocities, radii of curvature, and rotations of pitch. Statistics on locomotion, temporal & spatial scales, and diffusion rate show substantial differences between species. The scaling between turning radius and cell dimension can be explained by a distributed stokeslet model for a self-propelled body.

Spectrally resolved femtosecond photon echo spectroscopy of astaxanthin

NASA Astrophysics Data System (ADS)

Kumar, Ajitesh; Karthick Kumar, S. K.; Gupta, Aditya; Goswami, Debabrata

2010-12-01

We have studied the coherence and population dynamics of Astaxanthin solution in methanol and acetonitrile by spectrally resolving their photon echo signals. Our experiments indicate that methanol has a much stronger interaction with the ultrafast dynamics of Astaxanthin in comparison to that of acetonitrile.

Spectrally resolved femtosecond photon echo spectroscopy of astaxanthin

NASA Astrophysics Data System (ADS)

Kumar, Ajitesh; Karthick Kumar, S. K.; Gupta, Aditya; Goswami, Debabrata

2011-08-01

We have studied the coherence and population dynamics of Astaxanthin solution in methanol and acetonitrile by spectrally resolving their photon echo signals. Our experiments indicate that methanol has a much stronger interaction with the ultrafast dynamics of Astaxanthin in comparison to that of acetonitrile.

Is the Cortical Deficit in Amblyopia Due to Reduced Cortical Magnification, Loss of Neural Resolution, or Neural Disorganization?

PubMed

Clavagnier, Simon; Dumoulin, Serge O; Hess, Robert F

2015-11-04

The neural basis of amblyopia is a matter of debate. The following possibilities have been suggested: loss of foveal cells, reduced cortical magnification, loss of spatial resolution of foveal cells, and topographical disarray in the cellular map. To resolve this we undertook a population receptive field (pRF) functional magnetic resonance imaging analysis in the central field in humans with moderate-to-severe amblyopia. We measured the relationship between averaged pRF size and retinal eccentricity in retinotopic visual areas. Results showed that cortical magnification is normal in the foveal field of strabismic amblyopes. However, the pRF sizes are enlarged for the amblyopic eye. We speculate that the pRF enlargement reflects loss of cellular resolution or an increased cellular positional disarray within the representation of the amblyopic eye. The neural basis of amblyopia, a visual deficit affecting 3% of the human population, remains a matter of debate. We undertook the first population receptive field functional magnetic resonance imaging analysis in participants with amblyopia and compared the projections from the amblyopic and fellow normal eye in the visual cortex. The projection from the amblyopic eye was found to have a normal cortical magnification factor, enlarged population receptive field sizes, and topographic disorganization in all early visual areas. This is consistent with an explanation of amblyopia as an immature system with a normal complement of cells whose spatial resolution is reduced and whose topographical map is disordered. This bears upon a number of competing theories for the psychophysical defect and affects future treatment therapies. Copyright © 2015 the authors 0270-6474/15/3514740-16$15.00/0.

Hepatic macrophages in homeostasis and liver diseases: from pathogenesis to novel therapeutic strategies

PubMed Central

Ju, Cynthia; Tacke, Frank

2016-01-01

Macrophages represent a major cell type of innate immunity and have emerged as a critical player and therapeutic target in many chronic inflammatory diseases. Hepatic macrophages consist of Kupffer cells, which are originated from the fetal yolk-sack, and infiltrated bone marrow-derived monocytes/macrophages. Hepatic macrophages play a central role in maintaining homeostasis of the liver and in the pathogenesis of liver injury, making them an attractive therapeutic target for liver diseases. However, the various populations of hepatic macrophages display different phenotypes and exert distinct functions. Thus, more research is required to better understand these cells to guide the development of macrophage-based therapeutic interventions. This review article will summarize the current knowledge on the origins and composition of hepatic macrophages, their functions in maintaining hepatic homeostasis, and their involvement in both promoting and resolving liver inflammation, injury, and fibrosis. Finally, the current strategies being developed to target hepatic macrophages for the treatment of liver diseases will be reviewed. PMID:26908374

The History of the M31 Disk from Resolved Stellar Populations as Seen by PHAT

NASA Astrophysics Data System (ADS)

Lewis, A. R.; Dalcanton, J. J.; Dolphin, A. E.; Weisz, D. R.; Williams, B. F.; PHAT Collaboration

2014-03-01

The Panchromatic Hubble Andromeda Treasury (PHAT) is an HST multi-cycle treasury program that is mapping the resolved stellar populations of ˜1/3 of M31 from the UV through the near-IR. These data provide color and luminosity information for more than 150 million stars in the M31 disk. We use stellar evolution models to fit the luminous main sequence to derive spatially-resolved recent star formation histories (SFHs) over large areas of M31 with 50-100 pc resolution. These include individual star-forming regions as well as quiescent portions of the disk. We use the gridded SFHs to create movies of star formation activity to study the evolution of individual star-forming events across the disk. Outside of the star-forming regions, we use our resolved stellar photometry to derive the full SFHs of larger regions. These allow us to probe spatial and temporal trends in age and metallicity across a large radial baseline, providing constraints on the global formation and evolution of the disk over a Hubble time. M31 is the only large disk galaxy that is close enough to obtain the photometry necessary for this type of spatially-resolved SFH mapping.

Planar Diamond-Based Multiarrays to Monitor Neurotransmitter Release and Action Potential Firing: New Perspectives in Cellular Neuroscience.

PubMed

Carabelli, Valentina; Marcantoni, Andrea; Picollo, Federico; Battiato, Alfio; Bernardi, Ettore; Pasquarelli, Alberto; Olivero, Paolo; Carbone, Emilio

2017-02-15

High biocompatibility, outstanding electrochemical responsiveness, inertness, and transparency make diamond-based multiarrays (DBMs) first-rate biosensors for in vitro detection of electrochemical and electrical signals from excitable cells together, with potential for in vivo applications as neural interfaces and prostheses. Here, we will review the electrochemical and physical properties of various DBMs and how these devices have been employed for recording released neurotransmitter molecules and all-or-none action potentials from living cells. Specifically, we will overview how DBMs can resolve localized exocytotic events from subcellular compartments using high-density microelectrode arrays (MEAs), or monitoring oxidizable neurotransmitter release from populations of cells in culture and tissue slices using low-density MEAs. Interfacing DBMs with excitable cells is currently leading to the promising opportunity of recording electrical signals as well as creating neuronal interfaces through the same device. Given the recent increasingly growing development of newly available DBMs of various geometries to monitor electrical activity and neurotransmitter release in a variety of excitable and neuronal tissues, the discussion will be limited to planar DBMs.

Quantitative Magnetic Separation of Particles and Cells using Gradient Magnetic Ratcheting

PubMed Central

Murray, Coleman; Pao, Edward; Tseng, Peter; Aftab, Shayan; Kulkarni, Rajan; Rettig, Matthew; Di Carlo, Dino

2016-01-01

Extraction of rare target cells from biosamples is enabling for life science research. Traditional rare cell separation techniques, such as magnetic activated cell sorting (MACS), are robust but perform coarse, qualitative separations based on surface antigen expression. We report a quantitative magnetic separation technology using high-force magnetic ratcheting over arrays of magnetically soft micro-pillars with gradient spacing, and use the system to separate and concentrate magnetic beads based on iron oxide content (IOC) and cells based on surface expression. The system consists of a microchip of permalloy micro-pillar arrays with increasing lateral pitch and a mechatronic device to generate a cycling magnetic-field. Particles with higher IOC separate and equilibrate along the miro-pillar array at larger pitches. We develop a semi-analytical model that predicts behavior for particles and cells. Using the system, LNCaP cells were separated based on the bound quantity of 1μm anti-EpCAM particles as a metric for expression. The ratcheting cytometry system was able to resolve a ±13 bound particle differential, successfully distinguishing LNCaP from PC3 populations based on EpCAM expression, correlating with flow cytometry analysis. As a proof of concept, EpCAM-labeled cells from patient blood were isolated with 74% purity, demonstrating potential towards a quantitative magnetic separation instrument. PMID:26890496

Intracellular O2 sensing probe based on cell-penetrating phosphorescent nanoparticles.

PubMed

Fercher, Andreas; Borisov, Sergey M; Zhdanov, Alexander V; Klimant, Ingo; Papkovsky, Dmitri B

2011-07-26

A new intracellular O(2) (icO(2)) sensing probe is presented, which comprises a nanoparticle (NP) formulation of a cationic polymer Eudragit RL-100 and a hydrophobic phosphorescent dye Pt(II)-tetrakis(pentafluorophenyl)porphyrin (PtPFPP). Using the time-resolved fluorescence (TR-F) plate reader set-up, cell loading was investigated in detail, particularly the effects of probe concentration, loading time, serum content in the medium, cell type, density, etc. The use of a fluorescent analogue of the probe in conjunction with confocal microscopy and flow cytometry analysis, revealed that cellular uptake of the NPs is driven by nonspecific energy-dependent endocytosis and that the probe localizes inside the cell close to the nucleus. Probe calibration in biological environment was performed, which allowed conversion of measured phosphorescence lifetime signals into icO(2) concentration (μM). Its analytical performance in icO(2) sensing experiments was demonstrated by monitoring metabolic responses of mouse embryonic fibroblast cells under ambient and hypoxic macroenvironment. The NP probe was seen to generate stable and reproducible signals in different types of mammalian cells and robust responses to their metabolic stimulation, thus allowing accurate quantitative analysis. High brightness and photostability allow its use in screening experiments with cell populations on a commercial TR-F reader, and for single cell analysis on a fluorescent microscope.

Dynamic Properties of the Alkaline Vesicle Population at Hippocampal Synapses

PubMed Central

Röther, Mareike; Brauner, Jan M.; Ebert, Katrin; Welzel, Oliver; Jung, Jasmin; Bauereiss, Anna; Kornhuber, Johannes; Groemer, Teja W.

2014-01-01

In compensatory endocytosis, scission of vesicles from the plasma membrane to the cytoplasm is a prerequisite for intravesicular reacidification and accumulation of neurotransmitter molecules. Here, we provide time-resolved measurements of the dynamics of the alkaline vesicle population which appears upon endocytic retrieval. Using fast perfusion pH-cycling in live-cell microscopy, synapto-pHluorin expressing rat hippocampal neurons were electrically stimulated. We found that the relative size of the alkaline vesicle population depended significantly on the electrical stimulus size: With increasing number of action potentials the relative size of the alkaline vesicle population expanded. In contrast to that, increasing the stimulus frequency reduced the relative size of the population of alkaline vesicles. Measurement of the time constant for reacification and calculation of the time constant for endocytosis revealed that both time constants were variable with regard to the stimulus condition. Furthermore, we show that the dynamics of the alkaline vesicle population can be predicted by a simple mathematical model. In conclusion, here a novel methodical approach to analyze dynamic properties of alkaline vesicles is presented and validated as a convenient method for the detection of intracellular events. Using this method we show that the population of alkaline vesicles is highly dynamic and depends both on stimulus strength and frequency. Our results implicate that determination of the alkaline vesicle population size may provide new insights into the kinetics of endocytic retrieval. PMID:25079223

Tracing the spatiotemporally resolved inactivation of optically arranged bacteria by photofunctional microparticles at the single-cell level (Conference Presentation)

NASA Astrophysics Data System (ADS)

Barroso Peña, Alvaro; Grüner, Malte; Forbes, Taylor; Denz, Cornelia; Strassert, Cristian A.

2016-09-01

Antimicrobial Photodynamic Inactivation (PDI) represents an attractive alternative in the treatment of infections by antibiotic-resistant pathogenic bacteria. In PDI a photosensitizer (PS) is administered to the site of the biological target in order to generate cytotoxic singlet oxygen which reacts with the biological membrane upon application of harmless visible light. Established methods for testing the photoinduced cytotoxicity of PSs rely on the observation of the whole bacterial ensemble providing only a population-averaged information about the overall produced toxicity. However, for a deeper understanding of the processes that take place in PDI, new methods are required that provide simultaneous regulation of the ROS production, monitoring the subsequent damage induced in the bacteria cells, and full control of the distance between the bacteria and the center of the singlet oxygen production. Herein we present a novel method that enables the quantitative spatio-time-resolved analysis at the single cell level of the photoinduced damage produced by transparent microspheres functionalized with PSs. For this purpose, a methodology was introduced to monitor phototriggered changes with spatiotemporal resolution employing holographic optical tweezers and functional fluorescence microscopy. The defined distance between the photoactive particles and individual bacteria can be fixed under the microscope before the photosensitization process, and the photoinduced damage is monitored by tracing the fluorescence turn-on of a suitable marker. Our methodology constitutes a new tool for the in vitro design and analysis of photosensitizers, as it enables a quantitative response evaluation of living systems towards oxidative stress.

High-throughput single-molecule telomere characterization.

PubMed

McCaffrey, Jennifer; Young, Eleanor; Lassahn, Katy; Sibert, Justin; Pastor, Steven; Riethman, Harold; Xiao, Ming

2017-11-01

We have developed a novel method that enables global subtelomere and haplotype-resolved analysis of telomere lengths at the single-molecule level. An in vitro CRISPR/Cas9 RNA-directed nickase system directs the specific labeling of human (TTAGGG)n DNA tracts in genomes that have also been barcoded using a separate nickase enzyme that recognizes a 7-bp motif genome-wide. High-throughput imaging and analysis of large DNA single molecules from genomes labeled in this fashion using a nanochannel array system permits mapping through subtelomere repeat element (SRE) regions to unique chromosomal DNA while simultaneously measuring the (TTAGGG)n tract length at the end of each large telomere-terminal DNA segment. The methodology also permits subtelomere and haplotype-resolved analyses of SRE organization and variation, providing a window into the population dynamics and potential functions of these complex and structurally variant telomere-adjacent DNA regions. At its current stage of development, the assay can be used to identify and characterize telomere length distributions of 30-35 discrete telomeres simultaneously and accurately. The assay's utility is demonstrated using early versus late passage and senescent human diploid fibroblasts, documenting the anticipated telomere attrition on a global telomere-by-telomere basis as well as identifying subtelomere-specific biases for critically short telomeres. Similarly, we present the first global single-telomere-resolved analyses of two cancer cell lines. © 2017 McCaffrey et al.; Published by Cold Spring Harbor Laboratory Press.

Role of Alveolar Macrophages in Chronic Obstructive Pulmonary Disease

PubMed Central

Vlahos, Ross; Bozinovski, Steven

2014-01-01

Alveolar macrophages (AMs) represent a unique leukocyte population that responds to airborne irritants and microbes. This distinct microenvironment coordinates the maturation of long-lived AMs, which originate from fetal blood monocytes and self-renew through mechanisms dependent on GM-CSF and CSF-1 signaling. Peripheral blood monocytes can also replenish lung macrophages; however, this appears to occur in a stimuli specific manner. In addition to mounting an appropriate immune response during infection and injury, AMs actively coordinate the resolution of inflammation through efferocytosis of apoptotic cells. Any perturbation of this process can lead to deleterious responses. In chronic obstructive pulmonary disease (COPD), there is an accumulation of airway macrophages that do not conform to the classic M1/M2 dichotomy. There is also a skewed transcriptome profile that favors expression of wound-healing M2 markers, which is reflective of a deficiency to resolve inflammation. Endogenous mediators that can promote an imbalance in inhibitory M1 vs. healing M2 macrophages are discussed, as they are the plausible mechanisms underlying why AMs fail to effectively resolve inflammation and restore normal lung homeostasis in COPD. PMID:25309536

The evolution of sex-specific virulence in infectious diseases

PubMed Central

Úbeda, Francisco; Jansen, Vincent A. A.

2016-01-01

Fatality rates of infectious diseases are often higher in men than women. Although this difference is often attributed to a stronger immune response in women, we show that differences in the transmission routes that the sexes provide can result in evolution favouring pathogens with sex-specific virulence. Because women can transmit pathogens during pregnancy, birth or breast-feeding, pathogens adapt, evolving lower virulence in women. This can resolve the long-standing puzzle on progression from Human T-cell Lymphotropic Virus Type 1 (HTLV-1) infection to lethal Adult T-cell Leukaemia (ATL); a progression that is more likely in Japanese men than women, while it is equally likely in Caribbean women and men. We argue that breastfeeding, being more prolonged in Japan than in the Caribbean, may have driven the difference in virulence between the two populations. Our finding signifies the importance of investigating the differences in genetic expression profile of pathogens in males and females. PMID:27959327

The evolution of sex-specific virulence in infectious diseases.

PubMed

Úbeda, Francisco; Jansen, Vincent A A

2016-12-13

Fatality rates of infectious diseases are often higher in men than women. Although this difference is often attributed to a stronger immune response in women, we show that differences in the transmission routes that the sexes provide can result in evolution favouring pathogens with sex-specific virulence. Because women can transmit pathogens during pregnancy, birth or breast-feeding, pathogens adapt, evolving lower virulence in women. This can resolve the long-standing puzzle on progression from Human T-cell Lymphotropic Virus Type 1 (HTLV-1) infection to lethal Adult T-cell Leukaemia (ATL); a progression that is more likely in Japanese men than women, while it is equally likely in Caribbean women and men. We argue that breastfeeding, being more prolonged in Japan than in the Caribbean, may have driven the difference in virulence between the two populations. Our finding signifies the importance of investigating the differences in genetic expression profile of pathogens in males and females.

Effects of internal and external environment on health and well-being: from cell to society.

PubMed

Tomljenović, Andrea

2014-03-01

Stem cell fate in cell culture depends on the composition of the culturing media. Every single cell in an organism is influenced by its microenvironment and surrounding cells. Biology, psychology, emotions, spirit, energy, lifestyle, culture, economic and political influences, social interactions in family, work, living area and the possibilities to expresses oneself and live full life with a sense of well-being have influence on people appearances. Disease is as much social as biological. It is a reaction of an organism to unbalancing changes in the internal environment caused by the changes in the external environment and/or by the structural and functional failures or unfortunate legacies. Health gradient in the society depends on the every day circumstances in which people live and work. The health of the population is an insight into the society. The problem facing medicine in the complex society of today cannot be resolved without the aid of social sciences, as cultural, social, ecological and mental processes affect physiological responses and health outcomes. Anthropology could be a bridge between biomedicine and social sciences and influence strategies in public health to prevent rather than cure and in education for fulfillment in life and improvement of society.

Cytokinesis: breaking the ties that bind.

PubMed

McCollum, Dannel

2005-12-20

It has been unclear how cells complete cell division and resolve membrane connections to bring about cell separation. Recent work has shown that targeted secretion to the midbody is required to complete cell division.

Population structure of Vibrio fischeri within the light organs of Euprymna scolopes squid from Two Oahu (Hawaii) populations.

PubMed

Wollenberg, M S; Ruby, E G

2009-01-01

We resolved the intraspecific diversity of Vibrio fischeri, the bioluminescent symbiont of the Hawaiian sepiolid squid Euprymna scolopes, at two previously unexplored morphological and geographical scales. These scales ranged from submillimeter regions within the host light organ to the several kilometers encompassing two host populations around Oahu. To facilitate this effort, we employed both novel and standard genetic and phenotypic assays of light-organ symbiont populations. A V. fischeri-specific fingerprinting method and five phenotypic assays were used to gauge the genetic richness of V. fischeri populations; these methods confirmed that the symbiont population present in each adult host's light organ is polyclonal. Upon statistical analysis of these genetic and phenotypic population data, we concluded that the characteristics of symbiotic populations were more similar within individual host populations than between the two distinct Oahu populations of E. scolopes, providing evidence that local geographic symbiont population structure exists. Finally, to better understand the genesis of symbiont diversity within host light organs, the process of symbiosis initiation in newly hatched juvenile squid was examined both experimentally and by mathematical modeling. We concluded that, after the juvenile hatches, only one or two cells of V. fischeri enter each of six internal epithelium-lined crypts present in the developing light organ. We hypothesize that the expansion of different, crypt-segregated, clonal populations creates the polyclonal adult light-organ population structure observed in this study. The stability of the luminous-bacterium-sepiolid squid mutualism in the presence of a polyclonal symbiont population structure is discussed in the context of contemporary evolutionary theory.

Gold nanoparticle uptake in whole cells in liquid examined by environmental scanning electron microscopy.

PubMed

Peckys, Diana B; de Jonge, Niels

2014-02-01

The size of gold nanoparticles (AuNPs) can influence various aspects of their cellular uptake. Light microscopy is not capable of resolving most AuNPs, while electron microscopy (EM) is not practically capable of acquiring the necessary statistical data from many cells and the results may suffer from various artifacts. Here, we demonstrate the use of a fast EM method for obtaining high-resolution data from a much larger population of cells than is usually feasible with conventional EM. A549 (human lung carcinoma) cells were subjected to uptake protocols with 10, 15, or 30 nm diameter AuNPs with adsorbed serum proteins. After 20 min, 24 h, or 45 h, the cells were fixed and imaged in whole in a thin layer of liquid water with environmental scanning electron microscopy equipped with a scanning transmission electron microscopy detector. The fast preparation and imaging of 145 whole cells in liquid allowed collection of nanoscale data within an exceptionally small amount of time of ~80 h. Analysis of 1,041 AuNP-filled vesicles showed that the long-term AuNP storing lysosomes increased their average size by 80 nm when AuNPs with 30 nm diameter were uptaken, compared to lysosomes of cells incubated with AuNPs of 10 and 15 nm diameter.

Dynamics of tissue topology during cancer invasion and metastasis

NASA Astrophysics Data System (ADS)

Munn, Lance L.

2013-12-01

During tumor progression, cancer cells mix with other cell populations including epithelial and endothelial cells. Although potentially important clinically as well as for our understanding of basic tumor biology, the process of mixing is largely a mystery. Furthermore, there is no rigorous, analytical measure available for quantifying the mixing of compartments within a tumor. I present here a mathematical model of tissue repair and tumor growth based on collective cell migration that simulates a wide range of observed tumor behaviors with correct tissue compartmentalization and connectivity. The resulting dynamics are analyzed in light of the Euler characteristic number (χ), which describes key topological features such as fragmentation, looping and cavities. The analysis predicts a number of regimes in which the cancer cells can encapsulate normal tissue, form a co-interdigitating mass, or become fragmented and encapsulated by endothelial or epithelial structures. Key processes that affect the topological changes are the production of provisional matrix in the tumor, and the migration of endothelial or epithelial cells on this matrix. Furthermore, the simulations predict that topological changes during tumor invasion into blood vessels may contribute to metastasis. The topological analysis outlined here could be useful for tumor diagnosis or monitoring response to therapy and would only require high resolution, 3D image data to resolve and track the various cell compartments.

Intracellular pH Response to Weak Acid Stress in Individual Vegetative Bacillus subtilis Cells

PubMed Central

Pandey, Rachna; Vischer, Norbert O. E.; Smelt, Jan P. P. M.; van Beilen, Johan W. A.; Ter Beek, Alexander; De Vos, Winnok H.; Manders, Erik M. M.

2016-01-01

ABSTRACT Intracellular pH (pHi) critically affects bacterial cell physiology. Hence, a variety of food preservation strategies are aimed at perturbing pHi homeostasis. Unfortunately, accurate pHi quantification with existing methods is suboptimal, since measurements are averages across populations of cells, not taking into account interindividual heterogeneity. Yet, physiological heterogeneity in isogenic populations is well known to be responsible for differences in growth and division kinetics of cells in response to external stressors. To assess in this context the behavior of intracellular acidity, we have developed a robust method to quantify pHi at single-cell levels in Bacillus subtilis. Bacilli spoil food, cause disease, and are well known for their ability to form highly stress-resistant spores. Using an improved version of the genetically encoded ratiometric pHluorin (IpHluorin), we have quantified pHi in individual B. subtilis cells, cultured at an external pH of 6.4, in the absence or presence of weak acid stresses. In the presence of 3 mM potassium sorbate, a decrease in pHi and an increase in the generation time of growing cells were observed. Similar effects were observed when cells were stressed with 25 mM potassium acetate. Time-resolved analysis of individual bacteria in growing colonies shows that after a transient pH decrease, long-term pH evolution is highly cell dependent. The heterogeneity at the single-cell level shows the existence of subpopulations that might be more resistant and contribute to population survival. Our approach contributes to an understanding of pHi regulation in individual bacteria and may help scrutinizing effects of existing and novel food preservation strategies. IMPORTANCE This study shows how the physiological response to commonly used weak organic acid food preservatives, such as sorbic and acetic acids, can be measured at the single-cell level. These data are key to coupling often-observed single-cell heterogeneous growth behavior upon the addition of weak organic acid food preservatives. Generally, these data are gathered in the form of plate counting of samples incubated with the acids. Here, we visualize the underlying heterogeneity in cellular pH homeostasis, opening up avenues for mechanistic analyses of the heterogeneity in the weak acid stress response. Thus, microbial risk assessment can become more robust, widening the scope of use of these well-known weak organic acid food preservatives. PMID:27565617

Fas-Fas ligand interactions are essential for the binding to and killing of activated macrophages by gamma delta T cells.

PubMed

Dalton, Jane E; Howell, Gareth; Pearson, Jayne; Scott, Phillip; Carding, Simon R

2004-09-15

Gammadelta T cells have a direct role in resolving the host immune response to infection by eliminating populations of activated macrophages. Macrophage reactivity resides within the Vgamma1/Vdelta6.3 subset of gammadelta T cells, which have the ability to kill activated macrophages following infection with Listeria monocytogenes (Lm). However, it is not known how gammadelta T cell macrophage cytocidal activity is regulated, or what effector mechanisms gammadelta T cells use to kill activated macrophages. Using a macrophage-T cell coculture system in which peritoneal macrophages from naive or Lm-infected TCRdelta-/- mice were incubated with splenocytes from wild-type and Fas ligand (FasL)-deficient mice (gld), the ability of Vgamma1 T cells to bind macrophages was shown to be dependent upon Fas-FasL interactions. Combinations of anti-TCR and FasL Abs completely abolished binding to and killing of activated macrophages by Vgamma1 T cells. In addition, confocal microscopy showed that Fas and the TCR colocalized on Vgamma1 T cells at points of contact with macrophages. Collectively, these studies identify an accessory or coreceptor-like function for Fas-FasL that is essential for the interaction of Vgamma1 T cells with activated macrophages and their elimination during the resolution stage of pathogen-induced immune responses. Copyright 2004 The American Association of Immunologists, Inc.

Quantitative Temporal in Vivo Proteomics Deciphers the Transition of Virus-Driven Myeloid Cells into M2 Macrophages

PubMed Central

2017-01-01

Myeloid cells play a central role in the context of viral eradication, yet precisely how these cells differentiate throughout the course of acute infections is poorly understood. In this study, we have developed a novel quantitative temporal in vivo proteomics (QTiPs) platform to capture proteomic signatures of temporally transitioning virus-driven myeloid cells directly in situ, thus taking into consideration host–virus interactions throughout the course of an infection. QTiPs, in combination with phenotypic, functional, and metabolic analyses, elucidated a pivotal role for inflammatory CD11b+, Ly6G–, Ly6Chigh-low cells in antiviral immune response and viral clearance. Most importantly, the time-resolved QTiPs data set showed the transition of CD11b+, Ly6G–, Ly6Chigh-low cells into M2-like macrophages, which displayed increased antigen-presentation capacities and bioenergetic demands late in infection. We elucidated the pivotal role of myeloid cells in virus clearance and show how these cells phenotypically, functionally, and metabolically undergo a timely transition from inflammatory to M2-like macrophages in vivo. With respect to the growing appreciation for in vivo examination of viral–host interactions and for the role of myeloid cells, this study elucidates the use of quantitative proteomics to reveal the role and response of distinct immune cell populations throughout the course of virus infection. PMID:28768414

Single-cell paired-end genome sequencing reveals structural variation per cell cycle

PubMed Central

Voet, Thierry; Kumar, Parveen; Van Loo, Peter; Cooke, Susanna L.; Marshall, John; Lin, Meng-Lay; Zamani Esteki, Masoud; Van der Aa, Niels; Mateiu, Ligia; McBride, David J.; Bignell, Graham R.; McLaren, Stuart; Teague, Jon; Butler, Adam; Raine, Keiran; Stebbings, Lucy A.; Quail, Michael A.; D’Hooghe, Thomas; Moreau, Yves; Futreal, P. Andrew; Stratton, Michael R.; Vermeesch, Joris R.; Campbell, Peter J.

2013-01-01

The nature and pace of genome mutation is largely unknown. Because standard methods sequence DNA from populations of cells, the genetic composition of individual cells is lost, de novo mutations in cells are concealed within the bulk signal and per cell cycle mutation rates and mechanisms remain elusive. Although single-cell genome analyses could resolve these problems, such analyses are error-prone because of whole-genome amplification (WGA) artefacts and are limited in the types of DNA mutation that can be discerned. We developed methods for paired-end sequence analysis of single-cell WGA products that enable (i) detecting multiple classes of DNA mutation, (ii) distinguishing DNA copy number changes from allelic WGA-amplification artefacts by the discovery of matching aberrantly mapping read pairs among the surfeit of paired-end WGA and mapping artefacts and (iii) delineating the break points and architecture of structural variants. By applying the methods, we capture DNA copy number changes acquired over one cell cycle in breast cancer cells and in blastomeres derived from a human zygote after in vitro fertilization. Furthermore, we were able to discover and fine-map a heritable inter-chromosomal rearrangement t(1;16)(p36;p12) by sequencing a single blastomere. The methods will expedite applications in basic genome research and provide a stepping stone to novel approaches for clinical genetic diagnosis. PMID:23630320

Hydroxyl Radical Fluorescence and Quantum Yield Following Lyman-α Photoexcitation of Water Vapor in a Room Temperature Cell and Cooled in a Supersonic Expansion.

PubMed

Young, Justin W; Booth, Ryan S; Vogelhuber, Kristen M; Stearns, Jaime A; Annesley, Christopher J

2018-06-28

Photoexcitation of water by Lyman-α (121.6 nm) induces a dissociation reaction that produces OH(A 2 Σ + ) + H. Despite this reaction being part of numerous studies, a combined understanding of the product and fluorescence yields is still lacking. Here, the rotational and vibrational distributions of OH(A) are determined from dispersed fluorescence following photoexcitation of both room-temperature and jet-cooled water vapor, for the first time in the same experiment. This work compares new data of state-resolved fluorescence with literature molecular branching ratios and brings previous studies into agreement through careful consideration of OH(A) fluorescent and predissociation lifetimes and confirms a fluorescent quantum yield of 8%. Comparison of the room-temperature and jet-cooled OH(A) populations indicate the temperature of H 2 O prior to excitation has subtle effects on the OH(A) population distribution, such as altering the rotational distribution in the ν' = 0 population and affecting the population in the ν' = 1 state. These results indicate jet-cooled water vapor may have a 1% higher fluorescence quantum yield compared to room-temperature water vapor.

Population Structure of Vibrio fischeri within the Light Organs of Euprymna scolopes Squid from Two Oahu (Hawaii) Populations▿ †

PubMed Central

Wollenberg, M. S.; Ruby, E. G.

2009-01-01

We resolved the intraspecific diversity of Vibrio fischeri, the bioluminescent symbiont of the Hawaiian sepiolid squid Euprymna scolopes, at two previously unexplored morphological and geographical scales. These scales ranged from submillimeter regions within the host light organ to the several kilometers encompassing two host populations around Oahu. To facilitate this effort, we employed both novel and standard genetic and phenotypic assays of light-organ symbiont populations. A V. fischeri-specific fingerprinting method and five phenotypic assays were used to gauge the genetic richness of V. fischeri populations; these methods confirmed that the symbiont population present in each adult host's light organ is polyclonal. Upon statistical analysis of these genetic and phenotypic population data, we concluded that the characteristics of symbiotic populations were more similar within individual host populations than between the two distinct Oahu populations of E. scolopes, providing evidence that local geographic symbiont population structure exists. Finally, to better understand the genesis of symbiont diversity within host light organs, the process of symbiosis initiation in newly hatched juvenile squid was examined both experimentally and by mathematical modeling. We concluded that, after the juvenile hatches, only one or two cells of V. fischeri enter each of six internal epithelium-lined crypts present in the developing light organ. We hypothesize that the expansion of different, crypt-segregated, clonal populations creates the polyclonal adult light-organ population structure observed in this study. The stability of the luminous-bacterium-sepiolid squid mutualism in the presence of a polyclonal symbiont population structure is discussed in the context of contemporary evolutionary theory. PMID:18997024

Inequivalence of single-particle and population lifetimes in a cuprate superconductor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Shuolong; Sobota, J. A.; Leuenberger, D.

2015-06-15

We study optimally doped Bi-2212 (T c=96 K) using femtosecond time- and angle-resolved photoelectron spectroscopy. Energy-resolved population lifetimes are extracted and compared with single-particle lifetimes measured by equilibrium photoemission. The population lifetimes deviate from the single-particle lifetimes in the low excitation limit by 1–2 orders of magnitude. Fundamental considerations of electron scattering unveil that these two lifetimes are in general distinct, yet for systems with only electron-phonon scattering they should converge in the low-temperature, low-fluence limit. As a result, the qualitative disparity in our data, even in this limit, suggests that scattering channels beyond electron-phonon interactions play a significant rolemore » in the electron dynamics of cuprate superconductors.« less

Quantifying and resolving multiple vector transformants in S. cerevisiae plasmid libraries.

PubMed

Scanlon, Thomas C; Gray, Elizabeth C; Griswold, Karl E

2009-11-20

In addition to providing the molecular machinery for transcription and translation, recombinant microbial expression hosts maintain the critical genotype-phenotype link that is essential for high throughput screening and recovery of proteins encoded by plasmid libraries. It is known that Escherichia coli cells can be simultaneously transformed with multiple unique plasmids and thusly complicate recombinant library screening experiments. As a result of their potential to yield misleading results, bacterial multiple vector transformants have been thoroughly characterized in previous model studies. In contrast to bacterial systems, there is little quantitative information available regarding multiple vector transformants in yeast. Saccharomyces cerevisiae is the most widely used eukaryotic platform for cell surface display, combinatorial protein engineering, and other recombinant library screens. In order to characterize the extent and nature of multiple vector transformants in this important host, plasmid-born gene libraries constructed by yeast homologous recombination were analyzed by DNA sequencing. It was found that up to 90% of clones in yeast homologous recombination libraries may be multiple vector transformants, that on average these clones bear four or more unique mutant genes, and that these multiple vector cells persist as a significant proportion of library populations for greater than 24 hours during liquid outgrowth. Both vector concentration and vector to insert ratio influenced the library proportion of multiple vector transformants, but their population frequency was independent of transformation efficiency. Interestingly, the average number of plasmids born by multiple vector transformants did not vary with their library population proportion. These results highlight the potential for multiple vector transformants to dominate yeast libraries constructed by homologous recombination. The previously unrecognized prevalence and persistence of multiply transformed yeast cells have important implications for yeast library screens. The quantitative information described herein should increase awareness of this issue, and the rapid sequencing approach developed for these studies should be widely useful for identifying multiple vector transformants and avoiding complications associated with cells that have acquired more than one unique plasmid.

Quantitative Magnetic Separation of Particles and Cells Using Gradient Magnetic Ratcheting.

PubMed

Murray, Coleman; Pao, Edward; Tseng, Peter; Aftab, Shayan; Kulkarni, Rajan; Rettig, Matthew; Di Carlo, Dino

2016-04-13

Extraction of rare target cells from biosamples is enabling for life science research. Traditional rare cell separation techniques, such as magnetic activated cell sorting, are robust but perform coarse, qualitative separations based on surface antigen expression. A quantitative magnetic separation technology is reported using high-force magnetic ratcheting over arrays of magnetically soft micropillars with gradient spacing, and the system is used to separate and concentrate magnetic beads based on iron oxide content (IOC) and cells based on surface expression. The system consists of a microchip of permalloy micropillar arrays with increasing lateral pitch and a mechatronic device to generate a cycling magnetic field. Particles with higher IOC separate and equilibrate along the miropillar array at larger pitches. A semi-analytical model is developed that predicts behavior for particles and cells. Using the system, LNCaP cells are separated based on the bound quantity of 1 μm anti-epithelial cell adhesion molecule (EpCAM) particles as a metric for expression. The ratcheting cytometry system is able to resolve a ±13 bound particle differential, successfully distinguishing LNCaP from PC3 populations based on EpCAM expression, correlating with flow cytometry analysis. As a proof-of-concept, EpCAM-labeled cells from patient blood are isolated with 74% purity, demonstrating potential toward a quantitative magnetic separation instrument. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The ALHAMBRA survey: 2D analysis of the stellar populations in massive early-type galaxies at z < 0.3

NASA Astrophysics Data System (ADS)

San Roman, I.; Cenarro, A. J.; Díaz-García, L. A.; López-Sanjuan, C.; Varela, J.; González Delgado, R. M.; Sánchez-Blázquez, P.; Alfaro, E. J.; Ascaso, B.; Bonoli, S.; Borlaff, A.; Castander, F. J.; Cerviño, M.; Fernández-Soto, A.; Márquez, I.; Masegosa, J.; Muniesa, D.; Pović, M.; Viironen, K.; Aguerri, J. A. L.; Benítez, N.; Broadhurst, T.; Cabrera-Caño, J.; Cepa, J.; Cristóbal-Hornillos, D.; Infante, L.; Martínez, V. J.; Moles, M.; del Olmo, A.; Perea, J.; Prada, F.; Quintana, J. M.

2018-01-01

We present a technique that permits the analysis of stellar population gradients in a relatively low-cost way compared to integral field unit (IFU) surveys. We developed a technique to analyze unresolved stellar populations of spatially resolved galaxies based on photometric multi-filter surveys. This technique allows the analysis of vastly larger samples and out to larger galactic radii. We derived spatially resolved stellar population properties and radial gradients by applying a centroidal Voronoi tessellation and performing a multicolor photometry spectral energy distribution fitting. This technique has been successfully applied to a sample of 29 massive (M⋆ > 1010.5M⊙) early-type galaxies at z < 0.3 from the ALHAMBRA survey. We produced detailed 2D maps of stellar population properties (age, metallicity, and extinction), which allow us to identify galactic features. Radial structures were studied, and luminosity-weighted and mass-weighted gradients were derived out to 2-3.5 Reff. We find that the spatially resolved stellar population mass, age, and metallicity are well represented by their integrated values. We find the gradients of early-type galaxies to be on average flat in age (∇log AgeL = 0.02 ± 0.06 dex/Reff) and negative in metallicity (∇[Fe/H]L = -0.09 ± 0.06 dex/Reff). Overall,the extinction gradients are flat (∇Av = -0.03 ± 0.09 mag/Reff ) with a wide spread. These results are in agreement with previous studies that used standard long-slit spectroscopy, and with the most recent IFU studies. According to recent simulations, these results are consistent with a scenario where early-type galaxies were formed through major mergers and where their final gradients are driven by the older ages and higher metallicity of the accreted systems. We demonstrate the scientific potential of multi-filter photometry to explore the spatially resolved stellar populations of local galaxies and confirm previous spectroscopic trends from a complementary technique. Based on observations collected at the German-Spanish Astronomical Center, Calar Alto, jointly operated by the Max-Planck-Institut für Astronomie (MPIA) at Heidelberg and the Instituto de Astrofísica de Andalucía (CSIC).

Periodicity in Age-Resolved Populations

NASA Astrophysics Data System (ADS)

Esipov, Sergei

We discuss the interplay between the non-linear diffusion and age-resolved population dynamics. Depending on the age properties of collective migration the system may exhibit continuous joint expansion of all ages or continuous expansion with age segregation. Between these two obvious limiting regimes there is an interesting window of periodic expansion, which has been previously used by us in modeling bacterial colonies of Proteus mirabilis. In order to test whether the age-dependent collective migration leads to periodicity in other systems we performed a Fourier analysis of historical data on ethnic expansions and found multiple co-existing periods of activity.

Population Growth and Global Security: Toward an American Strategic Commitment.

ERIC Educational Resources Information Center

Mumford, Steven

1981-01-01

Addresses the world population problem by highlighting three crucial areas: the relationship between population growth control and national security issues, the role of American leadership in resolving the problem, and the barriers to effective action. One barrier discussed in detail is the Roman Catholic Church's stand on abortion and…

Epidermotropic presentation by splenic B-cell lymphoma: The importance of clinical-pathologic correlation.

PubMed

Hedayat, Amin A; Carter, Joi B; Lansigan, Frederick; LeBlanc, Robert E

2018-04-01

There are exceedingly rare reports of patients with epidermotropic B-cell lymphomas. A subset presented with intermittent, variably pruritic papular eruptions and involvement of their spleens, peripheral blood and bone marrow at the time of diagnosis. Furthermore, some experienced an indolent course despite dissemination of their lymphomas. We report a 66-year-old woman with a 12-year history of intermittent eruptions of non-pruritic, salmon-colored papules on her torso and proximal extremities that occurred in winter and resolved with outdoor activity in spring. Skin biopsy revealed an epidermotropic B-cell lymphoma with a non-specific B-cell phenotype and heavy chain class switching with IgG expression. On workup, our patient exhibited mild splenomegaly and low-level involvement of her peripheral blood and bone marrow by a kappa-restricted B-cell population. A splenic B-cell lymphoma was diagnosed. Considering her longstanding history and absences of cytopenias, our patient has been followed without splenectomy or systemic therapy. Furthermore, the papules have responded dramatically to narrowband UVB. Our case and a review of similar rare reports aim to raise awareness among dermatopathologists and dermatologists of a clinically distinct and indolent subset of epidermotropic splenic lymphomas with characteristic clinical and histologic findings. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Cancer stem cells: a metastasizing menace!

PubMed

Bandhavkar, Saurabh

2016-04-01

Cancer is one of the leading causes of death worldwide, and is estimated to be a reason of death of more than 18 billion people in the coming 5 years. Progress has been made in diagnosis and treatment of cancer; however, a sound understanding of the underlying cell biology still remains an unsolved mystery. Current treatments include a combination of radiation, surgery, and/or chemotherapy. However, these treatments are not a complete cure, aimed simply at shrinking the tumor and in majority of cases, there is a relapse of tumor. Several evidences suggest the presence of cancer stem cells (CSCs) or tumor-initiating stem-like cells, a small population of cells present in the tumor, capable of self-renewal and generation of differentiated progeny. The presence of these CSCs can be attributed to the failure of cancer treatments as these cells are believed to exhibit therapy resistance. As a result, increasing attention has been given to CSC research to resolve the therapeutic problems related to cancer. Progress in this field of research has led to the development of novel strategies to treat several malignancies and has become a hot topic of discussion. In this review, we will briefly focus on the main characteristics, therapeutic implications, and perspectives of CSCs in cancer therapy. © 2016 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

Cholinergic interneurons in the feeding system of the pond snail Lymnaea stagnalis. II. N1 interneurons make cholinergic synapses with feeding motoneurons.

PubMed

Elliott, C J; Kemenes, G

1992-05-29

The N1 neurons are a population of interneurons active during the protraction phase of the feeding rhythm. All the N1 neurons are coupled by electrical synapses which persist in a high Mg/low Ca saline which blocks chemical synapses. Individual N1 spikes produce discrete electrotonic postsynaptic potentials (PSPS) in other N1 cells, but the coupling is not strong enough to ensure 1:1 firing. Bursts of N1 spikes generate compound PSPS in the feeding motoneurons. The sign (excitation or inhibition) of the N1 input corresponds with the synaptic barrage recorded during the protraction phase. Discrete PSPS are only resolved in a Hi-Di saline. Their variation in latency and number can be explained by variation in electrotonic propagation within the electrically coupled network of N1 cells. The excitatory postsynaptic potentials (ESPS) in the 1 cell are reduced by 0.5 mM antagonists hexamethonium (HMT), atropine (ATR), curare (d-TC) and by methylxylocholine (MeXCh), all of which block the excitatory cholinergic receptor (Elliott et al. (Phil. Trans. R. Soc. Lond. 336, 157-166 (Preceding paper.) (1992)). The 1 cell EPSPS were transiently blocked by phenyltrimethylammonium (PTMA), which is both an agonist and antagonist at the 1 cell excitatory acetylcholine (ACh) receptor (Elliott et al. 1992). The inhibitory postsynaptic potential (IPSP) in the 3 cell is blocked by bath applications of MeXCh and PTMA, which both abolish the response of the 3 cell to ACh (Elliott et. al. 1992). The effects of the cholinergic antagonists on the response of 4 cluster and 5 cells to N1 stimulation matches their response to ACh (Elliott et al. 1992). It is concluded that the population of N1 cells are multiaction, premotor cholinergic interneurons.

Rapid Global Fitting of Large Fluorescence Lifetime Imaging Microscopy Datasets

PubMed Central

Warren, Sean C.; Margineanu, Anca; Alibhai, Dominic; Kelly, Douglas J.; Talbot, Clifford; Alexandrov, Yuriy; Munro, Ian; Katan, Matilda

2013-01-01

Fluorescence lifetime imaging (FLIM) is widely applied to obtain quantitative information from fluorescence signals, particularly using Förster Resonant Energy Transfer (FRET) measurements to map, for example, protein-protein interactions. Extracting FRET efficiencies or population fractions typically entails fitting data to complex fluorescence decay models but such experiments are frequently photon constrained, particularly for live cell or in vivo imaging, and this leads to unacceptable errors when analysing data on a pixel-wise basis. Lifetimes and population fractions may, however, be more robustly extracted using global analysis to simultaneously fit the fluorescence decay data of all pixels in an image or dataset to a multi-exponential model under the assumption that the lifetime components are invariant across the image (dataset). This approach is often considered to be prohibitively slow and/or computationally expensive but we present here a computationally efficient global analysis algorithm for the analysis of time-correlated single photon counting (TCSPC) or time-gated FLIM data based on variable projection. It makes efficient use of both computer processor and memory resources, requiring less than a minute to analyse time series and multiwell plate datasets with hundreds of FLIM images on standard personal computers. This lifetime analysis takes account of repetitive excitation, including fluorescence photons excited by earlier pulses contributing to the fit, and is able to accommodate time-varying backgrounds and instrument response functions. We demonstrate that this global approach allows us to readily fit time-resolved fluorescence data to complex models including a four-exponential model of a FRET system, for which the FRET efficiencies of the two species of a bi-exponential donor are linked, and polarisation-resolved lifetime data, where a fluorescence intensity and bi-exponential anisotropy decay model is applied to the analysis of live cell homo-FRET data. A software package implementing this algorithm, FLIMfit, is available under an open source licence through the Open Microscopy Environment. PMID:23940626

The eukaryotic fossil record in deep time

NASA Astrophysics Data System (ADS)

Butterfield, N.

2011-12-01

Eukaryotic organisms are defining constituents of the Phanerozoic biosphere, but they also extend well back into the Proterozoic record, primarily in the form of microscopic body fossils. Criteria for identifying pre-Ediacaran eukaryotes include large cell size, morphologically complex cell walls and/or the recognition of diagnostically eukaryotic cell division patterns. The oldest unambiguous eukaryote currently on record is an acanthomorphic acritarch (Tappania) from the Palaeoproterozoic Semri Group of central India. Older candidate eukaryotes are difficult to distinguish from giant bacteria, prokaryotic colonies or diagenetic artefacts. In younger Meso- and Neoproterozoic strata, the challenge is to recognize particular grades and clades of eukaryotes, and to document their macro-evolutionary expression. Distinctive unicellular forms include mid-Neoproterozoic testate amoebae and phosphate biomineralizing 'scale-microfossils' comparable to an extant green alga. There is also a significant record of seaweeds, possible fungi and problematica from this interval, documenting multiple independent experiments in eukaryotic multicellularity. Taxonomically resolved forms include a bangiacean red alga and probable vaucheriacean chromalveolate algae from the late Mesoproterozoic, and populations of hydrodictyacean and siphonocladalean green algae of mid Neoproterozoic age. Despite this phylogenetic breadth, however, or arguments from molecular clocks, there is no convincing evidence for pre-Ediacaran metazoans or metaphytes. The conspicuously incomplete nature of the Proterozoic record makes it difficult to resolve larger-scale ecological and evolutionary patterns. Even so, both body fossils and biomarker data point to a pre-Ediacaran biosphere dominated overwhelming by prokaryotes. Contemporaneous eukaryotes appear to be limited to conspicuously shallow water environments, and exhibit fundamentally lower levels of morphological diversity and evolutionary turnover than their Phanerozoic counterparts. I will argue here that this fundamental change of state was driven by the early Ediacaran appearance of Eumetazoa, a uniquely complex clade of heterotrophic eukaryotes that redefined how the planet worked.

CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging.

PubMed

Held, Michael; Schmitz, Michael H A; Fischer, Bernd; Walter, Thomas; Neumann, Beate; Olma, Michael H; Peter, Matthias; Ellenberg, Jan; Gerlich, Daniel W

2010-09-01

Fluorescence time-lapse imaging has become a powerful tool to investigate complex dynamic processes such as cell division or intracellular trafficking. Automated microscopes generate time-resolved imaging data at high throughput, yet tools for quantification of large-scale movie data are largely missing. Here we present CellCognition, a computational framework to annotate complex cellular dynamics. We developed a machine-learning method that combines state-of-the-art classification with hidden Markov modeling for annotation of the progression through morphologically distinct biological states. Incorporation of time information into the annotation scheme was essential to suppress classification noise at state transitions and confusion between different functional states with similar morphology. We demonstrate generic applicability in different assays and perturbation conditions, including a candidate-based RNA interference screen for regulators of mitotic exit in human cells. CellCognition is published as open source software, enabling live-cell imaging-based screening with assays that directly score cellular dynamics.

Asian population frequencies and haplotype distribution of killer cell immunoglobulin-like receptor (KIR) genes among Chinese, Malay, and Indian in Singapore.

PubMed

Lee, Yi Chuan; Chan, Soh Ha; Ren, Ee Chee

2008-11-01

Killer cell immunoglobulin-like receptors (KIR) gene frequencies have been shown to be distinctly different between populations and contribute to functional variation in the immune response. We have investigated KIR gene frequencies in 370 individuals representing three Asian populations in Singapore and report here the distribution of 14 KIR genes (2DL1, 2DL2, 2DL3, 2DL4, 2DL5, 2DS1, 2DS2, 2DS3, 2DS4, 2DS5, 3DL1, 3DL2, 3DL3, 3DS1) with two pseudogenes (2DP1, 3DP1) among Singapore Chinese (n = 210); Singapore Malay (n = 80), and Singapore Indian (n = 80). Four framework genes (KIR3DL3, 3DP1, 2DL4, 3DL2) and a nonframework pseudogene 2DP1 were detected in all samples while KIR2DS2, 2DL2, 2DL5, and 2DS5 had the greatest significant variation across the three populations. Fifteen significant linkage patterns, consistent with associations between genes of A and B haplotypes, were observed. Eighty-four distinct KIR profiles were determined in our populations, 38 of which had not been described in other populations. KIR haplotype studies were performed using nine Singapore Chinese families comprising 34 individuals. All genotypes could be resolved into corresponding pairs of existing haplotypes with eight distinct KIR genotypes and eight different haplotypes. The haplotype A2 with frequency of 63.9% was dominant in Singapore Chinese, comparable to that reported in Korean and Chinese Han. The A haplotypes predominate in Singapore Chinese, with ratio of A to B haplotypes of approximately 3:1. Comparison with KIR frequencies in other populations showed that Singapore Chinese shared similar distributions with Chinese Han, Japanese, and Korean; Singapore Indian was found to be comparable with North Indian Hindus while Singapore Malay resembled the Thai.

Scale-free flow of life: on the biology, economics, and physics of the cell

PubMed Central

Kurakin, Alexei

2009-01-01

The present work is intended to demonstrate that most of the paradoxes, controversies, and contradictions accumulated in molecular and cell biology over many years of research can be readily resolved if the cell and living systems in general are re-interpreted within an alternative paradigm of biological organization that is based on the concepts and empirical laws of nonequilibrium thermodynamics. In addition to resolving paradoxes and controversies, the proposed re-conceptualization of the cell and biological organization reveals hitherto unappreciated connections among many seemingly disparate phenomena and observations, and provides new and powerful insights into the universal principles governing the emergence and organizational dynamics of living systems on each and every scale of biological organizational hierarchy, from proteins and cells to economies and ecologies. PMID:19416527

Proteome reference maps of Medicago truncatula embryogenic cell cultures generated from single protoplasts.

PubMed

Imin, Nijat; De Jong, Femke; Mathesius, Ulrike; van Noorden, Giel; Saeed, Nasir A; Wang, Xin-Ding; Rose, Ray J; Rolfe, Barry G

2004-07-01

Using a combination of two-dimensional gel electrophoresis (2-DE) protein mapping and mass spectrometry (MS) analysis, we have established proteome reference maps of Medicago truncatula embryogenic tissue culture cells. The cultures were generated from single protoplasts, which provided a relatively homogeneous cell population. We used these to analyze protein expression at the globular stages of somatic embryogenesis, which is the earliest morphogenetic embryonic stage. Over 3000 proteins could reproducibly be resolved over a pI range of 4-11. Three hundred and twelve protein spots were extracted from colloidal Coomassie Blue-stained 2-DE gels and analyzed by matrix-assisted laser desorption/ionization-time of flight MS analysis and tandem MS sequencing. This enabled the identification of 169 protein spots representing 128 unique gene products using a publicly available expressed sequence tag database and the MASCOT search engine. These reference maps will be valuable for the investigation of the molecular events which occur during somatic embryogenesis in M. truncatula. The proteome reference maps and supplementary materials will be available and updated for public access at http://semele.anu.edu.au/.

Detection of Sendai virus receptor, the ganglioside GDla, in target tissue (mouse lung)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Markwell, M.A.K.; Sato, E.

1986-05-01

Previously the authors had shown that the gangliosides GDla, GTlb, and GQlb derived from brain function as receptors for the paramyxovirus Sendai virus by their ability to induce infection when incubated with receptor-deficient cells. Analyses of MDBK, HeLa, and MDCK cells in culture demonstrated that these putative receptors were present in host cells in the quantities required for infection. The primary site of infection for Sendai virus in the whole animal is the respiratory tract, culminating in the lung. Therefore, the ganglioside content of this target organ was analyzed to determine the endogenous receptor population available to Sendai virus. Themore » total ganglioside fraction of lung was resolved into individual species by HPTLC. Gangliosides of the gangliotetraose series were identified by the specific binding of /sup 125/I-labeled tetanus and cholera toxins before and after exposure with sialidase. In this manner one of the major resorcinol-positive bands was identified as GDla. Evidence of the more complex ganglioside receptors for Sendai virus was also seen.« less

Modern Perspectives on Numerical Modeling of Cardiac Pacemaker Cell

PubMed Central

Maltsev, Victor A.; Yaniv, Yael; Maltsev, Anna V.; Stern, Michael D.; Lakatta, Edward G.

2015-01-01

Cardiac pacemaking is a complex phenomenon that is still not completely understood. Together with experimental studies, numerical modeling has been traditionally used to acquire mechanistic insights in this research area. This review summarizes the present state of numerical modeling of the cardiac pacemaker, including approaches to resolve present paradoxes and controversies. Specifically we discuss the requirement for realistic modeling to consider symmetrical importance of both intracellular and cell membrane processes (within a recent “coupled-clock” theory). Promising future developments of the complex pacemaker system models include the introduction of local calcium control, mitochondria function, and biochemical regulation of protein phosphorylation and cAMP production. Modern numerical and theoretical methods such as multi-parameter sensitivity analyses within extended populations of models and bifurcation analyses are also important for the definition of the most realistic parameters that describe a robust, yet simultaneously flexible operation of the coupled-clock pacemaker cell system. The systems approach to exploring cardiac pacemaker function will guide development of new therapies, such as biological pacemakers for treating insufficient cardiac pacemaker function that becomes especially prevalent with advancing age. PMID:24748434

SOCS1 and SOCS3 Are Targeted by Hepatitis C Virus Core/gC1qR Ligation To Inhibit T-Cell Function

PubMed Central

Yao, Zhi Qiang; Waggoner, Stephen N.; Cruise, Michael W.; Hall, Caroline; Xie, Xuefang; Oldach, David W.; Hahn, Young S.

2005-01-01

T cells play an important role in the control of hepatitis C virus (HCV) infection. We have previously demonstrated that the HCV core inhibits T-cell responses through interaction with gC1qR. We show here that core proteins from chronic and resolved HCV patients differ in sequence, gC1qR-binding ability, and T-cell inhibition. Specifically, chronic core isolates bind to gC1qR more efficiently and inhibit T-cell proliferation as well as gamma interferon (IFN-γ) production more profoundly than resolved core isolates. This inhibition is mediated by the disruption of STAT phosphorylation through the induction of SOCS molecules. Silencing either SOCS1 or SOCS3 by small interfering RNA dramatically augments the production of IFN-γ in T cells, thereby abrogating the inhibitory effect of core. Additionally, the ability of core proteins from patients with chronic infections to induce SOCS proteins and suppress STAT activation greatly exceeds that of core proteins from patients with resolved infections. These results suggest that the HCV core/gC1qR-induced T-cell dysfunction involves the induction of SOCS, a powerful inhibitor of cytokine signaling, which represents a novel mechanism by which a virus usurps the host machinery for persistence. PMID:16306613

Striking parallels between carotid body glomus cell and adrenal chromaffin cell development.

PubMed

Hockman, Dorit; Adameyko, Igor; Kaucka, Marketa; Barraud, Perrine; Otani, Tomoki; Hunt, Adam; Hartwig, Anna C; Sock, Elisabeth; Waithe, Dominic; Franck, Marina C M; Ernfors, Patrik; Ehinger, Sean; Howard, Marthe J; Brown, Naoko; Reese, Jeffrey; Baker, Clare V H

2018-05-25

Carotid body glomus cells mediate essential reflex responses to arterial blood hypoxia. They are dopaminergic and secrete growth factors that support dopaminergic neurons, making the carotid body a potential source of patient-specific cells for Parkinson's disease therapy. Like adrenal chromaffin cells, which are also hypoxia-sensitive, glomus cells are neural crest-derived and require the transcription factors Ascl1 and Phox2b; otherwise, their development is little understood at the molecular level. Here, analysis in chicken and mouse reveals further striking molecular parallels, though also some differences, between glomus and adrenal chromaffin cell development. Moreover, histology has long suggested that glomus cell precursors are 'émigrés' from neighbouring ganglia/nerves, while multipotent nerve-associated glial cells are now known to make a significant contribution to the adrenal chromaffin cell population in the mouse. We present conditional genetic lineage-tracing data from mice supporting the hypothesis that progenitors expressing the glial marker proteolipid protein 1, presumably located in adjacent ganglia/nerves, also contribute to glomus cells. Finally, we resolve a paradox for the 'émigré' hypothesis in the chicken - where the nearest ganglion to the carotid body is the nodose, in which the satellite glia are neural crest-derived, but the neurons are almost entirely placode-derived - by fate-mapping putative nodose neuronal 'émigrés' to the neural crest. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Disrupted regulatory T cell homeostasis in inflammatory bowel diseases.

PubMed

Pedros, Christophe; Duguet, Fanny; Saoudi, Abdelhadi; Chabod, Marianne

2016-01-21

In the gut, where billions of non-self-antigens from the food and the microbiota are present, the immune response must be tightly regulated to ensure both host protection against pathogenic microorganisms and the absence of immune-related pathologies. It has been well documented that regulatory T cells (Tregs) play a pivotal role in this context. Indeed, Tregs are able to prevent excessive inflammation, which can lead to the rupture of intestinal homeostasis observed in inflammatory bowel diseases (IBDs). Both the worldwide incidence and prevalence of such diseases have increased throughout the latter part of the 20(th) century. Therefore, it is crucial to understand how Tregs suppress the colitogenic immune cells to establish new treatments for patients suffering from IBDs. In this review, we will first summarize the results obtained in animal model studies that highlight the importance of Tregs in maintaining intestinal homeostasis and describe the specific suppressive mechanisms involved. Next, our current knowledge about Tregs contribution to human IBDs will be reviewed, as well as the current therapeutic perspective on using Tregs for clinical IBD treatment and the challenges that remain to be resolved to ensure both the safety and effectiveness of these therapies in targeting this critical immune-regulatory cell population.

Low cytomegalovirus-specific T-cell counts at reactivation are associated with progression to high-level viremia or disease in seropositive recipients of hematopoietic cell grafts from seropositive but not seronegative donors.

PubMed

Hoegh-Petersen, Mette; Roa, Lina; Liu, Yiping; Zhou, Feng; Ugarte-Torres, Alejandra; Louie, Polly; Fonseca, Kevin; Khan, Faisal; Russell, James A; Storek, Jan

2012-02-01

Identifying patients who spontaneously resolve cytomegalovirus (CMV) reactivation could spare these patients from the toxicity of antiviral drugs such as ganciclovir. The role of CMV-specific T cells in clearing CMV viremia in patients who do not receive ganciclovir has not been evaluated. We assessed this in patients with CMV viremia between 50 and 50 000 genome copies/mL, because our threshold for initiating ganciclovir is 50 000 copies/mL. We enumerated CMV-specific T cells in 39 CMV seropositive hematopoietic cell transplantation (HCT) recipients within 4 days of the first positive CMV polymerase chain reaction (PCR). CMV-specific T cells were defined as cells that upon stimulation with CMV lysate or pp65 overlapping peptides produced interferon (IFN)-γ, tumor necrosis factor (TNF)-α or interleukin (IL)-2, alone or in combination. Among Donor (D+), Recipient (R+) patients, unifunctional CMV-specific CD4 T-cells were higher in patients who spontaneously resolved CMV viremia (did not receive ganciclovir) versus those who progressed (received ganciclovir) (median 0.20 versus 0.02/μL lysate-stimulated cells, P < 0.05, and 0.26 versus 0.05/μL pp65 peptide-stimulated cells, P<0.05). Among D- R+ patients, there was no difference between patients with spontaneous resolution or progression; all subsets of CMV-specific T cells measured were barely detectable, in both patients with spontaneous resolution and those with progression. Among D+ R+ patients (but not D- R+ patients), high CMV-specific CD4 T-cell counts identify patients who can spontaneously resolve CMV reactivation. In D- R+ patients, immune mechanisms other than T cells may control the progression from reactivation to high-level viremia/disease.

Loss of Elongation-Like Factor 1 Spontaneously Induces Diverse, RNase H-Related Suppressor Mutations in Schizosaccharomyces pombe.

PubMed

Marayati, Bahjat F; Drayton, Alena L; Tucker, James F; Huckabee, Reid H; Anderson, Alicia M; Pease, James B; Zeyl, Clifford W; Zhang, Ke

2018-05-29

A healthy individual may carry a detrimental genetic trait that is masked by another genetic mutation. Such suppressive genetic interactions, in which a mutant allele either partially or completely restores the fitness defect of a particular mutant, tend to occur between genes that have a confined functional connection. Here we investigate a self-recovery phenotype in Schizosaccharomyces pombe , mediated by suppressive genetic interactions that can be amplified during cell culture. Cells without Elf1, an AAA+ family ATPase, have severe growth defects initially, but quickly recover growth rates near to those of wild-type strains by acquiring suppressor mutations. elf1Δ cells accumulate RNAs within the nucleus and display effects of genome instability such as sensitivity to DNA damage, increased incidence of lagging chromosomes, and mini-chromosome loss. Notably, the rate of phenotypic recovery was further enhanced in elf1Δ cells when RNase H activities were abolished and significantly reduced upon overexpression of RNase H1, suggesting that loss of Elf1-related genome instability can be resolved by RNase H activities, likely through eliminating the potentially mutagenic DNA-RNA hybrids caused by RNA nuclear accumulation. Using whole genome sequencing, we mapped a few consistent suppressors of elf1Δ including mutated Cue2, Rpl2702, and SPBPJ4664.02, suggesting previously unknown functional connections between Elf1 and these proteins. Our findings describe a mechanism by which cells bearing mutations that cause fitness defects and genome instability may accelerate the fitness recovery of their population through quickly acquiring suppressors. We propose that this mechanism may be universally applicable to all microorganisms in large-population cultures. Copyright © 2018, Genetics.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tayebjee, Murad J. Y.; Sanders, Samuel N.; Kumarasamy, Elango

Singlet fission, in which two triplet excitons are generated from a single absorbed photon, is a key third-generation solar cell concept. Conservation of angular momentum requires that singlet fission populates correlated multiexciton states, which can subsequently dissociate to generate free triplets. However, little is known about electronic and spin correlations in these systems since, due to its typically short lifetime, the multiexciton state is challenging to isolate and study. Here, we use bridged pentacene dimers, which undergo intramolecular singlet fission while isolated in solution and in solid matrices, as a unimolecular model system that can trap long-lived multiexciton states. Wemore » also combine transient absorption and time-resolved electron spin resonance spectroscopies to show that spin correlations in the multiexciton state persist for hundreds of nanoseconds. Furthermore, we confirm long-standing predictions that singlet fission produces triplet pair states of quintet character. Finally, we compare two different pentacene–bridge–pentacene chromophores, systematically tuning the coupling between the pentacenes to understand how differences in molecular structure affect the population and dissociation of multiexciton quintet states.« less

B cell signatures of BCWD-resistant and susceptible lines of rainbow trout: a shift towards more EBF-expressing progenitors and fewer mature B cells in resistant animals.

PubMed

Zwollo, Patty; Ray, Jocelyn C; Sestito, Michael; Kiernan, Elizabeth; Wiens, Gregory D; Kaattari, Steve; StJacques, Brittany; Epp, Lidia

2015-01-01

Bacterial cold water disease (BCWD) is a chronic disease of rainbow trout, and is caused by the Gram-negative bacterium Flavobacterium psychrophilum (Fp), a common aquaculture pathogen. The National Center for Cool and Cold Water Aquaculture has bred two genetic lines of rainbow trout: a line of Fp-resistant trout (ARS-Fp-R or R-line trout) and a line of susceptible trout (ARS-Fp-S, or S-line). Little is known about how phenotypic selection alters immune response parameters or how such changes relate to genetic disease resistance. Herein, we quantify interindividual variation in the distribution and abundance of B cell populations (B cell signatures) and examine differences between genetic lines of naive animals. There are limited trout-specific cell surface markers currently available to resolve B cell subpopulations and thus we developed an alternative approach based on detection of differentially expressed transcription factors and intracellular cytokines. B cell signatures were compared between R-line and S-line trout by flow cytometry using antibodies against transcription factors early B cell factor-1 (EBF1) and paired domain box protein Pax5, the pro-inflammatory cytokine IL-1β, and the immunoglobulin heavy chain mu. R-line trout had higher percentages of EBF(+) B myeloid/ progenitor and pre-B cells in PBL, anterior and posterior kidney tissues compared to S-line trout. The opposite pattern was detected in more mature B cell populations: R-line trout had lower percentages of both IgM(+) mature B cells and IgM-secreting cells in anterior kidney and PBL compared to S-line trout. In vitro LPS-activation studies of PBL and spleen cell cultures revealed no significant induction differences between R-line and S-line trout. Together, our findings suggest that selective resistance to BCWD may be associated with shifts in naive animal developmental lineage commitment that result in decreased B lymphopoiesis and increased myelopoiesis in BCWD resistant trout relative to susceptible trout. Copyright © 2014 Elsevier Ltd. All rights reserved.

Promoting Health by Addressing Basic Needs: Effect of Problem Resolution on Contacting Health Referrals.

PubMed

Thompson, Tess; Kreuter, Matthew W; Boyum, Sonia

2016-04-01

Members of vulnerable populations have heightened needs for health services. One advantage of integrating health risk assessment and referrals into social service assistance systems such as 2-1-1 is that such systems help callers resolve problems in other areas (e.g., housing). Callers to 2-1-1 in Missouri (N= 1,090) with at least one behavioral risk factor or cancer screening need were randomly assigned to one of three health referral interventions: verbal referrals only, verbal referrals + a tailored mailed reminder, or verbal referrals + telephone health navigator. After 1 month, we assessed whether the nonhealth problems that prompted the 2-1-1 call had been resolved. Logistic regression estimated effects of having the problem resolved on calling a health referral. Callers were predominantly female (85%) and had a high school education or less (61%); nearly half (47%) had incomes under $10,000. The most common service requests were for utility assistance (35%), home/family problems (23%), and rent/mortgage assistance (12%). At follow-up, 38% of callers reported that all problems prompting their 2-1-1 call had been resolved, and 24% reported calling a health referral. Resolving all problems prompting the 2-1-1 call was associated with a higher odds of contacting a health referral (odds ratio = 1.44, 95% confidence interval [1.02, 2.05]) compared to people whose problems were not resolved. Multifaceted interventions that help meet non-health-related needs and provide support in reaching health-related goals may promote health in vulnerable populations. © 2015 Society for Public Health Education.

Promoting Health by Addressing Basic Needs: Effect of Problem Resolution on Contacting Health Referrals

PubMed Central

Thompson, Tess; Kreuter, Matthew; Boyum, Sonia

2016-01-01

Members of vulnerable populations have heightened needs for health services. One advantage of integrating health risk assessment and referrals into social service assistance systems such as 2-1-1 is that such systems help callers resolve problems in other areas (e.g. housing). Callers to 2-1-1 in Missouri (N=1090) with at least one behavioral risk factor or cancer screening need were randomly assigned to one of three health referral interventions: verbal referrals only, verbal referrals + a tailored mailed reminder, or verbal referrals + telephone health navigator. After one month, we assessed whether the non-health problems that prompted the 2-1-1 call had been resolved. Logistic regression estimated effects of having the problem resolved on calling a health referral. Callers were predominantly female (85%) and had a high school education or less (61%); nearly half (47%) had incomes under $10,000. The most common service requests were for utility assistance (35%), home/family problems (23%), and rent/mortgage assistance (12%). At follow-up, 38% of callers reported that all problems prompting their 2-1-1 call had been resolved, and 24% reported calling a health referral. Resolving all problems prompting the 2-1-1 call was associated with a higher odds of contacting a health referral (OR = 1.44, 95% CI 1.02-2.05) compared to people whose problems were not resolved. Multifaceted interventions that help meet non-health-related needs and provide support in reaching health-related goals may promote health in vulnerable populations. PMID:26293458

Time-resolved polarization imaging by pump-probe (stimulated emission) fluorescence microscopy.

PubMed Central

Buehler, C; Dong, C Y; So, P T; French, T; Gratton, E

2000-01-01

We report the application of pump-probe fluorescence microscopy in time-resolved polarization imaging. We derived the equations governing the pump-probe stimulated emission process and characterized the pump and probe laser power levels for signal saturation. Our emphasis is to use this novel methodology to image polarization properties of fluorophores across entire cells. As a feasibility study, we imaged a 15-microm orange latex sphere and found that there is depolarization that is possibly due to energy transfer among fluorescent molecules inside the sphere. We also imaged a mouse fibroblast labeled with CellTracker Orange CMTMR (5-(and-6)-(((4-chloromethyl)benzoyl)amino)tetramethyl-rhodamine). We observed that Orange CMTMR complexed with gluthathione rotates fast, indicating the relatively low fluid-phase viscosity of the cytoplasmic microenvironment as seen by Orange CMTMR. The measured rotational correlation time ranged from approximately 30 to approximately 150 ps. This work demonstrates the effectiveness of stimulated emission measurements in acquiring high-resolution, time-resolved polarization information across the entire cell. PMID:10866979

The role of CD133 in normal human prostate stem cells and malignant cancer-initiating cells.

PubMed

Vander Griend, Donald J; Karthaus, Wouter L; Dalrymple, Susan; Meeker, Alan; DeMarzo, Angelo M; Isaacs, John T

2008-12-01

Resolving the specific cell of origin for prostate cancer is critical to define rational targets for therapeutic intervention and requires the isolation and characterization of both normal human prostate stem cells and prostate cancer-initiating cells (CIC). Single epithelial cells from fresh normal human prostate tissue and prostate epithelial cell (PrEC) cultures derived from them were evaluated for the presence of subpopulations expressing stem cell markers and exhibiting stem-like growth characteristics. When epithelial cell suspensions containing cells expressing the stem cell marker CD133+ are inoculated in vivo, regeneration of stratified human prostate glands requires inductive prostate stromal cells. PrEC cultures contain a small subpopulation of CD133+ cells, and fluorescence-activated cell sorting-purified CD133+ PrECs self-renew and regenerate cell populations expressing markers of transit-amplifying cells (DeltaNp63), intermediate cells (prostate stem cell antigen), and neuroendocrine cells (CD56). Using a series of CD133 monoclonal antibodies, attachment and growth of CD133+ PrECs requires surface expression of full-length glycosylated CD133 protein. Within a series of androgen receptor-positive (AR+) human prostate cancer cell lines, CD133+ cells are present at a low frequency, self-renew, express AR, generate phenotypically heterogeneous progeny negative for CD133, and possess an unlimited proliferative capacity, consistent with CD133+ cells being CICs. Unlike normal adult prostate stem cells, prostate CICs are AR+ and do not require functional CD133. This suggests that (a) AR-expressing prostate CICs are derived from a malignantly transformed intermediate cell that acquires "stem-like activity" and not from a malignantly transformed normal stem cell and (b) AR signaling pathways are a therapeutic target for prostate CICs.

Cartograms Facilitate Communication of Climate Change Risks and Responsibilities

NASA Astrophysics Data System (ADS)

Döll, Petra

2017-12-01

Communication of climate change (CC) risks is challenging, in particular if global-scale spatially resolved quantitative information is to be conveyed. Typically, visualization of CC risks, which arise from the combination of hazard, exposure and vulnerability, is confined to showing only the hazards in the form of global thematic maps. This paper explores the potential of contiguous value-by-area cartograms, that is, distorted density-equalizing maps, for improving communication of CC risks and the countries' differentiated responsibilities for CC. Two global-scale cartogram sets visualize, as an example, groundwater-related CC risks in 0.5° grid cells, another one the correlation of (cumulative) fossil-fuel carbon dioxide emissions with the countries' population and gross domestic product. Viewers of the latter set visually recognize the lack of global equity and that the countries' wealth has been built on harmful emissions. I recommend that CC risks are communicated by bivariate gridded cartograms showing the hazard in color and population, or a combination of population and a vulnerability indicator, by distortion of grid cells. Gridded cartograms are also appropriate for visualizing the availability of natural resources to humans. For communicating complex information, sets of cartograms should be carefully designed instead of presenting single cartograms. Inclusion of a conventionally distorted map enhances the viewers' capability to take up the information represented by distortion. Empirical studies about the capability of global cartograms to convey complex information and to trigger moral emotions should be conducted, with a special focus on risk communication.

THE EDINGER-WESTPHAL NUCLEUS: A HISTORICAL, STRUCTURAL AND FUNCTIONAL PERSPECTIVE ON A DICHOTOMOUS TERMINOLOGY

PubMed Central

Kozicz, Tamás; Bittencourt, Jackson C.; May, Paul J.; Reiner, Anton; Gamlin, Paul D. R.; Palkovits, Miklós; Horn, Anja K.E.; Toledo, Claudio A. B.; Ryabinin, Andrey E.

2013-01-01

The eponymous term nucleus of Edinger-Westphal (EW) has come to be used to describe two juxtaposed and somewhat intermingled cell groups of the midbrain that differ dramatically in their connectivity and neurochemistry. On one hand, the classically defined EW is the part of the oculomotor complex that is the source of the parasympathetic preganglionic motoneuron input to the ciliary ganglion (CG), through which it controls pupil constriction and lens accommodation. On the other hand, EW is applied to a population of centrally projecting neurons involved in sympathetic, consumptive and stress-related functions. This terminology problem arose because the name EW has historically been applied to the most prominent cell collection above or between the somatic oculomotor nuclei (III), an assumption based on the known location of the preganglionic motoneurons in monkeys. However, in many mammals, the nucleus designated as EW is not made up of cholinergic, preganglionic motoneurons supplying the CG, and instead contains neurons using peptides, such as urocortin 1, with diverse central projections. As a result, the literature has become increasingly confusing. To resolve this problem, we suggest that the term EW be supplemented with terminology based on connectivity. Specifically, we recommend that: 1. The cholinergic, preganglionic neurons supplying the CG be termed the Edinger-Westphal preganglionic (EWpg) population, and 2. The centrally projecting, peptidergic neurons be termed the Edinger-Westphal centrally projecting (EWcp) population. The history of this nomenclature problem and the rationale for our solutions are discussed in this review. PMID:21452224

Kinetic theory of age-structured stochastic birth-death processes

NASA Astrophysics Data System (ADS)

Greenman, Chris D.; Chou, Tom

2016-01-01

Classical age-structured mass-action models such as the McKendrick-von Foerster equation have been extensively studied but are unable to describe stochastic fluctuations or population-size-dependent birth and death rates. Stochastic theories that treat semi-Markov age-dependent processes using, e.g., the Bellman-Harris equation do not resolve a population's age structure and are unable to quantify population-size dependencies. Conversely, current theories that include size-dependent population dynamics (e.g., mathematical models that include carrying capacity such as the logistic equation) cannot be easily extended to take into account age-dependent birth and death rates. In this paper, we present a systematic derivation of a new, fully stochastic kinetic theory for interacting age-structured populations. By defining multiparticle probability density functions, we derive a hierarchy of kinetic equations for the stochastic evolution of an aging population undergoing birth and death. We show that the fully stochastic age-dependent birth-death process precludes factorization of the corresponding probability densities, which then must be solved by using a Bogoliubov--Born--Green--Kirkwood--Yvon-like hierarchy. Explicit solutions are derived in three limits: no birth, no death, and steady state. These are then compared with their corresponding mean-field results. Our results generalize both deterministic models and existing master equation approaches by providing an intuitive and efficient way to simultaneously model age- and population-dependent stochastic dynamics applicable to the study of demography, stem cell dynamics, and disease evolution.

Gynaecomastia--pathophysiology, diagnosis and treatment.

PubMed

Narula, Harmeet S; Carlson, Harold E

2014-11-01

Gynaecomastia (enlargement of the male breast tissue) is a common finding in the general population. Most cases of gynaecomastia are benign and of cosmetic, rather than clinical, importance. However, the condition might cause local pain and tenderness, could occasionally be the result of a serious underlying illness or a medication, or be inherited. Breast cancer in men is much less common than benign gynaecomastia, and the two conditions can usually be distinguished by a careful physical examination. Estrogens are known to stimulate the growth of breast tissue, whereas androgens inhibit it; most cases of gynaecomastia result from deficient androgen action or excessive estrogen action in the breast tissue. In some cases, such as pubertal gynaecomastia, the breast enlargement resolves spontaneously. In other situations, more active treatment might be required to correct an underlying condition (such as hyperthyroidism or a benign Leydig cell tumour of the testis) or medications that could cause breast enlargement (such as spironolactone) might need to be discontinued. For men with hypogonadism, administration of androgens might be helpful, as might antiestrogen therapy in men with endogenous overproduction of estrogens. Surgery to remove the enlarged breast tissue might be necessary when gynaecomastia does not resolve spontaneously or with medical therapy.

Microfluidics-based, time-resolved mechanical phenotyping of cells using high-speed imaging

NASA Astrophysics Data System (ADS)

Belotti, Yuri; Conneely, Michael; Huang, Tianjun; McKenna, Stephen; Nabi, Ghulam; McGloin, David

2017-07-01

We demonstrate a single channel hydrodynamic stretching microfluidic device that relies on high-speed imaging to allow repeated dynamic cell deformation measurements. Experiments on prostate cancer cells suggest richer data than current approaches.

In vivo fluorescence imaging of primate retinal ganglion cells and retinal pigment epithelial cells

NASA Astrophysics Data System (ADS)

Gray, Daniel C.; Merigan, William; Wolfing, Jessica I.; Gee, Bernard P.; Porter, Jason; Dubra, Alfredo; Twietmeyer, Ted H.; Ahamd, Kamran; Tumbar, Remy; Reinholz, Fred; Williams, David R.

2006-08-01

The ability to resolve single cells noninvasively in the living retina has important applications for the study of normal retina, diseased retina, and the efficacy of therapies for retinal disease. We describe a new instrument for high-resolution, in vivo imaging of the mammalian retina that combines the benefits of confocal detection, adaptive optics, multispectral, and fluorescence imaging. The instrument is capable of imaging single ganglion cells and their axons through retrograde transport in ganglion cells of fluorescent dyes injected into the monkey lateral geniculate nucleus (LGN). In addition, we demonstrate a method involving simultaneous imaging in two spectral bands that allows the integration of very weak signals across many frames despite inter-frame movement of the eye. With this method, we are also able to resolve the smallest retinal capillaries in fluorescein angiography and the mosaic of retinal pigment epithelium (RPE) cells with lipofuscin autofluorescence.

Detection of single photoluminescent diamond nanoparticles in cells and study of the internalization pathway.

PubMed

Faklaris, Orestis; Garrot, Damien; Joshi, Vandana; Druon, Frédéric; Boudou, Jean-Paul; Sauvage, Thierry; Georges, Patrick; Curmi, Patrick A; Treussart, François

2008-12-01

Diamond nanoparticles are promising photoluminescent probes for tracking intracellular processes, due to embedded, perfectly photostable color centers. In this work, the spontaneous internalization of such nanoparticles (diameter 25 nm) in HeLa cancer cells is investigated by confocal microscopy and time-resolved techniques. Nanoparticles are observed inside the cell cytoplasm at the single-particle and single-color-center level, assessed by time-correlation intensity measurements. Improvement of the nanoparticle signal-to-noise ratio inside the cell is achieved using a pulsed-excitation laser and time-resolved detection taking advantage of the long radiative lifetime of the color-center excited state as compared to cell autofluorescence. The internalization pathways are also investigated, with endosomal marking and colocalization analyses. The low colocalization ratio observed proves that nanodiamonds are not trapped in endosomes, a promising result in prospect of drug delivery by these nanoparticles. Low cytotoxicity of these nanoparticles in this cell line is also shown.

Resolving a genetic paradox throughout preimplantation genetic diagnosis for autosomal dominant severe congenital neutropenia.

PubMed

Malcov, Mira; Reches, Adi; Ben-Yosef, Dalit; Cohen, Tania; Amit, Ami; Dgany, Orly; Tamary, Hannah; Yaron, Yuval

2010-03-01

Severe congenital neutropenia is an inherited disease characterized by low peripheral blood neutrophils, amenable to bone marrow transplantation. Genetic analysis in the family here described detected a ELA2 splice-site mutation in the affected child and also in his asymptomatic father. The parents requested preimplantation genetic diagnosis (PGD), coupled with HLA matching, to obtain a suitable bone marrow donor for the affected child. A PGD protocol was developed, based on multiplex nested PCR for direct analysis of the ELA2 mutation, flanking polymorphic markers and HLA typing. The amplification efficiency of the mutation was > 90% in single leukocytes from the affected child but only 67% in the father. Analysis of single haploid sperm cells from the father demonstrated three different sperm-cell populations: (1) sperm cells harboring the ELA2 mutation on the 'affected' haplotype, (2) sperm cells without the ELA2 mutation on the 'normal' haplotype, and (3) sperm cells without the ELA2 mutation on the 'affected' haplotype. These data demonstrate that the ELA2 mutation in the father occurred de novo during his embryonic development, resulting in somatic as well as germ-line mosaicism. This conclusion was also taken into consideration when PGD was performed. Copyright (c) 2010 John Wiley & Sons, Ltd.

A new hybrid electrospray Fourier transform mass spectrometer: design and performance characteristics.

PubMed

O'connor, Peter B; Pittman, Jason L; Thomson, Bruce A; Budnik, Bogdan A; Cournoyer, Jason C; Jebanathirajah, Judith; Lin, Cheng; Moyer, Susanne; Zhao, Cheng

2006-01-01

A new hybrid electrospray quadrupole Fourier transform mass spectrometry (FTMS) instrument design is shown and characterized. This instrument involves coupling an electrospray source and mass-resolving quadrupole, ion accumulation, and collision cell linear ion trap system developed by MDS Sciex with a home-built ion guide and ion cyclotron resonance (ICR) cell. The iterative progression of this design is shown. The final design involves a set of hexapole ion guides to transfer the ions from the accumulation/collision trap through the magnetic field gradient and into the cell. These hexapole ion guides are separated by a thin gate valve and two conduction limits to maintain the required <10(-9) mbar vacuum for FTICR. Low-attomole detection limits for a pure peptide are shown, 220 000 resolving power in broadband mode and 820 000 resolving power in narrow-band mode are demonstrated, and mass accuracy in the <2 ppm range is routinely available provided the signal is abundant, cleanly resolved, and internally calibrated. This instrument design provides high experimental flexibility, allowing Q2 CAD, SORI-CAD, IRMPD, and ECD experiments with selected ion accumulation as well as experiments such as nozzle skimmer dissociation. Initial top-down mass spectrometry experiments on a protein is shown using ECD.

Measurement of wood/plant cell or composite material attributes with computer assisted tomography

DOEpatents

West, Darrell C.; Paulus, Michael J.; Tuskan, Gerald A.; Wimmer, Rupert

2004-06-08

A method for obtaining wood-cell attributes from cellulose containing samples includes the steps of radiating a cellulose containing sample with a beam of radiation. Radiation attenuation information is collected from radiation which passes through the sample. The source is rotated relative to the sample and the radiation and collecting steps repeated. A projected image of the sample is formed from the collected radiation attenuation information, the projected image including resolvable features of the cellulose containing sample. Cell wall thickness, cell diameter (length) and cell vacoule diameter can be determined. A system for obtaining physical measures from cellulose containing samples includes a radiation source, a radiation detector, and structure for rotating the source relative to said sample. The system forms an image of the sample from the radiation attenuation information, the image including resolvable features of the sample.

Phylogenetic Diversity and Membership Patterns of Fecal and Environmental Bacteroidales Populations

EPA Science Inventory

Members of the Bacteroidales order have recently been targets of microbial source tracking assays. While several studies have documented that some populations exhibit preferential host-distribution, given the vast diversity of this bacterial group, it is still necessary to resolv...

Intracellular pH Response to Weak Acid Stress in Individual Vegetative Bacillus subtilis Cells.

PubMed

Pandey, Rachna; Vischer, Norbert O E; Smelt, Jan P P M; van Beilen, Johan W A; Ter Beek, Alexander; De Vos, Winnok H; Brul, Stanley; Manders, Erik M M

2016-11-01

Intracellular pH (pH i ) critically affects bacterial cell physiology. Hence, a variety of food preservation strategies are aimed at perturbing pH i homeostasis. Unfortunately, accurate pH i quantification with existing methods is suboptimal, since measurements are averages across populations of cells, not taking into account interindividual heterogeneity. Yet, physiological heterogeneity in isogenic populations is well known to be responsible for differences in growth and division kinetics of cells in response to external stressors. To assess in this context the behavior of intracellular acidity, we have developed a robust method to quantify pH i at single-cell levels in Bacillus subtilis Bacilli spoil food, cause disease, and are well known for their ability to form highly stress-resistant spores. Using an improved version of the genetically encoded ratiometric pHluorin (IpHluorin), we have quantified pH i in individual B. subtilis cells, cultured at an external pH of 6.4, in the absence or presence of weak acid stresses. In the presence of 3 mM potassium sorbate, a decrease in pH i and an increase in the generation time of growing cells were observed. Similar effects were observed when cells were stressed with 25 mM potassium acetate. Time-resolved analysis of individual bacteria in growing colonies shows that after a transient pH decrease, long-term pH evolution is highly cell dependent. The heterogeneity at the single-cell level shows the existence of subpopulations that might be more resistant and contribute to population survival. Our approach contributes to an understanding of pH i regulation in individual bacteria and may help scrutinizing effects of existing and novel food preservation strategies. This study shows how the physiological response to commonly used weak organic acid food preservatives, such as sorbic and acetic acids, can be measured at the single-cell level. These data are key to coupling often-observed single-cell heterogeneous growth behavior upon the addition of weak organic acid food preservatives. Generally, these data are gathered in the form of plate counting of samples incubated with the acids. Here, we visualize the underlying heterogeneity in cellular pH homeostasis, opening up avenues for mechanistic analyses of the heterogeneity in the weak acid stress response. Thus, microbial risk assessment can become more robust, widening the scope of use of these well-known weak organic acid food preservatives. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Intermittent Fluorescence Oscillations in Lipid Droplets in a Live Normal and Lung Cancer Cell: Time-Resolved Confocal Microscopy.

PubMed

Chowdhury, Rajdeep; Amin, Md Asif; Bhattacharyya, Kankan

2015-08-27

Intermittent structural oscillation in the lipid droplets of live lung cells is monitored using time-resolved confocal microscopy. Significant differences are observed between the lung cancer cell (A549) and normal (nonmalignant) lung cell (WI38). For this study, the lipid droplets are covalently labeled with a fluorescent dye, coumarin maleimide (7-diethylamino-3-(4-maleimido-phenyl)-4-methylcoumarin, CPM). The number of lipid droplets in the cancer cell is found to be ∼20-fold higher than that in the normal (nonmalignant) cell. The fluctuation in the fluorescence intensity of the dye (CPM) is attributed to the red-ox processes and periodic formation/rupture of the S-CPM bond. The amount of reactive oxygen species (ROS) is much higher in a cancer cell. This is manifested in faster oscillations (0.9 ± 0.3 s) in cancer cells compared to that in the normal cells (2.8 ± 0.7 s). Solvation dynamics in the lipid droplets of cancer cells is slower compared to that in the normal cell.

Multiple host defense defects in failure of C57BL/6 ep/ep (pale ear) mice to resolve visceral Leishmania donovani infection.

PubMed Central

Murray, H W; Hariprashad, J; McDermott, D F; Stoeckle, M Y

1996-01-01

Euthymic C57BL/L ep/ep (pale ear [PE]) mice halt the visceral replication of intracellular Leishmania donovani but fail to properly resolve infection. A previous study identified an isolated defect in tissue granuloma formation in these mice; CD4+ and CD8+ cell number, gamma interferon (IFN-gamma) production, and macrophage antimicrobial activity in vitro were all intact. New in vivo results reported here suggest a considerably more complex immune defect, with evidence indicating (i) enhanced control over L. donovani after transfer of normal C57BL/6 spleen cells, (ii) a partially suppressive Th2 cell-associated response mediated by interleukin-4 (IL-4) but not reversed by CD4+ cell depletion, (iii) absent responses to endogenous Th1 cell lymphokines (IFN-gamma and IL-2) but preserved responsiveness to endogenous tumor necrosis factor alpha, (iv) absent responses to exogenous treatment with recognized antileishmanial cytokines (IFN-gamma, IL-2, IL-12, and granulocyte-macrophage colony-stimulating factor [GM-CSF]) not corrected by transfer of C57BL/6 spleen cells, and (v) a deficient response to antimony chemotherapy. Defective hepatic granuloma formation was not corrected by transfer of C57BL/6 spleen cells or by anti-IL-4 administration. While treatment with IL-2 and GM-CSF modified the tissue reaction and induced selected effector cells to encase tissue macrophages, no antileishmanial activity resulted. Together, these observations suggest that the failure of PE mice to resolve visceral L. donovani infection likely represents expression of multiple suboptimal immune responses and/or partial defects, probably involving a combination of T-cell dysfunction, a Th2 cell response, and target cell (macrophage) hyporesponsiveness. PMID:8557335

Genome-Wide Studies Reveal that H3K4me3 Modification in Bivalent Genes Is Dynamically Regulated during the Pluripotent Cell Cycle and Stabilized upon Differentiation.

PubMed

Grandy, Rodrigo A; Whitfield, Troy W; Wu, Hai; Fitzgerald, Mark P; VanOudenhove, Jennifer J; Zaidi, Sayyed K; Montecino, Martin A; Lian, Jane B; van Wijnen, André J; Stein, Janet L; Stein, Gary S

2016-02-15

Stem cell phenotypes are reflected by posttranslational histone modifications, and this chromatin-related memory must be mitotically inherited to maintain cell identity through proliferative expansion. In human embryonic stem cells (hESCs), bivalent genes with both activating (H3K4me3) and repressive (H3K27me3) histone modifications are essential to sustain pluripotency. Yet, the molecular mechanisms by which this epigenetic landscape is transferred to progeny cells remain to be established. By mapping genomic enrichment of H3K4me3/H3K27me3 in pure populations of hESCs in G2, mitotic, and G1 phases of the cell cycle, we found striking variations in the levels of H3K4me3 through the G2-M-G1 transition. Analysis of a representative set of bivalent genes revealed that chromatin modifiers involved in H3K4 methylation/demethylation are recruited to bivalent gene promoters in a cell cycle-dependent fashion. Interestingly, bivalent genes enriched with H3K4me3 exclusively during mitosis undergo the strongest upregulation after induction of differentiation. Furthermore, the histone modification signature of genes that remain bivalent in differentiated cells resolves into a cell cycle-independent pattern after lineage commitment. These results establish a new dimension of chromatin regulation important in the maintenance of pluripotency. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Genome-Wide Studies Reveal that H3K4me3 Modification in Bivalent Genes Is Dynamically Regulated during the Pluripotent Cell Cycle and Stabilized upon Differentiation

PubMed Central

Grandy, Rodrigo A.; Whitfield, Troy W.; Wu, Hai; Fitzgerald, Mark P.; VanOudenhove, Jennifer J.; Zaidi, Sayyed K.; Montecino, Martin A.; Lian, Jane B.; van Wijnen, André J.; Stein, Janet L.

2015-01-01

Stem cell phenotypes are reflected by posttranslational histone modifications, and this chromatin-related memory must be mitotically inherited to maintain cell identity through proliferative expansion. In human embryonic stem cells (hESCs), bivalent genes with both activating (H3K4me3) and repressive (H3K27me3) histone modifications are essential to sustain pluripotency. Yet, the molecular mechanisms by which this epigenetic landscape is transferred to progeny cells remain to be established. By mapping genomic enrichment of H3K4me3/H3K27me3 in pure populations of hESCs in G2, mitotic, and G1 phases of the cell cycle, we found striking variations in the levels of H3K4me3 through the G2-M-G1 transition. Analysis of a representative set of bivalent genes revealed that chromatin modifiers involved in H3K4 methylation/demethylation are recruited to bivalent gene promoters in a cell cycle-dependent fashion. Interestingly, bivalent genes enriched with H3K4me3 exclusively during mitosis undergo the strongest upregulation after induction of differentiation. Furthermore, the histone modification signature of genes that remain bivalent in differentiated cells resolves into a cell cycle-independent pattern after lineage commitment. These results establish a new dimension of chromatin regulation important in the maintenance of pluripotency. PMID:26644406

Analysis of Faint Glints from Stabilized GEO Satellites

DTIC Science & Technology

2013-09-01

this regard temporal photometry (i.e., measurements of whole-object brightness as a function of time ) can be very valuable. For instance, GEO satellite ...INTRODUCTION Ground-based optical and radar sites routinely acquire resolved images of satellites , yielding a great deal of knowledge about orbiting...spacecraft. However, the important population of GEO satellites often cannot be resolved , and must be characterized using methods other than imagery. In

Cell cycle stage-specific differential expression of topoisomerase I in tobacco BY-2 cells and its ectopic overexpression and knockdown unravels its crucial role in plant morphogenesis and development.

PubMed

Singh, Badri Nath; Mudgil, Yashwanti; John, Riffat; Achary, V Mohan Murali; Tripathy, Manas Kumar; Sopory, Sudhir K; Reddy, Malireddy K; Kaul, Tanushri

2015-11-01

DNA topoisomerases catalyze the inter-conversion of different topological forms of DNA. Cell cycle coupled differential accumulation of topoisomerase I (Topo I) revealed biphasic expression maximum at S-phase and M/G1-phase of cultured synchronized tobacco BY-2 cells. This suggested its active role in resolving topological constrains during DNA replication (S-phase) and chromosome decondensation (M/G1 phase). Immuno-localization revealed high concentrations of Topo I in nucleolus. Propidium iodide staining and Br-UTP incorporation patterns revealed direct correlation between immunofluorescence intensity and rRNA transcription activity within nucleolus. Immuno-stained chromosomes during metaphase and anaphase suggested possible role of Topo I in resolving topological constrains during mitotic chromosome condensation. Inhibitor studies showed that in comparison to Topo I, Topo II was essential in resolving topological constrains during chromosome condensation. Probably, Topo II substituted Topo I functioning to certain extent during chromosome condensation, but not vice-versa. Transgenic Topo I tobacco lines revealed morphological abnormalities and highlighted its crucial role in plant morphogenesis and development. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Quantitative analyses of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy.

PubMed

Schmid, Volker J; Cremer, Marion; Cremer, Thomas

2017-07-01

Recent advancements of super-resolved fluorescence microscopy have revolutionized microscopic studies of cells, including the exceedingly complex structural organization of cell nuclei in space and time. In this paper we describe and discuss tools for (semi-) automated, quantitative 3D analyses of the spatial nuclear organization. These tools allow the quantitative assessment of highly resolved different chromatin compaction levels in individual cell nuclei, which reflect functionally different regions or sub-compartments of the 3D nuclear landscape, and measurements of absolute distances between sites of different chromatin compaction. In addition, these tools allow 3D mapping of specific DNA/RNA sequences and nuclear proteins relative to the 3D chromatin compaction maps and comparisons of multiple cell nuclei. The tools are available in the free and open source R packages nucim and bioimagetools. We discuss the use of masks for the segmentation of nuclei and the use of DNA stains, such as DAPI, as a proxy for local differences in chromatin compaction. We further discuss the limitations of 3D maps of the nuclear landscape as well as problems of the biological interpretation of such data. Copyright © 2017 Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rameau, J. D.; Freutel, S.; Kemper, A. F.

We report that in complex materials various interactions have important roles in determining electronic properties. Angle-resolved photoelectron spectroscopy (ARPES) is used to study these processes by resolving the complex single-particle self-energy and quantifying how quantum interactions modify bare electronic states. However, ambiguities in the measurement of the real part of the self-energy and an intrinsic inability to disentangle various contributions to the imaginary part of the self-energy can leave the implications of such measurements open to debate. Here we employ a combined theoretical and experimental treatment of femtosecond time-resolved ARPES (tr-ARPES) show how population dynamics measured using tr-ARPES can bemore » used to separate electron–boson interactions from electron–electron interactions. In conclusion, we demonstrate a quantitative analysis of a well-defined electron–boson interaction in the unoccupied spectrum of the cuprate Bi 2Sr 2CaCu 2O 8+x characterized by an excited population decay time that maps directly to a discrete component of the equilibrium self-energy not readily isolated by static ARPES experiments.« less

Consistency between the luminosity function of resolved millisecond pulsars and the galactic center excess

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ploeg, Harrison; Gordon, Chris; Crocker, Roland

Fermi Large Area Telescope data reveal an excess of GeV gamma rays from the direction of the Galactic Center and bulge. Several explanations have been proposed for this excess including an unresolved population of millisecond pulsars (MSPs) and self-annihilating dark matter. It has been claimed that a key discriminant for or against the MSP explanation can be extracted from the properties of the luminosity function describing this source population. Specifically, is the luminosity function of the putative MSPs in the Galactic Center consistent with that characterizing the resolved MSPs in the Galactic disk? To investigate this we have used amore » Bayesian Markov Chain Monte Carlo to evaluate the posterior distribution of the parameters of the MSP luminosity function describing both resolved MSPs and the Galactic Center excess. At variance with some other claims, our analysis reveals that, within current uncertainties, both data sets can be well fit with the same luminosity function.« less

Time-resolved x-ray absorption spectroscopy: Watching atoms dance

NASA Astrophysics Data System (ADS)

Milne, Chris J.; Pham, Van-Thai; Gawelda, Wojciech; van der Veen, Renske M.; El Nahhas, Amal; Johnson, Steven L.; Beaud, Paul; Ingold, Gerhard; Lima, Frederico; Vithanage, Dimali A.; Benfatto, Maurizio; Grolimund, Daniel; Borca, Camelia; Kaiser, Maik; Hauser, Andreas; Abela, Rafael; Bressler, Christian; Chergui, Majed

2009-11-01

The introduction of pump-probe techniques to the field of x-ray absorption spectroscopy (XAS) has allowed the monitoring of both structural and electronic dynamics of disordered systems in the condensed phase with unprecedented accuracy, both in time and in space. We present results on the electronically excited high-spin state structure of an Fe(II) molecular species, [FeII(bpy)3]2+, in aqueous solution, resolving the Fe-N bond distance elongation as 0.2 Å. In addition an analysis technique using the reduced χ2 goodness of fit between FEFF EXAFS simulations and the experimental transient absorption signal in energy space has been successfully tested as a function of excited state population and chemical shift, demonstrating its applicability in situations where the fractional excited state population cannot be determined through other measurements. Finally by using a novel ultrafast hard x-ray 'slicing' source the question of how the molecule relaxes after optical excitation has been successfully resolved using femtosecond XANES.

Selecting tandem partners for silicon solar cells [Selecting tandem partners for silicon solar cells using spectral efficiency

DOE PAGES

Yu, Zhengshan; Leilaeioun, Mehdi; Holman, Zachary

2016-09-26

Combining silicon and other materials in tandem solar cells is one approach to enhancing the overall power conversion efficiency of the cells. Here, we argue that top cell partners for silicon tandem solar cells should be selected on the basis of their spectral efficiency — their efficiency resolved by wavelength.

Selecting tandem partners for silicon solar cells [Selecting tandem partners for silicon solar cells using spectral efficiency

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Zhengshan; Leilaeioun, Mehdi; Holman, Zachary

Combining silicon and other materials in tandem solar cells is one approach to enhancing the overall power conversion efficiency of the cells. Here, we argue that top cell partners for silicon tandem solar cells should be selected on the basis of their spectral efficiency — their efficiency resolved by wavelength.

Time-resolved fluorescence monitoring of cholesterol in peripheral blood mononuclear cells

NASA Astrophysics Data System (ADS)

Martinakova, Z.; Horilova, J.; Lajdova, I.; Marcek Chorvatova, A.

2014-12-01

Precise evaluation of intracellular cholesterol distribution is crucial for improving diagnostics of diseased states associated with cholesterol alteration. Time-resolved fluorescence techniques are tested for non-invasive investigation of cholesterol in living cells. Fluorescent probe NBD attached to cholesterol was employed to evaluate cholesterol distribution in peripheral blood mononuclear cells (PBMC) isolated from the human blood. Fluorescence Lifetime Imaging Microscopy (FLIM) was successfully applied to simultaneously monitor the spatial distribution and the timeresolved characteristics of the NBD-cholesterol fluorescence in PBMC. Gathered data are the first step in the development of a new perspective non-invasive diagnostic method for evaluation of cholesterol modifications in diseases associated with disorders of lipid metabolism.

A Resolution to the Blue Whiting (Micromesistius poutassou) Population Paradox?

PubMed Central

Pointin, Fabien; Payne, Mark R.

2014-01-01

We provide the strongest evidence to date supporting the existence of two independent blue whiting (Micromesistius poutassou (Risso, 1827)) populations in the North Atlantic. In spite of extensive data collected in conjunction with the fishery, the population structure of blue whiting is poorly understood. On one hand, genetic, morphometric, otolith and drift modelling studies point towards the existence of two populations, but, on the other hand, observations of adult distributions point towards a single population. A paradox therefore arises in attempting to reconcile these two sets of information. Here we analyse 1100 observations of blue whiting larvae from the Continuous Plankton Recorder (CPR) from 1948–2005 using modern statistical techniques. We show a clear spatial separation between a northern spawning area, in the Rockall Trough, and a southern one, off the Porcupine Seabight. We further show a difference in the timing of spawning between these sites of at least a month, and meaningful differences in interannual variability. The results therefore support the two-population hypothesis. Furthermore, we resolve the paradox by showing that the acoustic observations cited in support of the single-population model are not capable of resolving both populations, as they occur too late in the year and do not extend sufficiently far south to cover the southern population: the confusion is the result of a simple observational artefact. We conclude that blue whiting in the North Atlantic comprises two populations. PMID:25184302

Regulation of pulmonary inflammation by mesenchymal cells.

PubMed

Alkhouri, Hatem; Poppinga, Wilfred Jelco; Tania, Navessa Padma; Ammit, Alaina; Schuliga, Michael

2014-12-01

Pulmonary inflammation and tissue remodelling are common elements of chronic respiratory diseases such as asthma, chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF), and pulmonary hypertension (PH). In disease, pulmonary mesenchymal cells not only contribute to tissue remodelling, but also have an important role in pulmonary inflammation. This review will describe the immunomodulatory functions of pulmonary mesenchymal cells, such as airway smooth muscle (ASM) cells and lung fibroblasts, in chronic respiratory disease. An important theme of the review is that pulmonary mesenchymal cells not only respond to inflammatory mediators, but also produce their own mediators, whether pro-inflammatory or pro-resolving, which influence the quantity and quality of the lung immune response. The notion that defective pro-inflammatory or pro-resolving signalling in these cells potentially contributes to disease progression is also discussed. Finally, the concept of specifically targeting pulmonary mesenchymal cell immunomodulatory function to improve therapeutic control of chronic respiratory disease is considered. Copyright © 2014 Elsevier Ltd. All rights reserved.

Mechanical Modulation of Nascent Stem Cell Lineage Commitment in Tissue Engineering Scaffolds

PubMed Central

Song, Min Jae; Dean, David; Tate, Melissa L. Knothe

2013-01-01

Taking inspiration from tissue morphogenesis in utero, this study tests the concept of using tissue engineering scaffolds as delivery devices to modulate emergent structure-function relationships at early stages of tissue genesis. We report on the use of a combined computational fluid dynamics (CFD) modeling, advanced manufacturing methods, and experimental fluid mechanics (micro-piv and strain mapping) for the prospective design of tissue engineering scaffold geometries that deliver spatially resolved mechanical cues to cells seeded within. When subjected to a constant magnitude global flow regime, the local scaffold geometry dictates the magnitudes of mechanical stresses and strains experienced by a given cell, and in a spatially resolved fashion, similar to patterning during morphogenesis. In addition, early markers of mesenchymal stem cell lineage commitment relate significantly to the local mechanical environment of the cell. Finally, by plotting the range of stress-strain states for all data corresponding to nascent cell lineage commitment (95% CI), we begin to “map the mechanome”, defining stress-strain states most conducive to targeted cell fates. In sum, we provide a library of reference mechanical cues that can be delivered to cells seeded on tissue engineering scaffolds to guide target tissue phenotypes in a temporally and spatially resolved manner. Knowledge of these effects allows for prospective scaffold design optimization using virtual models prior to prototyping and clinical implementation. Finally, this approach enables the development of next generation scaffolds cum delivery devices for genesis of complex tissues with heterogenous properties, e.g., organs, joints or interface tissues such as growth plates. PMID:23660249

Mechanical modulation of nascent stem cell lineage commitment in tissue engineering scaffolds.

PubMed

Song, Min Jae; Dean, David; Knothe Tate, Melissa L

2013-07-01

Taking inspiration from tissue morphogenesis in utero, this study tests the concept of using tissue engineering scaffolds as delivery devices to modulate emergent structure-function relationships at early stages of tissue genesis. We report on the use of a combined computational fluid dynamics (CFD) modeling, advanced manufacturing methods, and experimental fluid mechanics (micro-piv and strain mapping) for the prospective design of tissue engineering scaffold geometries that deliver spatially resolved mechanical cues to stem cells seeded within. When subjected to a constant magnitude global flow regime, the local scaffold geometry dictates the magnitudes of mechanical stresses and strains experienced by a given cell, and in a spatially resolved fashion, similar to patterning during morphogenesis. In addition, early markers of mesenchymal stem cell lineage commitment relate significantly to the local mechanical environment of the cell. Finally, by plotting the range of stress-strain states for all data corresponding to nascent cell lineage commitment (95% CI), we begin to "map the mechanome", defining stress-strain states most conducive to targeted cell fates. In sum, we provide a library of reference mechanical cues that can be delivered to cells seeded on tissue engineering scaffolds to guide target tissue phenotypes in a temporally and spatially resolved manner. Knowledge of these effects allows for prospective scaffold design optimization using virtual models prior to prototyping and clinical implementation. Finally, this approach enables the development of next generation scaffolds cum delivery devices for genesis of complex tissues with heterogenous properties, e.g., organs, joints or interface tissues such as growth plates. Copyright © 2013 Elsevier Ltd. All rights reserved.

Time-resolved rhodopsin activation currents in a unicellular expression system.

PubMed Central

Sullivan, J M; Shukla, P

1999-01-01

The early receptor current (ERC) is the charge redistribution occurring in plasma membrane rhodopsin during light activation of photoreceptors. Both the molecular mechanism of the ERC and its relationship to rhodopsin conformational activation are unknown. To investigate whether the ERC could be a time-resolved assay of rhodopsin structure-function relationships, the distinct sensitivity of modern electrophysiological tools was employed to test for flash-activated ERC signals in cells stably expressing normal human rod opsin after regeneration with 11-cis-retinal. ERCs are similar in waveform and kinetics to those found in photoreceptors. The action spectrum of the major R(2) charge motion is consistent with a rhodopsin photopigment. The R(1) phase is not kinetically resolvable and the R(2) phase, which overlaps metarhodopsin-II formation, has a rapid risetime and complex multiexponential decay. These experiments demonstrate, for the first time, kinetically resolved electrical state transitions during activation of expressed visual pigment in a unicellular environment (single or fused giant cells) containing only 6 x 10(6)-8 x 10(7) molecules of rhodopsin. This method improves measurement sensitivity 7 to 8 orders of magnitude compared to other time-resolved techniques applied to rhodopsin to study the role particular amino acids play in conformational activation and the forces that govern those transitions. PMID:10465746

Altered phenotype and function of NK cells infiltrating human papillomavirus (HPV)-associated genital warts during HIV infection.

PubMed

Bere, Alfred; Tayib, Shahila; Kriek, Jean-Mari; Masson, Lindi; Jaumdally, Shameem Z; Barnabas, Shaun L; Carr, William H; Allan, Bruce; Williamson, Anna-Lise; Denny, Lynette; Passmore, Jo-Ann S

2014-02-01

HIV-infected individuals experience more persistent HPV infections and are less likely to resolve genital warts. This study compared phenotype and functions of NK and T cells from genital warts and blood from 67 women. We compared in vitro functional responses of NK and T cells by multiparametric flow cytometry. HIV+ women had significantly lower frequencies of CD4 T cells in warts (p = 0.001) and blood (p = 0.001). While the distribution of NK cell subsets was similar, HIV+ women tended to have lower frequencies of CD56(Dim) NK cells in both blood (p = 0.0001) and warts (p = 0.006) than HIV- women. Wart NK cells from HIV+ women expressed significantly lower CD107a and produced IFN-γ. HAART status was not associated with differences in NK cell functionality. We conclude that wart NK cells from HIV+ women have defects in their ability to degranulate and/or secrete IFN-γ, which may provide insights into why HIV+ women fail to spontaneously resolve genital warts. Copyright © 2013 Elsevier Inc. All rights reserved.

Exosomes are released by bystander cells exposed to radiation-induced biophoton signals: Reconciling the mechanisms mediating the bystander effect

PubMed Central

Fernandez-Palomo, Cristian; McNeill, Fiona E.; Seymour, Colin B.; Rainbow, Andrew J.; Mothersill, Carmel E.

2017-01-01

Objective The objective of our study was to explore a possible molecular mechanism by which ultraviolet (UV) biophotons could elicit bystander responses in reporter cells and resolve the problem of seemingly mutually exclusive mechanisms of a physical UV signal & a soluble factor-mediated bystander signal. Methods The human colon carcinoma cell line, HCT116 p53 +/+, was directly irradiated with 0.5 Gy tritium beta particles to induce ultraviolet biophoton emission. Bystander cells were not directly irradiated but were exposed to the emitted UV biophotons. Medium was subsequently harvested from UV-exposed bystander cells. The exosomes extracted from this medium were incubated with reporter cell populations. These reporter cells were then assayed for clonogenic survival and mitochondrial membrane potential with and without prior treatment of the exosomes with RNase. Results Clonogenic cell survival was significantly reduced in reporter cells incubated with exosomes extracted from cells exposed to secondarily-emitted UV. These exosomes also induced significant mitochondrial membrane depolarization in receiving reporter cells. Conversely, exosomes extracted from non-UV-exposed cells did not produce bystander effects in reporter cells. The treatment of exosomes with RNase prior to their incubation with reporter cells effectively abolished bystander effects in reporter cells and this suggests a role for RNA in mediating the bystander response elicited by UV biophotons and their produced exosomes. Conclusion This study supports a role for exosomes released from UV biophoton-exposed bystander cells in eliciting bystander responses and also indicates a reconciliation between the UV-mediated bystander effect and the bystander effect which has been suggested in the literature to be mediated by soluble factors. PMID:28278290

The interaction of gamma delta T cells with activated macrophages is a property of the V gamma 1 subset.

PubMed

Dalton, Jane E; Pearson, Jayne; Scott, Phillip; Carding, Simon R

2003-12-15

Immunoregulation is an emerging paradigm of gammadelta T cell function. The mechanisms by which gammadelta T cells mediate this function, however, are not clear. Studies have identified a direct role for gammadelta T cells in resolving the host immune response to infection, by eliminating populations of activated macrophages. The aim of this study was to identify macrophage-reactive gammadelta T cells and establish the requirements/outcomes of macrophage-gammadelta T cell interactions during the immune response to the intracellular bacterium, Listeria monocytogenes (Lm). Using a macrophage-T cell coculture system in which peritoneal macrophages from naive or Lm-infected TCRdelta(-/-) mice were incubated with splenocytes from naive and Lm-infected alphabeta/gammadelta T cell-deficient and wild-type mice, the ability to bind macrophages was shown to be restricted to gammadelta T cells and the GV5S1 (Vgamma1) subset of gammadelta T cells. Macrophage adherence resulted in a 4- to 10-fold enrichment of Vgamma1(+) T cells. Enrichment of Vgamma1 T cells was dependent upon the activation status of macrophages, but independent of the activation status of gammadelta T cells. Vgamma1 T cells were cytotoxic for activated macrophages with both the binding to and killing of macrophages being TCR dependent because anti-TCRgammadelta Abs inhibited both Vgamma1 binding and killing activities. These studies establish the identity of macrophage cytotoxic gammadelta T cells, the conditions under which this interaction occurs, and the outcome of this interaction. These findings are concordant with the involvement of Vgamma1 T cells in macrophage homeostasis during the resolution of pathogen-mediated immune responses.

Exosomes are released by bystander cells exposed to radiation-induced biophoton signals: Reconciling the mechanisms mediating the bystander effect.

PubMed

Le, Michelle; Fernandez-Palomo, Cristian; McNeill, Fiona E; Seymour, Colin B; Rainbow, Andrew J; Mothersill, Carmel E

2017-01-01

The objective of our study was to explore a possible molecular mechanism by which ultraviolet (UV) biophotons could elicit bystander responses in reporter cells and resolve the problem of seemingly mutually exclusive mechanisms of a physical UV signal & a soluble factor-mediated bystander signal. The human colon carcinoma cell line, HCT116 p53 +/+, was directly irradiated with 0.5 Gy tritium beta particles to induce ultraviolet biophoton emission. Bystander cells were not directly irradiated but were exposed to the emitted UV biophotons. Medium was subsequently harvested from UV-exposed bystander cells. The exosomes extracted from this medium were incubated with reporter cell populations. These reporter cells were then assayed for clonogenic survival and mitochondrial membrane potential with and without prior treatment of the exosomes with RNase. Clonogenic cell survival was significantly reduced in reporter cells incubated with exosomes extracted from cells exposed to secondarily-emitted UV. These exosomes also induced significant mitochondrial membrane depolarization in receiving reporter cells. Conversely, exosomes extracted from non-UV-exposed cells did not produce bystander effects in reporter cells. The treatment of exosomes with RNase prior to their incubation with reporter cells effectively abolished bystander effects in reporter cells and this suggests a role for RNA in mediating the bystander response elicited by UV biophotons and their produced exosomes. This study supports a role for exosomes released from UV biophoton-exposed bystander cells in eliciting bystander responses and also indicates a reconciliation between the UV-mediated bystander effect and the bystander effect which has been suggested in the literature to be mediated by soluble factors.

Dynamics of the time-resolved stimulated Raman scattering spectrum in presence of transient vibronic inversion of population on the example of optically excited trans-β-apo-8{sup ′}-carotenal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kardaś, T. M., E-mail: kardas@chem.uw.edu.pl; Ratajska-Gadomska, B.; Gadomski, W.

2014-05-28

We have studied the effect of transient vibrational inversion of population in trans-β-apo-8{sup ′}-carotenal on the time-resolved femtosecond stimulated Raman scattering (TR-FSRS) signal. The experimental data are interpreted by applying a quantum mechanical approach, using the formalism of projection operators for constructing the theoretical model of TR-FSRS. Within this theoretical frame we explain the presence of transient Raman losses on the Stokes side of the TR-FSRS spectrum as the effect of vibrational inversion of population. In view of the obtained experimental and theoretical results, we conclude that the excited S{sub 2} electronic level of trans-β-apo-8{sup ′}-carotenal relaxes towards the S{submore » 0} ground state through a set of four vibrational sublevels of S{sub 1} state.« less

Core genome conservation of Staphylococcus haemolyticus limits sequence based population structure analysis.

PubMed

Cavanagh, Jorunn Pauline; Klingenberg, Claus; Hanssen, Anne-Merethe; Fredheim, Elizabeth Aarag; Francois, Patrice; Schrenzel, Jacques; Flægstad, Trond; Sollid, Johanna Ericson

2012-06-01

The notoriously multi-resistant Staphylococcus haemolyticus is an emerging pathogen causing serious infections in immunocompromised patients. Defining the population structure is important to detect outbreaks and spread of antimicrobial resistant clones. Currently, the standard typing technique is pulsed-field gel electrophoresis (PFGE). In this study we describe novel molecular typing schemes for S. haemolyticus using multi locus sequence typing (MLST) and multi locus variable number of tandem repeats (VNTR) analysis. Seven housekeeping genes (MLST) and five VNTR loci (MLVF) were selected for the novel typing schemes. A panel of 45 human and veterinary S. haemolyticus isolates was investigated. The collection had diverse PFGE patterns (38 PFGE types) and was sampled over a 20 year-period from eight countries. MLST resolved 17 sequence types (Simpsons index of diversity [SID]=0.877) and MLVF resolved 14 repeat types (SID=0.831). We found a low sequence diversity. Phylogenetic analysis clustered the isolates in three (MLST) and one (MLVF) clonal complexes, respectively. Taken together, neither the MLST nor the MLVF scheme was suitable to resolve the population structure of this S. haemolyticus collection. Future MLVF and MLST schemes will benefit from addition of more variable core genome sequences identified by comparing different fully sequenced S. haemolyticus genomes. Copyright © 2012 Elsevier B.V. All rights reserved.

Heterogeneous distribution of exocytotic microdomains in adrenal chromaffin cells resolved by high-density diamond ultra-microelectrode arrays.

PubMed

Gosso, Sara; Turturici, Marco; Franchino, Claudio; Colombo, Elisabetta; Pasquarelli, Alberto; Carbone, Emilio; Carabelli, Valentina

2014-08-01

Here we describe the ability of a high-density diamond microelectrode array targeted to resolve multi-site detection of fast exocytotic events from single cells. The array consists of nine boron-doped nanocrystalline diamond ultra-microelectrodes (9-Ch NCD-UMEA) radially distributed within a circular area of the dimensions of a single cell. The device can be operated in voltammetric or chronoamperometric configuration. Sensitivity to catecholamines, tested by dose-response calibrations, set the lowest detectable concentration of adrenaline to ∼5 μm. Catecholamine release from bovine or mouse chromaffin cells could be triggered by electrical stimulation or external KCl-enriched solutions. Spikes detected from the cell apex using carbon fibre microelectrodes showed an excellent correspondence with events measured at the bottom of the cell by the 9-Ch NCD-UMEA, confirming the ability of the array to resolve single quantal secretory events. Subcellular localization of exocytosis was provided by assigning each quantal event to one of the nine channels based on its location. The resulting mapping highlights the heterogeneous distribution of secretory activity in cell microdomains of 12-27 μm2. In bovine chromaffin cells, secretion was highly heterogeneous with zones of high and medium activity in 54% of the cell surface and zones of low or no activity in the remainder. The 'non-active' ('silent') zones covered 24% of the total and persisted for 6-8 min, indicating stable location. The 9-Ch NCD-UMEA therefore appears suitable for investigating the microdomain organization of neurosecretion with high spatial resolution. © 2014 The Authors. The Journal of Physiology © 2014 The Physiological Society.

Phagocytosis of microparticles by alveolar macrophages during acute lung injury requires MerTK.

PubMed

Mohning, Michael P; Thomas, Stacey M; Barthel, Lea; Mould, Kara J; McCubbrey, Alexandria L; Frasch, S Courtney; Bratton, Donna L; Henson, Peter M; Janssen, William J

2018-01-01

Microparticles are a newly recognized class of mediators in the pathophysiology of lung inflammation and injury, but little is known about the factors that regulate their accumulation and clearance. The primary objective of our study was to determine whether alveolar macrophages engulf microparticles and to elucidate the mechanisms by which this occurs. Alveolar microparticles were quantified in bronchoalveolar fluid of mice with lung injury induced by LPS and hydrochloric acid. Microparticle numbers were greatest at the peak of inflammation and declined as inflammation resolved. Isolated, fluorescently labeled particles were placed in culture with macrophages to evaluate ingestion in the presence of endocytosis inhibitors. Ingestion was blocked with cytochalasin D and wortmannin, consistent with a phagocytic process. In separate experiments, mice were treated intratracheally with labeled microparticles, and their uptake was assessed though microscopy and flow cytometry. Resident alveolar macrophages, not recruited macrophages, were the primary cell-ingesting microparticles in the alveolus during lung injury. In vitro, microparticles promoted inflammatory signaling in LPS primed epithelial cells, signifying the importance of microparticle clearance in resolving lung injury. Microparticles were found to have phosphatidylserine exposed on their surfaces. Accordingly, we measured expression of phosphatidylserine receptors on macrophages and found high expression of MerTK and Axl in the resident macrophage population. Endocytosis of microparticles was markedly reduced in MerTK-deficient macrophages in vitro and in vivo. In conclusion, microparticles are released during acute lung injury and peak in number at the height of inflammation. Resident alveolar macrophages efficiently clear these microparticles through MerTK-mediated phagocytosis.

A Biodosimeter for Multiparametric Determination of Radiation Dose, Radiation Quality, and Radiation Risk

NASA Technical Reports Server (NTRS)

Richmond, Robert; Cruz, Angela; Jansen, Heather; Bors, Karen

2003-01-01

Predicting risk of human cancer following exposure of an individual or a population to ionizing radiation is challenging. To an approximation, this is because uncertainties of uniform absorption of dose and the uniform processing of dose-related damage at the cellular level within a complex set of biological variables degrade the confidence of predicting the delayed expression of cancer as a relatively rare event. Cellular biodosimeters that simultaneously report: 1) the quantity of absorbed dose after exposure to ionizing radiation, 2) the quality of radiation delivering that dose, and 3) the risk of developing cancer by the cells absorbing that dose would therefore be useful. An approach to such a multiparametric biodosimeter will be reported. This is the demonstration of a dose responsive field effect of enhanced expression of keratin 18 (K18) in cultures of human mammary epithelial cells irradiated with cesium-1 37 gamma-rays. Dose response of enhanced K18 expression was experimentally extended over a range of 30 to 90 cGy for cells evaluated at mid-log phase. K18 has been reported to be a marker for tumor staging and for apoptosis, and thereby serves as an example of a potential marker for cancer risk, where the reality of such predictive value would require additional experimental development. Since observed radiogenic increase in expression of K18 is a field effect, ie., chronically present in all cells of the irradiated population, it may be hypothesized that K18 expression in specific cells absorbing particulate irradiation, such as the high-LET-producing atomic nuclei of space radiation, will report on both the single-cell distributions of those particles amongst cells within the exposed population, and that the relatively high dose per cell delivered by densely ionizing tracks of those intersecting particles will lead to cell-specific high-expression levels of K18, thereby providing analytical end points that may be used to resolve both the quantity and the quality of the radiation dose absorbed by individual cells. The principal value of this reported potential multiparametric cellular biodosimeter is suggested to be that it justifies a search for similar but more robust radiogenic assays. That is, K18 is only one radiation dose-sensitive expressed protein, whereas analytical techniques of genomics and proteomics can be used to simultaneously analyze multiple gene and protein expressions resulting from radiation-dose absorption. The potential usefulness of multiparametric cellular biodosimeters will be best realized from quantitatively profiling these multiple markers using these modern techniques.

Spatially Resolved Quantification of Chromatin Condensation through Differential Local Rheology in Cell Nuclei Fluorescence Lifetime Imaging

PubMed Central

Spagnol, Stephen T.; Dahl, Kris Noel

2016-01-01

The linear sequence of DNA encodes access to the complete set of proteins that carry out cellular functions. Yet, much of the functionality appropriate for each cell is nested within layers of dynamic regulation and organization, including a hierarchy of chromatin structural states and spatial arrangement within the nucleus. There remain limitations in our understanding of gene expression within the context of nuclear organization from an inability to characterize hierarchical chromatin organization in situ. Here we demonstrate the use of fluorescence lifetime imaging microscopy (FLIM) to quantify and spatially resolve chromatin condensation state using cell-permeable, DNA-binding dyes (Hoechst 33342 and PicoGreen). Through in vitro and in situ experiments we demonstrate the sensitivity of fluorescence lifetime to condensation state through the mechanical effects that accompany the structural changes and are reflected through altered viscosity. The establishment of FLIM for resolving and quantifying chromatin condensation state opens the door for single-measurement mechanical studies of the nucleus and for characterizing the role of genome structure and organization in nuclear processes that accompany physiological and pathological changes. PMID:26765322

Population Genetic Structure and Life History Variability in Oncorhynchus Nerka from the Snake River Basin, 1991-1993 Final Report.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Waples, Robin S.; Aebersold, Paul B.; Winans, Gary A.

A detailed examination of O. nerka from lakes in the Sawtooth Valley of Idaho was undertaken to help guide recovery planning for the endangered Redfish Lake population and to help resolve relationships between resident and anadromous forms.

Human T cell lymphotropic virus type I genomic expression and impact on intracellular signaling pathways during neurodegenerative disease and leukemia.

PubMed

Yao, J; Wigdahl, B

2000-01-01

HTLV-I has been identified as the etiologic agent of neoplasia within the human peripheral blood T lymphocyte population, and a progressive neurologic disorder based primarily within the central nervous system. We have examined the role of HTLV-I in these two distinctly different clinical syndromes by examining the life cycle of the virus, with emphasis on the regulation of viral gene expression within relevant target cell populations. In particular, we have examined the impact of specific viral gene products, particularly Tax, on cellular metabolic function. Tax is a highly promiscuous and pleiotropic viral oncoprotein, and is the most important factor contributing to the initial stages of viral-mediated transformation of T cells after HTLV-I infection. Tax, which weakly binds to Tax response element 1 (TRE-1) in the viral long terminal repeat (LTR), can dramatically trans-activate viral gene expression by interacting with cellular transcription factors, such as activated transcription factors and cyclic AMP response element binding proteins (ATF/CREB), CREB binding protein (CBP/p300), and factors involved with the basic transcription apparatus. At the same time, Tax alters cellular gene expression by directly or indirectly interacting with a variety of cellular transcription factors, cell cycle control elements, and cellular signal transduction molecules ultimately resulting in dysregulated cell proliferation. The mechanisms associated with HTLV-I infection, leading to tropical spastic paraparesis (TSP) are not as clearly resolved. Possible explanations of viral-induced neurologic disease range from central nervous system (CNS) damage caused by direct viral invasion of the CNS to bystander CNS damage caused by the immune response to HTLV-I infection. It is interesting to note that it is very rare for an HTLV-I infected individual to develop both adult T cell leukemia (ATL) and TSP in his/her life time, suggesting that the mechanisms governing development of these two diseases are mutually exclusive.

Nanophotothermolysis of multiple scattered cancer cells with carbon nanotubes guided by time-resolved infrared thermal imaging

PubMed Central

Biris, Alexandru S.; Boldor, Dorin; Palmer, Jason; Monroe, William T.; Mahmood, Meena; Dervishi, Enkeleda; Xu, Yang; Li, Zhongrui; Galanzha, Ekaterina I.; Zharov, Vladimir P.

2016-01-01

Nanophotothermolysis with long laser pulses for treatment of scattered cancer cells and their clusters is introduced with the main focus on real-time monitoring of temperature dynamics inside and around individual cancer cells labeled with carbon nanotubes. This technique utilizes advanced time- and spatially-resolved thermal radiometry imaging for the visualization of laser-induced temperature distribution in multiple-point absorbing targets. The capability of this approach was demonstrated for monitoring of thermal effects under long laser exposure (from millisecond to seconds, wavelength 1064 nm, maximum power 1 W) of cervical cancer HeLa cells labeled with carbon nanotubes in vitro. The applications are discussed with a focus on the nanophotothermolysis of small tumors, tumor margins, or micrometastases under the guidance of near-IR and microwave radiometry. PMID:19405720

[Excitation transfer between high-lying states in K2 in collisions with ground state K and H2 molecules].

PubMed

Shen, Xiao-Yan; Liu, Jing; Dai, Kang; Shen, Yi-Fan

2010-02-01

Pure potassium vapor or K-H2 mixture was irradiated in a glass fluorescence cell with pulses of 710 nm radiation from an OPO laser, populating K2 (1lambda(g)) state by two-photon absorption. Cross sections for 1lambda(g)-3lambda(g) transfer in K2 were determined using methods of molecular fluorescence. During the experiments with pure K vapor, the cell temperature was varied between 553 and 603 K. The K number density was determined spectroscopically by the white-light absorption measurement in the blue wing of the self-broadened resonance D2 line. The resulting fluorescence included a direct component emitted in the decay of the optically excitation and a sensitized component arising from the collisionally populated state. The decay signal of time-resolved fluorescence from1lambda(g) -->1 1sigma(u)+ transition was monitored. It was seen that just after the laser pulse the fluorescence of the photoexcited level decreased exponentially. The effective lifetimes of the 1lambda(g) state can be resolved. The plot of reciprocal of effective lifetimes of the 1lambda(g) state against K densities yielded the slope that indicated the total cross section for deactivation and the intercept that provided the radiative lifetime of the state. The radiative lifetime (20 +/- 2) ns was obtained. The cross section for deactivation of the K2(1lambda(g)) molecules by collisions with K is (2.5 +/- 0.3) x 10(-14) cm2. The time-resolved intensities of the K23lambda(g) --> 1 3sigma(u)+ (484 nm) line were measured. The radiative lifetime (16.0 +/- 3.2) ns and the total cross section (2.5 +/- 0.6) x 10(-14) cm2 for deactivation of the K2 (3lambda(g)) state can also be determined through the analogous procedure. The time-integrated intensities of 1lambda(g) --> 1 1sigma(u)+ and 3lambda(g) --> 1 3sigma(u)+ transitions were measured. The cross section (1.1 +/- 0.3) x10(-14) cm2 was obtained for K2 (1lambda(g))+ K --> K2 (3lambda(g)) + K collisions. During the experiments with K-H2 mixture, the cell temperature was kept constant at 553 K. The H2 pressure was varied between 40 and 400 Pa. The effects of K2-K collisions could not be neglected. These effects were subtracted out using the results of the pure K experiments. The cross section (2.7 +/- 1.1) x 10(-15) cm2 was obtained for K2 (1lambda(g)) + H2 --> K2 (3lambda(g))+H2 collisions. The cross section is (6.8 +/- 2.7) x 10(-15) cm2 for K2 (3lambda(g)) + H2 --> states out of K2 (3lambda(g)) + H2 collisions.

Resolving mixed mechanisms of protein subdiffusion at the T cell plasma membrane

NASA Astrophysics Data System (ADS)

Golan, Yonatan; Sherman, Eilon

2017-06-01

The plasma membrane is a complex medium where transmembrane proteins diffuse and interact to facilitate cell function. Membrane protein mobility is affected by multiple mechanisms, including crowding, trapping, medium elasticity and structure, thus limiting our ability to distinguish them in intact cells. Here we characterize the mobility and organization of a short transmembrane protein at the plasma membrane of live T cells, using single particle tracking and photoactivated-localization microscopy. Protein mobility is highly heterogeneous, subdiffusive and ergodic-like. Using mobility characteristics, we segment individual trajectories into subpopulations with distinct Gaussian step-size distributions. Particles of low-to-medium mobility consist of clusters, diffusing in a viscoelastic and fractal-like medium and are enriched at the centre of the cell footprint. Particles of high mobility undergo weak confinement and are more evenly distributed. This study presents a methodological approach to resolve simultaneous mixed subdiffusion mechanisms acting on polydispersed samples and complex media such as cell membranes.

Disrupted regulatory T cell homeostasis in inflammatory bowel diseases

PubMed Central

Pedros, Christophe; Duguet, Fanny; Saoudi, Abdelhadi; Chabod, Marianne

2016-01-01

In the gut, where billions of non-self-antigens from the food and the microbiota are present, the immune response must be tightly regulated to ensure both host protection against pathogenic microorganisms and the absence of immune-related pathologies. It has been well documented that regulatory T cells (Tregs) play a pivotal role in this context. Indeed, Tregs are able to prevent excessive inflammation, which can lead to the rupture of intestinal homeostasis observed in inflammatory bowel diseases (IBDs). Both the worldwide incidence and prevalence of such diseases have increased throughout the latter part of the 20th century. Therefore, it is crucial to understand how Tregs suppress the colitogenic immune cells to establish new treatments for patients suffering from IBDs. In this review, we will first summarize the results obtained in animal model studies that highlight the importance of Tregs in maintaining intestinal homeostasis and describe the specific suppressive mechanisms involved. Next, our current knowledge about Tregs contribution to human IBDs will be reviewed, as well as the current therapeutic perspective on using Tregs for clinical IBD treatment and the challenges that remain to be resolved to ensure both the safety and effectiveness of these therapies in targeting this critical immune-regulatory cell population. PMID:26811641

Preparation of the Nuclear Matrix for Parallel Microscopy and Biochemical Analyses.

PubMed

Wilson, Rosemary H C; Hesketh, Emma L; Coverley, Dawn

2016-01-04

Immobilized proteins within the nucleus are usually identified by treating cells with detergent. The detergent-resistant fraction is often assumed to be chromatin and is described as such in many studies. However, this fraction consists of both chromatin-bound and nuclear-matrix-bound proteins. To investigate nuclear-matrix-bound proteins alone, further separation of these fractions is required; the DNA must be removed so that the remaining proteins can be compared with those from untreated cells. This protocol uses a nonionic detergent (Triton X-100) to remove membranes and soluble proteins from cells under physiologically relevant salt concentrations, followed by extraction with 0.5 m NaCl, digestion with DNase I, and removal of fragmented DNA. It uses a specialized buffer (cytoskeletal buffer) to stabilize the cytoskeleton and nuclear matrix in relatively gentle conditions. Nuclear matrix proteins can then be assessed by either immunofluorescence (IF) and immunoblotting (IB). IB has the advantage of resolving different forms of a protein of interest, and the soluble fractions can be analyzed. The major advantage of IF analysis is that individual cells (rather than homogenized populations) can be monitored, and the spatial arrangement of proteins bound to residual nuclear structures can be revealed. © 2016 Cold Spring Harbor Laboratory Press.

Analysis of spectrally resolved autofluorescence images by support vector machines

NASA Astrophysics Data System (ADS)

Mateasik, A.; Chorvat, D.; Chorvatova, A.

2013-02-01

Spectral analysis of the autofluorescence images of isolated cardiac cells was performed to evaluate and to classify the metabolic state of the cells in respect to the responses to metabolic modulators. The classification was done using machine learning approach based on support vector machine with the set of the automatically calculated features from recorded spectral profile of spectral autofluorescence images. This classification method was compared with the classical approach where the individual spectral components contributing to cell autofluorescence were estimated by spectral analysis, namely by blind source separation using non-negative matrix factorization. Comparison of both methods showed that machine learning can effectively classify the spectrally resolved autofluorescence images without the need of detailed knowledge about the sources of autofluorescence and their spectral properties.

An integrated approach to improved toxicity prediction for the safety assessment during preclinical drug development using Hep G2 cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noor, Fozia; Niklas, Jens; Mueller-Vieira, Ursula

2009-06-01

Efficient and accurate safety assessment of compounds is extremely important in the preclinical development of drugs especially when hepatotoxicty is in question. Multiparameter and time resolved assays are expected to greatly improve the prediction of toxicity by assessing complex mechanisms of toxicity. An integrated approach is presented in which Hep G2 cells and primary rat hepatocytes are compared in frequently used cytotoxicity assays for parent compound toxicity. The interassay variability was determined. The cytotoxicity assays were also compared with a reliable alternative time resolved respirometric assay. The set of training compounds consisted of well known hepatotoxins; amiodarone, carbamazepine, clozapine, diclofenac,more » tacrine, troglitazone and verapamil. The sensitivity of both cell systems in each tested assay was determined. Results show that careful selection of assay parameters and inclusion of a kinetic time resolved assay improves prediction for non-metabolism mediated toxicity using Hep G2 cells as indicated by a sensitivity ratio of 1. The drugs with EC{sub 50} values 100 {mu}M or lower were considered toxic. The difference in the sensitivity of the two cell systems to carbamazepine which causes toxicity via reactive metabolites emphasizes the importance of human cell based in-vitro assays. Using the described system, primary rat hepatocytes do not offer advantage over the Hep G2 cells in parent compound toxicity evaluation. Moreover, respiration method is non invasive, highly sensitive and allows following the time course of toxicity. Respiration assay could serve as early indicator of changes that subsequently lead to toxicity.« less

Parallel Spectral Acquisition with an Ion Cyclotron Resonance Cell Array.

PubMed

Park, Sung-Gun; Anderson, Gordon A; Navare, Arti T; Bruce, James E

2016-01-19

Mass measurement accuracy is a critical analytical figure-of-merit in most areas of mass spectrometry application. However, the time required for acquisition of high-resolution, high mass accuracy data limits many applications and is an aspect under continual pressure for development. Current efforts target implementation of higher electrostatic and magnetic fields because ion oscillatory frequencies increase linearly with field strength. As such, the time required for spectral acquisition of a given resolving power and mass accuracy decreases linearly with increasing fields. Mass spectrometer developments to include multiple high-resolution detectors that can be operated in parallel could further decrease the acquisition time by a factor of n, the number of detectors. Efforts described here resulted in development of an instrument with a set of Fourier transform ion cyclotron resonance (ICR) cells as detectors that constitute the first MS array capable of parallel high-resolution spectral acquisition. ICR cell array systems consisting of three or five cells were constructed with printed circuit boards and installed within a single superconducting magnet and vacuum system. Independent ion populations were injected and trapped within each cell in the array. Upon filling the array, all ions in all cells were simultaneously excited and ICR signals from each cell were independently amplified and recorded in parallel. Presented here are the initial results of successful parallel spectral acquisition, parallel mass spectrometry (MS) and MS/MS measurements, and parallel high-resolution acquisition with the MS array system.

How to operate a nuclear pore complex by Kap-centric control

PubMed Central

Lim, Roderick Y H; Huang, Binlu; Kapinos, Larisa E

2015-01-01

Nuclear pore complexes (NPCs) mediate molecular transport between the nucleus and cytoplasm in eukaryotic cells. Tethered within each NPC lie numerous intrinsically disordered proteins known as FG nucleoporins (FG Nups) that are central to this process. Over two decades of investigation has converged on a view that a barrier mechanism consisting of FG Nups rejects non-specific macromolecules while promoting the speed and selectivity of karyopherin (Kaps) receptors (and their cargoes). Yet, the number of NPCs in the cell is exceedingly small compared to the number of Kaps, so that in fact there is a high likelihood the pores are always populated by Kaps. Here, we contemplate a view where Kaps actively participate in regulating the selectivity and speed of transport through NPCs. This so-called “Kap-centric” control of the NPC accounts for Kaps as essential barrier reinforcements that play a prerequisite role in facilitating fast transport kinetics. Importantly, Kap-centric control reconciles both mechanistic and kinetic requirements of the NPC, and in so doing potentially resolves incoherent aspects of FG-centric models. On this basis, we surmise that Kaps prime the NPC for nucleocytoplasmic transport by fine-tuning the NPC microenvironment according to the functional needs of the cell. PMID:26338152

Millisecond single-molecule localization microscopy combined with convolution analysis and automated image segmentation to determine protein concentrations in complexly structured, functional cells, one cell at a time.

PubMed

Wollman, Adam J M; Leake, Mark C

2015-01-01

We present a single-molecule tool called the CoPro (concentration of proteins) method that uses millisecond imaging with convolution analysis, automated image segmentation and super-resolution localization microscopy to generate robust estimates for protein concentration in different compartments of single living cells, validated using realistic simulations of complex multiple compartment cell types. We demonstrate its utility experimentally on model Escherichia coli bacteria and Saccharomyces cerevisiae budding yeast cells, and use it to address the biological question of how signals are transduced in cells. Cells in all domains of life dynamically sense their environment through signal transduction mechanisms, many involving gene regulation. The glucose sensing mechanism of S. cerevisiae is a model system for studying gene regulatory signal transduction. It uses the multi-copy expression inhibitor of the GAL gene family, Mig1, to repress unwanted genes in the presence of elevated extracellular glucose concentrations. We fluorescently labelled Mig1 molecules with green fluorescent protein (GFP) via chromosomal integration at physiological expression levels in living S. cerevisiae cells, in addition to the RNA polymerase protein Nrd1 with the fluorescent protein reporter mCherry. Using CoPro we make quantitative estimates of Mig1 and Nrd1 protein concentrations in the cytoplasm and nucleus compartments on a cell-by-cell basis under physiological conditions. These estimates indicate a ∼4-fold shift towards higher values in the concentration of diffusive Mig1 in the nucleus if the external glucose concentration is raised, whereas equivalent levels in the cytoplasm shift to smaller values with a relative change an order of magnitude smaller. This compares with Nrd1 which is not involved directly in glucose sensing, and which is almost exclusively localized in the nucleus under high and low external glucose levels. CoPro facilitates time-resolved quantification of protein concentrations in single functional cells, and enables the distributions of concentrations across a cell population to be measured. This could be useful in investigating several cellular processes that are mediated by proteins, especially where changes in protein concentration in a single cell in response to changes in the extracellular chemical environment are subtle and rapid and may be smaller than the variability across a cell population.

The Anemic Stellar Halo of M101

NASA Astrophysics Data System (ADS)

Holwerda, Benne

2014-10-01

Models of galaxy formation in a cosmological context predict that massive disk galaxies should have richly-structured extended stellar halos, containing ~10% of a galaxy's stars, originating in large part from the tidal disruption of dwarf galaxies. Observations of a number of nearby disk galaxies have generally agreed with these expectations. Recent new observations in integrated light with a novel array of low scattered-light telephoto lenses have failed to convincingly detect a stellar halo in the nearby massive face-on disk galaxy M101 (van Dokkum et al. 2014). They argue that any halo has to have <0.3% of the mass of the galaxy. This halo would be the least massive of any massive disk galaxy in the local Universe (by factors of several) -- such a halo is not predicted or naturally interpreted by the models, and would present a critical challenge to the picture of ubiquitous stellar halos formed from the debris of disrupting dwarf galaxies.We propose to resolve the stellar populations of this uniquely anemic stellar halo for 6 orbits with HST (ACS and WFC3), allowing us to reach surface brightness limits sufficient to clearly detect and characterize M101's stellar halo if it carries more than 0.1% of M101's mass. With resolved stellar populations, we can use the gradient of stellar populations as a function of radius to separate stellar halo from disk, which is impossible using integrated light observations. The resolved stellar populations will reveal the halo mass to much greater accuracy, measure the halo radial profile, constrain any halo lopsidedness, estimate the halo's stellar metallicity, and permit an analysis of outer disk stellar populations.

Insight into the Peopling of Mainland Southeast Asia from Thai Population Genetic Structure

PubMed Central

Chaichoompu, Kridsadakorn; Ngamphiw, Chumpol; Assawamakin, Anunchai; Nuinoon, Manit; Sripichai, Orapan; Svasti, Saovaros; Fucharoen, Suthat; Praphanphoj, Verayuth; Tongsima, Sissades

2013-01-01

There is considerable ethno-linguistic and genetic variation among human populations in Asia, although tracing the origins of this diversity is complicated by migration events. Thailand is at the center of Mainland Southeast Asia (MSEA), a region within Asia that has not been extensively studied. Genetic substructure may exist in the Thai population, since waves of migration from southern China throughout its recent history may have contributed to substantial gene flow. Autosomal SNP data were collated for 438,503 markers from 992 Thai individuals. Using the available self-reported regional origin, four Thai subpopulations genetically distinct from each other and from other Asian populations were resolved by Neighbor-Joining analysis using a 41,569 marker subset. Using an independent Principal Components-based unsupervised clustering approach, four major MSEA subpopulations were resolved in which regional bias was apparent. A major ancestry component was common to these MSEA subpopulations and distinguishes them from other Asian subpopulations. On the other hand, these MSEA subpopulations were admixed with other ancestries, in particular one shared with Chinese. Subpopulation clustering using only Thai individuals and the complete marker set resolved four subpopulations, which are distributed differently across Thailand. A Sino-Thai subpopulation was concentrated in the Central region of Thailand, although this constituted a minority in an otherwise diverse region. Among the most highly differentiated markers which distinguish the Thai subpopulations, several map to regions known to affect phenotypic traits such as skin pigmentation and susceptibility to common diseases. The subpopulation patterns elucidated have important implications for evolutionary and medical genetics. The subpopulation structure within Thailand may reflect the contributions of different migrants throughout the history of MSEA. The information will also be important for genetic association studies to account for population-structure confounding effects. PMID:24223962

Direct evaluation of influence of electron damage on the subcell performance in triple-junction solar cells using photoluminescence decays.

PubMed

Tex, David M; Nakamura, Tetsuya; Imaizumi, Mitsuru; Ohshima, Takeshi; Kanemitsu, Yoshihiko

2017-05-16

Tandem solar cells are suited for space applications due to their high performance, but also have to be designed in such a way to minimize influence of degradation by the high energy particle flux in space. The analysis of the subcell performance is crucial to understand the device physics and achieve optimized designs of tandem solar cells. Here, the radiation-induced damage of inverted grown InGaP/GaAs/InGaAs triple-junction solar cells for various electron fluences are characterized using conventional current-voltage (I-V) measurements and time-resolved photoluminescence (PL). The conversion efficiencies of the entire device before and after damage are measured with I-V curves and compared with the efficiencies predicted from the time-resolved method. Using the time-resolved data the change in the carrier dynamics in the subcells can be discussed. Our optical method allows to predict the absolute electrical conversion efficiency of the device with an accuracy of better than 5%. While both InGaP and GaAs subcells suffered from significant material degradation, the performance loss of the total device can be completely ascribed to the damage in the GaAs subcell. This points out the importance of high internal electric fields at the operating point.

Bright Lu2O3:Eu thin-film scintillators for high-resolution radioluminescence microscopy

PubMed Central

Sengupta, Debanti; Miller, Stuart; Marton, Zsolt; Chin, Frederick; Nagarkar, Vivek

2015-01-01

We investigate the performance of a new thin-film Lu2O3:Eu scintillator for single-cell radionuclide imaging. Imaging the metabolic properties of heterogeneous cell populations in real time is an important challenge with clinical implications. We have developed an innovative technique called radioluminescence microscopy, to quantitatively and sensitively measure radionuclide uptake in single cells. The most important component of this technique is the scintillator, which converts the energy released during radioactive decay into luminescent signals. The sensitivity and spatial resolution of the imaging system depend critically on the characteristics of the scintillator, i.e. the material used and its geometrical configuration. Scintillators fabricated using conventional methods are relatively thick, and therefore do not provide optimal spatial resolution. We compare a thin-film Lu2O3:Eu scintillator to a conventional 500 μm thick CdWO4 scintillator for radioluminescence imaging. Despite its thinness, the unique scintillation properties of the Lu2O3:Eu scintillator allow us to capture single positron decays with over fourfold higher sensitivity, a significant achievement. The thin-film Lu2O3:Eu scintillators also yield radioluminescence images where individual cells appear smaller and better resolved on average than with the CdWO4 scintillators. Coupled with the thin-film scintillator technology, radioluminescence microscopy can yield valuable and clinically relevant data on the metabolism of single cells. PMID:26183115

Mutual regulation of tumour vessel normalization and immunostimulatory reprogramming.

PubMed

Tian, Lin; Goldstein, Amit; Wang, Hai; Ching Lo, Hin; Sun Kim, Ik; Welte, Thomas; Sheng, Kuanwei; Dobrolecki, Lacey E; Zhang, Xiaomei; Putluri, Nagireddy; Phung, Thuy L; Mani, Sendurai A; Stossi, Fabio; Sreekumar, Arun; Mancini, Michael A; Decker, William K; Zong, Chenghang; Lewis, Michael T; Zhang, Xiang H-F

2017-04-13

Blockade of angiogenesis can retard tumour growth, but may also paradoxically increase metastasis. This paradox may be resolved by vessel normalization, which involves increased pericyte coverage, improved tumour vessel perfusion, reduced vascular permeability, and consequently mitigated hypoxia. Although these processes alter tumour progression, their regulation is poorly understood. Here we show that type 1 T helper (T H 1) cells play a crucial role in vessel normalization. Bioinformatic analyses revealed that gene expression features related to vessel normalization correlate with immunostimulatory pathways, especially T lymphocyte infiltration or activity. To delineate the causal relationship, we used various mouse models with vessel normalization or T lymphocyte deficiencies. Although disruption of vessel normalization reduced T lymphocyte infiltration as expected, reciprocal depletion or inactivation of CD4 + T lymphocytes decreased vessel normalization, indicating a mutually regulatory loop. In addition, activation of CD4 + T lymphocytes by immune checkpoint blockade increased vessel normalization. T H 1 cells that secrete interferon-γ are a major population of cells associated with vessel normalization. Patient-derived xenograft tumours growing in immunodeficient mice exhibited enhanced hypoxia compared to the original tumours in immunocompetent humans, and hypoxia was reduced by adoptive T H 1 transfer. Our findings elucidate an unexpected role of T H 1 cells in vasculature and immune reprogramming. T H 1 cells may be a marker and a determinant of both immune checkpoint blockade and anti-angiogenesis efficacy.

The axolotl limb blastema: cellular and molecular mechanisms driving blastema formation and limb regeneration in tetrapods

PubMed Central

McCusker, Catherine; Bryant, Susan V.

2015-01-01

Abstract The axolotl is one of the few tetrapods that are capable of regenerating complicated biological structures, such as complete limbs, throughout adulthood. Upon injury the axolotl generates a population of regeneration‐competent limb progenitor cells known as the blastema, which will grow, establish pattern, and differentiate into the missing limb structures. In this review we focus on the crucial early events that occur during wound healing, the neural−epithelial interactions that drive the formation of the early blastema, and how these mechanisms differ from those of other species that have restricted regenerative potential, such as humans. We also discuss how the presence of cells from the different axes of the limb is required for the continued growth and establishment of pattern in the blastema as described in the polar coordinate model, and how this positional information is reprogrammed in blastema cells during regeneration. Multiple cell types from the mature limb stump contribute to the blastema at different stages of regeneration, and we discuss the contribution of these types to the regenerate with reference to whether they are “pattern‐forming” or “pattern‐following” cells. Lastly, we explain how an engineering approach will help resolve unanswered questions in limb regeneration, with the goal of translating these concepts to developing better human regenerative therapies. PMID:27499868

Morphological plasticity of bacteria—Open questions

PubMed Central

Shen, Jie-Pan

2016-01-01

Morphological plasticity of bacteria is a cryptic phenomenon, by which bacteria acquire adaptive benefits for coping with changing environments. Some environmental cues were identified to induce morphological plasticity, but the underlying molecular mechanisms remain largely unknown. Physical and chemical factors causing morphological changes in bacteria have been investigated and mostly associated with potential pathways linked to the cell wall synthetic machinery. These include starvation, oxidative stresses, predation effectors, antimicrobial agents, temperature stresses, osmotic shock, and mechanical constraints. In an extreme scenario of morphological plasticity, bacteria can be induced to be shapeshifters when the cell walls are defective or deficient. They follow distinct developmental pathways and transform into assorted morphological variants, and most of them would eventually revert to typical cell morphology. It is suggested that phenotypic heterogeneity might play a functional role in the development of morphological diversity and/or plasticity within an isogenic population. Accordingly, phenotypic heterogeneity and inherited morphological plasticity are found to be survival strategies adopted by bacteria in response to environmental stresses. Here, microfluidic and nanofabrication technology is considered to provide versatile solutions to induce morphological plasticity, sort and isolate morphological variants, and perform single-cell analysis including transcriptional and epigenetic profiling. Questions such as how morphogenesis network is modulated or rewired (if epigenetic controls of cell morphogenesis apply) to induce bacterial morphological plasticity could be resolved with the aid of micro-nanofluidic platforms and optimization algorithms, such as feedback system control. PMID:27375812

Functional imaging with cellular resolution reveals precise micro-architecture in visual cortex

NASA Astrophysics Data System (ADS)

Ohki, Kenichi; Chung, Sooyoung; Ch'ng, Yeang H.; Kara, Prakash; Reid, R. Clay

2005-02-01

Neurons in the cerebral cortex are organized into anatomical columns, with ensembles of cells arranged from the surface to the white matter. Within a column, neurons often share functional properties, such as selectivity for stimulus orientation; columns with distinct properties, such as different preferred orientations, tile the cortical surface in orderly patterns. This functional architecture was discovered with the relatively sparse sampling of microelectrode recordings. Optical imaging of membrane voltage or metabolic activity elucidated the overall geometry of functional maps, but is averaged over many cells (resolution >100µm). Consequently, the purity of functional domains and the precision of the borders between them could not be resolved. Here, we labelled thousands of neurons of the visual cortex with a calcium-sensitive indicator in vivo. We then imaged the activity of neuronal populations at single-cell resolution with two-photon microscopy up to a depth of 400µm. In rat primary visual cortex, neurons had robust orientation selectivity but there was no discernible local structure; neighbouring neurons often responded to different orientations. In area 18 of cat visual cortex, functional maps were organized at a fine scale. Neurons with opposite preferences for stimulus direction were segregated with extraordinary spatial precision in three dimensions, with columnar borders one to two cells wide. These results indicate that cortical maps can be built with single-cell precision.

Cell therapy for heart failure: a comprehensive overview of experimental and clinical studies, current challenges, and future directions.

PubMed

Sanganalmath, Santosh K; Bolli, Roberto

2013-08-30

Despite significant therapeutic advances, the prognosis of patients with heart failure (HF) remains poor, and current therapeutic approaches are palliative in the sense that they do not address the underlying problem of the loss of cardiac tissue. Stem cell-based therapies have the potential to fundamentally transform the treatment of HF by achieving what would have been unthinkable only a few years ago-myocardial regeneration. For the first time since cardiac transplantation, a therapy is being developed to eliminate the underlying cause of HF, not just to achieve damage control. Since the initial report of cell therapy (skeletal myoblasts) in HF in 1998, research has proceeded at lightning speed, and numerous preclinical and clinical studies have been performed that support the ability of various stem cell populations to improve cardiac function and reduce infarct size in both ischemic and nonischemic cardiomyopathy. Nevertheless, we are still at the dawn of this therapeutic revolution. Many important issues (eg, mechanism(s) of action of stem cells, long-term engraftment, optimal cell type(s), and dose, route, and frequency of cell administration) remain to be resolved, and no cell therapy has been conclusively shown to be effective. The purpose of this article is to critically review the large body of work performed with respect to the use of stem/progenitor cells in HF, both at the experimental and clinical levels, and to discuss current controversies, unresolved issues, challenges, and future directions. The review focuses specifically on chronic HF; other settings (eg, acute myocardial infarction, refractory angina) are not discussed.

Population responses in primary auditory cortex simultaneously represent the temporal envelope and periodicity features in natural speech.

PubMed

Abrams, Daniel A; Nicol, Trent; White-Schwoch, Travis; Zecker, Steven; Kraus, Nina

2017-05-01

Speech perception relies on a listener's ability to simultaneously resolve multiple temporal features in the speech signal. Little is known regarding neural mechanisms that enable the simultaneous coding of concurrent temporal features in speech. Here we show that two categories of temporal features in speech, the low-frequency speech envelope and periodicity cues, are processed by distinct neural mechanisms within the same population of cortical neurons. We measured population activity in primary auditory cortex of anesthetized guinea pig in response to three variants of a naturally produced sentence. Results show that the envelope of population responses closely tracks the speech envelope, and this cortical activity more closely reflects wider bandwidths of the speech envelope compared to narrow bands. Additionally, neuronal populations represent the fundamental frequency of speech robustly with phase-locked responses. Importantly, these two temporal features of speech are simultaneously observed within neuronal ensembles in auditory cortex in response to clear, conversation, and compressed speech exemplars. Results show that auditory cortical neurons are adept at simultaneously resolving multiple temporal features in extended speech sentences using discrete coding mechanisms. Copyright © 2017 Elsevier B.V. All rights reserved.

Dual Roles for Spike Signaling in Cortical Neural Populations

PubMed Central

Ballard, Dana H.; Jehee, Janneke F. M.

2011-01-01

A prominent feature of signaling in cortical neurons is that of randomness in the action potential. The output of a typical pyramidal cell can be well fit with a Poisson model, and variations in the Poisson rate repeatedly have been shown to be correlated with stimuli. However while the rate provides a very useful characterization of neural spike data, it may not be the most fundamental description of the signaling code. Recent data showing γ frequency range multi-cell action potential correlations, together with spike timing dependent plasticity, are spurring a re-examination of the classical model, since precise timing codes imply that the generation of spikes is essentially deterministic. Could the observed Poisson randomness and timing determinism reflect two separate modes of communication, or do they somehow derive from a single process? We investigate in a timing-based model whether the apparent incompatibility between these probabilistic and deterministic observations may be resolved by examining how spikes could be used in the underlying neural circuits. The crucial component of this model draws on dual roles for spike signaling. In learning receptive fields from ensembles of inputs, spikes need to behave probabilistically, whereas for fast signaling of individual stimuli, the spikes need to behave deterministically. Our simulations show that this combination is possible if deterministic signals using γ latency coding are probabilistically routed through different members of a cortical cell population at different times. This model exhibits standard features characteristic of Poisson models such as orientation tuning and exponential interval histograms. In addition, it makes testable predictions that follow from the γ latency coding. PMID:21687798

On-chip immune cell activation and subsequent time-resolved magnetic bead-based cytokine detection.

PubMed

Kongsuphol, Patthara; Liu, Yunxiao; Ramadan, Qasem

2016-10-01

Cytokine profiling and immunophenotyping offer great potential for understanding many disease mechanisms, personalized diagnosis, and immunotherapy. Here, we demonstrate a time-resolved detection of cytokine from a single cell cluster using an in situ magnetic immune assay. An array of triple-layered microfluidic chambers was fabricated to enable simultaneous cell culture under perfusion flow and detection of the induced cytokines at multiple time-points. Each culture chamber comprises three fluidic compartments which are dedicated to, cell culture, perfusion and immunoassay. The three compartments are separated by porous membranes, which allow the diffusion of fresh nutrient from the perfusion compartment into the cell culture compartment and cytokines secretion from the cell culture compartment into the immune assay compartment. This structure hence enables capturing the released cytokines without disturbing the cell culture and without minimizing benefit gain from perfusion. Functionalized magnetic beads were used as a solid phase carrier for cytokine capturing and quantification. The cytokines released from differential stimuli were quantified in situ in non-differentiated U937 monocytes and differentiated macrophages.

ON THE INCORPORATION OF METALLICITY DATA INTO MEASUREMENTS OF STAR FORMATION HISTORY FROM RESOLVED STELLAR POPULATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dolphin, Andrew E., E-mail: adolphin@raytheon.com

The combination of spectroscopic stellar metallicities and resolved star color–magnitude diagrams (CMDs) has the potential to constrain the entire star formation history (SFH) of a galaxy better than fitting CMDs alone (as is most common in SFH studies using resolved stellar populations). In this paper, two approaches to incorporating external metallicity information into CMD-fitting techniques are presented. Overall, the joint fitting of metallicity and CMD information can increase the precision of measured age–metallicity relationships (AMRs) and star formation rates by 10% over CMD fitting alone. However, systematics in stellar isochrones and mismatches between spectroscopic and photometric determinations of metallicity canmore » reduce the accuracy of the recovered SFHs. I present a simple mitigation of these systematics that can reduce their amplitude to the level obtained from CMD fitting alone, while ensuring that the AMR is consistent with spectroscopic metallicities. As is the case in CMD-fitting analysis, improved stellar models and calibrations between spectroscopic and photometric metallicities are currently the primary impediment to gains in SFH precision from jointly fitting stellar metallicities and CMDs.« less

Energy dissipation from a correlated system driven out of equilibrium

DOE PAGES

Rameau, J. D.; Freutel, S.; Kemper, A. F.; ...

2016-12-20

We report that in complex materials various interactions have important roles in determining electronic properties. Angle-resolved photoelectron spectroscopy (ARPES) is used to study these processes by resolving the complex single-particle self-energy and quantifying how quantum interactions modify bare electronic states. However, ambiguities in the measurement of the real part of the self-energy and an intrinsic inability to disentangle various contributions to the imaginary part of the self-energy can leave the implications of such measurements open to debate. Here we employ a combined theoretical and experimental treatment of femtosecond time-resolved ARPES (tr-ARPES) show how population dynamics measured using tr-ARPES can bemore » used to separate electron–boson interactions from electron–electron interactions. In conclusion, we demonstrate a quantitative analysis of a well-defined electron–boson interaction in the unoccupied spectrum of the cuprate Bi 2Sr 2CaCu 2O 8+x characterized by an excited population decay time that maps directly to a discrete component of the equilibrium self-energy not readily isolated by static ARPES experiments.« less

Quintet multiexciton dynamics in singlet fission

DOE PAGES

Tayebjee, Murad J. Y.; Sanders, Samuel N.; Kumarasamy, Elango; ...

2016-10-17

Singlet fission, in which two triplet excitons are generated from a single absorbed photon, is a key third-generation solar cell concept. Conservation of angular momentum requires that singlet fission populates correlated multiexciton states, which can subsequently dissociate to generate free triplets. However, little is known about electronic and spin correlations in these systems since, due to its typically short lifetime, the multiexciton state is challenging to isolate and study. Here, we use bridged pentacene dimers, which undergo intramolecular singlet fission while isolated in solution and in solid matrices, as a unimolecular model system that can trap long-lived multiexciton states. Wemore » also combine transient absorption and time-resolved electron spin resonance spectroscopies to show that spin correlations in the multiexciton state persist for hundreds of nanoseconds. Furthermore, we confirm long-standing predictions that singlet fission produces triplet pair states of quintet character. Finally, we compare two different pentacene–bridge–pentacene chromophores, systematically tuning the coupling between the pentacenes to understand how differences in molecular structure affect the population and dissociation of multiexciton quintet states.« less

Examining Doctoral Students' Perceptions of Diversity in a Diversity Studies Specialization

ERIC Educational Resources Information Center

de Souza Correa, Daniel

2017-01-01

A recent challenge for contemporary education has been to efficiently educate the increasingly diverse American population (Holley, 2013). Seeking to resolve the problems related to the education of a diverse student population, colleges and universities across the United States have begun to require students to enroll in diversity courses…

Spatio-temporal dynamics of a tree-killing beetle and its predator

Treesearch

Aaron S. Weed; Matthew P. Ayres; Andrew M. Liebhold; Ronald F. Billings

2016-01-01

Resolving linkages between local-scale processes and regional-scale patterns in abundance of interacting species is important for understanding long-term population stability across spatial scales. Landscape patterning in consumer population dynamics may be largely the result of interactions between consumers and their predators, or driven by spatial variation in basal...

Diffusion lengths of silicon solar cells from luminescence images

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wuerfel, P.; Trupke, T.; Puzzer, T.

A method for spatially resolved measurement of the minority carrier diffusion length in silicon wafers and in silicon solar cells is introduced. The method, which is based on measuring the ratio of two luminescence images taken with two different spectral filters, is applicable, in principle, to both photoluminescence and electroluminescence measurements and is demonstrated experimentally by electroluminescence measurements on a multicrystalline silicon solar cell. Good agreement is observed with the diffusion length distribution obtained from a spectrally resolved light beam induced current map. In contrast to the determination of diffusion lengths from one single luminescence image, the method proposed heremore » gives absolute values of the diffusion length and, in comparison, it is much less sensitive to lateral voltage variations across the cell area as caused by local variations of the series resistance. It is also shown that measuring the ratio of two luminescence images allows distinguishing shunts or surface defects from bulk defects.« less

Finely Resolved On-Road PM2.5 and Estimated Premature Mortality in Central North Carolina.

PubMed

Chang, Shih Ying; Vizuete, William; Serre, Marc; Vennam, Lakshmi Pradeepa; Omary, Mohammad; Isakov, Vlad; Breen, Michael; Arunachalam, Saravanan

2017-12-01

To quantify the on-road PM 2.5 -related premature mortality at a national scale, previous approaches to estimate concentrations at a 12-km × 12-km or larger grid cell resolution may not fully characterize concentration hotspots that occur near roadways and thus the areas of highest risk. Spatially resolved concentration estimates from on-road emissions to capture these hotspots may improve characterization of the associated risk, but are rarely used for estimating premature mortality. In this study, we compared the on-road PM 2.5 -related premature mortality in central North Carolina with two different concentration estimation approaches-(i) using the Community Multiscale Air Quality (CMAQ) model to model concentration at a coarser resolution of a 36-km × 36-km grid resolution, and (ii) using a hybrid of a Gaussian dispersion model, CMAQ, and a space-time interpolation technique to provide annual average PM 2.5 concentrations at a Census-block level (∼105,000 Census blocks). The hybrid modeling approach estimated 24% more on-road PM 2.5 -related premature mortality than CMAQ. The major difference is from the primary on-road PM 2.5 where the hybrid approach estimated 2.5 times more primary on-road PM 2.5 -related premature mortality than CMAQ due to predicted exposure hotspots near roadways that coincide with high population areas. The results show that 72% of primary on-road PM 2.5 premature mortality occurs within 1,000 m from roadways where 50% of the total population resides, highlighting the importance to characterize near-road primary PM 2.5 and suggesting that previous studies may have underestimated premature mortality due to PM 2.5 from traffic-related emissions. © 2017 Society for Risk Analysis.

Motion-artifact-robust, polarization-resolved second-harmonic-generation microscopy based on rapid polarization switching with electro-optic Pockells cell and its application to in vivo visualization of collagen fiber orientation in human facial skin

PubMed Central

Tanaka, Yuji; Hase, Eiji; Fukushima, Shuichiro; Ogura, Yuki; Yamashita, Toyonobu; Hirao, Tetsuji; Araki, Tsutomu; Yasui, Takeshi

2014-01-01

Polarization-resolved second-harmonic-generation (PR-SHG) microscopy is a powerful tool for investigating collagen fiber orientation quantitatively with low invasiveness. However, the waiting time for the mechanical polarization rotation makes it too sensitive to motion artifacts and hence has hampered its use in various applications in vivo. In the work described in this article, we constructed a motion-artifact-robust, PR-SHG microscope based on rapid polarization switching at every pixel with an electro-optic Pockells cell (PC) in synchronization with step-wise raster scanning of the focus spot and alternate data acquisition of a vertical-polarization-resolved SHG signal and a horizontal-polarization-resolved one. The constructed PC-based PR-SHG microscope enabled us to visualize orientation mapping of dermal collagen fiber in human facial skin in vivo without the influence of motion artifacts. Furthermore, it implied the location and/or age dependence of the collagen fiber orientation in human facial skin. The robustness to motion artifacts in the collagen orientation measurement will expand the application scope of SHG microscopy in dermatology and collagen-related fields. PMID:24761292

Use of three-dimensional time-resolved phase-contrast magnetic resonance imaging with vastly undersampled isotropic projection reconstruction to assess renal blood flow in a renal cell carcinoma patient treated with sunitinib: a case report.

PubMed

Takayama, Tatsuya; Takehara, Yasuo; Sugiyama, Masataka; Sugiyama, Takayuki; Ishii, Yasuo; Johnson, Kevin E; Wieben, Oliver; Wakayama, Tetsuya; Sakahara, Harumi; Ozono, Seiichiro

2014-08-14

New imaging modalities to assess the efficacy of drugs that have molecular targets remain under development. Here, we describe for the first time the use of time-resolved three-dimensional phase-contrast magnetic resonance imaging to monitor changes in blood supply to a tumor during sunitinib treatment in a patient with localized renal cell carcinoma. A 43-year-old Japanese woman with a tumor-bearing but functional single kidney presented at our hospital in July 2012. Computed tomography and magnetic resonance imaging revealed a cT1aN0M0 renal cell carcinoma embedded in the upper central region of the left kidney. She was prescribed sunitinib as neoadjuvant therapy for 8 months, and then underwent partial nephrectomy. Tumor monitoring during this time was done using time-resolved three-dimensional phase-contrast magnetic resonance imaging, a recent technique which specifically measures blood flow in the various vessels of the kidney. This imaging allowed visualization of the redistribution of renal blood flow during treatment, and showed that flow to the tumor was decreased and flows to other areas increased. Of note, this change occurred in the absence of any change in tumor size. The ability of time-resolved three-dimensional phase-contrast magnetic resonance imaging to provide quantitative information on blood supply to tumors may be useful in monitoring the efficacy of sunitinib treatment.

The progenitors of quiescent galaxies at z~2: precision ages and star-formation histories from WFC3/IR spectroscopy

NASA Astrophysics Data System (ADS)

Barro, Guillermo

2013-10-01

The important "adolescent" epoch at redshifts z 1 to 2 bridges a universe of "adult" galaxies at z<1 to an earlier "childhood" period z>2 when galaxies were dramatically different. During this transition, the early quenching of star formation and later enlargement of compact quiescent galaxies since z 2 remain key unsolved mysteries. We have identified a population of compact star-forming galaxies at 2.5 whose structural properties and number densities suggest an evolutionary connection with the first quiescent galaxies. But demonstrating full consistency between progenitor to descendant populations requires high-precision redshifts, ages, and star formation histories to make reliable links in time. We thus propose adding a 56 orbit G102 survey to GOODS-North. The G102 grism meets the required spectral resolution to resolve stellar population ages and connect progenitors to quiescent galaxies, and perfectly bridges the gap for galaxies at 1

Cellular uptake of modified oligonucleotides: fluorescence approach

NASA Astrophysics Data System (ADS)

Kočišová, Eva; Praus, Petr; Rosenberg, Ivan; Seksek, Olivier; Sureau, Franck; Štěpánek, Josef; Turpin, Pierre-Yves

2005-06-01

Cellular uptake and intracellular distribution of the synthetic antisense analogue of dT 15 oligonucleotide (homogenously containing 3'-O-P-CH 2-O-5' internucleotide linkages and labeled with tetramethylrhodamine dye) was studied on B16 melanoma cell line by fluorescence micro-imaging and time-resolved microspectrofluorimetry. By using amphotericin B 3-dimethylaminopropyl amide as an enhancer molecule for the uptake process, homogenous staining of the cells with rather distinct nucleoli staining was achieved after 4 h of incubation. Two spectral components of 2.7 and 1.3 ns lifetime, respectively, were resolved in the emission collected from the cell nucleus. The way of staining and the long-lived component differed from our previous experiments demonstrating complexity of the intracellular oligonucleotide distribution and in particular of the binding inside the nucleus.

Characterization of an Adhesion-Associated Tumor Suppressor in Breast Cancer

DTIC Science & Technology

2001-08-01

Western blot analysis were invasive and associated with fibrous connective tissue (Fig. 4, B of whole cell lysates resolved by SDS-PAGE was...of breast cancer. Immunohistochemical analyses of archival, formalin-fixed paraffin-embedded specimens of benign and malignant breast tissues confirm...10A cells. In particular, EphA2 destabilizes cell-cell attachments while increasing cell interactions with extracellular matrix (ECM proteins). We have

Site-Dependent Fluorescence Decay of Malachite Green Doped in Onion Cell

NASA Astrophysics Data System (ADS)

Nakatsuka, Hiroki; Sekine, Masaya; Suzuki, Yuji; Hattori, Toshiaki

1999-03-01

Time-resolved fluorescence measurements of malachite green dye moleculesdoped in onion cells were carried out.The fluorescence decay time was dependent on the individual cell and on theposition of the dye in a cell, which reflect the microscopic dynamics of each boundsite.Upon cooling, the decay time increased and this increase was accelerated ataround the freezing point of the onion cell.

Tim-3 expression on PD-1+ HCV-specific human CTLs is associated with viral persistence, and its blockade restores hepatocyte-directed in vitro cytotoxicity

PubMed Central

McMahan, Rachel H.; Golden-Mason, Lucy; Nishimura, Michael I.; McMahon, Brian J.; Kemper, Michael; Allen, Todd M.; Gretch, David R.; Rosen, Hugo R.

2010-01-01

Having successfully developed mechanisms to evade immune clearance, hepatitis C virus (HCV) establishes persistent infection in approximately 75%–80% of patients. In these individuals, the function of HCV-specific CD8+ T cells is impaired by ligation of inhibitory receptors, the repertoire of which has expanded considerably in the past few years. We hypothesized that the coexpression of the negative regulatory receptors T cell immunoglobulin and mucin domain–containing molecule 3 (Tim-3) and programmed death 1 (PD-1) in HCV infection would identify patients at risk of developing viral persistence during and after acute HCV infection. The frequency of PD-1–Tim-3– HCV-specific CTLs greatly outnumbered PD-1+Tim-3+ CTLs in patients with acute resolving infection. Moreover, the population of PD-1+Tim-3+ T cells was enriched for within the central memory T cell subset and within the liver. Blockade of either PD-1 or Tim-3 enhanced in vitro proliferation of HCV-specific CTLs to a similar extent, whereas cytotoxicity against a hepatocyte cell line that expressed cognate HCV epitopes was increased exclusively by Tim-3 blockade. These results indicate that the coexpression of these inhibitory molecules tracks with defective T cell responses and that anatomical differences might account for lack of immune control of persistent pathogens, which suggests their manipulation may represent a rational target for novel immunotherapeutic approaches. PMID:21084749

A relation between the characteristic stellar ages of galaxies and their intrinsic shapes

NASA Astrophysics Data System (ADS)

van de Sande, Jesse; Scott, Nicholas; Bland-Hawthorn, Joss; Brough, Sarah; Bryant, Julia J.; Colless, Matthew; Cortese, Luca; Croom, Scott M.; d'Eugenio, Francesco; Foster, Caroline; Goodwin, Michael; Konstantopoulos, Iraklis S.; Lawrence, Jon S.; McDermid, Richard M.; Medling, Anne M.; Owers, Matt S.; Richards, Samuel N.; Sharp, Rob

2018-06-01

Stellar population and stellar kinematic studies provide unique but complementary insights into how galaxies build-up their stellar mass and angular momentum1-3. A galaxy's mean stellar age reveals when stars were formed, but provides little constraint on how the galaxy's mass was assembled. Resolved stellar dynamics4 trace the change in angular momentum due to mergers, but major mergers tend to obscure the effect of earlier interactions5. With the rise of large multi-object integral field spectroscopic surveys, such as SAMI6 and MaNGA7, and single-object integral field spectroscopic surveys (for example, ATLAS3D (ref. 8), CALIFA9, MASSIVE10), it is now feasible to connect a galaxy's star formation and merger history on the same resolved physical scales, over a large range in galaxy mass, morphology and environment4,11,12. Using the SAMI Galaxy Survey, here we present a combined study of spatially resolved stellar kinematics and global stellar populations. We find a strong correlation of stellar population age with location in the (V/σ, ɛe) diagram that links the ratio of ordered rotation to random motions in a galaxy to its observed ellipticity. For the large majority of galaxies that are oblate rotating spheroids, we find that characteristic stellar age follows the intrinsic ellipticity of galaxies remarkably well.

A relation between the characteristic stellar ages of galaxies and their intrinsic shapes

NASA Astrophysics Data System (ADS)

van de Sande, Jesse; Scott, Nicholas; Bland-Hawthorn, Joss; Brough, Sarah; Bryant, Julia J.; Colless, Matthew; Cortese, Luca; Croom, Scott M.; d'Eugenio, Francesco; Foster, Caroline; Goodwin, Michael; Konstantopoulos, Iraklis S.; Lawrence, Jon S.; McDermid, Richard M.; Medling, Anne M.; Owers, Matt S.; Richards, Samuel N.; Sharp, Rob

2018-04-01

Stellar population and stellar kinematic studies provide unique but complementary insights into how galaxies build-up their stellar mass and angular momentum1-3. A galaxy's mean stellar age reveals when stars were formed, but provides little constraint on how the galaxy's mass was assembled. Resolved stellar dynamics4 trace the change in angular momentum due to mergers, but major mergers tend to obscure the effect of earlier interactions5. With the rise of large multi-object integral field spectroscopic surveys, such as SAMI6 and MaNGA7, and single-object integral field spectroscopic surveys (for example, ATLAS3D (ref. 8), CALIFA9, MASSIVE10), it is now feasible to connect a galaxy's star formation and merger history on the same resolved physical scales, over a large range in galaxy mass, morphology and environment4,11,12. Using the SAMI Galaxy Survey, here we present a combined study of spatially resolved stellar kinematics and global stellar populations. We find a strong correlation of stellar population age with location in the (V/σ, ɛe) diagram that links the ratio of ordered rotation to random motions in a galaxy to its observed ellipticity. For the large majority of galaxies that are oblate rotating spheroids, we find that characteristic stellar age follows the intrinsic ellipticity of galaxies remarkably well.

Resolving the Milky Way and Nearby Galaxies with WFIRST

NASA Astrophysics Data System (ADS)

Kalirai, Jasonjot

High-resolution studies of nearby stellar populations have served as a foundation for our quest to understand the nature of galaxies. Today, studies of resolved stellar populations constrain fundamental relations -- such as the initial mass function of stars, the time scales of stellar evolution, the timing of mass loss and amount of energetic feedback, the color-magnitude relation and its dependency on age and metallicity, the stellar-dark matter connection in galaxy halos, and the build up of stellar populations over cosmic time -- that represent key ingredients in our prescription to interpret light from the Universe and to measure the physical state of galaxies. More than in any other area of astrophysics, WFIRST will yield a transformative impact in measuring and characterizing resolved stellar populations in the Milky Way and nearby galaxies. The proximity and level of detail that such populations need to be studied at directly map to all three pillars of WFIRST capabilities - sensitivity from a 2.4 meter space based telescope, resolution from 0.1" pixels, and large 0.3 degree field of view from multiple detectors. Our WFIRST GO Science Investigation Team (F) will develop three WFIRST (notional) GO programs related to resolved stellar populations to fully stress WFIRST's Wide Field Instrument. The programs will include a Survey of the Milky Way, a Survey of Nearby Galaxy Halos, and a Survey of Star-Forming Galaxies. Specific science goals for each program will be validated through a wide range of observational data sets, simulations, and new algorithms. As an output of this study, our team will deliver optimized strategies and tools to maximize stellar population science with WFIRST. This will include: new grids of IR-optimized stellar evolution and synthetic spectroscopic models; pipelines and algorithms for optimal data reduction at the WFIRST sensitivity and pixel scale; wide field simulations of MW environments and galaxy halos; cosmological simulations of nearby galaxy halos matched to WFIRST observations; strategies and automated algorithms to find substructure and dwarf galaxies in WFIRST IR data sets; and documentation. Our team will work closely with the WFIRST Science Center to translate our notional programs into inputs that can help achieve readiness for WFIRST science operations. This includes building full observing programs with target definitions, observing sequences, scheduling constraints, data processing needs, and calibration requirements. Our team has been chosen carefully. Team members are leading scientists in stellar population work that will be a core science theme for WFIRST and are also involved in all large future astronomy projects that will operate in the WFIRST era. The team is intentionally small, and each member will "own" significant science projects. The team will aggressively advocate for WFIRST through innovative initiatives. The team is also diverse in geographical location, observers and theorists, and gender.

Detection of rupture-prone atherosclerotic plaques by time-resolved laser-induced fluorescence spectroscopy.

PubMed

Marcu, Laura; Jo, Javier A; Fang, Qiyin; Papaioannou, Thanassis; Reil, Todd; Qiao, Jian-Hua; Baker, J Dennis; Freischlag, Julie A; Fishbein, Michael C

2009-05-01

Plaque with dense inflammatory cells, including macrophages, thin fibrous cap and superficial necrotic/lipid core is thought to be prone-to-rupture. We report a time-resolved laser-induced fluorescence spectroscopy (TR-LIFS) technique for detection of such markers of plaque vulnerability in human plaques. The autofluorescence of carotid plaques (65 endarterectomy patients) induced by a pulsed laser (337 nm, 0.7 ns) was measured from 831 distinct areas. The emission was resolved spectrally (360-550 nm range) and temporally (0.3 ns resolution) using a prototype fiber-optic TR-LIFS apparatus. Lesions were evaluated microscopically and quantified as to the % of different components (fibrous cap, necrotic core, inflammatory cells, foam cells, mature and degraded collagen, elastic fibers, calcification, and smooth muscle cell of the vessel wall). We determined that the spectral intensities and time-dependent parameters at discrete emission wavelengths (1) allow for discrimination (sensitivity >81%, specificity >94%) of various compositional and pathological features associated with plaque vulnerability including infiltration of macrophages into intima and necrotic/lipid core under a thin fibrous cap, and (2) show a linear correlation with plaque biochemical content: elastin (P<0.008), collagen (P<0.02), inflammatory cells (P<0.003), necrosis (P<0.004). Our results demonstrate the feasibility of TR-LIFS as a method for the identification of markers of plaque vulnerability. Current findings enable future development of TR-LIFS-based clinical devices for rapid investigation of atherosclerotic plaques and detection of those at high-risk.

Super-resolution binding activated localization microscopy through reversible change of DNA conformation.

PubMed

Szczurek, Aleksander; Birk, Udo; Knecht, Hans; Dobrucki, Jurek; Mai, Sabine; Cremer, Christoph

2018-01-01

Methods of super-resolving light microscopy (SRM) have found an exponentially growing range of applications in cell biology, including nuclear structure analyses. Recent developments have proven that Single Molecule Localization Microscopy (SMLM), a type of SRM, is particularly useful for enhanced spatial analysis of the cell nucleus due to its highest resolving capability combined with very specific fluorescent labeling. In this commentary we offer a brief review of the latest methodological development in the field of SMLM of chromatin designated DNA Structure Fluctuation Assisted Binding Activated Localization Microscopy (abbreviated as fBALM) as well as its potential future applications in biology and medicine.

Super-resolution binding activated localization microscopy through reversible change of DNA conformation

PubMed Central

Knecht, Hans; Dobrucki, Jurek; Mai, Sabine

2018-01-01

ABSTRACT Methods of super-resolving light microscopy (SRM) have found an exponentially growing range of applications in cell biology, including nuclear structure analyses. Recent developments have proven that Single Molecule Localization Microscopy (SMLM), a type of SRM, is particularly useful for enhanced spatial analysis of the cell nucleus due to its highest resolving capability combined with very specific fluorescent labeling. In this commentary we offer a brief review of the latest methodological development in the field of SMLM of chromatin designated DNA Structure Fluctuation Assisted Binding Activated Localization Microscopy (abbreviated as fBALM) as well as its potential future applications in biology and medicine. PMID:29297245

Eddy current imaging with an atomic radio-frequency magnetometer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wickenbrock, Arne, E-mail: wickenbr@uni-mainz.de; Leefer, Nathan; Blanchard, John W.

2016-05-02

We use a radio-frequency {sup 85}Rb alkali-vapor cell magnetometer based on a paraffin-coated cell with long spin-coherence time and a small, low-inductance driving coil to create highly resolved conductivity maps of different objects. We resolve sub-mm features in conductive objects, we characterize the frequency response of our technique, and by operating at frequencies up to 250 kHz we are able to discriminate between differently conductive materials based on the induced response. The method is suited to cover a wide range of driving frequencies and can potentially be used for detecting non-metallic objects with low DC conductivity.

Severe pernicious anaemia in an 8-year-old African girl.

PubMed

van Loon, M; Postels, D G; Heikens, G T; Molyneux, E

2009-09-01

An 8-year-old girl presented with severe muscular weakness, peripheral neuropathy, ataxia, fever and macrocytic anaemia. Clinically, vitamin B(12) (cobalamin) deficiency was considered. Despite the lack of pre-treatment laboratory confirmation of the diagnosis, a therapeutic trial of hydroxocobalamin injections was begun. After several days, a partial clinical response was seen. Within 5 months all symptoms had resolved. After treatment was initiated, laboratory analysis of pre-treatment blood samples confirmed the presence of vitamin B(12) deficiency. Auto-antibodies to intrinsic factor and parietal cells, pathognomonic for pernicious anaemia, were confirmed. Vitamin B(12) deficiency owing to dietary deficiency is not uncommon in children in developing countries. Although nutritional deficiency might have played a role in our patient, this case illustrates that the neurological manifestations of pernicious anaemia can present at a young age in African populations.

Molecular diversification of Trichuris spp. from Sigmodontinae (Cricetidae) rodents from Argentina based on mitochondrial DNA sequences.

PubMed

Callejón, Rocío; Robles, María Del Rosario; Panei, Carlos Javier; Cutillas, Cristina

2016-08-01

A molecular phylogenetic hypothesis is presented for the genus Trichuris based on sequence data from mitochondrial cytochrome c oxidase 1 (cox1) and cytochrome b (cob). The taxa consisted of nine populations of whipworm from five species of Sigmodontinae rodents from Argentina. Bayesian Inference, Maximum Parsimony, and Maximum Likelihood methods were used to infer phylogenies for each gene separately but also for the combined mitochondrial data and the combined mitochondrial and nuclear dataset. Phylogenetic results based on cox1 and cob mitochondrial DNA (mtDNA) revealed three clades strongly resolved corresponding to three different species (Trichuris navonae, Trichuris bainae, and Trichuris pardinasi) showing phylogeographic variation, but relationships among Trichuris species were poorly resolved. Phylogenetic reconstruction based on concatenated sequences had greater phylogenetic resolution for delimiting species and populations intra-specific of Trichuris than those based on partitioned genes. Thus, populations of T. bainae and T. pardinasi could be affected by geographical factors and co-divergence parasite-host.

Picosecond rotationally resolved stimulated emission pumping spectroscopy of nitric oxide

NASA Astrophysics Data System (ADS)

Tanjaroon, Chakree; Reeve, Scott W.; Ford, Alan; Murry, W. Dean; Lyon, Kevin; Yount, Bret; Britton, Dan; Burns, William A.; Allen, Susan D.; Bruce Johnson, J.

2012-01-01

Stimulated emission pumping (SEP) experiments were performed on the nitric oxide molecule in a flow cell environment using lasers with pulse widths of 17-25 ps. A lambda excitation scheme, or ''pump-dump" arrangement, was employed with the pump laser tuned to the T 00 vibronic band origin ( λ=226.35(1)nm) of the A2Σ+( v' = 0, J') ← X2Π1/2( v″ = 0, J″) and the dump laser scanned from 246-248 nm within the A2Σ+( v' = 0, J') → X2Π1/2( v″ = 2, J″) transition. The rotationally resolved SEP spectra were measured by observing the total fluorescence within the A2Σ+( v' = 0, J') → X2Π1/2( v″ = 1, J″) transition between 235 nm and 237.2 nm while scanning the dump laser wavelengths. Multiple rotational states were excited due to the broad laser bandwidth. Measurements showed that the resolved rotational structure depended on the energy and bandwidth of the applied pump and dump laser pulses. Analysis of the observed fluorescence depletion signals yielded an average percent fluorescence depletion of about 19% when λ=226.35(1)nm and λ=247.91(1)nm. This value reflects the percent transfer of the NO population from the A2Σ+( V' = 0, J') excited electronic state to the X2Π1/2( v″ = 2, J″) ground electronic state. The maximum expected depletion is 50% in the limit of dump saturation. Selective excitation of NO at the bandhead provides good spectral discrimination from the background emission and noise and unambiguously confirms the identity of the emitter.

Charge Separation and Triplet Exciton Formation Pathways in Small-Molecule Solar Cells as Studied by Time-Resolved EPR Spectroscopy

DOE PAGES

Thomson, Stuart A. J.; Niklas, Jens; Mardis, Kristy L.; ...

2017-09-13

Organic solar cells are a promising renewable energy technology, offering the advantages of mechanical flexibility and solution processability. An understanding of the electronic excited states and charge separation pathways in these systems is crucial if efficiencies are to be further improved. Here we use light induced electron paramagnetic resonance (LEPR) spectroscopy and density functional theory calculations (DFT) to study the electronic excited states, charge transfer (CT) dynamics and triplet exciton formation pathways in blends of the small molecule donors (DTS(FBTTh 2) 2, DTS(F2BTTh 2) 2, DTS(PTTh 2) 2, DTG(FBTTh 2) 2 and DTG(F2BTTh 2) 2) with the fullerene derivative PCmore » 61BM. Using high frequency EPR the g-tensor of the positive polaron on the donor molecules was determined. The experimental results are compared with DFT calculations which reveal that the spin density of the polaron is distributed over a dimer or trimer. Time-resolved EPR (TR-EPR) spectra attributed to singlet CT states were identified and the polarization patterns revealed similar charge separation dynamics in the four fluorobenzothiadiazole donors, while charge separation in the DTS(PTTh 2) 2 blend is slower. Using TR-EPR we also investigated the triplet exciton formation pathways in the blend. The polarization patterns reveal that the excitons originate from both intersystem crossing (ISC) and back electron transfer (BET) processes. The DTS(PTTh 2) 2 blend was found to contain substantially more triplet excitons formed by BET than the fluorobenzothiadiazole blends. As a result, the higher BET triplet exciton population in the DTS(PTTh 2) 2 blend is in accordance with the slower charge separation dynamics observed in this blend.« less

Charge Separation and Triplet Exciton Formation Pathways in Small Molecule Solar Cells as Studied by Time-resolved EPR Spectroscopy.

PubMed

Thomson, Stuart A J; Niklas, Jens; Mardis, Kristy L; Mallares, Christopher; Samuel, Ifor D W; Poluektov, Oleg G

2017-10-19

Organic solar cells are a promising renewable energy technology, offering the advantages of mechanical flexibility and solution processability. An understanding of the electronic excited states and charge separation pathways in these systems is crucial if efficiencies are to be further improved. Here we use light induced electron paramagnetic resonance (LEPR) spectroscopy and density functional theory calculations (DFT) to study the electronic excited states, charge transfer (CT) dynamics and triplet exciton formation pathways in blends of the small molecule donors (DTS(FBTTh 2 ) 2 , DTS(F 2 BTTh 2 ) 2 , DTS(PTTh 2 ) 2 , DTG(FBTTh 2 ) 2 and DTG(F 2 BTTh 2 ) 2 ) with the fullerene derivative PC 61 BM. Using high frequency EPR the g-tensor of the positive polaron on the donor molecules was determined. The experimental results are compared with DFT calculations which reveal that the spin density of the polaron is distributed over a dimer or trimer. Time-resolved EPR (TR-EPR) spectra attributed to singlet CT states were identified and the polarization patterns revealed similar charge separation dynamics in the four fluorobenzothiadiazole donors, while charge separation in the DTS(PTTh 2 ) 2 blend is slower. Using TR-EPR we also investigated the triplet exciton formation pathways in the blend. The polarization patterns reveal that the excitons originate from both intersystem crossing (ISC) and back electron transfer (BET) processes. The DTS(PTTh 2 ) 2 blend was found to contain substantially more triplet excitons formed by BET than the fluorobenzothiadiazole blends. The higher BET triplet exciton population in the DTS(PTTh 2 ) 2 blend is in accordance with the slower charge separation dynamics observed in this blend.

Charge Separation and Triplet Exciton Formation Pathways in Small-Molecule Solar Cells as Studied by Time-Resolved EPR Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thomson, Stuart A. J.; Niklas, Jens; Mardis, Kristy L.

Organic solar cells are a promising renewable energy technology, offering the advantages of mechanical flexibility and solution processability. An understanding of the electronic excited states and charge separation pathways in these systems is crucial if efficiencies are to be further improved. Here we use light induced electron paramagnetic resonance (LEPR) spectroscopy and density functional theory calculations (DFT) to study the electronic excited states, charge transfer (CT) dynamics and triplet exciton formation pathways in blends of the small molecule donors (DTS(FBTTh 2) 2, DTS(F2BTTh 2) 2, DTS(PTTh 2) 2, DTG(FBTTh 2) 2 and DTG(F2BTTh 2) 2) with the fullerene derivative PCmore » 61BM. Using high frequency EPR the g-tensor of the positive polaron on the donor molecules was determined. The experimental results are compared with DFT calculations which reveal that the spin density of the polaron is distributed over a dimer or trimer. Time-resolved EPR (TR-EPR) spectra attributed to singlet CT states were identified and the polarization patterns revealed similar charge separation dynamics in the four fluorobenzothiadiazole donors, while charge separation in the DTS(PTTh 2) 2 blend is slower. Using TR-EPR we also investigated the triplet exciton formation pathways in the blend. The polarization patterns reveal that the excitons originate from both intersystem crossing (ISC) and back electron transfer (BET) processes. The DTS(PTTh 2) 2 blend was found to contain substantially more triplet excitons formed by BET than the fluorobenzothiadiazole blends. As a result, the higher BET triplet exciton population in the DTS(PTTh 2) 2 blend is in accordance with the slower charge separation dynamics observed in this blend.« less

A Facile Droplet-Chip-Time-Resolved Inductively Coupled Plasma Mass Spectrometry Online System for Determination of Zinc in Single Cell.

PubMed

Wang, Han; Chen, Beibei; He, Man; Hu, Bin

2017-05-02

Single cell analysis is a significant research field in recent years reflecting the heterogeneity of cells in a biological system. In this work, a facile droplet chip was fabricated and online combined with time-resolved inductively coupled plasma mass spectrometry (ICPMS) via a microflow nebulizer for the determination of zinc in single HepG2 cells. On the focusing geometric designed PDMS microfluidic chip, the aqueous cell suspension was ejected and divided by hexanol to generate droplets. The droplets encapsulated single cells remain intact during the transportation into ICP for subsequent detection. Under the optimized conditions, the frequency of droplet generation is 3-6 × 10 6 min -1 , and the injected cell number is 2500 min -1 , which can ensure the single cell encapsulation. ZnO nanoparticles (NPs) were used for the quantification of zinc in single cells, and the accuracy was validated by conventional acid digestion-ICPMS method. The ZnO NPs incubated HepG2 cells were analyzed as model samples, and the results exhibit the heterogeneity of HepG2 cells in the uptake/adsorption of ZnO NPs. The developed online droplet-chip-ICPMS analysis system achieves stable single cell encapsulation and has high throughput for single cell analysis. It has the potential in monitoring the content as well as distribution of trace elements/NPs at the single cell level.

Photodynamic inactivation of Escherichia coli - Correlation of singlet oxygen kinetics and phototoxicity.

PubMed

Müller, Alexander; Preuß, Annegret; Röder, Beate

2018-01-01

Photodynamic inactivation (PDI) of bacteria may play a major role in facing the challenge of the ever expanding antibiotic resistances. Here we report about the direct correlation of singlet oxygen luminescence kinetics and phototoxicity in E. coli cell suspension under PDI using the widely applied cationic photosensitizer TMPyP. Through direct access to the microenvironment, the time resolved investigation of singlet oxygen luminescence plays a key role in understanding the photosensitization mechanism and inactivation pathway. Using the homemade set-up for highly sensitive time resolved singlet oxygen luminescence detection, we show that the cationic TMPyP is localized predominantly outside the bacterial cells but in their immediate vicinity prior to photodynamic inactivation. Throughout following light exposure, a clear change in singlet oxygen kinetics indicates a redistribution of photosensitizer molecules to at least one additional microenvironment. We found the signal kinetics mirrored in cell viability measurements of equally treated samples from same overnight cultures conducted in parallel: A significant drop in cell viability of the illuminated samples and stationary viability of dark controls. Thus, for the system investigated in this work - a Gram-negative model bacteria and a well-known PS for its PDI - singlet oxygen kinetics correlates with phototoxicity. This finding suggests that it is well possible to evaluate PDI efficiency directly via time resolved singlet oxygen detection. Copyright © 2017 Elsevier B.V. All rights reserved.

Time resolved study of cell death mechanisms induced by amine-modified polystyrene nanoparticles

NASA Astrophysics Data System (ADS)

Wang, Fengjuan; Bexiga, Mariana G.; Anguissola, Sergio; Boya, Patricia; Simpson, Jeremy C.; Salvati, Anna; Dawson, Kenneth A.

2013-10-01

Positively charged polymers and nanoparticles (NPs) can be toxic to cells in various systems. Using human astrocytoma cells, we have previously shown that 50 nm amine-modified polystyrene NPs damage mitochondria and induce cell death by apoptosis. Here we provide comprehensive details of the cellular events occurring after exposure to the NPs in a time-resolved manner. We demonstrate that the accumulation of NPs in lysosomes plays a central role in the observed cell death, leading to swelling of the lysosomes and release of cathepsins into the cytosol, which ultimately propagates the damage to the mitochondria with subsequent activation of apoptosis. This is accompanied and sustained by other events, such as increasing ROS levels and autophagy. Using various inhibitors, we also show the interplay between apoptosis and autophagy as a response to NP accumulation in lysosomes.Positively charged polymers and nanoparticles (NPs) can be toxic to cells in various systems. Using human astrocytoma cells, we have previously shown that 50 nm amine-modified polystyrene NPs damage mitochondria and induce cell death by apoptosis. Here we provide comprehensive details of the cellular events occurring after exposure to the NPs in a time-resolved manner. We demonstrate that the accumulation of NPs in lysosomes plays a central role in the observed cell death, leading to swelling of the lysosomes and release of cathepsins into the cytosol, which ultimately propagates the damage to the mitochondria with subsequent activation of apoptosis. This is accompanied and sustained by other events, such as increasing ROS levels and autophagy. Using various inhibitors, we also show the interplay between apoptosis and autophagy as a response to NP accumulation in lysosomes. Electronic supplementary information (ESI) available: additional analysis of flow cytometry results, western blots and experiments with cathepsin inhibitors. See DOI: 10.1039/c3nr03249c

Mechanisms of failed apoptotic cell clearance by phagocyte subsets in cardiovascular disease

PubMed Central

2013-01-01

Recent evidence in humans indicate that defective phagocytic clearance of dying cells is linked to progression of advanced atherosclerotic lesions, the precursor to atherothrombosis, ischemic heart disease, and leading cause of death in the industrialized world. During atherogenesis, apoptotic cell turnover in the vascular wall is counterbalanced by neighboring phagocytes with high clearance efficiency, thereby limiting cellularity and maintaining lesion integrity. However, as lesions mature, phagocytic removal of apoptotic cells (efferocytosis) becomes defective, leading to secondary necrosis, expansion of plaque necrotic cores, and susceptibility to rupture. Recent genetic causation studies in experimental rodents have implicated key molecular regulators of efferocytosis in atherosclerotic progression. These include MER tyrosine kinase (MERTK), milk fat globule-EGF factor 8 (MFGE8), and complement C1q. At the cellular level, atheromata are infiltrated by a heterogenous population of professional phagocytes, comprised of monocytes, differentiated macrophages, and CD11c+ dendritic-like cells. Each cell type is characterized by disparate clearance efficiencies and varying activities of key phagocytic signaling molecules. It is in this context that we outline a working model whereby plaque necrosis and destabilization is jointly promoted by (1) direct inhibition of core phagocytic signaling pathways and (2) expansion of phagocyte subsets with poor clearance capacity. Towards identifying targets for promoting efficient apoptotic cell clearance and resolving inflammation in atherosclerosis and during ischemic heart disease and post myocardial infarction, this review will discuss potential in vivo suppressors of efferocytosis at each stage of clearance and how these putative interventional targets may differentially affect uptake at the level of vascular phagocyte subsets. PMID:20552278

Time-resolved, single-cell analysis of induced and programmed cell death via non-invasive propidium iodide and counterstain perfusion.

PubMed

Krämer, Christina E M; Wiechert, Wolfgang; Kohlheyer, Dietrich

2016-09-01

Conventional propidium iodide (PI) staining requires the execution of multiple steps prior to analysis, potentially affecting assay results as well as cell vitality. In this study, this multistep analysis method has been transformed into a single-step, non-toxic, real-time method via live-cell imaging during perfusion with 0.1 μM PI inside a microfluidic cultivation device. Dynamic PI staining was an effective live/dead analytical tool and demonstrated consistent results for single-cell death initiated by direct or indirect triggers. Application of this method for the first time revealed the apparent antibiotic tolerance of wild-type Corynebacterium glutamicum cells, as indicated by the conversion of violet fluorogenic calcein acetoxymethyl ester (CvAM). Additional implementation of this method provided insight into the induced cell lysis of Escherichia coli cells expressing a lytic toxin-antitoxin module, providing evidence for non-lytic cell death and cell resistance to toxin production. Finally, our dynamic PI staining method distinguished necrotic-like and apoptotic-like cell death phenotypes in Saccharomyces cerevisiae among predisposed descendants of nutrient-deprived ancestor cells using PO-PRO-1 or green fluorogenic calcein acetoxymethyl ester (CgAM) as counterstains. The combination of single-cell cultivation, fluorescent time-lapse imaging, and PI perfusion facilitates spatiotemporally resolved observations that deliver new insights into the dynamics of cellular behaviour.

Angle-resolved light scattering of individual rod-shaped bacteria based on Fourier transform light scattering

NASA Astrophysics Data System (ADS)

Jo, Youngju; Jung, Jaehwang; Lee, Jee Woong; Shin, Della; Park, Hyunjoo; Nam, Ki Tae; Park, Ji-Ho; Park, Yongkeun

2014-05-01

Two-dimensional angle-resolved light scattering maps of individual rod-shaped bacteria are measured at the single-cell level. Using quantitative phase imaging and Fourier transform light scattering techniques, the light scattering patterns of individual bacteria in four rod-shaped species (Bacillus subtilis, Lactobacillus casei, Synechococcus elongatus, and Escherichia coli) are measured with unprecedented sensitivity in a broad angular range from -70° to 70°. The measured light scattering patterns are analyzed along the two principal axes of rod-shaped bacteria in order to systematically investigate the species-specific characteristics of anisotropic light scattering. In addition, the cellular dry mass of individual bacteria is calculated and used to demonstrate that the cell-to-cell variations in light scattering within bacterial species is related to the cellular dry mass and growth.

Single-cell genomics reveals co-metabolic interactions within uncultivated Marine Group A bacteria

NASA Astrophysics Data System (ADS)

Hawley, A. K.; Hallam, S. J.

2016-02-01

Marine Group A (MGA) bacteria represent a ubiquitous and abundant candidate phylum enriched in oxygen minimum zones (OMZs) and the deep ocean. Despite MGA prevalence little is known about their ecology and biogeochemistry. Here we chart the metabolic potential of 26 MGA single-cell amplified genomes sourced from different environments spanning ecothermodynamic gradients including open ocean waters, OMZs and methanogenic environments including a terephthalate-degrading bioreactor. Metagenomic contig recruitment to SAGs combined with tetra-nucleotide frequency distribution patterns resolved nine MGA population genome bins. All population genomes exhibited genomic streamlining with open ocean MGA being the most reduced. Different strategies for carbohydrate utilization, carbon fixation energy metabolism and respiratory pathways were identified between population genome bins, including various roles in the nitrogen and sulfur cycles. MGA inhabiting OMZ oxyclines encoded genes for partial denitrification with potential to feed into anammox and nitrification as well as a polysulfide reductase with a potential role in the cryptic sulfur cycle. MGA inhabiting anoxic waters, encoded NiFe hydrogenase and nitrous oxide reductase with the potential to complete partial denitrification pathways previously linked to sulfur oxidation in SUP05 bacteria. MGA from methanogenic environments encoded genes mediating cascading syntrophic interactions with fatty acid degraders and methanogens including reverse electron transport potential. The MGA phylum appears to have evolved alternative metabolic innovations adapting specific subgroups to occupy specific niches along ecothermodynamic gradients. Additionally, expression of MGA genes from different OMZ environments supports that these subgroups manifest an increasing propensity for co-metabolic interactions under energy limiting conditions that mandates a cooperative mode of existence with important implications for C, N and S cycling in marine ecosystems.

Electrochemical Quantification of Extracellular Local H2O2 Kinetics Originating from Single Cells.

PubMed

Bozem, Monika; Knapp, Phillip; Mirčeski, Valentin; Slowik, Ewa J; Bogeski, Ivan; Kappl, Reinhard; Heinemann, Christian; Hoth, Markus

2017-05-15

H 2 O 2 is produced by all eukaryotic cells under physiological and pathological conditions. Due to its enormous relevance for cell signaling at low concentrations and antipathogenic function at high concentrations, precise quantification of extracellular local H 2 O 2 concentrations ([H 2 O 2 ]) originating from single cells is required. Using a scanning electrochemical microscope and bare platinum disk ultramicroelectrodes, we established sensitive long-term measurements of extracellular [H 2 O 2 ] kinetics originating from single primary human monocytes (MCs) ex vivo. For the electrochemical techniques square wave voltammetry, cyclic and linear scan voltammetry, and chronoamperometry, detection limits for [H 2 O 2 ] were determined to be 5, 50, and 500 nM, respectively. Following phorbol ester stimulation, local [H 2 O 2 ] 5-8 μm above a single MC increased by 3.4 nM/s within the first 10 min before reaching a plateau. After extracellular addition of H 2 O 2 to an unstimulated MC, the local [H 2 O 2 ] decreased on average by 4.2 nM/s due to degradation processes of the cell. Using the scanning mode of the setup, we found that H 2 O 2 is evenly distributed around the producing cell and can still be detected up to 30 μm away from the cell. The electrochemical single-cell measurements were validated in MC populations using electron spin resonance spectroscopy and the Amplex ® UltraRed assay. Innovation and Conclusion: We demonstrate a highly sensitive, spatially, and temporally resolved electrochemical approach to monitor dynamics of production and degradation processes for H 2 O 2 separately. Local extracellular [H 2 O 2 ] kinetics originating from single cells is quantified in real time. Antioxid. Redox Signal. 00, 000-000.

Molecular phylogeography and cryptic speciation in the mosses, Mielichhoferia elongata and M. mielichhoferiana (Bryaceae).

PubMed

Shaw, A J

2000-05-01

Nucleotide sequence variation in the ITS1-5.8S-ITS2 region of nuclear ribosomal DNA (nrDNA) from 70 populations of Mielichhoferia elongata and M. mielichhoferiana, plus two outgroup species, was analysed using maximum parsimony and maximum likelihood methods. High levels of nucleotide substitution and numerous insertion-deletion events were detected within and between the two species. M. elongata is monophyletic with regard to nrDNA variation, but M. mielichhoferiana is paraphyletic. (M. elongata is nested within it.) A clade within M. mielichhoferiana provides evidence of vicariance, with North American and Scandinavian sister groups of populations. Two major clades are resolved in M. elongata by sequence data that are completely congruent with previous isozyme work. One clade includes populations from both North America and Europe whereas the other is strictly North American. These two clades, resolved by multiple independent loci, clearly represent cryptic species within the morphologically uniform M. elongata. Certain geographical areas, most notably southwestern Colorado in Ouray and San Juan Counties, harbour diverse populations of M. elongata with distinct phylogenetic and phylogeographical histories. Morphologically indistinguishable but phylogenetically distant populations were detected a few metres apart at one site. In contrast, all populations collected over hundreds of kilometres in California belong to a single clade. Arctic North American populations belong to a clade that includes disjunct populations in Alaska, northern Ellesmere Island, and the northeastern USA, but not subarctic Swedish populations, which are more closely related to plants from the Rocky Mountains. Morphological uniformity belies complex infraspecific phylogenetic patterns within M. elongata and M. mielichhoferiana.

Time resolved impedance spectroscopy analysis of lithium phosphorous oxynitride - LiPON layers under mechanical stress

NASA Astrophysics Data System (ADS)

Glenneberg, Jens; Bardenhagen, Ingo; Langer, Frederieke; Busse, Matthias; Kun, Robert

2017-08-01

In this paper we present investigations on the morphological and electrochemical changes of lithium phosphorous oxynitride (LiPON) under mechanically bent conditions. Therefore, two types of electrochemical cells with LiPON thin films were prepared by physical vapor deposition. First, symmetrical cells with two blocking electrodes (Cu/LiPON/Cu) were fabricated. Second, to simulate a more application-related scenario cells with one blocking and one non-blocking electrode (Cu/LiPON/Li/Cu) were analyzed. In order to investigate mechanical distortion induced transport property changes in LiPON layers the cells were deposited on a flexible polyimide substrate. Morphology of the as-prepared samples and deviations from the initial state after applying external stress by bending the cells over different radii were investigated by Focused Ion Beam- Scanning Electron Microscopy (FIB-SEM) cross-section and surface images. Mechanical stress induced changes in the impedance were evaluated by time-resolved electrochemical impedance spectroscopy (EIS). Due to the formation of a stable, ion-conducting solid electrolyte interphase (SEI), cells with lithium show decreased impedance values. Furthermore, applying mechanical stress to the cells results in a further reduction of the electrolyte resistance. These results are supported by finite element analysis (FEA) simulations.

Red Blood Cell Antigen Genotyping for Sickle Cell Disease, Thalassemia, and Other Transfusion Complications.

PubMed

Fasano, Ross M; Chou, Stella T

2016-10-01

Since the discovery of the ABO blood group in the early 20th century, more than 300 blood group antigens have been categorized among 35 blood group systems. The molecular basis for most blood group antigens has been determined and demonstrates tremendous genetic diversity, particularly in the ABO and Rh systems. Several blood group genotyping assays have been developed, and 1 platform has been approved by the Food and Drug Administration as a "test of record," such that no phenotype confirmation with antisera is required. DNA-based red blood cell (RBC) phenotyping can overcome certain limitations of hemagglutination assays and is beneficial in many transfusion settings. Genotyping can be used to determine RBC antigen phenotypes in patients recently transfused or with interfering allo- or autoantibodies, to resolve discrepant serologic typing, and/or when typing antisera are not readily available. Molecular RBC antigen typing can facilitate complex antibody evaluations and guide RBC selection for patients with sickle cell disease (SCD), thalassemia, and autoimmune hemolytic anemia. High-resolution RH genotyping can identify variant RHD and RHCE in patients with SCD, which have been associated with alloimmunization. In the future, broader access to cost-efficient, high-resolution RBC genotyping technology for both patient and donor populations may be transformative for the field of transfusion medicine. Copyright © 2016. Published by Elsevier Inc.

Subnuclear foci quantification using high-throughput 3D image cytometry

NASA Astrophysics Data System (ADS)

Wadduwage, Dushan N.; Parrish, Marcus; Choi, Heejin; Engelward, Bevin P.; Matsudaira, Paul; So, Peter T. C.

2015-07-01

Ionising radiation causes various types of DNA damages including double strand breaks (DSBs). DSBs are often recognized by DNA repair protein ATM which forms gamma-H2AX foci at the site of the DSBs that can be visualized using immunohistochemistry. However most of such experiments are of low throughput in terms of imaging and image analysis techniques. Most of the studies still use manual counting or classification. Hence they are limited to counting a low number of foci per cell (5 foci per nucleus) as the quantification process is extremely labour intensive. Therefore we have developed a high throughput instrumentation and computational pipeline specialized for gamma-H2AX foci quantification. A population of cells with highly clustered foci inside nuclei were imaged, in 3D with submicron resolution, using an in-house developed high throughput image cytometer. Imaging speeds as high as 800 cells/second in 3D were achieved by using HiLo wide-field depth resolved imaging and a remote z-scanning technique. Then the number of foci per cell nucleus were quantified using a 3D extended maxima transform based algorithm. Our results suggests that while most of the other 2D imaging and manual quantification studies can count only up to about 5 foci per nucleus our method is capable of counting more than 100. Moreover we show that 3D analysis is significantly superior compared to the 2D techniques.

The resolved stellar populations around 12 Type IIP supernovae

NASA Astrophysics Data System (ADS)

Maund, Justyn R.

2017-08-01

Core-collapse supernovae (SNe) are found in regions associated with recent massive star formation. The stellar population observed around the location of a SN can be used as a probe of the origins of the progenitor star. We apply a Bayesian mixture model to fit isochrones to the massive star population around 12 Type IIP SNe, for which constraints on the progenitors are also available from fortuitous pre-explosion images. Using the high-resolution Hubble Space Telescope Advanced Camera for Surveys and Wide Field Camera 3, we study the massive star population found within 100 pc of each of our target SNe. For most of the SNe in our sample, we find that there are multiple age components in the surrounding stellar populations. In the cases of SNe 2003gd and 2005cs, we find that the progenitor does not come from the youngest stellar population component and, in fact, these relatively low mass progenitors (˜8 M⊙) are found in close proximity to stars as massive as 15 and 50-60 M⊙, respectively. Overall, the field extinction (Galactic and host) derived for these populations is ˜0.3 mag higher than the extinction that was generally applied in previously reported progenitor analyses. We also find evidence, in particular for SN 2004dj, for significant levels of differential extinction. Our analysis for SN 2008bk suggests a significantly lower extinction for the population than the progenitor, but the lifetime of the population and mass determined from pre-explosion images agree. Overall, assuming that the appropriate age component can be suitably identified from the multiple stellar population components present, we find that our Bayesian approach to studying resolved stellar populations can match progenitor masses determined from direct imaging to within ±3 M⊙.

Relative information content of polymorphic microsatellites and mitochondrial DNA for inferring dispersal and population genetic structure in the olive sea snake, Aipysurus laevis.

PubMed

Lukoschek, V; Waycott, M; Keogh, J S

2008-07-01

Polymorphic microsatellites are widely considered more powerful for resolving population structure than mitochondrial DNA (mtDNA) markers, particularly for recently diverged lineages or geographically proximate populations. Weaker population subdivision for biparentally inherited nuclear markers than maternally inherited mtDNA may signal male-biased dispersal but can also be attributed to marker-specific evolutionary characteristics and sampling properties. We discriminated between these competing explanations with a population genetic study on olive sea snakes, Aipysurus laevis. A previous mtDNA study revealed strong regional population structure for A. laevis around northern Australia, where Pleistocene sea-level fluctuations have influenced the genetic signatures of shallow-water marine species. Divergences among phylogroups dated to the Late Pleistocene, suggesting recent range expansions by previously isolated matrilines. Fine-scale population structure within regions was, however, poorly resolved for mtDNA. In order to improve estimates of fine-scale genetic divergence and to compare population structure between nuclear and mtDNA, 354 olive sea snakes (previously sequenced for mtDNA) were genotyped for five microsatellite loci. F statistics and Bayesian multilocus genotype clustering analyses found similar regional population structure as mtDNA and, after standardizing microsatellite F statistics for high heterozygosities, regional divergence estimates were quantitatively congruent between marker classes. Over small spatial scales, however, microsatellites recovered almost no genetic structure and standardized F statistics were orders of magnitude smaller than for mtDNA. Three tests for male-biased dispersal were not significant, suggesting that recent demographic expansions to the typically large population sizes of A. laevis have prevented microsatellites from reaching mutation-drift equilibrium and local populations may still be diverging.

The Decennial Census: Potential Risks to Data Quality Resulting from Budget Reductions and Cost Increases

DTIC Science & Technology

1990-03-27

coding of certain population characteristic data and thus delay the publication of these data. This is similar to what happened in the 1980 census...when, because of budget shortfalls, the Bureau reduced the number of staff who coded population characteristic 5 data from questionnaires, contributing...Decennial Census: An Update, (GAO/T-GGD-89-15, Mar. 23, 1989). 6 missing population characteristic data would have been resolved either by telephone or a

Time-Resolved Analysis of Cytosolic and Surface-Associated Proteins of Staphylococcus aureus HG001 under Planktonic and Biofilm Conditions.

PubMed

Moche, Martin; Schlüter, Rabea; Bernhardt, Jörg; Plate, Kristina; Riedel, Katharina; Hecker, Michael; Becher, Dörte

2015-09-04

Staphylococcal biofilms are associated with persistent infections due to their capacity to protect bacteria against the host's immune system and antibiotics. Cell-surface-associated proteins are of great importance during biofilm formation. In the present study, an optimized biotinylation approach for quantitative GeLC-MS-based analysis of the staphylococcal cell-surface proteome was applied and the cytoplasmic protein fraction was analyzed to elucidate proteomic differences between colony biofilms and planktonic cells. The experimental setup enabled a time-resolved monitoring of the proteome under both culture conditions and the comparison of biofilm cells to planktonic cells at several time points. This allowed discrimination of differences attributed to delayed growth phases from responses provoked by biofilm conditions. Biofilm cells expressed CcpA-dependent catabolic proteins earlier than planktonic cells and strongly accumulated proteins that belong to the SigB stress regulon. The amount of the cell-surface protein and virulence gene regulator Rot decreased within biofilms and MgrA-dependent regulations appeared more pronounced. Biofilm cells simultaneously up-regulated activators (e.g., SarZ) as well as repressors (e.g., SarX) of RNAIII. A decreased amount of high-affinity iron uptake systems and an increased amount of the iron-storage protein FtnA possibly indicated a lower demand of iron in biofilms.

Validation of a time-resolved fluorescence spectroscopy apparatus in a rabbit atherosclerosis model

NASA Astrophysics Data System (ADS)

Fang, Qiyin; Jo, Javier A.; Papaioannou, Thanassis; Dorafshar, Amir; Reil, Todd; Qiao, Jian-Hua; Fishbein, Michael C.; Freischlag, Julie A.; Marcu, Laura

2004-07-01

Time-resolved laser-induced fluorescence spectroscopy (tr-LIFS) has been studied as a potential tool for in vivo diagnosis of atherosclerotic lesions. This study is to evaluate the potential of a compact fiber-optics based tr-LIFS instrument developed in our laboratory for in vivo analysis of atherosclerotic plaque composition. Time-resolved fluorescence spectroscopy studies were performed in vivo on fifteen New Zealand White rabbits (atherosclerotic: N=8, control: N=7). Time-resolved fluorescence spectra were acquired (range: 360-600 nm, increment: 5 nm, total acquisition time: 65 s) from normal aorta wall and lesions in the abdominal aorta. Data were analyzed in terms of fluorescence emission spectra and wavelength specific lifetimes. Following trichrome staining, tissue specimens were analyzed histopathologically in terms of intima/media thickness and biochemical composition (collagen, elastin, foam cells, and etc). Based on intimal thickness, the lesions were divided into thin and thick lesions. Each group was further separated into two categories: collagen rich lesions and foam cell rich lesions based on their biochemical composition. The obtained spectral and time domain fluorescence signatures were subsequently correlated to the histopathological findings. The results have shown that time-domain fluorescence spectral features can be used in vivo to separate atherosclerotic lesions from normal aorta wall as well discrimination within certain types of lesions.

Robustness of coevolution in resolving prisoner's dilemma games on interdependent networks subject to attack

NASA Astrophysics Data System (ADS)

Liu, Penghui; Liu, Jing

2017-08-01

Recently, coevolution between strategy and network structure has been established as a rule to resolve social dilemmas and reach optimal situations for cooperation. Many follow-up researches have focused on studying how coevolution helps networks reorganize to deter the defectors and many coevolution methods have been proposed. However, the robustness of the coevolution rules against attacks have not been studied much. Since attacks may directly influence the original evolutionary process of cooperation, the robustness should be an important index while evaluating the quality of a coevolution method. In this paper, we focus on investigating the robustness of an elementary coevolution method in resolving the prisoner's dilemma game upon the interdependent networks. Three different types of time-independent attacks, named as edge attacks, instigation attacks and node attacks have been employed to test its robustness. Through analyzing the simulation results obtained, we find this coevolution method is relatively robust against the edge attack and the node attack as it successfully maintains cooperation in the population over the entire attack range. However, when the instigation probability of the attacked individuals is large or the attack range of instigation attack is wide enough, coevolutionary rule finally fails in maintaining cooperation in the population.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Jesse S.; Sinogeikin, Stanislav V.; Lin, Chuanlong

Complementary advances in high pressure research apparatus and techniques make it possible to carry out time-resolved high pressure research using what would customarily be considered static high pressure apparatus. This work specifically explores time-resolved high pressure x-ray diffraction with rapid compression and/or decompression of a sample in a diamond anvil cell. Key aspects of the synchrotron beamline and ancillary equipment are presented, including source considerations, rapid (de)compression apparatus, high frequency imaging detectors, and software suitable for processing large volumes of data. A number of examples are presented, including fast equation of state measurements, compression rate dependent synthesis of metastable statesmore » in silicon and germanium, and ultrahigh compression rates using a piezoelectric driven diamond anvil cell.« less

Macrophage Phenotype and Function in Different Stages of Atherosclerosis

PubMed Central

Tabas, Ira; Bornfeldt, Karin E.

2016-01-01

The remarkable plasticity and plethora of biological functions performed by macrophages have enticed scientists to study these cells in relation to atherosclerosis for more than 50 years, and major discoveries continue to be made today. It is now understood that macrophages play important roles in all stages of atherosclerosis, from initiation of lesions and lesion expansion, to necrosis leading to rupture and the clinical manifestations of atherosclerosis, to resolution and regression of atherosclerotic lesions. Lesional macrophages are derived primarily from blood monocytes, although recent research has shown that lesional macrophage-like cells can also be derived from smooth muscle cells. Lesional macrophages take on different phenotypes depending on their environment and which intracellular signaling pathways are activated. Rather than a few distinct populations of macrophages, the phenotype of the lesional macrophage is more complex and likely changes during the different phases of atherosclerosis and with the extent of lipid and cholesterol loading, activation by a plethora of receptors, and metabolic state of the cells. These different phenotypes allow the macrophage to engulf lipids, dead cells, and other substances perceived as danger signals; efflux cholesterol to HDL; proliferate and migrate; undergo apoptosis and death; and secrete a large number of inflammatory and pro-resolving molecules. This review article, part of the Compendium on Atherosclerosis, discusses recent advances in our understanding of lesional macrophage phenotype and function in different stages of atherosclerosis. With the increasing understanding of the roles of lesional macrophages, new research areas and treatment strategies are beginning to emerge. PMID:26892964

Detection of Rupture-Prone Atherosclerotic Plaques by Time-Resolved Laser Induced Fluorescence Spectroscopy

PubMed Central

Marcu, Laura; Jo, Javier A.; Fang, Qiyin; Papaioannou, Thanassis; Reil, Todd; Qiao, Jian-Hua; Baker, J. Dennis; Freischlag, Julie A.; Fishbein, Michael C.

2009-01-01

Objective Plaque with dense inflammatory cells, including macrophages, thin fibrous cap and superficial necrotic/lipid core is thought to be prone-to-rupture. We report a time-resolved laser-induced fluorescence spectroscopy (TR-LIFS) technique for detection of such markers of plaque vulnerability in human plaques. Methods The autofluorescence of carotid plaques (65 endarterectomy patients) induced by a pulsed laser (337 nm, 0.7 ns) was measured from 831 distinct areas. The emission was resolved spectrally- (360–550 nm range) and temporally- (0.3 ns resolution) using a prototype fiber-optic TR-LIFS apparatus. Lesions were evaluated microscopically and quantified as to the % of different components (fibrous cap, necrotic core, inflammatory cells, foam cells, mature and degraded collagen, elastic fibers, calcification, and smooth muscle cell of the vessel wall). Results We determined that the spectral intensities and time-dependent parameters at discrete emission wavelengths 1) allow for discrimination (sensitivity >81%, specificity >94%) of various compositional and pathological features associated with plaque vulnerability including infiltration of macrophages into intima and necrotic/lipid core under a thin fibrous cap, and 2) show a linear correlation with plaque biochemical content: elastin (P<0.008), collagen (P<0.02), inflammatory cells (P<0.003), necrosis (P<0.004). Conclusion Our results demonstrate the feasibility of TR-LIFS as a method for the identification of markers of plaque vulnerability. Current findings enable future development of TR-LIFS based clinical devices for rapid investigation of atherosclerotic plaques and detection of those at high-risk. PMID:18926540

On mechanics and material length scales of failure in heterogeneous interfaces using a finite strain high performance solver

NASA Astrophysics Data System (ADS)

Mosby, Matthew; Matouš, Karel

2015-12-01

Three-dimensional simulations capable of resolving the large range of spatial scales, from the failure-zone thickness up to the size of the representative unit cell, in damage mechanics problems of particle reinforced adhesives are presented. We show that resolving this wide range of scales in complex three-dimensional heterogeneous morphologies is essential in order to apprehend fracture characteristics, such as strength, fracture toughness and shape of the softening profile. Moreover, we show that computations that resolve essential physical length scales capture the particle size-effect in fracture toughness, for example. In the vein of image-based computational materials science, we construct statistically optimal unit cells containing hundreds to thousands of particles. We show that these statistically representative unit cells are capable of capturing the first- and second-order probability functions of a given data-source with better accuracy than traditional inclusion packing techniques. In order to accomplish these large computations, we use a parallel multiscale cohesive formulation and extend it to finite strains including damage mechanics. The high-performance parallel computational framework is executed on up to 1024 processing cores. A mesh convergence and a representative unit cell study are performed. Quantifying the complex damage patterns in simulations consisting of tens of millions of computational cells and millions of highly nonlinear equations requires data-mining the parallel simulations, and we propose two damage metrics to quantify the damage patterns. A detailed study of volume fraction and filler size on the macroscopic traction-separation response of heterogeneous adhesives is presented.

Locating Noctiluca Miliaris in the Arabian Sea: An Optical Proxy Approach

NASA Technical Reports Server (NTRS)

Thibodeau, Patricia S.; Roesler, Collin S.; Drapeau, Susan L.; Matondkar, S. G. Prabhu; Goes, Joaquim I.; Werdell, P. Jeremy

2014-01-01

Coincident with shifting monsoon weather patterns over India, the phytoplankter Noctiluca miliaris has recently been observed to be dominating phytoplankton blooms in the northeastern Arabian Sea during the winter monsoons. Identifying the exact environmental and/or ecological conditions that favor this species has been hampered by the lack of concurrent environmental and biological observations on time and space scales relevant to ecologic and physiologic processes. We present a bio-optical proxy for N. miliaris measured on highly resolved depth scales coincident with hydrographic observations with the goal to identify conducive hydrographic conditions for the bloom. The proxy is derived from multichannel excitation chlorophyll a fluorescence and is validated with microscopy, pigment composition, and spectral absorption. Phytoplankton populations dominated by either diatoms or other dinoflagellates were additionally discerned. N. miliaris populations in full bloom were identified offshore in low-nutrient and low-N : P ratio surface waters within a narrow temperature and salinity range. These populations transitioned to high-biomass diatom-dominated coastal upwelling populations. A week later, the N. miliaris blooms were observed in declining phase, transitioning to very-low-biomass populations of non-N. miliaris dinoflagellates. There were no clear hydrographic conditions uniquely associated with the N. miliaris populations, although N. miliaris was not found in the upwelling or extremely oligotrophic waters. Taxonomic transitions were not discernible in the spatial structure of the bloom as identified by the ocean color Chl imagery, indicating that in situ observations may be necessary to resolve community structure, particularly for populations below the surface.

Pathogenetic and Clinical Aspects of Anti-Neutrophil Cytoplasmic Autoantibody-Associated Vasculitides

PubMed Central

Lamprecht, Peter; Kerstein, Anja; Klapa, Sebastian; Schinke, Susanne; Karsten, Christian M.; Yu, Xinhua; Ehlers, Marc; Epplen, Jörg T.; Holl-Ulrich, Konstanze; Wiech, Thorsten; Kalies, Kathrin; Lange, Tanja; Laudien, Martin; Laskay, Tamas; Gemoll, Timo; Schumacher, Udo; Ullrich, Sebastian; Busch, Hauke; Ibrahim, Saleh; Fischer, Nicole; Hasselbacher, Katrin; Pries, Ralph; Petersen, Frank; Weppner, Gesche; Manz, Rudolf; Humrich, Jens Y.; Nieberding, Relana; Riemekasten, Gabriela; Müller, Antje

2018-01-01

Anti-neutrophil cytoplasmic autoantibodies (ANCA) targeting proteinase 3 (PR3) and myeloperoxidase expressed by innate immune cells (neutrophils and monocytes) are salient diagnostic and pathogenic features of small vessel vasculitis, comprising granulomatosis with polyangiitis (GPA), microscopic polyangiitis, and eosinophilic GPA. Genetic studies suggest that ANCA-associated vasculitides (AAV) constitute separate diseases, which share common immunological and pathological features, but are otherwise heterogeneous. The successful therapeutic use of anti-CD20 antibodies emphasizes the prominent role of ANCA and possibly other autoantibodies in the pathogenesis of AAV. However, to elucidate causal effects in AAV, a better understanding of the complex interplay leading to the emergence of B lymphocytes that produce pathogenic ANCA remains a challenge. Different scenarios seem possible; e.g., the break of tolerance induced by a shift from non-pathogenic toward pathogenic autoantigen epitopes in inflamed tissue. This review gives a brief overview on current knowledge about genetic and epigenetic factors, barrier dysfunction and chronic non-resolving inflammation, necro-inflammatory auto-amplification of cellular death and inflammation, altered autoantigen presentation, alternative complement pathway activation, alterations within peripheral and inflamed tissue-residing T- and B-cell populations, ectopic lymphoid tissue neoformation, the characterization of PR3-specific T-cells, properties of ANCA, links between autoimmune disease and infection-triggered pathology, and animal models in AAV. PMID:29686675

Emerging Functions of Regulatory T Cells in Tissue Homeostasis

PubMed Central

Sharma, Amit; Rudra, Dipayan

2018-01-01

CD4+Foxp3+ regulatory T-cells (Tregs) are a unique subset of helper T-cells, which regulate immune response and establish peripheral tolerance. Tregs not only maintain the tone and tenor of an immune response by dominant tolerance but, in recent years, have also been identified as key players in resolving tissue inflammation and as mediators of tissue healing. Apart from being diverse in their origin (thymic and peripheral) and location (lymphoid and tissue resident), Tregs are also phenotypically heterogeneous as per the orientation of ongoing immune response. In this review, we discuss the recent advances in the field of Treg biology in general, and non-lymphoid and tissue-resident Tregs in particular. We elaborate upon well-known visceral adipose tissue, colon, skin, and tumor-infiltrating Tregs and newly identified tissue Treg populations as in lungs, skeletal muscle, placenta, and other tissues. Our attempt is to differentiate Tregs based on distinctive properties of their location, origin, ligand specificity, chemotaxis, and specific suppressive mechanisms. Despite ever expanding roles in maintaining systemic homeostasis, Tregs are employed by large varieties of tumors to dampen antitumor immunity. Thus, a comprehensive understanding of Treg biology in the context of inflammation can be instrumental in effectively managing tissue transplantation, autoimmunity, and antitumor immune responses. PMID:29887862

Development of a time-resolved fluorometric method for observing hybridization in living cells using fluorescence resonance energy transfer.

PubMed Central

Tsuji, A; Sato, Y; Hirano, M; Suga, T; Koshimoto, H; Taguchi, T; Ohsuka, S

2001-01-01

We previously showed that a specific kind of mRNA (c-fos) was detected in a living cell under a microscope by introducing two fluorescently labeled oligodeoxynucleotides, each labeled with donor or acceptor, into the cytoplasm, making them hybridize to adjacent locations on c-fos mRNA, and taking images of fluorescence resonance energy transfer (FRET) (A. Tsuji, H. Koshimoto, Y. Sato, M. Hirano. Y. Sei-Iida, S. Kondo, and K. Ishibashi, 2000, Biophys. J. 78:3260-3274). On the formed hybrid, the distance between donor and acceptor becomes close and FRET occurs. To observe small numbers of mRNA in living cells using this method, it is required that FRET fluorescence of hybrid must be distinguished from fluorescence of excess amounts of non-hybridizing probes and from cell autofluorescence. To meet these requirements, we developed a time-resolved method using acceptor fluorescence decays. When a combination of a donor having longer fluorescence lifetime and an acceptor having shorter lifetime is used, the measured fluorescence decays of acceptors under FRET becomes slower than the acceptor fluorescence decay with direct excitation. A combination of Bodipy493/503 and Cy5 was selected as donor and acceptor. When the formed hybrid had a configuration where the target RNA has no single-strand part between the two fluorophores, the acceptor fluorescence of hybrid had a sufficiently longer delay to detect fluorescence of hybrid in the presence of excess amounts of non-hybridizing probes. Spatial separation of 10-12 bases between two fluorophores on the hybrid is also required. The decay is also much slower than cell autofluorescence, and smaller numbers of hybrid were detected with less interference of cell autofluorescence in the cytoplasm of living cells under a time-resolved fluorescence microscope with a time-gated function equipped camera. The present method will be useful when observing induced expressions of mRNA in living cells. PMID:11423432

Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences.

PubMed

Nasser, Waleed; Beres, Stephen B; Olsen, Randall J; Dean, Melissa A; Rice, Kelsey A; Long, S Wesley; Kristinsson, Karl G; Gottfredsson, Magnus; Vuopio, Jaana; Raisanen, Kati; Caugant, Dominique A; Steinbakk, Martin; Low, Donald E; McGeer, Allison; Darenberg, Jessica; Henriques-Normark, Birgitta; Van Beneden, Chris A; Hoffmann, Steen; Musser, James M

2014-04-29

We sequenced the genomes of 3,615 strains of serotype Emm protein 1 (M1) group A Streptococcus to unravel the nature and timing of molecular events contributing to the emergence, dissemination, and genetic diversification of an unusually virulent clone that now causes epidemic human infections worldwide. We discovered that the contemporary epidemic clone emerged in stepwise fashion from a precursor cell that first contained the phage encoding an extracellular DNase virulence factor (streptococcal DNase D2, SdaD2) and subsequently acquired the phage encoding the SpeA1 variant of the streptococcal pyrogenic exotoxin A superantigen. The SpeA2 toxin variant evolved from SpeA1 by a single-nucleotide change in the M1 progenitor strain before acquisition by horizontal gene transfer of a large chromosomal region encoding secreted toxins NAD(+)-glycohydrolase and streptolysin O. Acquisition of this 36-kb region in the early 1980s into just one cell containing the phage-encoded sdaD2 and speA2 genes was the final major molecular event preceding the emergence and rapid intercontinental spread of the contemporary epidemic clone. Thus, we resolve a decades-old controversy about the type and sequence of genomic alterations that produced this explosive epidemic. Analysis of comprehensive, population-based contemporary invasive strains from seven countries identified strong patterns of temporal population structure. Compared with a preepidemic reference strain, the contemporary clone is significantly more virulent in nonhuman primate models of pharyngitis and necrotizing fasciitis. A key finding is that the molecular evolutionary events transpiring in just one bacterial cell ultimately have produced millions of human infections worldwide.

Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences

PubMed Central

Nasser, Waleed; Beres, Stephen B.; Olsen, Randall J.; Dean, Melissa A.; Rice, Kelsey A.; Long, S. Wesley; Kristinsson, Karl G.; Gottfredsson, Magnus; Vuopio, Jaana; Raisanen, Kati; Caugant, Dominique A.; Steinbakk, Martin; Low, Donald E.; McGeer, Allison; Darenberg, Jessica; Henriques-Normark, Birgitta; Van Beneden, Chris A.; Hoffmann, Steen; Musser, James M.

2014-01-01

We sequenced the genomes of 3,615 strains of serotype Emm protein 1 (M1) group A Streptococcus to unravel the nature and timing of molecular events contributing to the emergence, dissemination, and genetic diversification of an unusually virulent clone that now causes epidemic human infections worldwide. We discovered that the contemporary epidemic clone emerged in stepwise fashion from a precursor cell that first contained the phage encoding an extracellular DNase virulence factor (streptococcal DNase D2, SdaD2) and subsequently acquired the phage encoding the SpeA1 variant of the streptococcal pyrogenic exotoxin A superantigen. The SpeA2 toxin variant evolved from SpeA1 by a single-nucleotide change in the M1 progenitor strain before acquisition by horizontal gene transfer of a large chromosomal region encoding secreted toxins NAD+-glycohydrolase and streptolysin O. Acquisition of this 36-kb region in the early 1980s into just one cell containing the phage-encoded sdaD2 and speA2 genes was the final major molecular event preceding the emergence and rapid intercontinental spread of the contemporary epidemic clone. Thus, we resolve a decades-old controversy about the type and sequence of genomic alterations that produced this explosive epidemic. Analysis of comprehensive, population-based contemporary invasive strains from seven countries identified strong patterns of temporal population structure. Compared with a preepidemic reference strain, the contemporary clone is significantly more virulent in nonhuman primate models of pharyngitis and necrotizing fasciitis. A key finding is that the molecular evolutionary events transpiring in just one bacterial cell ultimately have produced millions of human infections worldwide. PMID:24733896

Elevation or Suppression? The Resolved Star Formation Main Sequence of Galaxies with Two Different Assembly Modes

NASA Astrophysics Data System (ADS)

Liu, Qing; Wang, Enci; Lin, Zesen; Gao, Yulong; Liu, Haiyang; Berhane Teklu, Berzaf; Kong, Xu

2018-04-01

We investigate the spatially resolved star formation main sequence in star-forming galaxies using Integral Field Spectroscopic observations from the Mapping Nearby Galaxies at the Apache Point Observatory survey. We demonstrate that the correlation between the stellar mass surface density (Σ*) and star formation rate surface density (ΣSFR) holds down to the sub-galactic scale, leading to the sub-galactic main sequence (SGMS). By dividing galaxies into two populations based on their recent mass assembly modes, we find the resolved main sequence in galaxies with the “outside-in” mode is steeper than that in galaxies with the “inside-out” mode. This is also confirmed on a galaxy-by-galaxy level, where we find the distributions of SGMS slopes for individual galaxies are clearly separated for the two populations. When normalizing and stacking the SGMS of individual galaxies on one panel for the two populations, we find that the inner regions of galaxies with the “inside-out” mode statistically exhibit a suppression in star formation, with a less significant trend in the outer regions of galaxies with the “outside-in” mode. In contrast, the inner regions of galaxies with “outside-in” mode and the outer regions of galaxies with “inside-out” mode follow a slightly sublinear scaling relation with a slope ∼0.9, which is in good agreement with previous findings, suggesting that they are experiencing a universal regulation without influences of additional physical processes.

PANCHROMATIC HUBBLE ANDROMEDA TREASURY. XVI. STAR CLUSTER FORMATION EFFICIENCY AND THE CLUSTERED FRACTION OF YOUNG STARS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, L. Clifton; Sandstrom, Karin; Seth, Anil C.

We use the Panchromatic Hubble Andromeda Treasury survey data set to perform spatially resolved measurements of star cluster formation efficiency (Γ), the fraction of stellar mass formed in long-lived star clusters. We use robust star formation history and cluster parameter constraints, obtained through color–magnitude diagram analysis of resolved stellar populations, to study Andromeda’s cluster and field populations over the last ∼300 Myr. We measure Γ of 4%–8% for young, 10–100 Myr-old populations in M31. We find that cluster formation efficiency varies systematically across the M31 disk, consistent with variations in mid-plane pressure. These Γ measurements expand the range of well-studiedmore » galactic environments, providing precise constraints in an H i-dominated, low-intensity star formation environment. Spatially resolved results from M31 are broadly consistent with previous trends observed on galaxy-integrated scales, where Γ increases with increasing star formation rate surface density (Σ{sub SFR}). However, we can explain observed scatter in the relation and attain better agreement between observations and theoretical models if we account for environmental variations in gas depletion time ( τ {sub dep}) when modeling Γ, accounting for the qualitative shift in star formation behavior when transitioning from a H{sub 2}-dominated to a H i-dominated interstellar medium. We also demonstrate that Γ measurements in high Σ{sub SFR} starburst systems are well-explained by τ {sub dep}-dependent fiducial Γ models.« less

A quantitative and spatially resolved analysis of the performance-bottleneck in high efficiency, planar hybrid perovskite solar cells

DOE PAGES

Draguta, Sergiu; Christians, Jeffrey A.; Morozov, Yurii V.; ...

2018-01-01

Hybrid perovskites represent a potential paradigm shift for the creation of low-cost solar cells. Current power conversion efficiencies (PCEs) exceed 22%. However, despite this, record PCEs are still far from their theoretical Shockley–Queisser limit of 31%. To increase these PCE values, there is a pressing need to understand, quantify and microscopically model charge recombination processes in full working devices. Here, we present a complete microscopic account of charge recombination processes in high efficiency (18–19% PCE) hybrid perovskite (mixed cation and methylammonium lead iodide) solar cells. We employ diffraction-limited optical measurements along with relevant kinetic modeling to establish, for the firstmore » time, local photoluminescence quantum yields, trap densities, trapping efficiencies, charge extraction efficiencies, quasi-Fermi-level splitting, and effective PCE estimates. Correlations between these spatially resolved parameters, in turn, allow us to conclude that intrinsic electron traps in the perovskite active layers limit the performance of these state-of-the-art hybrid perovskite solar cells.« less

Separating grain-boundary and bulk recombination with time-resolved photoluminescence microscopy

DOE PAGES

Kuciauskas, Darius; Lu, Dingyuan; Grover, Sachit; ...

2017-12-04

Two-photon excitation (2PE) microscopy allows contactless and non-destructive cross-sectional analysis of grain-boundary (GB) and grain-interior (GI) properties in polycrystalline solar cells, with measurements of doping uniformity, space-charge field distribution, and carrier dynamics in different regions of the device. Using 2PE time-resolved microscopy, we analyzed charge-carrier lifetimes near the GBs and in the GI of polycrystalline thin-film CdTe solar cells doped with As. When the grain radius is larger than the minority-carrier diffusion length, GI lifetimes are interpreted as the bulk lifetimes ..tau..B, and GB recombination velocity SGB is extracted by comparing recombination rates in the GI and near GBs. Inmore » As-doped CdTe solar cells, we find ..tau..B = 1.0-2.4 ns and S GB = (1-4) x 10 5 cm/s. The results imply the potential to improve solar cell voltage via GB passivation and reduced recombination center concentration in the GI.« less

Separating grain-boundary and bulk recombination with time-resolved photoluminescence microscopy

NASA Astrophysics Data System (ADS)

Kuciauskas, Darius; Lu, Dingyuan; Grover, Sachit; Xiong, Gang; Gloeckler, Markus

2017-12-01

Two-photon excitation (2PE) microscopy allows contactless and non-destructive cross-sectional analysis of grain-boundary (GB) and grain-interior (GI) properties in polycrystalline solar cells, with measurements of doping uniformity, space-charge field distribution, and carrier dynamics in different regions of the device. Using 2PE time-resolved microscopy, we analyzed charge-carrier lifetimes near the GBs and in the GI of polycrystalline thin-film CdTe solar cells doped with As. When the grain radius is larger than the minority-carrier diffusion length, GI lifetimes are interpreted as the bulk lifetimes τB, and GB recombination velocity SGB is extracted by comparing recombination rates in the GI and near GBs. In As-doped CdTe solar cells, we find τB = 1.0-2.4 ns and SGB = (1-4) × 105 cm/s. The results imply the potential to improve solar cell voltage via GB passivation and reduced recombination center concentration in the GI.

A quantitative and spatially resolved analysis of the performance-bottleneck in high efficiency, planar hybrid perovskite solar cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Draguta, Sergiu; Christians, Jeffrey A.; Morozov, Yurii V.

Hybrid perovskites represent a potential paradigm shift for the creation of low-cost solar cells. Current power conversion efficiencies (PCEs) exceed 22%. However, despite this, record PCEs are still far from their theoretical Shockley–Queisser limit of 31%. To increase these PCE values, there is a pressing need to understand, quantify and microscopically model charge recombination processes in full working devices. Here, we present a complete microscopic account of charge recombination processes in high efficiency (18–19% PCE) hybrid perovskite (mixed cation and methylammonium lead iodide) solar cells. We employ diffraction-limited optical measurements along with relevant kinetic modeling to establish, for the firstmore » time, local photoluminescence quantum yields, trap densities, trapping efficiencies, charge extraction efficiencies, quasi-Fermi-level splitting, and effective PCE estimates. Correlations between these spatially resolved parameters, in turn, allow us to conclude that intrinsic electron traps in the perovskite active layers limit the performance of these state-of-the-art hybrid perovskite solar cells.« less

Separating grain-boundary and bulk recombination with time-resolved photoluminescence microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuciauskas, Darius; Lu, Dingyuan; Grover, Sachit

Two-photon excitation (2PE) microscopy allows contactless and non-destructive cross-sectional analysis of grain-boundary (GB) and grain-interior (GI) properties in polycrystalline solar cells, with measurements of doping uniformity, space-charge field distribution, and carrier dynamics in different regions of the device. Using 2PE time-resolved microscopy, we analyzed charge-carrier lifetimes near the GBs and in the GI of polycrystalline thin-film CdTe solar cells doped with As. When the grain radius is larger than the minority-carrier diffusion length, GI lifetimes are interpreted as the bulk lifetimes ..tau..B, and GB recombination velocity SGB is extracted by comparing recombination rates in the GI and near GBs. Inmore » As-doped CdTe solar cells, we find ..tau..B = 1.0-2.4 ns and S GB = (1-4) x 10 5 cm/s. The results imply the potential to improve solar cell voltage via GB passivation and reduced recombination center concentration in the GI.« less

Diffusion maps for high-dimensional single-cell analysis of differentiation data.

PubMed

Haghverdi, Laleh; Buettner, Florian; Theis, Fabian J

2015-09-15

Single-cell technologies have recently gained popularity in cellular differentiation studies regarding their ability to resolve potential heterogeneities in cell populations. Analyzing such high-dimensional single-cell data has its own statistical and computational challenges. Popular multivariate approaches are based on data normalization, followed by dimension reduction and clustering to identify subgroups. However, in the case of cellular differentiation, we would not expect clear clusters to be present but instead expect the cells to follow continuous branching lineages. Here, we propose the use of diffusion maps to deal with the problem of defining differentiation trajectories. We adapt this method to single-cell data by adequate choice of kernel width and inclusion of uncertainties or missing measurement values, which enables the establishment of a pseudotemporal ordering of single cells in a high-dimensional gene expression space. We expect this output to reflect cell differentiation trajectories, where the data originates from intrinsic diffusion-like dynamics. Starting from a pluripotent stage, cells move smoothly within the transcriptional landscape towards more differentiated states with some stochasticity along their path. We demonstrate the robustness of our method with respect to extrinsic noise (e.g. measurement noise) and sampling density heterogeneities on simulated toy data as well as two single-cell quantitative polymerase chain reaction datasets (i.e. mouse haematopoietic stem cells and mouse embryonic stem cells) and an RNA-Seq data of human pre-implantation embryos. We show that diffusion maps perform considerably better than Principal Component Analysis and are advantageous over other techniques for non-linear dimension reduction such as t-distributed Stochastic Neighbour Embedding for preserving the global structures and pseudotemporal ordering of cells. The Matlab implementation of diffusion maps for single-cell data is available at https://www.helmholtz-muenchen.de/icb/single-cell-diffusion-map. fbuettner.phys@gmail.com, fabian.theis@helmholtz-muenchen.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Large Scale Flood Risk Analysis using a New Hyper-resolution Population Dataset

NASA Astrophysics Data System (ADS)

Smith, A.; Neal, J. C.; Bates, P. D.; Quinn, N.; Wing, O.

2017-12-01

Here we present the first national scale flood risk analyses, using high resolution Facebook Connectivity Lab population data and data from a hyper resolution flood hazard model. In recent years the field of large scale hydraulic modelling has been transformed by new remotely sensed datasets, improved process representation, highly efficient flow algorithms and increases in computational power. These developments have allowed flood risk analysis to be undertaken in previously unmodeled territories and from continental to global scales. Flood risk analyses are typically conducted via the integration of modelled water depths with an exposure dataset. Over large scales and in data poor areas, these exposure data typically take the form of a gridded population dataset, estimating population density using remotely sensed data and/or locally available census data. The local nature of flooding dictates that for robust flood risk analysis to be undertaken both hazard and exposure data should sufficiently resolve local scale features. Global flood frameworks are enabling flood hazard data to produced at 90m resolution, resulting in a mis-match with available population datasets which are typically more coarsely resolved. Moreover, these exposure data are typically focused on urban areas and struggle to represent rural populations. In this study we integrate a new population dataset with a global flood hazard model. The population dataset was produced by the Connectivity Lab at Facebook, providing gridded population data at 5m resolution, representing a resolution increase over previous countrywide data sets of multiple orders of magnitude. Flood risk analysis undertaken over a number of developing countries are presented, along with a comparison of flood risk analyses undertaken using pre-existing population datasets.

Novel methods of time-resolved fluorescence data analysis for in-vivo tissue characterization: application to atherosclerosis.

PubMed

Jo, J A; Fang, Q; Papaioannou, T; Qiao, J H; Fishbein, M C; Dorafshar, A; Reil, T; Baker, D; Freischlag, J; Marcu, L

2004-01-01

This study investigates the ability of new analytical methods of time-resolved laser-induced fluorescence spectroscopy (TR-LIFS) data to characterize tissue in-vivo, such as the composition of atherosclerotic vulnerable plaques. A total of 73 TR-LIFS measurements were taken in-vivo from the aorta of 8 rabbits, and subsequently analyzed using the Laguerre deconvolution technique. The investigated spots were classified as normal aorta, thin or thick lesions, and lesions rich in either collagen or macrophages/foam-cells. Different linear and nonlinear classification algorithms (linear discriminant analysis, stepwise linear discriminant analysis, principal component analysis, and feedforward neural networks) were developed using spectral and TR features (ratios of intensity values and Laguerre expansion coefficients, respectively). Normal intima and thin lesions were discriminated from thick lesions (sensitivity >90%, specificity 100%) using only spectral features. However, both spectral and time-resolved features were necessary to discriminate thick lesions rich in collagen from thick lesions rich in foam cells (sensitivity >85%, specificity >93%), and thin lesions rich in foam cells from normal aorta and thin lesions rich in collagen (sensitivity >85%, specificity >94%). Based on these findings, we believe that TR-LIFS information derived from the Laguerre expansion coefficients can provide a valuable additional dimension for in-vivo tissue characterization.

Xylem phenology and wood production: resolving the chicken-or-egg dilemma.

PubMed

Lupi, Carlo; Morin, Hubert; Deslauriers, Annie; Rossi, Sergio

2010-10-01

Delays in the start of the growing season reduce the period available for growth and the amount of xylem production. However, a higher number of developing tracheids could prolong cell differentiation and, consequently, lengthen the growing season. The relationship between the amount and duration of cell production in the xylem remains an unresolved issue. The aim of this study was to resolve the chicken-or-egg causality dilemma about duration of growth and cell production through simple- and double-cause models. This was achieved by (1) analysing the intra-annual growth dynamics of the xylem in Picea mariana (Mill.) BSP during 2006-2009 in two contrasting sites of the boreal forest of Quebec, Canada, and (2) extracting the dates of onset and ending of xylem formation and the number of radial cells along the tree ring. A higher number of cells was linked to an earlier onset (r=0.74) and later ending (r=0.61) of cell differentiation. The absence of a relationship between the residuals of the onset and ending of xylogenesis (r(p)=-0.06) indicated that cell production influenced the correlation between the two phenophases of the xylem. These results demonstrated that a higher number of cells produced delay the ending of xylem maturation, so extending the duration of wood formation. © 2010 Blackwell Publishing Ltd.

Photothermal optical coherence tomography for depth-resolved imaging of mesenchymal stem cells via single wall carbon nanotubes

NASA Astrophysics Data System (ADS)

Subhash, Hrebesh M.; Connolly, Emma; Murphy, Mary; Barron, Valerie; Leahy, Martin

2014-03-01

The progress in stem cell research over the past decade holds promise and potential to address many unmet clinical therapeutic needs. Tracking stem cell with modern imaging modalities are critically needed for optimizing stem cell therapy, which offers insight into various underlying biological processes such as cell migration, engraftment, homing, differentiation, and functions etc. In this study we report the feasibility of photothermal optical coherence tomography (PT-OCT) to image human mesenchymal stem cells (hMSCs) labeled with single-walled carbon nanotubes (SWNTs) for in vitro cell tracking in three dimensional scaffolds. PT-OCT is a functional extension of conventional OCT with extended capability of localized detection of absorbing targets from scattering background to provide depth-resolved molecular contrast imaging. A 91 kHz line rate, spectral domain PT-OCT system at 1310nm was developed to detect the photothermal signal generated by 800nm excitation laser. In general, MSCs do not have obvious optical absorption properties and cannot be directly visualized using PT-OCT imaging. However, the optical absorption properties of hMSCs can me modified by labeling with SWNTs. Using this approach, MSC were labeled with SWNT and the cell distribution imaged in a 3D polymer scaffold using PT-OCT.

Time-resolved diode laser infrared absorption spectroscopy of the nascent HCl in the infrared laser chemistry of 1,2-dichloro-1,1-difluoroethane

NASA Astrophysics Data System (ADS)

Dietrich, Peter; Quack, Martin; Seyfang, George

1990-04-01

The IR multiphoton excitation and the frequency, fluence and intensity dependence of the IR-laser chemical yields of CF 2ClCH 2Cl have been studied in the fluence range of 1 to 10 J cm -2 yielding a steady-state constant k(st)/ I=0.74×10 6 s -1 MW -1 cm 2 which is approximately independent of intensity. Time-resolved IR absorption spectroscopy with diode laser sources has been used to observe the nascent HCl during the first few 100 ns indicating a population inversion between the levels ν=1, J=4 and ν=2, J=5. At low reactant pressures ( p⩽10 Pa) the time-resolved measurement gives a steady-state rate constant consistent with the theoretical result adjusted to the static yield measurements. The capability of state-selective and time-resolved IR spectroscopy is thus demonstrated, giving real-time determinations of rate constants.

Spatially resolved, in situ potential measurements through porous electrodes as applied to fuel cells.

PubMed

Hess, Katherine C; Epting, William K; Litster, Shawn

2011-12-15

We report the development and use of a microstructured electrode scaffold (MES) to make spatially resolved, in situ, electrolyte potential measurements through the thickness of a polymer electrolyte fuel cell (PEFC) electrode. This new approach uses a microfabricated apparatus to analyze the coupled transport and electrochemical phenomena in porous electrodes at the microscale. In this study, the MES allows the fuel cell to run under near-standard operating conditions, while providing electrolyte potential measurements at discrete distances through the electrode's thickness. Here we use spatial distributions of electrolyte potential to evaluate the effects of Ohmic and mass transport resistances on the through-plane reaction distribution for various operating conditions. Additionally, we use the potential distributions to estimate the ionic conductivity of the electrode. Our results indicate the in situ conductivity is higher than typically estimated for PEFC electrodes based on bulk polymer electrolyte membrane (PEM) conductivity.

New large volume hydrothermal reaction cell for studying chemical processes under supercritical hydrothermal conditions using time-resolved in situ neutron diffraction.

PubMed

Ok, Kang Min; O'Hare, Dermot; Smith, Ronald I; Chowdhury, Mohammed; Fikremariam, Hanna

2010-12-01

The design and testing of a new large volume Inconel pressure cell for the in situ study of supercritical hydrothermal syntheses using time-resolved neutron diffraction is introduced for the first time. The commissioning of this new cell is demonstrated by the measurement of the time-of-flight neutron diffraction pattern for TiO(2) (Anatase) in supercritical D(2)O on the POLARIS diffractometer at the United Kingdom's pulsed spallation neutron source, ISIS, Rutherford Appleton Laboratory. The sample can be studied over a wide range of temperatures (25-450 °C) and pressures (1-355 bar). This novel apparatus will now enable us to study the kinetics and mechanisms of chemical syntheses under extreme environments such as supercritical water, and in particular to study the crystallization of a variety of technologically important inorganic materials.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiao, Kai; Ma, Ying -Zhong; Simpson, Mary Jane

Charge carrier trapping degrades the performance of organometallic halide perovskite solar cells. To characterize the locations of electronic trap states in a heterogeneous photoactive layer, a spatially resolved approach is essential. Here, we report a comparative study on methylammonium lead tri-iodide perovskite thin films subject to different thermal annealing times using a combined photoluminescence (PL) and femtosecond transient absorption microscopy (TAM) approach to spatially map trap states. This approach coregisters the initially populated electronic excited states with the regions that recombine radiatively. Although the TAM images are relatively homogeneous for both samples, the corresponding PL images are highly structured. Themore » remarkable variation in the PL intensities as compared to transient absorption signal amplitude suggests spatially dependent PL quantum efficiency, indicative of trapping events. Furthermore, detailed analysis enables identification of two trapping regimes: a densely packed trapping region and a sparse trapping area that appear as unique spatial features in scaled PL maps.« less

The quest for four-dimensional imaging in plant cell biology: it's just a matter of time

PubMed Central

Domozych, David S.

2012-01-01

Background Analysis of plant cell dynamics over time, or four-dimensional imaging (4-DI), represents a major goal of plant science. The ability to resolve structures in the third dimension within the cell or tissue during developmental events or in response to environmental or experimental stresses (i.e. 4-DI) is critical to our understanding of gene expression, post-expression modulations of macromolecules and sub-cellular system interactions. Scope Microscopy-based technologies have been profoundly integral to this type of investigation, and new and refined microscopy technologies now allow for the visualization of cell dynamics with unprecedented resolution, contrast and experimental versatility. However, certain realities of light and electron microscopy, choice of specimen and specimen preparation techniques limit the scope of readily attaining 4-DI. Today, the plant microscopist must use a combinatorial strategy whereby multiple microscopy-based investigations are used. Modern fluorescence, confocal laser scanning, transmission electron and scanning electron microscopy provide effective conduits for synthesizing data detailing live cell dynamics and highly resolved snapshots of specific cell structures that will ultimately lead to 4-DI. This review provides a synopsis of such technologies available. PMID:22628381

50 CFR 216.41 - Permits for scientific research and enhancement.

Code of Federal Regulations, 2010 CFR

2010-10-01

... ecology of the species or stock, or to identifying, evaluating, or resolving conservation problems for the... may authorize the release of any population of an endangered or threatened species outside the current...

50 CFR 216.41 - Permits for scientific research and enhancement.

Code of Federal Regulations, 2012 CFR

2012-10-01

... ecology of the species or stock, or to identifying, evaluating, or resolving conservation problems for the... may authorize the release of any population of an endangered or threatened species outside the current...

50 CFR 216.41 - Permits for scientific research and enhancement.

Code of Federal Regulations, 2011 CFR

2011-10-01

... ecology of the species or stock, or to identifying, evaluating, or resolving conservation problems for the... may authorize the release of any population of an endangered or threatened species outside the current...

50 CFR 216.41 - Permits for scientific research and enhancement.

Code of Federal Regulations, 2013 CFR

2013-10-01

... ecology of the species or stock, or to identifying, evaluating, or resolving conservation problems for the... may authorize the release of any population of an endangered or threatened species outside the current...

50 CFR 216.41 - Permits for scientific research and enhancement.

Code of Federal Regulations, 2014 CFR

2014-10-01

... ecology of the species or stock, or to identifying, evaluating, or resolving conservation problems for the... may authorize the release of any population of an endangered or threatened species outside the current...

Artificial insemination in captive Whooping Cranes: Results from genetic analyses

USGS Publications Warehouse

Jones, K.L.; Nicolich, Jane M.

2001-01-01

Artificial insemination has been used frequently in the captive whooping crane (Grus americana) population. In the 1980s, it was necessary at times to inseminate females with semen from several males during the breeding season or with semen from multiple males simultaneously due to unknown sperm viability of the breeding males. The goals of this study were to apply microsatellite DNA profiles to resolve uncertain paternities and to use these results to evaluate the current paternity assignment assumptions used by captive managers. Microsatellite DNA profiles were successful in resolving 20 of 23 paternity questions. When resolved paternities were coupled with data on insemination timing, substantial information was revealed on fertilization timing in captive whooping cranes. Delayed fertilization from inseminations 6+ days pre-oviposition suggests capability of sperm storage.

Concise Review: Conceptualizing Paralogous Stem-Cell Niches and Unfolding Bone Marrow Progenitor Cell Identities.

PubMed

Chen, Kevin G; Johnson, Kory R; McKay, Ronald D G; Robey, Pamela G

2018-01-01

Lineage commitment and differentiation of skeletal stem cells/bone marrow stromal cells (SSCs/BMSCs, often called bone marrow-derived "mesenchymal stem/stromal" cells) offer an important opportunity to study skeletal and hematopoietic diseases, and for tissue engineering and regenerative medicine. Currently, many studies in this field have relied on cell lineage tracing methods in mouse models, which have provided a significant advancement in our knowledge of skeletal and hematopoietic stem-cell niches in bone marrow (BM). However, there is a lack of agreement in numerous fundamental areas, including origins of various BM stem-cell niches, cell identities, and their physiological roles in the BM. In order to resolve these issues, we propose a new hypothesis of "paralogous" stem-cell niches (PSNs); that is, progressively altered parallel niches within an individual species throughout the life span of the organism. A putative PSN code seems to be plausible based on analysis of transcriptional signatures in two representative genes that encode Nes-GFP and leptin receptors, which are frequently used to monitor SSC lineage development in BM. Furthermore, we suggest a dynamic paralogous BM niche (PBMN) model that elucidates the coupling and uncoupling mechanisms between BM stem-cell niches and their zones of active regeneration during different developmental stages. Elucidation of these PBMNs would enable us to resolve the existing controversies, thus paving the way to achieving precision regenerative medicine and pharmaceutical applications based on these BM cell resources. Stem Cells 2018;36:11-21. © 2017 AlphaMed Press.

Population Dynamics of Viral Inactivation

NASA Astrophysics Data System (ADS)

Freeman, Krista; Li, Dong; Behrens, Manja; Streletzky, Kiril; Olsson, Ulf; Evilevitch, Alex

We have investigated the population dynamics of viral inactivation in vitrousing time-resolved cryo electron microscopy combined with light and X-ray scattering techniques. Using bacteriophage λ as a model system for pressurized double-stranded DNA viruses, we found that virions incubated with their cell receptor eject their genome in a stochastic triggering process. The triggering of DNA ejection occurs in a non synchronized manner after the receptor addition, resulting in an exponential decay of the number of genome-filled viruses with time. We have explored the characteristic time constant of this triggering process at different temperatures, salt conditions, and packaged genome lengths. Furthermore, using the temperature dependence we determined an activation energy for DNA ejections. The dependences of the time constant and activation energy on internal DNA pressure, affected by salt conditions and encapsidated genome length, suggest that the triggering process is directly dependent on the conformational state of the encapsidated DNA. The results of this work provide insight into how the in vivo kinetics of the spread of viral infection are influenced by intra- and extra cellular environmental conditions. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1252522.

HEALTH AND NUTRITIONAL ASSESSMENT OF FREE-RANGING EASTERN INDIGO SNAKES (DRYMARCHON COUPERI) IN GEORGIA, UNITED STATES.

PubMed

Knafo, S Emmanuelle; Norton, Terry M; Mitchell, Mark; Stevenson, Dirk J; Hyslop, Natalie; Poppenga, Robert; Oliva, Marcie; Chen, Tai; Cray, Carolyn; Gibbs, Samantha E J; Durden, Lance; Stedman, Nancy; Divers, Stephen; Dierenfeld, Ellen

2016-12-01

Clinical pathology and nutritional parameters are useful in evaluating and monitoring threatened and endangered wildlife populations, but reference ranges for most snake species are lacking. From 2001 to 2005, health assessments were performed on 58 eastern indigo snakes (EIS) (Drymarchon couperi) captured in the wild in southeastern Georgia, United States. Health and nutritional assessments performed included hematology, serum biochemistry, fat-soluble vitamins, heavy metals, pesticide contaminants, parasitology, and surveys of other pathogens. Significant differences in total solids, packed cell volume, glucose, blood urea nitrogen, albumin : globulin ratio, amylase, triglycerides, and bile acids between males and females were observed. Additionally, there was a significant difference between liver and kidney concentrations for vitamins A and E. As previously noted in captive EIS, total Ca was elevated in comparison to concentrations reported in other snake species. Parasitism was a common finding in sampled EIS, but the overall health status of this free-ranging population appeared good. A winter-time dermatitis was found in most snakes, which resolved in the summer months. This study represents the first health and nutritional assessment of free-ranging EIS, and provides needed data to guide monitoring and conservation efforts.

Ionization competition effects on population distribution and radiative opacity of mixture plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Yongjun; Gao, Cheng; Tian, Qinyun

2015-11-15

Ionization competition arising from the electronic shell structures of various atomic species in the mixture plasmas was investigated, taking SiO{sub 2} as an example. Using a detailed-level-accounting approximation, we studied the competition effects on the charge state population distribution and spectrally resolved and Planck and Rosseland mean radiative opacities of mixture plasmas. A set of coupled equations for ionization equilibria that include all components of the mixture plasmas are solved to determine the population distributions. For a given plasma density, competition effects are found at three distinct temperature ranges, corresponding to the ionization of M-, L-, and K-shell electrons ofmore » Si. Taking the effects into account, the spectrally resolved and Planck and Rosseland mean opacities are systematically investigated over a wide range of plasma densities and temperatures. For a given mass density, the Rosseland mean decreases monotonically with plasma temperature, whereas Planck mean does not. Although the overall trend is a decrease, the Planck mean increases over a finite intermediate temperature regime. A comparison with the available experimental and theoretical results is made.« less

Emergence of collective propulsion through cell-cell adhesion.

PubMed

Matsushita, Katsuyoshi

2018-04-01

The mechanisms driving the collective movement of cells remain poorly understood. To contribute toward resolving this mystery, a model was formulated to theoretically explore the possible functions of polarized cell-cell adhesion in collective cell migration. The model consists of an amoeba cell with polarized cell-cell adhesion, which is controlled by positive feedback with cell motion. This model cell has no persistent propulsion and therefore exhibits a simple random walk when in isolation. However, at high density, these cells acquire collective propulsion and form ordered movement. This result suggests that cell-cell adhesion has a potential function, which induces collective propulsion with persistence.

Emergence of collective propulsion through cell-cell adhesion

NASA Astrophysics Data System (ADS)

Matsushita, Katsuyoshi

2018-04-01

The mechanisms driving the collective movement of cells remain poorly understood. To contribute toward resolving this mystery, a model was formulated to theoretically explore the possible functions of polarized cell-cell adhesion in collective cell migration. The model consists of an amoeba cell with polarized cell-cell adhesion, which is controlled by positive feedback with cell motion. This model cell has no persistent propulsion and therefore exhibits a simple random walk when in isolation. However, at high density, these cells acquire collective propulsion and form ordered movement. This result suggests that cell-cell adhesion has a potential function, which induces collective propulsion with persistence.

Current focus of stem cell application in retinal repair

PubMed Central

Alonso-Alonso, María L; Srivastava, Girish K

2015-01-01

The relevance of retinal diseases, both in society’s economy and in the quality of people’s life who suffer with them, has made stem cell therapy an interesting topic for research. Embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs) and adipose derived mesenchymal stem cells (ADMSCs) are the focus in current endeavors as a source of different retinal cells, such as photoreceptors and retinal pigment epithelial cells. The aim is to apply them for cell replacement as an option for treating retinal diseases which so far are untreatable in their advanced stage. ESCs, despite the great potential for differentiation, have the dangerous risk of teratoma formation as well as ethical issues, which must be resolved before starting a clinical trial. iPSCs, like ESCs, are able to differentiate in to several types of retinal cells. However, the process to get them for personalized cell therapy has a high cost in terms of time and money. Researchers are working to resolve this since iPSCs seem to be a realistic option for treating retinal diseases. ADMSCs have the advantage that the procedures to obtain them are easier. Despite advancements in stem cell application, there are still several challenges that need to be overcome before transferring the research results to clinical application. This paper reviews recent research achievements of the applications of these three types of stem cells as well as clinical trials currently based on them. PMID:25914770

The time resolved SBS and SRS research in heavy water and its application in CARS

NASA Astrophysics Data System (ADS)

Liu, Jinbo; Gai, Baodong; Yuan, Hong; Sun, Jianfeng; Zhou, Xin; Liu, Di; Xia, Xusheng; Wang, Pengyuan; Hu, Shu; Chen, Ying; Guo, Jingwei; Jin, Yuqi; Sang, Fengting

2018-05-01

We present the time-resolved character of stimulated Brillouin scattering (SBS) and backward stimulated Raman scattering (BSRS) in heavy water and its application in Coherent Anti-Stokes Raman Scattering (CARS) technique. A nanosecond laser from a frequency-doubled Nd: YAG laser is introduced into a heavy water cell, to generate SBS and BSRS beams. The SBS and BSRS beams are collinear, and their time resolved characters are studied by a streak camera, experiment show that they are ideal source for an alignment-free CARS system, and the time resolved property of SBS and BSRS beams could affect the CARS efficiency significantly. By inserting a Dye cuvette to the collinear beams, the time-overlapping of SBS and BSRS could be improved, and finally the CARS efficiency is increased, even though the SBS energy is decreased. Possible methods to improve the efficiency of this CARS system are discussed too.

A dynamic urban air pollution population exposure assessment study using model and population density data derived by mobile phone traffic

NASA Astrophysics Data System (ADS)

Gariazzo, Claudio; Pelliccioni, Armando; Bolignano, Andrea

2016-04-01

A dynamic city-wide air pollution exposure assessment study has been carried out for the urban population of Rome, Italy, by using time resolved population distribution maps, derived by mobile phone traffic data, and modelled air pollutants (NO2, O3 and PM2.5) concentrations obtained by an integrated air dispersion modelling system. More than a million of persons were tracked during two months (March and April 2015) for their position within the city and its surroundings areas, with a time resolution of 15 min and mapped over an irregular grid system with a minimum resolution of 0.26 × 0.34 Km2. In addition, demographics information (as gender and age ranges) were available in a separated dataset not connected with the total population one. Such BigData were matched in time and space with air pollution model results and then used to produce hourly and daily resolved cumulative population exposures during the studied period. A significant mobility of population was identified with higher population densities in downtown areas during daytime increasing of up to 1000 people/Km2 with respect to nigh-time one, likely produced by commuters, tourists and working age population. Strong variability (up to ±50% for NO2) of population exposures were detected as an effect of both mobility and time/spatial changing in pollutants concentrations. A comparison with the correspondent stationary approach based on National Census data, allows detecting the inability of latter in estimating the actual variability of population exposure. Significant underestimations of the amount of population exposed to daily PM2.5 WHO guideline was identified for the Census approach. Very small differences (up to a few μg/m3) on exposure were detected for gender and age ranges population classes.

A multicenter retrospective analysis of the clinical features of pernicious anemia in a Korean population.

PubMed

Song, Ik-Chan; Lee, Hyo Jin; Kim, Han-Jo; Bae, Sang-Byung; Lee, Kyu-Taek; Yang, Young-Jun; Park, Suk-Young; Cho, Do-Yeun; Kim, Nae Yu; Cho, In-Sung; Jo, Deog-Yeon

2013-02-01

To determine the approximate incidence and clinical features of pernicious anemia in a Korean population, we retrospectively analyzed clinical data for patients with pernicious anemia who were diagnosed between 1995 and 2010 at five hospitals in Chungnam province. Ninety-seven patients were enrolled, who accounted for 24% of patients with vitamin B(12) deficiency anemia. The approximate annual incidence of pernicious anemia was 0.3 per 100,000. The median age was 66 (range, 32-98) yr, and the male/female ratio was 1.25. Anemia-associated discomfort was the most common symptom (79.4%), followed by gastrointestinal and neurological symptoms (78.4% and 38.1%, respectively). Pancytopenia was found in 36 patients (37.1%), and autoimmune disorders were found in 15 patients (15.5%). Antibody to intrinsic factor was detected in 62 (77.5%) of 80 patients examined, and antibody to parietal cells was detected in 35 (43.2%) of 81 patients examined. Of the 34 patients who underwent tests for Helicobacter pylori, 7 (12.5%) were positive. The anemia-associated and gastrointestinal symptoms resolved completely in all patients after intramuscular injection of cobalamin, whereas neurological symptoms remained in some. In conclusion, pernicious anemia is less frequent in Koreans than in Western populations; however, the clinical features of this disorder in Koreans do not differ from those of Western cases.

A Multicenter Retrospective Analysis of the Clinical Features of Pernicious Anemia in a Korean Population

PubMed Central

Song, Ik-Chan; Lee, Hyo Jin; Kim, Han-Jo; Bae, Sang-Byung; Lee, Kyu-Taek; Yang, Young-Jun; Park, Suk-Young; Cho, Do-Yeun; Kim, Nae Yu; Cho, In-Sung

2013-01-01

To determine the approximate incidence and clinical features of pernicious anemia in a Korean population, we retrospectively analyzed clinical data for patients with pernicious anemia who were diagnosed between 1995 and 2010 at five hospitals in Chungnam province. Ninety-seven patients were enrolled, who accounted for 24% of patients with vitamin B12 deficiency anemia. The approximate annual incidence of pernicious anemia was 0.3 per 100,000. The median age was 66 (range, 32-98) yr, and the male/female ratio was 1.25. Anemia-associated discomfort was the most common symptom (79.4%), followed by gastrointestinal and neurological symptoms (78.4% and 38.1%, respectively). Pancytopenia was found in 36 patients (37.1%), and autoimmune disorders were found in 15 patients (15.5%). Antibody to intrinsic factor was detected in 62 (77.5%) of 80 patients examined, and antibody to parietal cells was detected in 35 (43.2%) of 81 patients examined. Of the 34 patients who underwent tests for Helicobacter pylori, 7 (12.5%) were positive. The anemia-associated and gastrointestinal symptoms resolved completely in all patients after intramuscular injection of cobalamin, whereas neurological symptoms remained in some. In conclusion, pernicious anemia is less frequent in Koreans than in Western populations; however, the clinical features of this disorder in Koreans do not differ from those of Western cases. PMID:23400269

Mechanical Properties of Plant Cell Walls Probed by Relaxation Spectra1[W][OA

PubMed Central

Hansen, Steen Laugesen; Ray, Peter Martin; Karlsson, Anders Ola; Jørgensen, Bodil; Borkhardt, Bernhard; Petersen, Bent Larsen; Ulvskov, Peter

2011-01-01

Transformants and mutants with altered cell wall composition are expected to display a biomechanical phenotype due to the structural role of the cell wall. It is often quite difficult, however, to distinguish the mechanical behavior of a mutant's or transformant's cell walls from that of the wild type. This may be due to the plant’s ability to compensate for the wall modification or because the biophysical method that is often employed, determination of simple elastic modulus and breakstrength, lacks the resolving power necessary for detecting subtle mechanical phenotypes. Here, we apply a method, determination of relaxation spectra, which probes, and can separate, the viscoelastic properties of different cell wall components (i.e. those properties that depend on the elastic behavior of load-bearing wall polymers combined with viscous interactions between them). A computer program, BayesRelax, that deduces relaxation spectra from appropriate rheological measurements is presented and made accessible through a Web interface. BayesRelax models the cell wall as a continuum of relaxing elements, and the ability of the method to resolve small differences in cell wall mechanical properties is demonstrated using tuber tissue from wild-type and transgenic potatoes (Solanum tuberosum) that differ in rhamnogalacturonan I side chain structure. PMID:21075961

Decoding the dynamics of cellular metabolism and the action of 3-bromopyruvate and 2-deoxyglucose using pulsed stable isotope-resolved metabolomics.

PubMed

Pietzke, Matthias; Zasada, Christin; Mudrich, Susann; Kempa, Stefan

2014-01-01

Cellular metabolism is highly dynamic and continuously adjusts to the physiological program of the cell. The regulation of metabolism appears at all biological levels: (post-) transcriptional, (post-) translational, and allosteric. This regulatory information is expressed in the metabolome, but in a complex manner. To decode such complex information, new methods are needed in order to facilitate dynamic metabolic characterization at high resolution. Here, we describe pulsed stable isotope-resolved metabolomics (pSIRM) as a tool for the dynamic metabolic characterization of cellular metabolism. We have adapted gas chromatography-coupled mass spectrometric methods for metabolomic profiling and stable isotope-resolved metabolomics. In addition, we have improved robustness and reproducibility and implemented a strategy for the absolute quantification of metabolites. By way of examples, we have applied this methodology to characterize central carbon metabolism of a panel of cancer cell lines and to determine the mode of metabolic inhibition of glycolytic inhibitors in times ranging from minutes to hours. Using pSIRM, we observed that 2-deoxyglucose is a metabolic inhibitor, but does not directly act on the glycolytic cascade.

Particle-in-cell studies of fast-ion slowing-down rates in cool tenuous magnetized plasma

NASA Astrophysics Data System (ADS)

Evans, Eugene S.; Cohen, Samuel A.; Welch, Dale R.

2018-04-01

We report on 3D-3V particle-in-cell simulations of fast-ion energy-loss rates in a cold, weakly-magnetized, weakly-coupled plasma where the electron gyroradius, ρe, is comparable to or less than the Debye length, λDe, and the fast-ion velocity exceeds the electron thermal velocity, a regime in which the electron response may be impeded. These simulations use explicit algorithms, spatially resolve ρe and λDe, and temporally resolve the electron cyclotron and plasma frequencies. For mono-energetic dilute fast ions with isotropic velocity distributions, these scaling studies of the slowing-down time, τs, versus fast-ion charge are in agreement with unmagnetized slowing-down theory; with an applied magnetic field, no consistent anisotropy between τs in the cross-field and field-parallel directions could be resolved. Scaling the fast-ion charge is confirmed as a viable way to reduce the required computational time for each simulation. The implications of these slowing down processes are described for one magnetic-confinement fusion concept, the small, advanced-fuel, field-reversed configuration device.

Time-resolved correlative optical microscopy of charge-carrier transport, recombination, and space-charge fields in CdTe heterostructures

DOE PAGES

Kuciauskas, Darius; Myers, Thomas H.; Barnes, Teresa M.; ...

2017-02-20

From time- and spatially resolved optical measurements, we show that extended defects can have a large effect on the charge-carrier recombination in II-VI semiconductors. In CdTe double heterostructures grown by molecular beam epitaxy on the InSb (100)-orientation substrates, we characterized the extended defects and found that near stacking faults the space-charge field extends by 2-5 μm. Charge carriers drift (with the space-charge field strength of 730-1,360 V cm -1) and diffuse (with the mobility of 260 ± 30 cm 2 V -1 s -1) toward the extended defects, where the minority-carrier lifetime is reduced from 560 ns to 0.25 ns.more » Furthermore, the extended defects are nonradiative recombination sinks that affect areas significantly larger than the typical crystalline grains in II-VI solar cells. From the correlative time-resolved photoluminescence and second-harmonic generation microscopy data, we developed a band-diagram model that can be used to analyze the impact of extended defects on solar cells and other electronic devices.« less

Time-resolved correlative optical microscopy of charge-carrier transport, recombination, and space-charge fields in CdTe heterostructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuciauskas, Darius; Myers, Thomas H.; Barnes, Teresa M.

From time- and spatially resolved optical measurements, we show that extended defects can have a large effect on the charge-carrier recombination in II-VI semiconductors. In CdTe double heterostructures grown by molecular beam epitaxy on the InSb (100)-orientation substrates, we characterized the extended defects and found that near stacking faults the space-charge field extends by 2-5 μm. Charge carriers drift (with the space-charge field strength of 730-1,360 V cm -1) and diffuse (with the mobility of 260 ± 30 cm 2 V -1 s -1) toward the extended defects, where the minority-carrier lifetime is reduced from 560 ns to 0.25 ns.more » Furthermore, the extended defects are nonradiative recombination sinks that affect areas significantly larger than the typical crystalline grains in II-VI solar cells. From the correlative time-resolved photoluminescence and second-harmonic generation microscopy data, we developed a band-diagram model that can be used to analyze the impact of extended defects on solar cells and other electronic devices.« less

Identification of effective exciton-exciton annihilation in squaraine-squaraine copolymers.

PubMed

Hader, Kilian; May, Volkhard; Lambert, Christoph; Engel, Volker

2016-05-11

Ultrafast time-resolved transient absorption spectroscopy is able to monitor the fate of the excited state population in molecular aggregates or polymers. Due to many competing decay processes, the identification of exciton-exciton annihilation (EEA) is difficult. Here, we use a microscopic model to describe exciton annihilation processes in squaraine-squaraine copolymers. Transient absorption time traces measured at different laser powers exhibit an unusual time-dependence. The analysis points towards dynamics taking place on three time-scales. Immediately after laser-excitation a localization of excitons takes place within the femtosecond time-regime. This is followed by exciton-exciton annihilation which is responsible for a fast decay of the exciton population. At later times, excitations being localized on units which are not directly connected remain so that diffusion dominates the dynamics and leads to a slower decay. We thus provide evidence for EEA tracked by time-resolved spectroscopy which has not been reported that clearly before.

Vibrational frequencies and dephasing times in excited electronic states by femtosecond time-resolved four-wave mixing

NASA Astrophysics Data System (ADS)

Joo, Taiha; Albrecht, A. C.

1993-06-01

Time-resolved degenerate four-wave mixing (TRDFWM) for an electronically resonant system in a phase-matching configuration that measures population decay is reported. Because the spectral width of input light exceeds the vibrational Bohr frequency of a strong Raman active mode, the vibrational coherence produces strong oscillations in the TRDFWM signal together with the usual population decay from the excited electronic state. The data are analyzed in terms of a four-level system: ground and excited electronic states each split by a vibrational quantum of a Raman active mode. Absolute frequencies and their dephasing times of the vibrational modes at ≈590 cm -1 are obtained for the excited as well as the ground electronic state. The vibrational dephasing rate in the excited electronic state is about an order of magnitude faster than that in the ground state, the origin of which is speculated upon.

Discrimination, Crypticity and Incipient Taxa in Entamoeba1

PubMed Central

Espinosa, Avelina; Paz-y-Miño-C, Guillermo

2011-01-01

Persistent difficulties in resolving clear lineages in diverging populations of prokaryotes or unicellular eukaryotes (protistan polyphyletic groups) are challenging the classical species concept. Although multiple integrated approaches would render holistic taxonomies, most phylogenetic studies are still based on single-gene or morphological traits. Such methodologies conceal natural lineages, which are considered ‘cryptic’. The concept of species is considered artificial and inadequate to define natural populations. Social organisms display differential behaviors toward kin than to non-related individuals. In ‘social’ microbes, kin discrimination has been used to help resolve crypticity. Aggregative behavior could be explored in a non-social protist to define phylogenetic varieties that are considered ‘cryptic’. Two Entamoeba invadens strains, VK-1:NS and IP-1 are considered close populations of the same ‘species’. This study demonstrates that VK-1:NS and IP-1 trophozoites aggregate only with alike members and discriminate individuals from different strains based on behavioral and chemical signals. Combined morphological, behavioral/chemical and ecological studies could improve Archamoebae phylogenies and define cryptic varieties. Evolutionary processes in which selection acted continuously and cumulatively on ancestors of Entamoeba populations gave rise to behavioral and chemical signals that allowed individuals to discriminate non-population members and gradually, to new lineages; alternative views that claim a ‘Designer’ or ‘Creator’ as responsible for protistan diversity are unfounded. PMID:22299709

Time-resolved contrast-enhanced MRA (TWIST) with gadofosveset trisodium in the classification of soft-tissue vascular anomalies in the head and neck in children following updated 2014 ISSVA classification: first report on systematic evaluation of MRI and TWIST in a cohort of 47 children.

PubMed

Higgins, L J; Koshy, J; Mitchell, S E; Weiss, C R; Carson, K A; Huisman, T A G M; Tekes, A

2016-01-01

To evaluate the relative accuracy of contrast-enhanced time-resolved angiography with interleaved stochastic trajectories versus conventional contrast-enhanced magnetic resonance imaging (MRI) following International Society for the Study of Vascular Anomalies updated 2014-based classification of soft-tissue vascular anomalies in the head and neck in children. Time-resolved angiography with interleaved stochastic trajectories versus conventional contrast-enhanced MRI of children with diagnosis of soft-tissue vascular anomalies in the head and neck referred for MRI between 2008 and 2014 were retrospectively reviewed. Forty-seven children (0-18 years) were evaluated. Two paediatric neuroradiologists evaluated time-resolved MRA and conventional MRI in two different sessions (30 days apart). Blood-pool endovascular MRI contrast agent gadofosveset trisodium was used. The present cohort had the following diagnoses: infantile haemangioma (n=6), venous malformation (VM; n=23), lymphatic malformation (LM; n=16), arteriovenous malformation (AVM; n=2). Time-resolved MRA alone accurately classified 38/47 (81%) and conventional MRI 42/47 (89%), respectively. Although time-resolved MRA alone is slightly superior to conventional MRI alone for diagnosis of infantile haemangioma, conventional MRI is slightly better for diagnosis of venous and LMs. Neither time-resolved MRA nor conventional MRI was sufficient for accurate diagnosis of AVM in this cohort. Conventional MRI combined with time-resolved MRA accurately classified 44/47 cases (94%). Time-resolved MRA using gadofosveset trisodium can accurately classify soft-tissue vascular anomalies in the head and neck in children. The addition of time-resolved MRA to existing conventional MRI protocols provides haemodynamic information, assisting the diagnosis of vascular anomalies in the paediatric population at one-third of the dose of other MRI contrast agents. Copyright © 2015 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

Systems Imaging of the Immune Synapse.

PubMed

Ambler, Rachel; Ruan, Xiangtao; Murphy, Robert F; Wülfing, Christoph

2017-01-01

Three-dimensional live cell imaging of the interaction of T cells with antigen-presenting cells (APCs) visualizes the subcellular distributions of signaling intermediates during T cell activation at thousands of resolved positions within a cell. These information-rich maps of local protein concentrations are a valuable resource in understanding T cell signaling. Here, we describe a protocol for the efficient acquisition of such imaging data and their computational processing to create four-dimensional maps of local concentrations. This protocol allows quantitative analysis of T cell signaling as it occurs inside live cells with resolution in time and space across thousands of cells.

Thin film, concentrator, and multijunction space solar cells: Status and potential

NASA Technical Reports Server (NTRS)

Flood, Dennis J.

1991-01-01

Recent, rapid advances in a variety of solar cell technologies offer the potential for significantly enhancing, or enabling entirely new, mission capabilities. Thin film solar cells are of particular interest. A review is provided of the status of those thin film cell technologies of interest for space applications, and the issues to be resolved before mission planners can consider them. A short summary of recent developments in concentrator and multijunction space solar cell and array technology is given.

Thin film, concentrator and multijunction space solar cells: Status and potential

NASA Technical Reports Server (NTRS)

Flood, Dennis J.

1991-01-01

Recent, rapid advances in a variety of solar cell technologies offer the potential for significantly enhancing, or enabling entirely new, mission capabilities. Thin film solar cells are of particular interest in that regard. A review is provided of the status of those thin film cell technologies of interest for space applications, and the issues to be resolved before mission planners can consider them. A short summary is also given of recent developments in concentrator and multijunction space solar cell and array technology.

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput.

PubMed

Gierahn, Todd M; Wadsworth, Marc H; Hughes, Travis K; Bryson, Bryan D; Butler, Andrew; Satija, Rahul; Fortune, Sarah; Love, J Christopher; Shalek, Alex K

2017-04-01

Single-cell RNA-seq can precisely resolve cellular states, but applying this method to low-input samples is challenging. Here, we present Seq-Well, a portable, low-cost platform for massively parallel single-cell RNA-seq. Barcoded mRNA capture beads and single cells are sealed in an array of subnanoliter wells using a semipermeable membrane, enabling efficient cell lysis and transcript capture. We use Seq-Well to profile thousands of primary human macrophages exposed to Mycobacterium tuberculosis.

DNA Methylation as an Epigenetic Factor in the Development and Progression of Polycythemia Vera

DTIC Science & Technology

2008-10-01

vera and idiopathic myelofibrosis. Pathol Biol ( Paris ). 2001;49:164-166. 2. Spivak JL. Diagnosis of the myeloproliferative disorders: resolving...leukemia cell lines with different cellular origin (myeloid cell lines KG1, KG1a, HEL, K562, and TF1; T lymphoid cell lines CEM and JTAg; and B lymphoid...in the cell lines of lymphoid origin versus myeloid leukemia cell lines and a GM-CSF- Services Email this article to a friend Download to

Fluorescence Dynamics in the Endoplasmic Reticulum of a Live Cell: Time-Resolved Confocal Microscopy.

PubMed

Ghosh, Shirsendu; Nandi, Somen; Ghosh, Catherine; Bhattacharyya, Kankan

2016-09-19

Fluorescence dynamics in the endoplasmic reticulum (ER) of a live non-cancer lung cell (WI38) and a lung cancer cell (A549) are studied by using time-resolved confocal microscopy. To selectively study the organelle, ER, we have used an ER-Tracker dye. From the emission maximum (λmaxem) of the ER-Tracker dye, polarity (i.e. dielectric constant, ϵ) in the ER region of the cells (≈500 nm in WI38 and ≈510 nm in A549) is estimated to be similar to that of chloroform (λmaxem =506 nm, ϵ≈5). The red shift by 10 nm in λmaxem in the cancer cell (A549) suggests a slightly higher polarity compared to the non-cancer cell (WI38). The fluorescence intensity of the ER-Tracker dye exhibits prolonged intermittent oscillations on a timescale of 2-6 seconds for the cancer cell (A549). For the non-cancer cell (WI38), such fluorescence oscillations are much less prominent. The marked fluorescence intensity oscillations in the cancer cell are attributed to enhanced calcium oscillations. The average solvent relaxation time (<τs >) of the ER region in the lung cancer cell (A549, 250±50 ps) is about four times faster than that in the non-cancer cell (WI38, 1000±50 ps). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure-Preserving Variational Multiscale Modeling of Turbulent Incompressible Flow with Subgrid Vortices

NASA Astrophysics Data System (ADS)

Evans, John; Coley, Christopher; Aronson, Ryan; Nelson, Corey

2017-11-01

In this talk, a large eddy simulation methodology for turbulent incompressible flow will be presented which combines the best features of divergence-conforming discretizations and the residual-based variational multiscale approach to large eddy simulation. In this method, the resolved motion is represented using a divergence-conforming discretization, that is, a discretization that preserves the incompressibility constraint in a pointwise manner, and the unresolved fluid motion is explicitly modeled by subgrid vortices that lie within individual grid cells. The evolution of the subgrid vortices is governed by dynamical model equations driven by the residual of the resolved motion. Consequently, the subgrid vortices appropriately vanish for laminar flow and fully resolved turbulent flow. As the resolved velocity field and subgrid vortices are both divergence-free, the methodology conserves mass in a pointwise sense and admits discrete balance laws for energy, enstrophy, and helicity. Numerical results demonstrate the methodology yields improved results versus state-of-the-art eddy viscosity models in the context of transitional, wall-bounded, and rotational flow when a divergence-conforming B-spline discretization is utilized to represent the resolved motion.

Spatially resolved regression analysis of pre-treatment FDG, FLT and Cu-ATSM PET from post-treatment FDG PET: an exploratory study

PubMed Central

Bowen, Stephen R; Chappell, Richard J; Bentzen, Søren M; Deveau, Michael A; Forrest, Lisa J; Jeraj, Robert

2012-01-01

Purpose To quantify associations between pre-radiotherapy and post-radiotherapy PET parameters via spatially resolved regression. Materials and methods Ten canine sinonasal cancer patients underwent PET/CT scans of [18F]FDG (FDGpre), [18F]FLT (FLTpre), and [61Cu]Cu-ATSM (Cu-ATSMpre). Following radiotherapy regimens of 50 Gy in 10 fractions, veterinary patients underwent FDG PET/CT scans at three months (FDGpost). Regression of standardized uptake values in baseline FDGpre, FLTpre and Cu-ATSMpre tumour voxels to those in FDGpost images was performed for linear, log-linear, generalized-linear and mixed-fit linear models. Goodness-of-fit in regression coefficients was assessed by R2. Hypothesis testing of coefficients over the patient population was performed. Results Multivariate linear model fits of FDGpre to FDGpost were significantly positive over the population (FDGpost~0.17 FDGpre, p=0.03), and classified slopes of RECIST non-responders and responders to be different (0.37 vs. 0.07, p=0.01). Generalized-linear model fits related FDGpre to FDGpost by a linear power law (FDGpost~FDGpre0.93, p<0.001). Univariate mixture model fits of FDGpre improved R2 from 0.17 to 0.52. Neither baseline FLT PET nor Cu-ATSM PET uptake contributed statistically significant multivariate regression coefficients. Conclusions Spatially resolved regression analysis indicates that pre-treatment FDG PET uptake is most strongly associated with three-month post-treatment FDG PET uptake in this patient population, though associations are histopathology-dependent. PMID:22682748

Pituitary Stem Cell Update and Potential Implications for Treating Hypopituitarism

PubMed Central

Castinetti, Frederic; Davis, Shannon W.; Brue, Thierry

2011-01-01

Stem cells have been identified in organs with both low and high cell turnover rates. They are characterized by the expression of key marker genes for undifferentiated cells, the ability to self-renew, and the ability to regenerate tissue after cell loss. Several recent reports present evidence for the presence of pituitary stem cells. Here we offer a critical review of the field and suggest additional studies that could resolve points of debate. Recent reports have relied on different markers, including SOX2, nestin, GFRa2, and SCA1, to identify pituitary stem cells and progenitors. Future studies will be needed to resolve the relationships between cells expressing these markers. Members of the Sox family of transcription factors are likely involved in the earliest steps of pituitary stem cell proliferation and the earliest transitions to differentiation. The transcription factor PROP1 and the NOTCH signaling pathway may regulate the transition to differentiation. Identification of the stem cell niche is an important step in understanding organ development. The niche may be the marginal zone around the lumen of Rathke's pouch, between the anterior and intermediate lobes of mouse pituitary, because cells in this region apparently give birth to all six pituitary hormone cell lineages. Stem cells have been shown to play a role in recurrent malignancies in some tissues, and their role in pituitary hyperplasia, pituitary adenomas, and tumors is an important area for future investigation. From a therapeutic viewpoint, the ability to cultivate and grow stem cells in a pituitary predifferentiation state might also be helpful for the long-term treatment of pituitary deficiencies. PMID:21493869

Quenching and ram pressure stripping of simulated Milky Way satellite galaxies

NASA Astrophysics Data System (ADS)

Simpson, Christine; Grand, Robert; Gomez, Facundo; Marinacci, Federico; Pakmor, Rüdiger; Springel, Volker; Campbell, David; Frenk, Carlos; Auriga Project, Virgo Consortium

2018-01-01

We present predictions for the quenching of star formation in satellite galaxies of the Local Group from a suite of 30 cosmological zoom simulations of Milky Way-like host galaxies. The Auriga simulations resolve satellites down to the luminosity of the classical dwarf spheroidal galaxies of the Milky Way. We find strong mass-dependent and distance-dependent quenching signals, where dwarf systems beyond 600 kpc are only strongly quenched below a stellar mass of 107 M⊙. Ram pressure stripping appears to be the dominant quenching mechanism and 50% of quenched systems cease star formation within 1 Gyr of first infall. We demonstrate that systems within a host galaxy's R200 radius are comprised of two populations: (i) a first infall population that has entered the host halo within the past few Gyrs and (ii) a population of returning `backsplash' systems that have had a much more extended interaction with the host. Backsplash galaxies that do not return to the host galaxy by redshift zero exhibit quenching properties similar to galaxies within R200 and are distinct from other external systems. The simulated quenching trend with stellar mass has some tension with observations, but our simulations are able reproduce the range of quenching times measured from resolved stellar populations of Local Group dwarf galaxies.

Quenching and ram pressure stripping of simulated Milky Way satellite galaxies

NASA Astrophysics Data System (ADS)

Simpson, Christine M.; Grand, Robert J. J.; Gómez, Facundo A.; Marinacci, Federico; Pakmor, Rüdiger; Springel, Volker; Campbell, David J. R.; Frenk, Carlos S.

2018-07-01

We present predictions for the quenching of star formation in satellite galaxies of the Local Group from a suite of 30 cosmological zoom simulations of Milky Way-like host galaxies. The Auriga simulations resolve satellites down to the luminosity of the classical dwarf spheroidal galaxies of the Milky Way. We find strong mass-dependent and distance-dependent quenching signals, where dwarf systems beyond 600 kpc are only strongly quenched below a stellar mass of 107 M⊙. Ram pressure stripping appears to be the dominant quenching mechanism and 50 per cent of quenched systems cease star formation within 1 Gyr of first infall. We demonstrate that systems within a host galaxy's R200 radius are comprised of two populations: (i) a first infall population that has entered the host halo within the past few Gyrs and (ii) a population of returning `backsplash' systems that have had a much more extended interaction with the host. Backsplash galaxies that do not return to the host galaxy by redshift zero exhibit quenching properties similar to galaxies within R200 and are distinct from other external systems. The simulated quenching trend with stellar mass has some tension with observations, but our simulations are able reproduce the range of quenching times measured from resolved stellar populations of Local Group dwarf galaxies.

Quenching and ram pressure stripping of simulated Milky Way satellite galaxies

NASA Astrophysics Data System (ADS)

Simpson, Christine M.; Grand, Robert J. J.; Gómez, Facundo A.; Marinacci, Federico; Pakmor, Rüdiger; Springel, Volker; Campbell, David J. R.; Frenk, Carlos S.

2018-03-01

We present predictions for the quenching of star formation in satellite galaxies of the Local Group from a suite of 30 cosmological zoom simulations of Milky Way-like host galaxies. The Auriga simulations resolve satellites down to the luminosity of the classical dwarf spheroidal galaxies of the Milky Way. We find strong mass-dependent and distance-dependent quenching signals, where dwarf systems beyond 600 kpc are only strongly quenched below a stellar mass of 107 M⊙. Ram pressure stripping appears to be the dominant quenching mechanism and 50% of quenched systems cease star formation within 1 Gyr of first infall. We demonstrate that systems within a host galaxy's R200 radius are comprised of two populations: (i) a first infall population that has entered the host halo within the past few Gyrs and (ii) a population of returning `backsplash' systems that have had a much more extended interaction with the host. Backsplash galaxies that do not return to the host galaxy by redshift zero exhibit quenching properties similar to galaxies within R200 and are distinct from other external systems. The simulated quenching trend with stellar mass has some tension with observations, but our simulations are able reproduce the range of quenching times measured from resolved stellar populations of Local Group dwarf galaxies.

Internal energy of HCl upon photolysis of 2-chloropropene at 193 nm investigated with time-resolved Fourier-transform spectroscopy and quasiclassical trajectories

NASA Astrophysics Data System (ADS)

Chang, Chih-Min; Huang, Yu-Hsuan; Liu, Suet-Yi; Lee, Yuan-Pern; Pombar-Pérez, Marta; Martínez-Núñez, Emilio; Vázquez, Saulo A.

2008-12-01

Following photodissociation of 2-chloropropene (H2CCClCH3) at 193 nm, vibration-rotationally resolved emission spectra of HCl (υ ≤6) in the spectral region of 1900-2900 cm-1 were recorded with a step-scan time-resolved Fourier-transform spectrometer. All vibrational levels show a small low-J component corresponding to ˜400 K and a major high-J component corresponding to 7100-18 700 K with average rotational energy of 39±311 kJ mol-1. The vibrational population of HCl is inverted at υ =2, and the average vibrational energy is 86±5 kJ mol-1. Two possible channels of molecular elimination producing HCl+propyne or HCl+allene cannot be distinguished positively based on the observed internal energy distribution of HCl. The observed rotational distributions fit qualitatively with the distributions of both channels obtained with quasiclassical trajectories (QCTs), but the QCT calculations predict negligible populations for states at small J. The observed vibrational distribution agrees satisfactorily with the total QCT distribution obtained as a weighted sum of contributions from both four-center elimination channels. Internal energy distributions of HCl from 2-chloropropene and vinyl chloride are compared.

Addressing the [O III] / Hβ offset in metal poor star forming galaxies found in the RESOLVE survey and ECO catalog

NASA Astrophysics Data System (ADS)

Richardson, Chris T.; Kannappan, Sheila; Moffett, Amanda J.; RESOLVE survey team

2018-06-01

Metal poor star forming galaxies sit on the far left wing of the BPT diagram just below traditional demarcation lines. The basic approach to reproducing their emission lines by coupling photoionization models to stellar population synthesis models underestimates the observed [O III] / Hβ ratio by a factor 0.3-0.5 dex. We classified galaxies as metal poor in the REsolved Spectroscopy of a Local VolumE (RESOLVE) survey and the Environmental COntext (ECO) catalog by using the IZI code based off of Bayesian inference. We used a variety of stellar population synthesis codes to generate SEDs covering a range of starburst ages and metallicities including both secular and binary stellar evolution. Here, we show that multiple SPS codes can produce SEDs hard enough to reduce the offset assuming that simple, and perhaps unjustified, nebular conditions hold. Adopting more realistic nebular conditions shows that, despite the recent emphasis placed on binary evolution to fit high O III ratios, none of our SEDs can reduce the offset. We propose several new solutions including using ensembles of nebular clouds and improved microphysics to address this issue. This work is supported by National Science Foundation awards OCI-1053575, though XSEDE award TG-AST140040, and NSF awards AST-0955368 and CISE/ACI-1156614.

Application of Stable Isotope-Assisted Metabolomics for Cell Metabolism Studies

PubMed Central

You, Le; Zhang, Baichen; Tang, Yinjie J.

2014-01-01

The applications of stable isotopes in metabolomics have facilitated the study of cell metabolisms. Stable isotope-assisted metabolomics requires: (1) properly designed tracer experiments; (2) stringent sampling and quenching protocols to minimize isotopic alternations; (3) efficient metabolite separations; (4) high resolution mass spectrometry to resolve overlapping peaks and background noises; and (5) data analysis methods and databases to decipher isotopic clusters over a broad m/z range (mass-to-charge ratio). This paper overviews mass spectrometry based techniques for precise determination of metabolites and their isotopologues. It also discusses applications of isotopic approaches to track substrate utilization, identify unknown metabolites and their chemical formulas, measure metabolite concentrations, determine putative metabolic pathways, and investigate microbial community populations and their carbon assimilation patterns. In addition, 13C-metabolite fingerprinting and metabolic models can be integrated to quantify carbon fluxes (enzyme reaction rates). The fluxome, in combination with other “omics” analyses, may give systems-level insights into regulatory mechanisms underlying gene functions. More importantly, 13C-tracer experiments significantly improve the potential of low-resolution gas chromatography-mass spectrometry (GC-MS) for broad-scope metabolism studies. We foresee the isotope-assisted metabolomics to be an indispensable tool in industrial biotechnology, environmental microbiology, and medical research. PMID:24957020

Phase Reconstruction from FROG Using Genetic Algorithms[Frequency-Resolved Optical Gating

DOE Office of Scientific and Technical Information (OSTI.GOV)

Omenetto, F.G.; Nicholson, J.W.; Funk, D.J.

1999-04-12

The authors describe a new technique for obtaining the phase and electric field from FROG measurements using genetic algorithms. Frequency-Resolved Optical Gating (FROG) has gained prominence as a technique for characterizing ultrashort pulses. FROG consists of a spectrally resolved autocorrelation of the pulse to be measured. Typically a combination of iterative algorithms is used, applying constraints from experimental data, and alternating between the time and frequency domain, in order to retrieve an optical pulse. The authors have developed a new approach to retrieving the intensity and phase from FROG data using a genetic algorithm (GA). A GA is a generalmore » parallel search technique that operates on a population of potential solutions simultaneously. Operators in a genetic algorithm, such as crossover, selection, and mutation are based on ideas taken from evolution.« less

Resolving conflict realistically in today's health care environment.

PubMed

Smith, S B; Tutor, R S; Phillips, M L

2001-11-01

Conflict is a natural part of human interaction, and when properly addressed, results in improved interpersonal relationships and positive organizational culture. Unchecked conflict may escalate to verbal and physical violence. Conflict that is unresolved creates barriers for people, teams, organizational growth, and productivity, leading to cultural disintegration within the establishment. By relying on interdependence and professional collaboration, all parties involved grow and, in turn, benefit the organization and population served. When used in a constructive manner, conflict resolution can help all parties involved see the whole picture, thus allowing freedom for growth and change. Conflict resolution is accomplished best when emotions are controlled before entering into negotiation. Positive confrontation, problem solving, and negotiation are processes used to realistically resolve conflict. Everyone walks away a winner when conflict is resolved in a positive, professional manner (Stone, 1999).

Distinctive Capillary Action by Micro-channels in Bone-like Templates can Enhance Recruitment of Cells for Restoration of Large Bony Defect.

PubMed

Oh, Daniel S; Koch, Alia; Eisig, Sidney; Kim, Sahng Gyoon; Kim, Yoon Hyuk; Kim, Do-Gyoon; Shim, Jae Hyuck

2015-09-11

Without an active, thriving cell population that is well-distributed and stably anchored to the inserted template, exceptional bone regeneration does not occur. With conventional templates, the absence of internal micro-channels results in the lack of cell infiltration, distribution, and inhabitance deep inside the templates. Hence, a highly porous and uniformly interconnected trabecular-bone-like template with micro-channels (biogenic microenvironment template; BMT) has been developed to address these obstacles. The novel BMT was created by innovative concepts (capillary action) and fabricated with a sponge-template coating technique. The BMT consists of several structural components: inter-connected primary-pores (300-400 µm) that mimic pores in trabecular bone, micro-channels (25-70 µm) within each trabecula, and nanopores (100-400 nm) on the surface to allow cells to anchor. Moreover, the BMT has been documented by mechanical test study to have similar mechanical strength properties to those of human trabecular bone (~3.8 MPa)12. The BMT exhibited high absorption, retention, and habitation of cells throughout the bridge-shaped (Π) templates (3 cm height and 4 cm length). The cells that were initially seeded into one end of the templates immediately mobilized to the other end (10 cm distance) by capillary action of the BMT on the cell media. After 4 hr, the cells homogenously occupied the entire BMT and exhibited normal cellular behavior. The capillary action accounted for the infiltration of the cells suspended in the media and the distribution (active migration) throughout the BMT. Having observed these capabilities of the BMT, we project that BMTs will absorb bone marrow cells, growth factors, and nutrients from the periphery under physiological conditions. The BMT may resolve current limitations via rapid infiltration, homogenous distribution and inhabitance of cells in large, volumetric templates to repair massive skeletal defects.

Melatonin Decreases Glucose Metabolism in Prostate Cancer Cells: A 13C Stable Isotope-Resolved Metabolomic Study.

PubMed

Hevia, David; Gonzalez-Menendez, Pedro; Fernandez-Fernandez, Mario; Cueto, Sergio; Rodriguez-Gonzalez, Pablo; Garcia-Alonso, Jose I; Mayo, Juan C; Sainz, Rosa M

2017-07-26

The pineal neuroindole melatonin exerts an exceptional variety of systemic functions. Some of them are exerted through its specific membrane receptors type 1 and type 2 (MT1 and MT2) while others are mediated by receptor-independent mechanisms. A potential transport of melatonin through facilitative glucose transporters (GLUT/ SLC2A ) was proposed in prostate cancer cells. The prostate cells have a particular metabolism that changes during tumor progression. During the first steps of carcinogenesis, oxidative phosphorylation is reactivated while the switch to the "Warburg effect" only occurs in advanced tumors and in the metastatic stage. Here, we investigated whether melatonin might change prostate cancer cell metabolism. To do so, 13 C stable isotope-resolved metabolomics in androgen sensitive LNCaP and insensitive PC-3 prostate cancer cells were employed. In addition to metabolite 13 C-labeling, ATP/AMP levels, and lactate dehydrogenase or pentose phosphate pathway activity were measured. Melatonin reduces lactate labeling in androgen-sensitive cells and it also lowers 13 C-labeling of tricarboxylic acid cycle metabolites and ATP production. In addition, melatonin reduces lactate 13 C-labeling in androgen insensitive prostate cancer cells. Results demonstrated that melatonin limits glycolysis as well as the tricarboxylic acid cycle and pentose phosphate pathway in prostate cancer cells, suggesting that the reduction of glucose uptake is a major target of the indole in this tumor type.

Preface of the "Symposium on Mathematical Models and Methods to investigate Heterogeneity in Cell and Cell Population Biology"

NASA Astrophysics Data System (ADS)

Clairambault, Jean

2016-06-01

This session investigates hot topics related to mathematical representations of cell and cell population dynamics in biology and medicine, in particular, but not only, with applications to cancer. Methods in mathematical modelling and analysis, and in statistical inference using single-cell and cell population data, should contribute to focus this session on heterogeneity in cell populations. Among other methods are proposed: a) Intracellular protein dynamics and gene regulatory networks using ordinary/partial/delay differential equations (ODEs, PDEs, DDEs); b) Representation of cell population dynamics using agent-based models (ABMs) and/or PDEs; c) Hybrid models and multiscale models to integrate single-cell dynamics into cell population behaviour; d) Structured cell population dynamics and asymptotic evolution w.r.t. relevant traits; e) Heterogeneity in cancer cell populations: origin, evolution, phylogeny and methods of reconstruction; f) Drug resistance as an evolutionary phenotype: predicting and overcoming it in therapeutics; g) Theoretical therapeutic optimisation of combined drug treatments in cancer cell populations and in populations of other organisms, such as bacteria.

Regulatory complexity revealed by integrated cytological and RNA-seq analyses of meiotic substages in mouse spermatocytes.

PubMed

Ball, Robyn L; Fujiwara, Yasuhiro; Sun, Fengyun; Hu, Jianjun; Hibbs, Matthew A; Handel, Mary Ann; Carter, Gregory W

2016-08-12

The continuous and non-synchronous nature of postnatal male germ-cell development has impeded stage-specific resolution of molecular events of mammalian meiotic prophase in the testis. Here the juvenile onset of spermatogenesis in mice is analyzed by combining cytological and transcriptomic data in a novel computational analysis that allows decomposition of the transcriptional programs of spermatogonia and meiotic prophase substages. Germ cells from testes of individual mice were obtained at two-day intervals from 8 to 18 days post-partum (dpp), prepared as surface-spread chromatin and immunolabeled for meiotic stage-specific protein markers (STRA8, SYCP3, phosphorylated H2AFX, and HISTH1T). Eight stages were discriminated cytologically by combinatorial antibody labeling, and RNA-seq was performed on the same samples. Independent principal component analyses of cytological and transcriptomic data yielded similar patterns for both data types, providing strong evidence for substage-specific gene expression signatures. A novel permutation-based maximum covariance analysis (PMCA) was developed to map co-expressed transcripts to one or more of the eight meiotic prophase substages, thereby linking distinct molecular programs to cytologically defined cell states. Expression of meiosis-specific genes is not substage-limited, suggesting regulation of substage transitions at other levels. This integrated analysis provides a general method for resolving complex cell populations. Here it revealed not only features of meiotic substage-specific gene expression, but also a network of substage-specific transcription factors and relationships to potential target genes.

The involvement of Canadian physicians in promoting and providing unproven and unapproved stem cell interventions.

PubMed

Ogbogu, Ubaka; Du, Jenny; Koukio, Yonida

2018-05-02

Direct to consumer offerings of unproven stem cell interventions (SCIs) is a pressing scientific and policy issue. According to media reports, providers of SCIs have emerged in Canada. This study provides the first systematic scan of Canadian providers and associated trends and claims. The study sample consisted of 15 websites retrieved from a Google™ keyword search. The websites were assessed by a rater using a peer-reviewed coding frame that queried treatment location, stem cell offerings, treatment claims, supporting evidence, and legal and regulatory compliance. A second rater reviewed a subset of the websites for purposes of inter-rater reliability. Disagreements between raters were resolved by consensus. Data collected by the raters was analyzed in SPSS. Physicians are the dominant treatment providers in Canada. Providers operate in urban and semi-urban areas in the most populous provinces. SCIs provided are mainly autologous adult stem cells for multiple conditions including musculoskeletal disorders, spinal cord injury (SCI) and diabetes. Efficacy and benefits of treatment are prominently and positively portrayed, while risks are not mentioned or portrayed as trivial. Regulatory concerns are not discussed. The involvement of physicians in promoting and providing unproven and unapproved SCIs raises significant ethical, legal and regulatory concerns. Treatment claims and trends appear to contravene applicable professional standards, statutory obligations, and consumer protection laws. While the number of providers observed is still marginal, urgent and proactive regulatory response is needed to prevent proliferation of a potentially exploitative and harmful market for unproven SCIs in Canada.

Determination of Carrier Lifetimes in Organic-Inorganic Hybrid Solar Cells Based on Sb2S3 by Using the Time-Resolved Photocurrent

NASA Astrophysics Data System (ADS)

Jo, Hyun-Jun; Mun, Young Hee; Kim, Jong Su; Kim, Seung Hyun; Lee, Sang-Ju; Sung, Shi-Joon; Kim, Dae-Hwan

2018-03-01

This paper presents organic-inorganic hybrid solar cells (SCs) based on ZnO/Sb2S3/P3HT heterojunctions. The ZnO and the Sb2S3 layers were grown using atomic layer deposition (ALD). Although four cells were fabricated on one substrate by using the same process, their open-circuit voltages ( V OC ) and short-circuit current densities ( J SC ) were different. The SC with a high V OC has a low J SC . The causes of the changes in the V OC and the JSC were investigated by using photoluminescence (PL) spectroscopy and optically-biased time-resolved photocurrent (TRPC) measurements. The PL results at 300 K showed that the emission positions of the Sb2S3 layers in all cells were similar at approximately 1.71 eV. The carrier lifetime of the SCs was calculated from the TRPC results. The lifetime of cell 4 with the highest J SC decreased drastically with increasing intensity of the continuous-wave optical bias beam. Therefore, the defect states in the ZnO layer contribute to the J SC , but degrade the V OC .

Quantifying the correlation between spatially defined oxygen gradients and cell fate in an engineered three-dimensional culture model.

PubMed

Ardakani, Amir G; Cheema, Umber; Brown, Robert A; Shipley, Rebecca J

2014-09-06

A challenge in three-dimensional tissue culture remains the lack of quantitative information linking nutrient delivery and cellular distribution. Both in vivo and in vitro, oxygen is delivered by diffusion from its source (blood vessel or the construct margins). The oxygen level at a defined distance from its source depends critically on the balance of diffusion and cellular metabolism. Cells may respond to this oxygen environment through proliferation, death and chemotaxis, resulting in spatially resolved gradients in cellular density. This study extracts novel spatially resolved and simultaneous data on tissue oxygenation, cellular proliferation, viability and chemotaxis in three-dimensional spiralled, cellular collagen constructs. Oxygen concentration gradients drove preferential cellular proliferation rates and viability in the higher oxygen zones and induced chemotaxis along the spiral of the collagen construct; an oxygen gradient of 1.03 mmHg mm(-1) in the spiral direction induced a mean migratory speed of 1015 μm day(-1). Although this movement was modest, it was effective in balancing the system to a stable cell density distribution, and provided insights into the natural cell mechanism for adapting cell number and activity to a prevailing oxygen regime.

Resonant Soft X-ray Scattering of Cellulose Microstructure in Plant Primary Cell Walls

NASA Astrophysics Data System (ADS)

Ye, Dan; Kiemle, Sarah N.; Wang, Cheng; Cosgrove, Daniel J.; Gomez, Esther W.; Gomez, Enrique D.

Cellulosic biomass is the most abundant raw material available for the production of renewable and sustainable biofuels. Breaking down cellulose is the rate-limiting step in economical biofuel production; therefore, a detailed understanding of the microscopic structure of plant cell walls is required to develop efficient biofuel conversion methods. Primary cell walls are key determinants of plant growth and mechanics. Their structure is complex and heterogeneous, making it difficult to elucidate how various components such as pectin, hemicellulose, and cellulose contribute to the overall structure. The electron density of these wall components is similar; such that conventional hard X-ray scattering does not generate enough contrast to resolve the different elements of the polysaccharide network. The chemical specificity of resonant soft X-ray scattering allows contrast to be generated based on differences in chemistry of the different polysaccharides. By varying incident X-ray energies, we have achieved increased scattering contrast between cellulose and other polysaccharides from primary cell walls of onions. By performing scattering at certain energies, features of the network structure of the cell wall are resolved. From the soft X-ray scattering results, we obtained the packing distance of cellulose microfibrils embedded in the polysaccharide network.

Preliminary assessment of aerial photography techniques for canvasback population analysis

USGS Publications Warehouse

Munro, R.E.; Trauger, D.L.

1976-01-01

Recent intensive research on the canvasback has focused attention on the need for more precise estimates of population parameters. During the 1972-75 period, various types of aerial photographing equipment were evaluated to determine the problems and potentials for employing these techniques in appraisals of canvasback populations. The equipment and procedures available for automated analysis of aerial photographic imagery were also investigated. Serious technical problems remain to be resolved, but some promising results were obtained. Final conclusions about the feasibility of operational implementation await a more rigorous analysis of the data collected.

Novel physical chemistry approaches in biophysical researches with advanced application of lasers: Detection and manipulation.

PubMed

Iwata, Koichi; Terazima, Masahide; Masuhara, Hiroshi

2018-02-01

Novel methodologies utilizing pulsed or intense CW irradiation obtained from lasers have a major impact on biological sciences. In this article, recent development in biophysical researches fully utilizing the laser irradiation is described for three topics, time-resolved fluorescence spectroscopy, time-resolved thermodynamics, and manipulation of the biological assemblies by intense laser irradiation. First, experimental techniques for time-resolved fluorescence spectroscopy are concisely explained in Section 2. As an example of the recent application of time-resolved fluorescence spectroscopy to biological systems, evaluation of the viscosity of lipid bilayer membranes is described. The results of the spectroscopic experiments strongly suggest the presence of heterogeneous membrane structure with two different viscosity values in liposomes formed by a single phospholipid. Section 3 covers the time-resolved thermodynamics. Thermodynamical properties are important to characterize biomolecules. However, measurement of these quantities for short-lived intermediate species has been impossible by traditional thermodynamical techniques. Recently, development of a spectroscopic method based on the transient grating method enables us to measure these quantities and also to elucidate reaction kinetics which cannot be detected by other spectroscopic methods. The principle of the measurements and applications to some protein reactions are reviewed. Manipulation and fabrication of supramolecues, amino acids, proteins, and living cells by intense laser irradiation are described in Section 4. Unconventional assembly, crystallization and growth, amyloid fibril formation, and living cell manipulation are achieved by CW laser trapping and femtosecond laser-induced cavitation bubbling. Their spatio-temporal controllability is opening a new avenue in the relevant molecular and bioscience research fields. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017. Published by Elsevier B.V.

Unmixing of fluorescence spectra to resolve quantitative time-series measurements of gene expression in plate readers.

PubMed

Lichten, Catherine A; White, Rachel; Clark, Ivan B N; Swain, Peter S

2014-02-03

To connect gene expression with cellular physiology, we need to follow levels of proteins over time. Experiments typically use variants of Green Fluorescent Protein (GFP), and time-series measurements require specialist expertise if single cells are to be followed. Fluorescence plate readers, however, a standard in many laboratories, can in principle provide similar data, albeit at a mean, population level. Nevertheless, extracting the average fluorescence per cell is challenging because autofluorescence can be substantial. Here we propose a general method for correcting plate reader measurements of fluorescent proteins that uses spectral unmixing and determines both the fluorescence per cell and the errors on that fluorescence. Combined with strain collections, such as the GFP fusion collection for budding yeast, our methodology allows quantitative measurements of protein levels of up to hundreds of genes and therefore provides complementary data to high throughput studies of transcription. We illustrate the method by following the induction of the GAL genes in Saccharomyces cerevisiae for over 20 hours in different sugars and argue that the order of appearance of the Leloir enzymes may be to reduce build-up of the toxic intermediate galactose-1-phosphate. Further, we quantify protein levels of over 40 genes, again over 20 hours, after cells experience a change in carbon source (from glycerol to glucose). Our methodology is sensitive, scalable, and should be applicable to other organisms. By allowing quantitative measurements on a per cell basis over tens of hours and over hundreds of genes, it should increase our understanding of the dynamic changes that drive cellular behaviour.

Unmixing of fluorescence spectra to resolve quantitative time-series measurements of gene expression in plate readers

PubMed Central

2014-01-01

Background To connect gene expression with cellular physiology, we need to follow levels of proteins over time. Experiments typically use variants of Green Fluorescent Protein (GFP), and time-series measurements require specialist expertise if single cells are to be followed. Fluorescence plate readers, however, a standard in many laboratories, can in principle provide similar data, albeit at a mean, population level. Nevertheless, extracting the average fluorescence per cell is challenging because autofluorescence can be substantial. Results Here we propose a general method for correcting plate reader measurements of fluorescent proteins that uses spectral unmixing and determines both the fluorescence per cell and the errors on that fluorescence. Combined with strain collections, such as the GFP fusion collection for budding yeast, our methodology allows quantitative measurements of protein levels of up to hundreds of genes and therefore provides complementary data to high throughput studies of transcription. We illustrate the method by following the induction of the GAL genes in Saccharomyces cerevisiae for over 20 hours in different sugars and argue that the order of appearance of the Leloir enzymes may be to reduce build-up of the toxic intermediate galactose-1-phosphate. Further, we quantify protein levels of over 40 genes, again over 20 hours, after cells experience a change in carbon source (from glycerol to glucose). Conclusions Our methodology is sensitive, scalable, and should be applicable to other organisms. By allowing quantitative measurements on a per cell basis over tens of hours and over hundreds of genes, it should increase our understanding of the dynamic changes that drive cellular behaviour. PMID:24495318

Development of a ratiometric time-resolved luminescence sensor for pH based on lanthanide complexes.

PubMed

Liu, Mingjing; Ye, Zhiqiang; Xin, Chenglong; Yuan, Jingli

2013-01-25

Time-resolved luminescence bioassay technique using lanthanide complexes as luminescent probes/sensors has shown great utilities in clinical diagnostics and biotechnology discoveries. In this work, a novel terpyridine polyacid derivative that can form highly stable complexes with lanthanide ions in aqueous media, (4'-hydroxy-2,2':6',2''-terpyridine-6,6''-diyl) bis(methylenenitrilo) tetrakis(acetic acid) (HTTA), was designed and synthesized for developing time-resolved luminescence pH sensors based on its Eu(3+) and Tb(3+) complexes. The luminescence characterization results reveal that the luminescence intensity of HTTA-Eu(3+) is strongly dependent on the pH values in weakly acidic to neutral media (pK(a) = 5.8, pH 4.8-7.5), while that of HTTA-Tb(3+) is pH-independent. This unique luminescence response allows the mixture of HTTA-Eu(3+) and HTTA-Tb(3+) (the HTTA-Eu(3+)/Tb(3+) mixture) to be used as a ratiometric luminescence sensor for the time-resolved luminescence detection of pH with the intensity ratio of its Tb(3+) emission at 540 nm to its Eu(3+) emission at 610 nm, I(540 nm)/I(610 nm), as a signal. Moreover, the UV absorption spectrum changes of the HTTA-Eu(3+)/Tb(3+) mixture at different pHs (pH 4.0-7.0) also display a ratiometric response to the pH changes with the ratio of absorbance at 290 nm to that at 325 nm, A(290 nm)/A(325 nm), as a signal. This feature enables the HTTA-Eu(3+)/Tb(3+) mixture to have an additional function for the pH detection with the absorption spectrometry technique. For loading the complexes into the living cells, the acetoxymethyl ester of HTTA was synthesized and used for loading HTTA-Eu(3+) and HTTA-Tb(3+) into the cultured HeLa cells. The luminescence imaging results demonstrated the practical utility of the new sensor for the time-resolved luminescence cell imaging application. Copyright © 2012 Elsevier B.V. All rights reserved.

Imaging System For Measuring Macromolecule Crystal Growth Rates in Microgravity

NASA Technical Reports Server (NTRS)

Corder, Eric L.; Briscoe, Jeri

2004-01-01

In order to determine how macromolecule crystal quality improvement in microgravity is related to crystal growth characteristics, a team of scientists and engineers at NASA's Marshal Space Flight Center (MSFC) developed flight hardware capable of measuring the crystal growth rates of a population of crystals growing under the same conditions. As crystal growth rate is defined as the change or delta in a defined dimension or length (L) of crystal over time, the hardware was named Delta-L. Delta-L consists of three sub assemblies: a fluid unit including a temperature-controlled growth cell, an imaging unit, and a control unit (consisting of a Data Acquisition and Control Unit (DACU), and a thermal control unit). Delta-L will be used in connection with the Glovebox Integrated Microgravity Isolation Technology (g-LIMIT) inside the Microgravity Science Glovebox (MSG), onboard the International Space Station. This paper will describe the Delta-L imaging system. The Delta-L imaging system was designed to locate, resolve, and capture images of up to 10 individual crystals ranging in size from 10 to 500 microns with a point-to-point accuracy of +/- 2.0 microns within a quartz growth cell observation area of 20 mm x 10 mm x 1 mm. The optical imaging system is comprised of a video microscope camera mounted on computer controlled translation stages. The 3-axis translation stages and control units provide crewmembers the ability to search throughout the growth cell observation area for crystals forming in size of approximately 10 microns. Once the crewmember has selected ten crystals of interest, the growth of these crystals is tracked until the size reaches approximately 500 microns. In order to resolve these crystals an optical system with a magnification of 10X was designed. A black and white NTSC camera was utilized with a 20X microscope objective and a 0.5X custom designed relay lens with an inline light to meet the magnification requirement. The design allows a 500 pm crystal to be viewed in the vertical dimension on a standard NTSC monitor (4:3 aspect ratio). Images of the 10 crystals are collected periodically and stored in sets by the DACU.

Trojan Binaries

NASA Astrophysics Data System (ADS)

Noll, K. S.

2017-12-01

The Jupiter Trojans, in the context of giant planet migration models, can be thought of as an extension of the small body populations found beyond Neptune in the Kuiper Belt. Binaries are a distinctive feature of small body populations in the Kuiper Belt with an especially high fraction apparent among the brightest Cold Classicals. The binary fraction, relative sizes, and separations in the dynamically excited populations (Scattered, Resonant) reflects processes that may have eroded a more abundant initial population. This trend continues in the Centaurs and Trojans where few binaries have been found. We review new evidence including a third resolved Trojan binary and lightcurve studies to understand how the Trojans are related to the small body populations that originated in the outer protoplanetary disk.

Culture-Independent Investigation of the Microbiome Associated with the Nematode Acrobeloides maximus

PubMed Central

Baquiran, Jean-Paul; Thater, Brian; Sedky, Sammy; De Ley, Paul; Crowley, David; Orwin, Paul M.

2013-01-01

Background Symbioses between metazoans and microbes are widespread and vital to many ecosystems. Recent work with several nematode species has suggested that strong associations with microbial symbionts may also be common among members of this phylu. In this work we explore possible symbiosis between bacteria and the free living soil bacteriovorous nematode Acrobeloides maximus. Methodology We used a soil microcosm approach to expose A. maximus populations grown monoxenically on RFP labeled Escherichia coli in a soil slurry. Worms were recovered by density gradient separation and examined using both culture-independent and isolation methods. A 16S rRNA gene survey of the worm-associated bacteria was compared to the soil and to a similar analysis using Caenorhabditis elegans N2. Recovered A. maximus populations were maintained on cholesterol agar and sampled to examine the population dynamics of the microbiome. Results A consistent core microbiome was extracted from A. maximus that differed from those in the bulk soil or the C. elegans associated set. Three genera, Ochrobactrum, Pedobacter, and Chitinophaga, were identified at high levels only in the A. maximus populations, which were less diverse than the assemblage associated with C. elegans. Putative symbiont populations were maintained for at least 4 months post inoculation, although the levels decreased as the culture aged. Fluorescence in situ hybridization (FISH) using probes specific for Ochrobactrum and Pedobacter stained bacterial cells in formaldehyde fixed nematode guts. Conclusions Three microorganisms were repeatedly observed in association with Acrobeloides maximus when recovered from soil microcosms. We isolated several Ochrobactrum sp. and Pedobacter sp., and demonstrated that they inhabit the nematode gut by FISH. Although their role in A. maximus is not resolved, we propose possible mutualistic roles for these bacteria in protection of the host against pathogens and facilitating enzymatic digestion of other ingested bacteria. PMID:23894287

Spatially resolved density and ionization measurements of shocked foams using x-ray fluorescence

DOE Office of Scientific and Technical Information (OSTI.GOV)

MacDonald, M. J.; Keiter, P. A.; Montgomery, D. S.

2016-09-28

We present experiments at the Trident laser facility demonstrating the use of x-ray fluorescence (XRF) to simultaneously measure density, ionization state populations, and electron temperature in shocked foams. An imaging x-ray spectrometer obtained spatially resolved measurements of Ti K-α emission. Density profiles were measured from K-α intensity. Ti ionization state distributions and electron temperatures were inferred by fitting K-α spectra to spectra from CRETIN simulations. This work shows that XRF provides a powerful tool to complement other diagnostics to make equation of state measurements of shocked materials containing a suitable tracer element.

Tempo-spatially resolved cellular dynamics of human immunodeficiency virus transacting activator of transcription (Tat) peptide-modified nanocargos in living cells

NASA Astrophysics Data System (ADS)

Wei, Lin; Yang, Qiaoyu; Xiao, Lehui

2014-08-01

Understanding the cellular uptake mechanism and intracellular fate of nanocarriers in living cells is of great importance for the rational design of efficient drug delivery cargos as well as the development of robust biomedical diagnostic probes. In present study, with a dual wavelength view darkfield microscope (DWVD), the tempo-spatially resolved dynamics of Tat peptide-functionalized gold nanoparticles (TGNPs, with size similar to viruses) in living HeLa cells were extensively explored. It was found that energy-dependent endocytosis (both clathrin- and caveolae-mediated processes were involved) was the prevailing pathway for the cellular uptake of TGNPs. The time-correlated dynamic spatial distribution information revealed that TGNPs could not actively target the cell nuclei, which is contrary to previous observations based on fixed cell results. More importantly, the inheritance of TGNPs to the daughter cells through mitosis was found to be the major route to metabolize TGNPs by HeLa cells. These understandings on the cellular uptake mechanism and intracellular fate of nanocargos in living cells would provide deep insight on how to improve and controllably manipulate their translocation efficiency for targeted drug delivery.Understanding the cellular uptake mechanism and intracellular fate of nanocarriers in living cells is of great importance for the rational design of efficient drug delivery cargos as well as the development of robust biomedical diagnostic probes. In present study, with a dual wavelength view darkfield microscope (DWVD), the tempo-spatially resolved dynamics of Tat peptide-functionalized gold nanoparticles (TGNPs, with size similar to viruses) in living HeLa cells were extensively explored. It was found that energy-dependent endocytosis (both clathrin- and caveolae-mediated processes were involved) was the prevailing pathway for the cellular uptake of TGNPs. The time-correlated dynamic spatial distribution information revealed that TGNPs could not actively target the cell nuclei, which is contrary to previous observations based on fixed cell results. More importantly, the inheritance of TGNPs to the daughter cells through mitosis was found to be the major route to metabolize TGNPs by HeLa cells. These understandings on the cellular uptake mechanism and intracellular fate of nanocargos in living cells would provide deep insight on how to improve and controllably manipulate their translocation efficiency for targeted drug delivery. Electronic supplementary information (ESI) available: Experimental section and additional supporting results as noted in the text. See DOI: 10.1039/c4nr02732a

The Long and Complicated Relationship between Epstein-Barr Virus and Epithelial Cells.

PubMed

Hutt-Fletcher, Lindsey M

2017-01-01

The roles of epithelial cells in infection and persistence of the Epstein-Barr virus (EBV) have long been difficult to resolve. However, recent developments have reinforced the conclusion that these cells are a major site of virus replication and raised the possibility that, like papillomaviruses, EBV has evolved to take advantage of epithelial differentiation to ensure survival, persistence, and spread. Copyright © 2016 American Society for Microbiology.

Mapping the local organization of cell membranes using excitation-polarization-resolved confocal fluorescence microscopy.

PubMed

Kress, Alla; Wang, Xiao; Ranchon, Hubert; Savatier, Julien; Rigneault, Hervé; Ferrand, Patrick; Brasselet, Sophie

2013-07-02

Fluorescence anisotropy and linear dichroism imaging have been widely used for imaging biomolecular orientational distributions in protein aggregates, fibrillar structures of cells, and cell membranes. However, these techniques do not give access to complete orientational order information in a whole image, because their use is limited to parts of the sample where the average orientation of molecules is known a priori. Fluorescence anisotropy is also highly sensitive to depolarization mechanisms such as those induced by fluorescence energy transfer. A fully excitation-polarization-resolved fluorescence microscopy imaging that relies on the use of a tunable incident polarization and a nonpolarized detection is able to circumvent these limitations. We have developed such a technique in confocal epifluorescence microscopy, giving access to new regions of study in the complex and heterogeneous molecular organization of cell membranes. Using this technique, we demonstrate morphological changes at the subdiffraction scale in labeled COS-7 cell membranes whose cytoskeleton is perturbed. Molecular orientational order is also seen to be affected by cholesterol depletion, reflecting the strong interplay between lipid-packing regions and their nearby cytoskeleton. This noninvasive optical technique can reveal local organization in cell membranes when used as a complement to existing methods such as generalized polarization. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

In vivo flow cytometry and time-resolved near-IR angiography and lymphography

NASA Astrophysics Data System (ADS)

Galanzha, Ekaterina I.; Tuchin, Valery V.; Brock, Robert W.; Zharov, Vladimir P.

2007-05-01

Integration of photoacoustic and photothermal techniques with high-speed, high-resolution transmission and fluorescence microscopy shows great potential for in vivo flow cytometry and indocyanine green (ICG) near-infrared (IR) angiography of blood and lymph microvessels. In particular, the capabilities of in vivo flow cytometry using rat mesentery and nude mouse ear models are demonstrated for real-time quantitative detection of circulating and migrating individual blood and cancer cells in skin, mesentery, lymph nodes, liver, kidney; studying vascular dynamics with a focus on lymphatics; monitoring cell traffic between blood and lymph systems; high-speed imaging of cell deformability in flow; and label-free real-time monitoring of single cell extravasation from blood vessel lumen into tissue. As presented, the advantages of ICG IR-angiography include estimation of time resolved dye dynamics (appearance and clearance) in blood and lymph microvessels using fluorescent and photoacoustic modules of the integrated technique. These new approaches are important for monitoring and quantifying metastatic and apoptotic cells; comparative measurements of plasma and cell velocities; analysis of immune responses; monitoring of circulating macromolecules, chylomicrons, bacteria, viruses and nanoparticles; molecular imaging. In the future, we believe that the integrated technique presented will have great potential for translation to early disease diagnoses (e.g. cancer) or assessment of innovative therapeutic interventions in humans.

Automated processing of label-free Raman microscope images of macrophage cells with standardized regression for high-throughput analysis.

PubMed

Milewski, Robert J; Kumagai, Yutaro; Fujita, Katsumasa; Standley, Daron M; Smith, Nicholas I

2010-11-19

Macrophages represent the front lines of our immune system; they recognize and engulf pathogens or foreign particles thus initiating the immune response. Imaging macrophages presents unique challenges, as most optical techniques require labeling or staining of the cellular compartments in order to resolve organelles, and such stains or labels have the potential to perturb the cell, particularly in cases where incomplete information exists regarding the precise cellular reaction under observation. Label-free imaging techniques such as Raman microscopy are thus valuable tools for studying the transformations that occur in immune cells upon activation, both on the molecular and organelle levels. Due to extremely low signal levels, however, Raman microscopy requires sophisticated image processing techniques for noise reduction and signal extraction. To date, efficient, automated algorithms for resolving sub-cellular features in noisy, multi-dimensional image sets have not been explored extensively. We show that hybrid z-score normalization and standard regression (Z-LSR) can highlight the spectral differences within the cell and provide image contrast dependent on spectral content. In contrast to typical Raman imaging processing methods using multivariate analysis, such as single value decomposition (SVD), our implementation of the Z-LSR method can operate nearly in real-time. In spite of its computational simplicity, Z-LSR can automatically remove background and bias in the signal, improve the resolution of spatially distributed spectral differences and enable sub-cellular features to be resolved in Raman microscopy images of mouse macrophage cells. Significantly, the Z-LSR processed images automatically exhibited subcellular architectures whereas SVD, in general, requires human assistance in selecting the components of interest. The computational efficiency of Z-LSR enables automated resolution of sub-cellular features in large Raman microscopy data sets without compromise in image quality or information loss in associated spectra. These results motivate further use of label free microscopy techniques in real-time imaging of live immune cells.

A superior bright NIR luminescent nanoparticle preparation and indicating calcium signaling detection in cells and small animals.

PubMed

Zhang, Jian; Lakowicz, Joseph R

2018-01-01

Near-field fluorescence (NFF) effects were employed to develop a novel near-infrared (NIR) luminescent nanoparticle (LNP) with superior brightness. The LNP is used as imaging contrast agent for cellular and small animal imaging and furthermore suggested to use for detecting voltage-sensitive calcium in living cells and animals with high sensitivity. NIR Indocyanine green (ICG) dye was conjugated with human serum albumin (HSA) followed by covalently binding to gold nanorod (AuNR). The AuNR displayed dual plasmons from transverse and longitudinal axis, and the longitudinal plasmon was localized at the NIR region which could efficiently couple with the excitation and emission of ICG dye leading to a largely enhanced NFF. The enhancement factor was measured to be about 16-fold using both ensemble and single nanoparticle spectral methods. As an imaging contrast agent, the ICG-HSA-Au complex (abbreviate as ICG-Au) was conjugated on HeLa cells and fluorescence cell images were recorded on a time-resolved confocal microscope. The emission signals of ICG-Au complexes were distinctly resolved as the individual spots that were observed over the cellular backgrounds due to their strong brightness as well as shortened lifetime. The LNPs were also tested to have a low cytotoxicity. The ICG-Au complexes were injected below the skin surface of mouse showing emission spots 5-fold brighter than those from the same amount of free ICG-HSA conjugates. Based on the observations in this research, the excitation and emission of NIR ICG dyes were found to be able to sufficiently couple with the longitudinal plasmon of AuNRs leading to a largely enhanced NFF. Using the LNP with super-brightness as a contrast agent, the ICG-Au complex could be resolved from the background in the cell and small animal imaging. The novel NIR LNP has also a great potential for detection of voltage-gated calcium concentration in the cell and living animal with a high sensitivity.

Noninvasive in situ evaluation of osteogenic differentiation by time-resolved laser-induced fluorescence spectroscopy.

PubMed

Ashjian, Peter; Elbarbary, Amir; Zuk, Patricia; DeUgarte, Daniel A; Benhaim, Prosper; Marcu, Laura; Hedrick, Marc H

2004-01-01

The clinical implantation of bioengineered tissues requires an in situ nondestructive evaluation of the quality of tissue constructs developed in vitro before transplantation. Time-resolved laser-induced fluorescence spectroscopy (TR-LIFS) is demonstrated here to noninvasively monitor the formation of osteogenic extracellular matrix (ECM) produced by putative stem cells (PLA cells) derived from human adipose tissue. We show that this optical spectroscopy technique can assess the relative expression of collagens (types I, III, IV, and V) within newly forming osteogenic ECM. The results are consistent with those obtained by conventional histochemical techniques (immunofluorescence and Western blot) and demonstrate that TR-LIFS is a potential tool for monitoring the expression of distinct collagen types and the formation of collagen cross-links in intact tissue constructs.

Phase-sensitive flow cytometer

DOEpatents

Steinkamp, John A.

1993-01-01

A phase-sensitive flow cytometer (FCM) provides additional FCM capability to use the fluorescence lifetime of one or more fluorochromes bound to single cells to provide additional information regarding the cells. The resulting fluorescence emission can be resolved into individual fluorescence signals if two fluorochromes are present or can be converted directly to a decay lifetime from a single fluorochrome. The excitation light for the fluorochromes is modulated to produce an amplitude modulated fluorescence pulse as the fluorochrome is excited in the FCM. The modulation signal also forms a reference signal that is phase-shifted a selected amount for subsequent mixing with the output modulated fluorescence intensity signal in phase-sensitive detection circuitry. The output from the phase-sensitive circuitry is then an individual resolved fluorochrome signal or a single fluorochrome decay lifetime, depending on the applied phase shifts.

Capillary red blood cell velocimetry by phase-resolved optical coherence tomography.

PubMed

Tang, Jianbo; Erdener, Sefik Evren; Fu, Buyin; Boas, David A

2017-10-01

We present a phase-resolved optical coherence tomography (OCT) method to extend Doppler OCT for the accurate measurement of the red blood cell (RBC) velocity in cerebral capillaries. OCT data were acquired with an M-mode scanning strategy (repeated A-scans) to account for the single-file passage of RBCs in a capillary, which were then high-pass filtered to remove the stationary component of the signal to ensure an accurate measurement of phase shift of flowing RBCs. The angular frequency of the signal from flowing RBCs was then quantified from the dynamic component of the signal and used to calculate the axial speed of flowing RBCs in capillaries. We validated our measurement by RBC passage velocimetry using the signal magnitude of the same OCT time series data.

Comprehensive longitudinal analysis of hepatitis C virus (HCV)-specific T cell responses during acute HCV infection in the presence of existing HIV-1 infection.

PubMed

van den Berg, C H S B; Ruys, T A; Nanlohy, N M; Geerlings, S E; van der Meer, J T; Mulder, J-W; Lange, J A; van Baarle, D

2009-04-01

The aim of this study was to study the development of HCV-specific T cell immunity during acute HCV infection in the presence of an existing HIV-1 infection in four HIV-1 infected men having sex with men. A comprehensive analysis of HCV-specific T cell responses was performed at two time points during acute HCV infection using a T cell expansion assay with overlapping peptide pools spanning the entire HCV genome Three patients with (near) normal CD4+ T cell counts (range 400-970 x 10(6)/L) either resolved (n=1) or temporary suppressed HCV RNA. In contrast, one patient with low CD4+ T cell counts (330 x 10(6)/L), had sustained high HCV RNA levels. All four patients had low HCV-specific CD8+ T cell responses, and similar magnitudes of CD4+ T cell responses. Interestingly, individuals with resolved infection or temporary suppression of HCV-RNA had HCV-specific CD4+ T cell responses predominantly against nonstructural (NS) proteins. While the individual with high HCV RNA plasma concentrations had CD4+ T cell responses predominantly directed against Core. Our data show that an acute HCV infection in an HIV-1 infected person can be suppressed in the presence of HCV-specific CD4+ T cell response targeting non-structural proteins. However further research is needed in a larger group of patients to evaluate the role of HIV-1 on HCV-specific T cell responses in relation to outcome of acute HCV infection.

Fitness-Balanced Escape Determines Resolution of Dynamic Founder Virus Escape Processes in HIV-1 Infection

PubMed Central

Sunshine, Justine E.; Larsen, Brendan B.; Maust, Brandon; Casey, Ellie; Deng, Wenje; Chen, Lennie; Westfall, Dylan H.; Kim, Moon; Zhao, Hong; Ghorai, Suvankar; Lanxon-Cookson, Erinn; Rolland, Morgane; Collier, Ann C.; Maenza, Janine; Mullins, James I.

2015-01-01

ABSTRACT To understand the interplay between host cytotoxic T-lymphocyte (CTL) responses and the mechanisms by which HIV-1 evades them, we studied viral evolutionary patterns associated with host CTL responses in six linked transmission pairs. HIV-1 sequences corresponding to full-length p17 and p24 gag were generated by 454 pyrosequencing for all pairs near the time of transmission, and seroconverting partners were followed for a median of 847 days postinfection. T-cell responses were screened by gamma interferon/interleukin-2 (IFN-γ/IL-2) FluoroSpot using autologous peptide sets reflecting any Gag variant present in at least 5% of sequence reads in the individual's viral population. While we found little evidence for the occurrence of CTL reversions, CTL escape processes were found to be highly dynamic, with multiple epitope variants emerging simultaneously. We found a correlation between epitope entropy and the number of epitope variants per response (r = 0.43; P = 0.05). In cases in which multiple escape mutations developed within a targeted epitope, a variant with no fitness cost became fixed in the viral population. When multiple mutations within an epitope achieved fitness-balanced escape, these escape mutants were each maintained in the viral population. Additional mutations found to confer escape but undetected in viral populations incurred high fitness costs, suggesting that functional constraints limit the available sites tolerable to escape mutations. These results further our understanding of the impact of CTL escape and reversion from the founder virus in HIV infection and contribute to the identification of immunogenic Gag regions most vulnerable to a targeted T-cell attack. IMPORTANCE Rapid diversification of the viral population is a hallmark of HIV-1 infection, and understanding the selective forces driving the emergence of viral variants can provide critical insight into the interplay between host immune responses and viral evolution. We used deep sequencing to comprehensively follow viral evolution over time in six linked HIV transmission pairs. We then mapped T-cell responses to explore if mutations arose due to adaption to the host and found that escape processes were often highly dynamic, with multiple mutations arising within targeted epitopes. When we explored the impact of these mutations on replicative capacity, we found that dynamic escape processes only resolve with the selection of mutations that conferred escape with no fitness cost to the virus. These results provide further understanding of the complicated viral-host interactions that occur during early HIV-1 infection and may help inform the design of future vaccine immunogens. PMID:26223634

Rapid time-resolved diffraction studies of protein structures using synchrotron radiation

NASA Astrophysics Data System (ADS)

Bartunik, Hans D.; Bartunik, Lesley J.

1992-07-01

The crystal structure of intermediate states in biological reactions of proteins of multi-protein complexes may be studied by time-resolved X-ray diffraction techniques which make use of the high spectral brilliance, continuous wavelength distribution and pulsed time structure of synchrotron radiation. Laue diffraction methods provide a means of investigating intermediate structures with lifetimes in the millisecond time range at presently operational facilities. Third-generation storage rings which are under construction may permit one to reach a time resolution of one microsecond for non-cyclic and one nanosecond for cyclic reactions. The number of individual exposures required for exploring reciprocal space and hence the total time scale strongly depend on the lattice order that may be affected, e.g., by conformational changes. Time-resolved experiments require high population of a specific intermediate which has to be homogeneous over the crystal volume. A number of external excitation techniques have been developed including in situ liberation of active metabolites by laser pulse photolysis of photolabile inactive precursors. First applications to crystal structure analysis of catalytic intermediates of enzymes demonstrate the potential of time-resolved protein crystallography.

Appropriate Minimal Dose of Gadobutrol for 3D Time-Resolved MRA of the Supra-Aortic Arteries: Comparison with Conventional Single-Phase High-Resolution 3D Contrast-Enhanced MRA.

PubMed

Bak, S H; Roh, H G; Moon, W-J; Choi, J W; An, H S

2017-07-01

The development of nephrogenic systemic fibrosis and neural tissue deposition is gadolinium dose-dependent. The purpose of this study was to determine the appropriate minimal dose of gadobutrol with time-resolved MRA to assess supra-aortic arterial stenosis with contrast-enhanced MRA as a reference standard. Four hundred sixty-two consecutive patients underwent both standard-dose contrast-enhanced MRA and low-dose time-resolved MRA and were classified into 3 groups; group A (a constant dose of 1 mL for time-resolved MRA), group B (2 mL), or group C (3 mL). All studies were independently evaluated by 2 radiologists for image quality by using a 5-point scale (from 0 = failure to 4 = excellent), grading of arterial stenosis (0 = normal, 1 = mild [<30%], 2 = moderate [30%-69%], 3 = severe to occlusion [≥70%]), and signal-to-noise ratio. The image quality of time-resolved MRA was similar to that of contrast-enhanced MRA in groups B and C, but it was inferior to contrast-enhanced MRA in group A. For the grading of arterial stenosis, there was an excellent correlation between contrast-enhanced MRA and time-resolved MRA ( R = 0.957 for group A, R = 0.988 for group B, R = 0.991 for group C). The SNR of time-resolved MRA tended to be lower than that of contrast-enhanced MRA in groups A and B. However, SNR was higher for time-resolved MRA compared with contrast-enhanced MRA in group C. Low-dose time-resolved MRA is feasible in the evaluation of supra-aortic stenosis and could be used as an alternative to contrast-enhanced MRA for a diagnostic technique in high-risk populations. © 2017 by American Journal of Neuroradiology.

Photoinduced charge separation at polymer-fullerene interfaces of BHJ solar cells (Conference Presentation)

NASA Astrophysics Data System (ADS)

Poluektov, Oleg G.; Niklas, Jens; Mardis, Kristy

2016-09-01

While photovoltaic cells are highly promising man-made devices for direct solar energy utilization, a number of fundamental questions about how the organic bulk heterojunction cell enables efficient long-lived and long-range charge separation remain unanswered. These questions were address by employing an advanced suite of EPR spectroscopy in combination with DFT calculations to study mechanism of charge separation at the polymer-fullerene interfaces of photo-active BHJ. Observed charge delocalization in BHJ upon photoinduced ET is analogous to that in organic donor-acceptor material. This is an efficient mechanism of charge stabilization in photosynthetic assemblies. Time-resolved EPR spectra show a strong polarization pattern for all polymer-fullerene blends under study, which is caused by non-Boltzmann population of the electron spin energy levels in the radical pairs. The first observation of this phenomenon was reported in natural and artificial photosynthetic assemblies, and comparison with these systems allows us to better understand charge separation processes in OPVs. The spectral analysis presented here, in combination with DFT calculations, shows that CS processes in OPV materials are similar to that in organic photosynthetic systems. This work was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences, under Contract DE-AC02-06CH11357 at Argonne National Laboratory.

Static harmonization of dynamically harmonized Fourier transform ion cyclotron resonance cell.

PubMed

Zhdanova, Ekaterina; Kostyukevich, Yury; Nikolaev, Eugene

2017-08-01

Static harmonization in the Fourier transform ion cyclotron resonance cell improves the resolving power of the cell and prevents dephasing of the ion cloud in the case of any trajectory of the charged particle, not necessarily axisymmetric cyclotron (as opposed to dynamic harmonization). We reveal that the Fourier transform ion cyclotron resonance cell with dynamic harmonization (paracell) is proved to be statically harmonized. The volume of the statically harmonized potential distribution increases with an increase in the number of trap segments.

Visualization of HIV T Cell Virological Synapses and Virus-Containing Compartments by Three-Dimensional Correlative Light and Electron Microscopy

PubMed Central

Wang, Lili; Eng, Edward T.; Law, Kenneth; Gordon, Ronald E.; Rice, William J.

2016-01-01

ABSTRACT Virological synapses (VS) are adhesive structures that form between infected and uninfected cells to enhance the spread of HIV-1. During T cell VS formation, viral proteins are actively recruited to the site of cell-cell contact where the viral material is efficiently translocated to target cells into heterogeneous, protease-resistant, antibody-inaccessible compartments. Using correlative light and electron microscopy (CLEM), we define the membrane topography of the virus-containing compartments (VCC) where HIV is found following VS-mediated transfer. Focused ion beam scanning electron microscopy (FIB-SEM) and serial sectioning transmission electron microscopy (SS-TEM) were used to better resolve the fluorescent Gag-containing structures within the VCC. We found that small punctate fluorescent signals correlated with single viral particles in enclosed vesicular compartments or surface-localized virus particles and that large fluorescent signals correlated with membranous Gag-containing structures with unknown pathological function. CLEM imaging revealed distinct pools of newly deposited viral proteins within endocytic and nonendocytic compartments in VS target T cells. IMPORTANCE This study directly correlates individual virus-associated objects observed in light microscopy with ultrastructural features seen by electron microscopy in the HIV-1 virological synapse. This approach elucidates which infection-associated ultrastructural features represent bona fide HIV protein complexes. We define the morphology of some HIV cell-to-cell transfer intermediates as true endocytic compartments and resolve unique synapse-associated viral structures created by transfer across virological synapses. PMID:27847357

Fast, label-free super-resolution live-cell imaging using rotating coherent scattering (ROCS) microscopy

NASA Astrophysics Data System (ADS)

Jünger, Felix; Olshausen, Philipp V.; Rohrbach, Alexander

2016-07-01

Living cells are highly dynamic systems with cellular structures being often below the optical resolution limit. Super-resolution microscopes, usually based on fluorescence cell labelling, are usually too slow to resolve small, dynamic structures. We present a label-free microscopy technique, which can generate thousands of super-resolved, high contrast images at a frame rate of 100 Hertz and without any post-processing. The technique is based on oblique sample illumination with coherent light, an approach believed to be not applicable in life sciences because of too many interference artefacts. However, by circulating an incident laser beam by 360° during one image acquisition, relevant image information is amplified. By combining total internal reflection illumination with dark-field detection, structures as small as 150 nm become separable through local destructive interferences. The technique images local changes in refractive index through scattered laser light and is applied to living mouse macrophages and helical bacteria revealing unexpected dynamic processes.

Ddx19 links mRNA nuclear export with progression of transcription and replication and suppresses genomic instability upon DNA damage in proliferating cells.

PubMed

Hodroj, Dana; Serhal, Kamar; Maiorano, Domenico

2017-09-03

The DEAD-box Helicase 19 (Ddx19) gene codes for an RNA helicase involved in both mRNA (mRNA) export from the nucleus into the cytoplasm and in mRNA translation. In unperturbed cells, Ddx19 localizes in the cytoplasm and at the cytoplasmic face of the nuclear pore. Here we review recent findings related to an additional Ddx19 function in the nucleus in resolving RNA:DNA hybrids (R-loops) generated during collision between transcription and replication, and upon DNA damage. Activation of a DNA damage response pathway dependent upon the ATR kinase, a major regulator of replication fork progression, stimulates translocation of the Ddx19 protein from the cytoplasm into the nucleus. Only nuclear Ddx19 is competent to resolve R-loops, and down regulation of Ddx19 expression induces DNA double strand breaks only in proliferating cells. Overall these observations put forward Ddx19 as an important novel mediator of the crosstalk between transcription and replication.

Solid-state selective (13)C excitation and spin diffusion NMR to resolve spatial dimensions in plant cell walls.

PubMed

Foston, Marcus; Katahira, Rui; Gjersing, Erica; Davis, Mark F; Ragauskas, Arthur J

2012-02-15

The average spatial dimensions between major biopolymers within the plant cell wall can be resolved using a solid-state NMR technique referred to as a (13)C cross-polarization (CP) SELDOM (selectively by destruction of magnetization) with a mixing time delay for spin diffusion. Selective excitation of specific aromatic lignin carbons indicates that lignin is in close proximity to hemicellulose followed by amorphous and finally crystalline cellulose. (13)C spin diffusion time constants (T(SD)) were extracted using a two-site spin diffusion theory developed for (13)C nuclei under magic angle spinning (MAS) conditions. These time constants were then used to calculate an average lower-limit spin diffusion length between chemical groups within the plant cell wall. The results on untreated (13)C enriched corn stover stem reveal that the lignin carbons are, on average, located at distances ∼0.7-2.0 nm from the carbons in hemicellulose and cellulose, whereas the pretreated material had larger separations.

Fast, label-free super-resolution live-cell imaging using rotating coherent scattering (ROCS) microscopy

PubMed Central

Jünger, Felix; Olshausen, Philipp v.; Rohrbach, Alexander

2016-01-01

Living cells are highly dynamic systems with cellular structures being often below the optical resolution limit. Super-resolution microscopes, usually based on fluorescence cell labelling, are usually too slow to resolve small, dynamic structures. We present a label-free microscopy technique, which can generate thousands of super-resolved, high contrast images at a frame rate of 100 Hertz and without any post-processing. The technique is based on oblique sample illumination with coherent light, an approach believed to be not applicable in life sciences because of too many interference artefacts. However, by circulating an incident laser beam by 360° during one image acquisition, relevant image information is amplified. By combining total internal reflection illumination with dark-field detection, structures as small as 150 nm become separable through local destructive interferences. The technique images local changes in refractive index through scattered laser light and is applied to living mouse macrophages and helical bacteria revealing unexpected dynamic processes. PMID:27465033

Regulatory assembly of the vacuolar proton pump VoV1-ATPase in yeast cells by FLIM-FRET

NASA Astrophysics Data System (ADS)

Ernst, Stefan; Batisse, Claire; Zarrabi, Nawid; Böttcher, Bettina; Börsch, Michael

2010-02-01

We investigate the reversible disassembly of VOV1-ATPase in life yeast cells by time resolved confocal FRET imaging. VOV1-ATPase in the vacuolar membrane pumps protons from the cytosol into the vacuole. VOV1-ATPase is a rotary biological nanomotor driven by ATP hydrolysis. The emerging proton gradient is used for secondary transport processes as well as for pH and Ca2+ homoeostasis in the cell. The activity of the VOV1-ATPase is regulated through assembly / disassembly processes. During starvation the two parts of VOV1-ATPase start to disassemble. This process is reversed after addition of glucose. The exact mechanisms are unknown. To follow the disassembly / reassembly in vivo we tagged two subunits C and E with different fluorescent proteins. Cellular distributions of C and E were monitored using a duty cycle-optimized alternating laser excitation scheme (DCO-ALEX) for time resolved confocal FRET-FLIM measurements.

Network theory inspired analysis of time-resolved expression data reveals key players guiding P. patens stem cell development.

PubMed

Busch, Hauke; Boerries, Melanie; Bao, Jie; Hanke, Sebastian T; Hiss, Manuel; Tiko, Theodhor; Rensing, Stefan A

2013-01-01

Transcription factors (TFs) often trigger developmental decisions, yet, their transcripts are often only moderately regulated and thus not easily detected by conventional statistics on expression data. Here we present a method that allows to determine such genes based on trajectory analysis of time-resolved transcriptome data. As a proof of principle, we have analysed apical stem cells of filamentous moss (P. patens) protonemata that develop from leaflets upon their detachment from the plant. By our novel correlation analysis of the post detachment transcriptome kinetics we predict five out of 1,058 TFs to be involved in the signaling leading to the establishment of pluripotency. Among the predicted regulators is the basic helix loop helix TF PpRSL1, which we show to be involved in the establishment of apical stem cells in P. patens. Our methodology is expected to aid analysis of key players of developmental decisions in complex plant and animal systems.

Approach to a case of multiple irregular red cell antibodies in a liver transplant recipient: Need for developing competence

PubMed Central

Dara, Ravi C.; Tiwari, Aseem K.; Pandey, Prashant; Arora, Dinesh

2015-01-01

Liver transplant procedure acts as a challenge for transfusion services in terms of specialized blood components, serologic problems, and immunologic effects of transfusion. Red cell alloimmunization in patients awaiting a liver transplant complicate the process by undue delay or unavailability of compatible red blood cell units. Compatible blood units can be provided by well-equipped immunohematology laboratory, which has expertise in resolving these serological problems. This report illustrates resolution of a case with multiple alloantibodies using standard techniques, particularly rare antisera. Our case re-emphasizes the need for universal antibody screening in all patients as part of pretransfusion testing, which helps to identify atypical antibodies and plan for appropriate transfusion support well in time. We recommend that the centers, especially the ones that perform complex procedures like solid organ transplants and hematological transplants should have the necessary immunohematological reagents including rare antisera to resolve complex cases of multiple antibodies as illustrated in this case. PMID:25722585

Lithium-thionyl chloride battery safety

NASA Technical Reports Server (NTRS)

Carter, B.; Williams, R.; Tsay, F.; Rodriguez, A.; Frank, H.

1982-01-01

Primary lithium cells which use LiAlCl4/SOCl2 electrolyte exhibit high energy density and long life. Currently these cells pose a safety problem since they have been found to vent or explode. This paper summarizes experiments to resolve the safety problem of Li-SOCl2 cells by thermal modeling and identification of possibly hazardous intermediates formed during discharge of these cells. A thermal model and mechanism for the reduction of SOCl2 are presented, as well as a discussion of their application to Li-SOCl2 cell safety.

Murine gammadelta T cells in infections: beneficial or deleterious?

PubMed

Andrew, Elizabeth M; Carding, Simon R

2005-03-01

Although the importance of gammadelta T cells in pathogen-induced immune responses is becoming increasingly apparent, it is not clear that their involvement is always of benefit to the host. Here we review evidence for the protective and damaging roles of gammadelta T cells in infection and discuss how these disparate findings might be resolved by considering the nature and properties of the pathogen, the sites of infection and conditions under which gammadelta T cell responses are initiated, and the involvement of different subsets of gammadelta T cells.

Whole genome sequences are required to fully resolve the linkage disequilibrium structure of human populations.

PubMed

Pengelly, Reuben J; Tapper, William; Gibson, Jane; Knut, Marcin; Tearle, Rick; Collins, Andrew; Ennis, Sarah

2015-09-03

An understanding of linkage disequilibrium (LD) structures in the human genome underpins much of medical genetics and provides a basis for disease gene mapping and investigating biological mechanisms such as recombination and selection. Whole genome sequencing (WGS) provides the opportunity to determine LD structures at maximal resolution. We compare LD maps constructed from WGS data with LD maps produced from the array-based HapMap dataset, for representative European and African populations. WGS provides up to 5.7-fold greater SNP density than array-based data and achieves much greater resolution of LD structure, allowing for identification of up to 2.8-fold more regions of intense recombination. The absence of ascertainment bias in variant genotyping improves the population representativeness of the WGS maps, and highlights the extent of uncaptured variation using array genotyping methodologies. The complete capture of LD patterns using WGS allows for higher genome-wide association study (GWAS) power compared to array-based GWAS, with WGS also allowing for the analysis of rare variation. The impact of marker ascertainment issues in arrays has been greatest for Sub-Saharan African populations where larger sample sizes and substantially higher marker densities are required to fully resolve the LD structure. WGS provides the best possible resource for LD mapping due to the maximal marker density and lack of ascertainment bias. WGS LD maps provide a rich resource for medical and population genetics studies. The increasing availability of WGS data for large populations will allow for improved research utilising LD, such as GWAS and recombination biology studies.

Resolving Salmonella infection reveals dynamic and persisting changes in murine bone marrow progenitor cell phenotype and function

PubMed Central

Ross, Ewan A; Flores-Langarica, Adriana; Bobat, Saeeda; Coughlan, Ruth E; Marshall, Jennifer L; Hitchcock, Jessica R; Cook, Charlotte N; Carvalho-Gaspar, Manuela M; Mitchell, Andrea M; Clarke, Mary; Garcia, Paloma; Cobbold, Mark; Mitchell, Tim J; Henderson, Ian R; Jones, Nick D; Anderson, Graham; Buckley, Christopher D; Cunningham, Adam F

2014-01-01

The generation of immune cells from BM precursors is a carefully regulated process. This is essential to limit the potential for oncogenesis and autoimmunity yet protect against infection. How infection modulates this is unclear. Salmonella can colonize systemic sites including the BM and spleen. This resolving infection has multiple IFN-γ-mediated acute and chronic effects on BM progenitors, and during the first week of infection IFN-γ is produced by myeloid, NK, NKT, CD4+ T cells, and some lineage-negative cells. After infection, the phenotype of BM progenitors rapidly but reversibly alters, with a peak ∼30-fold increase in Sca-1hi progenitors and a corresponding loss of Sca-1lo/int subsets. Most strikingly, the capacity of donor Sca-1hi cells to reconstitute an irradiated host is reduced; the longer donor mice are exposed to infection, and Sca-1hic-kitint cells have an increased potential to generate B1a-like cells. Thus, Salmonella can have a prolonged influence on BM progenitor functionality not directly related to bacterial persistence. These results reflect changes observed in leucopoiesis during aging and suggest that BM functionality can be modulated by life-long, periodic exposure to infection. Better understanding of this process could offer novel therapeutic opportunities to modulate BM functionality and promote healthy aging. PMID:24825601

Why the dish makes a difference: quantitative comparison of polystyrene culture surfaces.

PubMed

Zeiger, Adam S; Hinton, Benjamin; Van Vliet, Krystyn J

2013-07-01

There is wide anecdotal recognition that biological cell viability and behavior can vary significantly as a function of the source of commercial tissue culture polystyrene (TCPS) culture vessels to which those cells adhere. However, this marked material dependency is typically resolved by selecting and then consistently using the same manufacturer's product - following protocol - rather than by investigating the material properties that may be responsible for such experimental variation. Here, we quantified several physical properties of TCPS surfaces obtained from a wide range of commercial sources and processing steps, through the use of atomic force microscopy (AFM)-based imaging and analysis, goniometry and protein adsorption quantification. We identify qualitative differences in surface features, as well as quantitative differences in surface roughness and wettability that cannot be attributed solely to differences in surface chemistry. We also find significant differences in cell morphology and proliferation among cells cultured on different TCPS surfaces, and resolve a correlation between nanoscale surface roughness and cell proliferation rate for both cell types considered. Interestingly, AFM images of living adherent cells on these nanotextured surfaces demonstrate direct interactions between cellular protrusions and topographically distinct features. These results illustrate and quantify the significant differences in material surface properties among these ubiquitous materials, allowing us to better understand why the dish can make a difference in biological experiments. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Concurrent Isolation of 3 Distinct Cardiac Stem Cell Populations From a Single Human Heart Biopsy.

PubMed

Monsanto, Megan M; White, Kevin S; Kim, Taeyong; Wang, Bingyan J; Fisher, Kristina; Ilves, Kelli; Khalafalla, Farid G; Casillas, Alexandria; Broughton, Kathleen; Mohsin, Sadia; Dembitsky, Walter P; Sussman, Mark A

2017-07-07

The relative actions and synergism between distinct myocardial-derived stem cell populations remain obscure. Ongoing debates on optimal cell population(s) for treatment of heart failure prompted implementation of a protocol for isolation of multiple stem cell populations from a single myocardial tissue sample to develop new insights for achieving myocardial regeneration. Establish a robust cardiac stem cell isolation and culture protocol to consistently generate 3 distinct stem cell populations from a single human heart biopsy. Isolation of 3 endogenous cardiac stem cell populations was performed from human heart samples routinely discarded during implantation of a left ventricular assist device. Tissue explants were mechanically minced into 1 mm 3 pieces to minimize time exposure to collagenase digestion and preserve cell viability. Centrifugation removes large cardiomyocytes and tissue debris producing a single cell suspension that is sorted using magnetic-activated cell sorting technology. Initial sorting is based on tyrosine-protein kinase Kit (c-Kit) expression that enriches for 2 c-Kit + cell populations yielding a mixture of cardiac progenitor cells and endothelial progenitor cells. Flowthrough c-Kit - mesenchymal stem cells are positively selected by surface expression of markers CD90 and CD105. After 1 week of culture, the c-Kit + population is further enriched by selection for a CD133 + endothelial progenitor cell population. Persistence of respective cell surface markers in vitro is confirmed both by flow cytometry and immunocytochemistry. Three distinct cardiac cell populations with individualized phenotypic properties consistent with cardiac progenitor cells, endothelial progenitor cells, and mesenchymal stem cells can be successfully concurrently isolated and expanded from a single tissue sample derived from human heart failure patients. © 2017 American Heart Association, Inc.

Multidimensional analysis of the frequencies and rates of cytokine secretion from single cells by quantitative microengraving.

PubMed

Han, Qing; Bradshaw, Elizabeth M; Nilsson, Björn; Hafler, David A; Love, J Christopher

2010-06-07

The large diversity of cells that comprise the human immune system requires methods that can resolve the individual contributions of specific subsets to an immunological response. Microengraving is process that uses a dense, elastomeric array of microwells to generate microarrays of proteins secreted from large numbers of individual live cells (approximately 10(4)-10(5) cells/assay). In this paper, we describe an approach based on this technology to quantify the rates of secretion from single immune cells. Numerical simulations of the microengraving process indicated an operating regime between 30 min-4 h that permits quantitative analysis of the rates of secretion. Through experimental validation, we demonstrate that microengraving can provide quantitative measurements of both the frequencies and the distribution in rates of secretion for up to four cytokines simultaneously released from individual viable primary immune cells. The experimental limits of detection ranged from 0.5 to 4 molecules/s for IL-6, IL-17, IFNgamma, IL-2, and TNFalpha. These multidimensional measures resolve the number and intensities of responses by cells exposed to stimuli with greater sensitivity than single-parameter assays for cytokine release. We show that cells from different donors exhibit distinct responses based on both the frequency and magnitude of cytokine secretion when stimulated under different activating conditions. Primary T cells with specific profiles of secretion can also be recovered after microengraving for subsequent expansion in vitro. These examples demonstrate the utility of quantitative, multidimensional profiles of single cells for analyzing the diversity and dynamics of immune responses in vitro and for identifying rare cells from clinical samples.

Introducing the Illustris Project: simulating the coevolution of dark and visible matter in the Universe

NASA Astrophysics Data System (ADS)

Vogelsberger, Mark; Genel, Shy; Springel, Volker; Torrey, Paul; Sijacki, Debora; Xu, Dandan; Snyder, Greg; Nelson, Dylan; Hernquist, Lars

2014-10-01

We introduce the Illustris Project, a series of large-scale hydrodynamical simulations of galaxy formation. The highest resolution simulation, Illustris-1, covers a volume of (106.5 Mpc)3, has a dark mass resolution of 6.26 × 106 M⊙, and an initial baryonic matter mass resolution of 1.26 × 106 M⊙. At z = 0 gravitational forces are softened on scales of 710 pc, and the smallest hydrodynamical gas cells have an extent of 48 pc. We follow the dynamical evolution of 2 × 18203 resolution elements and in addition passively evolve 18203 Monte Carlo tracer particles reaching a total particle count of more than 18 billion. The galaxy formation model includes: primordial and metal-line cooling with self-shielding corrections, stellar evolution, stellar feedback, gas recycling, chemical enrichment, supermassive black hole growth, and feedback from active galactic nuclei. Here we describe the simulation suite, and contrast basic predictions of our model for the present-day galaxy population with observations of the local universe. At z = 0 our simulation volume contains about 40 000 well-resolved galaxies covering a diverse range of morphologies and colours including early-type, late-type and irregular galaxies. The simulation reproduces reasonably well the cosmic star formation rate density, the galaxy luminosity function, and baryon conversion efficiency at z = 0. It also qualitatively captures the impact of galaxy environment on the red fractions of galaxies. The internal velocity structure of selected well-resolved disc galaxies obeys the stellar and baryonic Tully-Fisher relation together with flat circular velocity curves. In the well-resolved regime, the simulation reproduces the observed mix of early-type and late-type galaxies. Our model predicts a halo mass dependent impact of baryonic effects on the halo mass function and the masses of haloes caused by feedback from supernova and active galactic nuclei.

A New Approach to Model Pitch Perception Using Sparse Coding

PubMed Central

Furst, Miriam; Barak, Omri

2017-01-01

Our acoustical environment abounds with repetitive sounds, some of which are related to pitch perception. It is still unknown how the auditory system, in processing these sounds, relates a physical stimulus and its percept. Since, in mammals, all auditory stimuli are conveyed into the nervous system through the auditory nerve (AN) fibers, a model should explain the perception of pitch as a function of this particular input. However, pitch perception is invariant to certain features of the physical stimulus. For example, a missing fundamental stimulus with resolved or unresolved harmonics, or a low and high-level amplitude stimulus with the same spectral content–these all give rise to the same percept of pitch. In contrast, the AN representations for these different stimuli are not invariant to these effects. In fact, due to saturation and non-linearity of both cochlear and inner hair cells responses, these differences are enhanced by the AN fibers. Thus there is a difficulty in explaining how pitch percept arises from the activity of the AN fibers. We introduce a novel approach for extracting pitch cues from the AN population activity for a given arbitrary stimulus. The method is based on a technique known as sparse coding (SC). It is the representation of pitch cues by a few spatiotemporal atoms (templates) from among a large set of possible ones (a dictionary). The amount of activity of each atom is represented by a non-zero coefficient, analogous to an active neuron. Such a technique has been successfully applied to other modalities, particularly vision. The model is composed of a cochlear model, an SC processing unit, and a harmonic sieve. We show that the model copes with different pitch phenomena: extracting resolved and non-resolved harmonics, missing fundamental pitches, stimuli with both high and low amplitudes, iterated rippled noises, and recorded musical instruments. PMID:28099436

A New Approach to Model Pitch Perception Using Sparse Coding.

PubMed

Barzelay, Oded; Furst, Miriam; Barak, Omri

2017-01-01

Our acoustical environment abounds with repetitive sounds, some of which are related to pitch perception. It is still unknown how the auditory system, in processing these sounds, relates a physical stimulus and its percept. Since, in mammals, all auditory stimuli are conveyed into the nervous system through the auditory nerve (AN) fibers, a model should explain the perception of pitch as a function of this particular input. However, pitch perception is invariant to certain features of the physical stimulus. For example, a missing fundamental stimulus with resolved or unresolved harmonics, or a low and high-level amplitude stimulus with the same spectral content-these all give rise to the same percept of pitch. In contrast, the AN representations for these different stimuli are not invariant to these effects. In fact, due to saturation and non-linearity of both cochlear and inner hair cells responses, these differences are enhanced by the AN fibers. Thus there is a difficulty in explaining how pitch percept arises from the activity of the AN fibers. We introduce a novel approach for extracting pitch cues from the AN population activity for a given arbitrary stimulus. The method is based on a technique known as sparse coding (SC). It is the representation of pitch cues by a few spatiotemporal atoms (templates) from among a large set of possible ones (a dictionary). The amount of activity of each atom is represented by a non-zero coefficient, analogous to an active neuron. Such a technique has been successfully applied to other modalities, particularly vision. The model is composed of a cochlear model, an SC processing unit, and a harmonic sieve. We show that the model copes with different pitch phenomena: extracting resolved and non-resolved harmonics, missing fundamental pitches, stimuli with both high and low amplitudes, iterated rippled noises, and recorded musical instruments.

Resolving the detailed structure of cortical and thalamic neurons in the adult rat brain with refined biotinylated dextran amine labeling.

PubMed

Ling, Changying; Hendrickson, Michael L; Kalil, Ronald E

2012-01-01

Biotinylated dextran amine (BDA) has been used frequently for both anterograde and retrograde pathway tracing in the central nervous system. Typically, BDA labels axons and cell somas in sufficient detail to identify their topographical location accurately. However, BDA labeling often has proved to be inadequate to resolve the fine structural details of axon arbors or the dendrites of neurons at a distance from the site of BDA injection. To overcome this limitation, we varied several experimental parameters associated with the BDA labeling of neurons in the adult rat brain in order to improve the sensitivity of the method. Specifically, we compared the effect on labeling sensitivity of: (a) using 3,000 or 10,000 MW BDA; (b) injecting different volumes of BDA; (c) co-injecting BDA with NMDA; and (d) employing various post-injection survival times. Following the extracellular injection of BDA into the visual cortex, labeled cells and axons were observed in both cortical and thalamic areas of all animals studied. However, the detailed morphology of axon arbors and distal dendrites was evident only under optimal conditions for BDA labeling that take into account the: molecular weight of the BDA used, concentration and volume of BDA injected, post-injection survival time, and toning of the resolved BDA with gold and silver. In these instances, anterogradely labeled axons and retrogradely labeled dendrites were resolved in fine detail, approximating that which can be achieved with intracellularly injected compounds such as biocytin or fluorescent dyes.

Kinetics model for the wavelength-dependence of excited-state dynamics of hetero-FRET sensors

NASA Astrophysics Data System (ADS)

Schwarz, Jacob; Leighton, Ryan; Leopold, Hannah J.; Currie, Megan; Boersma, Arnold J.; Sheets, Erin D.; Heikal, Ahmed A.

2017-08-01

Foerster (or fluorescence) resonance energy transfer (FRET) is a powerful tool for investigating protein-protein interactions, in both living cells and in controlled environments. A typical hetero-FRET pair consists of a donor and acceptor tethered together with a linker. The corresponding energy transfer efficiency of a hetero-FRET pair probe depends upon the donor-acceptor distance, relative dipole orientation, and spectral overlap. Because of the sensitivity of the energy transfer efficiency on the donor-acceptor distance, FRET is often referred to as a "molecular ruler". Time-resolved fluorescence approach for measuring the excited-state lifetime of the donor and acceptor emissions is one of the most reliable approaches for quantitative assessment of the energy transfer efficiency in hetero-FRET pairs. In this contribution, we provide an analytical kinetics model that describes the excited-state depopulation of a FRET probe as a means to predicts the time-resolved fluorescence profile as a function of excitation and detection wavelengths. In addition, we used this developed kinetics model to simulate the time-dependence of the excited-state population of both the donor and acceptor. These results should serve as a guide for our ongoing studies of newly developed hetero-FRET sensors (mCerulean3-linker-mCitrine) that are designed specifically for in vivo studies of macromolecular crowding. The same model is applicable to other FRET pairs with the careful consideration of their steady-state spectroscopy and the experimental design for wavelength- dependence of the fluorescence lifetime measurements.

An empirical evaluation of genetic distance statistics using microsatellite data from bear (Ursidae) populations.

PubMed

Paetkau, D; Waits, L P; Clarkson, P L; Craighead, L; Strobeck, C

1997-12-01

A large microsatellite data set from three species of bear (Ursidae) was used to empirically test the performance of six genetic distance measures in resolving relationships at a variety of scales ranging from adjacent areas in a continuous distribution to species that diverged several million years ago. At the finest scale, while some distance measures performed extremely well, statistics developed specifically to accommodate the mutational processes of microsatellites performed relatively poorly, presumably because of the relatively higher variance of these statistics. At the other extreme, no statistic was able to resolve the close sister relationship of polar bears and brown bears from more distantly related pairs of species. This failure is most likely due to constraints on allele distributions at microsatellite loci. At intermediate scales, both within continuous distributions and in comparisons to insular populations of late Pleistocene origin, it was not possible to define the point where linearity was lost for each of the statistics, except that it is clearly lost after relatively short periods of independent evolution. All of the statistics were affected by the amount of genetic diversity within the populations being compared, significantly complicating the interpretation of genetic distance data.

An Empirical Evaluation of Genetic Distance Statistics Using Microsatellite Data from Bear (Ursidae) Populations

PubMed Central

Paetkau, D.; Waits, L. P.; Clarkson, P. L.; Craighead, L.; Strobeck, C.

1997-01-01

A large microsatellite data set from three species of bear (Ursidae) was used to empirically test the performance of six genetic distance measures in resolving relationships at a variety of scales ranging from adjacent areas in a continuous distribution to species that diverged several million years ago. At the finest scale, while some distance measures performed extremely well, statistics developed specifically to accommodate the mutational processes of microsatellites performed relatively poorly, presumably because of the relatively higher variance of these statistics. At the other extreme, no statistic was able to resolve the close sister relationship of polar bears and brown bears from more distantly related pairs of species. This failure is most likely due to constraints on allele distributions at microsatellite loci. At intermediate scales, both within continuous distributions and in comparisons to insular populations of late Pleistocene origin, it was not possible to define the point where linearity was lost for each of the statistics, except that it is clearly lost after relatively short periods of independent evolution. All of the statistics were affected by the amount of genetic diversity within the populations being compared, significantly complicating the interpretation of genetic distance data. PMID:9409849

Unraveling the electronic relaxation dynamics in photoexcited 2,4-difluoroaniline via femtosecond time-resolved photoelectron imaging

NASA Astrophysics Data System (ADS)

Ling, Fengzi; Li, Shuai; Wei, Jie; Liu, Kai; Wang, Yanmei; Zhang, Bing

2018-04-01

Time-resolved photoelectron imaging is employed to investigate the relaxation dynamics of the lowest two excited electronic states S1(ππ*) and S2(π3s/πσ*) in 2,4-difluoroaniline (24DFA). As the S1(ππ*) state is populated directly following 289 nm excitation, the population undergoes ultrafast intramolecular vibrational redistribution on a 540 fs time scale, followed by efficient intersystem crossing from S1(ππ*) to the triplet state within 379 ps, and the subsequent slower deactivation process of the triplet state. For excitation to the S2(π3s/πσ*) state at 238 nm, the population probably bifurcates into two decay channels. The dominant channel with 84 fs involves ultrafast internal conversion to the S1(ππ*) state, from which it relaxes to the electronic ground state on a 116 ps time scale. The other appears to involve motion along the S2(π3s/πσ*) potential energy surface. Our data also determine experimentally the electronic energies of S2(π3s/πσ*), S3(ππ*), and several Rydberg states in 24DFA.

Sensitivity simulations of superparameterised convection in a general circulation model

NASA Astrophysics Data System (ADS)

Rybka, Harald; Tost, Holger

2015-04-01

Cloud Resolving Models (CRMs) covering a horizontal grid spacing from a few hundred meters up to a few kilometers have been used to explicitly resolve small-scale and mesoscale processes. Special attention has been paid to realistically represent cloud dynamics and cloud microphysics involving cloud droplets, ice crystals, graupel and aerosols. The entire variety of physical processes on the small-scale interacts with the larger-scale circulation and has to be parameterised on the coarse grid of a general circulation model (GCM). Since more than a decade an approach to connect these two types of models which act on different scales has been developed to resolve cloud processes and their interactions with the large-scale flow. The concept is to use an ensemble of CRM grid cells in a 2D or 3D configuration in each grid cell of the GCM to explicitly represent small-scale processes avoiding the use of convection and large-scale cloud parameterisations which are a major source for uncertainties regarding clouds. The idea is commonly known as superparameterisation or cloud-resolving convection parameterisation. This study presents different simulations of an adapted Earth System Model (ESM) connected to a CRM which acts as a superparameterisation. Simulations have been performed with the ECHAM/MESSy atmospheric chemistry (EMAC) model comparing conventional GCM runs (including convection and large-scale cloud parameterisations) with the improved superparameterised EMAC (SP-EMAC) modeling one year with prescribed sea surface temperatures and sea ice content. The sensitivity of atmospheric temperature, precipiation patterns, cloud amount and types is observed changing the embedded CRM represenation (orientation, width, no. of CRM cells, 2D vs. 3D). Additionally, we also evaluate the radiation balance with the new model configuration, and systematically analyse the impact of tunable parameters on the radiation budget and hydrological cycle. Furthermore, the subgrid variability (individual CRM cell output) is analysed in order to illustrate the importance of a highly varying atmospheric structure inside a single GCM grid box. Finally, the convective transport of Radon is observed comparing different transport procedures and their influence on the vertical tracer distribution.

Acute Calcific Tendinitis of the Index Finger in a Child.

PubMed

Walocko, Frances M; Sando, Ian C; Haase, Steven C; Kozlow, Jeffrey H

2017-09-01

Calcific tendinitis is characterized by calcium hydroxyapatite crystal deposition within tendons and is a common cause of musculoskeletal pain in adults. Its clinical manifestations may be acute, chronic, or asymptomatic. Acute calcific tendinitis is self-resolving condition that is rarely reported in the pediatric population and may be overlooked for more common processes, leading to unnecessary treatment. A chart reivew was performed of a single case of acute calcific tendonitis of the index finger in a child. We describe a case of calcific tendinitis of the index finger in a 9-year-old boy who was referred to us for a second opinion after surgical exploration of an acutely inflamed digit was recommended based on his initial presentation. The calcifications and symptoms resolved over time without operative management. Although rare in children, acute calcific tendinitis can present similar to an infection. However, appropriate managment is non-operative as the symptoms and radiographic findings resolve over time.

Super-resolution of fluorescence-free plasmonic nanoparticles using enhanced dark-field illumination based on wavelength-modulation

DOE PAGES

Zhang, Peng; Lee, Seungah; Yu, Hyunung; ...

2015-06-15

Super-resolution imaging of fluorescence-free plasmonic nanoparticles (NPs) was achieved using enhanced dark-field (EDF) illumination based on wavelength-modulation. Indistinguishable adjacent EDF images of 103-nm gold nanoparticles (GNPs), 40-nm gold nanorods (GNRs), and 80-nm silver nanoparticles (SNPs) were modulated at their wavelengths of specific localized surface plasmon scattering. The coordinates (x, y) of each NP were resolved by fitting their point spread functions with a two-dimensional Gaussian. The measured localization precisions of GNPs, GNRs, and SNPs were 2.5 nm, 5.0 nm, and 2.9 nm, respectively. From the resolved coordinates of NPs and the corresponding localization precisions, super-resolution images were reconstructed. Depending onmore » the spontaneous polarization of GNR scattering, the orientation angle of GNRs in two-dimensions was resolved and provided more elaborate localization information. This novel fluorescence-free super-resolution method was applied to live HeLa cells to resolve NPs and provided remarkable subdiffraction limit images.« less

Emergence of cooperativity in a model biofilm

NASA Astrophysics Data System (ADS)

Rotrattanadumrong, Rachapun; Endres, Robert G.

2017-06-01

Evolution to multicellularity from an aggregate of cells involves altruistic cooperation between individual cells, which is in conflict with Darwinian evolution. How cooperation arises and how a cell community resolves such conflicts remains unclear. In this study, we investigated the spontaneous emergence of cell differentiation and the subsequent division of labour in evolving cellular metabolic networks. In spatially extended cell aggregates, our findings reveal that resource limitation can lead to the formation of subpopulations and cooperation of cells, and hence multicellular communities. A specific example of our model can explain the recently observed oscillatory growth in Bacillus subtilis biofilms.

ED(MF)n: Humidity-Convection Feedbacks in a Mass Flux Scheme Based on Resolved Size Densities

NASA Astrophysics Data System (ADS)

Neggers, R.

2014-12-01

Cumulus cloud populations remain at least partially unresolved in present-day numerical simulations of global weather and climate, and accordingly their impact on the larger-scale flow has to be represented through parameterization. Various methods have been developed over the years, ranging in complexity from the early bulk models relying on a single plume to more recent approaches that attempt to reconstruct the underlying probability density functions, such as statistical schemes and multiple plume approaches. Most of these "classic" methods capture key aspects of cumulus cloud populations, and have been successfully implemented in operational weather and climate models. However, the ever finer discretizations of operational circulation models, driven by advances in the computational efficiency of supercomputers, is creating new problems for existing sub-grid schemes. Ideally, a sub-grid scheme should automatically adapt its impact on the resolved scales to the dimension of the grid-box within which it is supposed to act. It can be argued that this is only possible when i) the scheme is aware of the range of scales of the processes it represents, and ii) it can distinguish between contributions as a function of size. How to conceptually represent this knowledge of scale in existing parameterization schemes remains an open question that is actively researched. This study considers a relatively new class of models for sub-grid transport in which ideas from the field of population dynamics are merged with the concept of multi plume modelling. More precisely, a multiple mass flux framework for moist convective transport is formulated in which the ensemble of plumes is created in "size-space". It is argued that thus resolving the underlying size-densities creates opportunities for introducing scale-awareness and scale-adaptivity in the scheme. The behavior of an implementation of this framework in the Eddy Diffusivity Mass Flux (EDMF) model, named ED(MF)n, is examined for a standard case of subtropical marine shallow cumulus. We ask if a system of multiple independently resolved plumes is able to automatically create the vertical profile of bulk (mass) flux at which the sub-grid scale transport balances the imposed larger-scale forcings in the cloud layer.

Use of Special Operations Forces in United Nations Missions: a Method to Resolve Complexity

DTIC Science & Technology

2015-05-21

physical stamina and psychological stability, followed by a rigorous training program are the imperatives to create SOF soldiers.42 Mark Bowden in...recommendation is that the United Nations should establish a Special Operations planning cell within the UN Department of Peacekeeping Operations. As of...now, the cell is nonexistent. This cell should be able to facilitate the integration of SOF into the overall peace operations concept. Finally, the

Particle-in-cell studies of fast-ion slowing-down rates in cool tenuous magnetized plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Evans, Eugene S.; Cohen, Samuel A.; Welch, Dale R.

We report on 3D-3V particle-in-cell simulations of fast-ion energy-loss rates in a cold, weakly-magnetized, weakly-coupled plasma where the electron gyroradius, ρe, is comparable to or less than the Debye length, λ De, and the fast-ion velocity exceeds the electron thermal velocity, a regime in which the electron response may be impeded. These simulations use explicit algorithms, spatially resolve ρ e and λ De, and temporally resolve the electron cyclotron and plasma frequencies. For mono-energetic dilute fast ions with isotropic velocity distributions, these scaling studies of the slowing-down time, τ s, versus fast-ion charge are in agreement with unmagnetized slowing-down theory;more » with an applied magnetic field, no consistent anisotropy between τs in the cross-field and field-parallel directions could be resolved. Scaling the fast-ion charge is confirmed as a viable way to reduce the required computational time for each simulation. In conclusion, the implications of these slowing down processes are described for one magnetic-confinement fusion concept, the small, advanced-fuel, field-reversed configuration device.« less

Homogeneous Time-resolved Förster Resonance Energy Transfer-based Assay for Detection of Insulin Secretion.

PubMed

Aslanoglou, Despoina; George, Emily W; Freyberg, Zachary

2018-05-10

The detection of insulin secretion is critical for elucidating mechanisms of regulated secretion as well as in studies of metabolism. Though numerous insulin assays have existed for decades, the recent advent of homogeneous time-resolved Förster Resonance Energy Transfer (HTRF) technology has significantly simplified these measurements. This is a rapid, cost-effective, reproducible, and robust optical assay reliant upon antibodies conjugated to bright fluorophores with long lasting emission which facilitates time-resolved Förster Resonance Energy Transfer. Moreover, HTRF insulin detection is amenable for the development of high-throughput screening assays. Here we use HTRF to detect insulin secretion in INS-1E cells, a rat insulinoma-derived cell line. This allows us to estimate basal levels of insulin and their changes in response to glucose stimulation. In addition, we use this insulin detection system to confirm the role of dopamine as a negative regulator of glucose-stimulated insulin secretion (GSIS). In a similar manner, other dopamine D2-like receptor agonists, quinpirole, and bromocriptine, reduce GSIS in a concentration-dependent manner. Our results highlight the utility of the HTRF insulin assay format in determining the role of numerous drugs in GSIS and their pharmacological profiles.

Time-resolved Analysis of Proteome Dynamics by Tandem Mass Tags and Stable Isotope Labeling in Cell Culture (TMT-SILAC) Hyperplexing*

PubMed Central

Welle, Kevin A.; Zhang, Tian; Hryhorenko, Jennifer R.; Shen, Shichen; Qu, Jun; Ghaemmaghami, Sina

2016-01-01

Recent advances in mass spectrometry have enabled system-wide analyses of protein turnover. By globally quantifying the kinetics of protein clearance and synthesis, these methodologies can provide important insights into the regulation of the proteome under varying cellular and environmental conditions. To facilitate such analyses, we have employed a methodology that combines metabolic isotopic labeling (Stable Isotope Labeling in Cell Culture - SILAC) with isobaric tagging (Tandem Mass Tags - TMT) for analysis of multiplexed samples. The fractional labeling of multiple time-points can be measured in a single mass spectrometry run, providing temporally resolved measurements of protein turnover kinetics. To demonstrate the feasibility of the approach, we simultaneously measured the kinetics of protein clearance and accumulation for more than 3000 proteins in dividing and quiescent human fibroblasts and verified the accuracy of the measurements by comparison to established non-multiplexed approaches. The results indicate that upon reaching quiescence, fibroblasts compensate for lack of cellular growth by globally downregulating protein synthesis and upregulating protein degradation. The described methodology significantly reduces the cost and complexity of temporally-resolved dynamic proteomic experiments and improves the precision of proteome-wide turnover data. PMID:27765818

Particle-in-cell studies of fast-ion slowing-down rates in cool tenuous magnetized plasma

DOE PAGES

Evans, Eugene S.; Cohen, Samuel A.; Welch, Dale R.

2018-04-05

We report on 3D-3V particle-in-cell simulations of fast-ion energy-loss rates in a cold, weakly-magnetized, weakly-coupled plasma where the electron gyroradius, ρe, is comparable to or less than the Debye length, λ De, and the fast-ion velocity exceeds the electron thermal velocity, a regime in which the electron response may be impeded. These simulations use explicit algorithms, spatially resolve ρ e and λ De, and temporally resolve the electron cyclotron and plasma frequencies. For mono-energetic dilute fast ions with isotropic velocity distributions, these scaling studies of the slowing-down time, τ s, versus fast-ion charge are in agreement with unmagnetized slowing-down theory;more » with an applied magnetic field, no consistent anisotropy between τs in the cross-field and field-parallel directions could be resolved. Scaling the fast-ion charge is confirmed as a viable way to reduce the required computational time for each simulation. In conclusion, the implications of these slowing down processes are described for one magnetic-confinement fusion concept, the small, advanced-fuel, field-reversed configuration device.« less

Human Prostate Side Population Cells Demonstrate Stem Cell Properties in Recombination with Urogenital Sinus Mesenchyme

PubMed Central

Foster, Barbara A.; Gangavarapu, Kalyan J.; Mathew, Grinu; Azabdaftari, Gissou; Morrison, Carl D.; Miller, Austin; Huss, Wendy J.

2013-01-01

Stem cell enrichment provides a tool to examine prostate stem cells obtained from benign and malignant tissue. Functional assays can enrich stem cells based on common stem cell phenotypes, such as high ATP binding cassette (ABC) transporter mediated efflux of Hoechst substrates (side population assay). This functional assay is based upon mechanisms that protect cells from environmental insult thus contributing to the survival and protection of the stem cell population. We have isolated and analyzed cells digested from twelve clinical prostate specimens based on the side population assay. Prostate stem cell properties of the isolated cells were tested by serial recombination with rat urogenital mesenchyme. Recombinants with side population cells demonstrate an increase in the frequency of human ductal growth and the number of glands per recombinant when compared to recombinants with non-side population cells. Isolated cells were capable of prostatic growth for up to three generations in the recombination assay with as little as 125 sorted prostate cells. The ability to reproducibly use cells isolated by fluorescence activated cell sorting from human prostate tissue is an essential step to a better understanding of human prostate stem cell biology. ABC transporter G2 (ABCG2) was expressed in recombinants from side population cells indicating the side population cells have self-renewal properties. Epithelial cell differentiation of recombinants was determined by immunohistochemical analysis for expression of the basal, luminal, and neuroendocrine markers, p63, androgen receptor, prostate specific antigen, and chromogranin A, respectively. Thus, the ABCG2 expressing side population demonstrates multipotency and self-renewal properties indicating stem cells are within this population. PMID:23383057

An open-source solution for advanced imaging flow cytometry data analysis using machine learning.

PubMed

Hennig, Holger; Rees, Paul; Blasi, Thomas; Kamentsky, Lee; Hung, Jane; Dao, David; Carpenter, Anne E; Filby, Andrew

2017-01-01

Imaging flow cytometry (IFC) enables the high throughput collection of morphological and spatial information from hundreds of thousands of single cells. This high content, information rich image data can in theory resolve important biological differences among complex, often heterogeneous biological samples. However, data analysis is often performed in a highly manual and subjective manner using very limited image analysis techniques in combination with conventional flow cytometry gating strategies. This approach is not scalable to the hundreds of available image-based features per cell and thus makes use of only a fraction of the spatial and morphometric information. As a result, the quality, reproducibility and rigour of results are limited by the skill, experience and ingenuity of the data analyst. Here, we describe a pipeline using open-source software that leverages the rich information in digital imagery using machine learning algorithms. Compensated and corrected raw image files (.rif) data files from an imaging flow cytometer (the proprietary .cif file format) are imported into the open-source software CellProfiler, where an image processing pipeline identifies cells and subcellular compartments allowing hundreds of morphological features to be measured. This high-dimensional data can then be analysed using cutting-edge machine learning and clustering approaches using "user-friendly" platforms such as CellProfiler Analyst. Researchers can train an automated cell classifier to recognize different cell types, cell cycle phases, drug treatment/control conditions, etc., using supervised machine learning. This workflow should enable the scientific community to leverage the full analytical power of IFC-derived data sets. It will help to reveal otherwise unappreciated populations of cells based on features that may be hidden to the human eye that include subtle measured differences in label free detection channels such as bright-field and dark-field imagery. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Making sense of snapshot data: ergodic principle for clonal cell populations

PubMed Central

2017-01-01

Population growth is often ignored when quantifying gene expression levels across clonal cell populations. We develop a framework for obtaining the molecule number distributions in an exponentially growing cell population taking into account its age structure. In the presence of generation time variability, the average acquired across a population snapshot does not obey the average of a dividing cell over time, apparently contradicting ergodicity between single cells and the population. Instead, we show that the variation observed across snapshots with known cell age is captured by cell histories, a single-cell measure obtained from tracking an arbitrary cell of the population back to the ancestor from which it originated. The correspondence between cells of known age in a population with their histories represents an ergodic principle that provides a new interpretation of population snapshot data. We illustrate the principle using analytical solutions of stochastic gene expression models in cell populations with arbitrary generation time distributions. We further elucidate that the principle breaks down for biochemical reactions that are under selection, such as the expression of genes conveying antibiotic resistance, which gives rise to an experimental criterion with which to probe selection on gene expression fluctuations. PMID:29187636

Making sense of snapshot data: ergodic principle for clonal cell populations.

PubMed

Thomas, Philipp

2017-11-01

Population growth is often ignored when quantifying gene expression levels across clonal cell populations. We develop a framework for obtaining the molecule number distributions in an exponentially growing cell population taking into account its age structure. In the presence of generation time variability, the average acquired across a population snapshot does not obey the average of a dividing cell over time, apparently contradicting ergodicity between single cells and the population. Instead, we show that the variation observed across snapshots with known cell age is captured by cell histories, a single-cell measure obtained from tracking an arbitrary cell of the population back to the ancestor from which it originated. The correspondence between cells of known age in a population with their histories represents an ergodic principle that provides a new interpretation of population snapshot data. We illustrate the principle using analytical solutions of stochastic gene expression models in cell populations with arbitrary generation time distributions. We further elucidate that the principle breaks down for biochemical reactions that are under selection, such as the expression of genes conveying antibiotic resistance, which gives rise to an experimental criterion with which to probe selection on gene expression fluctuations. © 2017 The Author(s).

Anatomical Analysis of the Retinal Specializations to a Crypto-Benthic, Micro-Predatory Lifestyle in the Mediterranean Triplefin Blenny Tripterygion delaisi

PubMed Central

Fritsch, Roland; Collin, Shaun P.; Michiels, Nico K.

2017-01-01

The environment and lifestyle of a species are known to exert selective pressure on the visual system, often demonstrating a tight link between visual morphology and ecology. Many studies have predicted the visual requirements of a species by examining the anatomical features of the eye. However, among the vast number of studies on visual specializations in aquatic animals, only a few have focused on small benthic fishes that occupy a heterogeneous and spatially complex visual environment. This study investigates the general retinal anatomy including the topography of both the photoreceptor and ganglion cell populations and estimates the spatial resolving power (SRP) of the eye of the Mediterranean triplefin Tripterygion delaisi. Retinal wholemounts were prepared to systematically and quantitatively analyze photoreceptor and retinal ganglion cell (RGC) densities using design-based stereology. To further examine the retinal structure, we also used magnetic resonance imaging (MRI) and histological examination of retinal cross sections. Observations of the triplefin’s eyes revealed them to be highly mobile, allowing them to view the surroundings without body movements. A rostral aphakic gap and the elliptical shape of the eye extend its visual field rostrally and allow for a rostro-caudal accommodatory axis, enabling this species to focus on prey at close range. Single and twin cones dominate the retina and are consistently arranged in one of two regular patterns, which may enhance motion detection and color vision. The retina features a prominent, dorso-temporal, convexiclivate fovea with an average density of 104,400 double and 30,800 single cones per mm2, and 81,000 RGCs per mm2. Based on photoreceptor spacing, SRP was calculated to be between 6.7 and 9.0 cycles per degree. Location and resolving power of the fovea would benefit the detection and identification of small prey in the lower frontal region of the visual field. PMID:29311852

Anatomical Analysis of the Retinal Specializations to a Crypto-Benthic, Micro-Predatory Lifestyle in the Mediterranean Triplefin Blenny Tripterygion delaisi.

PubMed

Fritsch, Roland; Collin, Shaun P; Michiels, Nico K

2017-01-01

The environment and lifestyle of a species are known to exert selective pressure on the visual system, often demonstrating a tight link between visual morphology and ecology. Many studies have predicted the visual requirements of a species by examining the anatomical features of the eye. However, among the vast number of studies on visual specializations in aquatic animals, only a few have focused on small benthic fishes that occupy a heterogeneous and spatially complex visual environment. This study investigates the general retinal anatomy including the topography of both the photoreceptor and ganglion cell populations and estimates the spatial resolving power (SRP) of the eye of the Mediterranean triplefin Tripterygion delaisi . Retinal wholemounts were prepared to systematically and quantitatively analyze photoreceptor and retinal ganglion cell (RGC) densities using design-based stereology. To further examine the retinal structure, we also used magnetic resonance imaging (MRI) and histological examination of retinal cross sections. Observations of the triplefin's eyes revealed them to be highly mobile, allowing them to view the surroundings without body movements. A rostral aphakic gap and the elliptical shape of the eye extend its visual field rostrally and allow for a rostro-caudal accommodatory axis, enabling this species to focus on prey at close range. Single and twin cones dominate the retina and are consistently arranged in one of two regular patterns, which may enhance motion detection and color vision. The retina features a prominent, dorso-temporal, convexiclivate fovea with an average density of 104,400 double and 30,800 single cones per mm 2 , and 81,000 RGCs per mm 2 . Based on photoreceptor spacing, SRP was calculated to be between 6.7 and 9.0 cycles per degree. Location and resolving power of the fovea would benefit the detection and identification of small prey in the lower frontal region of the visual field.

Comparisons of angularly and spectrally resolved Bremsstrahlung measurements to two-dimensional multi-stage simulations of short-pulse laser-plasma interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, C. D.; Kemp, A. J.; Pérez, F.

2013-05-15

A 2-D multi-stage simulation model incorporating realistic laser conditions and a fully resolved electron distribution handoff has been developed and compared to angularly and spectrally resolved Bremsstrahlung measurements from high-Z planar targets. For near-normal incidence and 0.5-1 × 10{sup 20} W/cm{sup 2} intensity, particle-in-cell (PIC) simulations predict the existence of a high energy electron component consistently directed away from the laser axis, in contrast with previous expectations for oblique irradiation. Measurements of the angular distribution are consistent with a high energy component when directed along the PIC predicted direction, as opposed to between the target normal and laser axis asmore » previously measured.« less

[Natural killer cell cytotoxic activity in critical pediatric patients with suspected hemophagocytic syndrome].

PubMed

Martínez, I; Fernández, L; Valentín, J; Castillo, C; Chamorro, C; Pérez-Martínez, A

2015-05-01

To determine the role of natural killer (NK) cytotoxic activity in patients with suspected hemophagocytic lymphohistiocytosis syndrome (HLH). A prospective study was conducted from September 2008 to February 2014. The study was carried out in the Hematological Oncology Laboratory of Hospital Infantil Universitario Niño Jesús, Madrid (Spain). We analyzed 30 peripheral blood samples from intensive care patients with suspected HLH. There were 18 males and 12 females, with a mean age of 4.7 years (range 0.2-22). NK cell cytotoxicity was compared with healthy controls according to age and sex. In vitro NK cell cytotoxicity against the K562 cell line was determined by time-resolved fluorescence (Europium-TDA) under resting conditions, after interleukin 15 stimulation, and following block with Fas ligand antibody. NK cell cytotoxicity. A total of 20 patients showed a significant decrease of NK cell activity compared with controls (P=.001). Nine of these patients were diagnosed with primary HLH. A total of 10 patients were diagnosed with secondary HLH. Cytotoxic activity was normal in 10 subjects. None of them were diagnosed with HLH. Interleukin 15 stimulation increased NK cell cytotoxicity in secondary HLH, and blocking Fas ligand on NK cells decreased cytotoxic activity in primary HLH patients (P=.001). In our experience, NK cell cytotoxic activity measured by time-resolved fluorescence is a simple and useful clinical diagnostic test for HLH. Interleukin 15 stimulation and Fas ligand blocking on NK cells could help differentiate between primary and secondary HLH. Copyright © 2014 Elsevier España, S.L.U. and SEMICYUC. All rights reserved.

On the reversibility of transitions between closed and open cellular convection

DOE PAGES

Feingold, G.; Koren, I.; Yamaguchi, T.; ...

2015-07-08

The two-way transition between closed and open cellular convection is addressed in an idealized cloud-resolving modeling framework. A series of cloud-resolving simulations shows that the transition between closed and open cellular states is asymmetrical and characterized by a rapid ("runaway") transition from the closed- to the open-cell state but slower recovery to the closed-cell state. Given that precipitation initiates the closed–open cell transition and that the recovery requires a suppression of the precipitation, we apply an ad hoc time-varying drop concentration to initiate and suppress precipitation. We show that the asymmetry in the two-way transition occurs even for very rapidmore » drop concentration replenishment. The primary barrier to recovery is the loss in turbulence kinetic energy (TKE) associated with the loss in cloud water (and associated radiative cooling) and the vertical stratification of the boundary layer during the open-cell period. In transitioning from the open to the closed state, the system faces the task of replenishing cloud water fast enough to counter precipitation losses, such that it can generate radiative cooling and TKE. It is hampered by a stable layer below cloud base that has to be overcome before water vapor can be transported more efficiently into the cloud layer. Recovery to the closed-cell state is slower when radiative cooling is inefficient such as in the presence of free tropospheric clouds or after sunrise, when it is hampered by the absorption of shortwave radiation. Tests suggest that recovery to the closed-cell state is faster when the drizzle is smaller in amount and of shorter duration, i.e., when the precipitation causes less boundary layer stratification. Cloud-resolving model results on recovery rates are supported by simulations with a simple predator–prey dynamical system analogue. It is suggested that the observed closing of open cells by ship effluent likely occurs when aerosol intrusions are large, when contact comes prior to the heaviest drizzle in the early morning hours, and when the free troposphere is cloud free.« less

Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentation

PubMed Central

Robidart, Julie C; Preston, Christina M; Paerl, Ryan W; Turk, Kendra A; Mosier, Annika C; Francis, Christopher A; Scholin, Christopher A; Zehr, Jonathan P

2012-01-01

Monterey Bay, CA is an Eastern boundary upwelling system that is nitrogen limited much of the year. In order to resolve population dynamics of microorganisms important for nutrient cycling in this region, we deployed the Environmental Sample Processor with quantitative PCR assays targeting both ribosomal RNA genes and functional genes for subclades of cyanobacteria (Synechococcus) and ammonia-oxidizing Archaea (Thaumarchaeota) populations. Results showed a strong correlation between Thaumarchaea abundances and nitrate during the spring upwelling but not the fall sampling period. In relatively stratified fall waters, the Thaumarchaeota community reached higher numbers than in the spring, and an unexpected positive correlation with chlorophyll concentration was observed. Further, we detected drops in Synechococcus abundance that occurred on short (that is, daily) time scales. Upwelling intensity and blooms of eukaryotic phytoplankton strongly influenced Synechococcus distributions in the spring and fall, revealing what appear to be the environmental limitations of Synechococcus populations in this region. Each of these findings has implications for Monterey Bay biogeochemistry. High-resolution sampling provides a better-resolved framework within which to observe changes in the plankton community. We conclude that controls on these ecosystems change on smaller scales than are routinely assessed, and that more predictable trends will be uncovered if they are evaluated within seasonal (monthly), rather than on annual or interannual scales. PMID:21975596

Dynamic positional fate map of the primary heart-forming region.

PubMed

Cui, Cheng; Cheuvront, Tracey J; Lansford, Rusty D; Moreno-Rodriguez, Ricardo A; Schultheiss, Thomas M; Rongish, Brenda J

2009-08-15

Here we show the temporal-spatial orchestration of early heart morphogenesis at cellular level resolution, in vivo, and reconcile conflicting positional fate mapping data regarding the primary heart-forming field(s). We determined the positional fates of precardiac cells using a precision electroporation approach in combination with wide-field time-lapse microscopy in the quail embryo, a warm-blooded vertebrate (HH Stages 4 through 10). Contrary to previous studies, the results demonstrate the existence of a "continuous" circle-shaped heart field that spans the midline, appearing at HH Stage 4, which then expands to form a wide arc of progenitors at HH Stages 5-7. Our time-resolved image data show that a subset of these cardiac progenitor cells do not overlap with the expression of common cardiogenic factors, Nkx-2.5 and Bmp-2, until HH Stage 10, when a tubular heart has formed, calling into question when cardiac fate is specified and by which key factors. Sub-groups and anatomical bands (cohorts) of heart precursor cells dramatically change their relative positions in a process largely driven by endodermal folding and other large-scale tissue deformations. Thus, our novel dynamic positional fate maps resolve the origin of cardiac progenitor cells in amniotes. The data also establish the concept that tissue motion contributes significantly to cellular position fate - i.e., much of the cellular displacement that occurs during assembly of a midline heart tube (HH Stage 9) is NOT due to "migration" (autonomous motility), a commonly held belief. Computational analysis of our time-resolved data lays the foundation for more precise analyses of how cardiac gene regulatory networks correlate with early heart tissue morphogenesis in birds and mammals.

Time-resolved delayed luminescence image microscopy using an europium ion chelate complex.

PubMed Central

Marriott, G.; Heidecker, M.; Diamandis, E. P.; Yan-Marriott, Y.

1994-01-01

Improvements and extended applications of time-resolved delayed luminescence imaging microscopy (TR-DLIM) in cell biology are described. The emission properties of europium ion complexed to a fluorescent chelating group capable of labeling proteins are exploited to provide high contrast images of biotin labeled ligands through detection of the delayed emission. The streptavidin-based macromolecular complex (SBMC) employs streptavidin cross-linked to thyroglobulin multiply labeled with the europium-fluorescent chelate. The fluorescent chelate is efficiently excited with 340-nm light, after which it sensitizes europium ion emission at 612 nm hundreds of microseconds later. The SBMC complex has a high quantum yield orders of magnitude higher than that of eosin, a commonly used delayed luminescent probe, and can be readily seen by the naked eye, even in specimens double-labeled with prompt fluorescent probes. Unlike triplet-state phosphorescent probes, sensitized europium ion emission is insensitive to photobleaching and quenching by molecular oxygen; these properties have been exploited to obtain delayed luminescence images of living cells in aerated medium thus complementing imaging studies using prompt fluorescent probes. Since TR-DLIM has the unique property of rejecting enormous signals that originate from scattered light, autofluorescence, and prompt fluorescence it has been possible to resolve double emission images of living amoeba cells containing an intensely stained lucifer yellow in pinocytosed vesicles and membrane surface-bound SBMC-labeled biotinylated concanavalin A. Images of fixed cells represented in terms of the time decay of the sensitized emission show the lifetime of the europium ion emission is sensitive to the environment in which it is found. Through the coupling of SBMC to streptavidin,a plethora of biotin-based tracer molecules are available for immunocytochemical studies. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 FIGURE 5 FIGURE 6 FIGURE 7 PMID:7811952

Time-resolved measurements of the hot-electron population in ignition-scale experiments on the National Ignition Facility (invited)

NASA Astrophysics Data System (ADS)

Hohenberger, M.; Albert, F.; Palmer, N. E.; Lee, J. J.; Döppner, T.; Divol, L.; Dewald, E. L.; Bachmann, B.; MacPhee, A. G.; LaCaille, G.; Bradley, D. K.; Stoeckl, C.

2014-11-01

In laser-driven inertial confinement fusion, hot electrons can preheat the fuel and prevent fusion-pellet compression to ignition conditions. Measuring the hot-electron population is key to designing an optimized ignition platform. The hot electrons in these high-intensity, laser-driven experiments, created via laser-plasma interactions, can be inferred from the bremsstrahlung generated by hot electrons interacting with the target. At the National Ignition Facility (NIF) [G. H. Miller, E. I. Moses, and C. R. Wuest, Opt. Eng. 43, 2841 (2004)], the filter-fluorescer x-ray (FFLEX) diagnostic-a multichannel, hard x-ray spectrometer operating in the 20-500 keV range-has been upgraded to provide fully time-resolved, absolute measurements of the bremsstrahlung spectrum with ˜300 ps resolution. Initial time-resolved data exhibited significant background and low signal-to-noise ratio, leading to a redesign of the FFLEX housing and enhanced shielding around the detector. The FFLEX x-ray sensitivity was characterized with an absolutely calibrated, energy-dispersive high-purity germanium detector using the high-energy x-ray source at NSTec Livermore Operations over a range of K-shell fluorescence energies up to 111 keV (U Kβ). The detectors impulse response function was measured in situ on NIF short-pulse (˜90 ps) experiments, and in off-line tests.

Development of a novel cell sorting method that samples population diversity in flow cytometry.

PubMed

Osborne, Geoffrey W; Andersen, Stacey B; Battye, Francis L

2015-11-01

Flow cytometry based electrostatic cell sorting is an important tool in the separation of cell populations. Existing instruments can sort single cells into multi-well collection plates, and keep track of cell of origin and sorted well location. However currently single sorted cell results reflect the population distribution and fail to capture the population diversity. Software was designed that implements a novel sorting approach, "Slice and Dice Sorting," that links a graphical representation of a multi-well plate to logic that ensures that single cells are sampled and sorted from all areas defined by the sort region/s. Therefore the diversity of the total population is captured, and the more frequently occurring or rarer cell types are all sampled. The sorting approach was tested computationally, and using functional cell based assays. Computationally we demonstrate that conventional single cell sorting can sample as little as 50% of the population diversity dependant on the population distribution, and that Slice and Dice sorting samples much more of the variety present within a cell population. We then show by sorting single cells into wells using the Slice and Dice sorting method that there are cells sorted using this method that would be either rarely sorted, or not sorted at all using conventional single cell sorting approaches. The present study demonstrates a novel single cell sorting method that samples much more of the population diversity than current methods. It has implications in clonal selection, stem cell sorting, single cell sequencing and any areas where population heterogeneity is of importance. © 2015 International Society for Advancement of Cytometry.

Investigation of energy transfer mechanisms between Bi(2+) and Tm(3+) by time-resolved spectrum.

PubMed

Li, Yang; Sharafudeen, Kaniyarakkal; Dong, Guoping; Ma, Zhijun; Qiu, Jianrong

2013-11-01

Here, we report for the first time the optical properties of Bi(2+) and Tm(3+) co-doped germanate glasses and elucidate the potential of this material as substrates to improve the performance of CdTe solar cell. A strong emission peak at 800nm is observed under the excitation of 450-700nm in this material. The energy transfer processes from the transitions of Bi(2+) [(2)P3/2(1)→(2)P1/2]: Tm(3+) [(3)H6→(3)H4] are investigated by time-resolved luminescence spectroscopy. A cover glass exhibiting an ultra-broadband response spectrum covering the entire solar visible wavelength region is suggested to enhance the conversion efficiency of CdTe solar cells significantly. Copyright © 2013 Elsevier B.V. All rights reserved.

Phase-sensitive flow cytometer

DOEpatents

Steinkamp, J.A.

1993-12-14

A phase-sensitive flow cytometer (FCM) provides additional FCM capability to use the fluorescence lifetime of one or more fluorochromes bound to single cells to provide additional information regarding the cells. The resulting fluorescence emission can be resolved into individual fluorescence signals if two fluorochromes are present or can be converted directly to a decay lifetime from a single fluorochrome. The excitation light for the fluorochromes is modulated to produce an amplitude modulated fluorescence pulse as the fluorochrome is excited in the FCM. The modulation signal also forms a reference signal that is phase-shifted a selected amount for subsequent mixing with the output modulated fluorescence intensity signal in phase-sensitive detection circuitry. The output from the phase-sensitive circuitry is then an individual resolved fluorochrome signal or a single fluorochrome decay lifetime, depending on the applied phase shifts. 15 figures.

Revealing the ultrafast charge carrier dynamics in organo metal halide perovskite solar cell materials using time resolved THz spectroscopy

NASA Astrophysics Data System (ADS)

Ponseca, C. S., Jr.; Sundström, V.

2016-03-01

Ultrafast charge carrier dynamics in organo metal halide perovskite has been probed using time resolved terahertz (THz) spectroscopy (TRTS). Current literature on its early time characteristics is unanimous: sub-ps charge carrier generation, highly mobile charges and very slow recombination rationalizing the exceptionally high power conversion efficiency for a solution processed solar cell material. Electron injection from MAPbI3 to nanoparticles (NP) of TiO2 is found to be sub-ps while Al2O3 NPs do not alter charge dynamics. Charge transfer to organic electrodes, Spiro-OMeTAD and PCBM, is sub-ps and few hundreds of ps respectively, which is influenced by the alignment of energy bands. It is surmised that minimizing defects/trap states is key in optimizing charge carrier extraction from these materials.

New developments in laser-heated diamond anvil cell with in situ synchrotron x-ray diffraction at High Pressure Collaborative Access Team

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meng, Yue; Hrubiak, Rostislav; Rod, Eric

An overview of the in situ laser heating system at the High Pressure Collaborative Access Team, with emphasis on newly developed capabilities, is presented. Since its establishment at the beamline 16-ID-B a decade ago, laser-heated diamond anvil cell coupled with in situ synchrotron x-ray diffraction has been widely used for studying the structural properties of materials under simultaneous high pressure and high temperature conditions. Recent developments in both continuous-wave and modulated heating techniques have been focusing on resolving technical issues of the most challenging research areas. Furthermore, the new capabilities have demonstrated clear benefits and provide new opportunities in researchmore » areas including high-pressure melting, pressure-temperature-volume equations of state, chemical reaction, and time resolved studies.« less

New developments in laser-heated diamond anvil cell with in situ synchrotron x-ray diffraction at High Pressure Collaborative Access Team

DOE PAGES

Meng, Yue; Hrubiak, Rostislav; Rod, Eric; ...

2015-07-17

An overview of the in situ laser heating system at the High Pressure Collaborative Access Team, with emphasis on newly developed capabilities, is presented. Since its establishment at the beamline 16-ID-B a decade ago, laser-heated diamond anvil cell coupled with in situ synchrotron x-ray diffraction has been widely used for studying the structural properties of materials under simultaneous high pressure and high temperature conditions. Recent developments in both continuous-wave and modulated heating techniques have been focusing on resolving technical issues of the most challenging research areas. Furthermore, the new capabilities have demonstrated clear benefits and provide new opportunities in researchmore » areas including high-pressure melting, pressure-temperature-volume equations of state, chemical reaction, and time resolved studies.« less

New developments in laser-heated diamond anvil cell with in situ synchrotron x-ray diffraction at High Pressure Collaborative Access Team

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meng, Yue; Hrubiak, Rostislav; Rod, Eric

An overview of the in situ laser heating system at the High Pressure Collaborative Access Team, with emphasis on newly developed capabilities, is presented. Since its establishment at the beamline 16-ID-B a decade ago, laser-heated diamond anvil cell coupled with in situ synchrotron x-ray diffraction has been widely used for studying the structural properties of materials under simultaneous high pressure and high temperature conditions. Recent developments in both continuous-wave and modulated heating techniques have been focusing on resolving technical issues of the most challenging research areas. The new capabilities have demonstrated clear benefits and provide new opportunities in research areasmore » including high-pressure melting, pressure-temperature-volume equations of state, chemical reaction, and time resolved studies.« less

A high-throughput platform for population reformatting and mammalian expression of phage display libraries to enable functional screening as full-length IgG.

PubMed

Xiao, Xiaodong; Douthwaite, Julie A; Chen, Yan; Kemp, Ben; Kidd, Sara; Percival-Alwyn, Jennifer; Smith, Alison; Goode, Kate; Swerdlow, Bonnie; Lowe, David; Wu, Herren; Dall'Acqua, William F; Chowdhury, Partha S

Phage display antibody libraries are a rich resource for discovery of potential therapeutic antibodies. Single-chain variable fragment (scFv) libraries are the most common format due to the efficient display of scFv by phage particles and the ease by which soluble scFv antibodies can be expressed for high-throughput screening. Typically, a cascade of screening and triaging activities are performed, beginning with the assessment of large numbers of E. coli-expressed scFv, and progressing through additional assays with individual reformatting of the most promising scFv to full-length IgG. However, use of high-throughput screening of scFv for the discovery of full-length IgG is not ideal because of the differences between these molecules. Furthermore, the reformatting step represents a bottle neck in the process because each antibody has to be handled individually to preserve the unique VH and VL pairing. These problems could be resolved if populations of scFv could be reformatted to full-length IgG before screening without disrupting the variable region pairing. Here, we describe a novel strategy that allows the reformatting of diverse populations of scFv from phage selections to full-length IgG in a batch format. The reformatting process maintains the diversity and variable region pairing with high fidelity, and the resulted IgG pool enables high-throughput expression of IgG in mammalian cells and cell-based functional screening. The improved process led to the discovery of potent candidates that are comparable or better than those obtained by traditional methods. This strategy should also be readily applicable to Fab-based phage libraries. Our approach, Screening in Product Format (SiPF), represents a substantial improvement in the field of antibody discovery using phage display.

Black carbon absorption at the global scale is affected by particle-scale diversity in composition.

PubMed

Fierce, Laura; Bond, Tami C; Bauer, Susanne E; Mena, Francisco; Riemer, Nicole

2016-09-01

Atmospheric black carbon (BC) exerts a strong, but uncertain, warming effect on the climate. BC that is coated with non-absorbing material absorbs more strongly than the same amount of BC in an uncoated particle, but the magnitude of this absorption enhancement (Eabs) is not well constrained. Modelling studies and laboratory measurements have found stronger absorption enhancement than has been observed in the atmosphere. Here, using a particle-resolved aerosol model to simulate diverse BC populations, we show that absorption is overestimated by as much as a factor of two if diversity is neglected and population-averaged composition is assumed across all BC-containing particles. If, instead, composition diversity is resolved, we find Eabs=1-1.5 at low relative humidity, consistent with ambient observations. This study offers not only an explanation for the discrepancy between modelled and observed absorption enhancement, but also demonstrates how particle-scale simulations can be used to develop relationships for global-scale models.

Black Carbon Absorption at the Global Scale Is Affected by Particle-Scale Diversity in Composition

NASA Technical Reports Server (NTRS)

Fierce, Laura; Bond, Tami C.; Bauer, Susanne E.; Mena, Francisco; Riemer, Nicole

2016-01-01

Atmospheric black carbon (BC) exerts a strong, but uncertain, warming effect on the climate. BC that is coated with non-absorbing material absorbs more strongly than the same amount of BC in an uncoated particle, but the magnitude of this absorption enhancement (E(sub abs)) is not well constrained. Modelling studies and laboratory measurements have found stronger absorption enhancement than has been observed in the atmosphere. Here, using a particle-resolved aerosol model to simulate diverse BC populations, we show that absorption is overestimated by as much as a factor of two if diversity is neglected and population-averaged composition is assumed across all BC-containing particles. If, instead, composition diversity is resolved, we find E(sub abs) = 1 - 1.5 at low relative humidity, consistent with ambient observations. This study offers not only an explanation for the discrepancy between modelled and observed absorption enhancement, but also demonstrates how particle-scale simulations can be used to develop relationships for global-scale models.

[Acetyl-11-keto-beta-boswellic acid and arsenic trioxide regulate the productions and activities of matrix metalloproteinases in human skin fibroblasts and human leukemia cell line THP-1].

PubMed

Liang, Ya-hui; Li, Ping; Zhao, Jing-xia; Liu, Xin; Huang, Qi-fu

2010-11-01

In order to reveal the treatment mechanism of Chinese medicine with the effect of activating blood and resolving putridity, we selected acetyl-11-keto-beta-boswellic acid (AKBA) and arsenic trioxide (ATO), the main monomeric components of frankincense and arsenolite which are two most commonly used Chinese medicine with effect of activating blood and resolving putridity. We combined AKBA and ATO as a compound, and explored its regulatory role in productions and activities of matrix metalloproteinase (MMP)-1, MMP-2 and MMP-9 in human skin fibroblasts (HSFbs) and human acute monocytic leukemia cell line THP-1 in inflammatory state. In order to simulate the inflammatory micro-environment of chronic wounds, we established 3 cell models: HSFb model activated by tumor necrosis factor-alpha (TNF-α), THP-1 cell model activated by phorbol-12-myristate-13-acetate (PMA) and HSFb-THP-1 cell coculture system. AKBA and ATO were cocultured with these cell models. Enzyme-linked immunosorbent assay (ELISA), gelatin zymography assay and reverse transcription-polymerase chain reaction (RT-PCR) were used to test the secretions, activities and mRNA expressions of MMP-1, MMP-2 and MMP-9. In the study of the regulatory mechanism of AKBA and ATO on MMPs, AKBA and ATO were cocultured with the cell models. ELISA was used to test the secretions of TNF-α and interleukin-1beta (IL-β) and Western blot was used to test the phosphorylation levels of extracellular signal-regulated kinases 1 and 2 (ERK1/2) and p38 mitogen-activated proteinkinase (p38MAPK). Compound of AKBA and ATO inhibited MMP-1, MMP-2 and MMP-9 mRNA expressions, secretions and activities respectively in HSFbs and THP-1 cells in inflammatory state (P<0.05, P<0.01). Also compound of AKBA and ATO inhibited secretions of TNF-α and IL-1β in THP-1 cells and cell coculture system (P<0.01). It also decreased the phosphorylation of ERK1/2 and p38 MAPK in HSFbs and THP-1 cells (P<0.05, P<0.01). The combined use of AKBA and ATO which in line with the rule of activating blood and resolving putridity inhibits fibroblasts and inflammatory cells in producing MMPs in inflammatory state through inhibiting the release of inflammatory factors and MAPK cascade pathway.

Effect of pressure on infrared spectra of ice 7

NASA Technical Reports Server (NTRS)

Holzapfel, W. B.; Seiler, B.; Nicol, M.

1983-01-01

The effect of pressure on the infrared spectra of H2O and D2O ice VII was studied at room temperature and pressures between 2 and 15 GPa with a Fourier transform infrared spectrometer and a diamond anvil high pressure cell. Two librational modes, one bending mode, and various overtone bands are well resolved. The stretching modes, nu sub 1 and nu sub 3 are poorly resolved due to overlap with diamond window absorption. Differences between the spectra of H2O and D2O are discussed.

Time-resolved experiments in the frequency domain using synchrotron radiation (invited)

NASA Astrophysics Data System (ADS)

De Stasio, Gelsomina; Giusti, A. M.; Parasassi, T.; Ravagnan, G.; Sapora, O.

1992-01-01

PLASTIQUE is the only synchrotron radiation beam line in the world that performs time-resolved fluorescence experiments in frequency domain. These experiments are extremely valuable sources of information on the structure and the dynamics of molecules. This technique measures fluorescence lifetimes with picosecond resolution in the near UV spectral range. Such accurate measurements are rendered possible by taking phase and modulation data, and by the advantages of the cross-correlation technique. A successful experiment demonstrated the radiation damage induced by low doses of radiation on rabbit blood cell membranes.

Time-resolved fluorescence decay measurements for flowing particles

DOEpatents

Deka, C.; Steinkamp, J.A.

1999-06-01

Time-resolved fluorescence decay measurements are disclosed for flowing particles. An apparatus and method for the measurement and analysis of fluorescence for individual cells and particles in flow are described, wherein the rapid measurement capabilities of flow cytometry and the robust measurement and analysis procedures of time-domain fluorescence lifetime spectroscopy are combined. A pulse-modulated CW laser is employed for excitation of the particles. The characteristics and the repetition rate of the excitation pulses can be readily adjusted to accommodate for fluorescence decays having a wide range of lifetimes. 12 figs.

Time-resolved fluorescence decay measurements for flowing particles

DOEpatents

Deka, Chiranjit; Steinkamp, John A.

1999-01-01

Time-resolved fluorescence decay measurements for flowing particles. An apparatus and method for the measurement and analysis of fluorescence for individual cells and particles in flow are described, wherein the rapid measurement capabilities of flow cytometry and the robust measurement and analysis procedures of time-domain fluorescence lifetime spectroscopy are combined. A pulse-modulated cw laser is employed for excitation of the particles. The characteristics and the repetition rate of the excitation pulses can be readily adjusted to accommodate for fluorescence decays having a wide range of lifetimes.

Beam-dynamics codes used at DARHT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ekdahl, Jr., Carl August

Several beam simulation codes are used to help gain a better understanding of beam dynamics in the DARHT LIAs. The most notable of these fall into the following categories: for beam production – Tricomp Trak orbit tracking code, LSP Particle in cell (PIC) code, for beam transport and acceleration – XTR static envelope and centroid code, LAMDA time-resolved envelope and centroid code, LSP-Slice PIC code, for coasting-beam transport to target – LAMDA time-resolved envelope code, LSP-Slice PIC code. These codes are also being used to inform the design of Scorpius.

Identification of handheld objects for electro-optic/FLIR applications

NASA Astrophysics Data System (ADS)

Moyer, Steve K.; Flug, Eric; Edwards, Timothy C.; Krapels, Keith A.; Scarbrough, John

2004-08-01

This paper describes research on the determination of the fifty-percent probability of identification cycle criterion (N50) for two sets of handheld objects. The first set consists of 12 objects which are commonly held in a single hand. The second set consists of 10 objects commonly held in both hands. These sets consist of not only typical civilian handheld objects but also objects that are potentially lethal. A pistol, a cell phone, a rocket propelled grenade (RPG) launcher, and a broom are examples of the objects in these sets. The discrimination of these objects is an inherent part of homeland security, force protection, and also general population security. Objects were imaged from each set in the visible and mid-wave infrared (MWIR) spectrum. Various levels of blur are then applied to these images. These blurred images were then used in a forced choice perception experiment. Results were analyzed as a function of blur level and target size to give identification probability as a function of resolvable cycles on target. These results are applicable to handheld object target acquisition estimates for visible imaging systems and MWIR systems. This research provides guidance in the design and analysis of electro-optical systems and forward-looking infrared (FLIR) systems for use in homeland security, force protection, and also general population security.

A multiscale computational model of spatially resolved calcium cycling in cardiac myocytes: from detailed cleft dynamics to the whole cell concentration profiles

PubMed Central

Vierheller, Janine; Neubert, Wilhelm; Falcke, Martin; Gilbert, Stephen H.; Chamakuri, Nagaiah

2015-01-01

Mathematical modeling of excitation-contraction coupling (ECC) in ventricular cardiac myocytes is a multiscale problem, and it is therefore difficult to develop spatially detailed simulation tools. ECC involves gradients on the length scale of 100 nm in dyadic spaces and concentration profiles along the 100 μm of the whole cell, as well as the sub-millisecond time scale of local concentration changes and the change of lumenal Ca2+ content within tens of seconds. Our concept for a multiscale mathematical model of Ca2+ -induced Ca2+ release (CICR) and whole cardiomyocyte electrophysiology incorporates stochastic simulation of individual LC- and RyR-channels, spatially detailed concentration dynamics in dyadic clefts, rabbit membrane potential dynamics, and a system of partial differential equations for myoplasmic and lumenal free Ca2+ and Ca2+-binding molecules in the bulk of the cell. We developed a novel computational approach to resolve the concentration gradients from dyadic space to cell level by using a quasistatic approximation within the dyad and finite element methods for integrating the partial differential equations. We show whole cell Ca2+-concentration profiles using three previously published RyR-channel Markov schemes. PMID:26441674

A multiphysics microstructure-resolved model for silicon anode lithium-ion batteries

NASA Astrophysics Data System (ADS)

Wang, Miao; Xiao, Xinran; Huang, Xiaosong

2017-04-01

Silicon (Si) is one of the most promising next generation anode materials for lithium-ion batteries (LIBs), but the use of Si in LIBs has been rather limited. The main challenge is its large volume change (up to 300%) during battery cycling. This can lead to the fracture of Si, failure at the interfaces between electrode components, and large dimensional change on the cell level. To optimize the Si electrode/battery design, a model that considers the interactions of different cell components is needed. This paper presents the development of a multiphysics microstructure-resolved model (MRM) for LIB cells with a-Si anode. The model considered the electrochemical reactions, Li transports in electrolyte and electrodes, dimensional changes and stresses, property evolution with the structure, and the coupling relationships. Important model parameters, such as the diffusivity, reaction rate constant, and apparent transfer coefficient, were determined by correlating the simulation results to experiments. The model was validated with experimental results in the literature. The use of this model was demonstrated in a parameter study of Si nanowall|Li cells. The specific and volumetric capacities of the cell as a function of the size, length/size ratio, spacing of the nanostructure, and Li+ concentration in electrolyte were investigated.

Dynamic organization of myristoylated Src in the live cell plasma membrane

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Adam W.; Huang, Hector H.; Endres, Nicholas F.

The spatial organization of lipid-anchored proteins in the plasma membrane directly influences cell signaling, but measuring such organization in situ is experimentally challenging. The canonical oncogene, c-Src, is a lipid anchored protein that plays a key role in integrin-mediated signal transduction within focal adhesions and cell–cell junctions. Because of its activity in specific plasma membrane regions, structural motifs within the protein have been hypothesized to play an important role in its subcellular localization. This study used a combination of time-resolved fluorescence fluctuation spectroscopy and super-resolution microscopy to quantify the dynamic organization of c-Src in live cell membranes. Pulsed-interleaved excitation fluorescencemore » cross-correlation spectroscopy (PIE–FCCS) showed that a small fraction of c-Src transiently sorts into membrane clusters that are several times larger than the monomers. Photoactivated localization microscopy (PALM) confirmed that c-Src partitions into clusters with low probability and showed that the characteristic size of the clusters is 10–80 nm. Finally, time-resolved fluorescence anisotropy measurements were used to quantify the rotational mobility of c-Src to determine how it interacts with its local environment. Altogether, these results build a quantitative description of the mobility and clustering behavior of the c-Src nonreceptor tyrosine kinase in the live cell plasma membrane.« less

Dynamic organization of myristoylated Src in the live cell plasma membrane

DOE PAGES

Smith, Adam W.; Huang, Hector H.; Endres, Nicholas F.; ...

2016-01-15

The spatial organization of lipid-anchored proteins in the plasma membrane directly influences cell signaling, but measuring such organization in situ is experimentally challenging. The canonical oncogene, c-Src, is a lipid anchored protein that plays a key role in integrin-mediated signal transduction within focal adhesions and cell–cell junctions. Because of its activity in specific plasma membrane regions, structural motifs within the protein have been hypothesized to play an important role in its subcellular localization. This study used a combination of time-resolved fluorescence fluctuation spectroscopy and super-resolution microscopy to quantify the dynamic organization of c-Src in live cell membranes. Pulsed-interleaved excitation fluorescencemore » cross-correlation spectroscopy (PIE–FCCS) showed that a small fraction of c-Src transiently sorts into membrane clusters that are several times larger than the monomers. Photoactivated localization microscopy (PALM) confirmed that c-Src partitions into clusters with low probability and showed that the characteristic size of the clusters is 10–80 nm. Finally, time-resolved fluorescence anisotropy measurements were used to quantify the rotational mobility of c-Src to determine how it interacts with its local environment. Altogether, these results build a quantitative description of the mobility and clustering behavior of the c-Src nonreceptor tyrosine kinase in the live cell plasma membrane.« less

Fine- and hyperfine-structure effects in molecular photoionization. I. General theory and direct photoionization.

PubMed

Germann, Matthias; Willitsch, Stefan

2016-07-28

We develop a model for predicting fine- and hyperfine intensities in the direct photoionization of molecules based on the separability of electron and nuclear spin states from vibrational-electronic states. Using spherical tensor algebra, we derive highly symmetrized forms of the squared photoionization dipole matrix elements from which we derive the salient selection and propensity rules for fine- and hyperfine resolved photoionizing transitions. Our theoretical results are validated by the analysis of the fine-structure resolved photoelectron spectrum of O2 reported by Palm and Merkt [Phys. Rev. Lett. 81, 1385 (1998)] and are used for predicting hyperfine populations of molecular ions produced by photoionization.

Spatially resolved density and ionization measurements of shocked foams using x-ray fluorescence

DOE Office of Scientific and Technical Information (OSTI.GOV)

MacDonald, M. J.; Keiter, P. A.; Montgomery, D. S.

2016-09-22

We present experiments at the Trident laser facility demonstrating the use of x-ray fluorescence (XRF) to simultaneously measure density, ionization state populations, and electron temperature in shocked foams. An imaging x-ray spectrometer was used to obtain spatially-resolved measurements of Ti K-more » $$\\alpha$$ emission. Density profiles were measured from K-$$\\alpha$$ intensity. Ti ionization state distributions and electron temperatures were inferred by fitting K-$$\\alpha$$ spectra to spectra from CRETIN simulations. This study shows that XRF provides a powerful tool to complement other diagnostics to make equation of state measurements of shocked materials containing a suitable tracer element.« less

Calibration of a time-resolved hard-x-ray detector using radioactive sources

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stoeckl, C., E-mail: csto@lle.rochester.edu; Theobald, W.; Regan, S. P.

A four-channel, time-resolved, hard x-ray detector (HXRD) has been operating at the Laboratory for Laser Energetics for more than a decade. The slope temperature of the hot-electron population in direct-drive inertial confinement fusion experiments is inferred by recording the hard x-ray radiation generated in the interaction of the electrons with the target. Measuring the energy deposited by hot electrons requires an absolute calibration of the hard x-ray detector. A novel method to obtain an absolute calibration of the HXRD using single photons from radioactive sources was developed, which uses a thermoelectrically cooled, low-noise, charge-sensitive amplifier.

Isolation of a novel cell wall architecture mutant of rice with defective Arabidopsis COBL4 ortholog BC1 required for regulated deposition of secondary cell wall components.

PubMed

Sato, Kanna; Suzuki, Ryu; Nishikubo, Nobuyuki; Takenouchi, Sachi; Ito, Sachiko; Nakano, Yoshimi; Nakaba, Satoshi; Sano, Yuzou; Funada, Ryo; Kajita, Shinya; Kitano, Hidemi; Katayama, Yoshihiro

2010-06-01

The plant secondary cell wall is a highly ordered structure composed of various polysaccharides, phenolic components and proteins. Its coordinated regulation of a number of complex metabolic pathways and assembly has not been resolved. To understand the molecular mechanisms that regulate secondary cell wall synthesis, we isolated a novel rice mutant, cell wall architecture1 (cwa1), that exhibits an irregular thickening pattern in the secondary cell wall of sclerenchyma, as well as culm brittleness and reduced cellulose content in mature internodes. Light and transmission electron microscopy revealed that the cwa1 mutant plant has regions of local aggregation in the secondary cell walls of the cortical fibers in its internodes, showing uneven thickness. Ultraviolet microscopic observation indicated that localization of cell wall phenolic components was perturbed and that these components abundantly deposited at the aggregated cell wall regions in sclerenchyma. Therefore, regulation of deposition and assembly of secondary cell wall materials, i.e. phenolic components, appear to be disturbed by mutation of the cwa1 gene. Genetic analysis showed that cwa1 is allelic to brittle culm1 (bc1), which encodes the glycosylphosphatidylinositol-anchored COBRA-like protein specifically in plants. BC1 is known as a regulator that controls the culm mechanical strength and cellulose content in the secondary cell walls of sclerenchyma, but the precise function of BC1 has not been resolved. Our results suggest that CWA1/BC1 has an essential role in assembling cell wall constituents at their appropriate sites, thereby enabling synthesis of solid and flexible internodes in rice.

Depletion of pro-inflammatory CD161(+) double negative (CD3(+)CD4(-)CD8(-)) T cells in AIDS patients is ameliorated by expansion of the γδ T cell population.

PubMed

Singleterry, Will L; Henderson, Harold; Cruse, Julius M

2012-02-01

In this present investigation, flow cytometry was utilized to evaluate 13 healthy controls and 31 HIV-1 infected patients who had advanced to the AIDS stage of infection (CD4 count below 200 cells/mm(3)), for the expression of CD161 on CD3(+) double negative (DN) (CD3(+)CD4(-)CD8(-)) T cells, CD4(+) T cells, CD8(+) T cells and γδ T cells. The observed depletion of CD161(+) T cells from peripheral circulation was due primarily to the loss of CD4(+)CD161(+) T cells; as these cells represented 8.67±0.74% of the total healthy control peripheral T cell population, while the CD4(+)CD161(+) T cells of the AIDS group represented only 3.35±0.41% (p=<0.0001) of the total peripheral T cell population. We have also shown here that the DN T cell population was more than doubled in the AIDS group, with the DN T cell population expanding from 3.29±0.45% of the healthy control peripheral T cell population to 8.64±1.16% (p=0.0001) of the AIDS group peripheral T cell population. By evaluating the expression of CD161 on the surface of the DN T cells we showed that within the healthy control group, 47.4±4.99% of the DN T cells were positive for the expression of CD161, while only 26.4±3.54% (p=0.002) of the AIDS group's DN T cells expressed CD161. Despite CD161 expression being halved on the DN T cells of the AIDS group, when we compared the total peripheral T cell percentage of CD161(+) DN T cells between the healthy control group and the AIDS group, there was no statistical difference. Even though only 26.4% DN T cells within the AIDS group were positive for CD161(+), the overall DN T cell population had expanded to such an extent that there was no statistical difference between the groups with regard to CD161(+) DN T cells as a percentage of the total peripheral T cell population. Furthermore, we showed that within the DN T cell population, there was an approximate 2:1 ratio of γδ to αβ T cells, and this ratio was maintained in both the healthy control group and the AIDS group. While evaluating γδ T cells we also discovered that CD8(+) γδ T cells were expanded from 0.62±.09% of the healthy control peripheral T cell population to 5.01±.88% (p=<0.0001) of the peripheral T cell population of the AIDS group; and that this population of CD8(+) γδ T cells underwent the same reduction in percentage of cells expressing CD161(+), further demonstrated that the phenomenon of CD161(+) percentage reduction and compensatory increase in total cell population was affecting the entire circulating γδ T cell population. Copyright © 2011 Elsevier Inc. All rights reserved.

Highly sensitive detection of human papillomavirus type 16 DNA using time-resolved fluorescence microscopy and long lifetime probes

NASA Astrophysics Data System (ADS)

Wang, Xue F.; Periasamy, Ammasi; Wodnicki, Pawel; Siadat-Pajouh, M.; Herman, Brian

1995-04-01

We have been interested in the role of Human Papillomavirus (HPV) in cervical cancer and its diagnosis; to that end we have been developing microscopic imaging and fluorescent in situ hybridization (FISH) techniques to genotype and quantitate the amount of HPV present at a single cell level in cervical PAP smears. However, we have found that low levels of HPV DNA are difficult to detect accurately because theoretically obtainable sensitivity is never achieved due to nonspecific autofluorescence, fixative induced fluorescence of cells and tissues, and autofluorescence of the optical components in the microscopic system. In addition, the absorption stains used for PAP smears are intensely autofluorescent. Autofluorescence is a rapidly decaying process with lifetimes in the range of 1-100 nsec, whereas phosphorescence and delayed fluorescence have lifetimes in the range of 1 microsecond(s) ec-10 msec. The ability to discriminate between specific fluorescence and autofluorescence in the time-domain has improved the sensitivity of diagnostic test such that they perform comparably to, or even more sensitive than radioisotopic assays. We have developed a novel time-resolved fluorescence microscope to improve the sensitivity of detection of specific molecules of interest in slide based specimens. This time-resolved fluorescence microscope is based on our recently developed fluorescence lifetime imaging microscopy (FILM) in conjunction with the use of long lifetime fluorescent labels. By using fluorescence in situ hybridization and the long lifetime probe (europium), we have demonstrated the utility of this technique for detection of HPV DNA in cervicovaginal cells. Our results indicate that the use of time-resolved fluorescence microscopy and long lifetime probes increases the sensitivity of detection by removing autofluorescence and will thus lead to improved early diagnosis of cervical cancer. Since the highly sensitive detection of DNA in clinical samples using fluorescence in situ hybridization image is useful for the diagnosis of many other type of diseases, the system we have developed should find numerous applications for the diagnosis of disease states.

Micro-optical coherence tomography of the mammalian cochlea

PubMed Central

Iyer, Janani S.; Batts, Shelley A.; Chu, Kengyeh K.; Sahin, Mehmet I.; Leung, Hui Min; Tearney, Guillermo J.; Stankovic, Konstantina M.

2016-01-01

The mammalian cochlea has historically resisted attempts at high-resolution, non-invasive imaging due to its small size, complex three-dimensional structure, and embedded location within the temporal bone. As a result, little is known about the relationship between an individual’s cochlear pathology and hearing function, and otologists must rely on physiological testing and imaging methods that offer limited resolution to obtain information about the inner ear prior to performing surgery. Micro-optical coherence tomography (μOCT) is a non-invasive, low-coherence interferometric imaging technique capable of resolving cellular-level anatomic structures. To determine whether μOCT is capable of resolving mammalian intracochlear anatomy, fixed guinea pig inner ears were imaged as whole temporal bones with cochlea in situ. Anatomical structures such as the tunnel of Corti, space of Nuel, modiolus, scalae, and cell groupings were visualized, in addition to individual cell types such as neuronal fibers, hair cells, and supporting cells. Visualization of these structures, via volumetrically-reconstructed image stacks and endoscopic perspective videos, represents an improvement over previous efforts using conventional OCT. These are the first μOCT images of mammalian cochlear anatomy, and they demonstrate μOCT’s potential utility as an imaging tool in otology research. PMID:27633610

Highly luminescent, biocompatible ytterbium(iii) complexes as near-infrared fluorophores for living cell imaging.

PubMed

Ning, Yingying; Tang, Juan; Liu, Yi-Wei; Jing, Jing; Sun, Yuansheng; Zhang, Jun-Long

2018-04-21

Herein, we report the design and synthesis of biocompatible Yb 3+ complexes for near-infrared (NIR) living cell imaging. Upon excitation at either the visible (Soret band) or red region (Q band), these β-fluorinated Yb 3+ complexes display high NIR luminescence (quantum yields up to 23% and 13% in dimethyl sulfoxide and water, respectively) and have higher stabilities and prolonged decay lifetimes (up to 249 μs) compared to the β-non-fluorinated counterparts. This renders the β-fluorinated Yb 3+ complexes as a new class of biological optical probes in both steady-state imaging and time-resolved fluorescence lifetime imaging (FLIM). NIR confocal fluorescence images showed strong and specific intracellular Yb 3+ luminescence signals when the biocompatible Yb 3+ complexes were uptaken into the living cells. Importantly, FLIM measurements showed an intracellular lifetime distribution between 100 and 200 μs, allowing an effective discrimination from cell autofluorescence, and afforded high signal-to-noise ratios as firstly demonstrated in the NIR region. These results demonstrated the prospects of NIR lanthanide complexes as biological probes for NIR steady-state fluorescence and time-resolved fluorescence lifetime imaging.

Complete hydatidiform mole with a surviving coexistent twin in a woman with sickle cell disease: a case report.

PubMed

Mahmoud, Mohamad S; Merhi, Zaher

2007-06-01

Twin pregnancy with an apparently healthy fetus and complete hydatidiform mole (CHMTF) is a rare condition. We present the first reported case in a woman with sickle cell disease. An 18-year-old woman, para 1, gravida 0, with sickle cell disease was diagnosed at 19 weeks as having a complete molar pregnancy with a coexistent live fetus. The patient presented with abdominal pain, nausea, headaches, body aches, joint pain and chest pain on 2 different occasions. She denied having vaginal bleeding. Whether the patient was having a sickle cell crisis or molar pregnancy symptoms (i.e., thyrotoxicosis) was not clear. She was given intravenous hydration and pain management. All her symptoms resolved, confirming sickle cell crisis as the final diagnosis. The pregnancy was uneventful until 35 weeks, when oligohydramnios prompted induction of labor. Suction curettage was performed after delivery for removal of the molar pregnancy. The patient did not show any evidence of persistent trophoblastic disease 2 months after delivery. CHMTF in sickle cell disease patients is challenging. Adequate intravenous hydration and pain management should be started when one suspects a crisis. If the symptoms resolved, thyrotoxicosis due to the molar pregnancy is unlikely. In addition to proper medical management, proper counseling of the patient and close monitoring of both fetus and mother should be undertaken.

Comparison of TiO₂ and ZnO solar cells sensitized with an indoline dye: time-resolved laser spectroscopy studies of partial charge separation processes.

PubMed

Sobuś, Jan; Burdziński, Gotard; Karolczak, Jerzy; Idígoras, Jesús; Anta, Juan A; Ziółek, Marcin

2014-03-11

Time-resolved laser spectroscopy techniques in the time range from femtoseconds to seconds were applied to investigate the charge separation processes in complete dye-sensitized solar cells (DSC) made with iodide/iodine liquid electrolyte and indoline dye D149 interacting with TiO2 or ZnO nanoparticles. The aim of the studies was to explain the differences in the photocurrents of the cells (3-4 times higher for TiO2 than for ZnO ones). Electrochemical impedance spectroscopy and nanosecond flash photolysis studies revealed that the better performance of TiO2 samples is not due to the charge collection and dye regeneration processes. Femtosecond transient absorption results indicated that after first 100 ps the number of photoinduced electrons in the semiconductor is 3 times higher for TiO2 than for ZnO solar cells. Picosecond emission studies showed that the lifetime of the D149 excited state is about 3 times longer for ZnO than for TiO2 samples. Therefore, the results indicate that lower performance of ZnO solar cells is likely due to slower electron injection. The studies show how to correlate the laser spectroscopy methodology with global parameters of the solar cells and should help in better understanding of the behavior of alternative materials for porous electrodes for DSC and related devices.

The orally active and bioavailable ATR kinase inhibitor AZD6738 potentiates the anti-tumor effects of cisplatin to resolve ATM-deficient non-small cell lung cancer in vivo.

PubMed

Vendetti, Frank P; Lau, Alan; Schamus, Sandra; Conrads, Thomas P; O'Connor, Mark J; Bakkenist, Christopher J

2015-12-29

ATR and ATM are DNA damage signaling kinases that phosphorylate several thousand substrates. ATR kinase activity is increased at damaged replication forks and resected DNA double-strand breaks (DSBs). ATM kinase activity is increased at DSBs. ATM has been widely studied since ataxia telangiectasia individuals who express no ATM protein are the most radiosensitive patients identified. Since ATM is not an essential protein, it is widely believed that ATM kinase inhibitors will be well-tolerated in the clinic. ATR has been widely studied, but advances have been complicated by the finding that ATR is an essential protein and it is widely believed that ATR kinase inhibitors will be toxic in the clinic. We describe AZD6738, an orally active and bioavailable ATR kinase inhibitor. AZD6738 induces cell death and senescence in non-small cell lung cancer (NSCLC) cell lines. AZD6738 potentiates the cytotoxicity of cisplatin and gemcitabine in NSCLC cell lines with intact ATM kinase signaling, and potently synergizes with cisplatin in ATM-deficient NSCLC cells. In contrast to expectations, daily administration of AZD6738 and ATR kinase inhibition for 14 consecutive days is tolerated in mice and enhances the therapeutic efficacy of cisplatin in xenograft models. Remarkably, the combination of cisplatin and AZD6738 resolves ATM-deficient lung cancer xenografts.

The role of cell size in density gradient electrophoretic separation of mouse leukemia cells according to position in the cell cycle

NASA Technical Reports Server (NTRS)

Plank, L. D.; Kunze, M. E.; Todd, P. W.

1985-01-01

Cultured mouse leukemia cells line L5178Y were subjected to upward electrophoresis in a density gradient and the slower migrating cell populations were enriched in G2 cells. It is indicated that this cell line does not change electrophoretic mobility through the cell cycle. The possibility that increased sedimentation downward on the part of the larger G2 cells caused this separation was explored. Two different cell populations were investigated. The log phase population was found to migrate upward faster than the G2 population, and a similar difference between their velocities and calculated on the basis of a 1 um diameter difference between the two cell populations. The G2 and G1 enriched populations were isolated by Ficoll density gradient sedimentation. The bottom fraction was enriched in G2 cells and the top fraction was enriched with G1 cells, especially when compared with starting materials. The electrophoretic mobilities of these two cell populations did not differ significantly from one another. Cell diameter dependent migration curves were calculated and were found to be different. Families of migration curves that differ when cell size is considered as a parameter are predicted.

Solving Navigational Uncertainty Using Grid Cells on Robots

PubMed Central

Milford, Michael J.; Wiles, Janet; Wyeth, Gordon F.

2010-01-01

To successfully navigate their habitats, many mammals use a combination of two mechanisms, path integration and calibration using landmarks, which together enable them to estimate their location and orientation, or pose. In large natural environments, both these mechanisms are characterized by uncertainty: the path integration process is subject to the accumulation of error, while landmark calibration is limited by perceptual ambiguity. It remains unclear how animals form coherent spatial representations in the presence of such uncertainty. Navigation research using robots has determined that uncertainty can be effectively addressed by maintaining multiple probabilistic estimates of a robot's pose. Here we show how conjunctive grid cells in dorsocaudal medial entorhinal cortex (dMEC) may maintain multiple estimates of pose using a brain-based robot navigation system known as RatSLAM. Based both on rodent spatially-responsive cells and functional engineering principles, the cells at the core of the RatSLAM computational model have similar characteristics to rodent grid cells, which we demonstrate by replicating the seminal Moser experiments. We apply the RatSLAM model to a new experimental paradigm designed to examine the responses of a robot or animal in the presence of perceptual ambiguity. Our computational approach enables us to observe short-term population coding of multiple location hypotheses, a phenomenon which would not be easily observable in rodent recordings. We present behavioral and neural evidence demonstrating that the conjunctive grid cells maintain and propagate multiple estimates of pose, enabling the correct pose estimate to be resolved over time even without uniquely identifying cues. While recent research has focused on the grid-like firing characteristics, accuracy and representational capacity of grid cells, our results identify a possible critical and unique role for conjunctive grid cells in filtering sensory uncertainty. We anticipate our study to be a starting point for animal experiments that test navigation in perceptually ambiguous environments. PMID:21085643

Calcium channel blockers ameliorate iron overload-associated hepatic fibrosis by altering iron transport and stellate cell apoptosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Ying

Liver fibrosis is the principal cause of morbidity and mortality in patients with iron overload. Calcium channel blockers (CCBs) can antagonize divalent cation entry into renal and myocardial cells and inhibit fibrogenic gene expression. We investigated the potential of CCBs to resolve iron overload-associated hepatic fibrosis. Kunming mice were assigned to nine groups (n = 8 per group): control, iron overload, deferoxamine, high and low dose verapamil, high and low dose nimodipine, and high and low dose diltiazem. Iron deposition and hepatic fibrosis were measured in mouse livers. Expression levels of molecules associated with transmembrane iron transport were determined bymore » molecular biology approaches. In vitro HSC-T6 cells were randomized into nine groups (the same groups as the mice). Changes in proliferation, apoptosis, and metalloproteinase expression in cells were detected to assess the anti-fibrotic effects of CCBs during iron overload conditions. We found that CCBs reduced hepatic iron content, intracellular iron deposition, the number of hepatic fibrotic areas, collagen expression levels, and hydroxyproline content. CCBs rescued abnormal expression of α1C protein in L-type voltage-dependent calcium channel (LVDCC) and down-regulated divalent metal transporter-1 (DMT-1) expression in mouse livers. In iron-overloaded HSC-T6 cells, CCBs reduced iron deposition, inhibited proliferation, induced apoptosis, and elevated expression of matrix metalloproteinase-13 (MMP-13) and tissue inhibitor of metalloproteinase-1 (TIMP-1). CCBs are potential therapeutic agents that can be used to address hepatic fibrosis during iron overload. They resolve hepatic fibrosis probably correlated with regulating transmembrane iron transport and inhibiting HSC growth. - Highlights: • Calcium channel blockers (CCBs) reduced hepatic iron content. • CCBs decreased hepatic fibrotic areas and collagen expression levels. • CCBs resolve fibrosis by regulating iron transport and inhibiting HSC growth.« less

Breakdown voltage mapping through voltage dependent ReBEL intensity imaging of multi-crystalline Si solar cells

NASA Astrophysics Data System (ADS)

Dix-Peek, RM.; van Dyk, EE.; Vorster, FJ.; Pretorius, CJ.

2018-04-01

Device material quality affects both the efficiency and the longevity of photovoltaic (PV) cells. Therefore, identifying these defects can be beneficial in the development of more efficient and longer lasting PV cells. In this study, a combination of spatially-resolved, electroluminescence (EL), and light beam induced current (LBIC) measurements, were used to identify specific defects and features of a multi-crystalline Si PV cells. In this study, a novel approach is used to map the breakdown voltage of a PV cell through voltage dependent Reverse Bias EL (ReBEL) intensity imaging.

Isolation and culture of human multipotent stromal cells from the pancreas.

PubMed

Seeberger, Karen L; Eshpeter, Alana; Korbutt, Gregory S

2011-01-01

Mesenchymal stem cells, also termed multipotent mesenchymal stromal cells (MSCs), can be isolated from most adult tissues. Although the exact origin of MSCs expanded from the human pancreas has not been resolved, we have developed protocols to isolate and expand MSCs from human pancreatic tissue that remains after islet procurement. Similar to techniques used to isolate MSCs from bone marrow, pancreatic MSCs are isolated based on their cell adherence, expression of several cell surface antigens, and multilineage differentiation. The protocols for isolating, characterizing, and differentiating MSCs from the pancreas are presented in this chapter.

Human Leukocyte Antigen Typing Using a Knowledge Base Coupled with a High-Throughput Oligonucleotide Probe Array Analysis

PubMed Central

Zhang, Guang Lan; Keskin, Derin B.; Lin, Hsin-Nan; Lin, Hong Huang; DeLuca, David S.; Leppanen, Scott; Milford, Edgar L.; Reinherz, Ellis L.; Brusic, Vladimir

2014-01-01

Human leukocyte antigens (HLA) are important biomarkers because multiple diseases, drug toxicity, and vaccine responses reveal strong HLA associations. Current clinical HLA typing is an elimination process requiring serial testing. We present an alternative in situ synthesized DNA-based microarray method that contains hundreds of thousands of probes representing a complete overlapping set covering 1,610 clinically relevant HLA class I alleles accompanied by computational tools for assigning HLA type to 4-digit resolution. Our proof-of-concept experiment included 21 blood samples, 18 cell lines, and multiple controls. The method is accurate, robust, and amenable to automation. Typing errors were restricted to homozygous samples or those with very closely related alleles from the same locus, but readily resolved by targeted DNA sequencing validation of flagged samples. High-throughput HLA typing technologies that are effective, yet inexpensive, can be used to analyze the world’s populations, benefiting both global public health and personalized health care. PMID:25505899

High-definition reconstruction of clonal composition in cancer.

PubMed

Fischer, Andrej; Vázquez-García, Ignacio; Illingworth, Christopher J R; Mustonen, Ville

2014-06-12

The extensive genetic heterogeneity of cancers can greatly affect therapy success due to the existence of subclonal mutations conferring resistance. However, the characterization of subclones in mixed-cell populations is computationally challenging due to the short length of sequence reads that are generated by current sequencing technologies. Here, we report cloneHD, a probabilistic algorithm for the performance of subclone reconstruction from data generated by high-throughput DNA sequencing: read depth, B-allele counts at germline heterozygous loci, and somatic mutation counts. The algorithm can exploit the added information present in correlated longitudinal or multiregion samples and takes into account correlations along genomes caused by events such as copy-number changes. We apply cloneHD to two case studies: a breast cancer sample and time-resolved samples of chronic lymphocytic leukemia, where we demonstrate that monitoring the response of a patient to therapy regimens is feasible. Our work provides new opportunities for tracking cancer development. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Two types of amorphous protein particles facilitate crystal nucleation.

PubMed

Yamazaki, Tomoya; Kimura, Yuki; Vekilov, Peter G; Furukawa, Erika; Shirai, Manabu; Matsumoto, Hiroaki; Van Driessche, Alexander E S; Tsukamoto, Katsuo

2017-02-28

Nucleation, the primary step in crystallization, dictates the number of crystals, the distribution of their sizes, the polymorph selection, and other crucial properties of the crystal population. We used time-resolved liquid-cell transmission electron microscopy (TEM) to perform an in situ examination of the nucleation of lysozyme crystals. Our TEM images revealed that mesoscopic clusters, which are similar to those previously assumed to consist of a dense liquid and serve as nucleation precursors, are actually amorphous solid particles (ASPs) and act only as heterogeneous nucleation sites. Crystalline phases never form inside them. We demonstrate that a crystal appears within a noncrystalline particle assembling lysozyme on an ASP or a container wall, highlighting the role of heterogeneous nucleation. These findings represent a significant departure from the existing formulation of the two-step nucleation mechanism while reaffirming the role of noncrystalline particles. The insights gained may have significant implications in areas that rely on the production of protein crystals, such as structural biology, pharmacy, and biophysics, and for the fundamental understanding of crystallization mechanisms.

Odor identity coding by distributed ensembles of neurons in the mouse olfactory cortex

PubMed Central

Roland, Benjamin; Deneux, Thomas; Franks, Kevin M; Bathellier, Brice; Fleischmann, Alexander

2017-01-01

Olfactory perception and behaviors critically depend on the ability to identify an odor across a wide range of concentrations. Here, we use calcium imaging to determine how odor identity is encoded in olfactory cortex. We find that, despite considerable trial-to-trial variability, odor identity can accurately be decoded from ensembles of co-active neurons that are distributed across piriform cortex without any apparent spatial organization. However, piriform response patterns change substantially over a 100-fold change in odor concentration, apparently degrading the population representation of odor identity. We show that this problem can be resolved by decoding odor identity from a subpopulation of concentration-invariant piriform neurons. These concentration-invariant neurons are overrepresented in piriform cortex but not in olfactory bulb mitral and tufted cells. We therefore propose that distinct perceptual features of odors are encoded in independent subnetworks of neurons in the olfactory cortex. DOI: http://dx.doi.org/10.7554/eLife.26337.001 PMID:28489003

Biology and management of transient abnormal myelopoiesis (TAM) in children with Down syndrome.

PubMed

Roy, Anindita; Roberts, Irene; Vyas, Paresh

2012-08-01

Children with Down syndrome (DS) have an increased risk of Acute Myeloid Leukaemia (ML-DS), particularly megakaryoblastic leukaemia, which is clonally -related to the neonatal myeloproliferative syndrome, Transient Abnormal Myelopoiesis (TAM) unique to infants with DS. Molecular, biological, and clinical data indicate that TAM is initiated before birth when fetal liver haematopoietic cells trisomic for chromosome 21 acquire mutations in GATA1. TAM usually resolves spontaneously by 6 months; however 20-30% subsequently develop ML-DS harbouring the same GATA1 mutation(s). This review focuses on recent studies describing haematological, clinical and biological features of TAM and discusses approaches to diagnose, treat and monitor minimal residual disease in TAM. An important unanswered question is whether ML-DS is always preceded by TAM as it may be clinically and possibly haematologically 'silent'. We have briefly discussed the role of population-based screening for TAM and development of treatment strategies to eliminate the preleukaemic TAM clone, thereby preventing ML-DS. Copyright © 2012 Elsevier Ltd. All rights reserved.

Imaging electronic trap states in perovskite thin films with combined fluorescence and femtosecond transient absorption microscopy

DOE PAGES

Xiao, Kai; Ma, Ying -Zhong; Simpson, Mary Jane; ...

2016-04-22

Charge carrier trapping degrades the performance of organometallic halide perovskite solar cells. To characterize the locations of electronic trap states in a heterogeneous photoactive layer, a spatially resolved approach is essential. Here, we report a comparative study on methylammonium lead tri-iodide perovskite thin films subject to different thermal annealing times using a combined photoluminescence (PL) and femtosecond transient absorption microscopy (TAM) approach to spatially map trap states. This approach coregisters the initially populated electronic excited states with the regions that recombine radiatively. Although the TAM images are relatively homogeneous for both samples, the corresponding PL images are highly structured. Themore » remarkable variation in the PL intensities as compared to transient absorption signal amplitude suggests spatially dependent PL quantum efficiency, indicative of trapping events. Furthermore, detailed analysis enables identification of two trapping regimes: a densely packed trapping region and a sparse trapping area that appear as unique spatial features in scaled PL maps.« less

Spatially- and Temporally-Resolved Measurements of Roadway Air Pollution Using a Zero-Emission Electric Vehicle

EPA Science Inventory

Vehicle-related air pollution has an intrinsically dynamic nature. Recent field measurements and modeling work have demonstrated that near-road topography may modify levels of air pollutants reaching populations residing and working in close proximity to roadways. However, the ma...

A research perspective on white-tailed deer overabundance in the northeastern United States

Treesearch

William M. Healy; David S. deCalesta; Susan L. Stout

1997-01-01

Resolving issues of deer (Odocoileus spp.) over-abundance will require gaining more reliable knowledge about their role in ecosystem dynamics. Science can contribute by advancing knowledge in 4 overlapping spheres of research: model development, measurement techniques, population management, and human behavior.

Clinical Outcomes of Transplanted Modified Bone Marrow-Derived Mesenchymal Stem Cells in Stroke: A Phase 1/2a Study.

PubMed

Steinberg, Gary K; Kondziolka, Douglas; Wechsler, Lawrence R; Lunsford, L Dade; Coburn, Maria L; Billigen, Julia B; Kim, Anthony S; Johnson, Jeremiah N; Bates, Damien; King, Bill; Case, Casey; McGrogan, Michael; Yankee, Ernest W; Schwartz, Neil E

2016-07-01

Preclinical data suggest that cell-based therapies have the potential to improve stroke outcomes. Eighteen patients with stable, chronic stroke were enrolled in a 2-year, open-label, single-arm study to evaluate the safety and clinical outcomes of surgical transplantation of modified bone marrow-derived mesenchymal stem cells (SB623). All patients in the safety population (N=18) experienced at least 1 treatment-emergent adverse event. Six patients experienced 6 serious treatment-emergent adverse events; 2 were probably or definitely related to surgical procedure; none were related to cell treatment. All serious treatment-emergent adverse events resolved without sequelae. There were no dose-limiting toxicities or deaths. Sixteen patients completed 12 months of follow-up at the time of this analysis. Significant improvement from baseline (mean) was reported for: (1) European Stroke Scale: mean increase 6.88 (95% confidence interval, 3.5-10.3; P<0.001), (2) National Institutes of Health Stroke Scale: mean decrease 2.00 (95% confidence interval, -2.7 to -1.3; P<0.001), (3) Fugl-Meyer total score: mean increase 19.20 (95% confidence interval, 11.4-27.0; P<0.001), and (4) Fugl-Meyer motor function total score: mean increase 11.40 (95% confidence interval, 4.6-18.2; P<0.001). No changes were observed in modified Rankin Scale. The area of magnetic resonance T2 fluid-attenuated inversion recovery signal change in the ipsilateral cortex 1 week after implantation significantly correlated with clinical improvement at 12 months (P<0.001 for European Stroke Scale). In this interim report, SB623 cells were safe and associated with improvement in clinical outcome end points at 12 months. URL: https://www.clinicaltrials.gov. Unique identifier: NCT01287936. © 2016 American Heart Association, Inc.

Atomic Force Microscopy in Imaging of Viruses and Virus-Infected Cells

PubMed Central

Kuznetsov, Yurii G.; McPherson, Alexander

2011-01-01

Summary: Atomic force microscopy (AFM) can visualize almost everything pertinent to structural virology and at resolutions that approach those for electron microscopy (EM). Membranes have been identified, RNA and DNA have been visualized, and large protein assemblies have been resolved into component substructures. Capsids of icosahedral viruses and the icosahedral capsids of enveloped viruses have been seen at high resolution, in some cases sufficiently high to deduce the arrangement of proteins in the capsomeres as well as the triangulation number (T). Viruses have been recorded budding from infected cells and suffering the consequences of a variety of stresses. Mutant viruses have been examined and phenotypes described. Unusual structural features have appeared, and the unexpectedly great amount of structural nonconformity within populations of particles has been documented. Samples may be imaged in air or in fluids (including culture medium or buffer), in situ on cell surfaces, or after histological procedures. AFM is nonintrusive and nondestructive, and it can be applied to soft biological samples, particularly when the tapping mode is employed. In principle, only a single cell or virion need be imaged to learn of its structure, though normally images of as many as is practical are collected. While lateral resolution, limited by the width of the cantilever tip, is a few nanometers, height resolution is exceptional, at approximately 0.5 nm. AFM produces three-dimensional, topological images that accurately depict the surface features of the virus or cell under study. The images resemble common light photographic images and require little interpretation. The structures of viruses observed by AFM are consistent with models derived by X-ray crystallography and cryo-EM. PMID:21646429

On the formation of anions: frequency-, angle-, and time-resolved photoelectron imaging of the menadione radical anion† †Electronic supplementary information (ESI) available: A summary of the ground-state geometries and molecular orbitals from the ab initio calculations; fitted residuals from the FA-PI simulation; plots of all spectra included in the frequency-resolved two-dimensional figure; and example time-resolved PE spectra from the 3.10 + 1.55 eV pump-probe experiments. See DOI: 10.1039/c4sc03491k Click here for additional data file.

PubMed Central

Bull, James N.; West, Christopher W.

2015-01-01

Frequency-, angle-, and time-resolved photoelectron imaging of gas-phase menadione (vitamin K3) radical anions was used to show that quasi-bound resonances of the anion can act as efficient doorway states to produce metastable ground electronic state anions on a sub-picosecond timescale. Several anion resonances have been experimentally observed and identified with the assistance of ab initio calculations, and ground state anion recovery was observed across the first 3 eV above threshold. Time-resolved measurements revealed the mechanism of electronic ground state anion formation, which first involves a cascade of very fast internal conversion processes to a bound electronic state that, in turn, decays by slower internal conversion to the ground state. Autodetachment processes from populated resonances are inefficient compared with electronic relaxation through internal conversion. The mechanistic understanding gained provides insight into the formation of radical anions in biological and astrochemical systems. PMID:29560245

Phospho-Bcl-xL(Ser62) influences spindle assembly and chromosome segregation during mitosis.

PubMed

Wang, Jianfang; Beauchemin, Myriam; Bertrand, Richard

2014-01-01

Functional analysis of a series of phosphorylation mutants reveals that Bcl-xL(Ser62Ala) influences cell entry into anaphase and mitotic exit in taxol-exposed cells compared with cells expressing wild-type Bcl-xL or a series of other phosphorylation mutants, an effect that appears to be independent of its anti-apoptotic activity. During normal mitosis progression, Bcl-xL(Ser62) is strongly phosphorylated by PLK1 and MAPK14/SAPKp38α at the prometaphase, metaphase, and the anaphase boundaries, while it is de-phosphorylated at telophase and cytokinesis. Phospho-Bcl-xL(Ser62) localizes in centrosomes with γ-tubulin and in the mitotic cytosol with some spindle-assembly checkpoint signaling components, including PLK1, BubR1, and Mad2. In taxol- and nocodazole-exposed cells, phospho-Bcl-xL(Ser62) also binds to Cdc20- Mad2-, BubR1-, and Bub3-bound complexes, while Bcl-xL(Ser62Ala) does not. Silencing Bcl-xL expression and expressing the phosphorylation mutant Bcl-xL(Ser62Ala) lead to an increased number of cells harboring mitotic spindle defects including multipolar spindle, chromosome lagging and bridging, aneuploidy with micro-, bi-, or multi-nucleated cells, and cells that fail to resolve undergo mitosis within 6 h. Together, the data indicate that during mitosis, Bcl-xL(Ser62) phosphorylation impacts on spindle assembly and chromosome segregation, influencing chromosome stability. Observations of mitotic cells harboring aneuploidy with micro-, bi-, or multi-nucleated cells, and cells that fail to resolve undergo mitosis within 6 h were also made with cells expressing the phosphorylation mutant Bcl-xL(Ser49Ala) and dual mutant Bcl-xL(Ser49/62Ala).

The blood-brain barrier internalises Cryptococcus neoformans via the EphA2-tyrosine kinase receptor.

PubMed

Aaron, Phylicia A; Jamklang, Mantana; Uhrig, John P; Gelli, Angie

2018-03-01

Cryptococcus neoformans is an opportunistic fungal pathogen that causes life-threatening meningitis most commonly in populations with impaired immunity. Here, we resolved the transcriptome of the human brain endothelium challenged with C. neoformans to establish whether C. neoformans invades the CNS by co-opting particular signalling pathways as a means to promote its own entry. Among the 5 major pathways targeted by C. neoformans, the EPH-EphrinA1 (EphA2) tyrosine kinase receptor-signalling pathway was examined further. Silencing the EphA2 receptor transcript in a human brain endothelial cell line or blocking EphA2 activity with an antibody or chemical inhibitor prevented transmigration of C. neoformans in an in vitro model of the blood-brain barrier (BBB). In contrast, treating brain endothelial cells with an EphA2 chemical agonist or an EphA2 ligand promoted greater migration of fungal cells across the BBB. C. neoformans activated the EPH-tyrosine kinase pathway through a CD44-dependent phosphorylation of EphA2, promoting clustering and internalisation of EphA2 receptors. Moreover, HEK293T cells expressing EphA2 revealed an association between EphA2 and C. neoformans that boosted internalisation of C. neoformans. Collectively, the results suggest that C. neoformans promotes EphA2 activity via CD44, and this in turn creates a permeable barrier that facilitates the migration of C. neoformans across the BBB. © 2017 John Wiley & Sons Ltd.

Quantitative Fluorescence Studies in Living Cells: Extending Fluorescence Fluctuation Spectroscopy to Peripheral Membrane Proteins

NASA Astrophysics Data System (ADS)

Smith, Elizabeth Myhra

The interactions of peripheral membrane proteins with both membrane lipids and proteins are vital for many cellular processes including membrane trafficking, cellular signaling, and cell growth/regulation. Building accurate biophysical models of these processes requires quantitative characterization of the behavior of peripheral membrane proteins, yet methods to quantify their interactions inside living cells are very limited. Because peripheral membrane proteins usually exist both in membrane-bound and cytoplasmic forms, the separation of these two populations is a key challenge. This thesis aims at addressing this challenge by extending fluorescence fluctuation spectroscopy (FFS) to simultaneously measure the oligomeric state of peripheral membrane proteins in the cytoplasm and at the plasma membrane. We developed a new method based on z-scan FFS that accounts for the fluorescence contributions from cytoplasmic and membrane layers by incorporating a fluorescence intensity z-scan through the cell. H-Ras-EGFP served as a model system to demonstrate the feasibility of the technique. The resolvability and stability of z-scanning was determined as well as the oligomeric state of H-Ras-EGFP at the plasma membrane and in the cytoplasm. Further, we successfully characterized the binding affinity of a variety of proteins to the plasma membrane by quantitative analysis of the z-scan fluorescence intensity profile. This analysis method, which we refer to as z-scan fluorescence profile deconvoution, was further used in combination with dual-color competition studies to determine the lipid specificity of protein binding. Finally, we applied z-scan FFS to provide insight into the early assembly steps of the HTLV-1 retrovirus.

Method for rapid isolation of sensitive mutants

DOEpatents

Freyer, James P.

1997-01-01

Sensitive mammalian cell mutants are rapidly isolated using flow cytometry. A first population of clonal spheroids is established to contain both normal and mutant cells. The population may be naturally occurring or may arise from mutagenized cells. The first population is then flow sorted by size to obtain a second population of clonal spheroids of a first uniform size. The second population is then exposed to a DNA-damaging agent that is being investigated. The exposed second population is placed in a growth medium to form a third population of clonal spheroids comprising spheroids of increased size from the mammalian cells that are resistant to the DNA-damaging agent and spheroids of substantially the first uniform size formed from the mammalian cells that are sensitive to the DNA-damaging agent. The third population is not flow sorted to differentiate the spheroids formed from resistant mammalian cells from spheroids formed from sensitive mammalian cells. The spheroids formed from sensitive mammalian cells are now treated to recover viable sensitive cells from which a sensitive cell line can be cloned.

Method for rapid isolation of sensitive mutants

DOEpatents

Freyer, J.P.

1997-07-29

Sensitive mammalian cell mutants are rapidly isolated using flow cytometry. A first population of clonal spheroids is established to contain both normal and mutant cells. The population may be naturally occurring or may arise from mutagenized cells. The first population is then flow sorted by size to obtain a second population of clonal spheroids of a first uniform size. The second population is then exposed to a DNA-damaging agent that is being investigated. The exposed second population is placed in a growth medium to form a third population of clonal spheroids comprising spheroids of increased size from the mammalian cells that are resistant to the DNA-damaging agent and spheroids of substantially the first uniform size formed from the mammalian cells that are sensitive to the DNA-damaging agent. The third population is not flow sorted to differentiate the spheroids formed from resistant mammalian cells from spheroids formed from sensitive mammalian cells. The spheroids formed from sensitive mammalian cells are now treated to recover viable sensitive cells from which a sensitive cell line can be cloned. 15 figs.

Internalization of aggregated photosensitizers by tumor cells: subcellular time-resolved fluorescence spectroscopy on derivatives of pyropheophorbide-a ethers and chlorin e6 under femtosecond one- and two-photon excitations.

PubMed

Kelbauskas, L; Dietel, W

2002-12-01

Amphiphilic sensitizers self-associate in aqueous environments and form aggregated species that exhibit no or only negligible photodynamic activity. However, amphiphilic photosensitizers number among the most potent agents of photodynamic therapy. The processes by which these sensitizers are internalized into tumor cells have yet to be fully elucidated and thus remain the subject of debate. In this study the uptake of photosensitizer aggregates into tumor cells was examined directly using subcellular time-resolved fluorescence spectroscopy with a high temporal resolution (20-30 ps) and high sensitivity (time-correlated single-photon counting). The investigations were performed on selected sensitizers that exhibit short fluorescence decay times (< 50 ps) in aggregated form. Derivatives of pyropheophorbide-a ether and chlorin e6 with varying lipophilicity were used for the study. The characteristic fluorescence decay times and spectroscopic features of the sensitizer aggregates measured in aqueous solution also could be observed in A431 human endothelial carcinoma cells administered with these photosensitizers. This shows that tumor cells can internalize sensitizers in aggregated form. Uptake of aggregates and their monomerization inside cells were demonstrated directly for the first time by means of fluorescence lifetime imaging with a high temporal resolution. Internalization of the aggregates seems to be endocytosis mediated. The degree of their monomerization in tumor cells is strongly influenced by the lipophilicity of the compounds.

Time-resolved photoelectron spectroscopy of IR-driven electron dynamics in a charge transfer model system.

PubMed

Falge, Mirjam; Fröbel, Friedrich Georg; Engel, Volker; Gräfe, Stefanie

2017-08-02

If the adiabatic approximation is valid, electrons smoothly adapt to molecular geometry changes. In contrast, as a characteristic of diabatic dynamics, the electron density does not follow the nuclear motion. Recently, we have shown that the asymmetry in time-resolved photoelectron spectra serves as a tool to distinguish between these dynamics [Falge et al., J. Phys. Chem. Lett., 2012, 3, 2617]. Here, we investigate the influence of an additional, moderately intense infrared (IR) laser field, as often applied in attosecond time-resolved experiments, on such asymmetries. This is done using a simple model for coupled electronic-nuclear motion. We calculate time-resolved photoelectron spectra and their asymmetries and demonstrate that the spectra directly map the bound electron-nuclear dynamics. From the asymmetries, we can trace the IR field-induced population transfer and both the field-driven and intrinsic (non-)adiabatic dynamics. This holds true when considering superposition states accompanied by electronic coherences. The latter are observable in the asymmetries for sufficiently short XUV pulses to coherently probe the coupled states. It is thus documented that the asymmetry is a measure for phases in bound electron wave packets and non-adiabatic dynamics.

REMOVING BIASES IN RESOLVED STELLAR MASS MAPS OF GALAXY DISKS THROUGH SUCCESSIVE BAYESIAN MARGINALIZATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martínez-García, Eric E.; González-Lópezlira, Rosa A.; Bruzual A, Gustavo

2017-01-20

Stellar masses of galaxies are frequently obtained by fitting stellar population synthesis models to galaxy photometry or spectra. The state of the art method resolves spatial structures within a galaxy to assess the total stellar mass content. In comparison to unresolved studies, resolved methods yield, on average, higher fractions of stellar mass for galaxies. In this work we improve the current method in order to mitigate a bias related to the resolved spatial distribution derived for the mass. The bias consists in an apparent filamentary mass distribution and a spatial coincidence between mass structures and dust lanes near spiral arms.more » The improved method is based on iterative Bayesian marginalization, through a new algorithm we have named Bayesian Successive Priors (BSP). We have applied BSP to M51 and to a pilot sample of 90 spiral galaxies from the Ohio State University Bright Spiral Galaxy Survey. By quantitatively comparing both methods, we find that the average fraction of stellar mass missed by unresolved studies is only half what previously thought. In contrast with the previous method, the output BSP mass maps bear a better resemblance to near-infrared images.« less

PROSPECTS FOR MEASURING THE MASS OF BLACK HOLES AT HIGH REDSHIFTS WITH RESOLVED KINEMATICS USING GRAVITATIONAL LENSING

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hezaveh, Yashar D.

2014-08-20

Application of the most robust method of measuring black hole masses, spatially resolved kinematics of gas and stars, is presently limited to nearby galaxies. The Atacama Large Millimeter/sub-millimeter Array (ALMA) and 30m class telescopes (the Thirty Meter Telescope, the Giant Magellan Telescope, and the European Extremely Large Telescope) with milli-arcsecond resolution are expected to extend such measurements to larger distances. Here, we study the possibility of exploiting the angular magnification provided by strong gravitational lensing to measure black hole masses at high redshifts (z ∼ 1-6), using resolved gas kinematics with these instruments. We show that in ∼15% and ∼20%more » of strongly lensed galaxies, the inner 25 and 50 pc could be resolved, allowing the mass of ≳ 10{sup 8} M {sub ☉} black holes to be dynamically measured with ALMA, if moderately bright molecular gas is present at these small radii. Given the large number of strong lenses discovered in current millimeter surveys and future optical surveys, this fraction could constitute a statistically significant population for studying the evolution of the M-σ relation at high redshifts.« less

Computational electrodynamics in material media with constraint-preservation, multidimensional Riemann solvers and sub-cell resolution - Part II, higher order FVTD schemes

NASA Astrophysics Data System (ADS)

Balsara, Dinshaw S.; Garain, Sudip; Taflove, Allen; Montecinos, Gino

2018-02-01

The Finite Difference Time Domain (FDTD) scheme has served the computational electrodynamics community very well and part of its success stems from its ability to satisfy the constraints in Maxwell's equations. Even so, in the previous paper of this series we were able to present a second order accurate Godunov scheme for computational electrodynamics (CED) which satisfied all the same constraints and simultaneously retained all the traditional advantages of Godunov schemes. In this paper we extend the Finite Volume Time Domain (FVTD) schemes for CED in material media to better than second order of accuracy. From the FDTD method, we retain a somewhat modified staggering strategy of primal variables which enables a very beneficial constraint-preservation for the electric displacement and magnetic induction vector fields. This is accomplished with constraint-preserving reconstruction methods which are extended in this paper to third and fourth orders of accuracy. The idea of one-dimensional upwinding from Godunov schemes has to be significantly modified to use the multidimensionally upwinded Riemann solvers developed by the first author. In this paper, we show how they can be used within the context of a higher order scheme for CED. We also report on advances in timestepping. We show how Runge-Kutta IMEX schemes can be adapted to CED even in the presence of stiff source terms brought on by large conductivities as well as strong spatial variations in permittivity and permeability. We also formulate very efficient ADER timestepping strategies to endow our method with sub-cell resolving capabilities. As a result, our method can be stiffly-stable and resolve significant sub-cell variation in the material properties within a zone. Moreover, we present ADER schemes that are applicable to all hyperbolic PDEs with stiff source terms and at all orders of accuracy. Our new ADER formulation offers a treatment of stiff source terms that is much more efficient than previous ADER schemes. The computer algebra system scripts for generating ADER time update schemes for any general PDE with stiff source terms are also given in the electronic supplements to this paper. Second, third and fourth order accurate schemes for numerically solving Maxwell's equations in material media are presented in this paper. Several stringent tests are also presented to show that the method works and meets its design goals even when material permittivity and permeability vary by an order of magnitude over just a few zones. Furthermore, since the method is unconditionally stable and sub-cell-resolving in the presence of stiff source terms (i.e. for problems involving giant variations in conductivity over just a few zones), it can accurately handle such problems without any reduction in timestep. We also show that increasing the order of accuracy offers distinct advantages for resolving sub-cell variations in material properties. Most importantly, we show that when the accuracy requirements are stringent the higher order schemes offer the shortest time to solution. This makes a compelling case for the use of higher order, sub-cell resolving schemes in CED.

The ultimate picture-the combination of live cell superresolution microscopy and single molecule tracking yields highest spatio-temporal resolution.

PubMed

Dersch, Simon; Graumann, Peter L

2018-06-01

We are witnessing a breathtaking development in light (fluorescence) microscopy, where structures can be resolved down to the size of a ribosome within cells. This has already yielded surprising insight into the subcellular structure of cells, including the smallest cells, bacteria. Moreover, it has become possible to visualize and track single fluorescent protein fusions in real time, and quantify molecule numbers within individual cells. Combined, super resolution and single molecule tracking are pushing the limits of our understanding of the spatio-temporal organization even of the smallest cells to an unprecedented depth. Copyright © 2017 Elsevier Ltd. All rights reserved.

Systems Biology Analysis of Heterocellular Signaling.

PubMed

Tape, Christopher J

2016-08-01

Tissues comprise multiple heterotypic cell types (e.g., epithelial, mesenchymal, and immune cells). Communication between heterotypic cell types is essential for biological cohesion and is frequently dysregulated in disease. Despite the importance of heterocellular communication, most systems biology techniques do not report cell-specific signaling data from mixtures of cells. As a result, our existing perspective of cellular behavior under-represents the influence of heterocellular signaling. Recent technical advances now permit the resolution of systems-level cell-specific signaling data. This review discusses how new physical, spatial, and isotopic resolving methods are facilitating unique systems biology studies of heterocellular communication. Copyright © 2016 Elsevier Ltd. All rights reserved.

The role of stromal cells in the persistence of chronic inflammation

PubMed Central

Naylor, A J; Filer, A; Buckley, C D

2013-01-01

Inflammation is an unstable state; it either resolves or persists. Inflammatory reactions often have a propensity for specific anatomical sites. Why inflammation persists with specific tissue tropism remains obscure. Increasing evidence suggests that stromal cells which define tissue architecture are the key cells involved, and therefore make attractive therapeutic targets. Research on stromal cells in general and fibroblasts in particular has so far been hampered by a lack of fibroblast-specific cell markers. This review highlights our increasing understanding of the role of fibroblasts in inflammation, and suggests that these cells provide the cellular basis for site specific chronic inflammation. PMID:23199320

Bacterial spread from cell to cell: beyond actin-based motility.

PubMed

Kuehl, Carole J; Dragoi, Ana-Maria; Talman, Arthur; Agaisse, Hervé

2015-09-01

Several intracellular pathogens display the ability to propagate within host tissues by displaying actin-based motility in the cytosol of infected cells. As motile bacteria reach cell-cell contacts they form plasma membrane protrusions that project into adjacent cells and resolve into vacuoles from which the pathogen escapes, thereby achieving spread from cell to cell. Seminal studies have defined the bacterial and cellular factors that support actin-based motility. By contrast, the mechanisms supporting the formation of protrusions and their resolution into vacuoles have remained elusive. Here, we review recent advances in the field showing that Listeria monocytogenes and Shigella flexneri have evolved pathogen-specific mechanisms of bacterial spread from cell to cell. Copyright © 2015 Elsevier Ltd. All rights reserved.

Steady state and time resolved optical characterization studies of Zn 2SnO 4 nanowires for solar cell applications

DOE PAGES

Yakami, Baichhabi R.; Poudyal, Uma; Nandyala, Shashank R.; ...

2016-10-25

Nanowires are a promising option for sensitized solar cells, sensors, and display technology. Most of the work thus far has focused on binary oxides for these nanowires, but ternary oxides have advantages in additional control of optical and electronic properties. Here, we report on the diffuse reflectance, Low Temperature and Room Temperature Photoluminescence (PL), PL excitation spectrum, and Time Resolved PL (TRPL) of Zinc Tin Oxide (ZTO) nanowires grown by Chemical Vapor Deposition. The PL from the ZTO nanowires does not exhibit any band gap or near gap emission, and the diffuse reflectance measurement confirms that these ZTO nanowires havemore » a direct forbidden transition. The broad PL spectrum reveals two Gaussian peaks centered at 1.86 eV (red) and 2.81 eV (blue), representing two distinct defect states or complexes. The PL spectra were further studied by the Time Resolved Emission Spectrum and intensity dependent PL and TRPL. The time resolved measurements show complex non-exponential decays at all wavelengths, indicative of defect to defect transitions, and the red emissive states decay much slower than the blue emissive states. The effects of annealing in air and vacuum are studied to investigate the origin of the defect states in the nanowires, showing that the blue states are related to oxygen vacancies. We propose an energy band model for the nanowires containing defect states within the band gap and the associated transitions between these states that are consistent with our measurements.« less

Resolving the Detailed Structure of Cortical and Thalamic Neurons in the Adult Rat Brain with Refined Biotinylated Dextran Amine Labeling

PubMed Central

Ling, Changying; Hendrickson, Michael L.; Kalil, Ronald E.

2012-01-01

Biotinylated dextran amine (BDA) has been used frequently for both anterograde and retrograde pathway tracing in the central nervous system. Typically, BDA labels axons and cell somas in sufficient detail to identify their topographical location accurately. However, BDA labeling often has proved to be inadequate to resolve the fine structural details of axon arbors or the dendrites of neurons at a distance from the site of BDA injection. To overcome this limitation, we varied several experimental parameters associated with the BDA labeling of neurons in the adult rat brain in order to improve the sensitivity of the method. Specifically, we compared the effect on labeling sensitivity of: (a) using 3,000 or 10,000 MW BDA; (b) injecting different volumes of BDA; (c) co-injecting BDA with NMDA; and (d) employing various post-injection survival times. Following the extracellular injection of BDA into the visual cortex, labeled cells and axons were observed in both cortical and thalamic areas of all animals studied. However, the detailed morphology of axon arbors and distal dendrites was evident only under optimal conditions for BDA labeling that take into account the: molecular weight of the BDA used, concentration and volume of BDA injected, post-injection survival time, and toning of the resolved BDA with gold and silver. In these instances, anterogradely labeled axons and retrogradely labeled dendrites were resolved in fine detail, approximating that which can be achieved with intracellularly injected compounds such as biocytin or fluorescent dyes. PMID:23144777

Steady state and time resolved optical characterization studies of Zn 2SnO 4 nanowires for solar cell applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yakami, Baichhabi R.; Poudyal, Uma; Nandyala, Shashank R.

Nanowires are a promising option for sensitized solar cells, sensors, and display technology. Most of the work thus far has focused on binary oxides for these nanowires, but ternary oxides have advantages in additional control of optical and electronic properties. Here, we report on the diffuse reflectance, Low Temperature and Room Temperature Photoluminescence (PL), PL excitation spectrum, and Time Resolved PL (TRPL) of Zinc Tin Oxide (ZTO) nanowires grown by Chemical Vapor Deposition. The PL from the ZTO nanowires does not exhibit any band gap or near gap emission, and the diffuse reflectance measurement confirms that these ZTO nanowires havemore » a direct forbidden transition. The broad PL spectrum reveals two Gaussian peaks centered at 1.86 eV (red) and 2.81 eV (blue), representing two distinct defect states or complexes. The PL spectra were further studied by the Time Resolved Emission Spectrum and intensity dependent PL and TRPL. The time resolved measurements show complex non-exponential decays at all wavelengths, indicative of defect to defect transitions, and the red emissive states decay much slower than the blue emissive states. The effects of annealing in air and vacuum are studied to investigate the origin of the defect states in the nanowires, showing that the blue states are related to oxygen vacancies. We propose an energy band model for the nanowires containing defect states within the band gap and the associated transitions between these states that are consistent with our measurements.« less

Improving the accuracy and efficiency of time-resolved electronic spectra calculations: cellular dephasing representation with a prefactor.

PubMed

Zambrano, Eduardo; Šulc, Miroslav; Vaníček, Jiří

2013-08-07

Time-resolved electronic spectra can be obtained as the Fourier transform of a special type of time correlation function known as fidelity amplitude, which, in turn, can be evaluated approximately and efficiently with the dephasing representation. Here we improve both the accuracy of this approximation-with an amplitude correction derived from the phase-space propagator-and its efficiency-with an improved cellular scheme employing inverse Weierstrass transform and optimal scaling of the cell size. We demonstrate the advantages of the new methodology by computing dispersed time-resolved stimulated emission spectra in the harmonic potential, pyrazine, and the NCO molecule. In contrast, we show that in strongly chaotic systems such as the quartic oscillator the original dephasing representation is more appropriate than either the cellular or prefactor-corrected methods.

Fully quantum-state resolved study of NO{sub 2} photodissociation. Correlated NO({sup 2}{Pi}{sub {Omega}}, {nu} = 0 J,A) + O({sup 3}P{sub j}) distributions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanov, A.; Bieler, C.R.; Reisler, H.

1995-09-14

Relative O({sup 3}P{sub j} = 2.1.0) spin-orbit populations correlated with specific NO[{sup 2}{Pi}{sub {Omega}} = {1/2}, 3/2; {nu} = 0; f; {Lambda} = {Pi}(A{prime}), {Pi}(A{double_prime})] product states were obtained following photolysis of NO{sub 2} at excess energies E{sup {+-}} = 390, 425, and 1054 cm{sup -1}. These fully quantum state-resolved measurements were carried out by recording spatial profiles of recoiling NO({sup 2}{Pi}{sub {Omega}}, J, {Lambda}) products using polarized radiation for photolysis and state-selective laser ionization detection. The relative O({sup 3}P{sub j}) populations correlated with each NO({sup 2}{Pi}{sub {Omega}}, J, {Lambda}) state show marked fluctuations at each excess energy as amore » function of rotational state and {Lambda}-doublet component. The relative populations also fluctuate as a function of excess energy. The O({sup 3}P{sub j}) spin-orbit population ratios, when averaged over all measurements, exhibit distributions that are colder than statistical, in agreement with previous results. In particular, we find that, on average, O({sup 3}P{sub 1}):O({sup 3}P{sub 2}) population ratios correlated with the ground NO({sup 2}{Pi}{sub {1/2}}) state are colder than the corresponding ratios correlated with the excited NO({sup 2}{Pi}{sub 3/2}) spin-orbit state. These results are in agreement with the state-specific calculations of Katigiri and Kato. 45 refs., 12 figs., 3 tabs.« less

Timing the formation and assembly of early-type galaxies via spatially resolved stellar populations analysis

NASA Astrophysics Data System (ADS)

Martín-Navarro, Ignacio; Vazdekis, Alexandre; Falcón-Barroso, Jesús; La Barbera, Francesco; Yıldırım, Akın; van de Ven, Glenn

2018-04-01

To investigate star formation and assembly processes of massive galaxies, we present here a spatially resolved stellar population analysis of a sample of 45 elliptical galaxies (Es) selected from the Calar Alto Legacy Integral Field Area survey. We find rather flat age and [Mg/Fe] radial gradients, weakly dependent on the effective velocity dispersion of the galaxy within half-light radius. However, our analysis shows that metallicity gradients become steeper with increasing galaxy velocity dispersion. In addition, we have homogeneously compared the stellar population gradients of our sample of Es to a sample of nearby relic galaxies, i.e. local remnants of the high-z population of red nuggets. This comparison indicates that, first, the cores of present-day massive galaxies were likely formed in gas-rich, rapid star formation events at high redshift (z ≳ 2). This led to radial metallicity variations steeper than observed in the local Universe, and positive [Mg/Fe] gradients. Secondly, our analysis also suggests that a later sequence of minor dry mergers, populating the outskirts of early-type galaxies (ETGs), flattened the pristine [Mg/Fe] and metallicity gradients. Finally, we find a tight age-[Mg/Fe] relation, supporting that the duration of the star formation is the main driver of the [Mg/Fe] enhancement in massive ETGs. However, the star formation time-scale alone is not able to fully explain our [Mg/Fe] measurements. Interestingly, our results match the expected effect that a variable stellar initial mass function would have on the [Mg/Fe] ratio.

Phylogenetic and population genetic analyses of diploid Leucaena (Leguminosae; Mimosoideae) reveal cryptic species diversity and patterns of divergent allopatric speciation.

PubMed

Govindarajulu, Rajanikanth; Hughes, Colin E; Bailey, C Donovan

2011-12-01

Leucaena comprises 17 diploid species, five tetraploid species, and a complex series of hybrids whose evolutionary histories have been influenced by human seed translocation, cultivation, and subsequent spontaneous hybridization. Here we investigated patterns of evolutionary divergence among diploid Leucaena through comprehensively sampled multilocus phylogenetic and population genetic approaches to address species delimitation, interspecific relationships, hybridization, and the predominant mode of speciation among diploids. Parsimony- and maximum-likelihood-based phylogenetic approaches were applied to 59 accessions sequenced for six SCAR-based nuclear loci, nrDNA ITS, and four cpDNA regions. Population genetic comparisons included 1215 AFLP loci representing 42 populations and 424 individuals. Phylogenetic results provided a well-resolved hypothesis of divergent species relationships, recovering previously recognized clades of diploids as well as newly resolved relationships. Phylogenetic and population genetic assessments identified two cryptic species that are consistent with geography and morphology. Findings from this study highlight the importance and utility of multilocus data in the recovery of complex evolutionary histories. The results are consistent with allopatric divergence representing the predominant mode of speciation among diploid Leucaena. These findings contrast with the potential hybrid origin of several tetraploid species and highlight the importance of human translocation of seed to the origin of these tetraploids. The recognition of one previously unrecognized species (L. cruziana) and the elevation of another taxon (L. collinsii subsp. zacapana) to specific status (L. zacapana) is consistent with a growing number of newly diagnosed species from neotropical seasonally dry forests, suggesting these communities harbor greater species diversity than previously recognized.

Quantifying selection in evolving populations using time-resolved genetic data

NASA Astrophysics Data System (ADS)

Illingworth, Christopher J. R.; Mustonen, Ville

2013-01-01

Methods which uncover the molecular basis of the adaptive evolution of a population address some important biological questions. For example, the problem of identifying genetic variants which underlie drug resistance, a question of importance for the treatment of pathogens, and of cancer, can be understood as a matter of inferring selection. One difficulty in the inference of variants under positive selection is the potential complexity of the underlying evolutionary dynamics, which may involve an interplay between several contributing processes, including mutation, recombination and genetic drift. A source of progress may be found in modern sequencing technologies, which confer an increasing ability to gather information about evolving populations, granting a window into these complex processes. One particularly interesting development is the ability to follow evolution as it happens, by whole-genome sequencing of an evolving population at multiple time points. We here discuss how to use time-resolved sequence data to draw inferences about the evolutionary dynamics of a population under study. We begin by reviewing our earlier analysis of a yeast selection experiment, in which we used a deterministic evolutionary framework to identify alleles under selection for heat tolerance, and to quantify the selection acting upon them. Considering further the use of advanced intercross lines to measure selection, we here extend this framework to cover scenarios of simultaneous recombination and selection, and of two driver alleles with multiple linked neutral, or passenger, alleles, where the driver pair evolves under an epistatic fitness landscape. We conclude by discussing the limitations of the approach presented and outlining future challenges for such methodologies.

Applications of nonlinear science and kinetic equations to the spread of epidemics

NASA Astrophysics Data System (ADS)

Macinnis, David Robert

The study of the spread of epidemics is currently growing into a successful subfield of a combination of nonlinear science and statistical mechanics. Topics studied in this field include kinetic and mean field levels of epidemiological models. This thesis consists of the analysis of such topics and specifically directed at the Hantavirus, West Nile virus, and the Bubonic Plague. A successful reaction-diffusion equation approach developed recently by Abramson and Kenkre was able to describe spatiotemporal patterns of the Hantavirus model. From measurements of the parameters of their model it was found that the mice, the carriers of the infection, must be regarded as moving diffusively within attractive potentials representative of home ranges. Several attempts have been made to incorporate home ranges into their model. Two of these attempts are discussed within this thesis. A model to explain the transmission of the West Nile virus within bird and mosquito populations was recently developed by Kenkre, Parmenter, Peixoto, and Sadasiv who showed how spatially resolved issues could be discussed but restricted their analysis to mean field considerations. This thesis extends that study by investigating spatial resolution of the infected populations. Traveling waves of the bird and mosquito populations are found in the West Nile context. Infection control of various epidemics has become increasingly important to limit the potential force of infection into the human population. This thesis contains a quantitative attempt at a theory of such control (for the West Nile virus) via spraying of the mosquito population. Mean field and kinetic level models are proposed in this thesis to describe the transmission of the Bubonic Plague which involves flea and mammal populations. The various populations are found to undergo a variety of bifurcations as well as hysteresis in their steady state regime. Spatially resolved analysis of the populations is also presented.

Seismic hazard and risks based on the Unified Scaling Law for Earthquakes

NASA Astrophysics Data System (ADS)

Kossobokov, Vladimir; Nekrasova, Anastasia

2014-05-01

Losses from natural disasters continue to increase mainly due to poor understanding by majority of scientific community, decision makers and public, the three components of Risk, i.e., Hazard, Exposure, and Vulnerability. Contemporary Science is responsible for not coping with challenging changes of Exposures and their Vulnerability inflicted by growing population, its concentration, etc., which result in a steady increase of Losses from Natural Hazards. Scientists owe to Society for lack of knowledge, education, and communication. In fact, Contemporary Science can do a better job in disclosing Natural Hazards, assessing Risks, and delivering such knowledge in advance catastrophic events. Any kind of risk estimates R(g) at location g results from a convolution of the natural hazard H(g) with the exposed object under consideration O(g) along with its vulnerability V(O(g)). Note that g could be a point, or a line, or a cell on or under the Earth surface and that distribution of hazards, as well as objects of concern and their vulnerability, could be time-dependent. There exist many different risk estimates even if the same object of risk and the same hazard are involved. It may result from the different laws of convolution, as well as from different kinds of vulnerability of an object of risk under specific environments and conditions. Both conceptual issues must be resolved in a multidisciplinary problem oriented research performed by specialists in the fields of hazard, objects of risk, and object vulnerability, i.e. specialists in earthquake engineering, social sciences and economics. To illustrate this general concept, we first construct seismic hazard assessment maps based on the Unified Scaling Law for Earthquakes (USLE). The parameters A, B, and C of USLE, i.e. log N(M,L) = A - B•(M-6) + C•log L, where N(M,L) is the expected annual number of earthquakes of a certain magnitude M within an area of linear size L, are used to estimate the expected maximum magnitude in 50 years and the corresponding expected ground shaking intensity in a cell g of a uniform grid of the region of interest. Then such a seismic hazard map is used to generate earthquake risk maps based on the exposed population density. Some oversimplified convolutions R(g) = H(g)•gP•F(gP) of seismic hazard assessment maps H(g) are applied in a few regions with population density distribution P of vulnerability V=F(gP), where g is a cell of a uniform grid and gP is the integral of the population density over the cell g.

Triangle Geometry Processing for Surface Modeling and Cartesian Grid Generation

NASA Technical Reports Server (NTRS)

Aftosmis, Michael J. (Inventor); Melton, John E. (Inventor); Berger, Marsha J. (Inventor)

2002-01-01

Cartesian mesh generation is accomplished for component based geometries, by intersecting components subject to mesh generation to extract wetted surfaces with a geometry engine using adaptive precision arithmetic in a system which automatically breaks ties with respect to geometric degeneracies. During volume mesh generation, intersected surface triangulations are received to enable mesh generation with cell division of an initially coarse grid. The hexagonal cells are resolved, preserving the ability to directionally divide cells which are locally well aligned.

Basal cell carcinomas in elderly patients treated by cryotherapy

PubMed Central

Chiriac, Anca; Mihaila, Doina; Foia, Liliana; Solovan, Caius

2013-01-01

Basal cell carcinoma is a malignant skin tumor with high incidence in our country, especially in rural areas, on sun-exposed skin (particularly on the face) in elderly patients. We present three cases of basal cell carcinoma with good results with cryotherapy. This report aims to outline and to prove that in some difficult situations, a simple, inexpensive, easy-to-perform procedure with no contraindications and with minimal side effects (erythema, mild pain) can be applied and resolve such cases. PMID:23569366

Triangle geometry processing for surface modeling and cartesian grid generation

DOEpatents

Aftosmis, Michael J [San Mateo, CA; Melton, John E [Hollister, CA; Berger, Marsha J [New York, NY

2002-09-03

Cartesian mesh generation is accomplished for component based geometries, by intersecting components subject to mesh generation to extract wetted surfaces with a geometry engine using adaptive precision arithmetic in a system which automatically breaks ties with respect to geometric degeneracies. During volume mesh generation, intersected surface triangulations are received to enable mesh generation with cell division of an initially coarse grid. The hexagonal cells are resolved, preserving the ability to directionally divide cells which are locally well aligned.

Toward a Standardized Internet Measurement.

ERIC Educational Resources Information Center

Chen, Hsiang; Tan, Zixiang

This paper investigates measurement issues related to elements of the Internet and calls for a standardized measuring scheme to resolve the problem of the measurement. The dilemmas in measuring the elements of the Internet are identified, and previous studies are reviewed. Elements of the Internet are categorized into population, usage, protocol…

Redistribution on the thallium scan in myocardial sarcoidosis: concise communication

DOE Office of Scientific and Technical Information (OSTI.GOV)

Makler, P.T.; Lavine, S.J.; Denenberg, B.S.

1981-05-01

Resting and redistribution thallium studies were performed in four young patients with sarcoidosis to evaluate the possibility of myocardial involvement. In each case the resting scan showed marked defects that resolved on the redistribution studies. In a different patient population, these results would have implied significant coronary artery disease.

Implementation of Conflict Resolution and Mediation Process at a Community College

ERIC Educational Resources Information Center

Metellus, Frantz H.

2017-01-01

Conflicts are inevitable when diverse populations of students, administrators, and staff function in close proximity in the community college setting. Effective methods of resolving conflicts focus on supporting both sides in a dispute while creating an environment within which the participating stakeholders benefit from their interactions. Common…

Review of quantitative phase-digital holographic microscopy: promising novel imaging technique to resolve neuronal network activity and identify cellular biomarkers of psychiatric disorders

PubMed Central

Marquet, Pierre; Depeursinge, Christian; Magistretti, Pierre J.

2014-01-01

Abstract. Quantitative phase microscopy (QPM) has recently emerged as a new powerful quantitative imaging technique well suited to noninvasively explore a transparent specimen with a nanometric axial sensitivity. In this review, we expose the recent developments of quantitative phase-digital holographic microscopy (QP-DHM). Quantitative phase-digital holographic microscopy (QP-DHM) represents an important and efficient quantitative phase method to explore cell structure and dynamics. In a second part, the most relevant QPM applications in the field of cell biology are summarized. A particular emphasis is placed on the original biological information, which can be derived from the quantitative phase signal. In a third part, recent applications obtained, with QP-DHM in the field of cellular neuroscience, namely the possibility to optically resolve neuronal network activity and spine dynamics, are presented. Furthermore, potential applications of QPM related to psychiatry through the identification of new and original cell biomarkers that, when combined with a range of other biomarkers, could significantly contribute to the determination of high risk developmental trajectories for psychiatric disorders, are discussed. PMID:26157976

Microscopic time-resolved imaging of singlet oxygen by delayed fluorescence in living cells.

PubMed

Scholz, Marek; Dědic, Roman; Hála, Jan

2017-11-08

Singlet oxygen is a highly reactive species which is involved in a number of processes, including photodynamic therapy of cancer. Its very weak near-infrared emission makes imaging of singlet oxygen in biological systems a long-term challenge. We address this challenge by introducing Singlet Oxygen Feedback Delayed Fluorescence (SOFDF) as a novel modality for semi-direct microscopic time-resolved wide-field imaging of singlet oxygen in biological systems. SOFDF has been investigated in individual fibroblast cells incubated with a well-known photosensitizer aluminium phthalocyanine tetrasulfonate. The SOFDF emission from the cells is several orders of magnitude stronger and much more readily detectable than the very weak near-infrared phosphorescence of singlet oxygen. Moreover, the analysis of SOFDF kinetics enables us to estimate the lifetimes of the involved excited states. Real-time SOFDF images with micrometer spatial resolution and submicrosecond temporal-resolution have been recorded. Interestingly, a steep decrease in the SOFDF intensity after the photodynamically induced release of a photosensitizer from lysosomes has been demonstrated. This effect could be potentially employed as a valuable diagnostic tool for monitoring and dosimetry in photodynamic therapy.

Carotenoid Distribution in Living Cells of Haematococcus pluvialis (Chlorophyceae)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Collins, Aaron M.; Jones, Howland D. T.; Han, Danxiang

Haematococcus pluvialis is a freshwater unicellular green microalga belonging to the class Chlorophyceae and is of commercial interest for its ability to accumulate massive amounts of the red ketocarotenoid astaxanthin (3,3'-dihydroxy-β,β-carotene-4,4'-dione). Using confocal Raman microscopy and multivariate analysis, we demonstrate the ability to spectrally resolve resonance–enhanced Raman signatures associated with astaxanthin and β-carotene along with chlorophyll fluorescence. By mathematically isolating these spectral signatures, in turn, it is possible to locate these species independent of each other in living cells of H. pluvialis in various stages of the life cycle. Chlorophyll emission was found only in the chloroplast whereas astaxanthin wasmore » identified within globular and punctate regions of the cytoplasmic space. Moreover, we found evidence for β-carotene to be co-located with both the chloroplast and astaxanthin in the cytosol. These observations imply that β-carotene is a precursor for astaxanthin and the synthesis of astaxanthin occurs outside the chloroplast. Finally, our work demonstrates the broad utility of confocal Raman microscopy to resolve spectral signatures of highly similar chromophores in living cells.« less

Review of quantitative phase-digital holographic microscopy: promising novel imaging technique to resolve neuronal network activity and identify cellular biomarkers of psychiatric disorders.

PubMed

Marquet, Pierre; Depeursinge, Christian; Magistretti, Pierre J

2014-10-01

Quantitative phase microscopy (QPM) has recently emerged as a new powerful quantitative imaging technique well suited to noninvasively explore a transparent specimen with a nanometric axial sensitivity. In this review, we expose the recent developments of quantitative phase-digital holographic microscopy (QP-DHM). Quantitative phase-digital holographic microscopy (QP-DHM) represents an important and efficient quantitative phase method to explore cell structure and dynamics. In a second part, the most relevant QPM applications in the field of cell biology are summarized. A particular emphasis is placed on the original biological information, which can be derived from the quantitative phase signal. In a third part, recent applications obtained, with QP-DHM in the field of cellular neuroscience, namely the possibility to optically resolve neuronal network activity and spine dynamics, are presented. Furthermore, potential applications of QPM related to psychiatry through the identification of new and original cell biomarkers that, when combined with a range of other biomarkers, could significantly contribute to the determination of high risk developmental trajectories for psychiatric disorders, are discussed.