Peculiarities of data interpretation upon direct tissue analysis by Fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Chagovets, Vtaliy; Kononikhin, Aleksey; Starodubtseva, Nataliia; Kostyukevich, Yury; Popov, Igor; Frankevich, Vladimir; Nikolaev, Eugene

2016-01-01

The importance of high-resolution mass spectrometry for the correct data interpretation of a direct tissue analysis is demonstrated with an example of its clinical application for an endometriosis study. Multivariate analysis of the data discovers lipid species differentially expressed in different tissues under investigation. High-resolution mass spectrometry allows unambiguous separation of peaks with close masses that correspond to proton and sodium adducts of phosphatidylcholines and to phosphatidylcholines differing in double bond number.

Mars Surface Compositional Units and Some Geological Implications from the Mars Express High Resolution Stereo Camera (HRSC)

NASA Astrophysics Data System (ADS)

McCord, T. B.; Combe, J.-P.; Hayne, P. O.

We are investigating the composition of the Martian surface partly by mapping the small spatial variations of water ice and salt minerals using the spectral images provided by the High Resolution Stereo Camera (HRSC). In order to identify the main mineral components, high spectral resolution data from the Observatoire pour la Mineralogie, l'Eau, les Glaces et l'Activite (OMEGA) imaging spectrometer are used. The join analysis of these two dataset makes the most of their respective abilities and, because of that, it requires a close agreement of their calibration [1]. The first part of this work is a comparison of HRSC and OMEGA measurements, exploration of atmosphere effects and checks of calibration. Then, an attempt to detect and map quantitatively at high spatial resolution (1) water ice both at the poles and in equatorial regions and (2) salts minerals is performed by exploring the spectral types evidenced in HRSC color data. For a given region, these two materials do or could represent additional endmember compositional units detectable with HRSC in addition to the basic units so far: 1) dark rock (basalt) and 2) red rock (iron oxide-rich material) [1]. Both materials also have been reported detected by OMEGA, but at much lower spatial resolution than HRSC. An ice mapping of the north polar regions is performed with OMEGA data by using a spectral index calibrated to ice fraction by using a set of linear combinations of various categories of materials with ice. In addition, a linear spectral unmixing model is used on HRSC data. Both ice fraction maps produce similar quantitative results, allowing us to interpret HRSC data at their full spatial resolution. Low-latitude sites are also explored where past but recent glacial activities have been reported as possible evidence of current water-ice. This includes looking for fresh frost and changes with time. The salt detection with HRSC firstly focused on the Candor Chasma area, where salt have been reported by using OMEGA [2]. The present work extends the analysis to other regions in order to constrain better the general geology and climate of Mars. References: [1] McCord T. B., et al. (2006). The Mars Express High Resolution Stereo Camera spectrophotometric data: Characteristics and science analysis, JGR, submitted. [2] Gendrin, A., N. Mangold, J-P. Bibring, Y. Langevin, B. Gondet, F. Poulet, G. Bonello, C. Quantin, J. Mustard, R. Arvidson, S. LeMouelic (2005), Sulfates in Martian layered terrains: The OMEGA/Mars Express View, Science, 307, 1587-1591

Expression-dependent susceptibility to face distortions in processing of facial expressions of emotion.

PubMed

Guo, Kun; Soornack, Yoshi; Settle, Rebecca

2018-03-05

Our capability of recognizing facial expressions of emotion under different viewing conditions implies the existence of an invariant expression representation. As natural visual signals are often distorted and our perceptual strategy changes with external noise level, it is essential to understand how expression perception is susceptible to face distortion and whether the same facial cues are used to process high- and low-quality face images. We systematically manipulated face image resolution (experiment 1) and blur (experiment 2), and measured participants' expression categorization accuracy, perceived expression intensity and associated gaze patterns. Our analysis revealed a reasonable tolerance to face distortion in expression perception. Reducing image resolution up to 48 × 64 pixels or increasing image blur up to 15 cycles/image had little impact on expression assessment and associated gaze behaviour. Further distortion led to decreased expression categorization accuracy and intensity rating, increased reaction time and fixation duration, and stronger central fixation bias which was not driven by distortion-induced changes in local image saliency. Interestingly, the observed distortion effects were expression-dependent with less deterioration impact on happy and surprise expressions, suggesting this distortion-invariant facial expression perception might be achieved through the categorical model involving a non-linear configural combination of local facial features. Copyright © 2018 Elsevier Ltd. All rights reserved.

External optical imaging of freely moving mice with green fluorescent protein-expressing metastatic tumors

NASA Astrophysics Data System (ADS)

Yang, Meng; Baranov, Eugene; Shimada, Hiroshi; Moossa, A. R.; Hoffman, Robert M.

2000-04-01

We report here a new approach to genetically engineering tumors to become fluorescence such that they can be imaged externally in freely-moving animals. We describe here external high-resolution real-time fluorescent optical imaging of metastatic tumors in live mice. Stable high-level green flourescent protein (GFP)-expressing human and rodent cell lines enable tumors and metastasis is formed from them to be externally imaged from freely-moving mice. Real-time tumor and metastatic growth were quantitated from whole-body real-time imaging in GFP-expressing melanoma and colon carcinoma models. This GFP optical imaging system is highly appropriate for high throughput in vivo drug screening.

Analytical Calculation of the Lower Bound on Timing Resolution for PET Scintillation Detectors Comprising High-Aspect-Ratio Crystal Elements

PubMed Central

Cates, Joshua W.; Vinke, Ruud; Levin, Craig S.

2015-01-01

Excellent timing resolution is required to enhance the signal-to-noise ratio (SNR) gain available from the incorporation of time-of-flight (ToF) information in image reconstruction for positron emission tomography (PET). As the detector’s timing resolution improves, so does SNR, reconstructed image quality, and accuracy. This directly impacts the challenging detection and quantification tasks in the clinic. The recognition of these benefits has spurred efforts within the molecular imaging community to determine to what extent the timing resolution of scintillation detectors can be improved and develop near-term solutions for advancing ToF-PET. Presented in this work, is a method for calculating the Cramér-Rao lower bound (CRLB) on timing resolution for scintillation detectors with long crystal elements, where the influence of the variation in optical path length of scintillation light on achievable timing resolution is non-negligible. The presented formalism incorporates an accurate, analytical probability density function (PDF) of optical transit time within the crystal to obtain a purely mathematical expression of the CRLB with high-aspect-ratio (HAR) scintillation detectors. This approach enables the statistical limit on timing resolution performance to be analytically expressed for clinically-relevant PET scintillation detectors without requiring Monte Carlo simulation-generated photon transport time distributions. The analytically calculated optical transport PDF was compared with detailed light transport simulations, and excellent agreement was found between the two. The coincidence timing resolution (CTR) between two 3×3×20 mm3 LYSO:Ce crystals coupled to analogue SiPMs was experimentally measured to be 162±1 ps FWHM, approaching the analytically calculated lower bound within 6.5%. PMID:26083559

Analytical calculation of the lower bound on timing resolution for PET scintillation detectors comprising high-aspect-ratio crystal elements

NASA Astrophysics Data System (ADS)

Cates, Joshua W.; Vinke, Ruud; Levin, Craig S.

2015-07-01

Excellent timing resolution is required to enhance the signal-to-noise ratio (SNR) gain available from the incorporation of time-of-flight (ToF) information in image reconstruction for positron emission tomography (PET). As the detector’s timing resolution improves, so does SNR, reconstructed image quality, and accuracy. This directly impacts the challenging detection and quantification tasks in the clinic. The recognition of these benefits has spurred efforts within the molecular imaging community to determine to what extent the timing resolution of scintillation detectors can be improved and develop near-term solutions for advancing ToF-PET. Presented in this work, is a method for calculating the Cramér-Rao lower bound (CRLB) on timing resolution for scintillation detectors with long crystal elements, where the influence of the variation in optical path length of scintillation light on achievable timing resolution is non-negligible. The presented formalism incorporates an accurate, analytical probability density function (PDF) of optical transit time within the crystal to obtain a purely mathematical expression of the CRLB with high-aspect-ratio (HAR) scintillation detectors. This approach enables the statistical limit on timing resolution performance to be analytically expressed for clinically-relevant PET scintillation detectors without requiring Monte Carlo simulation-generated photon transport time distributions. The analytically calculated optical transport PDF was compared with detailed light transport simulations, and excellent agreement was found between the two. The coincidence timing resolution (CTR) between two 3× 3× 20 mm3 LYSO:Ce crystals coupled to analogue SiPMs was experimentally measured to be 162+/- 1 ps FWHM, approaching the analytically calculated lower bound within 6.5%.

Some unique surface patterns on ignimbrites on Earth: A "bird's eye" view as a guide for planetary mappers

NASA Astrophysics Data System (ADS)

de Silva, Shanaka L.; Bailey, John E.

2017-08-01

Observations of terrestrial analogs are critical to aiding planetary mappers in interpreting surface lithologies on other planets. For instance, the presence of ignimbrites on Mars has been debated for over three decades and is supported by analogy with deposits on Earth. Critical evidence includes the geomorphic and surface expression of the deposits, and those in the Central Andes of South America are amongst the most-cited analogs. Herein we describe some prominent surface textures and patterns seen in ignimbrites on the scale of high-resolution remotely sensed data (10-1 m per pixel). These include pervasive joints and fractures that contribute to yardang form and development as well as prominent mounds, fissures, and fracture networks ("spiders", "bugs", "boxworks") on ignimbrite surfaces. While all these features are related to intrinsic cooling and degassing processes, the involvement of external water buried by hot pyroclastic flows enhances fumarolic activity, advective cooling, and joint development. Observations of these geomorphic expressions using remote sensing are only possible with the highest resolution data and limited surface erosion. For Mars, where similarly high resolution datasets are available (for example, the High Resolution Imaging Sensor Experiment or HiRISE) extensive dust cover may limit the recognition of similar features there. However significant relief on some of these features on Earth indicate they might still be detectable on Mars.

High resolution Chromatin Immunoprecipitation (ChIP) sequencing reveals novel bindings targets and prognostic role for SOX11 in Mantle cell lymphoma

PubMed Central

Kuo, Pei-Yu; Leshchenko, Violetta V.; Fazzari, Melissa J.; Perumal, Deepak; Gellen, Tobias; He, Tianfang; Iqbal, Javeed; Baumgartner-Wennerholm, Stefanie; Nygren, Lina; Zhang, Fan; Zhang, Weijia; Suh, K. Stephen; Goy, Andre; Yang, David T.; Chan, Wing-Chung; Kahl, Brad S.; Verma, Amit K.; Gascoyne, Randy D.; Kimby, Eva; Sander, Birgitta; Ye, B. Hilda; Melnick, Ari M.; Parekh, Samir

2015-01-01

SOX11 (Sex determining region Y-box 11) expression is specific for MCL as compared to other Non-Hodgkin's lymphomas. However, the function and direct binding targets of SOX11 in MCL are largely unknown. We used high-resolution ChIP-Seq to identify the direct target genes of SOX11 in a genome-wide, unbiased manner and elucidate its functional significance. Pathway analysis identified WNT, PKA and TGF-beta signaling pathways as significantly enriched by SOX11 target genes. qCHIP and promoter reporter assays confirmed that SOX11 directly binds to individual genes and modulates their transcription activities in these pathways in MCL. Functional studies using RNA interference demonstrate that SOX11 directly regulates WNT in MCL. We analyzed SOX11 expression in three independent well-annotated tissue microarrays from the University of Wisconsin (UW), Karolinska Institute and British Columbia Cancer Agency (BCCA). Our findings suggest that high SOX11 expression is associated with improved survival in a subset of MCL patients, particularly those treated with intensive chemotherapy. Transcriptional regulation of WNT and other biological pathways affected by SOX11 target genes may help explain the impact of SOX11 expression on patient outcomes. PMID:24681958

Analysis of the precipitation and streamflow extremes in Northern Italy using high resolution reanalysis dataset Express-Hydro

NASA Astrophysics Data System (ADS)

Silvestro, Francesco; Parodi, Antonio; Campo, Lorenzo

2017-04-01

The characterization of the hydrometeorological extremes, both in terms of rainfall and streamflow, in a given region plays a key role in the environmental monitoring provided by the flood alert services. In last years meteorological simulations (both near real-time and historical reanalysis) were available at increasing spatial and temporal resolutions, making possible long-period hydrological reanalysis in which the meteo dataset is used as input in distributed hydrological models. In this work, a very high resolution meteorological reanalysis dataset, namely Express-Hydro (CIMA, ISAC-CNR, GAUSS Special Project PR45DE), was employed as input in the hydrological model Continuum in order to produce long time series of streamflows in the Liguria territory, located in the Northern part of Italy. The original dataset covers the whole Europe territory in the 1979-2008 period, at 4 km of spatial resolution and 3 hours of time resolution. Analyses in terms of comparison between the rainfall estimated by the dataset and the observations (available from the local raingauges network) were carried out, and a bias correction was also performed in order to better match the observed climatology. An extreme analysis was eventually carried on the streamflows time series obtained by the simulations, by comparing them with the results of the same hydrological model fed with the observed time series of rainfall. The results of the analysis are shown and discussed.

Measurement of high-dynamic temperature field using high-speed quadriwave lateral shearing interferometer

NASA Astrophysics Data System (ADS)

Cui, Bo-chuan; Wang, Jian-li; Yao, Kai-nan; Chen, Tao

2018-03-01

An approach to measure a high-dynamic two-dimensional (2D) temperature field using a high-speed quadriwave lateral shearing interferometer (QWLSI) is proposed. The detailed theoretical derivation to express the wavefront reconstruct principle of the proposed method is presented. The comparison experiment with thermocouples shows that the temperature field measurement using QWLSI has a precision of ±0.5 °C. An experiment for measuring the highdynamic temperature field generated by an electrical heater is carried out. A 200 frame rate temperature field video with 512 × 512 resolution is obtained finally. Experimental results show that the temperature field measurement system using a QWLSI has the advantage of high sensitivity and high resolution.

Enhanced Beetle Luciferase for High-Resolution Bioluminescence Imaging

PubMed Central

Nakajima, Yoshihiro; Yamazaki, Tomomi; Nishii, Shigeaki; Noguchi, Takako; Hoshino, Hideto; Niwa, Kazuki; Viviani, Vadim R.; Ohmiya, Yoshihiro

2010-01-01

We developed an enhanced green-emitting luciferase (ELuc) to be used as a bioluminescence imaging (BLI) probe. ELuc exhibits a light signal in mammalian cells that is over 10-fold stronger than that of the firefly luciferase (FLuc), which is the most widely used luciferase reporter gene. We showed that ELuc produces a strong light signal in primary cells and tissues and that it enables the visualization of gene expression with high temporal resolution at the single-cell level. Moreover, we successfully imaged the nucleocytoplasmic shuttling of importin α by fusing ELuc at the intracellular level. These results demonstrate that the use of ELuc allows a BLI spatiotemporal resolution far greater than that provided by FLuc. PMID:20368807

Gingival transcriptome patterns during induction and resolution of experimental gingivitis in humans.

PubMed

Offenbacher, Steven; Barros, Silvana P; Paquette, David W; Winston, J Leslie; Biesbrock, Aaron R; Thomason, Ryan G; Gibb, Roger D; Fulmer, Andy W; Tiesman, Jay P; Juhlin, Kenton D; Wang, Shuo L; Reichling, Tim D; Chen, Ker-Sang; Ho, Begonia

2009-12-01

To our knowledge, changes in the patterns of whole-transcriptome gene expression that occur during the induction and resolution of experimental gingivitis in humans were not previously explored using bioinformatic tools. Gingival biopsy samples collected from 14 subjects during a 28-day stent-induced experimental gingivitis model, followed by treatment, and resolution at days 28 through 35 were analyzed using gene-expression arrays. Biopsy samples were collected at different sites within each subject at baseline (day 0), at the peak of gingivitis (day 28), and at resolution (day 35) and processed using whole-transcriptome gene-expression arrays. Gene-expression data were analyzed to identify biologic themes and pathways associated with changes in gene-expression profiles that occur during the induction and resolution of experimental gingivitis using bioinformatic tools. During disease induction and resolution, the dominant expression pathway was the immune response, with 131 immune response genes significantly up- or downregulated during induction, during resolution, or during both at P <0.05. During induction, there was significant transient increase in the expression of inflammatory and oxidative stress mediators, including interleukin (IL)-1 alpha (IL1A), IL-1 beta (IL1B), IL8, RANTES, colony stimulating factor 3 (CSF3), and superoxide dismutase 2 (SOD2), and a decreased expression of IP10, interferon inducible T-cell alpha chemoattractant (ITAC), matrix metalloproteinase 10 (MMP10), and beta 4 defensin (DEFB4). These genes reversed expression patterns upon resolution in parallel with the reversal of gingival inflammation. A relatively small subset (11.9%) of the immune response genes analyzed by array was transiently activated in response to biofilm overgrowth, suggesting a degree of specificity in the transcriptome-expression response. The fact that this same subset demonstrates a reversal in expression patterns during clinical resolution implicates these genes as being critical for maintaining tissue homeostasis at the biofilm-gingival interface. In addition to the immune response pathway as the dominant response theme, new candidate genes and pathways were identified as being selectively modulated in experimental gingivitis, including neural processes, epithelial defenses, angiogenesis, and wound healing.

Integrated analysis of copy number alteration and RNA expression profiles of cancer using a high-resolution whole-genome oligonucleotide array.

PubMed

Jung, Seung-Hyun; Shin, Seung-Hun; Yim, Seon-Hee; Choi, Hye-Sun; Lee, Sug-Hyung; Chung, Yeun-Jun

2009-07-31

Recently, microarray-based comparative genomic hybridization (array-CGH) has emerged as a very efficient technology with higher resolution for the genome-wide identification of copy number alterations (CNA). Although CNAs are thought to affect gene expression, there is no platform currently available for the integrated CNA-expression analysis. To achieve high-resolution copy number analysis integrated with expression profiles, we established human 30k oligoarray-based genome-wide copy number analysis system and explored the applicability of this system for integrated genome and transcriptome analysis using MDA-MB-231 cell line. We compared the CNAs detected by the oligoarray with those detected by the 3k BAC array for validation. The oligoarray identified the single copy difference more accurately and sensitively than the BAC array. Seventeen CNAs detected by both platforms in MDA-MB-231 such as gains of 5p15.33-13.1, 8q11.22-8q21.13, 17p11.2, and losses of 1p32.3, 8p23.3-8p11.21, and 9p21 were consistently identified in previous studies on breast cancer. There were 122 other small CNAs (mean size 1.79 mb) that were detected by oligoarray only, not by BAC-array. We performed genomic qPCR targeting 7 CNA regions, detected by oligoarray only, and one non-CNA region to validate the oligoarray CNA detection. All qPCR results were consistent with the oligoarray-CGH results. When we explored the possibility of combined interpretation of both DNA copy number and RNA expression profiles, mean DNA copy number and RNA expression levels showed a significant correlation. In conclusion, this 30k oligoarray-CGH system can be a reasonable choice for analyzing whole genome CNAs and RNA expression profiles at a lower cost.

NorWood: a gene expression resource for evo-devo studies of conifer wood development.

PubMed

Jokipii-Lukkari, Soile; Sundell, David; Nilsson, Ove; Hvidsten, Torgeir R; Street, Nathaniel R; Tuominen, Hannele

2017-10-01

The secondary xylem of conifers is composed mainly of tracheids that differ anatomically and chemically from angiosperm xylem cells. There is currently no high-spatial-resolution data available profiling gene expression during wood formation for any coniferous species, which limits insight into tracheid development. RNA-sequencing data from replicated, high-spatial-resolution section series throughout the cambial and woody tissues of Picea abies were used to generate the NorWood.conGenIE.org web resource, which facilitates exploration of the associated gene expression profiles and co-expression networks. Integration within PlantGenIE.org enabled a comparative regulomics analysis, revealing divergent co-expression networks between P. abies and the two angiosperm species Arabidopsis thaliana and Populus tremula for the secondary cell wall (SCW) master regulator NAC Class IIB transcription factors. The SCW cellulose synthase genes (CesAs) were located in the neighbourhoods of the NAC factors in A. thaliana and P. tremula, but not in P. abies. The NorWood co-expression network enabled identification of potential SCW CesA regulators in P. abies. The NorWood web resource represents a powerful community tool for generating evo-devo insights into the divergence of wood formation between angiosperms and gymnosperms and for advancing understanding of the regulation of wood development in P. abies. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

A high resolution atlas of gene expression in the domestic sheep (Ovis aries)

PubMed Central

Farquhar, Iseabail L.; Young, Rachel; Lefevre, Lucas; Pridans, Clare; Tsang, Hiu G.; Afrasiabi, Cyrus; Watson, Mick; Whitelaw, C. Bruce; Freeman, Tom C.; Archibald, Alan L.; Hume, David A.

2017-01-01

Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The Ovis aries reference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset. Network-based cluster analysis of this dataset grouped genes according to their expression pattern. The principle of ‘guilt by association’ was used to infer the function of uncharacterised genes from their co-expression with genes of known function. We describe the overall transcriptional signatures present in the sheep gene expression atlas and assign those signatures, where possible, to specific cell populations or pathways. The findings are related to innate immunity by focusing on clusters with an immune signature, and to the advantages of cross-breeding by examining the patterns of genes exhibiting the greatest expression differences between purebred and crossbred animals. This high-resolution gene expression atlas for sheep is, to our knowledge, the largest transcriptomic dataset from any livestock species to date. It provides a resource to improve the annotation of the current reference genome for sheep, presenting a model transcriptome for ruminants and insight into gene, cell and tissue function at multiple developmental stages. PMID:28915238

A high resolution atlas of gene expression in the domestic sheep (Ovis aries).

PubMed

Clark, Emily L; Bush, Stephen J; McCulloch, Mary E B; Farquhar, Iseabail L; Young, Rachel; Lefevre, Lucas; Pridans, Clare; Tsang, Hiu G; Wu, Chunlei; Afrasiabi, Cyrus; Watson, Mick; Whitelaw, C Bruce; Freeman, Tom C; Summers, Kim M; Archibald, Alan L; Hume, David A

2017-09-01

Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The Ovis aries reference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset. Network-based cluster analysis of this dataset grouped genes according to their expression pattern. The principle of 'guilt by association' was used to infer the function of uncharacterised genes from their co-expression with genes of known function. We describe the overall transcriptional signatures present in the sheep gene expression atlas and assign those signatures, where possible, to specific cell populations or pathways. The findings are related to innate immunity by focusing on clusters with an immune signature, and to the advantages of cross-breeding by examining the patterns of genes exhibiting the greatest expression differences between purebred and crossbred animals. This high-resolution gene expression atlas for sheep is, to our knowledge, the largest transcriptomic dataset from any livestock species to date. It provides a resource to improve the annotation of the current reference genome for sheep, presenting a model transcriptome for ruminants and insight into gene, cell and tissue function at multiple developmental stages.

High-resolution time series of Pseudomonas aeruginosa gene expression and rhamnolipid secretion through growth curve synchronization.

PubMed

van Ditmarsch, Dave; Xavier, João B

2011-06-17

Online spectrophotometric measurements allow monitoring dynamic biological processes with high-time resolution. Contrastingly, numerous other methods require laborious treatment of samples and can only be carried out offline. Integrating both types of measurement would allow analyzing biological processes more comprehensively. A typical example of this problem is acquiring quantitative data on rhamnolipid secretion by the opportunistic pathogen Pseudomonas aeruginosa. P. aeruginosa cell growth can be measured by optical density (OD600) and gene expression can be measured using reporter fusions with a fluorescent protein, allowing high time resolution monitoring. However, measuring the secreted rhamnolipid biosurfactants requires laborious sample processing, which makes this an offline measurement. Here, we propose a method to integrate growth curve data with endpoint measurements of secreted metabolites that is inspired by a model of exponential cell growth. If serial diluting an inoculum gives reproducible time series shifted in time, then time series of endpoint measurements can be reconstructed using calculated time shifts between dilutions. We illustrate the method using measured rhamnolipid secretion by P. aeruginosa as endpoint measurements and we integrate these measurements with high-resolution growth curves measured by OD600 and expression of rhamnolipid synthesis genes monitored using a reporter fusion. Two-fold serial dilution allowed integrating rhamnolipid measurements at a ~0.4 h-1 frequency with high-time resolved data measured at a 6 h-1 frequency. We show how this simple method can be used in combination with mutants lacking specific genes in the rhamnolipid synthesis or quorum sensing regulation to acquire rich dynamic data on P. aeruginosa virulence regulation. Additionally, the linear relation between the ratio of inocula and the time-shift between curves produces high-precision measurements of maximum specific growth rates, which were determined with a precision of ~5.4%. Growth curve synchronization allows integration of rich time-resolved data with endpoint measurements to produce time-resolved quantitative measurements. Such data can be valuable to unveil the dynamic regulation of virulence in P. aeruginosa. More generally, growth curve synchronization can be applied to many biological systems thus helping to overcome a key obstacle in dynamic regulation: the scarceness of quantitative time-resolved data.

High resolution atomic force microscopy of double-stranded RNA.

PubMed

Ares, Pablo; Fuentes-Perez, Maria Eugenia; Herrero-Galán, Elías; Valpuesta, José M; Gil, Adriana; Gomez-Herrero, Julio; Moreno-Herrero, Fernando

2016-06-09

Double-stranded (ds) RNA mediates the suppression of specific gene expression, it is the genetic material of a number of viruses, and a key activator of the innate immune response against viral infections. The ever increasing list of roles played by dsRNA in the cell and its potential biotechnological applications over the last decade has raised an interest for the characterization of its mechanical properties and structure, and that includes approaches using Atomic Force Microscopy (AFM) and other single-molecule techniques. Recent reports have resolved the structure of dsDNA with AFM at unprecedented resolution. However, an equivalent study with dsRNA is still lacking. Here, we have visualized the double helix of dsRNA under near-physiological conditions and at sufficient resolution to resolve the A-form sub-helical pitch periodicity. We have employed different high-sensitive force-detection methods and obtained images with similar spatial resolution. Therefore, we show here that the limiting factors for high-resolution AFM imaging of soft materials in liquid medium are, rather than the imaging mode, the force between the tip and the sample and the sharpness of the tip apex.

Theory and design of interferometric synthetic aperture radars

NASA Technical Reports Server (NTRS)

Rodriguez, E.; Martin, J. M.

1992-01-01

A derivation of the signal statistics, an optimal estimator of the interferometric phase, and the expression necessary to calculate the height-error budget are presented. These expressions are used to derive methods of optimizing the parameters of the interferometric synthetic aperture radar system (InSAR), and are then employed in a specific design example for a system to perform high-resolution global topographic mapping with a one-year mission lifetime, subject to current technological constraints. A Monte Carlo simulation of this InSAR system is performed to evaluate its performance for realistic topography. The results indicate that this system has the potential to satisfy the stringent accuracy and resolution requirements for geophysical use of global topographic data.

Thermodynamical effects and high resolution methods for compressible fluid flows

NASA Astrophysics Data System (ADS)

Li, Jiequan; Wang, Yue

2017-08-01

One of the fundamental differences of compressible fluid flows from incompressible fluid flows is the involvement of thermodynamics. This difference should be manifested in the design of numerical schemes. Unfortunately, the role of entropy, expressing irreversibility, is often neglected even though the entropy inequality, as a conceptual derivative, is verified for some first order schemes. In this paper, we refine the GRP solver to illustrate how the thermodynamical variation is integrated into the design of high resolution methods for compressible fluid flows and demonstrate numerically the importance of thermodynamic effects in the resolution of strong waves. As a by-product, we show that the GRP solver works for generic equations of state, and is independent of technical arguments.

Light-sheet Bayesian microscopy enables deep-cell super-resolution imaging of heterochromatin in live human embryonic stem cells.

PubMed

Hu, Ying S; Zhu, Quan; Elkins, Keri; Tse, Kevin; Li, Yu; Fitzpatrick, James A J; Verma, Inder M; Cang, Hu

2013-01-01

Heterochromatin in the nucleus of human embryonic cells plays an important role in the epigenetic regulation of gene expression. The architecture of heterochromatin and its dynamic organization remain elusive because of the lack of fast and high-resolution deep-cell imaging tools. We enable this task by advancing instrumental and algorithmic implementation of the localization-based super-resolution technique. We present light-sheet Bayesian super-resolution microscopy (LSBM). We adapt light-sheet illumination for super-resolution imaging by using a novel prism-coupled condenser design to illuminate a thin slice of the nucleus with high signal-to-noise ratio. Coupled with a Bayesian algorithm that resolves overlapping fluorophores from high-density areas, we show, for the first time, nanoscopic features of the heterochromatin structure in both fixed and live human embryonic stem cells. The enhanced temporal resolution allows capturing the dynamic change of heterochromatin with a lateral resolution of 50-60 nm on a time scale of 2.3 s. Light-sheet Bayesian microscopy opens up broad new possibilities of probing nanometer-scale nuclear structures and real-time sub-cellular processes and other previously difficult-to-access intracellular regions of living cells at the single-molecule, and single cell level.

Light-sheet Bayesian microscopy enables deep-cell super-resolution imaging of heterochromatin in live human embryonic stem cells

PubMed Central

Hu, Ying S; Zhu, Quan; Elkins, Keri; Tse, Kevin; Li, Yu; Fitzpatrick, James A J; Verma, Inder M; Cang, Hu

2016-01-01

Background Heterochromatin in the nucleus of human embryonic cells plays an important role in the epigenetic regulation of gene expression. The architecture of heterochromatin and its dynamic organization remain elusive because of the lack of fast and high-resolution deep-cell imaging tools. We enable this task by advancing instrumental and algorithmic implementation of the localization-based super-resolution technique. Results We present light-sheet Bayesian super-resolution microscopy (LSBM). We adapt light-sheet illumination for super-resolution imaging by using a novel prism-coupled condenser design to illuminate a thin slice of the nucleus with high signal-to-noise ratio. Coupled with a Bayesian algorithm that resolves overlapping fluorophores from high-density areas, we show, for the first time, nanoscopic features of the heterochromatin structure in both fixed and live human embryonic stem cells. The enhanced temporal resolution allows capturing the dynamic change of heterochromatin with a lateral resolution of 50–60 nm on a time scale of 2.3 s. Conclusion Light-sheet Bayesian microscopy opens up broad new possibilities of probing nanometer-scale nuclear structures and real-time sub-cellular processes and other previously difficult-to-access intracellular regions of living cells at the single-molecule, and single cell level. PMID:27795878

SRRF: Universal live-cell super-resolution microscopy.

PubMed

Culley, Siân; Tosheva, Kalina L; Matos Pereira, Pedro; Henriques, Ricardo

2018-08-01

Super-resolution microscopy techniques break the diffraction limit of conventional optical microscopy to achieve resolutions approaching tens of nanometres. The major advantage of such techniques is that they provide resolutions close to those obtainable with electron microscopy while maintaining the benefits of light microscopy such as a wide palette of high specificity molecular labels, straightforward sample preparation and live-cell compatibility. Despite this, the application of super-resolution microscopy to dynamic, living samples has thus far been limited and often requires specialised, complex hardware. Here we demonstrate how a novel analytical approach, Super-Resolution Radial Fluctuations (SRRF), is able to make live-cell super-resolution microscopy accessible to a wider range of researchers. We show its applicability to live samples expressing GFP using commercial confocal as well as laser- and LED-based widefield microscopes, with the latter achieving long-term timelapse imaging with minimal photobleaching. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

High-level expression, purification, crystallization and preliminary X-ray crystallographic studies of the receptor binding domain of botulinum neurotoxin serotype D

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

Zhang, Yanfeng; Gao, Xiaoli; Qin, Lin

2010-12-01

Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and can cause neuroparalytic disease botulism. Due to the limitations of production and manipulation of holoenzymes, expressing non-toxic heavy chain receptor binding domains (HCR) has become a common strategy for vaccine and antibody development. Meanwhile, large quantities and highly purified soluble proteins are required for research areas such as antibody maturation and structural biology. We present high level expression and purification of the BoNT serotype D HCR in E. coli using a codon-optimized cDNA. By varying expression conditions, especially at low temperature, the protein was expressed at a high level withmore » high solubility. About 150-200 mg protein was purified to >90% purity from 1 L cell culture. The recombinant D_HCR was crystallized and the crystals diffracted to 1.65 Å resolution. The crystals belong to space group P212121 with unit cell dimensions a = 60.8 Å, b = 89.7 Å, c = 93.9 Å. Preliminary crystallographic data analysis revealed one molecule in asymmetric unit.« less

Using high-resolution multibeam bathymetry to identify seafloor surface rupture along the Palos Verdes fault complex in offshore Southern California

USGS Publications Warehouse

Marlow, M. S.; Gardner, J.V.; Normark, W.R.

2000-01-01

Recently acquired high-resolution multibeam bathymetric data reveal several linear traces that are the surficial expressions of seafloor rupture of Holocene faults on the upper continental slope southeast of the Palos Verdes Peninsula. High-resolution multichannel and boomer seismic-reflection profiles show that these linear ruptures are the surficial expressions of Holocene faults with vertical to steep dips. The most prominent fault on the multibeam bathymetry is about 10 km to the west of the mapped trace of the Palos Verdes fault and extends for at least 14 km between the shelf edge and the base of the continental slope. This fault is informally called the Avalon Knoll fault for the nearby geographic feature of that name. Seismic-reflection profiles show that the Avalon Knoll fault is part of a northwest-trending complex of faults and anticlinal uplifts that are evident as scarps and bathymetric highs on the multibeam bathymetry. This fault complex may extend onshore and contribute to the missing balance of Quaternary uplift determined for the Palos Verdes Hills and not accounted for by vertical uplift along the onshore Palos Verdes fault. We investigate the extent of the newly located offshore Avalon Knoll fault and use this mapped fault length to estimate likely minimum magnitudes for events along this fault.

Light-patterning of synthetic tissues with single droplet resolution.

PubMed

Booth, Michael J; Restrepo Schild, Vanessa; Box, Stuart J; Bayley, Hagan

2017-08-24

Synthetic tissues can be generated by forming networks of aqueous droplets in lipid-containing oil. Each droplet contains a cell-free expression system and is connected to its neighbor through a lipid bilayer. In the present work, we have demonstrated precise external control of such networks by activating protein expression within single droplets, by using light-activated DNA to encode either a fluorescent or a pore-forming protein. By controlling the extent of activation, synthetic tissues were generated with graded levels of protein expression in patterns of single droplets. Further, we have demonstrated reversible activation within individual compartments in synthetic tissues by turning a fluorescent protein on-and-off. This is the first example of the high-resolution patterning of droplet networks, following their formation. Single-droplet control will be essential to power subsets of compartments within synthetic tissues or to stimulate subsets of cells when synthetic tissues are interfaced with living tissues.

Microscopy and microanalysis 1996

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

Bailey, G.W.; Corbett, J.M.; Dimlich, R.V.W.

1996-12-31

The Proceedings of this Annual Meeting contain paper of members from the three societies. These proceedings emphasizes the common research interests and attempts to eliminate some unwanted overlap. Topics covered are: microscopic analysis of animals with altered gene expression and in-situ gene and antibody localizations, high-resolution elemental mapping of nucleoprofein interactions, plant biology and pathology, quantitative HREM analysis of perfect and defected materials, computational methods for TEM image analysis, high-resolution FESM in materials research, frontiers in polymer microscopy and microanalysis, oxidation and corrosion, micro XRD and XRF, molecular microspectroscopy and spectral imaging, advances in confocal and multidimensional light microscopy, analyticalmore » electron microscopy in biology, correlative microscopy in biological sciences, grain-boundary microengineering, surfaces and interfaces, telepresence microscopy in education and research, MSA educational outreach, quantitative electron probe microanalysis, frontiers of analytical electron microscopy, critical issues in ceramic microstructures, dynamic organization of the cell, pathology, microbiology, high-resolution biological and cryo SEM, and scanning-probe microscopy.« less

Rachiplusia nu larva as a biofactory to achieve high level expression of horseradish peroxidase.

PubMed

Romero, Lucía Virginia; Targovnik, Alexandra Marisa; Wolman, Federico Javier; Cascone, Osvaldo; Miranda, María Victoria

2011-05-01

A process based on orally-infected Rachiplusia nu larvae as biological factories for expression and one-step purification of horseradish peroxidase isozyme C (HRP-C) is described. The process allows obtaining high levels of pure HRP-C by membrane chromatography purification. The introduction of the partial polyhedrin homology sequence element in the target gene increased HRP-C expression level by 2.8-fold whereas it increased 1.8-fold when the larvae were reared at 27 °C instead of at 24 °C, summing up a 4.6-fold overall increase in the expression level. Additionally, HRP-C purification by membrane chromatography at a high flow rate greatly increase D the productivity without affecting the resolution. The V(max) and K(m) values of the recombinant HRP-C were similar to those of the HRP from Armoracia rusticana roots. © Springer Science+Business Media B.V. 2011

Expression, Purification, and Structural Insights for the Human Uric Acid Transporter, GLUT9, Using the Xenopus laevis Oocytes System

PubMed Central

Clémençon, Benjamin; Lüscher, Benjamin P.; Fine, Michael; Baumann, Marc U.; Surbek, Daniel V.; Bonny, Olivier; Hediger, Matthias A.

2014-01-01

The urate transporter, GLUT9, is responsible for the basolateral transport of urate in the proximal tubule of human kidneys and in the placenta, playing a central role in uric acid homeostasis. GLUT9 shares the least homology with other members of the glucose transporter family, especially with the glucose transporting members GLUT1-4 and is the only member of the GLUT family to transport urate. The recently published high-resolution structure of XylE, a bacterial D-xylose transporting homologue, yields new insights into the structural foundation of this GLUT family of proteins. While this represents a huge milestone, it is unclear if human GLUT9 can benefit from this advancement through subsequent structural based targeting and mutagenesis. Little progress has been made toward understanding the mechanism of GLUT9 since its discovery in 2000. Before work can begin on resolving the mechanisms of urate transport we must determine methods to express, purify and analyze hGLUT9 using a model system adept in expressing human membrane proteins. Here, we describe the surface expression, purification and isolation of monomeric protein, and functional analysis of recombinant hGLUT9 using the Xenopus laevis oocyte system. In addition, we generated a new homology-based high-resolution model of hGLUT9 from the XylE crystal structure and utilized our purified protein to generate a low-resolution single particle reconstruction. Interestingly, we demonstrate that the functional protein extracted from the Xenopus system fits well with the homology-based model allowing us to generate the predicted urate-binding pocket and pave a path for subsequent mutagenesis and structure-function studies. PMID:25286413

Farewell to the Earth and the Moon -ESA's Mars Express successfully tests its instruments

NASA Astrophysics Data System (ADS)

2003-07-01

The routine check-outs of Mars Express's instruments and of the Beagle-2 lander, performed during the last weeks, have been very successful. "As in all space missions little problems have arisen, but they have been carefully evaluated and solved. Mars Express continues on its way to Mars performing beautifully", comments Chicarro. The views of the Earth/Moon system were taken on 3 July 2003 by Mars Express's High Resolution Stereo Camera (HRSC), when the spacecraft was 8 million kilometres from Earth. The image taken shows true colours; the Pacific Ocean appears in blue, and the clouds near the Equator and in mid to northern latitudes in white to light grey. The image was processed by the Instrument Team at the Institute of Planetary Research of DLR, Berlin (Germany). It was built by combining a super resolution black and white HRSC snap-shot image of the Earth and the Moon with colour information obtained by the blue, green, and red sensors of the instrument. “The pictures and the information provided by the data prove the camera is working very well. They provide a good indication of what to expect once the spacecraft is in its orbit around Mars, at altitudes of only 250-300 kilometres: very high resolution images with brilliant true colour and in 3D,” says the Principal Investigator of the HRSC, Gerhard Neukum, of the Freie Universität of Berlin (Germany). This camera will be able to distinguish details of up to 2 metres on the Martian surface. Another striking demonstration of Mars Express's instruments high performance are the data taken by the OMEGA spectrometer. Once at Mars, this instrument will provide the best map of the molecular and mineralogical composition of the whole planet, with 5% of the planetary surface in high resolution. Minerals and other compounds such as water will be charted as never before. As the Red Planet is still too far away, the OMEGA team devised an ingenious test for their instrument: to detect the Earth’s surface components. As expected, OMEGA made a direct and unambiguous detection of major and minor constituents of the Earth’s atmosphere, such as molecular oxygen, water and carbon dioxide, ozone and methane, among other molecules. "The sensitivity demonstrated by OMEGA on these Earth spectra should reveal really minute amounts of water in both Martian surface materials and atmosphere," says the Principal Investigator of OMEGA, Jean Pierre Bibring , from the Institut d'Astrophysique Spatiale, Orsay, France. The experts will carry on testing Mars Express’s instruments up till the arrival to the Red Planet, next December. The scientists agree on the fact that these instruments will enormously increase our understanding of the morphology and topography of the Martian surface, of the geological structures and processes - active now and in the past, and eventually of Mars’s geological evolution. With such tools, Mars Express is also able to address the important “water” question, namely how much water there is today and how much there was in the past. Ultimately, this will also tell us whether Mars had environmental conditions that could favour the evolution of life. Note to editors The Mars Express High Resolution Stereo Camera (HRSC) was developed by the German Aerospace Centre (DLR) and built by EADS-Astrium GmbH in Friedrichshafen, Germany. The Mars Express OMEGA spectrometer was developed and built by the Institut d'Astrophysique Spatiale, Orsay, France, in cooperation with LESIA at Meudon/Paris Observatory, France, IFSI in Frascati, Italy, and IKI in Moscow, Russia.

Detecting differential allelic expression using high-resolution melting curve analysis: application to the breast cancer susceptibility gene CHEK2

PubMed Central

2011-01-01

Background The gene CHEK2 encodes a checkpoint kinase playing a key role in the DNA damage pathway. Though CHEK2 has been identified as an intermediate breast cancer susceptibility gene, only a small proportion of high-risk families have been explained by genetic variants located in its coding region. Alteration in gene expression regulation provides a potential mechanism for generating disease susceptibility. The detection of differential allelic expression (DAE) represents a sensitive assay to direct the search for a functional sequence variant within the transcriptional regulatory elements of a candidate gene. We aimed to assess whether CHEK2 was subject to DAE in lymphoblastoid cell lines (LCLs) from high-risk breast cancer patients for whom no mutation in BRCA1 or BRCA2 had been identified. Methods We implemented an assay based on high-resolution melting (HRM) curve analysis and developed an analysis tool for DAE assessment. Results We observed allelic expression imbalance in 4 of the 41 LCLs examined. All four were carriers of the truncating mutation 1100delC. We confirmed previous findings that this mutation induces non-sense mediated mRNA decay. In our series, we ruled out the possibility of a functional sequence variant located in the promoter region or in a regulatory element of CHEK2 that would lead to DAE in the transcriptional regulatory milieu of freely proliferating LCLs. Conclusions Our results support that HRM is a sensitive and accurate method for DAE assessment. This approach would be of great interest for high-throughput mutation screening projects aiming to identify genes carrying functional regulatory polymorphisms. PMID:21569354

iGen: An automated generator of simplified models with provable error bounds.

NASA Astrophysics Data System (ADS)

Tang, D.; Dobbie, S.

2009-04-01

Climate models employ various simplifying assumptions and parameterisations in order to increase execution speed. However, in order to draw conclusions about the Earths climate from the results of a climate simulation it is necessary to have information about the error that these assumptions and parameterisations introduce. A novel computer program, called iGen, is being developed which automatically generates fast, simplified models by analysing the source code of a slower, high resolution model. The resulting simplified models have provable bounds on error compared to the high resolution model and execute at speeds that are typically orders of magnitude faster. iGen's input is a definition of the prognostic variables of the simplified model, a set of bounds on acceptable error and the source code of a model that captures the behaviour of interest. In the case of an atmospheric model, for example, this would be a global cloud resolving model with very high resolution. Although such a model would execute far too slowly to be used directly in a climate model, iGen never executes it. Instead, it converts the code of the resolving model into a mathematical expression which is then symbolically manipulated and approximated to form a simplified expression. This expression is then converted back into a computer program and output as a simplified model. iGen also derives and reports formal bounds on the error of the simplified model compared to the resolving model. These error bounds are always maintained below the user-specified acceptable error. Results will be presented illustrating the success of iGen's analysis of a number of example models. These extremely encouraging results have lead on to work which is currently underway to analyse a cloud resolving model and so produce an efficient parameterisation of moist convection with formally bounded error.

Neuregulin: First Steps Towards a Structure

NASA Technical Reports Server (NTRS)

Ferree, D. S.; Malone, C. C.; Karr, L. J.

2003-01-01

Neuregulins are growth factor domain proteins with diverse bioactivities, such as cell proliferation, receptor binding, and differentiation. Neureguh- 1 binds to two members of the ErbB class I tyrosine kinase receptors, ErbB3 and ErbB4. A number of human cancers overexpress the ErbB receptors, and neuregulin can modulate the growth of certain cancer types. Neuregulin-1 has been shown to promote the migration of invasive gliomas of the central nervous system. Neuregulin has also been implicated in schizophrenia, multiple sclerosis and abortive cardiac abnormalities. The full function of neuregulin-1 is not known. In this study we are inserting a cDNA clone obtained from American Type Culture Collection into E.coli expression vectors to express neuregulin- 1 protein. Metal chelate affinity chromatography is used for recombinant protein purification. Crystallization screening will proceed for X-ray diffraction studies following expression, optimization, and protein purification. In spite of medical and scholarly interest in the neuregulins, there are currently no high-resolution structures available for these proteins. Here we present the first steps toward attaining a high-resolution structure of neuregulin- 1, which will help enable us to better understand its function

Arabidopsis Defense against Botrytis cinerea: Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis[C][W

PubMed Central

Windram, Oliver; Madhou, Priyadharshini; McHattie, Stuart; Hill, Claire; Hickman, Richard; Cooke, Emma; Jenkins, Dafyd J.; Penfold, Christopher A.; Baxter, Laura; Breeze, Emily; Kiddle, Steven J.; Rhodes, Johanna; Atwell, Susanna; Kliebenstein, Daniel J.; Kim, Youn-sung; Stegle, Oliver; Borgwardt, Karsten; Zhang, Cunjin; Tabrett, Alex; Legaie, Roxane; Moore, Jonathan; Finkenstadt, Bärbel; Wild, David L.; Mead, Andrew; Rand, David; Beynon, Jim; Ott, Sascha; Buchanan-Wollaston, Vicky; Denby, Katherine J.

2012-01-01

Transcriptional reprogramming forms a major part of a plant’s response to pathogen infection. Many individual components and pathways operating during plant defense have been identified, but our knowledge of how these different components interact is still rudimentary. We generated a high-resolution time series of gene expression profiles from a single Arabidopsis thaliana leaf during infection by the necrotrophic fungal pathogen Botrytis cinerea. Approximately one-third of the Arabidopsis genome is differentially expressed during the first 48 h after infection, with the majority of changes in gene expression occurring before significant lesion development. We used computational tools to obtain a detailed chronology of the defense response against B. cinerea, highlighting the times at which signaling and metabolic processes change, and identify transcription factor families operating at different times after infection. Motif enrichment and network inference predicted regulatory interactions, and testing of one such prediction identified a role for TGA3 in defense against necrotrophic pathogens. These data provide an unprecedented level of detail about transcriptional changes during a defense response and are suited to systems biology analyses to generate predictive models of the gene regulatory networks mediating the Arabidopsis response to B. cinerea. PMID:23023172

Peace Education and Conflict Resolution through the Expressive Arts in Early Childhood Education and Teacher Education.

ERIC Educational Resources Information Center

Hinitz, Blythe F.; Stomfay-Stitz, Aline M.

Several modes of expressive arts may be especially appropriate for peace education and conflict resolution instruction in early childhood and teacher education classrooms. This paper explores the integration of the concepts and processes of peace education and conflict resolution through an examination of current research and professional…

Evaluating planetary digital terrain models-The HRSC DTM test

USGS Publications Warehouse

Heipke, C.; Oberst, J.; Albertz, J.; Attwenger, M.; Dorninger, P.; Dorrer, E.; Ewe, M.; Gehrke, S.; Gwinner, K.; Hirschmuller, H.; Kim, J.R.; Kirk, R.L.; Mayer, H.; Muller, Jan-Peter; Rengarajan, R.; Rentsch, M.; Schmidt, R.; Scholten, F.; Shan, J.; Spiegel, M.; Wahlisch, M.; Neukum, G.

2007-01-01

The High Resolution Stereo Camera (HRSC) has been orbiting the planet Mars since January 2004 onboard the European Space Agency (ESA) Mars Express mission and delivers imagery which is being used for topographic mapping of the planet. The HRSC team has conducted a systematic inter-comparison of different alternatives for the production of high resolution digital terrain models (DTMs) from the multi look HRSC push broom imagery. Based on carefully chosen test sites the test participants have produced DTMs which have been subsequently analysed in a quantitative and a qualitative manner. This paper reports on the results obtained in this test. ?? 2007 Elsevier Ltd. All rights reserved.

Cone arrestin confers cone vision of high temporal resolution in zebrafish larvae.

PubMed

Renninger, Sabine L; Gesemann, Matthias; Neuhauss, Stephan C F

2011-02-01

Vision of high temporal resolution depends on careful regulation of photoresponse kinetics, beginning with the lifetime of activated photopigment. The activity of rhodopsin is quenched by high-affinity binding of arrestin to photoexcited phosphorylated photopigment, which effectively terminates the visual transduction cascade. This regulation mechanism is well established for rod photoreceptors, yet its role for cone vision is still controversial. In this study we therefore analyzed arrestin function in the cone-dominated vision of larval zebrafish. For both rod (arrS ) and cone (arr3 ) arrestin we isolated two paralogs, each expressed in the respective subset of photoreceptors. Labeling with paralog-specific antibodies revealed subfunctionalized expression of Arr3a in M- and L-cones, and Arr3b in S- and UV-cones. The inactivation of arr3a by morpholino knockdown technology resulted in a severe delay in photoresponse recovery which, under bright light conditions, was rate-limiting. Comparison to opsin phosphorylation-deficient animals confirmed the role of cone arrestin in late cone response recovery. Arr3a activity partially overlapped with the function of the cone-specific kinase Grk7a involved in initial response recovery. Behavioral measurements further revealed Arr3a deficiency to be sufficient to reduce temporal contrast sensitivity, providing evidence for the importance of arrestin in cone vision of high temporal resolution. © 2011 The Authors. European Journal of Neuroscience © 2011 Federation of European Neuroscience Societies and Blackwell Publishing Ltd.

A Two-Stage Framework for 3D Face Reconstruction from RGBD Images.

PubMed

Wang, Kangkan; Wang, Xianwang; Pan, Zhigeng; Liu, Kai

2014-08-01

This paper proposes a new approach for 3D face reconstruction with RGBD images from an inexpensive commodity sensor. The challenges we face are: 1) substantial random noise and corruption are present in low-resolution depth maps; and 2) there is high degree of variability in pose and face expression. We develop a novel two-stage algorithm that effectively maps low-quality depth maps to realistic face models. Each stage is targeted toward a certain type of noise. The first stage extracts sparse errors from depth patches through the data-driven local sparse coding, while the second stage smooths noise on the boundaries between patches and reconstructs the global shape by combining local shapes using our template-based surface refinement. Our approach does not require any markers or user interaction. We perform quantitative and qualitative evaluations on both synthetic and real test sets. Experimental results show that the proposed approach is able to produce high-resolution 3D face models with high accuracy, even if inputs are of low quality, and have large variations in viewpoint and face expression.

Spatially resolved RNA-sequencing of the embryonic heart identifies a role for Wnt/β-catenin signaling in autonomic control of heart rate

PubMed Central

Burkhard, Silja Barbara

2018-01-01

Development of specialized cells and structures in the heart is regulated by spatially -restricted molecular pathways. Disruptions in these pathways can cause severe congenital cardiac malformations or functional defects. To better understand these pathways and how they regulate cardiac development we used tomo-seq, combining high-throughput RNA-sequencing with tissue-sectioning, to establish a genome-wide expression dataset with high spatial resolution for the developing zebrafish heart. Analysis of the dataset revealed over 1100 genes differentially expressed in sub-compartments. Pacemaker cells in the sinoatrial region induce heart contractions, but little is known about the mechanisms underlying their development. Using our transcriptome map, we identified spatially restricted Wnt/β-catenin signaling activity in pacemaker cells, which was controlled by Islet-1 activity. Moreover, Wnt/β-catenin signaling controls heart rate by regulating pacemaker cellular response to parasympathetic stimuli. Thus, this high-resolution transcriptome map incorporating all cell types in the embryonic heart can expose spatially restricted molecular pathways critical for specific cardiac functions. PMID:29400650

High Resolution Observations of Escaping Ions in the Martian Magnetotail

NASA Astrophysics Data System (ADS)

Halekas, J. S.; Raman, C.; Brain, D.; DiBraccio, G. A.; Harada, Y.; McFadden, J. P.; Mitchell, D. L.; Connerney, J. E. P.; Jakosky, B. M.

2016-12-01

Ions escape from the Martian upper atmosphere via a number of channels, including the central plasmasheet of the magnetotail. Mars Express observations show that the heavy ions O+ and O2+ escaping through the central tail often have approximately the same energy, suggesting acceleration in a quasi-static electric field, which has been interpreted as a Hall electric field. The Solar Wind Ion Analyzer (SWIA) on MAVEN was designed to measure the upstream solar wind. However, during orbit segments with appropriate spacecraft attitude, SWIA can also make high resolution measurements of escaping ions in the tail. During the prime mission, these observations were only returned sporadically, during periods of intense escaping fluxes that fortuitously triggered a mode switch. Now, in the extended mission, we return high resolution observations from SWIA routinely. Some of these high resolution measurements reveal slight differences in both the direction and energy of escaping O+ and O2+ ions, which may help determine the acceleration process(es). We investigate the location and solar wind conditions for which the escaping ions separate in energy and angle and the systematics of their energies and flow vectors, and discuss the implications for ion acceleration and the overall picture of Martian atmospheric escape.

Combined lineage mapping and gene expression profiling of embryonic brain patterning using ultrashort pulse microscopy and image registration

NASA Astrophysics Data System (ADS)

Gibbs, Holly C.; Dodson, Colin R.; Bai, Yuqiang; Lekven, Arne C.; Yeh, Alvin T.

2014-12-01

During embryogenesis, presumptive brain compartments are patterned by dynamic networks of gene expression. The spatiotemporal dynamics of these networks, however, have not been characterized with sufficient resolution for us to understand the regulatory logic resulting in morphogenetic cellular behaviors that give the brain its shape. We have developed a new, integrated approach using ultrashort pulse microscopy [a high-resolution, two-photon fluorescence (2PF)-optical coherence microscopy (OCM) platform using 10-fs pulses] and image registration to study brain patterning and morphogenesis in zebrafish embryos. As a demonstration, we used time-lapse 2PF to capture midbrain-hindbrain boundary morphogenesis and a wnt1 lineage map from embryos during brain segmentation. We then performed in situ hybridization to deposit NBT/BCIP, where wnt1 remained actively expressed, and reimaged the embryos with combined 2PF-OCM. When we merged these datasets using morphological landmark registration, we found that the mechanism of boundary formation differs along the dorsoventral axis. Dorsally, boundary sharpening is dominated by changes in gene expression, while ventrally, sharpening may be accomplished by lineage sorting. We conclude that the integrated visualization of lineage reporter and gene expression domains simultaneously with brain morphology will be useful for understanding how changes in gene expression give rise to proper brain compartmentalization and structure.

Combined lineage mapping and gene expression profiling of embryonic brain patterning using ultrashort pulse microscopy and image registration.

PubMed

Gibbs, Holly C; Dodson, Colin R; Bai, Yuqiang; Lekven, Arne C; Yeh, Alvin T

2014-12-01

During embryogenesis, presumptive brain compartments are patterned by dynamic networks of gene expression. The spatiotemporal dynamics of these networks, however, have not been characterized with sufficient resolution for us to understand the regulatory logic resulting in morphogenetic cellular behaviors that give the brain its shape. We have developed a new, integrated approach using ultrashort pulse microscopy [a high-resolution, two-photon fluorescence (2PF)-optical coherence microscopy (OCM) platform using 10-fs pulses] and image registration to study brain patterning and morphogenesis in zebrafish embryos. As a demonstration, we used time-lapse 2PF to capture midbrain-hindbrain boundary morphogenesis and a wnt1 lineage map from embryos during brain segmentation. We then performed in situ hybridization to deposit NBT/BCIP, where wnt1 remained actively expressed, and reimaged the embryos with combined 2PF-OCM. When we merged these datasets using morphological landmark registration, we found that the mechanism of boundary formation differs along the dorsoventral axis. Dorsally, boundary sharpening is dominated by changes in gene expression, while ventrally, sharpening may be accomplished by lineage sorting. We conclude that the integrated visualization of lineage reporter and gene expression domains simultaneously with brain morphology will be useful for understanding how changes in gene expression give rise to proper brain compartmentalization and structure.

A quick and simple FISH protocol with hybridization-sensitive fluorescent linear oligodeoxynucleotide probes

PubMed Central

Wang, Dan Ohtan; Matsuno, Hitomi; Ikeda, Shuji; Nakamura, Akiko; Yanagisawa, Hiroyuki; Hayashi, Yasunori; Okamoto, Akimitsu

2012-01-01

Fluorescence in situ hybridization (FISH) is a powerful tool used in karyotyping, cytogenotyping, cancer diagnosis, species specification, and gene-expression analysis. Although widely used, conventional FISH protocols are cumbersome and time consuming. We have now developed a FISH method using exciton-controlled hybridization-sensitive fluorescent oligodeoxynucleotide (ECHO) probes. ECHO–FISH uses a 25-min protocol from fixation to mounting that includes no stringency washing steps. We use ECHO–FISH to detect both specific DNA and RNA sequences with multicolor probes. ECHO–FISH is highly reproducible, stringent, and compatible with other fluorescent cellular labeling techniques. The resolution allows detection of intranuclear speckles of poly(A) RNA in HeLa cells and dissociated hippocampal primary cultures, and mRNAs in the distal dendrites of hippocampal neurons. We also demonstrate detection of telomeric and centromeric DNA on metaphase mouse chromosomes. The simplicity of the ECHO–FISH method will likely accelerate cytogenetic and gene-expression analysis with high resolution. PMID:22101241

Cloning, expression, purification, and characterisation of the HEAT-repeat domain of TOR from the thermophilic eukaryote Chaetomium thermophilum.

PubMed

Robinson, Graham C; Vegunta, Yogesh; Gabus, Caroline; Gaubitz, Christl; Thore, Stéphane

2017-05-01

The Target of Rapamycin Complex is a central controller of cell growth and differentiation in eukaryotes. Its global architecture has been described by cryoelectron microscopy, and regions of its central TOR protein have been described by X-ray crystallography. However, the N-terminal region of this protein, which consists of a series of HEAT repeats, remains uncharacterised at high resolution, most likely due to the absence of a suitable purification procedure. Here, we present a robust method for the preparation of the HEAT-repeat domain, utilizing the thermophilic fungus Chaetomium thermophilum as a source organism. We describe construct design and stable expression in insect cells. An efficient two-step purification procedure is presented, and the purified product is characterised by SEC and MALDI-TOF MS. The methods described pave the way for a complete high-resolution characterisation of this elusive region of the TOR protein. Copyright © 2017 Elsevier Inc. All rights reserved.

High-resolution molecular validation of self-renewal and spontaneous differentiation in adipose-tissue derived human mesenchymal stem cells cultured in human platelet lysate

PubMed Central

Dudakovic, Amel Dudakovic; Camilleri, Emily; Riester, Scott M.; Lewallen, Eric A.; Kvasha, Sergiy; Chen, Xiaoyue; Radel, Darcie J.; Anderson, Jarett M.; Nair, Asha A.; Evans, Jared M.; Krych, Aaron J.; Smith, Jay; Deyle, David R.; Stein, Janet L.; Stein, Gary S.; Im, Hee-Jeong; Cool, Simon M.; Westendorf, Jennifer J.; Kakar, Sanjeev; Dietz, Allan B.; van Wijnen, Andre J.

2014-01-01

Improving the effectiveness of adipose-tissue derived human mesenchymal stromal/stem cells (AMSCs) for skeletal therapies requires a detailed characterization of mechanisms supporting cell proliferation and multi-potency. We investigated the molecular phenotype of AMSCs that were either actively proliferating in platelet lysate or in a basal non-proliferative state. Flow cytometry combined with high-throughput RNA sequencing (RNASeq) and RT-qPCR analyses validate that AMSCs express classic mesenchymal cell surface markers (e.g., CD44, CD73/NT5E, CD90/THY1 and CD105/ENG). Expression of CD90 is selectively elevated at confluence. Self-renewing AMSCs express a standard cell cycle program that successively mediates DNA replication, chromatin packaging, cyto-architectural enlargement and mitotic division. Confluent AMSCs preferentially express genes involved in extracellular matrix (ECM) formation and cellular communication. For example, cell cycle-related biomarkers (e.g., cyclins E2 and B2, transcription factor E2F1) and histone-related genes (e.g., H4, HINFP, NPAT) are elevated in proliferating AMSCs, while ECM genes are strongly upregulated (>10 fold) in quiescent AMSCs. AMSCs also express pluripotency genes (e.g., POU5F1, NANOG, KLF4) and early mesenchymal markers (e.g., NES, ACTA2) consistent with their multipotent phenotype. Strikingly, AMSCs modulate expression of WNT signaling components and switch production of WNT ligands (from WNT5A/WNT5B/WNT7B to WNT2/WNT2B), while up-regulating WNT-related genes (WISP2, SFRP2 and SFRP4). Furthermore, post-proliferative AMSCs spontaneously express fibroblastic, osteogenic, chondrogenic and adipogenic biomarkers when maintained in confluent cultures. Our findings validate the biological properties of self-renewing and multi-potent AMSCs by providing high-resolution quality control data that support their clinical versatility. PMID:24905804

Sparsity of the normal matrix in the refinement of macromolecules at atomic and subatomic resolution.

PubMed

Jelsch, C

2001-09-01

The normal matrix in the least-squares refinement of macromolecules is very sparse when the resolution reaches atomic and subatomic levels. The elements of the normal matrix, related to coordinates, thermal motion and charge-density parameters, have a global tendency to decrease rapidly with the interatomic distance between the atoms concerned. For instance, in the case of the protein crambin at 0.54 A resolution, the elements are reduced by two orders of magnitude for distances above 1.5 A. The neglect a priori of most of the normal-matrix elements according to a distance criterion represents an approximation in the refinement of macromolecules, which is particularly valid at very high resolution. The analytical expressions of the normal-matrix elements, which have been derived for the coordinates and the thermal parameters, show that the degree of matrix sparsity increases with the diffraction resolution and the size of the asymmetric unit.

Microscopic Optical Projection Tomography In Vivo

PubMed Central

Meyer, Heiko; Ripoll, Jorge; Tavernarakis, Nektarios

2011-01-01

We describe a versatile optical projection tomography system for rapid three-dimensional imaging of microscopic specimens in vivo. Our tomographic setup eliminates the in xy and z strongly asymmetric resolution, resulting from optical sectioning in conventional confocal microscopy. It allows for robust, high resolution fluorescence as well as absorption imaging of live transparent invertebrate animals such as C. elegans. This system offers considerable advantages over currently available methods when imaging dynamic developmental processes and animal ageing; it permits monitoring of spatio-temporal gene expression and anatomical alterations with single-cell resolution, it utilizes both fluorescence and absorption as a source of contrast, and is easily adaptable for a range of small model organisms. PMID:21559481

iCLIP: Protein–RNA interactions at nucleotide resolution

PubMed Central

Huppertz, Ina; Attig, Jan; D’Ambrogio, Andrea; Easton, Laura E.; Sibley, Christopher R.; Sugimoto, Yoichiro; Tajnik, Mojca; König, Julian; Ule, Jernej

2014-01-01

RNA-binding proteins (RBPs) are key players in the post-transcriptional regulation of gene expression. Precise knowledge about their binding sites is therefore critical to unravel their molecular function and to understand their role in development and disease. Individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) identifies protein–RNA crosslink sites on a genome-wide scale. The high resolution and specificity of this method are achieved by an intramolecular cDNA circularization step that enables analysis of cDNAs that truncated at the protein–RNA crosslink sites. Here, we describe the improved iCLIP protocol and discuss critical optimization and control experiments that are required when applying the method to new RBPs. PMID:24184352

Retinal Prosthetics, Optogenetics, and Chemical Photoswitches

PubMed Central

2015-01-01

Three technologies have emerged as therapies to restore light sensing to profoundly blind patients suffering from late-stage retinal degenerations: (1) retinal prosthetics, (2) optogenetics, and (3) chemical photoswitches. Prosthetics are the most mature and the only approach in clinical practice. Prosthetic implants require complex surgical intervention and provide only limited visual resolution but can potentially restore navigational ability to many blind patients. Optogenetics uses viral delivery of type 1 opsin genes from prokaryotes or eukaryote algae to restore light responses in survivor neurons. Targeting and expression remain major problems, but are potentially soluble. Importantly, optogenetics could provide the ultimate in high-resolution vision due to the long persistence of gene expression achieved in animal models. Nevertheless, optogenetics remains challenging to implement in human eyes with large volumes, complex disease progression, and physical barriers to viral penetration. Now, a new generation of photochromic ligands or chemical photoswitches (azobenzene-quaternary ammonium derivatives) can be injected into a degenerated mouse eye and, in minutes to hours, activate light responses in neurons. These photoswitches offer the potential for rapidly and reversibly screening the vision restoration expected in an individual patient. Chemical photoswitch variants that persist in the cell membrane could make them a simple therapy of choice, with resolution and sensitivity equivalent to optogenetics approaches. A major complexity in treating retinal degenerations is retinal remodeling: pathologic network rewiring, molecular reprogramming, and cell death that compromise signaling in the surviving retina. Remodeling forces a choice between upstream and downstream targeting, each engaging different benefits and defects. Prosthetics and optogenetics can be implemented in either mode, but the use of chemical photoswitches is currently limited to downstream implementations. Even so, given the high density of human foveal ganglion cells, the ultimate chemical photoswitch treatment could deliver cost-effective, high-resolution vision for the blind. PMID:25089879

The Martian Neutral Atmosphere from the Radio Science Experiment MaRS on Mars Express

NASA Astrophysics Data System (ADS)

Tellmann, Silvia; Paetzold, Martin; Haeusler, Bernd; Tyler, G. L.; Hinson, David P.

The Mars Express Radio Science Experiment (MaRS) has been sounding the Martian atmo-sphere and ionosphere by means of radio occultation since 2004. To date more than 570 sound-ings covering all latitudes during almost all seasons have been obtained in seven occultation seasons, mostly in the northern hemisphere. The highly elliptical orbit of Mars Express provides access to a large range of local times and locations which we use to investigate latitudinal, diurnal, and seasonal behavior of the atmosphere. Observed radial profiles of neutral number density, n[r], are used to obtain accurate measurements of temperature, T[r], and pressure, p[r], from the surface boundary layer to altitudes of 50 km with a vertical resolution of only a few hundred metres. Typical measurement accuracies of the temperature are in the range of ten percent at the upper boundary and fractions of a Kelvin near the surface. Several soundings are located in the polar regions of both hemispheres. These measurements will be used to examine the seasonal variations at high latitudes. The high vertical resolution and accuracy of the temperature profiles allows us to investigate the CO2 supersaturation and condensation near the poles. Atmospheric waves can be identified and will be investigated with regard to their spatial oc-currence over all latitude ranges. The MaRS experiment is funded by DLR under grant 50QM0701.

It’s about This and That: A Description of Anaphoric Expressions in Clinical Text

PubMed Central

Wang, Yan; Melton, Genevieve B.; Pakhomov, Serguei

2011-01-01

Although anaphoric expressions are very common in biomedical and clinical documents, little work has been done to systematically characterize their use in clinical text. Samples of ‘it’, ‘this’, and ‘that’ expressions occurring in inpatient clinical notes from four metropolitan hospitals were analyzed using a combination of semi-automated and manual annotation techniques. We developed a rule-based approach to filter potential non-referential expressions. A physician then manually annotated 1000 potential referential instances to determine referent status and the antecedent of each referent expression. A distributional analysis of the three referring expressions in the entire corpus of notes demonstrates a high prevalence of anaphora and large variance in distributions of referential expressions with different notes. Our results confirm that anaphoric expressions are common in clinical texts. Effective co-reference resolution with anaphoric expressions remains an important challenge in medical natural language processing research. PMID:22195211

Hydrogel-Tissue Chemistry: Principles and Applications.

PubMed

Gradinaru, Viviana; Treweek, Jennifer; Overton, Kristin; Deisseroth, Karl

2018-05-20

Over the past five years, a rapidly developing experimental approach has enabled high-resolution and high-content information retrieval from intact multicellular animal (metazoan) systems. New chemical and physical forms are created in the hydrogel-tissue chemistry process, and the retention and retrieval of crucial phenotypic information regarding constituent cells and molecules (and their joint interrelationships) are thereby enabled. For example, rich data sets defining both single-cell-resolution gene expression and single-cell-resolution activity during behavior can now be collected while still preserving information on three-dimensional positioning and/or brain-wide wiring of those very same neurons-even within vertebrate brains. This new approach and its variants, as applied to neuroscience, are beginning to illuminate the fundamental cellular and chemical representations of sensation, cognition, and action. More generally, reimagining metazoans as metareactants-or positionally defined three-dimensional graphs of constituent chemicals made available for ongoing functionalization, transformation, and readout-is stimulating innovation across biology and medicine.

Whole genome DNA methylation: beyond genes silencing.

PubMed

Tirado-Magallanes, Roberto; Rebbani, Khadija; Lim, Ricky; Pradhan, Sriharsa; Benoukraf, Touati

2017-01-17

The combination of DNA bisulfite treatment with high-throughput sequencing technologies has enabled investigation of genome-wide DNA methylation at near base pair level resolution, far beyond that of the kilobase-long canonical CpG islands that initially revealed the biological relevance of this covalent DNA modification. The latest high-resolution studies have revealed a role for very punctual DNA methylation in chromatin plasticity, gene regulation and splicing. Here, we aim to outline the major biological consequences of DNA methylation recently discovered. We also discuss the necessity of tuning DNA methylation resolution into an adequate scale to ease the integration of the methylome information with other chromatin features and transcription events such as gene expression, nucleosome positioning, transcription factors binding dynamic, gene splicing and genomic imprinting. Finally, our review sheds light on DNA methylation heterogeneity in cell population and the different approaches used for its assessment, including the contribution of single cell DNA analysis technology.

Whole genome DNA methylation: beyond genes silencing

PubMed Central

Tirado-Magallanes, Roberto; Rebbani, Khadija; Lim, Ricky; Pradhan, Sriharsa; Benoukraf, Touati

2017-01-01

The combination of DNA bisulfite treatment with high-throughput sequencing technologies has enabled investigation of genome-wide DNA methylation at near base pair level resolution, far beyond that of the kilobase-long canonical CpG islands that initially revealed the biological relevance of this covalent DNA modification. The latest high-resolution studies have revealed a role for very punctual DNA methylation in chromatin plasticity, gene regulation and splicing. Here, we aim to outline the major biological consequences of DNA methylation recently discovered. We also discuss the necessity of tuning DNA methylation resolution into an adequate scale to ease the integration of the methylome information with other chromatin features and transcription events such as gene expression, nucleosome positioning, transcription factors binding dynamic, gene splicing and genomic imprinting. Finally, our review sheds light on DNA methylation heterogeneity in cell population and the different approaches used for its assessment, including the contribution of single cell DNA analysis technology. PMID:27895318

Application of laser scanning speckle-microscopy for high-resolution express diagnostics of chlamydial infection

NASA Astrophysics Data System (ADS)

Ulyanov, Sergey; Larionova, Olga; Ulianova, Onega; Zaitsev, Sergey; Saltykov, Yury; Polyanina, Tatiana; Lyapina, Anna; Filonova, Nadezhda; Subbotina, Irina; Kalduzova, Irina; Utz, Sergey; Moiseeva, Yulia; Feodorova, Valentina

2018-04-01

Method of speckle-microscopy has been adapted to the problem of detection of Chlamydia trachomatis microbial cells in clinical samples. Prototype of laser scanning speckle-microscope has been designed. Spatial resolution and output characteristics of this microscope have been analyzed for the case of scanning of C. trachomatis bacteria inclusions - Elementary Bodies (EBs) inside the human cells, fixed on the glass. It has been demonstrated, that presence of C. trachomatis microbial cells in the sample can be easily detected using speckle microscopy.

The development and application of new crystallization method for tobacco mosaic virus coat protein.

PubMed

Li, Xiangyang; Song, Baoan; Hu, Deyu; Wang, Zhenchao; Zeng, Mengjiao; Yu, Dandan; Chen, Zhuo; Jin, Linhong; Yang, Song

2012-11-21

Although tobacco mosaic virus (TMV) coat protein (CP) has been isolated from virus particles and its crystals have grown in ammonium sulfate buffers for many years, to date, no one has reported on the crystallization of recombinant TMV-CP connecting peptides expressed in E. coli. In the present papers genetically engineered TMV-CP was expressed, into which hexahistidine (His) tags or glutathione-S-transferase (GST) tags were incorporated. Considering that GST-tags are long peptides and His-tags are short peptides, an attempt was made to grow crystals of TMV-CP cleaved GST-tags (WT-TMV-CP32) and TMV-CP incorporated His-tags (WT-His-TMV-CP12) simultaneously in ammonium sulfate buffers and commercial crystallization reagents. It was found that the 20S disk form of WT-TMV-CP32 and WT-His-TMV-CP12 did not form high resolution crystals by using various crystallization buffers and commercial crystallization reagents. Subsequently, a new experimental method was adopted in which a range of truncated TMV-CP was constructed by removing several amino acids from the N- or the C-terminal, and high resolution crystals were grown in ammonium sulfate buffers and commercial crystallization reagents. The new crystallization method was developed and 3.0 Å resolution macromolecular crystal was thereby obtained by removing four amino acids at the C-terminal of His-TMV-CP and connecting six His-tags at the N-terminal of His-TMV-CP (TR-His-TMV-CP19). The Four-layer aggregate disk structure of TR-His-TMV-CP19 was solved. This phenomenon showed that peptides at the C-terminus hindered the growth of high resolution crystals and the peptides interactions at the N-terminus were attributed to the quality of TMV-CP crystals. A 3.0 Å resolution macromolecular crystal of TR-His-TMV-CP19 was obtained and the corresponding structure was solved by removing four amino acids at the C-terminus of TMV-CP and connecting His-tags at the N-terminus of TMV-CP. It indicated that short peptides influenced the resolution of TMV-CP crystals.

Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins

PubMed Central

Handfield, Louis-François; Chong, Yolanda T.; Simmons, Jibril; Andrews, Brenda J.; Moses, Alan M.

2013-01-01

Protein subcellular localization has been systematically characterized in budding yeast using fluorescently tagged proteins. Based on the fluorescence microscopy images, subcellular localization of many proteins can be classified automatically using supervised machine learning approaches that have been trained to recognize predefined image classes based on statistical features. Here, we present an unsupervised analysis of protein expression patterns in a set of high-resolution, high-throughput microscope images. Our analysis is based on 7 biologically interpretable features which are evaluated on automatically identified cells, and whose cell-stage dependency is captured by a continuous model for cell growth. We show that it is possible to identify most previously identified localization patterns in a cluster analysis based on these features and that similarities between the inferred expression patterns contain more information about protein function than can be explained by a previous manual categorization of subcellular localization. Furthermore, the inferred cell-stage associated to each fluorescence measurement allows us to visualize large groups of proteins entering the bud at specific stages of bud growth. These correspond to proteins localized to organelles, revealing that the organelles must be entering the bud in a stereotypical order. We also identify and organize a smaller group of proteins that show subtle differences in the way they move around the bud during growth. Our results suggest that biologically interpretable features based on explicit models of cell morphology will yield unprecedented power for pattern discovery in high-resolution, high-throughput microscopy images. PMID:23785265

Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution.

PubMed

Ma, Wenxiu; Ay, Ferhat; Lee, Choli; Gulsoy, Gunhan; Deng, Xinxian; Cook, Savannah; Hesson, Jennifer; Cavanaugh, Christopher; Ware, Carol B; Krumm, Anton; Shendure, Jay; Blau, C Anthony; Disteche, Christine M; Noble, William S; Duan, ZhiJun

2018-06-01

The folding and three-dimensional (3D) organization of chromatin in the nucleus critically impacts genome function. The past decade has witnessed rapid advances in genomic tools for delineating 3D genome architecture. Among them, chromosome conformation capture (3C)-based methods such as Hi-C are the most widely used techniques for mapping chromatin interactions. However, traditional Hi-C protocols rely on restriction enzymes (REs) to fragment chromatin and are therefore limited in resolution. We recently developed DNase Hi-C for mapping 3D genome organization, which uses DNase I for chromatin fragmentation. DNase Hi-C overcomes RE-related limitations associated with traditional Hi-C methods, leading to improved methodological resolution. Furthermore, combining this method with DNA capture technology provides a high-throughput approach (targeted DNase Hi-C) that allows for mapping fine-scale chromatin architecture at exceptionally high resolution. Hence, targeted DNase Hi-C will be valuable for delineating the physical landscapes of cis-regulatory networks that control gene expression and for characterizing phenotype-associated chromatin 3D signatures. Here, we provide a detailed description of method design and step-by-step working protocols for these two methods. Copyright © 2018 Elsevier Inc. All rights reserved.

Precise Spatiotemporal Control of Optogenetic Activation Using an Acousto-Optic Device

PubMed Central

Guo, Yanmeng; Song, Peipei; Zhang, Xiaohui; Zeng, Shaoqun; Wang, Zuoren

2011-01-01

Light activation and inactivation of neurons by optogenetic techniques has emerged as an important tool for studying neural circuit function. To achieve a high resolution, new methods are being developed to selectively manipulate the activity of individual neurons. Here, we report that the combination of an acousto-optic device (AOD) and single-photon laser was used to achieve rapid and precise spatiotemporal control of light stimulation at multiple points in a neural circuit with millisecond time resolution. The performance of this system in activating ChIEF expressed on HEK 293 cells as well as cultured neurons was first evaluated, and the laser stimulation patterns were optimized. Next, the spatiotemporally selective manipulation of multiple neurons was achieved in a precise manner. Finally, we demonstrated the versatility of this high-resolution method in dissecting neural circuits both in the mouse cortical slice and the Drosophila brain in vivo. Taken together, our results show that the combination of AOD-assisted laser stimulation and optogenetic tools provides a flexible solution for manipulating neuronal activity at high efficiency and with high temporal precision. PMID:22174813

A Conserved Developmental Patterning Network Produces Quantitatively Different Output in Multiple Species of Drosophila

PubMed Central

Meyer, Miriah; Wunderlich, Zeba; Simirenko, Lisa; Luengo Hendriks, Cris L.; Keränen, Soile V. E.; Henriquez, Clara; Knowles, David W.; Biggin, Mark D.; Eisen, Michael B.; DePace, Angela H.

2011-01-01

Differences in the level, timing, or location of gene expression can contribute to alternative phenotypes at the molecular and organismal level. Understanding the origins of expression differences is complicated by the fact that organismal morphology and gene regulatory networks could potentially vary even between closely related species. To assess the scope of such changes, we used high-resolution imaging methods to measure mRNA expression in blastoderm embryos of Drosophila yakuba and Drosophila pseudoobscura and assembled these data into cellular resolution atlases, where expression levels for 13 genes in the segmentation network are averaged into species-specific, cellular resolution morphological frameworks. We demonstrate that the blastoderm embryos of these species differ in their morphology in terms of size, shape, and number of nuclei. We present an approach to compare cellular gene expression patterns between species, while accounting for varying embryo morphology, and apply it to our data and an equivalent dataset for Drosophila melanogaster. Our analysis reveals that all individual genes differ quantitatively in their spatio-temporal expression patterns between these species, primarily in terms of their relative position and dynamics. Despite many small quantitative differences, cellular gene expression profiles for the whole set of genes examined are largely similar. This suggests that cell types at this stage of development are conserved, though they can differ in their relative position by up to 3–4 cell widths and in their relative proportion between species by as much as 5-fold. Quantitative differences in the dynamics and relative level of a subset of genes between corresponding cell types may reflect altered regulatory functions between species. Our results emphasize that transcriptional networks can diverge over short evolutionary timescales and that even small changes can lead to distinct output in terms of the placement and number of equivalent cells. PMID:22046143

Using Small Unmanned Aerial Systems to Advance Hydrological Models in Coastal Watersheds

NASA Astrophysics Data System (ADS)

Moorhead, R.; Hathcock, L.; Coffey, J. J.; Hood, R. E.; van Cooten, S.; Choate, K.; Rawson, H.; Kosturock, A.

2014-12-01

Small unmanned aerial systems (sUASs) have the potential to provide highly useful information for models of earth systems that vary over time intervals of days and for which sub-meter resolution is crucial. In particular, the state of coastal watershed plains are highly dependent on vegetation type and cover, soil type, weather, river flooding, and coastal inundation. The vegetation type and cover affect the drying potential, as well as the watershed's resistance to flood water movement. The soil type, soil moisture, and pond depths affect the ability of the watershed to absorb river flood waters and inundation from the sea. In this presentation we will describe a data collection campaign and model modification effort for hydrological models in a coastal watershed. The data collection campaign is obtaining data bimonthly using multiple UASs to capture the state of the watershed quicker. In particular, the vegetation cover and the extent of the water surface expression are captured at approximately a 1 inch spatial resolution over a few days with sUASs that can image 1-2 square miles per hour. The vegetation data provides a time-varying input to improve the estimation of the roughness coefficient and the dry potential from the traditionally static datasets. By correlating the high spatio-temporal resolution surface water expression with data from approximately ten river gauges, models can be improved and validated under more conditions. The presentation will also discuss the requisite sUAS capabilities and our experience in using them.

A multi-step strategy to obtain crystals of the dengue virus RNA-dependent RNA polymerase that diffract to high resolution

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

Yap, Thai Leong; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551; Chen, Yen Liang

Crystals of the RNA-dependent RNA polymerase catalytic domain from the dengue virus NS5 protein have been obtained using a strategy that included expression screening of naturally occurring serotype variants of the protein, the addition of divalent metal ions and crystal dehydration. These crystals diffract to 1.85 Å resolution and are thus suitable for a structure-based drug-design program. Dengue virus, a member of the Flaviviridae genus, causes dengue fever, an important emerging disease with several million infections occurring annually for which no effective therapy exists. The viral RNA-dependent RNA polymerase NS5 plays an important role in virus replication and represents anmore » interesting target for the development of specific antiviral compounds. Crystals that diffract to 1.85 Å resolution that are suitable for three-dimensional structure determination and thus for a structure-based drug-design program have been obtained using a strategy that included expression screening of naturally occurring serotype variants of the protein, the addition of divalent metal ions and crystal dehydration.« less

Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq

PubMed Central

Dumelie, Jason G

2017-01-01

R-loops are features of chromatin consisting of a strand of DNA hybridized to RNA, as well as the expelled complementary DNA strand. R-loops are enriched at promoters where they have recently been shown to have important roles in modifying gene expression. However, the location of promoter-associated R-loops and the genomic domains they perturb to modify gene expression remain unclear. To resolve this issue, we developed a bisulfite-based approach, bisDRIP-seq, to map R-loops across the genome at near-nucleotide resolution in MCF-7 cells. We found the location of promoter-associated R-loops is dependent on the presence of introns. In intron-containing genes, R-loops are bounded between the transcription start site and the first exon-intron junction. In intronless genes, the 3' boundary displays gene-specific heterogeneity. Moreover, intronless genes are often associated with promoter-associated R-loop formation. Together, these studies provide a high-resolution map of R-loops and identify gene structure as a critical determinant of R-loop formation. PMID:29072160

Aeromagnetic Expression of Buried Basaltic Volcanoes Near Yucca Mountain, Nevada

USGS Publications Warehouse

O'Leary, Dennis W.; Mankinen, E.A.; Blakely, R.J.; Langenheim, V.E.; Ponce, D.A.

2002-01-01

A high-resolution aeromagnetic survey has defined a number of small dipolar anomalies indicating the presence of magnetic bodies buried beneath the surface of Crater Flat and the Amargosa Desert. Results of potential-field modeling indicate that isolated, small-volume, highly magnetic bodies embedded within the alluvial deposits of both areas produce the anomalies. Their physical characteristics and the fact that they tend to be aligned along major structural trends provide strong support for the hypothesis that the anomalies reflect buried basaltic volcanic centers. Other, similar anomalies are identified as possible targets for further investigation. High-resolution gravity and ground-magnetic surveys, perhaps along with drilling sources of selected anomalies and radiometric age determinations, can provide valuable constraints in estimating potential volcanic hazard to the potential nuclear waste repository at Yucca Mountain.

Thermographic Sensing For On-Line Industrial Control

NASA Astrophysics Data System (ADS)

Holmsten, Dag

1986-10-01

It is today's emergence of thermoelectrically cooled, highly accurate infrared linescanners and imaging systems that has definitely made on-line Infraread Thermography (IRT) possible. Specifically designed for continuous use, these scanners are equipped with dedicated software capable of monitoring and controlling highly complex thermodynamic situations. This paper will outline some possible implications of using IRT on-line by describing some uses of this technology in the steel-making (hot rolling) and automotive industries (machine-vision). A warning is also expressed that IRT technology not originally designed for automated applications e.g. high resolution, imaging systems, should not be directly applied to an on-line measurement situation without having its measurement resolution, accuracy and especially its repeatability, reliably proven. Some suitable testing procedures are briefly outlined at the end of the paper.

Ultramicroscopy as a novel tool to unravel the tropism of AAV gene therapy vectors in the brain.

PubMed

Alves, Sandro; Bode, Julia; Bemelmans, Alexis-Pierre; von Kalle, Christof; Cartier, Nathalie; Tews, Björn

2016-06-20

Recombinant adeno-associated viral (AAV) vectors have advanced to the vanguard of gene therapy. Numerous naturally occurring serotypes have been used to target cells in various tissues. There is a strong need for fast and dynamic methods which efficiently unravel viral tropism in whole organs. Ultramicroscopy (UM) is a novel fluorescence microscopy technique that images optically cleared undissected specimens, achieving good resolutions at high penetration depths while being non-destructive. UM was applied to obtain high-resolution 3D analysis of AAV transduction in adult mouse brains, especially in the hippocampus, a region of interest for Alzheimer's disease therapy. We separately or simultaneously compared transduction efficacies for commonly used serotypes (AAV9 and AAVrh10) using fluorescent reporter expression. We provide a detailed comparative and quantitative analysis of the transduction profiles. UM allowed a rapid analysis of marker fluorescence expression in neurons with intact projections deep inside the brain, in defined anatomical structures. Major hippocampal neuronal transduction was observed with both vectors, with slightly better efficacy for AAV9 in UM. Glial response and synaptic marker expression did not change post transduction.We propose UM as a novel valuable complementary tool to efficiently and simultaneously unravel tropism of different viruses in a single non-dissected adult rodent brain.

Spatial coherence effect on layer thickness determination in narrowband full-field optical coherence tomography.

PubMed

Safrani, Avner; Abdulhalim, Ibrahim

2011-06-20

Longitudinal spatial coherence (LSC) is determined by the spatial frequency content of an optical beam. The use of lenses with a high numerical aperture (NA) in full-field optical coherence tomography and a narrowband light source makes the LSC length much shorter than the temporal coherence length, hence suggesting that high-resolution 3D images of biological and multilayered samples can be obtained based on the low LSC. A simplified model is derived, supported by experimental results, which describes the expected interference output signal of multilayered samples when high-NA lenses are used together with a narrowband light source. An expression for the correction factor for the layer thickness determination is found valid for high-NA objectives. Additionally, the method was applied to a strongly scattering layer, demonstrating the potential of this method for high-resolution imaging of scattering media.

Coregistration of high-resolution Mars orbital images

NASA Astrophysics Data System (ADS)

Sidiropoulos, Panagiotis; Muller, Jan-Peter

2015-04-01

The systematic orbital imaging of the Martian surface started 4 decades ago from NASA's Viking Orbiter 1 & 2 missions, which were launched in August 1975, and acquired orbital images of the planet between 1976 and 1980. The result of this reconnaissance was the first medium-resolution (i.e. ≤ 300m/pixel) global map of Mars, as well as a variety of high-resolution images (reaching up to 8m/pixel) of special regions of interest. Over the last two decades NASA has sent 3 more spacecraft with onboard instruments for high-resolution orbital imaging: Mars Global Surveyor (MGS) having onboard the Mars Orbital Camera - Narrow Angle (MOC-NA), Mars Odyssey having onboard the Thermal Emission Imaging System - Visual (THEMIS-VIS) and the Mars Reconnaissance Orbiter (MRO) having on board two distinct high-resolution cameras, Context Camera (CTX) and High-Resolution Imaging Science Experiment (HiRISE). Moreover, ESA has the multispectral High resolution Stereo Camera (HRSC) onboard ESA's Mars Express with resolution up to 12.5m since 2004. Overall, this set of cameras have acquired more than 400,000 high-resolution images, i.e. with resolution better than 100m and as fine as 25 cm/pixel. Notwithstanding the high spatial resolution of the available NASA orbital products, their accuracy of areo-referencing is often very poor. As a matter of fact, due to pointing inconsistencies, usually form errors in roll attitude, the acquired products may actually image areas tens of kilometers far away from the point that they are supposed to be looking at. On the other hand, since 2004, the ESA Mars Express has been acquiring stereo images through the High Resolution Stereo Camera (HRSC), with resolution that is usually 12.5-25 metres per pixel. The achieved coverage is more than 64% for images with resolution finer than 20 m/pixel, while for ~40% of Mars, Digital Terrain Models (DTMs) have been produced with are co-registered with MOLA [Gwinner et al., 2010]. The HRSC images and DTMs represent the best available 3D reference frame for Mars showing co-registration with MOLA<25m (loc.cit.). In our work, the reference generated by HRSC terrain corrected orthorectified images is used as a common reference frame to co-register all available high-resolution orbital NASA products into a common 3D coordinate system, thus allowing the examination of the changes that happen on the surface of Mars over time (such as seasonal flows [McEwen et al., 2011] or new impact craters [Byrne, et al., 2009]). In order to accomplish such a tedious manual task, we have developed an automatic co-registration pipeline that produces orthorectified versions of the NASA images in realistic time (i.e. from ~15 minutes to 10 hours per image depending on size). In the first step of this pipeline, tie-points are extracted from the target NASA image and the reference HRSC image or image mosaic. Subsequently, the HRSC areo-reference information is used to transform the HRSC tie-points pixel coordinates into 3D "world" coordinates. This way, a correspondence between the pixel coordinates of the target NASA image and the 3D "world" coordinates is established for each tie-point. This set of correspondences is used to estimate a non-rigid, 3D to 2D transformation model, which transforms the target image into the HRSC reference coordinate system. Finally, correlation of the transformed target image and the HRSC image is employed to fine-tune the orthorectification results, thus generating results with sub-pixel accuracy. This method, which has been proven to be accurate, robust to resolution differences and reliable when dealing with partially degraded data and fast, will be presented, along with some example co-registration results that have been achieved by using it. Acknowledgements: The research leading to these results has received partial funding from the STFC "MSSL Consolidated Grant" ST/K000977/1 and partial support from the European Union's Seventh Framework Programme (FP7/2007-2013) under iMars grant agreement n° 607379. References: [1] K. F. Gwinner, et al. (2010) Topography of Mars from global mapping by HRSC high-resolution digital terrain models and orthoimages: characteristics and performance. Earth and Planetary Science Letters 294, 506-519, doi:10.1016/j.epsl.2009.11.007. [2] A. McEwen, et al. (2011) Seasonal flows on warm martian slopes. Science , 333 (6043): 740-743. [3] S. Byrne, et al. (2009) Distribution of mid-latitude ground ice on mars from new impact craters. Science, 325(5948):1674-1676.

Mapping whole-brain activity with cellular resolution by light-sheet microscopy and high-throughput image analysis (Conference Presentation)

NASA Astrophysics Data System (ADS)

Silvestri, Ludovico; Rudinskiy, Nikita; Paciscopi, Marco; Müllenbroich, Marie Caroline; Costantini, Irene; Sacconi, Leonardo; Frasconi, Paolo; Hyman, Bradley T.; Pavone, Francesco S.

2016-03-01

Mapping neuronal activity patterns across the whole brain with cellular resolution is a challenging task for state-of-the-art imaging methods. Indeed, despite a number of technological efforts, quantitative cellular-resolution activation maps of the whole brain have not yet been obtained. Many techniques are limited by coarse resolution or by a narrow field of view. High-throughput imaging methods, such as light sheet microscopy, can be used to image large specimens with high resolution and in reasonable times. However, the bottleneck is then moved from image acquisition to image analysis, since many TeraBytes of data have to be processed to extract meaningful information. Here, we present a full experimental pipeline to quantify neuronal activity in the entire mouse brain with cellular resolution, based on a combination of genetics, optics and computer science. We used a transgenic mouse strain (Arc-dVenus mouse) in which neurons which have been active in the last hours before brain fixation are fluorescently labelled. Samples were cleared with CLARITY and imaged with a custom-made confocal light sheet microscope. To perform an automatic localization of fluorescent cells on the large images produced, we used a novel computational approach called semantic deconvolution. The combined approach presented here allows quantifying the amount of Arc-expressing neurons throughout the whole mouse brain. When applied to cohorts of mice subject to different stimuli and/or environmental conditions, this method helps finding correlations in activity between different neuronal populations, opening the possibility to infer a sort of brain-wide 'functional connectivity' with cellular resolution.

Localization microscopy of DNA in situ using Vybrant{sup ®} DyeCycle™ Violet fluorescent probe: A new approach to study nuclear nanostructure at single molecule resolution

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

Żurek-Biesiada, Dominika; Szczurek, Aleksander T.; Prakash, Kirti

Higher order chromatin structure is not only required to compact and spatially arrange long chromatids within a nucleus, but have also important functional roles, including control of gene expression and DNA processing. However, studies of chromatin nanostructures cannot be performed using conventional widefield and confocal microscopy because of the limited optical resolution. Various methods of superresolution microscopy have been described to overcome this difficulty, like structured illumination and single molecule localization microscopy. We report here that the standard DNA dye Vybrant{sup ®} DyeCycle™ Violet can be used to provide single molecule localization microscopy (SMLM) images of DNA in nuclei ofmore » fixed mammalian cells. This SMLM method enabled optical isolation and localization of large numbers of DNA-bound molecules, usually in excess of 10{sup 6} signals in one cell nucleus. The technique yielded high-quality images of nuclear DNA density, revealing subdiffraction chromatin structures of the size in the order of 100 nm; the interchromatin compartment was visualized at unprecedented optical resolution. The approach offers several advantages over previously described high resolution DNA imaging methods, including high specificity, an ability to record images using a single wavelength excitation, and a higher density of single molecule signals than reported in previous SMLM studies. The method is compatible with DNA/multicolor SMLM imaging which employs simple staining methods suited also for conventional optical microscopy. - Highlights: • Super-resolution imaging of nuclear DNA with Vybrant Violet and blue excitation. • 90nm resolution images of DNA structures in optically thick eukaryotic nuclei. • Enhanced resolution confirms the existence of DNA-free regions inside the nucleus. • Optimized imaging conditions enable multicolor super-resolution imaging.« less

Neutron and high-resolution room-temperature X-ray data collection from crystallized lytic polysaccharide monooxygenase

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

Bacik, John -Paul; Mekasha, Sophanit; Forsberg, Zarah

Bacteria and fungi express lytic polysaccharide monooxgyenase (LPMO) enzymes that act in conjunction with canonical hydrolytic sugar-processing enzymes to rapidly convert polysaccharides such as chitin, cellulose and starch to single monosaccharide products. In order to gain a better understanding of the structure and oxidative mechanism of these enzymes, large crystals (1–3 mm 3) of a chitin-processing LPMO from the Gram-positive soil bacterium Jonesia denitrificans were grown and screened for their ability to diffract neutrons. In addition to the collection of neutron diffraction data, which were processed to 2.1 Å resolution, a high-resolution room-temperature X-ray diffraction data set was collected andmore » processed to 1.1 Å resolution in space group P2 12 12 1. To our knowledge, this work marks the first successful neutron crystallographic experiment on an LPMO. As a result, joint X-ray/neutron refinement of the resulting data will reveal new details of the structure and mechanism of this recently discovered class of enzymes.« less

Neutron and high-resolution room-temperature X-ray data collection from crystallized lytic polysaccharide monooxygenase

DOE PAGES

Bacik, John -Paul; Mekasha, Sophanit; Forsberg, Zarah; ...

2015-01-01

Bacteria and fungi express lytic polysaccharide monooxgyenase (LPMO) enzymes that act in conjunction with canonical hydrolytic sugar-processing enzymes to rapidly convert polysaccharides such as chitin, cellulose and starch to single monosaccharide products. In order to gain a better understanding of the structure and oxidative mechanism of these enzymes, large crystals (1–3 mm 3) of a chitin-processing LPMO from the Gram-positive soil bacterium Jonesia denitrificans were grown and screened for their ability to diffract neutrons. In addition to the collection of neutron diffraction data, which were processed to 2.1 Å resolution, a high-resolution room-temperature X-ray diffraction data set was collected andmore » processed to 1.1 Å resolution in space group P2 12 12 1. To our knowledge, this work marks the first successful neutron crystallographic experiment on an LPMO. As a result, joint X-ray/neutron refinement of the resulting data will reveal new details of the structure and mechanism of this recently discovered class of enzymes.« less

Recent Advancements in DNA Damage-Transcription Crosstalk and High-Resolution Mapping of DNA Breaks.

PubMed

Vitelli, Valerio; Galbiati, Alessandro; Iannelli, Fabio; Pessina, Fabio; Sharma, Sheetal; d'Adda di Fagagna, Fabrizio

2017-08-31

Until recently, DNA damage arising from physiological DNA metabolism was considered a detrimental by-product for cells. However, an increasing amount of evidence has shown that DNA damage could have a positive role in transcription activation. In particular, DNA damage has been detected in transcriptional elements following different stimuli. These physiological DNA breaks are thought to be instrumental for the correct expression of genomic loci through different mechanisms. In this regard, although a plethora of methods are available to precisely map transcribed regions and transcription start sites, commonly used techniques for mapping DNA breaks lack sufficient resolution and sensitivity to draw a robust correlation between DNA damage generation and transcription. Recently, however, several methods have been developed to map DNA damage at single-nucleotide resolution, thus providing a new set of tools to correlate DNA damage and transcription. Here, we review how DNA damage can positively regulate transcription initiation, the current techniques for mapping DNA breaks at high resolution, and how these techniques can benefit future studies of DNA damage and transcription.

qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells.

PubMed

Andrews, J O; Conway, W; Cho, W -K; Narayanan, A; Spille, J -H; Jayanth, N; Inoue, T; Mullen, S; Thaler, J; Cissé, I I

2018-05-09

We present qSR, an analytical tool for the quantitative analysis of single molecule based super-resolution data. The software is created as an open-source platform integrating multiple algorithms for rigorous spatial and temporal characterizations of protein clusters in super-resolution data of living cells. First, we illustrate qSR using a sample live cell data of RNA Polymerase II (Pol II) as an example of highly dynamic sub-diffractive clusters. Then we utilize qSR to investigate the organization and dynamics of endogenous RNA Polymerase I (Pol I) in live human cells, throughout the cell cycle. Our analysis reveals a previously uncharacterized transient clustering of Pol I. Both stable and transient populations of Pol I clusters co-exist in individual living cells, and their relative fraction vary during cell cycle, in a manner correlating with global gene expression. Thus, qSR serves to facilitate the study of protein organization and dynamics with very high spatial and temporal resolutions directly in live cell.

iCLIP: protein-RNA interactions at nucleotide resolution.

PubMed

Huppertz, Ina; Attig, Jan; D'Ambrogio, Andrea; Easton, Laura E; Sibley, Christopher R; Sugimoto, Yoichiro; Tajnik, Mojca; König, Julian; Ule, Jernej

2014-02-01

RNA-binding proteins (RBPs) are key players in the post-transcriptional regulation of gene expression. Precise knowledge about their binding sites is therefore critical to unravel their molecular function and to understand their role in development and disease. Individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) identifies protein-RNA crosslink sites on a genome-wide scale. The high resolution and specificity of this method are achieved by an intramolecular cDNA circularization step that enables analysis of cDNAs that truncated at the protein-RNA crosslink sites. Here, we describe the improved iCLIP protocol and discuss critical optimization and control experiments that are required when applying the method to new RBPs. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

A High-Resolution In Vivo Atlas of the Human Brain's Serotonin System.

PubMed

Beliveau, Vincent; Ganz, Melanie; Feng, Ling; Ozenne, Brice; Højgaard, Liselotte; Fisher, Patrick M; Svarer, Claus; Greve, Douglas N; Knudsen, Gitte M

2017-01-04

The serotonin (5-hydroxytryptamine, 5-HT) system modulates many important brain functions and is critically involved in many neuropsychiatric disorders. Here, we present a high-resolution, multidimensional, in vivo atlas of four of the human brain's 5-HT receptors (5-HT 1A , 5-HT 1B , 5-HT 2A , and 5-HT 4 ) and the 5-HT transporter (5-HTT). The atlas is created from molecular and structural high-resolution neuroimaging data consisting of positron emission tomography (PET) and magnetic resonance imaging (MRI) scans acquired in a total of 210 healthy individuals. Comparison of the regional PET binding measures with postmortem human brain autoradiography outcomes showed a high correlation for the five 5-HT targets and this enabled us to transform the atlas to represent protein densities (in picomoles per milliliter). We also assessed the regional association between protein concentration and mRNA expression in the human brain by comparing the 5-HT density across the atlas with data from the Allen Human Brain atlas and identified receptor- and transporter-specific associations that show the regional relation between the two measures. Together, these data provide unparalleled insight into the serotonin system of the human brain. We present a high-resolution positron emission tomography (PET)- and magnetic resonance imaging-based human brain atlas of important serotonin receptors and the transporter. The regional PET-derived binding measures correlate strongly with the corresponding autoradiography protein levels. The strong correlation enables the transformation of the PET-derived human brain atlas into a protein density map of the serotonin (5-hydroxytryptamine, 5-HT) system. Next, we compared the regional receptor/transporter protein densities with mRNA levels and uncovered unique associations between protein expression and density at high detail. This new in vivo neuroimaging atlas of the 5-HT system not only provides insight in the human brain's regional protein synthesis, transport, and density, but also represents a valuable source of information for the neuroscience community as a comparative instrument to assess brain disorders. Copyright © 2017 the authors 0270-6474/17/370120-09$15.00/0.

Between Anaphora and Deixis ... The Resolution of the Demonstrative Noun Phrase "That N"

ERIC Educational Resources Information Center

Fossard, Marion; Garnham, Alan; Cowles, H. Wind

2012-01-01

Three experiments examined the hypothesis that the demonstrative noun phrase (NP) that N, as an anadeictic expression, preferentially refers to the less salient referent in a discourse representation when used anaphorically, whereas the anaphoric pronoun he or she preferentially refers to the highly-focused referent. The findings, from a sentence…

Evidence from the Mars Express High Resolution Stereo Camera for a frozen sea close to Mars' equator.

PubMed

Murray, John B; Muller, Jan-Peter; Neukum, Gerhard; Werner, Stephanie C; van Gasselt, Stephan; Hauber, Ernst; Markiewicz, Wojciech J; Head, James W; Foing, Bernard H; Page, David; Mitchell, Karl L; Portyankina, Ganna

2005-03-17

It is thought that the Cerberus Fossae fissures on Mars were the source of both lava and water floods two to ten million years ago. Evidence for the resulting lava plains has been identified in eastern Elysium, but seas and lakes from these fissures and previous water flooding events were presumed to have evaporated and sublimed away. Here we present High Resolution Stereo Camera images from the European Space Agency Mars Express spacecraft that indicate that such lakes may still exist. We infer that the evidence is consistent with a frozen body of water, with surface pack-ice, around 5 degrees north latitude and 150 degrees east longitude in southern Elysium. The frozen lake measures about 800 x 900 km in lateral extent and may be up to 45 metres deep--similar in size and depth to the North Sea. From crater counts, we determined its age to be 5 +/- 2 million years old. If our interpretation is confirmed, this is a place that might preserve evidence of primitive life, if it has ever developed on Mars.

TLM-Quant: an open-source pipeline for visualization and quantification of gene expression heterogeneity in growing microbial cells.

PubMed

Piersma, Sjouke; Denham, Emma L; Drulhe, Samuel; Tonk, Rudi H J; Schwikowski, Benno; van Dijl, Jan Maarten

2013-01-01

Gene expression heterogeneity is a key driver for microbial adaptation to fluctuating environmental conditions, cell differentiation and the evolution of species. This phenomenon has therefore enormous implications, not only for life in general, but also for biotechnological applications where unwanted subpopulations of non-producing cells can emerge in large-scale fermentations. Only time-lapse fluorescence microscopy allows real-time measurements of gene expression heterogeneity. A major limitation in the analysis of time-lapse microscopy data is the lack of fast, cost-effective, open, simple and adaptable protocols. Here we describe TLM-Quant, a semi-automatic pipeline for the analysis of time-lapse fluorescence microscopy data that enables the user to visualize and quantify gene expression heterogeneity. Importantly, our pipeline builds on the open-source packages ImageJ and R. To validate TLM-Quant, we selected three possible scenarios, namely homogeneous expression, highly 'noisy' heterogeneous expression, and bistable heterogeneous expression in the Gram-positive bacterium Bacillus subtilis. This bacterium is both a paradigm for systems-level studies on gene expression and a highly appreciated biotechnological 'cell factory'. We conclude that the temporal resolution of such analyses with TLM-Quant is only limited by the numbers of recorded images.

Identification and resolution of artifacts in the interpretation of imprinted gene expression.

PubMed

Proudhon, Charlotte; Bourc'his, Déborah

2010-12-01

Genomic imprinting refers to genes that are epigenetically programmed in the germline to express exclusively or preferentially one allele in a parent-of-origin manner. Expression-based genome-wide screening for the identification of imprinted genes has failed to uncover a significant number of new imprinted genes, probably because of the high tissue- and developmental-stage specificity of imprinted gene expression. A very large number of technical and biological artifacts can also lead to the erroneous evidence of imprinted gene expression. In this article, we focus on three common sources of potential confounding effects: (i) random monoallelic expression in monoclonal cell populations, (ii) genetically determined monoallelic expression and (iii) contamination or infiltration of embryonic tissues with maternal material. This last situation specifically applies to genes that occur as maternally expressed in the placenta. Beside the use of reciprocal crosses that are instrumental to confirm the parental specificity of expression, we provide additional methods for the detection and elimination of these situations that can be misinterpreted as cases of imprinted expression.

Preparation, crystallization and preliminary X-ray analysis of the methionine synthase (MetE) from Streptococcus mutans

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

Fu, Tian-Min; Zhang, Xiao-Yan; Li, Lan-Fen

2006-10-01

Methionine synthase (MetE) from S. mutans was expressed, purified and crystallized. Diffraction data have been collected to 2.2 Å resolution. The Streptococcus mutans metE gene encodes methionine synthase (MetE), which catalyzes the direct transfer of a methyl group from methyltetrahydrofolate to homocysteine in the last step of methionine synthesis. metE was cloned into pET28a and the gene product was expressed at high levels in the Escherichia coli strain BL21 (DE3). MetE was purified to homogeneity using Ni{sup 2+}-chelating chromatography followed by size-exclusion chromatography. Crystals of the protein were obtained by the hanging-drop vapour-diffusion method and diffracted to 2.2 Å resolution.more » The crystal belongs to space group P2{sub 1}, with unit-cell parameters a = 52.85, b = 99.48, c = 77.88 Å, β = 94.55°.« less

High-resolution, preparative purification of PEGylated protein using a laterally-fed membrane chromatography device.

PubMed

Madadkar, Pedram; Nino, Sergio Luna; Ghosh, Raja

2016-11-01

We discuss the use of a laterally-fed membrane chromatography (or LFMC) device for single-step purification of mono-PEGylated lysozyme. Recent studies have shown such LFMC devices to be suitable for high-resolution, multi-component separation of proteins in the bind-and-elute mode. The device used in this study contained a stack of rectangular cation-exchange membranes having 9.25mL bed volume. PEGylation of lysozyme was carried out in batch mode using 5kDa methoxy-polyethyleneglycol propionaldehyde (or m-PEG propionaldehyde) in the presence of sodium cyanoborohydride as reducing agent. Membrane chromatographic separation was carried out at 1.62 membrane bed volumes per minute flow rate, in the bind-and-elute mode. When a salt gradient was applied, the higher PEGylated forms of lysozyme (i.e. the byproducts) eluted earlier than mono-PEGylated lysozyme (the target product), while lysozyme eluted last. Under elution conditions optimized for resolution and speed, the separation could be carried out in less than 15 membrane bed volumes. High purity and recovery of mono-PEGylated lysozyme was obtained. The resolution of separation of mono-PEGylated lysozyme obtained under the above condition was comparable to that reported in the literature for equivalent cation-exchange resin columns while the flow rate expressed in bed volumes/min was 21.7 times higher. Also, the number of theoretical plates per meter was significantly higher with the LFMC device. Therefore the LFMC based purification process discussed in this paper combined high-productivity with high-resolution. Copyright © 2016 Elsevier B.V. All rights reserved.

Telomere length profiles in primary human peritoneal mesothelial cells are consistent with senescence.

PubMed

Lopez-Anton, Melisa; Rudolf, András; Baird, Duncan M; Roger, Laureline; Jones, Rhiannon E; Witowski, Janusz; Fraser, Donald J; Bowen, Timothy

2017-06-01

Mesothelial cell (MC) senescence contributes to malignancy and tissue fibrosis. The role of telomere erosion in MC senescence remains controversial, with evidence for both telomere-dependent and telomere-independent mechanisms reported. Single telomere length analysis revealed considerable telomere length heterogeneity in freshly isolated human peritoneal MCs, reflecting a heterogeneous proliferative history and providing high-resolution evidence for telomere-dependent senescence. By contrast the attenuated replicative lifespan, lack of telomere erosion and induction of p16 expression in in vitro-aged cells was consistent with stress-induced senescence. Given the potential pathophysiological impact of senescence in mesothelial tissues, high-resolution MC telomere length analysis may provide clinically useful information. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Comparative Study of Regulatory Circuits in Two Sea Urchin Species Reveals Tight Control of Timing and High Conservation of Expression Dynamics

PubMed Central

Gildor, Tsvia; Ben-Tabou de-Leon, Smadar

2015-01-01

Accurate temporal control of gene expression is essential for normal development and must be robust to natural genetic and environmental variation. Studying gene expression variation within and between related species can delineate the level of expression variability that development can tolerate. Here we exploit the comprehensive model of sea urchin gene regulatory networks and generate high-density expression profiles of key regulatory genes of the Mediterranean sea urchin, Paracentrotus lividus (Pl). The high resolution of our studies reveals highly reproducible gene initiation times that have lower variation than those of maximal mRNA levels between different individuals of the same species. This observation supports a threshold behavior of gene activation that is less sensitive to input concentrations. We then compare Mediterranean sea urchin gene expression profiles to those of its Pacific Ocean relative, Strongylocentrotus purpuratus (Sp). These species shared a common ancestor about 40 million years ago and show highly similar embryonic morphologies. Our comparative analyses of five regulatory circuits operating in different embryonic territories reveal a high conservation of the temporal order of gene activation but also some cases of divergence. A linear ratio of 1.3-fold between gene initiation times in Pl and Sp is partially explained by scaling of the developmental rates with temperature. Scaling the developmental rates according to the estimated Sp-Pl ratio and normalizing the expression levels reveals a striking conservation of relative dynamics of gene expression between the species. Overall, our findings demonstrate the ability of biological developmental systems to tightly control the timing of gene activation and relative dynamics and overcome expression noise induced by genetic variation and growth conditions. PMID:26230518

Nanometric depth resolution from multi-focal images in microscopy.

PubMed

Dalgarno, Heather I C; Dalgarno, Paul A; Dada, Adetunmise C; Towers, Catherine E; Gibson, Gavin J; Parton, Richard M; Davis, Ilan; Warburton, Richard J; Greenaway, Alan H

2011-07-06

We describe a method for tracking the position of small features in three dimensions from images recorded on a standard microscope with an inexpensive attachment between the microscope and the camera. The depth-measurement accuracy of this method is tested experimentally on a wide-field, inverted microscope and is shown to give approximately 8 nm depth resolution, over a specimen depth of approximately 6 µm, when using a 12-bit charge-coupled device (CCD) camera and very bright but unresolved particles. To assess low-flux limitations a theoretical model is used to derive an analytical expression for the minimum variance bound. The approximations used in the analytical treatment are tested using numerical simulations. It is concluded that approximately 14 nm depth resolution is achievable with flux levels available when tracking fluorescent sources in three dimensions in live-cell biology and that the method is suitable for three-dimensional photo-activated localization microscopy resolution. Sub-nanometre resolution could be achieved with photon-counting techniques at high flux levels.

Nanometric depth resolution from multi-focal images in microscopy

PubMed Central

Dalgarno, Heather I. C.; Dalgarno, Paul A.; Dada, Adetunmise C.; Towers, Catherine E.; Gibson, Gavin J.; Parton, Richard M.; Davis, Ilan; Warburton, Richard J.; Greenaway, Alan H.

2011-01-01

We describe a method for tracking the position of small features in three dimensions from images recorded on a standard microscope with an inexpensive attachment between the microscope and the camera. The depth-measurement accuracy of this method is tested experimentally on a wide-field, inverted microscope and is shown to give approximately 8 nm depth resolution, over a specimen depth of approximately 6 µm, when using a 12-bit charge-coupled device (CCD) camera and very bright but unresolved particles. To assess low-flux limitations a theoretical model is used to derive an analytical expression for the minimum variance bound. The approximations used in the analytical treatment are tested using numerical simulations. It is concluded that approximately 14 nm depth resolution is achievable with flux levels available when tracking fluorescent sources in three dimensions in live-cell biology and that the method is suitable for three-dimensional photo-activated localization microscopy resolution. Sub-nanometre resolution could be achieved with photon-counting techniques at high flux levels. PMID:21247948

DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states.

PubMed

White, Eric J; Emanuelsson, Olof; Scalzo, David; Royce, Thomas; Kosak, Steven; Oakeley, Edward J; Weissman, Sherman; Gerstein, Mark; Groudine, Mark; Snyder, Michael; Schübeler, Dirk

2004-12-21

Duplication of the genome during the S phase of the cell cycle does not occur simultaneously; rather, different sequences are replicated at different times. The replication timing of specific sequences can change during development; however, the determinants of this dynamic process are poorly understood. To gain insights into the contribution of developmental state, genomic sequence, and transcriptional activity to replication timing, we investigated the timing of DNA replication at high resolution along an entire human chromosome (chromosome 22) in two different cell types. The pattern of replication timing was correlated with respect to annotated genes, gene expression, novel transcribed regions of unknown function, sequence composition, and cytological features. We observed that chromosome 22 contains regions of early- and late-replicating domains of 100 kb to 2 Mb, many (but not all) of which are associated with previously described chromosomal bands. In both cell types, expressed sequences are replicated earlier than nontranscribed regions. However, several highly transcribed regions replicate late. Overall, the DNA replication-timing profiles of the two different cell types are remarkably similar, with only nine regions of difference observed. In one case, this difference reflects the differential expression of an annotated gene that resides in this region. Novel transcribed regions with low coding potential exhibit a strong propensity for early DNA replication. Although the cellular function of such transcripts is poorly understood, our results suggest that their activity is linked to the replication-timing program.

Unprecedented high-resolution view of bacterial operon architecture revealed by RNA sequencing.

PubMed

Conway, Tyrrell; Creecy, James P; Maddox, Scott M; Grissom, Joe E; Conkle, Trevor L; Shadid, Tyler M; Teramoto, Jun; San Miguel, Phillip; Shimada, Tomohiro; Ishihama, Akira; Mori, Hirotada; Wanner, Barry L

2014-07-08

We analyzed the transcriptome of Escherichia coli K-12 by strand-specific RNA sequencing at single-nucleotide resolution during steady-state (logarithmic-phase) growth and upon entry into stationary phase in glucose minimal medium. To generate high-resolution transcriptome maps, we developed an organizational schema which showed that in practice only three features are required to define operon architecture: the promoter, terminator, and deep RNA sequence read coverage. We precisely annotated 2,122 promoters and 1,774 terminators, defining 1,510 operons with an average of 1.98 genes per operon. Our analyses revealed an unprecedented view of E. coli operon architecture. A large proportion (36%) of operons are complex with internal promoters or terminators that generate multiple transcription units. For 43% of operons, we observed differential expression of polycistronic genes, despite being in the same operons, indicating that E. coli operon architecture allows fine-tuning of gene expression. We found that 276 of 370 convergent operons terminate inefficiently, generating complementary 3' transcript ends which overlap on average by 286 nucleotides, and 136 of 388 divergent operons have promoters arranged such that their 5' ends overlap on average by 168 nucleotides. We found 89 antisense transcripts of 397-nucleotide average length, 7 unannotated transcripts within intergenic regions, and 18 sense transcripts that completely overlap operons on the opposite strand. Of 519 overlapping transcripts, 75% correspond to sequences that are highly conserved in E. coli (>50 genomes). Our data extend recent studies showing unexpected transcriptome complexity in several bacteria and suggest that antisense RNA regulation is widespread. Importance: We precisely mapped the 5' and 3' ends of RNA transcripts across the E. coli K-12 genome by using a single-nucleotide analytical approach. Our resulting high-resolution transcriptome maps show that ca. one-third of E. coli operons are complex, with internal promoters and terminators generating multiple transcription units and allowing differential gene expression within these operons. We discovered extensive antisense transcription that results from more than 500 operons, which fully overlap or extensively overlap adjacent divergent or convergent operons. The genomic regions corresponding to these antisense transcripts are highly conserved in E. coli (including Shigella species), although it remains to be proven whether or not they are functional. Our observations of features unearthed by single-nucleotide transcriptome mapping suggest that deeper layers of transcriptional regulation in bacteria are likely to be revealed in the future. Copyright © 2014 Conway et al.

Innovation and fusion of x-ray and optical tomography for mouse studies of breast cancer

NASA Astrophysics Data System (ADS)

Wang, Ge; Cong, Wenxiang; Yang, Qingsong; Pian, Qi; Zhu, Shouping; Liang, Jimin; Barroso, Margarida; Intes, Xavier

2016-10-01

For early detection and targeted therapy, receptor expression profiling is instrumental to classifying breast cancer into sub-groups. In particular, human epidermal growth factor receptor 2 (HER2) expression has been shown to have both prognostic and predictive values. Recently, an increasingly more complex view of HER2 in breast cancer has emerged from genome sequencing that highlights the role of inter- and intra-tumor heterogeneity in therapy resistance. Studies on such heterogeneity demand high-content, high-resolution functional and molecular imaging in vivo, which cannot be achieved using any single imaging tool. Clearly, there is a critical need to develop a multimodality approach for breast cancer imaging. Since 2006, grating-based x-ray imaging has been developed for much-improved x-ray images. In 2014, the demonstration of fluorescence molecular tomography (FMT) guided by x-ray grating-based micro-CT was reported with encouraging results and major drawbacks. In this paper, we propose to integrate grating-based x-ray tomography (GXT) and high-dimensional optical tomography (HOT) into the first-of-its-kind truly-fused GXT-HOT (pronounced as "Get Hot") system for imaging of breast tumor heterogeneity, HER2 expression and dimerization, and therapeutic response. The primary innovation lies in developing a brand-new high-content, high-throughput x-ray optical imager based on several contemporary techniques to have MRI-type soft tissue contrast, PET-like sensitivity and specificity, and micro-CT-equivalent resolution. This system consists of two orthogonal x-ray Talbot-Lau interferometric imaging chains and a hyperspectral time-resolved single-pixel optical imager. Both the system design and pilot results will be reported in this paper, along with relevant issues under further investigation.

Kuiper Belt Objects Along the Pluto Express Path

NASA Technical Reports Server (NTRS)

Jewitt, David C.

1998-01-01

The science objective of this work was to identify objects in the Kuiper Belt which will, in the 5 years following Pluto encounter, be close to the flight path of NASA's Pluto-Kuiper Express. Currently, launch is scheduled for 2004 with a flight time of about 1 decade. Early identification of post-Pluto targets is important for mission design and orbit refinement. An object or objects close enough to the flight path can be visited and studied at high resolution, using only residual gas in the thrusters to affect a close encounter.

Do Gender-Specific and High-Resolution Three Dimensional Body Charts Facilitate the Communication of Pain for Women? A Quantitative and Qualitative Study

PubMed Central

Egsgaard, Line Lindhardt

2016-01-01

Background Chronic pain is more prevalent among women; however, the majority of standardized pain drawings are often collected using male-like androgynous body representations. Objective The purpose of this study was to assess whether gender-specific and high-resolution three-dimensional (3D) body charts facilitate the communication of pain for women. Methods Using mixed-methods and a cross-over design, female patients with chronic pain were asked to provide detailed drawings of their current pain on masculine and feminine two-dimensional (2D) body schemas (N=41, Part I) or on female 2D and 3D high-resolution body schemas (N=41, Part II) on a computer tablet. The consistency of the drawings between body charts were assessed by intraclass correlation coefficient (ICC) and Bland-Altman plots. Semistructured interviews and a preference questionnaire were then used to obtain qualitative and quantitative responses of the drawing experience. Results The consistency between body charts were high (Part I: ICC=0.980, Part II: ICC=0.994). The preference ratio for the masculine to feminine body schemas were 6:35 and 18:23 for the 2D to 3D female body charts. Patients reported that the 3D body chart enabled a more accurate expression of their pain due to the detailed contours of the musculature and bone structure, however, patients also reported the 3D body chart was too human and believed that skin-like appearance limited ‘deep pain’ expressions. Conclusions Providing gender-specific body charts may facilitate the communication of pain and the level of detail (2D vs 3D body charts) should be used according to patients’ needs. PMID:27440737

Recent and episodic volcanic and glacial activity on Mars revealed by the High Resolution Stereo Camera.

PubMed

Neukum, G; Jaumann, R; Hoffmann, H; Hauber, E; Head, J W; Basilevsky, A T; Ivanov, B A; Werner, S C; van Gasselt, S; Murray, J B; McCord, T

2004-12-23

The large-area coverage at a resolution of 10-20 metres per pixel in colour and three dimensions with the High Resolution Stereo Camera Experiment on the European Space Agency Mars Express Mission has made it possible to study the time-stratigraphic relationships of volcanic and glacial structures in unprecedented detail and give insight into the geological evolution of Mars. Here we show that calderas on five major volcanoes on Mars have undergone repeated activation and resurfacing during the last 20 per cent of martian history, with phases of activity as young as two million years, suggesting that the volcanoes are potentially still active today. Glacial deposits at the base of the Olympus Mons escarpment show evidence for repeated phases of activity as recently as about four million years ago. Morphological evidence is found that snow and ice deposition on the Olympus construct at elevations of more than 7,000 metres led to episodes of glacial activity at this height. Even now, water ice protected by an insulating layer of dust may be present at high altitudes on Olympus Mons.

Exploring image data assimilation in the prospect of high-resolution satellite data

NASA Astrophysics Data System (ADS)

Verron, J. A.; Duran, M.; Gaultier, L.; Brankart, J. M.; Brasseur, P.

2016-02-01

Many recent works show the key importance of studying the ocean at fine scales including the meso- and submesoscales. Satellite observations such as ocean color data provide informations on a wide range of scales but do not directly provide information on ocean dynamics. Satellite altimetry provide informations on the ocean dynamic topography (SSH) but so far with a limited resolution in space and even more, in time. However, in the near future, high-resolution SSH data (e.g. SWOT) will give a vision of the dynamic topography at such fine space resolution. This raises some challenging issues for data assimilation in physical oceanography: develop reliable methodology to assimilate high resolution data, make integrated use of various data sets including biogeochemical data, and even more simply, solve the challenge of handling large amont of data and huge state vectors. In this work, we propose to consider structured information rather than pointwise data. First, we take an image data assimilation approach in studying the feasibility of inverting tracer observations from Sea Surface Temperature and/or Ocean Color datasets, to improve the description of mesoscale dynamics provided by altimetric observations. Finite Size Lyapunov Exponents are used as an image proxy. The inverse problem is formulated in a Bayesian framework and expressed in terms of a cost function measuring the misfits between the two images. Second, we explore the inversion of SWOT-like high resolution SSH data and more especially the various possible proxies of the actual SSH that could be used to control the ocean circulation at various scales. One focus is made on controlling the subsurface ocean from surface only data. A key point lies in the errors and uncertainties that are associated to SWOT data.

A high-resolution anatomical ontology of the developing murine genitourinary tract

PubMed Central

Little, Melissa H.; Brennan, Jane; Georgas, Kylie; Davies, Jamie A.; Davidson, Duncan R.; Baldock, Richard A.; Beverdam, Annemiek; Bertram, John F.; Capel, Blanche; Chiu, Han Sheng; Clements, Dave; Cullen-McEwen, Luise; Fleming, Jean; Gilbert, Thierry; Houghton, Derek; Kaufman, Matt H.; Kleymenova, Elena; Koopman, Peter A.; Lewis, Alfor G.; McMahon, Andrew P.; Mendelsohn, Cathy L.; Mitchell, Eleanor K.; Rumballe, Bree A.; Sweeney, Derina E.; Valerius, M. Todd; Yamada, Gen; Yang, Yiya; Yu., Jing

2007-01-01

Cataloguing gene expression during development of the genitourinary tract will increase our understanding not only of this process but also of congenital defects and disease affecting this organ system. We have developed a high-resolution ontology with which to describe the subcompartments of the developing murine genitourinary tract. This ontology incorporates what can be defined histologically and begins to encompass other structures and cell types already identified at the molecular level. The ontology is being used to annotate in situ hybridisation data generated as part of the Genitourinary Development Molecular Anatomy Project (GUDMAP), a publicly available data resource on gene and protein expression during genitourinary development. The GUDMAP ontology encompasses Theiler stage (TS) 17 to 27 of development as well as the sexually mature adult. It has been written as a partonomic, text-based, hierarchical ontology that, for the embryological stages, has been developed as a high-resolution expansion of the existing Edinburgh Mouse Atlas Project (EMAP) ontology. It also includes group terms for well-characterised structural and/or functional units comprising several sub-structures, such as the nephron and juxtaglomerular complex. Each term has been assigned a unique identification number. Synonyms have been used to improve the success of query searching and maintain wherever possible existing EMAP terms relating to this organ system. We describe here the principles and structure of the ontology and provide representative diagrammatic, histological, and whole mount and section RNA in situ hybridisation images to clarify the terms used within the ontology. Visual examples of how terms appear in different specimen types are also provided. PMID:17452023

Identification of novel non-coding small RNAs from Streptococcus pneumoniae TIGR4 using high-resolution genome tiling arrays

PubMed Central

2010-01-01

Background The identification of non-coding transcripts in human, mouse, and Escherichia coli has revealed their widespread occurrence and functional importance in both eukaryotic and prokaryotic life. In prokaryotes, studies have shown that non-coding transcripts participate in a broad range of cellular functions like gene regulation, stress and virulence. However, very little is known about non-coding transcripts in Streptococcus pneumoniae (pneumococcus), an obligate human respiratory pathogen responsible for significant worldwide morbidity and mortality. Tiling microarrays enable genome wide mRNA profiling as well as identification of novel transcripts at a high-resolution. Results Here, we describe a high-resolution transcription map of the S. pneumoniae clinical isolate TIGR4 using genomic tiling arrays. Our results indicate that approximately 66% of the genome is expressed under our experimental conditions. We identified a total of 50 non-coding small RNAs (sRNAs) from the intergenic regions, of which 36 had no predicted function. Half of the identified sRNA sequences were found to be unique to S. pneumoniae genome. We identified eight overrepresented sequence motifs among sRNA sequences that correspond to sRNAs in different functional categories. Tiling arrays also identified approximately 202 operon structures in the genome. Conclusions In summary, the pneumococcal operon structures and novel sRNAs identified in this study enhance our understanding of the complexity and extent of the pneumococcal 'expressed' genome. Furthermore, the results of this study open up new avenues of research for understanding the complex RNA regulatory network governing S. pneumoniae physiology and virulence. PMID:20525227

Control of transcription elongation by GreA determines rate of gene expression in Streptococcus pneumoniae.

PubMed

Yuzenkova, Yulia; Gamba, Pamela; Herber, Martijn; Attaiech, Laetitia; Shafeeq, Sulman; Kuipers, Oscar P; Klumpp, Stefan; Zenkin, Nikolay; Veening, Jan-Willem

2014-01-01

Transcription by RNA polymerase may be interrupted by pauses caused by backtracking or misincorporation that can be resolved by the conserved bacterial Gre-factors. However, the consequences of such pausing in the living cell remain obscure. Here, we developed molecular biology and transcriptome sequencing tools in the human pathogen Streptococcus pneumoniae and provide evidence that transcription elongation is rate-limiting on highly expressed genes. Our results suggest that transcription elongation may be a highly regulated step of gene expression in S. pneumoniae. Regulation is accomplished via long-living elongation pauses and their resolution by elongation factor GreA. Interestingly, mathematical modeling indicates that long-living pauses cause queuing of RNA polymerases, which results in 'transcription traffic jams' on the gene and thus blocks its expression. Together, our results suggest that long-living pauses and RNA polymerase queues caused by them are a major problem on highly expressed genes and are detrimental for cell viability. The major and possibly sole function of GreA in S. pneumoniae is to prevent formation of backtracked elongation complexes. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Microtopographic characterization of ice-wedge polygon landscape in Barrow, Alaska: a digital map of troughs, rims, centers derived from high resolution (0.25 m) LiDAR data

DOE Data Explorer

Gangodagamage, Chandana; Wullschleger, Stan

2014-07-03

The dataset represents microtopographic characterization of the ice-wedge polygon landscape in Barrow, Alaska. Three microtopographic features are delineated using 0.25 m high resolution digital elevation dataset derived from LiDAR. The troughs, rims, and centers are the three categories in this classification scheme. The polygon troughs are the surface expression of the ice-wedges that are in lower elevations than the interior polygon. The elevated shoulders of the polygon interior immediately adjacent to the polygon troughs are the polygon rims for the low center polygons. In case of high center polygons, these features are the topographic highs. In this classification scheme, both topographic highs and rims are considered as polygon rims. The next version of the dataset will include more refined classification scheme including separate classes for rims ad topographic highs. The interior part of the polygon just adjacent to the polygon rims are the polygon centers.

Zero-crossing approach to high-resolution reconstruction in frequency-domain optical-coherence tomography.

PubMed

Krishnan, Sunder Ram; Seelamantula, Chandra Sekhar; Bouwens, Arno; Leutenegger, Marcel; Lasser, Theo

2012-10-01

We address the problem of high-resolution reconstruction in frequency-domain optical-coherence tomography (FDOCT). The traditional method employed uses the inverse discrete Fourier transform, which is limited in resolution due to the Heisenberg uncertainty principle. We propose a reconstruction technique based on zero-crossing (ZC) interval analysis. The motivation for our approach lies in the observation that, for a multilayered specimen, the backscattered signal may be expressed as a sum of sinusoids, and each sinusoid manifests as a peak in the FDOCT reconstruction. The successive ZC intervals of a sinusoid exhibit high consistency, with the intervals being inversely related to the frequency of the sinusoid. The statistics of the ZC intervals are used for detecting the frequencies present in the input signal. The noise robustness of the proposed technique is improved by using a cosine-modulated filter bank for separating the input into different frequency bands, and the ZC analysis is carried out on each band separately. The design of the filter bank requires the design of a prototype, which we accomplish using a Kaiser window approach. We show that the proposed method gives good results on synthesized and experimental data. The resolution is enhanced, and noise robustness is higher compared with the standard Fourier reconstruction.

Increase of Myoglobin in Rat Gastrocnemius Muscles with Immobilization-induced Atrophy

PubMed Central

Lee, Jeong-Uk; Kim, Ju-Hyun; Kim, Mee-Young; Lee, Lim-Kyu; Yang, Seung-Min; Jeon, Hye-Joo; Lee, Won-Deok; Noh, Ji-Woong; Lee, Tae-Hyun; Kwak, Taek-Yong; Kim, Bokyung; Kim, Junghwan

2014-01-01

[Purpose] Atrophy is a common phenomenon caused by prolonged muscle disuse associated with bed-rest, aging, and immobilization. However, changes in the expression of atrophy-related myoglobin are still poorly understood. In the present study, we examined whether or not myoglobin expression is altered in the gastrocnemius muscles of rats after seven days of cast immobilization. [Methods] We conducted a protein expression and high-resolution differential proteomic analysis using, two-dimensional gel electrophoresis and matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry, and western blotting. [Results] The density and expression of myoglobin increased significantly more in atrophic gastrocnemius muscle strips than they did in the control group. [Conclusion] The results suggest that cast immobilization-induced atrophy may be related to changes in the expression of myoglobin in rat gastrocnemius muscles. PMID:24409033

Rapid differentiation of citrus Hop stunt viroid variants by use of real-time RT-PCR and high resolution melting analysis

USDA-ARS?s Scientific Manuscript database

The RNA genome of Hop stunt viroid (HSVd) contains five to six nucleotides in a variable (V) domain, called the cachexia expression motif, which is associated with pathogenic and non-pathogenic variants in citrus. Current methods to differentiate HSVd variants rely on lengthy greenhouse biological i...

Genome Comparisons Reveal a Dominant Mechanism of Chromosome Number Reduction in Grasses and Accelerated Genome Evolution in Triticeae

USDA-ARS?s Scientific Manuscript database

Single nucleotide polymorphism was employed in the construction of a high-resolution, expressed sequence tag (EST) map of Aegilops tauschii, the diploid source of the wheat D genome. Comparison of the map with the rice and sorghum genome sequences revealed 50 inversions and translocations; 2, 8, and...

Near-Seafloor Magnetic Exploration of Submarine Hydrothermal Systems in the Kermadec Arc

NASA Astrophysics Data System (ADS)

Caratori Tontini, F.; de Ronde, C. E. J.; Tivey, M.; Kinsey, J. C.

2014-12-01

Magnetic data can provide important information about hydrothermal systems because hydrothermal alteration can drastically reduce the magnetization of the host volcanic rocks. Near-seafloor data (≤70 m altitude) are required to map hydrothermal systems in detail; Autonomous Underwater Vehicles (AUVs) are the ideal platform to provide this level of resolution. Here, we show the results of high-resolution magnetic surveys by the ABE and Sentry AUVs for selected submarine volcanoes of the Kermadec arc. 3-D magnetization models derived from the inversion of magnetic data, when combined with high resolution seafloor bathymetry derived from multibeam surveys, provide important constraints on the subseafloor geometry of hydrothermal upflow zones and the structural control on the development of seafloor hydrothermal vent sites as well as being a tool for the discovery of previously unknown hydrothermal sites. Significant differences exist between the magnetic expressions of hydrothermal sites at caldera volcanoes ("donut" pattern) and cones ("Swiss cheese" pattern), respectively. Subseafloor 3-D magnetization models also highlight structural differences between focused and diffuse vent sites.

High-Resolution Topomapping of Mars: Life After MER Site Selection

NASA Technical Reports Server (NTRS)

Kirk, R. L.; Howington-Kraus, E.; Hare, T. M.; Soricone, R.; Ross, K.; Weller, L.; Rosiek, M.; Redding, B.; Galuszka, D.; Haldemann, A. F. C.

2004-01-01

In this abstract we describe our ongoing use of high-resolution images from the Mars Global Surveyor Mars Orbiter Camera Narrow-Angle subsystem (MGS MOC-NA) to derive quantitative topographic and slope data for the martian surface at 3 - 10-m resolution. Our efforts over the past several years focused on assessment of candidate landing sites for the Mars Exploration Rovers (MER) and culminated in the selection of sites in Gusev crater and Meridiani Planum as safe as well as scientifically compelling. As of this writing, MER-A (Spirit) has landed safely in Gusev and we are performing a limited amount of additional mapping near the landing point to support localization of the lander and rover operations planning. The primary focus of our work, however, has been extending our techniques to sample a variety of geologic terrains planetwide to support both a variety of geoscientific studies and planning and data analysis for missions such as Mars Express, Mars Reconnaissance Orbiter, and Phoenix.

A quantitative image cytometry technique for time series or population analyses of signaling networks.

PubMed

Ozaki, Yu-ichi; Uda, Shinsuke; Saito, Takeshi H; Chung, Jaehoon; Kubota, Hiroyuki; Kuroda, Shinya

2010-04-01

Modeling of cellular functions on the basis of experimental observation is increasingly common in the field of cellular signaling. However, such modeling requires a large amount of quantitative data of signaling events with high spatio-temporal resolution. A novel technique which allows us to obtain such data is needed for systems biology of cellular signaling. We developed a fully automatable assay technique, termed quantitative image cytometry (QIC), which integrates a quantitative immunostaining technique and a high precision image-processing algorithm for cell identification. With the aid of an automated sample preparation system, this device can quantify protein expression, phosphorylation and localization with subcellular resolution at one-minute intervals. The signaling activities quantified by the assay system showed good correlation with, as well as comparable reproducibility to, western blot analysis. Taking advantage of the high spatio-temporal resolution, we investigated the signaling dynamics of the ERK pathway in PC12 cells. The QIC technique appears as a highly quantitative and versatile technique, which can be a convenient replacement for the most conventional techniques including western blot, flow cytometry and live cell imaging. Thus, the QIC technique can be a powerful tool for investigating the systems biology of cellular signaling.

HRSC: High resolution stereo camera

USGS Publications Warehouse

Neukum, G.; Jaumann, R.; Basilevsky, A.T.; Dumke, A.; Van Gasselt, S.; Giese, B.; Hauber, E.; Head, J. W.; Heipke, C.; Hoekzema, N.; Hoffmann, H.; Greeley, R.; Gwinner, K.; Kirk, R.; Markiewicz, W.; McCord, T.B.; Michael, G.; Muller, Jan-Peter; Murray, J.B.; Oberst, J.; Pinet, P.; Pischel, R.; Roatsch, T.; Scholten, F.; Willner, K.

2009-01-01

The High Resolution Stereo Camera (HRSC) on Mars Express has delivered a wealth of image data, amounting to over 2.5 TB from the start of the mapping phase in January 2004 to September 2008. In that time, more than a third of Mars was covered at a resolution of 10-20 m/pixel in stereo and colour. After five years in orbit, HRSC is still in excellent shape, and it could continue to operate for many more years. HRSC has proven its ability to close the gap between the low-resolution Viking image data and the high-resolution Mars Orbiter Camera images, leading to a global picture of the geological evolution of Mars that is now much clearer than ever before. Derived highest-resolution terrain model data have closed major gaps and provided an unprecedented insight into the shape of the surface, which is paramount not only for surface analysis and geological interpretation, but also for combination with and analysis of data from other instruments, as well as in planning for future missions. This chapter presents the scientific output from data analysis and highlevel data processing, complemented by a summary of how the experiment is conducted by the HRSC team members working in geoscience, atmospheric science, photogrammetry and spectrophotometry. Many of these contributions have been or will be published in peer-reviewed journals and special issues. They form a cross-section of the scientific output, either by summarising the new geoscientific picture of Mars provided by HRSC or by detailing some of the topics of data analysis concerning photogrammetry, cartography and spectral data analysis.

Bistatic synthetic aperture radar

NASA Astrophysics Data System (ADS)

Yates, Gillian

Synthetic aperture radar (SAR) allows all-weather, day and night, surface surveillance and has the ability to detect, classify and geolocate objects at long stand-off ranges. Bistatic SAR, where the transmitter and the receiver are on separate platforms, is seen as a potential means of countering the vulnerability of conventional monostatic SAR to electronic countermeasures, particularly directional jamming, and avoiding physical attack of the imaging platform. As the receiving platform can be totally passive, it does not advertise its position by RF emissions. The transmitter is not susceptible to jamming and can, for example, operate at long stand-off ranges to reduce its vulnerability to physical attack. This thesis examines some of the complications involved in producing high-resolution bistatic SAR imagery. The effect of bistatic operation on resolution is examined from a theoretical viewpoint and analytical expressions for resolution are developed. These expressions are verified by simulation work using a simple 'point by point' processor. This work is extended to look at using modern practical processing engines for bistatic geometries. Adaptations of the polar format algorithm and range migration algorithm are considered. The principal achievement of this work is a fully airborne demonstration of bistatic SAR. The route taken in reaching this is given, along with some results. The bistatic SAR imagery is analysed and compared to the monostatic imagery collected at the same time. Demonstrating high-resolution bistatic SAR imagery using two airborne platforms represents what I believe to be a European first and is likely to be the first time that this has been achieved outside the US (the UK has very little insight into US work on this topic). Bistatic target characteristics are examined through the use of simulations. This also compares bistatic imagery with monostatic and gives further insight into the utility of bistatic SAR.

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

Ono, Kenji; Fuma, Kazuya; Tabata, Kaori

Magnetic resonance imaging (MRI) is a minimally invasive way to provide high spatial resolution tomograms. However, MRI has been considered to be useless for gene expression imaging compared to optical imaging. In this study, we used a ferritin reporter, binding with biogenic iron, to make it a powerful tool for gene expression imaging in MRI studies. GL261 mouse glioma cells were over-expressed with dual-reporter ferritin-DsRed under {beta}-actin promoter, then gene expression was observed by optical imaging and MRI in a brain tumor model. GL261 cells expressing ferritin-DsRed fusion protein showed enhanced visualizing effect by reducing T2-weighted signal intensity for inmore » vitro and in vivo MRI studies, as well as DsRed fluorescence for optical imaging. Furthermore, a higher contrast was achieved on T2-weighted images when permeating the plasma membrane of ferritin-DsRed-expressing GL261. Thus, a ferritin expression vector can be used as an MRI reporter to monitor in vivo gene expression.« less

Unmixing of spectral components affecting AVIRIS imagery of Tampa Bay

NASA Astrophysics Data System (ADS)

Carder, Kendall L.; Lee, Z. P.; Chen, Robert F.; Davis, Curtiss O.

1993-09-01

According to Kirk's as well as Morel and Gentili's Monte Carlo simulations, the popular simple expression, R approximately equals 0.33 bb/a, relating subsurface irradiance reflectance (R) to the ratio of the backscattering coefficient (bb) to absorption coefficient (a), is not valid for bb/a > 0.25. This means that it may no longer be valid for values of remote-sensing reflectance (above-surface ratio of water-leaving radiance to downwelling irradiance) where Rrs4/ > 0.01. Since there has been no simple Rrs expression developed for very turbid waters, we developed one based in part on Monte Carlo simulations and empirical adjustments to an Rrs model and applied it to rather turbid coastal waters near Tampa Bay to evaluate its utility for unmixing the optical components affecting the water- leaving radiance. With the high spectral (10 nm) and spatial (20 m2) resolution of Airborne Visible-InfraRed Imaging Spectrometer (AVIRIS) data, the water depth and bottom type were deduced using the model for shallow waters. This research demonstrates the necessity of further research to improve interpretations of scenes with highly variable turbid waters, and it emphasizes the utility of high spectral-resolution data as from AVIRIS for better understanding complicated coastal environments such as the west Florida shelf.

Marine algae are `taught' the basics of angular momentum

NASA Astrophysics Data System (ADS)

Allen, John Taylor

2017-11-01

Advanced modelling studies and high-resolution observations have shown that flows related to instability of the mesoscale ( 1-10 km scale) may provide both the fertilisation mechanism for nutrient-depleted (oligotrophic) surface waters and a subduction mechanism for the rapid export of phytoplankton biomass to the deep ocean. Here, a detailed multidisciplinary analysis of the data from an example high-resolution observational campaign is presented. The data provide direct observations of the transport of phytoplankton through baroclinic instability. Furthermore, the data confirm that this transport is constrained by the requirement to conserve angular momentum, expressed in a stratified water column as the conservation of potential vorticity. This constraint is clearly seen to produce long thin filaments of phytoplankton populations strained out along isopycnal vorticity annuli associated with mesoscale frontal instabilities.

Strain, magnetic anisotropy, and anisotropic magnetoresistance in (Ga,Mn)As on high-index substrates: Application to (113)A -oriented layers

NASA Astrophysics Data System (ADS)

Dreher, L.; Donhauser, D.; Daeubler, J.; Glunk, M.; Rapp, C.; Schoch, W.; Sauer, R.; Limmer, W.

2010-06-01

Based on a detailed theoretical examination of the lattice distortion in high-index epilayers in terms of continuum mechanics, expressions are deduced that allow the calculation and experimental determination of the strain tensor for (hhl) -oriented (Ga,Mn)As layers. Analytical expressions are derived for the strain-dependent free-energy density and for the resistivity tensor for monoclinic and orthorhombic crystal symmetries, phenomenologically describing the magnetic anisotropy and anisotropic magnetoresistance by appropriate anisotropy and resistivity parameters, respectively. Applying the results to (113)A orientation with monoclinic crystal symmetry, the expressions are used to determine the strain tensor and the shear angle of a series of (113)A -oriented (Ga,Mn)As layers by high-resolution x-ray diffraction and to probe the magnetic anisotropy and anisotropic magnetoresistance at 4.2 K by means of angle-dependent magnetotransport. Whereas the transverse-resistivity parameters are nearly unaffected by the magnetic field, the parameters describing the longitudinal resistivity are strongly field dependent.

High-level Expression Purification Crystallization and Preliminary X-ray Crystallographic Studies of the Receptor Binding Domain of botulinum neurotoxin Serotype D

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

Y Zhang; X Gao; G Buchko

2011-12-31

Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and animals that are responsible for the deadly neuroparalytic disease botulism. Here, details of the expression and purification of the receptor-binding domain (HCR) of BoNT/D in Escherichia coli are presented. Using a codon-optimized cDNA, BoNT/D{_}HCR was expressed at a high level (150-200 mg per litre of culture) in the soluble fraction. Following a three-step purification protocol, very pure (>98%) BoNT/D{_}HCR was obtained. The recombinant BoNT/D{_}HCR was crystallized and the crystals diffracted to 1.65 {angstrom} resolution. The crystals belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 60.8,more » b = 89.7, c = 93.9 {angstrom}. Preliminary crystallographic data analysis revealed the presence of one molecule in the asymmetric unit.« less

High-level expression, purification, crystallization and preliminary X-ray crystallographic studies of the receptor-binding domain of botulinum neurotoxin serotype D

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

Zhang, Y.; Robinson, H.; Gao, X.

2010-12-01

Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and animals that are responsible for the deadly neuroparalytic disease botulism. Here, details of the expression and purification of the receptor-binding domain (HCR) of BoNT/D in Escherichia coli are presented. Using a codon-optimized cDNA, BoNT/D{_}HCR was expressed at a high level (150-200 mg per litre of culture) in the soluble fraction. Following a three-step purification protocol, very pure (>98%) BoNT/D{_}HCR was obtained. The recombinant BoNT/D{_}HCR was crystallized and the crystals diffracted to 1.65 {angstrom} resolution. The crystals belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 60.8,more » b = 89.7, c = 93.9 {angstrom}. Preliminary crystallographic data analysis revealed the presence of one molecule in the asymmetric unit.« less

Immunocytochemistry of the amphibian embryo--from overview to ultrastructure.

PubMed

Kurth, Thomas

2003-06-01

Amphibian embryos are standard research objects to study pattern formation and morphogenesis. Due to their external development and robust nature, experimental manipulations such as microinjections or transplantations can be easily performed. However, most immunocytochemical approaches addressing the specific localization of proteins are hampered by the fragility of the large and yolky embryonic cells which render high resolution staining difficult. Immunocytochemical data are therefore often restricted to either overall patterns in whole embryo preparations or to immunofluorescent localization with limited resolution on sections. High resolution or ultrastructural protein localization data are rare and can be achieved only with time consuming procedures. Here, a comparative study of immunocytochemical methods suitable for light and electron microscopy using different kinds of plastic resins is presented. Three main approaches are described: preembedding staining of whole embryos, postembedding staining of ultrathin sections and preembedding staining of vibratome sections. All the procedures are designed to study protein expression in early amphibian embryos en gros as well as en detail and the described techniques are suitable to combine two or three levels of resolution on the very same biological specimen. Examples are presented and advantages and disadvantages of the different protocols are discussed.

Supramolecular organization and chiral resolution of p-terphenyl-m-dicarbonitrile on the Ag(111) surface.

PubMed

Marschall, Matthias; Reichert, Joachim; Seufert, Knud; Auwärter, Willi; Klappenberger, Florian; Weber-Bargioni, Alexander; Klyatskaya, Svetlana; Zoppellaro, Giorgio; Nefedov, Alexei; Strunskus, Thomas; Wöll, Christof; Ruben, Mario; Barth, Johannes V

2010-05-17

The supramolecular organization and layer formation of the non-linear, prochiral molecule [1, 1';4',1'']-terphenyl-3,3"-dicarbonitrile adsorbed on the Ag(111) surface is investigated by scanning tunneling microscopy (STM) and near-edge X-ray absorption fine-structure spectroscopy (NEXAFS). Upon two-dimensional confinement the molecules are deconvoluted in three stereoisomers, that is, two mirror-symmetric trans- and one cis-species. STM measurements reveal large and regular islands following room temperature deposition, whereby NEXAFS confirms a flat adsorption geometry with the electronic pi-system parallel to the surface plane. The ordering within the expressed supramolecular arrays reflects a substrate templating effect, steric constraints and the operation of weak lateral interactions mainly originating from the carbonitrile endgroups. High-resolution data at room temperature reveal enantiormorphic characteristics of the molecular packing schemes in different domains of the arrays, indicative of chiral resolution during the 2D molecular self-assembly process. At submonolayer coverage supramolecular islands coexist with a disordered fluid phase of highly mobile molecules. Following thermal quenching (down to 6 K) we find extended supramolecular ribbons stabilised again by attractive and directional noncovalent interactions, the formation of which reflects a chiral resolution of trans-species.

TLM-Quant: An Open-Source Pipeline for Visualization and Quantification of Gene Expression Heterogeneity in Growing Microbial Cells

PubMed Central

Piersma, Sjouke; Denham, Emma L.; Drulhe, Samuel; Tonk, Rudi H. J.; Schwikowski, Benno; van Dijl, Jan Maarten

2013-01-01

Gene expression heterogeneity is a key driver for microbial adaptation to fluctuating environmental conditions, cell differentiation and the evolution of species. This phenomenon has therefore enormous implications, not only for life in general, but also for biotechnological applications where unwanted subpopulations of non-producing cells can emerge in large-scale fermentations. Only time-lapse fluorescence microscopy allows real-time measurements of gene expression heterogeneity. A major limitation in the analysis of time-lapse microscopy data is the lack of fast, cost-effective, open, simple and adaptable protocols. Here we describe TLM-Quant, a semi-automatic pipeline for the analysis of time-lapse fluorescence microscopy data that enables the user to visualize and quantify gene expression heterogeneity. Importantly, our pipeline builds on the open-source packages ImageJ and R. To validate TLM-Quant, we selected three possible scenarios, namely homogeneous expression, highly ‘noisy’ heterogeneous expression, and bistable heterogeneous expression in the Gram-positive bacterium Bacillus subtilis. This bacterium is both a paradigm for systems-level studies on gene expression and a highly appreciated biotechnological ‘cell factory’. We conclude that the temporal resolution of such analyses with TLM-Quant is only limited by the numbers of recorded images. PMID:23874729

Would you like to play together? Adults' attachment and the mirror game.

PubMed

Feniger-Schaal, Rinat; Noy, Lior; Hart, Yuval; Koren-Karie, Nina; Mayo, Avraham E; Alon, Uri

2016-01-01

Why is it easy for some people to play together and difficult for others? In this interdisciplinary pilot study, we looked at dyadic interaction in motion as a paradigm to explore the expression of attachment in adulthood. We used a device that gives simple, quantitative and automated indicators for the quality of interaction while playing the mirror game. Forty-seven participants played the mirror game with the same gender-matched expert players. In addition, participants were interviewed on the Adult Attachment Interview to assess their quality of attachment. Using high resolution kinematic measures, we found that secure attachment was correlated with high complexity of the game and low synchrony compared to insecure attachment. The findings suggest that security of attachment is related to a more exploratory and less rigid game than insecure-dismissing attachment. These preliminary findings imply that high resolution analysis of simple movement interaction could carry information about attachment behavior.

Temporally precise single-cell resolution optogenetics

PubMed Central

Shemesh, Or A.; Tanese, Dimitrii; Zampini, Valeria; Linghu, Changyang; Piatkevich, Kiryl; Ronzitti, Emiliano; Papagiakoumou, Eirini; Boyden, Edward S.; Emiliani, Valentina

2017-01-01

Optogenetic control of individual neurons with high temporal precision, within intact mammalian brain circuitry, would enable powerful explorations of how neural circuits operate. Two-photon computer generated holography enables precise sculpting of light, and could in principle enable simultaneous illumination of many neurons in a network, with the requisite temporal precision to simulate accurate neural codes. We designed a high efficacy soma-targeted opsin, finding that fusing the N-terminal 150 residues of kainate receptor subunit 2 (KA2) to the recently discovered high-photocurrent channelrhodopsin CoChR restricted expression of this opsin primarily to the cell body of mammalian cortical neurons. In combination with two-photon holographic stimulation, we found that this somatic CoChR (soCoChR) enabled photostimulation of individual cells in intact cortical circuits with single cell resolution and <1 millisecond temporal precision, and use soCoChR to perform connectivity mapping on intact cortical circuits. PMID:29184208

Simultaneously achieve soluble expression and biomimetic immobilization of Candida antarctica lipase B by introducing polyamine tags.

PubMed

Zhou, Xiaoxue; Han, Yu; Lv, Zheng; Tian, Xuemei; Li, Han; Xie, Panpan; Zheng, Liangyu

2017-05-10

Polyamine tags fused in Candida antarctica lipase B (CalB) can help achieve high soluble expression of CalB in E. coli and can directly mediate silicification, which leads to rapid formation of a CalB-silica particle complex through a one-step approach. After optimization experiments, the fused lipase CalB tagged with 6-histidine at the N terminal and 10-lysine at the C terminal (6His-CalB-10Lys) is effectively expressed with high solubility (0.1mg/mL) and specific activity (10.1U/mg), and easily cross-linked in silica particles with a high immobilization efficiency of 96.8% and activity recovery of 81.5%. The immobilized lipase 6His-CalB-10Lys exhibits excellent performance at broad temperature ranges, high thermal and storage stabilities, and superior reusability. Michaelis-Menten kinetics indicates that the affinity and enantioselectivity of the free and immobilized 6His-CalB-10Lys toward the substrate are better than that of commercial Novozym 435 in enantioselective resolution of (S)-N-(2-ethyl-6-methylphenyl) alanine ((S)-NEMPA). The strategies described in this paper are useful for the facile expression and construction of diverse enzyme systems with high efficiency and excellent recyclability. Copyright © 2017 Elsevier B.V. All rights reserved.

Identification and resolution of artifacts in the interpretation of imprinted gene expression

PubMed Central

Proudhon, Charlotte

2010-01-01

Genomic imprinting refers to genes that are epigenetically programmed in the germline to express exclusively or preferentially one allele in a parent-of-origin manner. Expression-based genome-wide screening for the identification of imprinted genes has failed to uncover a significant number of new imprinted genes, probably because of the high tissue- and developmental-stage specificity of imprinted gene expression. A very large number of technical and biological artifacts can also lead to the erroneous evidence of imprinted gene expression. In this article, we focus on three common sources of potential confounding effects: (i) random monoallelic expression in monoclonal cell populations, (ii) genetically determined monoallelic expression and (iii) contamination or infiltration of embryonic tissues with maternal material. This last situation specifically applies to genes that occur as maternally expressed in the placenta. Beside the use of reciprocal crosses that are instrumental to confirm the parental specificity of expression, we provide additional methods for the detection and elimination of these situations that can be misinterpreted as cases of imprinted expression. PMID:20829207

Low-resolution expression recognition based on central oblique average CS-LBP with adaptive threshold

NASA Astrophysics Data System (ADS)

Han, Sheng; Xi, Shi-qiong; Geng, Wei-dong

2017-11-01

In order to solve the problem of low recognition rate of traditional feature extraction operators under low-resolution images, a novel algorithm of expression recognition is proposed, named central oblique average center-symmetric local binary pattern (CS-LBP) with adaptive threshold (ATCS-LBP). Firstly, the features of face images can be extracted by the proposed operator after pretreatment. Secondly, the obtained feature image is divided into blocks. Thirdly, the histogram of each block is computed independently and all histograms can be connected serially to create a final feature vector. Finally, expression classification is achieved by using support vector machine (SVM) classifier. Experimental results on Japanese female facial expression (JAFFE) database show that the proposed algorithm can achieve a recognition rate of 81.9% when the resolution is as low as 16×16, which is much better than that of the traditional feature extraction operators.

Angular resolution of stacked resistive plate chambers

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

Samuel, Deepak; Onikeri, Pratibha B.; Murgod, Lakshmi P., E-mail: deepaksamuel@cuk.ac.in, E-mail: pratibhaonikeri@gmail.com, E-mail: lakshmipmurgod@gmail.com

We present here detailed derivations of mathematical expressions for the accuracy in the arrival direction of particles estimated using a set of stacked resistive plate chambers (RPCs). The expressions are validated against experimental results using data collected from the prototype detectors (without magnet) of the upcoming India-based Neutrino Observatory (INO). We also present a theoretical estimate of angular resolution of such a setup. In principle, these expressions can be used for any other detector with an architecture similar to that of RPCs.

Toward Active Control of Noise from Hot Supersonic Jets

DTIC Science & Technology

2012-11-15

Instruments PXIe (PCI extensions for Instrumentation-express) system. The PXIe system has four PXIe-4331 cards (8 channels, 24 bits of resolution...üiüj) _ dxjdx ■j \\ düi düj dxj dxi düi du dii dx ?)■ (7) Our intention is to use (7) as an indicator of sound production in high speed

Optogenetic pacing in Drosophila melanogaster

PubMed Central

Alex, Aneesh; Li, Airong; Tanzi, Rudolph E.; Zhou, Chao

2015-01-01

Electrical stimulation is currently the gold standard for cardiac pacing. However, it is invasive and nonspecific for cardiac tissues. We recently developed a noninvasive cardiac pacing technique using optogenetic tools, which are widely used in neuroscience. Optogenetic pacing of the heart provides high spatial and temporal precisions, is specific for cardiac tissues, avoids artifacts associated with electrical stimulation, and therefore promises to be a powerful tool in basic cardiac research. We demonstrated optogenetic control of heart rhythm in a well-established model organism, Drosophila melanogaster. We developed transgenic flies expressing a light-gated cation channel, channelrhodopsin-2 (ChR2), specifically in their hearts and demonstrated successful optogenetic pacing of ChR2-expressing Drosophila at different developmental stages, including the larva, pupa, and adult stages. A high-speed and ultrahigh-resolution optical coherence microscopy imaging system that is capable of providing images at a rate of 130 frames/s with axial and transverse resolutions of 1.5 and 3.9 μm, respectively, was used to noninvasively monitor Drosophila cardiac function and its response to pacing stimulation. The development of a noninvasive integrated optical pacing and imaging system provides a novel platform for performing research studies in developmental cardiology. PMID:26601299

High-resolution face verification using pore-scale facial features.

PubMed

Li, Dong; Zhou, Huiling; Lam, Kin-Man

2015-08-01

Face recognition methods, which usually represent face images using holistic or local facial features, rely heavily on alignment. Their performances also suffer a severe degradation under variations in expressions or poses, especially when there is one gallery per subject only. With the easy access to high-resolution (HR) face images nowadays, some HR face databases have recently been developed. However, few studies have tackled the use of HR information for face recognition or verification. In this paper, we propose a pose-invariant face-verification method, which is robust to alignment errors, using the HR information based on pore-scale facial features. A new keypoint descriptor, namely, pore-Principal Component Analysis (PCA)-Scale Invariant Feature Transform (PPCASIFT)-adapted from PCA-SIFT-is devised for the extraction of a compact set of distinctive pore-scale facial features. Having matched the pore-scale features of two-face regions, an effective robust-fitting scheme is proposed for the face-verification task. Experiments show that, with one frontal-view gallery only per subject, our proposed method outperforms a number of standard verification methods, and can achieve excellent accuracy even the faces are under large variations in expression and pose.

High LMD GCM Resolution Modeling of the Seasonal Evolution of the Martian Northern Permanent Cap: Comparison with Mars Express OMEGA Observations

NASA Technical Reports Server (NTRS)

Levrard, B.; Forget, F.; Montmessin, F.; Schmitt, B.; Doute, S.; Langevin, Y.; Poulet, F.; Bibring, J. P.; Gondet, B.

2005-01-01

Analyses of imaging data from Mariner, Viking and MGS have shown that surface properties (albedo, temperature) of the northern cap present significant differences within the summer season and between Mars years. These observations include differential brightening and/or darkening between polar areas from the end of the spring to midsummer. These differences are attributed to changes in grain size or dust content of surface ice. To better understand the summer behavior of the permanent northern polar cap, we perfomed a high resolution modeling (approximately 1 deg x 1 deg.) of northern cap in the Martian Climate/water cycle as simulated by the Laboratoire de Meteorologie Dynamique (LMD) global climate model. We compare the predicted properties of the surface ice (ice thickness, temperature) with the Mars Express Omega summer observations of the northern cap. albedo and thermal inertia svariations model. In particular, albedo variations could be constrained by OMEGA data. Meteorological predictions of the LMD GCM wil be presented at the conference to interpret the unprecedently resolved OMEGA observations. The specific evolution of regions of interest (cap center, Chasma Boreal...) and the possibility of late summer global cap brightening will be discussed.

Micropreparative capillary gel electrophoresis of DNA: rapid expressed sequence tag library construction.

PubMed

Shi, Liang; Khandurina, Julia; Ronai, Zsolt; Li, Bi-Yu; Kwan, Wai King; Wang, Xun; Guttman, András

2003-01-01

A capillary gel electrophoresis based automated DNA fraction collection technique was developed to support a novel DNA fragment-pooling strategy for expressed sequence tag (EST) library construction. The cDNA population is first cleaved by BsaJ I and EcoR I restriction enzymes, and then subpooled by selective ligation with specific adapters followed by polymerase chain reaction (PCR) amplification and labeling. Combination of this cDNA fingerprinting method with high-resolution capillary gel electrophoresis separation and precise fractionation of individual cDNA transcript representatives avoids redundant fragment selection and concomitant repetitive sequencing of abundant transcripts. Using a computer-controlled capillary electrophoresis device the transcript representatives were separated by their size and fractions were automatically collected in every 30 s into 96-well plates. The high resolving power of the sieving matrix ensured sequencing grade separation of the DNA fragments (i.e., single-base resolution) and successful fraction collection. Performance and precision of the fraction collection procedure was validated by PCR amplification of the collected DNA fragments followed by capillary electrophoresis analysis for size and purity verification. The collected and PCR-amplified transcript representatives, ranging up to several hundred base pairs, were then sequenced to create an EST library.

Diverse profiles of N-acyl-homoserine lactones in biofilm forming strains of Cronobacter sakazakii.

PubMed

Singh, Niharika; Patil, Amrita; Prabhune, Asmita A; Raghav, Mamta; Goel, Gunjan

2017-04-03

The present study investigates the role of quorum sensing (QS) molecules expressed by C. sakazakii in biofilm formation and extracellular polysaccharide expression. The QS signaling was detected using Chromobacterium violaceum 026 and Agrobacterium tumefaciens NTL4(pZLR4) based bioassay. Long chain N-acyl-homoserine lactones (AHLs) with C6- C18 chain length were identified using High Performance Liquid Chromatography and Liquid Chromatography-High Resolution Mass Spectrometry. A higher Specific Biofilm Formation (SBF) index (p < 0.05) with the presence of genes associated with cellulose biosynthesis (bcsA, bcsC and bcsG) was observed in the strains. AHLs and their mechanisms can serve as novel targets for developing technologies to eradicate and prevent biofilm formation by C. sakazakii.

Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development.

PubMed

Obudulu, Ogonna; Bygdell, Joakim; Sundberg, Björn; Moritz, Thomas; Hvidsten, Torgeir R; Trygg, Johan; Wingsle, Gunnar

2016-02-18

Wood development is of outstanding interest both to basic research and industry due to the associated cellulose and lignin biomass production. Efforts to elucidate wood formation (which is essential for numerous aspects of both pure and applied plant science) have been made using transcriptomic analyses and/or low-resolution sampling. However, transcriptomic data do not correlate perfectly with levels of expressed proteins due to effects of post-translational modifications and variations in turnover rates. In addition, high-resolution analysis is needed to characterize key transitions. In order to identify protein profiles across the developmental region of wood formation, an in-depth and tissue specific sampling was performed. We examined protein profiles, using an ultra-performance liquid chromatography/quadrupole time of flight mass spectrometry system, in high-resolution tangential sections spanning all wood development zones in Populus tremula from undifferentiated cambium to mature phloem and xylem, including cell expansion and cell death zones. In total, we analyzed 482 sections, 20-160 μm thick, from four 47-year-old trees growing wild in Sweden. We obtained high quality expression profiles for 3,082 proteins exhibiting consistency across the replicates, considering that the trees were growing in an uncontrolled environment. A combination of Principal Component Analysis (PCA), Orthogonal Projections to Latent Structures (OPLS) modeling and an enhanced stepwise linear modeling approach identified several major transitions in global protein expression profiles, pinpointing (for example) locations of the cambial division leading to phloem and xylem cells, and secondary cell wall formation zones. We also identified key proteins and associated pathways underlying these developmental landmarks. For example, many of the lignocellulosic related proteins were upregulated in the expansion to the early developmental xylem zone, and for laccases with a rapid decrease in early xylem zones. We observed upregulation of two forms of xylem cysteine protease (Potri.002G005700.1 and Potri.005G256000.2; Pt-XCP2.1) in early xylem and their downregulation in late maturing xylem. Our data also show that Pt-KOR1.3 (Potri.003G151700.2) exhibits an expression pattern that supports the hypothesis put forward in previous studies that this is a key xyloglucanase involved in cellulose biosynthesis in primary cell walls and reduction of cellulose crystallinity in secondary walls. Our novel multivariate approach highlights important processes and provides confirmatory insights into the molecular foundations of wood development.

Structural Characterization of the 1918 Influenza H1N1 Neuraminidase

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

Xu, X.; Zhu, X.; Dwek, R.A.

2009-05-28

Influenza virus neuraminidase (NA) plays a crucial role in facilitating the spread of newly synthesized virus in the host and is an important target for controlling disease progression. The NA crystal structure from the 1918 'Spanish flu' (A/Brevig Mission/1/18 H1N1) and that of its complex with zanamivir (Relenza) at 1.65-{angstrom} and 1.45-{angstrom} resolutions, respectively, corroborated the successful expression of correctly folded NA tetramers in a baculovirus expression system. An additional cavity adjacent to the substrate-binding site is observed in N1, compared to N2 and N9 NAs, including H5N1. This cavity arises from an open conformation of the 150 loop (Gly147more » to Asp151) and appears to be conserved among group 1 NAs (N1, N4, N5, and N8). It closes upon zanamivir binding. Three calcium sites were identified, including a novel site that may be conserved in N1 and N4. Thus, these high-resolution structures, combined with our recombinant expression system, provide new opportunities to augment the limited arsenal of therapeutics against influenza.« less

Compact high-resolution echelle-AOTF NIR spectrometer for atmospheric measurements

NASA Astrophysics Data System (ADS)

Korablev, Oleg I.; Bertaux, Jean-Loup; Vinogradov, Imant I.; Kalinnikov, Yurii K.; Nevejans, D.; Neefs, E.; Le Barbu, T.; Durry, G.

2017-11-01

A new concept of a high-resolution near-IR spectrometer consisting of an echelle grating combined with an acousto-optic tunable filter (AOTF) for separation of diffraction orders, is developed for space-borne studies of planetary atmospheres. A compact design with no moving parts within the mass budget of 3-5 kg allows to reach the resolving power λ/Δλ of 20000-30000. Only a small piece of spectrum in high diffraction orders can be measured at a time, but thanks to flexibility of the AOTF electrical tuning, such pieces of spectrum can be measured randomly and rapidly within the spectral range. This development can be used for accurate measurements of important atmospheric gases, such as CO2 in terrestrial atmosphere, isotopic ratios and minor gases. A spectrometer, based on this principle, SOIR (Solar Occultation InfraRed) is being built for Venus Express (2005) ESA mission. Instruments based on this principle have high potential for the studies of the Earth, in particular for measurements of isotopes of water in the lower atmosphere, either in solar occultation profiling (tangent altitude <10 km), or observing solar glint for integral quantities of the components. Small size of hardware makes them ideal for micro-satellites, which are now agile enough to provide necessary pointing for solar occultation or glint observations. Also, the atmosphere of Mars has never been observed at local scales with such a high spectral resolution. A laboratory prototype consisting of 275-mm echelle spectrometer with Hamamatsu InGaAs 512-pixel linear array and the AOTF has demonstrated λ/Δλ≍30000 in the spectral range of 1-1.7 μm. The next set up, covering the spectral ranges of 1-1.7 μm and 2.3-4.3 μm, and the Venus Express SOIR are briefly discussed.

Medium-throughput processing of whole mount in situ hybridisation experiments into gene expression domains.

PubMed

Crombach, Anton; Cicin-Sain, Damjan; Wotton, Karl R; Jaeger, Johannes

2012-01-01

Understanding the function and evolution of developmental regulatory networks requires the characterisation and quantification of spatio-temporal gene expression patterns across a range of systems and species. However, most high-throughput methods to measure the dynamics of gene expression do not preserve the detailed spatial information needed in this context. For this reason, quantification methods based on image bioinformatics have become increasingly important over the past few years. Most available approaches in this field either focus on the detailed and accurate quantification of a small set of gene expression patterns, or attempt high-throughput analysis of spatial expression through binary pattern extraction and large-scale analysis of the resulting datasets. Here we present a robust, "medium-throughput" pipeline to process in situ hybridisation patterns from embryos of different species of flies. It bridges the gap between high-resolution, and high-throughput image processing methods, enabling us to quantify graded expression patterns along the antero-posterior axis of the embryo in an efficient and straightforward manner. Our method is based on a robust enzymatic (colorimetric) in situ hybridisation protocol and rapid data acquisition through wide-field microscopy. Data processing consists of image segmentation, profile extraction, and determination of expression domain boundary positions using a spline approximation. It results in sets of measured boundaries sorted by gene and developmental time point, which are analysed in terms of expression variability or spatio-temporal dynamics. Our method yields integrated time series of spatial gene expression, which can be used to reverse-engineer developmental gene regulatory networks across species. It is easily adaptable to other processes and species, enabling the in silico reconstitution of gene regulatory networks in a wide range of developmental contexts.

New approaches for the reliable in vitro assessment of binding affinity based on high-resolution real-time data acquisition of radioligand-receptor binding kinetics.

PubMed

Zeilinger, Markus; Pichler, Florian; Nics, Lukas; Wadsak, Wolfgang; Spreitzer, Helmut; Hacker, Marcus; Mitterhauser, Markus

2017-12-01

Resolving the kinetic mechanisms of biomolecular interactions have become increasingly important in early-phase drug development. Since traditional in vitro methods belong to dose-dependent assessments, binding kinetics is usually overlooked. The present study aimed at the establishment of two novel experimental approaches for the assessment of binding affinity of both, radiolabelled and non-labelled compounds targeting the A 3 R, based on high-resolution real-time data acquisition of radioligand-receptor binding kinetics. A novel time-resolved competition assay was developed and applied to determine the K i of eight different A 3 R antagonists, using CHO-K1 cells stably expressing the hA 3 R. In addition, a new kinetic real-time cell-binding approach was established to quantify the rate constants k on and k off , as well as the dedicated K d of the A 3 R agonist [ 125 I]-AB-MECA. Furthermore, lipophilicity measurements were conducted to control influences due to physicochemical properties of the used compounds. Two novel real-time cell-binding approaches were successfully developed and established. Both experimental procedures were found to visualize the kinetic binding characteristics with high spatial and temporal resolution, resulting in reliable affinity values, which are in good agreement with values previously reported with traditional methods. Taking into account the lipophilicity of the A 3 R antagonists, no influences on the experimental performance and the resulting affinity were investigated. Both kinetic binding approaches comprise tracer administration and subsequent binding to living cells, expressing the dedicated target protein. Therefore, the experiments resemble better the true in vivo physiological conditions and provide important markers of cellular feedback and biological response.

Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci.

PubMed

Canver, Matthew C; Lessard, Samuel; Pinello, Luca; Wu, Yuxuan; Ilboudo, Yann; Stern, Emily N; Needleman, Austen J; Galactéros, Frédéric; Brugnara, Carlo; Kutlar, Abdullah; McKenzie, Colin; Reid, Marvin; Chen, Diane D; Das, Partha Pratim; A Cole, Mitchel; Zeng, Jing; Kurita, Ryo; Nakamura, Yukio; Yuan, Guo-Cheng; Lettre, Guillaume; Bauer, Daniel E; Orkin, Stuart H

2017-04-01

Cas9-mediated, high-throughput, saturating in situ mutagenesis permits fine-mapping of function across genomic segments. Disease- and trait-associated variants identified in genome-wide association studies largely cluster at regulatory loci. Here we demonstrate the use of multiple designer nucleases and variant-aware library design to interrogate trait-associated regulatory DNA at high resolution. We developed a computational tool for the creation of saturating-mutagenesis libraries with single or multiple nucleases with incorporation of variants. We applied this methodology to the HBS1L-MYB intergenic region, which is associated with red-blood-cell traits, including fetal hemoglobin levels. This approach identified putative regulatory elements that control MYB expression. Analysis of genomic copy number highlighted potential false-positive regions, thus emphasizing the importance of off-target analysis in the design of saturating-mutagenesis experiments. Together, these data establish a widely applicable high-throughput and high-resolution methodology to identify minimal functional sequences within large disease- and trait-associated regions.

High-resolution NMR structures of the domains of Saccharomyces cerevisiae Tho1

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

Jacobsen, Julian O. B.; Allen, Mark D.; Freund, Stefan M. V.

2016-05-23

In this study, high-resolution structures of both the N-terminal DNA-binding SAP domain and the C-terminal RNA-binding domain of S. cerevisiae Tho1 have been determined. THO is a multi-protein complex involved in the formation of messenger ribonuclear particles (mRNPs) by coupling transcription with mRNA processing and export. THO is thought to be formed from five subunits, Tho2p, Hpr1p, Tex1p, Mft1p and Thp2p, and recent work has determined a low-resolution structure of the complex [Poulsen et al. (2014 ▸), PLoS One, 9, e103470]. A number of additional proteins are thought to be involved in the formation of mRNP in yeast, including Tho1,more » which has been shown to bind RNA in vitro and is recruited to actively transcribed chromatin in vivo in a THO-complex and RNA-dependent manner. Tho1 is known to contain a SAP domain at the N-terminus, but the ability to suppress the expression defects of the hpr1Δ mutant of THO was shown to reside in the RNA-binding C-terminal region. In this study, high-resolution structures of both the N-terminal DNA-binding SAP domain and C-terminal RNA-binding domain have been determined.« less

Early to middle Miocene climate evolution: benthic oxygen and carbon isotope records from Walvis Ridge Site 1264.

NASA Astrophysics Data System (ADS)

Lourens, L. J.; Beddow, H.; Liebrand, D.; Schrader, C.; Hilgen, F. J.

2016-12-01

Across the early to middle Miocene, high-resolution records from the Pacific Ocean indicate a dynamic climate system, encompassing a 2 Myr global warming event from 17 Ma to 14.7 Ma, followed by a major Cenozoic cooling step at 14.2 Ma -13.8 Ma. Currently, no high-resolution benthic record from the Atlantic Ocean exists covering both events, limiting global coverage of this intriguing period in Cenozoic climate evolution. Here, we present the first early to middle Miocene high-resolution from the Atlantic basin. These records, from Site 1264 on the Walvis Ridge, span a 5.5 Myr long interval (13.24-18.90 ma) in high temporal resolution ( 4 kyr) and are tuned to eccentricity. The d18O record shows a sudden (high-latitude) warming/deglaciation on Antarctica at 17.1 Ma, a rapid cooling/glaciation of Antarctica at 13.8 Ma, and high-amplitude ( 1‰) variability on astronomical time-scales throughout this interval. Together with other records from this time interval located in the Pacific, which show similar features, the data strongly suggests a highly dynamic global climate system. We find cooling steps in d18O at 14.7, 14.2 and 13.8 Ma, suggesting concurrent cooling in the Pacific and Atlantic deep waters during the MMCT. The benthic foraminiferal stable isotope records reveal that the dominant astronomical frequencies present at ODP Site 1264 during the early to middle Miocene interval are the 405 kyr and 110 kyr eccentricity periodicities. This is a contrast to other early to middle Miocene records from drill-sites in the Pacific and South China Sea, which show a strong expression of obliquity in particular between 14.2 and 14.7 Ma.

Combining structure-from-motion derived point clouds from satellites and unmanned aircraft systems images with ground-truth data to create high-resolution digital elevation models

NASA Astrophysics Data System (ADS)

Palaseanu, M.; Thatcher, C.; Danielson, J.; Gesch, D. B.; Poppenga, S.; Kottermair, M.; Jalandoni, A.; Carlson, E.

2016-12-01

Coastal topographic and bathymetric (topobathymetric) data with high spatial resolution (1-meter or better) and high vertical accuracy are needed to assess the vulnerability of Pacific Islands to climate change impacts, including sea level rise. According to the Intergovernmental Panel on Climate Change reports, low-lying atolls in the Pacific Ocean are extremely vulnerable to king tide events, storm surge, tsunamis, and sea-level rise. The lack of coastal topobathymetric data has been identified as a critical data gap for climate vulnerability and adaptation efforts in the Republic of the Marshall Islands (RMI). For Majuro Atoll, home to the largest city of RMI, the only elevation dataset currently available is the Shuttle Radar Topography Mission data which has a 30-meter spatial resolution and 16-meter vertical accuracy (expressed as linear error at 90%). To generate high-resolution digital elevation models (DEMs) in the RMI, elevation information and photographic imagery have been collected from field surveys using GNSS/total station and unmanned aerial vehicles for Structure-from-Motion (SfM) point cloud generation. Digital Globe WorldView II imagery was processed to create SfM point clouds to fill in gaps in the point cloud derived from the higher resolution UAS photos. The combined point cloud data is filtered and classified to bare-earth and georeferenced using the GNSS data acquired on roads and along survey transects perpendicular to the coast. A total station was used to collect elevation data under tree canopies where heavy vegetation cover blocked the view of GNSS satellites. A subset of the GPS / total station data was set aside for error assessment of the resulting DEM.

Light Controlled Modulation of Gene Expression by Chemical Optoepigenetic Probes

PubMed Central

Reis, Surya A.; Ghosh, Balaram; Hendricks, J. Adam; Szantai-Kis, D. Miklos; Törk, Lisa; Ross, Kenneth N.; Lamb, Justin; Read-Button, Willis; Zheng, Baixue; Wang, Hongtao; Salthouse, Christopher; Haggarty, Stephen J.; Mazitschek, Ralph

2016-01-01

Epigenetic gene regulation is a dynamic process orchestrated by chromatin-modifying enzymes. Many of these master regulators exert their function through covalent modification of DNA and histone proteins. Aberrant epigenetic processes have been implicated in the pathophysiology of multiple human diseases. Small-molecule inhibitors have been essential to advancing our understanding of the underlying molecular mechanisms of epigenetic processes. However, the resolution offered by small molecules is often insufficient to manipulate epigenetic processes with high spatio-temporal control. Here, we present a novel and generalizable approach, referred to as ‘Chemo-Optical Modulation of Epigenetically-regulated Transcription’ (COMET), enabling high-resolution, optical control of epigenetic mechanisms based on photochromic inhibitors of human histone deacetylases using visible light. COMET probes may translate into novel therapeutic strategies for diseases where conditional and selective epigenome modulation is required. PMID:26974814

High-resolution identification and abundance profiling of cassava (Manihot esculenta Crantz) microRNAs.

PubMed

Khatabi, Behnam; Arikit, Siwaret; Xia, Rui; Winter, Stephan; Oumar, Doungous; Mongomake, Kone; Meyers, Blake C; Fondong, Vincent N

2016-01-28

Small RNAs (sRNAs) are endogenous sRNAs that play regulatory roles in plant growth, development, and biotic and abiotic stress responses. In plants, one subset of sRNAs, microRNAs (miRNAs) exhibit tissue-differential expression and regulate gene expression mainly through direct cleavage of mRNA or indirectly via production of secondary phased siRNAs (phasiRNAs) that silence cognate target transcripts in trans. Here, we have identified cassava (Manihot esculenta Crantz) miRNAs using high resolution sequencing of sRNA libraries from leaf, stem, callus, male and female flower tissues. To analyze the data, we built a cassava genome database and, via sequence analysis and secondary structure prediction, 38 miRNAs not previously reported in cassava were identified. These new cassava miRNAs included two miRNAs not previously been reported in any plant species. The miRNAs exhibited tissue-differential accumulation as confirmed by quantitative RT-PCR and Northern blot analysis, largely reflecting levels observed in sequencing data. Some of the miRNAs identified were predicted to trigger production of secondary phased siRNAs (phasiRNAs) from 80 PHAS loci. Cassava is a woody perennial shrub, grown principally for its starch-rich storage roots, which are rich in calories. In this study, new miRNAs were identified and their expression was validated using qRT-PCR of RNA from five different tissues. The data obtained expand the list of annotated miRNAs and provide additional new resources for cassava improvement research.

The effect of Aspergillus fumigatus infection on vitamin D receptor expression in cystic fibrosis.

PubMed

Coughlan, Catherine A; Chotirmall, Sanjay H; Renwick, Julie; Hassan, Tidi; Low, Teck Boon; Bergsson, Gudmundur; Eshwika, Ahmed; Bennett, Kathleen; Dunne, Katie; Greene, Catherine M; Gunaratnam, Cedric; Kavanagh, Kevin; Logan, Patrick M; Murphy, Philip; Reeves, Emer P; McElvaney, Noel G

2012-11-15

Aspergillus fumigatus (A. fumigatus) in cystic fibrosis (CF) is increasingly recognized. Although allergic bronchopulmonary aspergillosis (ABPA) leads to deterioration of pulmonary function, the effect of A. fumigatus colonization in the absence of ABPA remains unclear. To address this, we examined individuals with CF with A. fumigatus who were ABPA negative to identify the effects of itraconazole therapy on Aspergillus-induced lung inflammation. The effect of A. fumigatus on nuclear vitamin D receptor (VDR) expression was investigated using qRT-PCR and Western blotting. IL-5 and IL-13 levels were quantified by ELISA. The effect of itraconazole was assessed by a combination of high-resolution computed tomography, lung function test, and microbiological analysis. We demonstrate that A. fumigatus down-regulates VDR in macrophages and airway epithelial cells and that the fungal metabolite gliotoxin (Gt) is the main causative agent. Gt overcame the positive effect of 1,25-OH vitamin D(3) on VDR expression in vitro, resulting in increased IL-5 and IL-13 production. In vivo, A. fumigatus positivity was associated with increased Gt in CF bronchoalveolar lavage fluid and increased bronchoalveolar lavage fluid levels of IL-5 and IL-13. After airway eradication of A. fumigatus with itraconazole, we observed decreased Gt, IL-5 and IL-13, improved respiratory symptoms, and diminished high-resolution computed tomography mosaic pattern consistent with sustained pulmonary function. This study provides a rationale for the therapeutic effect of itraconazole and implied that the therapeutic potential of vitamin D supplementation in preventing ABPA is only feasible with concurrent elimination of A. fumigatus to permit VDR expression and its positive functional consequences.

"We Were Very Afraid": The Confederated Salish and Kootenai Politics, Identity, and the Perception of Termination, 1971-2003

ERIC Educational Resources Information Center

Puisto, Jaakko

2009-01-01

The federal policy of termination against Native Americans was on a high roll from 1946 to 1954. The policy received explicit expression in House Concurrent Resolution 108, passed in 1953, which stated that "Indians should be made subject to the same laws and entitled to the same privileges and responsibilities as are applicable to other…

Multifaceted Therapeutic Benefits of Factors Derived From Dental Pulp Stem Cells for Mouse Liver Fibrosis.

PubMed

Hirata, Marina; Ishigami, Masatoshi; Matsushita, Yoshihiro; Ito, Takanori; Hattori, Hisashi; Hibi, Hideharu; Goto, Hidemi; Ueda, Minoru; Yamamoto, Akihito

2016-10-01

: Chronic liver injury from various causes often results in liver fibrosis (LF). Although the liver possesses endogenous tissue-repairing activities, these can be overcome by sustained inflammation and excessive fibrotic scar formation. Advanced LF leads to irreversible cirrhosis and subsequent liver failure and/or hepatic cancer. Here, using the mouse carbon tetrachloride (CCl 4 )-induced LF model, we showed that a single intravenous administration of stem cells derived from human exfoliated deciduous teeth (SHEDs) or of SHED-derived serum-free conditioned medium (SHED-CM) resulted in fibrotic scar resolution. SHED-CM suppressed the gene expression of proinflammatory mediators, such as TNF-α, IL-1β, and iNOS, and eliminated activated hepatic stellate cells by inducing their apoptosis, but protected parenchymal hepatocytes from undergoing apoptosis. In addition, SHED-CM induced tissue-repairing macrophages that expressed high levels of the profibrinolytic factor, matrix metalloproteinase 13. Furthermore, SHED-CM suppressed the CCl 4 -induced apoptosis of primary cultured hepatocytes. SHED-CM contained a high level of hepatocyte growth factor (HGF). Notably, HGF-depleted SHED-CM (dHGF-CM) did not suppress the proinflammatory response or resolve fibrotic scarring. Furthermore, SHED-CM, but not dHGF-CM, inhibited CCl 4 -induced hepatocyte apoptosis. These results suggest that HGF plays a central role in the SHED-CM-mediated resolution of LF. Taken together, our findings suggest that SHED-CM provides multifaceted therapeutic benefits for the treatment of LF. This study demonstrated that a single intravenous administration of stem cells from human exfoliated deciduous teeth (SHEDs) or of the serum-free conditioned medium (CM) derived from SHEDs markedly improved mouse liver fibrosis (LF). SHED-CM suppressed chronic inflammation, eliminated activated hepatic stellate cells by inducing their apoptosis, protected hepatocytes from undergoing apoptosis, and induced differentiation of tissue-repairing macrophages expressing high levels of the profibrinolytic factor matrix metalloproteinase 13. Furthermore, hepatocyte growth factor played a central role in the SHED-CM-mediated resolution of LF. This is the first report demonstrating the multifaceted therapeutic benefits of secreted factors derived from SHEDs for LF. ©AlphaMed Press.

Modular Detection of GFP-Labeled Proteins for Rapid Screening by Electron Microscopy in Cells and Organisms.

PubMed

Ariotti, Nicholas; Hall, Thomas E; Rae, James; Ferguson, Charles; McMahon, Kerrie-Ann; Martel, Nick; Webb, Robyn E; Webb, Richard I; Teasdale, Rohan D; Parton, Robert G

2015-11-23

Reliable and quantifiable high-resolution protein localization is critical for understanding protein function. However, the time required to clone and characterize any protein of interest is a significant bottleneck, especially for electron microscopy (EM). We present a modular system for enzyme-based protein tagging that allows for improved speed and sampling for analysis of subcellular protein distributions using existing clone libraries to EM-resolution. We demonstrate that we can target a modified soybean ascorbate peroxidase (APEX) to any GFP-tagged protein of interest by engineering a GFP-binding peptide (GBP) directly to the APEX-tag. We demonstrate that APEX-GBP (1) significantly reduces the time required to characterize subcellular protein distributions of whole libraries to less than 3 days, (2) provides remarkable high-resolution localization of proteins to organelle subdomains, and (3) allows EM localization of GFP-tagged proteins, including proteins expressed at endogenous levels, in vivo by crossing existing GFP-tagged transgenic zebrafish lines with APEX-GBP transgenic lines. Copyright © 2015 Elsevier Inc. All rights reserved.

Early Spring Post-Fire Snow Albedo Dynamics in High Latitude Boreal Forests Using Landsat-8 OLI Data

NASA Technical Reports Server (NTRS)

Wang, Zhuosen; Erb, Angela M.; Schaaf, Crystal B.; Sun, Qingsong; Liu, Yan; Yang, Yun; Shuai, Yanmin; Casey, Kimberly A.; Roman, Miguel O.

2016-01-01

Taking advantage of the improved radiometric resolution of Landsat-8 OLI which, unlike previous Landsat sensors, does not saturate over snow, the progress of fire recovery progress at the landscape scale (less than 100 m) is examined. High quality Landsat-8 albedo retrievals can now capture the true reflective and layered character of snow cover over a full range of land surface conditions and vegetation densities. This new capability particularly improves the assessment of post-fire vegetation dynamics across low- to high-burn severity gradients in Arctic and boreal regions in the early spring, when the albedos during recovery show the greatest variation. We use 30 m resolution Landsat-8 surface reflectances with concurrent coarser resolution (500 m) MODIS high quality full inversion surface Bidirectional Reflectance Distribution Functions (BRDF) products to produce higher resolution values of surface albedo. The high resolution full expression shortwave blue sky albedo product performs well with an overall RMSE of 0.0267 between tower and satellite measures under both snow-free and snow-covered conditions. While the importance of post-fire albedo recovery can be discerned from the MODIS albedo product at regional and global scales, our study addresses the particular importance of early spring post-fire albedo recovery at the landscape scale by considering the significant spatial heterogeneity of burn severity, and the impact of snow on the early spring albedo of various vegetation recovery types. We found that variations in early spring albedo within a single MODIS gridded pixel can be larger than 0.6. Since the frequency and severity of wildfires in Arctic and boreal systems is expected to increase in the coming decades, the dynamics of albedo in response to these rapid surface changes will increasingly impact the energy balance and contribute to other climate processes and physical feedback mechanisms. Surface radiation products derived from Landsat-8 data will thus play an important role in characterizing the carbon cycle and ecosystem processes of high latitude systems.

Early spring post-fire snow albedo dynamics in high latitude boreal forests using Landsat-8 OLI data

PubMed Central

Wang, Zhuosen; Erb, Angela M.; Schaaf, Crystal B.; Sun, Qingsong; Liu, Yan; Yang, Yun; Shuai, Yanmin; Casey, Kimberly A.; Román, Miguel O.

2018-01-01

Taking advantage of the improved radiometric resolution of Landsat-8 OLI which, unlike previous Landsat sensors, does not saturate over snow, the progress of fire recovery progress at the landscape scale (< 100m) is examined. High quality Landsat-8 albedo retrievals can now capture the true reflective and layered character of snow cover over a full range of land surface conditions and vegetation densities. This new capability particularly improves the assessment of post-fire vegetation dynamics across low- to high- burn severity gradients in Arctic and boreal regions in the early spring, when the albedos during recovery show the greatest variation. We use 30 m resolution Landsat-8 surface reflectances with concurrent coarser resolution (500m) MODIS high quality full inversion surface Bidirectional Reflectance Distribution Functions (BRDF) products to produce higher resolution values of surface albedo. The high resolution full expression shortwave blue sky albedo product performs well with an overall RMSE of 0.0267 between tower and satellite measures under both snow-free and snow-covered conditions. While the importance of post-fire albedo recovery can be discerned from the MODIS albedo product at regional and global scales, our study addresses the particular importance of early spring post-fire albedo recovery at the landscape scale by considering the significant spatial heterogeneity of burn severity, and the impact of snow on the early spring albedo of various vegetation recovery types. We found that variations in early spring albedo within a single MODIS gridded pixel can be larger than 0.6. Since the frequency and severity of wildfires in Arctic and boreal systems is expected to increase in the coming decades, the dynamics of albedo in response to these rapid surface changes will increasingly impact the energy balance and contribute to other climate processes and physical feedback mechanisms. Surface radiation products derived from Landsat-8 data will thus play an important role in characterizing the carbon cycle and ecosystem processes of high latitude systems. PMID:29769751

Early spring post-fire snow albedo dynamics in high latitude boreal forests using Landsat-8 OLI data.

PubMed

Wang, Zhuosen; Erb, Angela M; Schaaf, Crystal B; Sun, Qingsong; Liu, Yan; Yang, Yun; Shuai, Yanmin; Casey, Kimberly A; Román, Miguel O

2016-11-01

Taking advantage of the improved radiometric resolution of Landsat-8 OLI which, unlike previous Landsat sensors, does not saturate over snow, the progress of fire recovery progress at the landscape scale (< 100m) is examined. High quality Landsat-8 albedo retrievals can now capture the true reflective and layered character of snow cover over a full range of land surface conditions and vegetation densities. This new capability particularly improves the assessment of post-fire vegetation dynamics across low- to high- burn severity gradients in Arctic and boreal regions in the early spring, when the albedos during recovery show the greatest variation. We use 30 m resolution Landsat-8 surface reflectances with concurrent coarser resolution (500m) MODIS high quality full inversion surface Bidirectional Reflectance Distribution Functions (BRDF) products to produce higher resolution values of surface albedo. The high resolution full expression shortwave blue sky albedo product performs well with an overall RMSE of 0.0267 between tower and satellite measures under both snow-free and snow-covered conditions. While the importance of post-fire albedo recovery can be discerned from the MODIS albedo product at regional and global scales, our study addresses the particular importance of early spring post-fire albedo recovery at the landscape scale by considering the significant spatial heterogeneity of burn severity, and the impact of snow on the early spring albedo of various vegetation recovery types. We found that variations in early spring albedo within a single MODIS gridded pixel can be larger than 0.6. Since the frequency and severity of wildfires in Arctic and boreal systems is expected to increase in the coming decades, the dynamics of albedo in response to these rapid surface changes will increasingly impact the energy balance and contribute to other climate processes and physical feedback mechanisms. Surface radiation products derived from Landsat-8 data will thus play an important role in characterizing the carbon cycle and ecosystem processes of high latitude systems.

[64Cu]NOTA-pentixather enables high resolution PET imaging of CXCR4 expression in a preclinical lymphoma model.

PubMed

Poschenrieder, Andreas; Schottelius, Margret; Osl, Theresa; Schwaiger, Markus; Wester, Hans-Jürgen

2017-01-01

The chemokine receptor 4 (CXCR4) is an important molecular target for both visualization and therapy of tumors. The aim of the present study was the synthesis and preclinical evaluation of a 64 Cu-labeled, CXCR4-targeting peptide for positron emission tomography (PET) imaging of CXCR4 expression in vivo. For this purpose, 1,4,7-triazacyclononane,1-glutaric acid-4,7-acetic acid (NODAGA), or 1,4,7-triazacyclononane-triacetic acid (NOTA) was conjugated to the highly affine CXCR4-targeting pentixather scaffold. Affinities were determined using Jurkat T-lymphocytes in competitive binding assays employing [ 125 I]FC131 as the radioligand. Internalization and efflux studies of [ 64 Cu]NOTA-pentixather were performed in chem-1 cells, stably transfected with hCXCR4. The stability of the tracer was evaluated in vitro and in vivo . Small-animal PET and biodistribution studies at different time points were performed in Daudi lymphoma-bearing severe combined immunodeficiency (SCID) mice. [ 64 Cu]NOTA-pentixather was rapidly radiolabeled at 60 °C with high radiochemical yields ≥90% and purities >99%. [ 64 Cu]NOTA-pentixather offered the highest affinity of the evaluated peptides in this study (IC 50  = 14.9 ± 2.1 nM), showed efficient CXCR4-targeting in vitro and was stable in blood and urine with high resistance to transchelation in ethylenediaminetetraacetic acid (EDTA) challenge studies. Due to the enhanced lipophilicity of [ 64 Cu]NOTA-pentixather (logP = -1.2), biodistribution studies showed some nonspecific accumulation in the liver and intestines. However, tumor accumulation (13.1 ± 1.5% ID/g, 1.5 h p.i.) was CXCR4-specific and higher than in all other organs and resulted in high resolution delineation of Daudi tumors in PET/CT images in vivo. [ 64 Cu]NOTA-pentixather was fast and efficiently radiolabeled, showed effective CXCR4-targeting, high stability in vitro and in vivo and resulted in high resolution PET/CT images accompanied with a suitable biodistribution profile, making [ 64 Cu]NOTA-pentixather a promising tracer for future application in humans.

MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data.

PubMed

Zou, Dong; Sun, Shixiang; Li, Rujiao; Liu, Jiang; Zhang, Jing; Zhang, Zhang

2015-01-01

DNA methylation plays crucial roles during embryonic development. Here we present MethBank (http://dnamethylome.org), a DNA methylome programming database that integrates the genome-wide single-base nucleotide methylomes of gametes and early embryos in different model organisms. Unlike extant relevant databases, MethBank incorporates the whole-genome single-base-resolution methylomes of gametes and early embryos at multiple different developmental stages in zebrafish and mouse. MethBank allows users to retrieve methylation levels, differentially methylated regions, CpG islands, gene expression profiles and genetic polymorphisms for a specific gene or genomic region. Moreover, it offers a methylome browser that is capable of visualizing high-resolution DNA methylation profiles as well as other related data in an interactive manner and thus is of great helpfulness for users to investigate methylation patterns and changes of gametes and early embryos at different developmental stages. Ongoing efforts are focused on incorporation of methylomes and related data from other organisms. Together, MethBank features integration and visualization of high-resolution DNA methylation data as well as other related data, enabling identification of potential DNA methylation signatures in different developmental stages and accordingly providing an important resource for the epigenetic and developmental studies. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Adaptive-optics SLO imaging combined with widefield OCT and SLO enables precise 3D localization of fluorescent cells in the mouse retina.

PubMed

Zawadzki, Robert J; Zhang, Pengfei; Zam, Azhar; Miller, Eric B; Goswami, Mayank; Wang, Xinlei; Jonnal, Ravi S; Lee, Sang-Hyuck; Kim, Dae Yu; Flannery, John G; Werner, John S; Burns, Marie E; Pugh, Edward N

2015-06-01

Adaptive optics scanning laser ophthalmoscopy (AO-SLO) has recently been used to achieve exquisite subcellular resolution imaging of the mouse retina. Wavefront sensing-based AO typically restricts the field of view to a few degrees of visual angle. As a consequence the relationship between AO-SLO data and larger scale retinal structures and cellular patterns can be difficult to assess. The retinal vasculature affords a large-scale 3D map on which cells and structures can be located during in vivo imaging. Phase-variance OCT (pv-OCT) can efficiently image the vasculature with near-infrared light in a label-free manner, allowing 3D vascular reconstruction with high precision. We combined widefield pv-OCT and SLO imaging with AO-SLO reflection and fluorescence imaging to localize two types of fluorescent cells within the retinal layers: GFP-expressing microglia, the resident macrophages of the retina, and GFP-expressing cone photoreceptor cells. We describe in detail a reflective afocal AO-SLO retinal imaging system designed for high resolution retinal imaging in mice. The optical performance of this instrument is compared to other state-of-the-art AO-based mouse retinal imaging systems. The spatial and temporal resolution of the new AO instrumentation was characterized with angiography of retinal capillaries, including blood-flow velocity analysis. Depth-resolved AO-SLO fluorescent images of microglia and cone photoreceptors are visualized in parallel with 469 nm and 663 nm reflectance images of the microvasculature and other structures. Additional applications of the new instrumentation are discussed.

High-resolution raster scan optoacoustic mesoscopy of genetically modified drosophila pupae

NASA Astrophysics Data System (ADS)

Omar, Murad; Gateau, Jérôme; Ntziachristos, Vasilis

2014-03-01

Optoacoutic mesoscopy aims to bridge the gap between optoacoustic microscopy and optoacoustic tomography. We have developed a setup for optoacoustic mesoscopy where we use a high frequency, high numerical aperture spherically focused ultrasound transducer, with a wide bandwidth of 25-125 MHz. The excitation is performed using a diode laser capable of >500 μJ/pulse, 1.8ns pulse width, 1.4 kHz pulse repetition rate, at 515 nm. The system is capable to penetrate more than 5 mm with a resolution of 7 μm axially and 30 μm transversally. Using high-speed stages and scanning the transducer in a quasi-continuous mode, a field of view of 2×2 mm2 is scanned in less than 2 minutes. The system is suitable for imaging biological samples that have a diameter of 1-5 mm; zebrafish, drosophila melanogaster, and thin biological samples such as the mouse ear and mouse extremities. We have used our mesoscopic setup to generate 3- dimensional images of genetically modified drosophila fly, and drosophila pupae expressing GFP from the wings, high resolution images were generated in both cases, in the fly we can see the wings, the legs, the eyes, and the shape of the body. In the pupae the outline of the pupae, the spiracles at both ends and a strong signal corresponding to the location of the future wings are observed.

New Insight of Common Regulatory Pathways in Human Trabecular Meshwork Cells in Response to Dexamethasone and Prednisolone Using an Integrated Quantitative Proteomics: SWATH and MRM-HR Mass Spectrometry.

PubMed

Shan, Sze Wan; Do, Chi Wai; Lam, Thomas Chuen; Kong, Ricky Pak Wing; Li, King Kit; Chun, Ka Man; Stamer, William Daniel; To, Chi Ho

2017-10-06

The molecular pathophysiology of corticosteroid-induced ocular hypertension (CIH) is not well understood. To determine the biological mechanisms of CIH, this study investigated protein expression profiles of human trabecular meshwork (hTM) cells in response to dexamethasone and prednisolone treatment. Both discovery-based sequential windowed data independent acquisition of the total high-resolution mass spectra (SWATH-MS) and targeted based high resolution multiple reaction monitoring (MRM-HR) confirmation were applied using a hybrid quadrupole-time-of-flight mass spectrometer. A comprehensive list of 1759 proteins (1% FDR) was generated from the hTM. Quantitative proteomics revealed 20 differentially expressed proteins (p-value ≤ 0.05 and fold-change ≥ 1.5 or ≤ 0.67) commonly induced by prednisolone and dexamethasone, both at 300 nM. These included connective tissue growth factor (CTGF) and thrombospondin-1 (THBS1), two proteins previously implicated in ocular hypertension, glaucoma, and the transforming growth factor-β pathway. Their gene expressions in response to corticosteroids were further confirmed using reverse-transcription polymerase chain reaction. Together with other novel proteins identified in the data sets, additional pathways implicated by these regulated proteins were the phosphatidylinositol 3-kinase (PI3K)-protein kinase B (Akt) signaling pathway, integrin cell surface interaction, extracellular matrix (ECM) proteoglycans, and ECM-receptor interaction. Our results indicated that an integrated platform of SWATH-MS and MRM-HR allows high throughput identification and confirmation of novel and known corticosteroid-regulated proteins in trabecular meshwork cells, demonstrating the power of this technique in extending the current understanding of the pathogenesis of CIH.

Identifying microbially mediated transformations of DOC across season and tide from simultaneous changes in whole community gene expression and in mass spectra generated by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS)

NASA Astrophysics Data System (ADS)

Ballantyne, F.; Medeiros, P. M.; Moran, M. A.; Song, C.; Whitman, W. B.; Washington, B.; Yu, M.; Lee, J.

2017-12-01

Despite the advent of methods enabling high resolution characterization of metabolic activity and of organic matter, linking microbial metabolism to organic matter transformations remains a challenge. By sequencing metatranscriptomes and using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS) to characterize organic matter (OM) at the beginning and at the end of incubations of estuarine water across tide and season, we sought to link observed a changes in OM composition to microbial metabolism. We used linear models and K means clustering to identify clusters of genes that responded coherently across season, which accounted for most of the variability in gene expression, over tidal regime, which explained the majority of the remaining variation, and over time during the 24 hour incubations. We used an approach from the field of signal processing, that to our knowledge has not been used to analyze FTICR-MS data, to identify formulae of compounds that changed in concentration during the incubations. This approach, based on the discrete wavelet transform (DWT), allowed us to overcome some of the challenges associated with analyzing FTICR-MS data: variable ionization of organic compounds, signal suppression by high concentration compounds, and uncertainty about how to normalize changes across spectra. We were able to link clusters of metabolic and transporter genes to changes in OM composition, and uniquely identify genes based on their cross correlation with changes in FTICR mass spectra. Our approach for analyzing FTICR- MS data enables more robust inference about OM transformations, and linking high resolution changes in gene expression and in OM data during incubations represents an important step toward formulating models of microbial metabolism relevant for predicting biogeochemically relevant C fluxes.

Laminar and dorsoventral molecular organization of the medial entorhinal cortex revealed by large-scale anatomical analysis of gene expression.

PubMed

Ramsden, Helen L; Sürmeli, Gülşen; McDonagh, Steven G; Nolan, Matthew F

2015-01-01

Neural circuits in the medial entorhinal cortex (MEC) encode an animal's position and orientation in space. Within the MEC spatial representations, including grid and directional firing fields, have a laminar and dorsoventral organization that corresponds to a similar topography of neuronal connectivity and cellular properties. Yet, in part due to the challenges of integrating anatomical data at the resolution of cortical layers and borders, we know little about the molecular components underlying this organization. To address this we develop a new computational pipeline for high-throughput analysis and comparison of in situ hybridization (ISH) images at laminar resolution. We apply this pipeline to ISH data for over 16,000 genes in the Allen Brain Atlas and validate our analysis with RNA sequencing of MEC tissue from adult mice. We find that differential gene expression delineates the borders of the MEC with neighboring brain structures and reveals its laminar and dorsoventral organization. We propose a new molecular basis for distinguishing the deep layers of the MEC and show that their similarity to corresponding layers of neocortex is greater than that of superficial layers. Our analysis identifies ion channel-, cell adhesion- and synapse-related genes as candidates for functional differentiation of MEC layers and for encoding of spatial information at different scales along the dorsoventral axis of the MEC. We also reveal laminar organization of genes related to disease pathology and suggest that a high metabolic demand predisposes layer II to neurodegenerative pathology. In principle, our computational pipeline can be applied to high-throughput analysis of many forms of neuroanatomical data. Our results support the hypothesis that differences in gene expression contribute to functional specialization of superficial layers of the MEC and dorsoventral organization of the scale of spatial representations.

Laminar and Dorsoventral Molecular Organization of the Medial Entorhinal Cortex Revealed by Large-scale Anatomical Analysis of Gene Expression

PubMed Central

Ramsden, Helen L.; Sürmeli, Gülşen; McDonagh, Steven G.; Nolan, Matthew F.

2015-01-01

Neural circuits in the medial entorhinal cortex (MEC) encode an animal’s position and orientation in space. Within the MEC spatial representations, including grid and directional firing fields, have a laminar and dorsoventral organization that corresponds to a similar topography of neuronal connectivity and cellular properties. Yet, in part due to the challenges of integrating anatomical data at the resolution of cortical layers and borders, we know little about the molecular components underlying this organization. To address this we develop a new computational pipeline for high-throughput analysis and comparison of in situ hybridization (ISH) images at laminar resolution. We apply this pipeline to ISH data for over 16,000 genes in the Allen Brain Atlas and validate our analysis with RNA sequencing of MEC tissue from adult mice. We find that differential gene expression delineates the borders of the MEC with neighboring brain structures and reveals its laminar and dorsoventral organization. We propose a new molecular basis for distinguishing the deep layers of the MEC and show that their similarity to corresponding layers of neocortex is greater than that of superficial layers. Our analysis identifies ion channel-, cell adhesion- and synapse-related genes as candidates for functional differentiation of MEC layers and for encoding of spatial information at different scales along the dorsoventral axis of the MEC. We also reveal laminar organization of genes related to disease pathology and suggest that a high metabolic demand predisposes layer II to neurodegenerative pathology. In principle, our computational pipeline can be applied to high-throughput analysis of many forms of neuroanatomical data. Our results support the hypothesis that differences in gene expression contribute to functional specialization of superficial layers of the MEC and dorsoventral organization of the scale of spatial representations. PMID:25615592

Recanalization and flow regulate venous thrombus resolution and Matrix metalloproteinases expression in vivo

PubMed Central

Chabasse, Christine; Siefert, Suzanne A.; Chaudry, Mohammed; Hoofnagle, Mark H.; Lal, Brajesh K.; Sarkar, Rajabrata

2016-01-01

Objective We examined the role of thrombus recanalization and ongoing blood flow in the process of thrombus resolution by comparing two murine in vivo models of deep venous thrombosis. Design of study In CD1 mice, we performed surgical inferior vena cava (IVC) ligation (stasis thrombosis), stenosis (thrombosis with recanalization) or sham procedure. We analyzed thrombus weight over time as a measure of thrombus resolution, and quantified the mRNA and protein levels of Membrane-Type Matrix Metalloproteinases (MT-MMPs) as well as effectors of the plasmin complex at day 4, 8 and 12 post-surgery. Results Despite similar initial thrombus size, the presence of ongoing blood flow (stenosis model) was associated with a 45.91% subsequent improvement in thrombus resolution at day 8, and 12.57% at day 12, as compared with stasis thrombosis (ligation model). Immunoblot and real-time PCR demonstrated a difference in MMP-2 and MMP-9 activity at day 8 between the two models (P=.03 and P=.006 respectively), as well as a difference in MT2-MMP gene expression at day 8 (P=.044) and day 12 (P=0.03) and MT1-MMP protein expression at day 4 (P=.021). Histological analyses revealed distinct areas of recanalization in the thrombi of the stenosis model compared to the ligation model, as well as the recruitment of inflammatory cells, especially macrophages, and a focal pattern of localized expression of MT1-MMP and MT3-MMP proteins surrounding the areas of recanalization in the stenosis model. Conclusions Recanalization and ongoing blood flow accelerate deep venous thrombus resolution in vivo, and are associated with distinct patterns of MT1- and MT3-MMP expression and macrophages localization in areas of intra-thrombus recanalization. PMID:26993683

Recanalization and flow regulate venous thrombus resolution and matrix metalloproteinase expression in vivo.

PubMed

Chabasse, Christine; Siefert, Suzanne A; Chaudry, Mohammed; Hoofnagle, Mark H; Lal, Brajesh K; Sarkar, Rajabrata

2015-01-01

We examined the role of thrombus recanalization and ongoing blood flow in the process of thrombus resolution by comparing two murine in vivo models of deep venous thrombosis. In CD1 mice, we performed surgical inferior vena cava ligation (stasis thrombosis), stenosis (thrombosis with recanalization), or sham procedure. We analyzed thrombus weight over time as a measure of thrombus resolution and quantified the messenger RNA and protein levels of membrane-type matrix metalloproteinases (MT-MMPs) as well as effectors of the plasmin complex at days 4, 8, and 12 after surgery. Despite similar initial thrombus size, the presence of ongoing blood flow (stenosis model) was associated with a 45.91% subsequent improvement in thrombus resolution at day 8 and 12.57% at day 12 compared with stasis thrombosis (ligation model). Immunoblot and real-time polymerase chain reaction analysis demonstrated a difference in MMP-2 and MMP-9 activity at day 8 between the two models (P = .03 and P = .006, respectively) as well as a difference in MT2-MMP gene expression at day 8 (P = .044) and day 12 (P = .03) and MT1-MMP protein expression at day 4 (P = .021). Histologic analyses revealed distinct areas of recanalization in the thrombi of the stenosis model compared with the ligation model as well as the recruitment of inflammatory cells, especially macrophages, and a focal pattern of localized expression of MT1-MMP and MT3-MMP proteins surrounding the areas of recanalization in the stenosis model. Recanalization and ongoing blood flow accelerate deep venous thrombus resolution in vivo and are associated with distinct patterns of MT1-MMP and MT3-MMP expression and macrophage localization in areas of intrathrombus recanalization. Copyright © 2015 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

Tumor Lysing Genetically Engineered T Cells Loaded with Multi-Modal Imaging Agents

NASA Astrophysics Data System (ADS)

Bhatnagar, Parijat; Alauddin, Mian; Bankson, James A.; Kirui, Dickson; Seifi, Payam; Huls, Helen; Lee, Dean A.; Babakhani, Aydin; Ferrari, Mauro; Li, King C.; Cooper, Laurence J. N.

2014-03-01

Genetically-modified T cells expressing chimeric antigen receptors (CAR) exert anti-tumor effect by identifying tumor-associated antigen (TAA), independent of major histocompatibility complex. For maximal efficacy and safety of adoptively transferred cells, imaging their biodistribution is critical. This will determine if cells home to the tumor and assist in moderating cell dose. Here, T cells are modified to express CAR. An efficient, non-toxic process with potential for cGMP compliance is developed for loading high cell number with multi-modal (PET-MRI) contrast agents (Super Paramagnetic Iron Oxide Nanoparticles - Copper-64; SPION-64Cu). This can now be potentially used for 64Cu-based whole-body PET to detect T cell accumulation region with high-sensitivity, followed by SPION-based MRI of these regions for high-resolution anatomically correlated images of T cells. CD19-specific-CAR+SPIONpos T cells effectively target in vitro CD19+ lymphoma.

A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data

PubMed Central

Skelly, Daniel A.; Johansson, Marnie; Madeoy, Jennifer; Wakefield, Jon; Akey, Joshua M.

2011-01-01

Variation in gene expression is thought to make a significant contribution to phenotypic diversity among individuals within populations. Although high-throughput cDNA sequencing offers a unique opportunity to delineate the genome-wide architecture of regulatory variation, new statistical methods need to be developed to capitalize on the wealth of information contained in RNA-seq data sets. To this end, we developed a powerful and flexible hierarchical Bayesian model that combines information across loci to allow both global and locus-specific inferences about allele-specific expression (ASE). We applied our methodology to a large RNA-seq data set obtained in a diploid hybrid of two diverse Saccharomyces cerevisiae strains, as well as to RNA-seq data from an individual human genome. Our statistical framework accurately quantifies levels of ASE with specified false-discovery rates, achieving high reproducibility between independent sequencing platforms. We pinpoint loci that show unusual and biologically interesting patterns of ASE, including allele-specific alternative splicing and transcription termination sites. Our methodology provides a rigorous, quantitative, and high-resolution tool for profiling ASE across whole genomes. PMID:21873452

Expression of ribosomopathy genes during Xenopus tropicalis embryogenesis.

PubMed

Robson, Andrew; Owens, Nick D L; Baserga, Susan J; Khokha, Mustafa K; Griffin, John N

2016-10-26

Because ribosomes are ubiquitously required for protein production, it was long assumed that any inherited defect in ribosome manufacture would be embryonically lethal. However, several human congenital diseases have been found to be associated with mutations in ribosome biogenesis factors. Surprisingly, despite the global requirement for ribosomes, these "ribosomopathies" are characterized by distinct and tissue specific phenotypes. The reasons for such tissue proclivity in ribosomopathies remain mysterious but may include differential expression of ribosome biogenesis factors in distinct tissues. Here we use in situ hybridization of labeled antisense mRNA probes and ultra high temporal resolution RNA-Seq data to examine and compare expression of 13 disease associated ribosome biogenesis factors at six key stages in Xenopus tropicalis development. Rather than being ubiquitously expressed during development, mRNAs of all examined ribosome biogenesis factors were highly enriched in specific tissues, including the cranial neural crest and ventral blood islands. Interestingly, expression of ribosome biogenesis factors demonstrates clear differences in timing, transcript number and tissue localization. Ribosome biogenesis factor expression is more spatiotemporally regulated during embryonic development than previously expected and correlates closely with many of the common ribosomopathy phenotypes. Our findings provide information on the dynamic use of ribosome production machinery components during development and advance our understanding of their roles in disease.

Synthetic dual-input mammalian genetic circuits enable tunable and stringent transcription control by chemical and light.

PubMed

Chen, Xianjun; Li, Ting; Wang, Xue; Du, Zengmin; Liu, Renmei; Yang, Yi

2016-04-07

Programmable transcription factors can enable precise control of gene expression triggered by a chemical inducer or light. To obtain versatile transgene system with combined benefits of a chemical inducer and light inducer, we created various chimeric promoters through the assembly of different copies of the tet operator and Gal4 operator module, which simultaneously responded to a tetracycline-responsive transcription factor and a light-switchable transactivator. The activities of these chimeric promoters can be regulated by tetracycline and blue light synergistically or antagonistically. Further studies of the antagonistic genetic circuit exhibited high spatiotemporal resolution and extremely low leaky expression, which therefore could be used to spatially and stringently control the expression of highly toxic protein Diphtheria toxin A for light regulated gene therapy. When transferring plasmids engineered for the gene switch-driven expression of a firefly luciferase (Fluc) into mice, the Fluc expression levels of the treated animals directly correlated with the tetracycline and light input program. We suggest that dual-input genetic circuits using TET and light that serve as triggers to achieve expression profiles may enable the design of robust therapeutic gene circuits for gene- and cell-based therapies. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

In Situ Detection of MicroRNA Expression with RNAscope Probes.

PubMed

Yin, Viravuth P

2018-01-01

Elucidating the spatial resolution of gene transcripts provides important insight into potential gene function. MicroRNAs are short, singled-stranded noncoding RNAs that control gene expression through base-pair complementarity with target mRNAs in the 3' untranslated region (UTR) and inhibiting protein expression. However, given their small size of ~22- to 24-nt and low expression levels, standard in situ hybridization detection methods are not amendable for microRNA spatial resolution. Here, I describe a technique that employs RNAscope probe design and propriety amplification technology that provides simultaneous single molecule detection of individual microRNA and its target gene. This method allows for rapid and sensitive detection of noncoding RNA transcripts in frozen tissue sections.

Language in context: Characterizing the comprehension of referential expressions with MEG.

PubMed

Brodbeck, Christian; Pylkkänen, Liina

2017-02-15

A critical component of comprehending language in context is identifying the entities that individual linguistic expressions refer to. While previous research has shown that language comprehenders resolve reference quickly and incrementally, little is currently known about the neural basis of successful reference resolution. Using source localized MEG, we provide evidence across 3 experiments and 2 languages that successful reference resolution in simple visual displays is associated with increased activation in the medial parietal lobe. In each trial, participants saw a simple visual display containing three objects which constituted the referential domain. Target referential expressions were embedded in questions about the displays. By varying the displays, we manipulated referential status while keeping the linguistic expressions constant. Follow-up experiments addressed potential interactions of reference resolution with linguistic predictiveness and pragmatic plausibility. Notably, we replicated the effect in Arabic, a language that differs in a structurally informative way from English while keeping referential aspects parallel to our two English studies. Distributed minimum norm estimates of MEG data consistently indicated that reference resolution is associated with increased activity in the medial parietal lobe. With one exception, the timing of the onset of the medial parietal response fell into a mid-latency time-window at 350-500ms after the onset of the resolving word. Through concurrent EEG recordings on a subset of subjects we also describe the EEG topography of the effect of reference resolution, which makes the result available for comparison with a larger existing literature. Our results extend previous reports that medial parietal lobe is involved in referential language processing, indicating that it is relevant for reference resolution to individual referents, and suggests avenues for future research. Copyright © 2016 Elsevier Inc. All rights reserved.

Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference

PubMed Central

Campbell, Kieran R.

2016-01-01

Single cell gene expression profiling can be used to quantify transcriptional dynamics in temporal processes, such as cell differentiation, using computational methods to label each cell with a ‘pseudotime’ where true time series experimentation is too difficult to perform. However, owing to the high variability in gene expression between individual cells, there is an inherent uncertainty in the precise temporal ordering of the cells. Pre-existing methods for pseudotime estimation have predominantly given point estimates precluding a rigorous analysis of the implications of uncertainty. We use probabilistic modelling techniques to quantify pseudotime uncertainty and propagate this into downstream differential expression analysis. We demonstrate that reliance on a point estimate of pseudotime can lead to inflated false discovery rates and that probabilistic approaches provide greater robustness and measures of the temporal resolution that can be obtained from pseudotime inference. PMID:27870852

Development of tyrosinase-based reporter genes for preclinical photoacoustic imaging of mesenchymal stem cells

NASA Astrophysics Data System (ADS)

Märk, Julia; Ruschke, Karen; Dortay, Hakan; Schreiber, Isabelle; Sass, Andrea; Qazi, Taimoor; Pumberger, Matthias; Laufer, Jan

2014-03-01

The capability to image stem cells in vivo in small animal models over extended periods of time is important to furthering our understanding of the processes involved in tissue regeneration. Photoacoustic imaging is suited to this application as it can provide high resolution (tens of microns) absorption-based images of superficial tissues (cm depths). However, stem cells are rare, highly migratory, and can divide into more specialised cells. Genetic labelling strategies are therefore advantageous for their visualisation. In this study, methods for the transfection and viral transduction of mesenchymal stem cells with reporter genes for the co-expression of tyrosinase and a fluorescent protein (mCherry). Initial photoacoustic imaging experiments of tyrosinase expressing cells in small animal models of tissue regeneration were also conducted. Lentiviral transduction methods were shown to result in stable expression of tyrosinase and mCherry in mesenchymal stem cells. The results suggest that photoacoustic imaging using reporter genes is suitable for the study of stem cell driven tissue regeneration in small animals.

Preliminary frequency-domain analysis for the reconstructed spatial resolution of muon tomography

NASA Astrophysics Data System (ADS)

Yu, B.; Zhao, Z.; Wang, X.; Wang, Y.; Wu, D.; Zeng, Z.; Zeng, M.; Yi, H.; Luo, Z.; Yue, X.; Cheng, J.

2014-11-01

Muon tomography is an advanced technology to non-destructively detect high atomic number materials. It exploits the multiple Coulomb scattering information of muon to reconstruct the scattering density image of the traversed object. Because of the statistics of muon scattering, the measurement error of system and the data incompleteness, the reconstruction is always accompanied with a certain level of interference, which will influence the reconstructed spatial resolution. While statistical noises can be reduced by extending the measuring time, system parameters determine the ultimate spatial resolution that one system can reach. In this paper, an effective frequency-domain model is proposed to analyze the reconstructed spatial resolution of muon tomography. The proposed method modifies the resolution analysis in conventional computed tomography (CT) to fit the different imaging mechanism in muon scattering tomography. The measured scattering information is described in frequency domain, then a relationship between the measurements and the original image is proposed in Fourier domain, which is named as "Muon Central Slice Theorem". Furthermore, a preliminary analytical expression of the ultimate reconstructed spatial is derived, and the simulations are performed for validation. While the method is able to predict the ultimate spatial resolution of a given system, it can also be utilized for the optimization of system design and construction.

High-resolution magnetic resonance imaging of carotid atherosclerotic plaques - a correlation study with histopathology.

PubMed

Xia, Zhangyong; Yang, Hua; Yuan, Xiaochun; Wang, Jiyue; Zhang, Shigang; Zhang, Liyong; Qu, Yang; Chen, Jun; Jiao, Liqun; Wang, Le-Xin; Du, Yifeng

2017-07-01

This study aimed to utilize high-resolution magnetic resonance imaging (MRI) to investigate the characteristics of stable and vulnerable carotid arteriosclerotic plaques, with correlations to histopathological findings. High-resolution MRI was performed in 817 patients, using three-dimensional magnetic resonance angiography. Plaque composition was evaluated by measuring the areas occupied by calcification, a lipid-rich necrotic core, intra-plaque haemorrhage, and fibrous cap rupture. Plaque morphology was analysed by measuring vessel wall area, thickness, and luminal area at the bifurcation of the common carotid artery. Plaque tissues were sampled during carotid endarterectomy and examined using haematoxylin-eosin, Oil Red O, Masson trichrome staining, and immunohistochemical staining for CD68. Patients were divided into stable plaque group (n = 462) and vulnerable plaque group (n = 355), based on intraoperative observations and postoperative histopathological findings. Compared to the stable plaque group, the vulnerable plaque group exhibited increased vessel wall areas and thickness, and decreased mean luminal areas (P < 0.001). The vulnerable plaque group also had a lower collagen content, a higher lipid content, and higher CD68 expression in plaque tissues on histological examinations (P < 0.01). Incidences of lipid-rich necrotic core (38.1 % vs. 34.3 %), intra-plaque haemorrhage (26.9 % vs. 22.8 %), plaque calcification (45.2 % vs. 40.9 %), and fibrous cap rupture (36.0 % vs 39.8 %) in the plaques were concordant with MRI observations and histopathological findings (p > 0.05). Stable and vulnerable carotid plaques had different morphologies and compositions. High-resolution MRI can assess such differences qualitatively and quantitatively in vivo and provide guidance for risk stratification and management.

Validation of dye-binding/high-resolution thermal denaturation for the identification of mutations in the SLC22A5 gene.

PubMed

Dobrowolski, Steven F; McKinney, Jason T; Amat di San Filippo, Cristina; Giak Sim, Keow; Wilcken, Bridget; Longo, Nicola

2005-03-01

Primary carnitine deficiency is an autosomal recessive disorder of fatty acid oxidation resulting from defective carnitine transport. This disease is caused by mutations in the OCTN2 carnitine transporter encoded by the SLC22A5 gene. Here we validate dye-binding/high-resolution thermal denaturation as a screening procedure to identify novel mutations in this gene. This procedure is based on the amplification of DNA by PCR in capillaries with the dsDNA binding dye LCGreen I. The PCR reaction is then analyzed in the same capillary by high-resolution thermal denaturation. Samples with abnormal melting profiles are sequenced. This technique correctly identified all known patients who were compound heterozygotes for different mutations in the carnitine transporter gene and about 30% of homozygous patients. The remaining 70% of homozygous patients were identified by a second amplification, in which the patient's DNA was mixed with the DNA of a normal control. This screening system correctly identified eight novel mutations and both abnormal alleles in six new families with primary carnitine deficiency. The causative role of the missense mutations identified (c.3G>T/p.M1I, c.695C>T/p.T232M, and c.1403 C>G/p.T468R) was confirmed by expression in Chinese hamster ovary (CHO) cells. These results expand the mutational spectrum in primary carnitine deficiency and indicate dye-binding/high-resolution thermal denaturation as an ideal system to screen for mutations in diseases with no prevalent molecular alteration. (c) 2005 Wiley-Liss, Inc.

The Crista Fenestra and Its Impact on the Surgical Approach to the Scala Tympani during Cochlear Implantation.

PubMed

Angeli, Roberto D; Lavinsky, Joel; Setogutti, Enio T; Lavinsky, Luiz

2017-01-01

The aim of this work was to describe the dimensions of the crista fenestra and determine its presence by means of high-resolution computed tomography (CT) for the purpose of cochlear implantation via the round window approach. A series of 10 adult human temporal bones underwent high-resolution CT scanning and were further dissected for microscopic study of the round window niche. In all of the specimens, the round window membrane was fully visualized after the complete removal of bony overhangs. The crista fenestra was identified as a sharp bony crest located in the anterior and inferior borders of the niche; its area ranged from 0.28 to 0.80 mm2 (mean 0.51 ± 0.18). The proportion of the area occupied by the crista fenestra in the whole circumference of the round window ranged from 23 to 50% (mean 36%). We found a moderate positive correlation between the area of the niche and the dimensions of the crista fenestra (Spearman rho: 0.491). In every case, high-resolution CT scanning was unable to determine the presence of the crista fenestra. The crista fenestra occupies a variable but expressive area within the bony round window niche. Narrower round window niches tended to house smaller crests. The presence of the crista fenestra is an important obstacle to adequate access to the scala tympani. Nevertheless, a high-resolution CT scan provides no additional preoperative information with regard to its presence for the purpose of surgical access to the scala tympani via the round window niche. © 2017 S. Karger AG, Basel.

A resolution expressing sympathy for the people of Poland in the aftermath of the devastating plane crash that killed the country's President, First Lady, and 94 other high ranking government, military, and civic leaders on April 10, 2010.

THOMAS, 111th Congress

Sen. Durbin, Richard J. [D-IL

2010-04-14

Senate - 04/14/2010 Submitted in the Senate, considered, and agreed to without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

Developing a Drosophila Model of Schwannomatosis

DTIC Science & Technology

2013-02-01

Drosophila melanogaster has become an important model system for cancer studies. Reduced redundancy in the Drosophila genome compared with that of...of high-resolution deletion coverage of the Drosophila melanogaster genome . Nat. Genet. 36, 288-292. Pastor-Pareja, J. C., Wu, M. and Xu. T. (2008...microarray analysis of the entire Drosophila melanogaster genome and compared gene expression profiles of wild type, dCap-D3 and rbf1 mutant

Two-photon imaging in living brain slices.

PubMed

Mainen, Z F; Maletic-Savatic, M; Shi, S H; Hayashi, Y; Malinow, R; Svoboda, K

1999-06-01

Two-photon excitation laser scanning microscopy (TPLSM) has become the tool of choice for high-resolution fluorescence imaging in intact neural tissues. Compared with other optical techniques, TPLSM allows high-resolution imaging and efficient detection of fluorescence signal with minimal photobleaching and phototoxicity. The advantages of TPLSM are especially pronounced in highly scattering environments such as the brain slice. Here we describe our approaches to imaging various aspects of synaptic function in living brain slices. To combine several imaging modes together with patch-clamp electrophysiological recordings we found it advantageous to custom-build an upright microscope. Our design goals were primarily experimental convenience and efficient collection of fluorescence. We describe our TPLSM imaging system and its performance in detail. We present dynamic measurements of neuronal morphology of neurons expressing green fluorescent protein (GFP) and GFP fusion proteins as well as functional imaging of calcium dynamics in individual dendritic spines. Although our microscope is a custom instrument, its key advantages can be easily implemented as a modification of commercial laser scanning microscopes. Copyright 1999 Academic Press.

Transcript expression and genetic variability analysis of caspases in breast carcinomas suggests CASP9 as the most interesting target.

PubMed

Brynychova, Veronika; Hlavac, Viktor; Ehrlichova, Marie; Vaclavikova, Radka; Nemcova-Furstova, Vlasta; Pecha, Vaclav; Trnkova, Marketa; Mrhalova, Marcela; Kodet, Roman; Vrana, David; Gatek, Jiri; Bendova, Marie; Vernerova, Zdenka; Kovar, Jan; Soucek, Pavel

2017-01-01

Apoptosis plays a critical role in cancer cell survival and tumor development. We provide a hypothesis-generating screen for further research by exploring the expression profile and genetic variability of caspases (2, 3, 7, 8, 9, and 10) in breast carcinoma patients. This study addressed isoform-specific caspase transcript expression and genetic variability in regulatory sequences of caspases 2 and 9. Gene expression profiling was performed by quantitative real-time PCR in tumor and paired non-malignant tissues of two independent groups of patients. Genetic variability was determined by high resolution melting, allelic discrimination, and sequencing analysis in tumor and peripheral blood lymphocyte DNA of the patients. CASP3 A+B and S isoforms were over-expressed in tumors of both patient groups. The CASP9 transcript was down-regulated in tumors of both groups of patients and significantly associated with expression of hormonal receptors and with the presence of rs4645978-rs2020903-rs4646034 haplotype in the CASP9 gene. Patients with a low intratumoral CASP9A/B isoform expression ratio (predicted to shift equilibrium towards anti-apoptotic isoform) subsequently treated with adjuvant chemotherapy had a significantly shorter disease-free survival than those with the high ratio (p=0.04). Inheritance of CC genotype of rs2020903 in CASP9 was associated with progesterone receptor expression in tumors (p=0.003). Genetic variability in CASP9 and expression of its splicing variants present targets for further study.

Recombinant expression of Ixolaris, a Kunitz-type inhibitor from the tick salivary gland, for NMR studies.

PubMed

De Paula, V S; Silva, F H S; Francischetti, I M B; Monteiro, R Q; Valente, A P

2017-11-01

Ixolaris is an anticoagulant protein identified in the tick saliva of Ixodes scapularis. Ixolaris contains 2 Kunitz like domains and binds to Factor Xa or Factor X as a scaffold for inhibition of the Tissue Factor (TF)/Factor VIIa (FVIIa). In contrast to tissue factor pathway inhibitor (TFPI), however, Ixolaris does not bind to the active site cleft of FXa. Instead, complex formation is mediated by the FXa heparin-binding exosite. Due to its potent and long-lasting antithrombotic activity, Ixolaris is a promising agent for anticoagulant therapy. Although numerous functional studies of Ixolaris exist, three-dimensional structure of Ixolaris has not been obtained at atomic resolution. Using the pET32 vector, we successfully expressed a TRX-His 6 -Ixolaris fusion protein. By combining Ni-NTA chromatography, enterokinase protease cleavage, and reverse phase HPLC (RP-HPLC), we purified isotopically labeled Ixolaris for NMR studies. 1D 1 H and 2D 15 N- 1 H NMR analysis yielded high quality 2D 15 N- 1 H HSQC spectra revealing that the recombinant protein is folded. These studies represent the first steps in obtaining high-resolution structural information by NMR for Ixolaris enabling the investigation of the molecular basis for Ixolaris-coagulation factors interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

Gut Microbiota Contributes to Resistance Against Pneumococcal Pneumonia in Immunodeficient Rag-/- Mice.

PubMed

Felix, Krysta M; Jaimez, Ivan A; Nguyen, Thuy-Vi V; Ma, Heqing; Raslan, Walid A; Klinger, Christina N; Doyle, Kristian P; Wu, Hsin-Jung J

2018-01-01

Streptococcus pneumoniae causes infection-related mortality worldwide. Immunocompromised individuals, including young children, the elderly, and those with immunodeficiency, are especially vulnerable, yet little is known regarding S. pneumoniae- related pathogenesis and protection in immunocompromised hosts. Recently, strong interest has emerged in the gut microbiota's impact on lung diseases, or the "gut-lung axis." However, the mechanisms of gut microbiota protection against gut-distal lung diseases like pneumonia remain unclear. We investigated the role of the gut commensal, segmented filamentous bacteria (SFB), against pneumococcal pneumonia in immunocompetent and immunocompromised mouse models. For the latter, we chose the Rag -/- model, with adaptive immune deficiency. Immunocompetent adaptive protection against S. pneumoniae infection is based on antibodies against pneumococcal capsular polysaccharides, prototypical T cell independent-II (TI-II) antigens. Although SFB colonization enhanced TI-II antibodies in C57BL/6 mice, our data suggest that SFB did not further protect these immunocompetent animals. Indeed, basal B cell activity in hosts without SFB is sufficient for essential protection against S. pneumoniae . However, in immunocompromised Rag -/- mice, we demonstrate a gut-lung axis of communication, as SFB influenced lung protection by regulating innate immunity. Neutrophil resolution is crucial to recovery, since an unchecked neutrophil response causes severe tissue damage. We found no early neutrophil recruitment differences between hosts with or without SFB; however, we observed a significant drop in lung neutrophils in the resolution phase of S. pneumoniae infection, which corresponded with lower CD47 expression, a molecule that inhibits phagocytosis of apoptotic cells, in SFB-colonized Rag -/- mice. SFB promoted a shift in lung neutrophil phenotype from inflammatory neutrophils expressing high levels of CD18 and low levels of CD62L, to pro-resolution neutrophils with low CD18 and high CD62L. Blocking CD47 in SFB(-) mice increased pro-resolution neutrophils, suggesting CD47 down-regulation may be one neutrophil-modulating mechanism SFB utilizes. The SFB-induced lung neutrophil phenotype remained similar with heat-inactivated S. pneumoniae treatment, indicating these SFB-induced changes in neutrophil phenotype during the resolution phase are not simply secondary to better bacterial clearance in SFB(+) than SFB(-) mice. Together, these data demonstrate that the gut commensal SFB may provide much-needed protection in immunocompromised hosts in part by promoting neutrophil resolution post lung infection.

Arrays of microscopic organic LEDs for high-resolution optogenetics

PubMed Central

Steude, Anja; Witts, Emily C.; Miles, Gareth B.; Gather, Malte C.

2016-01-01

Optogenetics is a paradigm-changing new method to study and manipulate the behavior of cells with light. Following major advances of the used genetic constructs over the last decade, the light sources required for optogenetic control are now receiving increased attention. We report a novel optogenetic illumination platform based on high-density arrays of microscopic organic light-emitting diodes (OLEDs). Because of the small dimensions of each array element (6 × 9 μm2) and the use of ultrathin device encapsulation, these arrays enable illumination of cells with unprecedented spatiotemporal resolution. We show that adherent eukaryotic cells readily proliferate on these arrays, and we demonstrate specific light-induced control of the ionic current across the membrane of individual live cells expressing different optogenetic constructs. Our work paves the way for the use of OLEDs for cell-specific optogenetic control in cultured neuronal networks and for acute brain slices, or as implants in vivo. PMID:27386540

Watching stem cells at work with a flexible multiphoton tomograph

NASA Astrophysics Data System (ADS)

Uchugonova, Aisada; Hoffmann, Robert; Weinigel, Martin; König, Karsten

2012-03-01

There is a high demand for non-invasive imaging techniques that allow observation of stem cells in their native environment without significant input on cell metabolism, reproduction, and behavior. Easy accessible hair follicle pluripotent stem cells in the bulge area and dermal papilla are potential sources for stem cell based therapy. It has been shown that these cells are able to generate hair, non-follicle skin cells, nerves, vessels, smooth muscles etc. and may participate in wound healing processes. We report on the finding of nestin-GFP expressing stem cells in their native niche in the bulge of the hair follicle of living mice by using high-resolution in-vivo multiphoton tomography. The 3D imaging with submicron resolution was based on two-photon induced fluorescence and second harmonic generation (SHG) of collagen. Migrating stem cells from the bulge to their microenvironment have been detected inside the skin during optical deep tissue sectioning.

Probing Chemical Bonding in Uranium Dioxide by Means of High-Resolution X-ray Absorption Spectroscopy

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

Butorin, Sergei M.; Modin, Anders; Vegelius, Johan R.

Here, a systematic X-ray absorption study at the U 3d, 4d, and 4f edges of UO 2 was performed, and the data were analyzed within framework of the Anderson impurity model. By applying the high-energy-resolution fluorescence-detection (HERFD) mode of X-ray absorption spectroscopy (XAS) at the U 3d 3/2 edge and conducting the XAS measurements at the shallower U 4f levels, fine details of the XAS spectra were resolved resulting from reduced core-hole lifetime broadening. This multiedge study enabled a far more effective analysis of the electronic structure at the U sites and characterization of the chemical bonding and degree ofmore » the 5f localization in UO 2. The results support the covalent character of UO 2 and do not agree with the suggestions of rather ionic bonding in this compound as expressed in some publications.« less

High-resolution analysis of locomotor activity rhythms in disconnected, a visual-system mutant of Drosophila melanogaster.

PubMed

Dowse, H B; Dushay, M S; Hall, J C; Ringo, J M

1989-07-01

Free-running locomotor activity and eclosion rhythms of Drosophila melanogaster, mutant at the disconnected (disco) locus, are substantially different from the wild-type phenotype. Initial periodogram analysis revealed little or no rhythmicity (Dushay et al., 1989). We have reanalyzed the locomotor activity data using high-resolution signal analysis (maximum-entropy spectral analysis, or MESA). These analyses, corroborated by autocorrelograms, uncovered significant residual circadian rhythmicity and strong ultradian rhythms in most of the animals tested. In this regard the disco mutants are much like flies expressing mutant alleles of the period gene, as well as wild-type flies reared throughout life in constant darkness. We hypothesize that light normally triggers the coupling of multiple ultradian oscillators into a functional circadian clock and that this process is disrupted in disco flies as a result of the neural lesion.

Probing Chemical Bonding in Uranium Dioxide by Means of High-Resolution X-ray Absorption Spectroscopy

DOE PAGES

Butorin, Sergei M.; Modin, Anders; Vegelius, Johan R.; ...

2016-11-30

Here, a systematic X-ray absorption study at the U 3d, 4d, and 4f edges of UO 2 was performed, and the data were analyzed within framework of the Anderson impurity model. By applying the high-energy-resolution fluorescence-detection (HERFD) mode of X-ray absorption spectroscopy (XAS) at the U 3d 3/2 edge and conducting the XAS measurements at the shallower U 4f levels, fine details of the XAS spectra were resolved resulting from reduced core-hole lifetime broadening. This multiedge study enabled a far more effective analysis of the electronic structure at the U sites and characterization of the chemical bonding and degree ofmore » the 5f localization in UO 2. The results support the covalent character of UO 2 and do not agree with the suggestions of rather ionic bonding in this compound as expressed in some publications.« less

Single-cell imaging tools for brain energy metabolism: a review

PubMed Central

San Martín, Alejandro; Sotelo-Hitschfeld, Tamara; Lerchundi, Rodrigo; Fernández-Moncada, Ignacio; Ceballo, Sebastian; Valdebenito, Rocío; Baeza-Lehnert, Felipe; Alegría, Karin; Contreras-Baeza, Yasna; Garrido-Gerter, Pamela; Romero-Gómez, Ignacio; Barros, L. Felipe

2014-01-01

Abstract. Neurophotonics comes to light at a time in which advances in microscopy and improved calcium reporters are paving the way toward high-resolution functional mapping of the brain. This review relates to a parallel revolution in metabolism. We argue that metabolism needs to be approached both in vitro and in vivo, and that it does not just exist as a low-level platform but is also a relevant player in information processing. In recent years, genetically encoded fluorescent nanosensors have been introduced to measure glucose, glutamate, ATP, NADH, lactate, and pyruvate in mammalian cells. Reporting relative metabolite levels, absolute concentrations, and metabolic fluxes, these sensors are instrumental for the discovery of new molecular mechanisms. Sensors continue to be developed, which together with a continued improvement in protein expression strategies and new imaging technologies, herald an exciting era of high-resolution characterization of metabolism in the brain and other organs. PMID:26157964

Ranging performance of satellite laser altimeters

NASA Technical Reports Server (NTRS)

Gardner, Chester S.

1992-01-01

Topographic mapping of the earth, moon and planets can be accomplished with high resolution and accuracy using satellite laser altimeters. These systems employ nanosecond laser pulses and microradian beam divergences to achieve submeter vertical range resolution from orbital altitudes of several hundred kilometers. Here, we develop detailed expressions for the range and pulse width measurement accuracies and use the results to evaluate the ranging performances of several satellite laser altimeters currently under development by NASA for launch during the next decade. Our analysis includes the effects of the target surface characteristics, spacecraft pointing jitter and waveform digitizer characteristics. The results show that ranging accuracy is critically dependent on the pointing accuracy and stability of the altimeter especially over high relief terrain where surface slopes are large. At typical orbital altitudes of several hundred kilometers, single-shot accuracies of a few centimeters can be achieved only when the pointing jitter is on the order of 10 mu rad or less.

Confocal fluorescence microscope with dual-axis architecture and biaxial postobjective scanning

PubMed Central

Wang, Thomas D.; Contag, Christopher H.; Mandella, Michael J.; Chan, Ning Y.; Kino, Gordon S.

2007-01-01

We present a novel confocal microscope that has dual-axis architecture and biaxial postobjective scanning for the collection of fluorescence images from biological specimens. This design uses two low-numerical-aperture lenses to achieve high axial resolution and long working distance, and the scanning mirror located distal to the lenses rotates along the orthogonal axes to produce arc-surface images over a large field of view (FOV). With fiber optic coupling, this microscope can potentially be scaled down to millimeter dimensions via microelectromechanical systems (MEMS) technology. We demonstrate a benchtop prototype with a spatial resolution ≤4.4 μm that collects fluorescence images with a high SNR and a good contrast ratio from specimens expressing GFP. Furthermore, the scanning mechanism produces only small differences in aberrations over the image FOV. These results demonstrate proof of concept of the dual-axis confocal architecture for in vivo molecular and cellular imaging. PMID:15250760

High-resolution transcript profiling reveals shoot abscission process of spruce dwarf mistletoe Arceuthobium sichuanense in response to ethephon

PubMed Central

Wang, Yonglin; Xiong, Dianguang; Jiang, Ning; Li, Xuewu; Yang, Qiqing; Tian, Chengming

2016-01-01

Arceuthobium (dwarf mistletoes) are hemiparasites that may cause great damage to infected trees belonging to Pinaceae and Cupressaceae. Currently, dwarf mistletoe control involves the use of the ethylene-producing product ethephon (ETH), which acts by inducing dwarf mistletoe shoot abscission. However, the process by which ETH functions is mostly unknown. Therefore, the transcriptome of the ETH-exposed plants was compared to non-exposed controls to identify genes associated with the response to ethephon. In this study, the reference transcriptome was contained 120,316 annotated unigenes, with a total of 21,764 ETH-responsive differentially expressed unigenes were identified. These ETH-associated genes clustered into 20 distinctly expressed pattern groups, providing a view of molecular events with good spatial and temporal resolution. As expected, the greatest number of unigenes with changed expression were observed at the onset of abscission, suggesting induction by ethylene. ETH also affected genes associated with shoot abscission processes including hormone biosynthesis and signaling, cell wall hydrolysis and modification, lipid transference, and more. The comprehensive transcriptome data set provides a wealth of genomic resources for dwarf mistletoe communities and contributes to a better understanding of the molecular regulatory mechanism of ethylene-caused shoots abscission. PMID:27941945

Identification of Fur, Aconitase, and Other Proteins Expressed by Mycobacterium tuberculosis under Conditions of Low and High Concentrations of Iron by Combined Two-Dimensional Gel Electrophoresis and Mass Spectrometry

PubMed Central

Wong, Diane K.; Lee, Bai-Yu; Horwitz, Marcus A.; Gibson, Bradford W.

1999-01-01

Iron plays a critical role in the pathophysiology of Mycobacterium tuberculosis. To gain a better understanding of iron regulation by this organism, we have used two-dimensional (2-D) gel electrophoresis, mass spectrometry, and database searching to study protein expression in M. tuberculosis under conditions of high and low iron concentration. Proteins in cellular extracts from M. tuberculosis Erdman strain grown under low-iron (1 μM) and high-iron (70 μM) conditions were separated by 2-D polyacrylamide gel electrophoresis, which allowed high-resolution separation of several hundred proteins, as visualized by Coomassie staining. The expression of at least 15 proteins was induced, and the expression of at least 12 proteins was decreased under low-iron conditions. In-gel trypsin digestion was performed on these differentially expressed proteins, and the digestion mixtures were analyzed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry to determine the molecular masses of the resulting tryptic peptides. Partial sequence data on some of the peptides were obtained by using after source decay and/or collision-induced dissociation. The fragmentation data were used to search computerized peptide mass and protein sequence databases for known proteins. Ten iron-regulated proteins were identified, including Fur and aconitase proteins, both of which are known to be regulated by iron in other bacterial systems. Our study shows that, where large protein sequence databases are available from genomic studies, the combined use of 2-D gel electrophoresis, mass spectrometry, and database searching to analyze proteins expressed under defined environmental conditions is a powerful tool for identifying expressed proteins and their physiologic relevance. PMID:9864233

Investigation of subcellular localization and dynamics of membrane proteins in living bacteria by combining optical micromanipulation and high-resolution microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Barroso Peña, Álvaro; Nieves, Marcos; Teper, Konrad; Wedlich-Soldner, Roland; Denz, Cornelia

2016-09-01

The plasma membrane serves as protective interface between cells and their environment. It also constitutes a hub for selective nutrient uptake and signal transduction. Increasing evidence over the last years indicates that, similar to eukaryotic cells, lateral membrane organization plays an important role in the regulation of prokaryotic signaling pathways. However, the mechanisms underlying this phenomenon are still poorly understood. Spatiotemporal characterization of bacterial signal transduction demands very sensitive high-resolution microscopy techniques due to the low expression levels of most signaling proteins and the small size of bacterial cells. In addition, direct study of subcellular confinement and dynamics of bacterial signaling proteins during the different stages of the signal transduction also requires immobilization in order to avoid cell displacement caused by Brownian motion, local fluid flows and bacterial self-propulsion. In this work we present a novel approach based on the combination of high resolution imaging and optical manipulation that enables the investigation of the distribution and dynamics of proteins at the bacterial plasma membrane. For this purpose, we combine the versatility of holographic optical tweezers (HOT) with the sensitivity and resolution of total internal reflection fluorescence (TIRF) microscopy. Furthermore, we discuss the implementation of microfluidic devices in our integrated HOT+TIRF system for the control of growth conditions of bacterial cells. The capabilities of our workstation provides thus new valuable insights into the fundamental cellular and physical mechanisms underlying the regulation of bacterial signal transduction.

Localization microscopy of DNA in situ using Vybrant(®) DyeCycle™ Violet fluorescent probe: A new approach to study nuclear nanostructure at single molecule resolution.

PubMed

Żurek-Biesiada, Dominika; Szczurek, Aleksander T; Prakash, Kirti; Mohana, Giriram K; Lee, Hyun-Keun; Roignant, Jean-Yves; Birk, Udo J; Dobrucki, Jurek W; Cremer, Christoph

2016-05-01

Higher order chromatin structure is not only required to compact and spatially arrange long chromatids within a nucleus, but have also important functional roles, including control of gene expression and DNA processing. However, studies of chromatin nanostructures cannot be performed using conventional widefield and confocal microscopy because of the limited optical resolution. Various methods of superresolution microscopy have been described to overcome this difficulty, like structured illumination and single molecule localization microscopy. We report here that the standard DNA dye Vybrant(®) DyeCycle™ Violet can be used to provide single molecule localization microscopy (SMLM) images of DNA in nuclei of fixed mammalian cells. This SMLM method enabled optical isolation and localization of large numbers of DNA-bound molecules, usually in excess of 10(6) signals in one cell nucleus. The technique yielded high-quality images of nuclear DNA density, revealing subdiffraction chromatin structures of the size in the order of 100nm; the interchromatin compartment was visualized at unprecedented optical resolution. The approach offers several advantages over previously described high resolution DNA imaging methods, including high specificity, an ability to record images using a single wavelength excitation, and a higher density of single molecule signals than reported in previous SMLM studies. The method is compatible with DNA/multicolor SMLM imaging which employs simple staining methods suited also for conventional optical microscopy. Copyright © 2016. Published by Elsevier Inc.

Io’s volcanoes at high spatial, spectral, and temporal resolution from ground-based observations

NASA Astrophysics Data System (ADS)

de Kleer, Katherine R.; de Pater, Imke

2017-10-01

Io’s dynamic volcanic eruptions provide a laboratory for studying large-scale volcanism on a body vastly different from Earth, and for unraveling the connections between tidal heating and the geological activity it powers. Ground-based near-infrared observatories allow for high-cadence, long-time-baseline observing programs using diverse instrumentation, and yield new information into the nature and variability of this activity. I will summarize results from four years of ground-based observations of Io’s volcanism, including: (1) A multi-year cadence observing campaign using adaptive optics on 8-10 meter telescopes, which places constraints on tidal heating models through sampling the spatial distribution of Io’s volcanic heat flow, and provides estimates of the occurrence rate of Io’s most energetic eruptions; (2) High-spectral-resolution (R~25,000) studies of Io’s volcanic SO gas emission at 1.7 microns, which resolves this rovibronic line into its different branches, and thus contains detailed information on the temperature and thermal state of the gas; and (3) The highest-spatial-resolution map ever produced of the entire Loki Patera, a 20,000 km2 volcanic feature on Io, derived from adaptive-optics observations of an occultation of Io by Europa. The map achieves a spatial resolution of ~10 km and indicates compositional differences across the patera. These datasets both reveal specific characteristics of Io’s individual eruptions, and provide clues into the sub-surface systems connecting Io’s tidally-heated interior to its surface expressions of volcanism.

The RNA-Seq-based high resolution gene expression atlas of chickpea (Cicer arietinum L.) reveals dynamic spatio-temporal changes associated with growth and development.

PubMed

Kudapa, Himabindu; Garg, Vanika; Chitikineni, Annapurna; Varshney, Rajeev K

2018-04-10

Chickpea is one of the world's largest cultivated food legumes and is an excellent source of high-quality protein to the human diet. Plant growth and development are controlled by programmed expression of a suite of genes at the given time, stage, and tissue. Understanding how the underlying genome sequence translates into specific plant phenotypes at key developmental stages, information on gene expression patterns is crucial. Here, we present a comprehensive Cicer arietinum Gene Expression Atlas (CaGEA) across different plant developmental stages and organs covering the entire life cycle of chickpea. One of the widely used drought tolerant cultivars, ICC 4958 has been used to generate RNA-Seq data from 27 samples at 5 major developmental stages of the plant. A total of 816 million raw reads were generated and of these, 794 million filtered reads after quality control (QC) were subjected to downstream analysis. A total of 15,947 unique number of differentially expressed genes across different pairwise tissue combinations were identified. Significant differences in gene expression patterns contributing in the process of flowering, nodulation, and seed and root development were inferred in this study. Furthermore, differentially expressed candidate genes from "QTL-hotspot" region associated with drought stress response in chickpea were validated. © 2018 The Authors. Plant, Cell & Environment Published by John Wiley & Sons Ltd.

Integrated analysis of chromosome copy number variation and gene expression in cervical carcinoma

PubMed Central

Yan, Deng; Yi, Song; Chiu, Wang Chi; Qin, Liu Gui; Kin, Wong Hoi; Kwok Hung, Chung Tony; Linxiao, Han; Wai, Choy Kwong; Yi, Sui; Tao, Yang; Tao, Tang

2017-01-01

Objective This study was conducted to explore chromosomal copy number variations (CNV) and transcript expression and to examine pathways in cervical pathogenesis using genome-wide high resolution microarrays. Methods Genome-wide chromosomal CNVs were investigated in 6 cervical cancer cell lines by Human Genome CGH Microarray Kit (4x44K). Gene expression profiles in cervical cancer cell lines, primary cervical carcinoma and normal cervical epithelium tissues were also studied using the Whole Human Genome Microarray Kit (4x44K). Results Fifty common chromosomal CNVs were identified in the cervical cancer cell lines. Correlation analysis revealed that gene up-regulation or down-regulation is significantly correlated with genomic amplification (P=0.009) or deletion (P=0.006) events. Expression profiles were identified through cluster analysis. Gene annotation analysis pinpointed cell cycle pathways was significantly (P=1.15E-08) affected in cervical cancer. Common CNVs were associated with cervical cancer. Conclusion Chromosomal CNVs may contribute to their transcript expression in cervical cancer. PMID:29312578

Genetically encoded reporters for hyperpolarized xenon magnetic resonance imaging

NASA Astrophysics Data System (ADS)

Shapiro, Mikhail G.; Ramirez, R. Matthew; Sperling, Lindsay J.; Sun, George; Sun, Jinny; Pines, Alexander; Schaffer, David V.; Bajaj, Vikram S.

2014-07-01

Magnetic resonance imaging (MRI) enables high-resolution non-invasive observation of the anatomy and function of intact organisms. However, previous MRI reporters of key biological processes tied to gene expression have been limited by the inherently low molecular sensitivity of conventional 1H MRI. This limitation could be overcome through the use of hyperpolarized nuclei, such as in the noble gas xenon, but previous reporters acting on such nuclei have been synthetic. Here, we introduce the first genetically encoded reporters for hyperpolarized 129Xe MRI. These expressible reporters are based on gas vesicles (GVs), gas-binding protein nanostructures expressed by certain buoyant microorganisms. We show that GVs are capable of chemical exchange saturation transfer interactions with xenon, which enables chemically amplified GV detection at picomolar concentrations (a 100- to 10,000-fold improvement over comparable constructs for 1H MRI). We demonstrate the use of GVs as heterologously expressed indicators of gene expression and chemically targeted exogenous labels in MRI experiments performed on living cells.

Integrated analysis of chromosome copy number variation and gene expression in cervical carcinoma.

PubMed

Yan, Deng; Yi, Song; Chiu, Wang Chi; Qin, Liu Gui; Kin, Wong Hoi; Kwok Hung, Chung Tony; Linxiao, Han; Wai, Choy Kwong; Yi, Sui; Tao, Yang; Tao, Tang

2017-12-12

This study was conducted to explore chromosomal copy number variations (CNV) and transcript expression and to examine pathways in cervical pathogenesis using genome-wide high resolution microarrays. Genome-wide chromosomal CNVs were investigated in 6 cervical cancer cell lines by Human Genome CGH Microarray Kit (4x44K). Gene expression profiles in cervical cancer cell lines, primary cervical carcinoma and normal cervical epithelium tissues were also studied using the Whole Human Genome Microarray Kit (4x44K). Fifty common chromosomal CNVs were identified in the cervical cancer cell lines. Correlation analysis revealed that gene up-regulation or down-regulation is significantly correlated with genomic amplification ( P =0.009) or deletion ( P =0.006) events. Expression profiles were identified through cluster analysis. Gene annotation analysis pinpointed cell cycle pathways was significantly ( P =1.15E-08) affected in cervical cancer. Common CNVs were associated with cervical cancer. Chromosomal CNVs may contribute to their transcript expression in cervical cancer.

Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population

PubMed Central

Serin, Elise A. R.; Snoek, L. B.; Nijveen, Harm; Willems, Leo A. J.; Jiménez-Gómez, Jose M.; Hilhorst, Henk W. M.; Ligterink, Wilco

2017-01-01

High-density genetic maps are essential for high resolution mapping of quantitative traits. Here, we present a new genetic map for an Arabidopsis Bayreuth × Shahdara recombinant inbred line (RIL) population, built on RNA-seq data. RNA-seq analysis on 160 RILs of this population identified 30,049 single-nucleotide polymorphisms (SNPs) covering the whole genome. Based on a 100-kbp window SNP binning method, 1059 bin-markers were identified, physically anchored on the genome. The total length of the RNA-seq genetic map spans 471.70 centimorgans (cM) with an average marker distance of 0.45 cM and a maximum marker distance of 4.81 cM. This high resolution genotyping revealed new recombination breakpoints in the population. To highlight the advantages of such high-density map, we compared it to two publicly available genetic maps for the same population, comprising 69 PCR-based markers and 497 gene expression markers derived from microarray data, respectively. In this study, we show that SNP markers can effectively be derived from RNA-seq data. The new RNA-seq map closes many existing gaps in marker coverage, saturating the previously available genetic maps. Quantitative trait locus (QTL) analysis for published phenotypes using the available genetic maps showed increased QTL mapping resolution and reduced QTL confidence interval using the RNA-seq map. The new high-density map is a valuable resource that facilitates the identification of candidate genes and map-based cloning approaches. PMID:29259624

Advanced astigmatism-corrected tandem Wadsworth mounting for small-scale spectral broadband imaging spectrometer.

PubMed

Lei, Yu; Lin, Guan-yu

2013-01-01

Tandem gratings of double-dispersion mount make it possible to design an imaging spectrometer for the weak light observation with high spatial resolution, high spectral resolution, and high optical transmission efficiency. The traditional tandem Wadsworth mounting is originally designed to match the coaxial telescope and large-scale imaging spectrometer. When it is used to connect the off-axis telescope such as off-axis parabolic mirror, it presents lower imaging quality than to connect the coaxial telescope. It may also introduce interference among the detector and the optical elements as it is applied to the short focal length and small-scale spectrometer in a close volume by satellite. An advanced tandem Wadsworth mounting has been investigated to deal with the situation. The Wadsworth astigmatism-corrected mounting condition for which is expressed as the distance between the second concave grating and the imaging plane is calculated. Then the optimum arrangement for the first plane grating and the second concave grating, which make the anterior Wadsworth condition fulfilling each wavelength, is analyzed by the geometric and first order differential calculation. These two arrangements comprise the advanced Wadsworth mounting condition. The spectral resolution has also been calculated by these conditions. An example designed by the optimum theory proves that the advanced tandem Wadsworth mounting performs excellently in spectral broadband.

A resolution recognizing the threats to freedom of the press and expression in the People's Republic of China and urging the Government of the People's Republic of China to take meaningful steps to improve freedom of expression as fitting of a responsible international stakeholder.

THOMAS, 113th Congress

Sen. Cardin, Benjamin L. [D-MD

2014-02-24

Senate - 04/08/2014 Resolution agreed to in Senate with an amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

Non-Parametric Model Drift Detection

DTIC Science & Technology

2016-07-01

de,la,n,o,the,m, facto ,et,des,of Group num: 42, TC(X;Y_j): 0.083 42:resolution,council,resolutions,draft,recalling,pursuant,reaffirming,sponsors...Y_j): 0.019 80: posts ,cost, post ,expenditure,overall,infrastructure,expected,operational,external, savings Group num: 81, TC(X;Y_j): 0.018 81...90, TC(X;Y_j): 0.014 90:its,expresses,mandate,reiterates,appreciation,expressing,endorsed,reiterated, ex peditiously,literature Group num: 91, TC(X

A High-Resolution Proteomic Landscaping of Primary Human Dental Stem Cells: Identification of SHED- and PDLSC-Specific Biomarkers.

PubMed

Taraslia, Vasiliki; Lymperi, Stefania; Pantazopoulou, Vasiliki; Anagnostopoulos, Athanasios K; Papassideri, Issidora S; Basdra, Efthimia K; Bei, Marianna; Kontakiotis, Evangelos G; Tsangaris, George Th; Stravopodis, Dimitrios J; Anastasiadou, Ema

2018-01-05

Dental stem cells (DSCs) have emerged as a promising tool for basic research and clinical practice. A variety of adult stem cell (ASC) populations can be isolated from different areas within the dental tissue, which, due to their cellular and molecular characteristics, could give rise to different outcomes when used in potential applications. In this study, we performed a high-throughput molecular comparison of two primary human adult dental stem cell (hADSC) sub-populations: Stem Cells from Human Exfoliated Deciduous Teeth (SHEDs) and Periodontal Ligament Stem Cells (PDLSCs). A detailed proteomic mapping of SHEDs and PDLSCs, via employment of nano-LC tandem-mass spectrometry (MS/MS) revealed 2032 identified proteins in SHEDs and 3235 in PDLSCs. In total, 1516 proteins were expressed in both populations, while 517 were unique for SHEDs and 1721 were exclusively expressed in PDLSCs. Further analysis of the recorded proteins suggested that SHEDs predominantly expressed molecules that are involved in organizing the cytoskeletal network, cellular migration and adhesion, whereas PDLSCs are highly energy-producing cells, vastly expressing proteins that are implicated in various aspects of cell metabolism and proliferation. Applying the Rho-GDI signaling pathway as a paradigm, we propose potential biomarkers for SHEDs and for PDLSCs, reflecting their unique features, properties and engaged molecular pathways.

A High-Resolution Proteomic Landscaping of Primary Human Dental Stem Cells: Identification of SHED- and PDLSC-Specific Biomarkers

PubMed Central

Taraslia, Vasiliki; Lymperi, Stefania; Pantazopoulou, Vasiliki; Anagnostopoulos, Athanasios K.; Basdra, Efthimia K.; Bei, Marianna; Kontakiotis, Evangelos G.; Tsangaris, George Th.; Stravopodis, Dimitrios J.; Anastasiadou, Ema

2018-01-01

Dental stem cells (DSCs) have emerged as a promising tool for basic research and clinical practice. A variety of adult stem cell (ASC) populations can be isolated from different areas within the dental tissue, which, due to their cellular and molecular characteristics, could give rise to different outcomes when used in potential applications. In this study, we performed a high-throughput molecular comparison of two primary human adult dental stem cell (hADSC) sub-populations: Stem Cells from Human Exfoliated Deciduous Teeth (SHEDs) and Periodontal Ligament Stem Cells (PDLSCs). A detailed proteomic mapping of SHEDs and PDLSCs, via employment of nano-LC tandem-mass spectrometry (MS/MS) revealed 2032 identified proteins in SHEDs and 3235 in PDLSCs. In total, 1516 proteins were expressed in both populations, while 517 were unique for SHEDs and 1721 were exclusively expressed in PDLSCs. Further analysis of the recorded proteins suggested that SHEDs predominantly expressed molecules that are involved in organizing the cytoskeletal network, cellular migration and adhesion, whereas PDLSCs are highly energy-producing cells, vastly expressing proteins that are implicated in various aspects of cell metabolism and proliferation. Applying the Rho-GDI signaling pathway as a paradigm, we propose potential biomarkers for SHEDs and for PDLSCs, reflecting their unique features, properties and engaged molecular pathways. PMID:29304003

Brain BLAQ: Post-hoc thick-section histochemistry for localizing optogenetic constructs in neurons and their distal terminals

PubMed Central

Kupferschmidt, David A.; Cody, Patrick A.; Lovinger, David M.; Davis, Margaret I.

2015-01-01

Optogenetic constructs have revolutionized modern neuroscience, but the ability to accurately and efficiently assess their expression in the brain and associate it with prior functional measures remains a challenge. High-resolution imaging of thick, fixed brain sections would make such post-hoc assessment and association possible; however, thick sections often display autofluorescence that limits their compatibility with fluorescence microscopy. We describe and evaluate a method we call “Brain BLAQ” (Block Lipids and Aldehyde Quench) to rapidly reduce autofluorescence in thick brain sections, enabling efficient axon-level imaging of neurons and their processes in conventional tissue preparations using standard epifluorescence microscopy. Following viral-mediated transduction of optogenetic constructs and fluorescent proteins in mouse cortical pyramidal and dopaminergic neurons, we used BLAQ to assess innervation patterns in the striatum, a region in which autofluorescence often obscures the imaging of fine neural processes. After BLAQ treatment of 250–350 μm-thick brain sections, axons and puncta of labeled afferents were visible throughout the striatum using a standard epifluorescence stereomicroscope. BLAQ histochemistry confirmed that motor cortex (M1) projections preferentially innervated the matrix component of lateral striatum, whereas medial prefrontal cortex projections terminated largely in dorsal striosomes and distinct nucleus accumbens subregions. Ventral tegmental area dopaminergic projections terminated in a similarly heterogeneous pattern within nucleus accumbens and ventral striatum. Using a minimal number of easily manipulated and visualized sections, and microscopes available in most neuroscience laboratories, BLAQ enables simple, high-resolution assessment of virally transduced optogenetic construct expression, and post-hoc association of this expression with molecular markers, physiology and behavior. PMID:25698938

Multi-layer sparse representation for weighted LBP-patches based facial expression recognition.

PubMed

Jia, Qi; Gao, Xinkai; Guo, He; Luo, Zhongxuan; Wang, Yi

2015-03-19

In this paper, a novel facial expression recognition method based on sparse representation is proposed. Most contemporary facial expression recognition systems suffer from limited ability to handle image nuisances such as low resolution and noise. Especially for low intensity expression, most of the existing training methods have quite low recognition rates. Motivated by sparse representation, the problem can be solved by finding sparse coefficients of the test image by the whole training set. Deriving an effective facial representation from original face images is a vital step for successful facial expression recognition. We evaluate facial representation based on weighted local binary patterns, and Fisher separation criterion is used to calculate the weighs of patches. A multi-layer sparse representation framework is proposed for multi-intensity facial expression recognition, especially for low-intensity expressions and noisy expressions in reality, which is a critical problem but seldom addressed in the existing works. To this end, several experiments based on low-resolution and multi-intensity expressions are carried out. Promising results on publicly available databases demonstrate the potential of the proposed approach.

Single cell transcriptome analysis of MCF-7 reveals consistently and inconsistently expressed gene groups each associated with distinct cellular localization and functions

PubMed Central

Chen, Tzu-Han; Shiau, Hsin-Chieh

2018-01-01

Single cell transcriptome (SCT) analysis provides superior resolution to illustrate tumor cell heterogeneity for clinical implications. We characterized four SCTs of MCF-7 using 143 housekeeping genes (HKGs) as control, of which lactate dehydrogenase B (LDHB) expression is silenced. These SCT libraries mapped to 11,423, 11,486, 10,380, and 11,306 RefSeq genes (UCSC), respectively. High consistency in HKG expression levels across all four SCTs, along with transcriptional silencing of LDHB, was observed, suggesting a high sensitivity and reproducibility of the SCT analysis. Cross-library comparison on expression levels by scatter plotting revealed a linear correlation and an 83–94% overlap in transcript isoforms and expressed genes were also observed. To gain insight of transcriptional diversity among the SCTs, expressed genes were split into consistently expressed (CE) (expressed in all SCTs) and inconsistently expressed (IE) (expressed in some but not all SCTs) genes for further characterization, along with the 142 expressed HKGs as a reference. Distinct transcriptional strengths were found among these groups, with averages of 1,612.0, 88.0 and 1.2 FPKM for HKGs, CE and IE, respectively. Comparison between CE and IE groups further indicated that expressions of CE genes vary more significantly than that of IE genes. Gene Ontology analysis indicated that proteins encoded by CE genes are mainly involved in fundamental intracellular activities, while proteins encoded by IE genes are mainly for extracellular activities, especially acting as receptors or ion channels. The diversified gene expressions, especially for those encoded by IE genes, may contribute to cancer drug resistance. PMID:29920548

Pseudotemporal Ordering of Single Cells Reveals Metabolic Control of Postnatal β Cell Proliferation.

PubMed

Zeng, Chun; Mulas, Francesca; Sui, Yinghui; Guan, Tiffany; Miller, Nathanael; Tan, Yuliang; Liu, Fenfen; Jin, Wen; Carrano, Andrea C; Huising, Mark O; Shirihai, Orian S; Yeo, Gene W; Sander, Maike

2017-05-02

Pancreatic β cell mass for appropriate blood glucose control is established during early postnatal life. β cell proliferative capacity declines postnatally, but the extrinsic cues and intracellular signals that cause this decline remain unknown. To obtain a high-resolution map of β cell transcriptome dynamics after birth, we generated single-cell RNA-seq data of β cells from multiple postnatal time points and ordered cells based on transcriptional similarity using a new analytical tool. This analysis captured signatures of immature, proliferative β cells and established high expression of amino acid metabolic, mitochondrial, and Srf/Jun/Fos transcription factor genes as their hallmark feature. Experimental validation revealed high metabolic activity in immature β cells and a role for reactive oxygen species and Srf/Jun/Fos transcription factors in driving postnatal β cell proliferation and mass expansion. Our work provides the first high-resolution molecular characterization of state changes in postnatal β cells and paves the way for the identification of novel therapeutic targets to stimulate β cell regeneration. Copyright © 2017 Elsevier Inc. All rights reserved.

Analysis of antigen-specific B-cell memory directly ex vivo.

PubMed

McHeyzer-Williams, Louise J; McHeyzer-Williams, Michael G

2004-01-01

Helper T-cell-regulated B-cell memory develops in response to initial antigen priming as a cellular product of the germinal center (GC) reaction. On antigen recall, memory response precursors expand rapidly with exaggerated differentiation into plasma cells to produce the high-titer, high-affinity antibody(Ab) that typifies the memory B-cell response in vivo. We have devised a high-resolution flow cytometric strategy to quantify the emergence and maintenance of antigen-specific memory B cells directly ex vivo. Extended cell surface phenotype establishes a level of cellular diversity not previously appreciated for the memory B-cell compartment. Using an "exclusion transfer" strategy, we ascertain the capacity of two distinct memory B-cell populations to transfer antigen-specific memory into naive adoptive hosts. Finally, we sequence expressed messenger ribonucleic acid (mRNA) from single cells within the population to estimate the level of somatic hypermutation as the best molecular indicator of B-cell memory. In this chapter, we describe the methods used in each of these four sections that serve to provide high-resolution quantification of antigen-specific B-cell memory responses directly ex vivo.

Expression, purification and crystallization of a lyssavirus matrix (M) protein

PubMed Central

Assenberg, René; Delmas, Olivier; Graham, Stephen C.; Verma, Anil; Berrow, Nick; Stuart, David I.; Owens, Raymond J.; Bourhy, Hervé; Grimes, Jonathan M.

2008-01-01

The matrix (M) proteins of lyssaviruses (family Rhabdoviridae) are crucial to viral morphogenesis as well as in modulating replication and transcription of the viral genome. To date, no high-resolution structural information has been obtained for full-length rhabdovirus M. Here, the cloning, expression and purification of the matrix proteins from three lyssaviruses, Lagos bat virus (LAG), Mokola virus and Thailand dog virus, are described. Crystals have been obtained for the full-length M protein from Lagos bat virus (LAG M). Successful crystallization depended on a number of factors, in particular the addition of an N-terminal SUMO fusion tag to increase protein solubility. Diffraction data have been recorded from crystals of native and selenomethionine-labelled LAG M to 2.75 and 3.0 Å resolution, respectively. Preliminary analysis indicates that these crystals belong to space group P6122 or P6522, with unit-cell parameters a = b = 56.9–57.2, c = 187.9–188.6 Å, consistent with the presence of one molecule per asymmetric unit, and structure determination is currently in progress. PMID:18391421

Fast evaluation of solid harmonic Gaussian integrals for local resolution-of-the-identity methods and range-separated hybrid functionals.

PubMed

Golze, Dorothea; Benedikter, Niels; Iannuzzi, Marcella; Wilhelm, Jan; Hutter, Jürg

2017-01-21

An integral scheme for the efficient evaluation of two-center integrals over contracted solid harmonic Gaussian functions is presented. Integral expressions are derived for local operators that depend on the position vector of one of the two Gaussian centers. These expressions are then used to derive the formula for three-index overlap integrals where two of the three Gaussians are located at the same center. The efficient evaluation of the latter is essential for local resolution-of-the-identity techniques that employ an overlap metric. We compare the performance of our integral scheme to the widely used Cartesian Gaussian-based method of Obara and Saika (OS). Non-local interaction potentials such as standard Coulomb, modified Coulomb, and Gaussian-type operators, which occur in range-separated hybrid functionals, are also included in the performance tests. The speed-up with respect to the OS scheme is up to three orders of magnitude for both integrals and their derivatives. In particular, our method is increasingly efficient for large angular momenta and highly contracted basis sets.

Fast evaluation of solid harmonic Gaussian integrals for local resolution-of-the-identity methods and range-separated hybrid functionals

NASA Astrophysics Data System (ADS)

Golze, Dorothea; Benedikter, Niels; Iannuzzi, Marcella; Wilhelm, Jan; Hutter, Jürg

2017-01-01

An integral scheme for the efficient evaluation of two-center integrals over contracted solid harmonic Gaussian functions is presented. Integral expressions are derived for local operators that depend on the position vector of one of the two Gaussian centers. These expressions are then used to derive the formula for three-index overlap integrals where two of the three Gaussians are located at the same center. The efficient evaluation of the latter is essential for local resolution-of-the-identity techniques that employ an overlap metric. We compare the performance of our integral scheme to the widely used Cartesian Gaussian-based method of Obara and Saika (OS). Non-local interaction potentials such as standard Coulomb, modified Coulomb, and Gaussian-type operators, which occur in range-separated hybrid functionals, are also included in the performance tests. The speed-up with respect to the OS scheme is up to three orders of magnitude for both integrals and their derivatives. In particular, our method is increasingly efficient for large angular momenta and highly contracted basis sets.

Crystallization and preliminary X-ray diffraction analysis of a high-affinity phosphate-binding protein endowed with phosphatase activity from Pseudomonas aeruginosa PAO1

PubMed Central

Djeghader, Ahmed; Gotthard, Guillaume; Suh, Andrew; Gonzalez, Daniel; Scott, Ken; Chabriere, Eric; Elias, Mikael

2013-01-01

In prokaryotes, phosphate starvation induces the expression of numerous phosphate-responsive genes, such as the pst operon including the high-affinity phosphate-binding protein (PBP or pstS) and alkaline phosphatases such as PhoA. This response increases the cellular inorganic phosphate import efficiency. Notably, some Pseudomonas species secrete, via a type-2 secretion system, a phosphate-binding protein dubbed LapA endowed with phosphatase activity. Here, the expression, purification, crystallization and X-ray data collection at 0.87 Å resolution of LapA are described. Combined with biochemical and enzymatic characterization, the structure of this intriguing phosphate-binding protein will help to elucidate the molecular origin of its phosphatase activity and to decipher its putative role in phosphate uptake. PMID:24100568

A stele-enriched gene regulatory network in the Arabidopsis root

PubMed Central

Brady, Siobhan M; Zhang, Lifang; Megraw, Molly; Martinez, Natalia J; Jiang, Eric; Yi, Charles S; Liu, Weilin; Zeng, Anna; Taylor-Teeples, Mallorie; Kim, Dahae; Ahnert, Sebastian; Ohler, Uwe; Ware, Doreen; Walhout, Albertha J M; Benfey, Philip N

2011-01-01

Tightly controlled gene expression is a hallmark of multicellular development and is accomplished by transcription factors (TFs) and microRNAs (miRNAs). Although many studies have focused on identifying downstream targets of these molecules, less is known about the factors that regulate their differential expression. We used data from high spatial resolution gene expression experiments and yeast one-hybrid (Y1H) and two-hybrid (Y2H) assays to delineate a subset of interactions occurring within a gene regulatory network (GRN) that determines tissue-specific TF and miRNA expression in plants. We find that upstream TFs are expressed in more diverse cell types than their targets and that promoters that are bound by a relatively large number of TFs correspond to key developmental regulators. The regulatory consequence of many TFs for their target was experimentally determined using genetic analysis. Remarkably, molecular phenotypes were identified for 65% of the TFs, but morphological phenotypes were associated with only 16%. This indicates that the GRN is robust, and that gene expression changes may be canalized or buffered. PMID:21245844

Progress toward heterologous expression of active G-protein-coupled receptors in Saccharomyces cerevisiae: Linking cellular stress response with translocation and trafficking

PubMed Central

O'Malley, Michelle A; Mancini, J Dominic; Young, Carissa L; McCusker, Emily C; Raden, David; Robinson, Anne S

2009-01-01

High-level expression of mammalian G-protein-coupled receptors (GPCRs) is a necessary step toward biophysical characterization and high-resolution structure determination. Even though many heterologous expression systems have been used to express mammalian GPCRs at high levels, many receptors are improperly trafficked or are inactive in these systems. En route to engineering a robust microbial host for GPCR expression, we have investigated the expression of 12 GPCRs in the yeast Saccharomyces cerevisiae, where all receptors are expressed at the mg/L scale. However, only the human adenosine A2a (hA2aR) receptor is active for ligand-binding and located primarily at the plasma membrane, whereas other tested GPCRs are mainly retained within the cell. Selective receptors associate with BiP, an ER-resident chaperone, and activated the unfolded protein response (UPR) pathway, which suggests that a pool of receptors may be folded incorrectly. Leader sequence cleavage of the expressed receptors was complete for the hA2aR, as expected, and partially cleaved for hA2bR, hCCR5R, and hD2LR. Ligand-binding assays conducted on the adenosine family (hA1R, hA2aR, hA2bR, and hA3R) of receptors show that hA2aR and hA2bR, the only adenosine receptors that demonstrate leader sequence processing, display activity. Taken together, these studies point to translocation as a critical limiting step in the production of active mammalian GPCRs in S. cerevisiae. PMID:19760666

Sort-Seq Approach to Engineering a Formaldehyde-Inducible Promoter for Dynamically Regulated Escherichia coli Growth on Methanol

PubMed Central

2017-01-01

Tight and tunable control of gene expression is a highly desirable goal in synthetic biology for constructing predictable gene circuits and achieving preferred phenotypes. Elucidating the sequence–function relationship of promoters is crucial for manipulating gene expression at the transcriptional level, particularly for inducible systems dependent on transcriptional regulators. Sort-seq methods employing fluorescence-activated cell sorting (FACS) and high-throughput sequencing allow for the quantitative analysis of sequence–function relationships in a robust and rapid way. Here we utilized a massively parallel sort-seq approach to analyze the formaldehyde-inducible Escherichia coli promoter (Pfrm) with single-nucleotide resolution. A library of mutated formaldehyde-inducible promoters was cloned upstream of gfp on a plasmid. The library was partitioned into bins via FACS on the basis of green fluorescent protein (GFP) expression level, and mutated promoters falling into each expression bin were identified with high-throughput sequencing. The resulting analysis identified two 19 base pair repressor binding sites, one upstream of the −35 RNA polymerase (RNAP) binding site and one overlapping with the −10 site, and assessed the relative importance of each position and base therein. Key mutations were identified for tuning expression levels and were used to engineer formaldehyde-inducible promoters with predictable activities. Engineered variants demonstrated up to 14-fold lower basal expression, 13-fold higher induced expression, and a 3.6-fold stronger response as indicated by relative dynamic range. Finally, an engineered formaldehyde-inducible promoter was employed to drive the expression of heterologous methanol assimilation genes and achieved increased biomass levels on methanol, a non-native substrate of E. coli. PMID:28463494

Systematic characterization of maturation time of fluorescent proteins in living cells

PubMed Central

Balleza, Enrique; Kim, J. Mark; Cluzel, Philippe

2017-01-01

Slow maturation time of fluorescent proteins limits accurate measurement of rapid gene expression dynamics and effectively reduces fluorescence signal in growing cells. We used high-precision time-lapse microscopy to characterize, at two different temperatures in E. coli, the maturation kinetics of 50 FPs that span the visible spectrum. We identified fast-maturing FPs that yield the highest signal-to-noise ratio and temporal resolution in individual growing cells. PMID:29320486

Estimation of a Constant False Alarm Rate Processing Loss for a High-Resolution Maritime Radar System

DTIC Science & Technology

2008-08-01

a sample with clutter of mean level y0 and noise of variance σ 2, with a threshold CACA zt β= . Using the results presented in [15, 16, 23], it can...level y0 and noise of variance σ 2, with a threshold CACA zt β= . Using (3.107) and (3.98), the expression for the expected Pd of a Swerling 2 target can

Classification and Compression of Multi-Resolution Vectors: A Tree Structured Vector Quantizer Approach

DTIC Science & Technology

2002-01-01

their expression profile and for classification of cells into tumerous and non- tumerous classes. Then we will present a parallel tree method for... cancerous cells. We will use the same dataset and use tree structured classifiers with multi-resolution analysis for classifying cancerous from non- cancerous ...cells. We have the expressions of 4096 genes from 98 different cell types. Of these 98, 72 are cancerous while 26 are non- cancerous . We are interested

Resolvin E1-induced intestinal alkaline phosphatase promotes resolution of inflammation through LPS detoxification

PubMed Central

Campbell, Eric L.; MacManus, Christopher F.; Kominsky, Douglas J.; Keely, Simon; Glover, Louise E.; Bowers, Brittelle E.; Scully, Melanie; Bruyninckx, Walter J.; Colgan, Sean P.

2010-01-01

Resolvin-E1 (RvE1) has been demonstrated to promote inflammatory resolution in numerous disease models. Given the importance of epithelial cells to coordination of mucosal inflammation, we hypothesized that RvE1 elicits an epithelial resolution signature. Initial studies revealed that the RvE1-receptor (ChemR23) is expressed on intestinal epithelial cells (IECs) and that microarray profiling of cells exposed to RvE1 revealed regulation of inflammatory response gene expression. Notably, RvE1 induced intestinal alkaline phosphatase (ALPI) expression and significantly enhanced epithelial ALPI enzyme activity. One role recently attributed to ALPI is the detoxification of bacterial LPS. In our studies, RvE1-exposed epithelia detoxified LPS (assessed by attenuation of NF-κB signaling). Furthermore, in epithelial-bacterial interaction assays, we determined that ALPI retarded the growth of Escherichia coli. To define these features in vivo, we used a murine dextran sulfate sodium (DSS) model of colitis. Compared with vehicle controls, administration of RvE1 resulted in significant improvement of disease activity indices (e.g., body weight, colon length) concomitant with increased ALPI expression in the intestinal epithelium. Moreover, inhibition of ALPI activity resulted in increased severity of colitis in DSS-treated animals and partially abrogated the protective influence of RvE1. Together, these data implicate a previously unappreciated role for ALPI in RvE1-mediated inflammatory resolution. PMID:20660763

Resolvin E1-induced intestinal alkaline phosphatase promotes resolution of inflammation through LPS detoxification.

PubMed

Campbell, Eric L; MacManus, Christopher F; Kominsky, Douglas J; Keely, Simon; Glover, Louise E; Bowers, Brittelle E; Scully, Melanie; Bruyninckx, Walter J; Colgan, Sean P

2010-08-10

Resolvin-E1 (RvE1) has been demonstrated to promote inflammatory resolution in numerous disease models. Given the importance of epithelial cells to coordination of mucosal inflammation, we hypothesized that RvE1 elicits an epithelial resolution signature. Initial studies revealed that the RvE1-receptor (ChemR23) is expressed on intestinal epithelial cells (IECs) and that microarray profiling of cells exposed to RvE1 revealed regulation of inflammatory response gene expression. Notably, RvE1 induced intestinal alkaline phosphatase (ALPI) expression and significantly enhanced epithelial ALPI enzyme activity. One role recently attributed to ALPI is the detoxification of bacterial LPS. In our studies, RvE1-exposed epithelia detoxified LPS (assessed by attenuation of NF-kappaB signaling). Furthermore, in epithelial-bacterial interaction assays, we determined that ALPI retarded the growth of Escherichia coli. To define these features in vivo, we used a murine dextran sulfate sodium (DSS) model of colitis. Compared with vehicle controls, administration of RvE1 resulted in significant improvement of disease activity indices (e.g., body weight, colon length) concomitant with increased ALPI expression in the intestinal epithelium. Moreover, inhibition of ALPI activity resulted in increased severity of colitis in DSS-treated animals and partially abrogated the protective influence of RvE1. Together, these data implicate a previously unappreciated role for ALPI in RvE1-mediated inflammatory resolution.

High-resolution copy number variation analysis of schizophrenia in Japan.

PubMed

Kushima, I; Aleksic, B; Nakatochi, M; Shimamura, T; Shiino, T; Yoshimi, A; Kimura, H; Takasaki, Y; Wang, C; Xing, J; Ishizuka, K; Oya-Ito, T; Nakamura, Y; Arioka, Y; Maeda, T; Yamamoto, M; Yoshida, M; Noma, H; Hamada, S; Morikawa, M; Uno, Y; Okada, T; Iidaka, T; Iritani, S; Yamamoto, T; Miyashita, M; Kobori, A; Arai, M; Itokawa, M; Cheng, M-C; Chuang, Y-A; Chen, C-H; Suzuki, M; Takahashi, T; Hashimoto, R; Yamamori, H; Yasuda, Y; Watanabe, Y; Nunokawa, A; Someya, T; Ikeda, M; Toyota, T; Yoshikawa, T; Numata, S; Ohmori, T; Kunimoto, S; Mori, D; Iwata, N; Ozaki, N

2017-03-01

Recent schizophrenia (SCZ) studies have reported an increased burden of de novo copy number variants (CNVs) and identified specific high-risk CNVs, although with variable phenotype expressivity. However, the pathogenesis of SCZ has not been fully elucidated. Using array comparative genomic hybridization, we performed a high-resolution genome-wide CNV analysis on a mainly (92%) Japanese population (1699 SCZ cases and 824 controls) and identified 7066 rare CNVs, 70.0% of which were small (<100 kb). Clinically significant CNVs were significantly more frequent in cases than in controls (odds ratio=3.04, P=9.3 × 10 -9 , 9.0% of cases). We confirmed a significant association of X-chromosome aneuploidies with SCZ and identified 11 de novo CNVs (e.g., MBD5 deletion) in cases. In patients with clinically significant CNVs, 41.7% had a history of congenital/developmental phenotypes, and the rate of treatment resistance was significantly higher (odds ratio=2.79, P=0.0036). We found more severe clinical manifestations in patients with two clinically significant CNVs. Gene set analysis replicated previous findings (e.g., synapse, calcium signaling) and identified novel biological pathways including oxidative stress response, genomic integrity, kinase and small GTPase signaling. Furthermore, involvement of multiple SCZ candidate genes and biological pathways in the pathogenesis of SCZ was suggested in established SCZ-associated CNV loci. Our study shows the high genetic heterogeneity of SCZ and its clinical features and raises the possibility that genomic instability is involved in its pathogenesis, which may be related to the increased burden of de novo CNVs and variable expressivity of CNVs.

Ultrastructural localisation of protein interactions using conditionally stable nanobodies.

PubMed

Ariotti, Nicholas; Rae, James; Giles, Nichole; Martel, Nick; Sierecki, Emma; Gambin, Yann; Hall, Thomas E; Parton, Robert G

2018-04-01

We describe the development and application of a suite of modular tools for high-resolution detection of proteins and intracellular protein complexes by electron microscopy (EM). Conditionally stable GFP- and mCherry-binding nanobodies (termed csGBP and csChBP, respectively) are characterized using a cell-free expression and analysis system and subsequently fused to an ascorbate peroxidase (APEX) enzyme. Expression of these cassettes alongside fluorescently labelled proteins results in recruitment and stabilisation of APEX, whereas unbound APEX nanobodies are efficiently degraded by the proteasome. This greatly simplifies correlative analyses, enables detection of less-abundant proteins, and eliminates the need to balance expression levels between fluorescently labelled and APEX nanobody proteins. Furthermore, we demonstrate the application of this system to bimolecular complementation ('EM split-fluorescent protein'), for localisation of protein-protein interactions at the ultrastructural level.

Ultrastructural localisation of protein interactions using conditionally stable nanobodies

PubMed Central

Ariotti, Nicholas; Rae, James; Giles, Nichole; Martel, Nick; Sierecki, Emma; Gambin, Yann; Parton, Robert G.

2018-01-01

We describe the development and application of a suite of modular tools for high-resolution detection of proteins and intracellular protein complexes by electron microscopy (EM). Conditionally stable GFP- and mCherry-binding nanobodies (termed csGBP and csChBP, respectively) are characterized using a cell-free expression and analysis system and subsequently fused to an ascorbate peroxidase (APEX) enzyme. Expression of these cassettes alongside fluorescently labelled proteins results in recruitment and stabilisation of APEX, whereas unbound APEX nanobodies are efficiently degraded by the proteasome. This greatly simplifies correlative analyses, enables detection of less-abundant proteins, and eliminates the need to balance expression levels between fluorescently labelled and APEX nanobody proteins. Furthermore, we demonstrate the application of this system to bimolecular complementation (‘EM split-fluorescent protein’), for localisation of protein–protein interactions at the ultrastructural level. PMID:29621251

Gene networks and the evolution of plant morphology.

PubMed

Das Gupta, Mainak; Tsiantis, Miltos

2018-06-06

Elaboration of morphology depends on the precise orchestration of gene expression by key regulatory genes. The hierarchy and relationship among the participating genes is commonly known as gene regulatory network (GRN). Therefore, the evolution of morphology ultimately occurs by the rewiring of gene network structures or by the co-option of gene networks to novel domains. The availability of high-resolution expression data combined with powerful statistical tools have opened up new avenues to formulate and test hypotheses on how diverse gene networks influence trait development and diversity. Here we summarize recent studies based on both big-data and genetics approaches to understand the evolution of plant form and physiology. We also discuss recent genome-wide investigations on how studying open-chromatin regions may help study the evolution of gene expression patterns. Copyright © 2018. Published by Elsevier Ltd.

A high-resolution structure of the DNA-binding domain of AhrC, the arginine repressor/activator protein from Bacillus subtilis

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

Garnett, James A.; Baumberg, Simon; Stockley, Peter G.

2007-11-01

The structure of the winged helix–turn–helix DNA-binding domain of AhrC has been determined at 1.0 Å resolution. The largely hydrophobic β-wing shows high B factors and may mediate the dimer interface in operator complexes. In Bacillus subtilis the concentration of l-arginine is controlled by the transcriptional regulator AhrC, which interacts with 18 bp DNA operator sites called ARG boxes in the promoters of arginine biosynthetic and catabolic operons. AhrC is a 100 kDa homohexamer, with each subunit having two domains. The C-terminal domains form the core, mediating intersubunit interactions and binding of the co-repressor l-arginine, whilst the N-terminal domains containmore » a winged helix–turn–helix DNA-binding motif and are arranged around the periphery. The N-terminal domain of AhrC has been expressed, purified and characterized and it has been shown that the fragment still binds DNA operators as a recombinant monomer. The DNA-binding domain has also been crystallized and the crystal structure refined to 1.0 Å resolution is presented.« less

Note: Large active area solid state photon counter with 20 ps timing resolution and 60 fs detection delay stability

NASA Astrophysics Data System (ADS)

Prochazka, Ivan; Kodet, Jan; Eckl, Johann; Blazej, Josef

2017-10-01

We are reporting on the design, construction, and performance of a photon counting detector system, which is based on single photon avalanche diode detector technology. This photon counting device has been optimized for very high timing resolution and stability of its detection delay. The foreseen application of this detector is laser ranging of space objects, laser time transfer ground to space and fundamental metrology. The single photon avalanche diode structure, manufactured on silicon using K14 technology, is used as a sensor. The active area of the sensor is circular with 200 μm diameter. Its photon detection probability exceeds 40% in the wavelength range spanning from 500 to 800 nm. The sensor is operated in active quenching and gating mode. A new control circuit was optimized to maintain high timing resolution and detection delay stability. In connection to this circuit, timing resolution of the detector is reaching 20 ps FWHM. In addition, the temperature change of the detection delay is as low as 70 fs/K. As a result, the detection delay stability of the device is exceptional: expressed in the form of time deviation, detection delay stability of better than 60 fs has been achieved. Considering the large active area aperture of the detector, this is, to our knowledge, the best timing performance reported for a solid state photon counting detector so far.

Local and Systemic CD4+ T Cell Exhaustion Reverses with Clinical Resolution of Pulmonary Sarcoidosis

PubMed Central

Hawkins, Charlene; Shaginurova, Guzel; Shelton, D. Auriel; Herazo-Maya, Jose D.; Oswald-Richter, Kyra A.; Young, Anjuli; Celada, Lindsay J.; Kaminski, Naftali; Sevin, Carla

2017-01-01

Investigation of the Th1 immune response in sarcoidosis CD4+ T cells has revealed reduced proliferative capacity and cytokine expression upon TCR stimulation. In other disease models, such cellular dysfunction has been associated with a step-wise, progressive loss of T cell function that results from chronic antigenic stimulation. T cell exhaustion is defined by decreased cytokine production upon TCR activation, decreased proliferation, increased expression of inhibitory cell surface receptors, and increased susceptibility to apoptosis. We characterized sarcoidosis CD4+ T cell immune function in systemic and local environments among subjects undergoing disease progression compared to those experiencing disease resolution. Spontaneous and TCR-stimulated Th1 cytokine expression and proliferation assays were performed in 53 sarcoidosis subjects and 30 healthy controls. PD-1 expression and apoptosis were assessed by flow cytometry. Compared to healthy controls, sarcoidosis CD4+ T cells demonstrated reductions in Th1 cytokine expression, proliferative capacity (p < 0.05), enhanced apoptosis (p < 0.01), and increased PD-1 expression (p < 0.001). BAL-derived CD4+ T cells also demonstrated multiple facets of T cell exhaustion (p < 0.05). Reversal of CD4+ T cell exhaustion was observed in subjects undergoing spontaneous resolution (p < 0.05). Sarcoidosis CD4+ T cells exhibit loss of cellular function during progressive disease that follows the archetype of T cell exhaustion. PMID:29234685

In vivo Magnetic Resonance Imaging of Tumor Protease Activity

PubMed Central

Haris, Mohammad; Singh, Anup; Mohammed, Imran; Ittyerah, Ranjit; Nath, Kavindra; Nanga, Ravi Prakash Reddy; Debrosse, Catherine; Kogan, Feliks; Cai, Kejia; Poptani, Harish; Reddy, Damodar; Hariharan, Hari; Reddy, Ravinder

2014-01-01

Increased expression of cathepsins has diagnostic as well as prognostic value in several types of cancer. Here, we demonstrate a novel magnetic resonance imaging (MRI) method, which uses poly-L-glutamate (PLG) as an MRI probe to map cathepsin expression in vivo, in a rat brain tumor model. This noninvasive, high-resolution and non-radioactive method exploits the differences in the CEST signals of PLG in the native form and cathepsin mediated cleaved form. The method was validated in phantoms with known physiological concentrations, in tumor cells and in an animal model of brain tumor along with immunohistochemical analysis. Potential applications in tumor diagnosis and evaluation of therapeutic response are outlined. PMID:25124082

Application of Strep-Tactin XT for affinity purification of Twin-Strep-tagged CB2, a G protein-coupled cannabinoid receptor.

PubMed

Yeliseev, Alexei; Zoubak, Lioudmila; Schmidt, Thomas G M

2017-03-01

Human cannabinoid receptor CB 2 belongs to the class A of G protein-coupled receptor (GPCR). CB 2 is predominantly expressed in membranes of cells of immune origin and is implicated in regulation of metabolic pathways of inflammation, neurodegenerative disorders and pain sensing. High resolution structural studies of CB 2 require milligram quantities of purified, structurally intact protein. While we previously reported on the methodology for expression of the recombinant CB 2 and its stabilization in a functional state, here we describe an efficient protocol for purification of this protein using the Twin-Strep-tag/Strep-Tactin XT system. To improve the affinity of interaction of the recombinant CB 2 with the resin, the double repeat of the Strep-tag (a sequence of eight amino acids WSHPQFEK), named the Twin-Strep-tag was attached either to the N- or C-terminus of CB 2 via a short linker, and the recombinant protein was expressed in cytoplasmic membranes of E. coli as a fusion with the N-terminal maltose binding protein (MBP). The CB 2 was isolated at high purity from dilute solutions containing high concentrations of detergents, glycerol and salts, by capturing onto the Strep-Tactin XT resin, and was eluted from the resin under mild conditions upon addition of biotin. Surface plasmon resonance studies performed on the purified protein demonstrate the high affinity of interaction between the Twin-Strep-tag fused to the CB 2 and Strep-Tactin XT with an estimated Kd in the low nanomolar range. The affinity of binding did not vary significantly in response to the position of the tag at either N- or C-termini of the fusion. The binding capacity of the resin was several-fold higher for the tag located at the N-terminus of the protein as opposed to the C-terminus- or middle of the fusion. The variation in the length of the linker between the double repeats of the Strep-tag from 6 to 12 amino acid residues did not significantly affect the binding. The novel purification protocol reported here enables efficient isolation of a recombinant GPCR expressed at low titers in host cells. This procedure is suitable for preparation of milligram quantities of stable isotope-labelled receptor for high-resolution NMR studies. Published by Elsevier Inc.

Coupled Transcriptome and Proteome Analysis of Human Lymphotropic Tumor Viruses: Insights on the Detection and Discovery of Viral Genes

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

Dresang, Lindsay R.; Teuton, Jeremy R.; Feng, Huichen

Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV) are related human tumor viruses that cause primary effusion lymphomas (PEL) and Burkitt's lymphomas (BL), respectively. Viral genes expressed in naturally-infected cancer cells contribute to disease pathogenesis; knowing which viral genes are expressed is critical in understanding how these viruses cause cancer. To evaluate the expression of viral genes, we used high-resolution separation and mass spectrometry coupled with custom tiling arrays to align the viral proteomes and transcriptomes of three PEL and two BL cell lines under latent and lytic culture conditions. Results The majority of viral genes were efficiently detected atmore » the transcript and/or protein level on manipulating the viral life cycle. Overall the correlation of expressed viral proteins and transcripts was highly complementary in both validating and providing orthogonal data with latent/lytic viral gene expression. Our approach also identified novel viral genes in both KSHV and EBV, and extends viral genome annotation. Several previously uncharacterized genes were validated at both transcript and protein levels. Conclusions This systems biology approach coupling proteome and transcriptome measurements provides a comprehensive view of viral gene expression that could not have been attained using each methodology independently. Detection of viral proteins in combination with viral transcripts is a potentially powerful method for establishing virus-disease relationships.« less

Detecting Circular RNAs by RNA Fluorescence In Situ Hybridization.

PubMed

Zirkel, Anne; Papantonis, Argyris

2018-01-01

Fluorescence in situ hybridization (FISH) coupled to high-resolution microscopy is a powerful method for analyzing the subcellular localization of RNA. However, the detection of circular RNAs (circRNAs) using microscopy is challenging because the only feature of a circRNA that can be used for the probe design is its junction. Circular RNAs are expressed at varying levels, and for their efficient monitoring by FISH, background fluorescence levels need to be kept low. Here, we describe a FISH protocol coupled to high-precision localizations using a single fluorescently labeled probe spanning the circRNA junction; this allows circRNA detection in mammalian cells with high signal-to-noise ratios.

Soil erodibility in Europe: a high-resolution dataset based on LUCAS.

PubMed

Panagos, Panos; Meusburger, Katrin; Ballabio, Cristiano; Borrelli, Pasqualle; Alewell, Christine

2014-05-01

The greatest obstacle to soil erosion modelling at larger spatial scales is the lack of data on soil characteristics. One key parameter for modelling soil erosion is the soil erodibility, expressed as the K-factor in the widely used soil erosion model, the Universal Soil Loss Equation (USLE) and its revised version (RUSLE). The K-factor, which expresses the susceptibility of a soil to erode, is related to soil properties such as organic matter content, soil texture, soil structure and permeability. With the Land Use/Cover Area frame Survey (LUCAS) soil survey in 2009 a pan-European soil dataset is available for the first time, consisting of around 20,000 points across 25 Member States of the European Union. The aim of this study is the generation of a harmonised high-resolution soil erodibility map (with a grid cell size of 500 m) for the 25 EU Member States. Soil erodibility was calculated for the LUCAS survey points using the nomograph of Wischmeier and Smith (1978). A Cubist regression model was applied to correlate spatial data such as latitude, longitude, remotely sensed and terrain features in order to develop a high-resolution soil erodibility map. The mean K-factor for Europe was estimated at 0.032 thahha(-1)MJ(-1)mm(-1) with a standard deviation of 0.009 thahha(-1)MJ(-1)mm(-1). The yielded soil erodibility dataset compared well with the published local and regional soil erodibility data. However, the incorporation of the protective effect of surface stone cover, which is usually not considered for the soil erodibility calculations, resulted in an average 15% decrease of the K-factor. The exclusion of this effect in K-factor calculations is likely to result in an overestimation of soil erosion, particularly for the Mediterranean countries, where highest percentages of surface stone cover were observed. Copyright © 2014. Published by Elsevier B.V.

Multi-temporal database of High Resolution Stereo Camera (HRSC) images - Alpha version

NASA Astrophysics Data System (ADS)

Erkeling, G.; Luesebrink, D.; Hiesinger, H.; Reiss, D.; Jaumann, R.

2014-04-01

Image data transmitted to Earth by Martian spacecraft since the 1970s, for example by Mariner and Viking, Mars Global Surveyor (MGS), Mars Express (MEx) and the Mars Reconnaissance Orbiter (MRO) showed, that the surface of Mars has changed dramatically and actually is continually changing [e.g., 1-8]. The changes are attributed to a large variety of atmospherical, geological and morphological processes, including eolian processes [9,10], mass wasting processes [11], changes of the polar caps [12] and impact cratering processes [13]. In addition, comparisons between Mariner, Viking and Mars Global Surveyor images suggest that more than one third of the Martian surface has brightened or darkened by at least 10% [6]. Albedo changes can have effects on the global heat balance and the circulation of winds, which can result in further surface changes [14-15]. The High Resolution Stereo Camera (HRSC) [16,17] on board Mars Express (MEx) covers large areas at high resolution and is therefore suited to detect the frequency, extent and origin of Martian surface changes. Since 2003 HRSC acquires highresolution images of the Martian surface and contributes to Martian research, with focus on the surface morphology, the geology and mineralogy, the role of liquid water on the surface and in the atmosphere, on volcanism, as well as on the proposed climate change throughout the Martian history and has improved our understanding of the evolution of Mars significantly [18-21]. The HRSC data are available at ESA's Planetary Science Archive (PSA) as well as through the NASA Planetary Data System (PDS). Both data platforms are frequently used by the scientific community and provide additional software and environments to further generate map-projected and geometrically calibrated HRSC data. However, while previews of the images are available, there is no possibility to quickly and conveniently see the spatial and temporal availability of HRSC images in a specific region, which is important to detect the surface changes that occurred between two or more images.

Systems biology of embryonic development: Prospects for a complete understanding of the Caenorhabditis elegans embryo.

PubMed

Murray, John Isaac

2018-05-01

The convergence of developmental biology and modern genomics tools brings the potential for a comprehensive understanding of developmental systems. This is especially true for the Caenorhabditis elegans embryo because its small size, invariant developmental lineage, and powerful genetic and genomic tools provide the prospect of a cellular resolution understanding of messenger RNA (mRNA) expression and regulation across the organism. We describe here how a systems biology framework might allow large-scale determination of the embryonic regulatory relationships encoded in the C. elegans genome. This framework consists of two broad steps: (a) defining the "parts list"-all genes expressed in all cells at each time during development and (b) iterative steps of computational modeling and refinement of these models by experimental perturbation. Substantial progress has been made towards defining the parts list through imaging methods such as large-scale green fluorescent protein (GFP) reporter analysis. Imaging results are now being augmented by high-resolution transcriptome methods such as single-cell RNA sequencing, and it is likely the complete expression patterns of all genes across the embryo will be known within the next few years. In contrast, the modeling and perturbation experiments performed so far have focused largely on individual cell types or genes, and improved methods will be needed to expand them to the full genome and organism. This emerging comprehensive map of embryonic expression and regulatory function will provide a powerful resource for developmental biologists, and would also allow scientists to ask questions not accessible without a comprehensive picture. This article is categorized under: Invertebrate Organogenesis > Worms Technologies > Analysis of the Transcriptome Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics. © 2018 Wiley Periodicals, Inc.

Functional imaging of hippocampal place cells at cellular resolution during virtual navigation

PubMed Central

Dombeck, Daniel A.; Harvey, Christopher D.; Tian, Lin; Looger, Loren L.; Tank, David W.

2010-01-01

Spatial navigation is a widely employed behavior in rodent studies of neuronal circuits underlying cognition, learning and memory. In vivo microscopy combined with genetically-encoded indicators provides important new tools to study neuronal circuits, but has been technically difficult to apply during navigation. We describe methods to image the activity of hippocampal CA1 neurons with sub-cellular resolution in behaving mice. Neurons expressing the genetically encoded calcium indicator GCaMP3 were imaged through a chronic hippocampal window. Head-fixed mice performed spatial behaviors within a setup combining a virtual reality system and a custom built two-photon microscope. Populations of place cells were optically identified, and the correlation between the location of their place fields in the virtual environment and their anatomical location in the local circuit was measured. The combination of virtual reality and high-resolution functional imaging should allow for a new generation of studies to probe neuronal circuit dynamics during behavior. PMID:20890294

Gene expression profiling in the early phases of DMD: a constant molecular signature characterizes DMD muscle from early postnatal life throughout disease progression.

PubMed

Pescatori, Mario; Broccolini, Aldobrando; Minetti, Carlo; Bertini, Enrico; Bruno, Claudio; D'amico, Adele; Bernardini, Camilla; Mirabella, Massimiliano; Silvestri, Gabriella; Giglio, Vincenzo; Modoni, Anna; Pedemonte, Marina; Tasca, Giorgio; Galluzzi, Giuliana; Mercuri, Eugenio; Tonali, Pietro A; Ricci, Enzo

2007-04-01

Genome-wide gene expression profiling of skeletal muscle from Duchenne muscular dystrophy (DMD) patients has been used to describe muscle tissue alterations in DMD children older than 5 years. By studying the expression profile of 19 patients younger than 2 years, we describe with high resolution the gene expression signature that characterizes DMD muscle during the initial or "presymptomatic" phase of the disease. We show that in the first 2 years of the disease, DMD muscle is already set to express a distinctive gene expression pattern considerably different from the one expressed by normal, age-matched muscle. This "dystrophic" molecular signature is characterized by a coordinate induction of genes involved in the inflammatory response, extracellular matrix (ECM) remodeling and muscle regeneration, and the reduced transcription of those involved in energy metabolism. Despite the lower degree of muscle dysfunction experienced, our younger patients showed abnormal expression of most of the genes reported as differentially expressed in more advanced stages of the disease. By analyzing our patients as a time series, we provide evidence that some genes, including members of three pathways involved in morphogenetic signaling-Wnt, Notch, and BMP-are progressively induced or repressed in the natural history of DMD.

Overexpression of MutSα Complex Proteins Predicts Poor Prognosis in Oral Squamous Cell Carcinoma.

PubMed

Wagner, Vivian Petersen; Webber, Liana Preto; Salvadori, Gabriela; Meurer, Luise; Fonseca, Felipe Paiva; Castilho, Rogério Moraes; Squarize, Cristiane Helena; Vargas, Pablo Agustin; Martins, Manoela Domingues

2016-05-01

The DNA mismatch repair (MMR) system is responsible for the detection and correction of errors created during DNA replication, thereby avoiding the incorporation of mutations in dividing cells. The prognostic value of alterations in MMR system has not previously been analyzed in oral squamous cell carcinoma (OSCC).The study comprised 115 cases of OSCC diagnosed between 1996 and 2010. The specimens collected were constructed into tissue microarray blocks. Immunohistochemical staining for MutSα complex proteins hMSH2 and hMSH6 was performed. The slides were subsequently scanned into high-resolution images, and nuclear staining of hMSH2 and hMSH6 was analyzed using the Nuclear V9 algorithm. Univariable and multivariable Cox proportional hazard regression models were performed to evaluate the prognostic value of hMSH2 and hMSH6 in OSCC.All cases in the present cohort were positive for hMSH2 and hMSH6 and a direct correlation was found between the expression of the proteins (P < 0.05). The mean number of positive cells for hMSH2 and hMSH6 was 64.44 ± 15.21 and 31.46 ± 22.38, respectively. These values were used as cutoff points to determine high protein expression. Cases with high expression of both proteins simultaneously were classified as having high MutSα complex expression. In the multivariable analysis, high expression of the MutSα complex was an independent prognostic factor for poor overall survival (hazard ratio: 2.75, P = 0.02).This study provides a first insight of the prognostic value of alterations in MMR system in OSCC. We found that MutSα complex may constitute a molecular marker for the poor prognosis of OSCC.

Tunable diode-laser absorption measurements of methane at elevated temperatures

NASA Astrophysics Data System (ADS)

Nagali, V.; Chou, S. I.; Baer, D. S.; Hanson, R. K.; Segall, J.

1996-07-01

A diode-laser sensor system based on absorption spectroscopy techniques has been developed to monitor CH4 nonintrusively in high-temperature environments. Fundamental spectroscopic parameters, including the line strengths of the transitions in the R(6) manifold of the 2 nu 3 band near 1.646 mu m, have been determined from high-resolution absorption measurements in a heated static cell. In addition, a corrected expression for the CH 4 partition function has been validated experimentally over the temperature range from 400 to 915 K. Potential applications of the diode-laser sensor system include process control, combustion measurements, and atmospheric monitoring.

Cell Fate Decision as High-Dimensional Critical State Transition

PubMed Central

Zhou, Joseph; Castaño, Ivan G.; Leong-Quong, Rebecca Y. Y.; Chang, Hannah; Trachana, Kalliopi; Giuliani, Alessandro; Huang, Sui

2016-01-01

Cell fate choice and commitment of multipotent progenitor cells to a differentiated lineage requires broad changes of their gene expression profile. But how progenitor cells overcome the stability of their gene expression configuration (attractor) to exit the attractor in one direction remains elusive. Here we show that commitment of blood progenitor cells to the erythroid or myeloid lineage is preceded by the destabilization of their high-dimensional attractor state, such that differentiating cells undergo a critical state transition. Single-cell resolution analysis of gene expression in populations of differentiating cells affords a new quantitative index for predicting critical transitions in a high-dimensional state space based on decrease of correlation between cells and concomitant increase of correlation between genes as cells approach a tipping point. The detection of “rebellious cells” that enter the fate opposite to the one intended corroborates the model of preceding destabilization of a progenitor attractor. Thus, early warning signals associated with critical transitions can be detected in statistical ensembles of high-dimensional systems, offering a formal theory-based approach for analyzing single-cell molecular profiles that goes beyond current computational pattern recognition, does not require knowledge of specific pathways, and could be used to predict impending major shifts in development and disease. PMID:28027308

Imaging Molecular Signatures of Breast Cancer With X-ray Activated Nano-Phosphors

DTIC Science & Technology

2011-09-01

high resolution with a decrease in X-ray dose to healthy tissue. For the first-year training goals, this grant has provided for extensive study in...europium (red) were studied . The light emission was imaged in a clinical X-ray scanner with a cooled CCD camera and a spectrophotometer; dose...Indeed, in a preliminary study , these phosphor were targeted to the Folate receptor (commonly expressed in breast cancer), and uptaken by live cells

Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum.

PubMed

Rosengarten, Rafael David; Santhanam, Balaji; Fuller, Danny; Katoh-Kurasawa, Mariko; Loomis, William F; Zupan, Blaz; Shaulsky, Gad

2015-04-13

Development of the soil amoeba Dictyostelium discoideum is triggered by starvation. When placed on a solid substrate, the starving solitary amoebae cease growth, communicate via extracellular cAMP, aggregate by tens of thousands and develop into multicellular organisms. Early phases of the developmental program are often studied in cells starved in suspension while cAMP is provided exogenously. Previous studies revealed massive shifts in the transcriptome under both developmental conditions and a close relationship between gene expression and morphogenesis, but were limited by the sampling frequency and the resolution of the methods. Here, we combine the superior depth and specificity of RNA-seq-based analysis of mRNA abundance with high frequency sampling during filter development and cAMP pulsing in suspension. We found that the developmental transcriptome exhibits mostly gradual changes interspersed by a few instances of large shifts. For each time point we treated the entire transcriptome as single phenotype, and were able to characterize development as groups of similar time points separated by gaps. The grouped time points represented gradual changes in mRNA abundance, or molecular phenotype, and the gaps represented times during which many genes are differentially expressed rapidly, and thus the phenotype changes dramatically. Comparing developmental experiments revealed that gene expression in filter developed cells lagged behind those treated with exogenous cAMP in suspension. The high sampling frequency revealed many genes whose regulation is reproducibly more complex than indicated by previous studies. Gene Ontology enrichment analysis suggested that the transition to multicellularity coincided with rapid accumulation of transcripts associated with DNA processes and mitosis. Later development included the up-regulation of organic signaling molecules and co-factor biosynthesis. Our analysis also demonstrated a high level of synchrony among the developing structures throughout development. Our data describe D. discoideum development as a series of coordinated cellular and multicellular activities. Coordination occurred within fields of aggregating cells and among multicellular bodies, such as mounds or migratory slugs that experience both cell-cell contact and various soluble signaling regimes. These time courses, sampled at the highest temporal resolution to date in this system, provide a comprehensive resource for studies of developmental gene expression.

High-resolution telomere fluorescence in situ hybridization reveals intriguing anomalies in germ cell tumors.

PubMed

Shekhani, Mohammed Talha; Barber, John R; Bezerra, Stephania M; Heaphy, Christopher M; Gonzalez Roibon, Nilda Diana; Taheri, Diana; Reis, Leonardo O; Guner, Gunes; Joshu, Corinne E; Netto, George J; Meeker, Alan K

2016-08-01

Testicular germ cell tumor (TGCT) is the most common malignancy of young men. Most patients are completely cured, which distinguishes these from most other malignancies. Orchiectomy specimens (n=76) were evaluated using high-resolution (single-cell discriminative) telomere-specific fluorescence in situ hybridization (FISH) with simultaneous Oct4 immunofluorescence to describe telomere length phenotype in TGCT neoplastic cells. For the first time, the TGCT precursor lesion, germ cell neoplasia in situ (GCNIS) is also evaluated in depth. The intensity of the signals from cancerous cells was compared to the same patient's reference cells-namely, healthy germ cells (defined as "medium" length) and interstitial/somatic cells (defined as "short" telomere length). We observed short telomeres in most GCNIS and pure seminomas (P=.006 and P=.0005, respectively). In contrast, nonseminomas displayed longer telomeres. Lesion-specific telomere lengths were documented in mixed tumor cases. Embryonal carcinoma (EC) demonstrated the longest telomeres. A fraction of EC displays the telomerase-independent alternative lengthening of telomeres (ALT) phenotype (24% of cases). Loss of ATRX or DAXX nuclear expression was strongly associated with ALT; however, nuclear expression of both proteins was retained in half of ALT-positive ECs. The particular distribution of telomere lengths among TGCT and GCNIS precursors implicate telomeres anomalies in pathogenesis. These results may advise management decisions as well. Copyright © 2016. Published by Elsevier Inc.

Spatially resolved proteome mapping of laser capture microdissected tissue with automated sample transfer to nanodroplets.

PubMed

Zhu, Ying; Dou, Maowei; Piehowski, Paul D; Liang, Yiran; Wang, Fangjun; Chu, Rosalie K; Chrisler, Will; Smith, Jordan N; Schwarz, Kaitlynn C; Shen, Yufeng; Shukla, Anil K; Moore, Ronald J; Smith, Richard D; Qian, Wei-Jun; Kelly, Ryan T

2018-06-24

Current mass spectrometry (MS)-based proteomics approaches are ineffective for mapping protein expression in tissue sections with high spatial resolution due to the limited overall sensitivity of conventional workflows. Here we report an integrated and automated method to advance spatially resolved proteomics by seamlessly coupling laser capture microdissection (LCM) with a recently developed nanoliter-scale sample preparation system termed nanoPOTS (Nanodroplet Processing in One pot for Trace Samples). The workflow is enabled by prepopulating nanowells with DMSO, which serves as a sacrificial capture liquid for microdissected tissues. The DMSO droplets efficiently collect laser-pressure catapulted LCM tissues as small as 20 µm in diameter with success rates >87%. We also demonstrate that tissue treatment with DMSO can significantly improve proteome coverage, likely due to its ability to dissolve lipids from tissue and enhance protein extraction efficiency. The LCM-nanoPOTS platform was able to identify 180, 695, and 1827 protein groups on average from 12-µm-thick rat brain cortex tissue sections with diameters of 50, 100, and 200 µm, respectively. We also analyzed 100-µm-diameter sections corresponding to 10-18 cells from three different regions of rat brain and comparatively quantified ~1000 proteins, demonstrating the potential utility for high-resolution spatially resolved mapping of protein expression in tissues. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Determination of lipophilic marine toxins in mussels. Quantification and confirmation criteria using high resolution mass spectrometry.

PubMed

Domènech, Albert; Cortés-Francisco, Nuria; Palacios, Oscar; Franco, José M; Riobó, Pilar; Llerena, José J; Vichi, Stefania; Caixach, Josep

2014-02-07

A multitoxin method has been developed for quantification and confirmation of lipophilic marine biotoxins in mussels by liquid chromatography coupled to high resolution mass spectrometry (HRMS), using an Orbitrap-Exactive HCD mass spectrometer. Okadaic acid (OA), yessotoxin, azaspiracid-1, gymnodimine, 13-desmethyl spirolide C, pectenotoxin-2 and Brevetoxin B were analyzed as representative compounds of each lipophilic toxin group. HRMS identification and confirmation criteria were established. Fragment and isotope ions and ion ratios were studied and evaluated for confirmation purpose. In depth characterization of full scan and fragmentation spectrum of the main toxins were carried out. Accuracy (trueness and precision), linearity, calibration curve check, limit of quantification (LOQ) and specificity were the parameters established for the method validation. The validation was performed at 0.5 times the current European Union permitted levels. The method performed very well for the parameters investigated. The trueness, expressed as recovery, ranged from 80% to 94%, the precision, expressed as intralaboratory reproducibility, ranged from 5% to 22% and the LOQs range from 0.9 to 4.8pg on column. Uncertainty of the method was also estimated for OA, using a certified reference material. A top-down approach considering two main contributions: those arising from the trueness studies and those coming from the precision's determination, was used. An overall expanded uncertainty of 38% was obtained. Copyright © 2014 Elsevier B.V. All rights reserved.

Expression, crystallization and preliminary X-ray diffraction studies of recombinant Clostridium perfringens β2-toxin

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

Gurjar, Abhijit A.; Yennawar, Neela H.; Yennawar, Hemant P.

2007-06-01

The cloning, expression, purification and crystallization of recombinant Clostridium perfringens β2-toxin is described. The crystals diffracted to 2.9 Å resolution. Clostridium perfringens is a Gram-positive sporulating anaerobic bacterium that is responsible for a wide spectrum of diseases in animals, birds and humans. The virulence of C. perfringens is associated with the production of several enterotoxins and exotoxins. β2-toxin is a 28 kDa exotoxin produced by C. perfringens. It is implicated in necrotic enteritis in animals and humans, a disease characterized by a sudden acute onset with lethal hemorrhagic mucosal ulceration. The recombinant expression, purification and crystallization of β2-toxin using themore » batch-under-oil technique are reported here. Native X-ray diffraction data were obtained to 2.9 Å resolution on a synchrotron beamline at the F2 station at Cornell High Energy Synchrotron Source (CHESS) using an ADSC Quantum-210 CCD detector. The crystals belong to space group R3, with a dimer in the asymmetric unit; the unit-cell parameters are a = b = 103.71, c = 193.48 Å, α = β = 90, γ = 120° using the hexagonal axis setting. A self-rotation function shows that the two molecules are related by a noncrystallographic twofold axis with polar angles ω = 90.0, ϕ = 210.3°.« less

The Separate Physics and Dynamics Experiment (SPADE) framework for determining resolution awareness: A case study of microphysics

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

Gustafson, William I.; Ma, Po-Lun; Xiao, Heng

2013-08-29

The ability to use multi-resolution dynamical cores for weather and climate modeling is pushing the atmospheric community towards developing scale aware or, more specifically, resolution aware parameterizations that will function properly across a range of grid spacings. Determining the resolution dependence of specific model parameterizations is difficult due to strong resolution dependencies in many pieces of the model. This study presents the Separate Physics and Dynamics Experiment (SPADE) framework that can be used to isolate the resolution dependent behavior of specific parameterizations without conflating resolution dependencies from other portions of the model. To demonstrate the SPADE framework, the resolution dependencemore » of the Morrison microphysics from the Weather Research and Forecasting model and the Morrison-Gettelman microphysics from the Community Atmosphere Model are compared for grid spacings spanning the cloud modeling gray zone. It is shown that the Morrison scheme has stronger resolution dependence than Morrison-Gettelman, and that the ability of Morrison-Gettelman to use partial cloud fractions is not the primary reason for this difference. This study also discusses how to frame the issue of resolution dependence, the meaning of which has often been assumed, but not clearly expressed in the atmospheric modeling community. It is proposed that parameterization resolution dependence can be expressed in terms of "resolution dependence of the first type," RA1, which implies that the parameterization behavior converges towards observations with increasing resolution, or as "resolution dependence of the second type," RA2, which requires that the parameterization reproduces the same behavior across a range of grid spacings when compared at a given coarser resolution. RA2 behavior is considered the ideal, but brings with it serious implications due to limitations of parameterizations to accurately estimate reality with coarse grid spacing. The type of resolution awareness developers should target in their development depends upon the particular modeler’s application.« less

Comprehensive single cell-resolution analysis of the role of chromatin regulators in early C. elegans embryogenesis.

PubMed

Krüger, Angela V; Jelier, Rob; Dzyubachyk, Oleh; Zimmerman, Timo; Meijering, Erik; Lehner, Ben

2015-02-15

Chromatin regulators are widely expressed proteins with diverse roles in gene expression, nuclear organization, cell cycle regulation, pluripotency, physiology and development, and are frequently mutated in human diseases such as cancer. Their inhibition often results in pleiotropic effects that are difficult to study using conventional approaches. We have developed a semi-automated nuclear tracking algorithm to quantify the divisions, movements and positions of all nuclei during the early development of Caenorhabditis elegans and have used it to systematically study the effects of inhibiting chromatin regulators. The resulting high dimensional datasets revealed that inhibition of multiple regulators, including F55A3.3 (encoding FACT subunit SUPT16H), lin-53 (RBBP4/7), rba-1 (RBBP4/7), set-16 (MLL2/3), hda-1 (HDAC1/2), swsn-7 (ARID2), and let-526 (ARID1A/1B) affected cell cycle progression and caused chromosome segregation defects. In contrast, inhibition of cir-1 (CIR1) accelerated cell division timing in specific cells of the AB lineage. The inhibition of RNA polymerase II also accelerated these division timings, suggesting that normal gene expression is required to delay cell cycle progression in multiple lineages in the early embryo. Quantitative analyses of the dataset suggested the existence of at least two functionally distinct SWI/SNF chromatin remodeling complex activities in the early embryo, and identified a redundant requirement for the egl-27 and lin-40 MTA orthologs in the development of endoderm and mesoderm lineages. Moreover, our dataset also revealed a characteristic rearrangement of chromatin to the nuclear periphery upon the inhibition of multiple general regulators of gene expression. Our systematic, comprehensive and quantitative datasets illustrate the power of single cell-resolution quantitative tracking and high dimensional phenotyping to investigate gene function. Furthermore, the results provide an overview of the functions of essential chromatin regulators during the early development of an animal. Copyright © 2014 Elsevier Inc. All rights reserved.

Gene gymnastics

PubMed Central

Vijayachandran, Lakshmi S; Thimiri Govinda Raj, Deepak B; Edelweiss, Evelina; Gupta, Kapil; Maier, Josef; Gordeliy, Valentin; Fitzgerald, Daniel J; Berger, Imre

2013-01-01

Most essential activities in eukaryotic cells are catalyzed by large multiprotein assemblies containing up to ten or more interlocking subunits. The vast majority of these protein complexes are not easily accessible for high resolution studies aimed at unlocking their mechanisms, due to their low cellular abundance and high heterogeneity. Recombinant overproduction can resolve this bottleneck and baculovirus expression vector systems (BEVS) have emerged as particularly powerful tools for the provision of eukaryotic multiprotein complexes in high quality and quantity. Recently, synthetic biology approaches have begun to make their mark in improving existing BEVS reagents by de novo design of streamlined transfer plasmids and by engineering the baculovirus genome. Here we present OmniBac, comprising new custom designed reagents that further facilitate the integration of heterologous genes into the baculovirus genome for multiprotein expression. Based on comparative genome analysis and data mining, we herein present a blueprint to custom design and engineer the entire baculovirus genome for optimized production properties using a bottom-up synthetic biology approach. PMID:23328086

Droplet barcoding for single cell transcriptomics applied to embryonic stem cells

PubMed Central

Klein, Allon M; Mazutis, Linas; Akartuna, Ilke; Tallapragada, Naren; Veres, Adrian; Li, Victor; Peshkin, Leonid; Weitz, David A; Kirschner, Marc W

2015-01-01

Summary It has long been the dream of biologists to map gene expression at the single cell level. With such data one might track heterogeneous cell sub-populations, and infer regulatory relationships between genes and pathways. Recently, RNA sequencing has achieved single cell resolution. What is limiting is an effective way to routinely isolate and process large numbers of individual cells for quantitative in-depth sequencing. We have developed a high-throughput droplet-microfluidic approach for barcoding the RNA from thousands of individual cells for subsequent analysis by next-generation sequencing. The method shows a surprisingly low noise profile and is readily adaptable to other sequencing-based assays. We analyzed mouse embryonic stem cells, revealing in detail the population structure and the heterogeneous onset of differentiation after LIF withdrawal. The reproducibility of these high-throughput single cell data allowed us to deconstruct cell populations and infer gene expression relationships. PMID:26000487

Transcriptional Landscape of the Prenatal Human Brain

PubMed Central

Miller, Jeremy A.; Ding, Song-Lin; Sunkin, Susan M.; Smith, Kimberly A; Ng, Lydia; Szafer, Aaron; Ebbert, Amanda; Riley, Zackery L.; Aiona, Kaylynn; Arnold, James M.; Bennet, Crissa; Bertagnolli, Darren; Brouner, Krissy; Butler, Stephanie; Caldejon, Shiella; Carey, Anita; Cuhaciyan, Christine; Dalley, Rachel A.; Dee, Nick; Dolbeare, Tim A.; Facer, Benjamin A. C.; Feng, David; Fliss, Tim P.; Gee, Garrett; Goldy, Jeff; Gourley, Lindsey; Gregor, Benjamin W.; Gu, Guangyu; Howard, Robert E.; Jochim, Jayson M.; Kuan, Chihchau L.; Lau, Christopher; Lee, Chang-Kyu; Lee, Felix; Lemon, Tracy A.; Lesnar, Phil; McMurray, Bergen; Mastan, Naveed; Mosqueda, Nerick F.; Naluai-Cecchini, Theresa; Ngo, Nhan-Kiet; Nyhus, Julie; Oldre, Aaron; Olson, Eric; Parente, Jody; Parker, Patrick D.; Parry, Sheana E.; Player, Allison Stevens; Pletikos, Mihovil; Reding, Melissa; Royall, Joshua J.; Roll, Kate; Sandman, David; Sarreal, Melaine; Shapouri, Sheila; Shapovalova, Nadiya V.; Shen, Elaine H.; Sjoquist, Nathan; Slaughterbeck, Clifford R.; Smith, Michael; Sodt, Andy J.; Williams, Derric; Zöllei, Lilla; Fischl, Bruce; Gerstein, Mark B.; Geschwind, Daniel H.; Glass, Ian A.; Hawrylycz, Michael J.; Hevner, Robert F.; Huang, Hao; Jones, Allan R.; Knowles, James A.; Levitt, Pat; Phillips, John W.; Sestan, Nenad; Wohnoutka, Paul; Dang, Chinh; Bernard, Amy; Hohmann, John G.; Lein, Ed S.

2014-01-01

Summary The anatomical and functional architecture of the human brain is largely determined by prenatal transcriptional processes. We describe an anatomically comprehensive atlas of mid-gestational human brain, including de novo reference atlases, in situ hybridization, ultra-high resolution magnetic resonance imaging (MRI) and microarray analysis on highly discrete laser microdissected brain regions. In developing cerebral cortex, transcriptional differences are found between different proliferative and postmitotic layers, wherein laminar signatures reflect cellular composition and developmental processes. Cytoarchitectural differences between human and mouse have molecular correlates, including species differences in gene expression in subplate, although surprisingly we find minimal differences between the inner and human-expanded outer subventricular zones. Both germinal and postmitotic cortical layers exhibit fronto-temporal gradients, with particular enrichment in frontal lobe. Finally, many neurodevelopmental disorder and human evolution-related genes show patterned expression, potentially underlying unique features of human cortical formation. These data provide a rich, freely-accessible resource for understanding human brain development. PMID:24695229

Public Outreach and Archiving of Data from the High Resolution Stereo Camera Onboard Mars Express: 2004 The First Year

NASA Technical Reports Server (NTRS)

Koehler, U.; Neukum, G.; Gasselt, S. v.; Jaumann, R.; Roatsch, Th.; Hoffmann, H.; Zender, J.; Acton, C.; Drigani, F.

2005-01-01

During the first year of operation, corresponding to the calendar year 2004, the HRSC imaging experiment onboard ESA's Mars Express mission recorded 23 Gigabyte of 8-bit compressed raw data. After processing, the amount of data increased to more than 344 Gigabyte of decompressed and radiometrically calibrated scientifically useable image products. Every six months these HRSC Level 2 data are fed into ESA's Planetary Science Archive (PSA) that sends all data also to the Planetary Data System (PDS) to ensure easy availability to the interested user. On their respective web portals, the European Space Agency published in cooperation with the Principal Investigator-Group at Freie Universitat Berlin and the German Space Agency (DLR) almost 40 sets of high-level image scenes and movies for PR needs that have been electronically visited many hundred thousand times.

Rainfall erosivity in Europe.

PubMed

Panagos, Panos; Ballabio, Cristiano; Borrelli, Pasquale; Meusburger, Katrin; Klik, Andreas; Rousseva, Svetla; Tadić, Melita Perčec; Michaelides, Silas; Hrabalíková, Michaela; Olsen, Preben; Aalto, Juha; Lakatos, Mónika; Rymszewicz, Anna; Dumitrescu, Alexandru; Beguería, Santiago; Alewell, Christine

2015-04-01

Rainfall is one the main drivers of soil erosion. The erosive force of rainfall is expressed as rainfall erosivity. Rainfall erosivity considers the rainfall amount and intensity, and is most commonly expressed as the R-factor in the USLE model and its revised version, RUSLE. At national and continental levels, the scarce availability of data obliges soil erosion modellers to estimate this factor based on rainfall data with only low temporal resolution (daily, monthly, annual averages). The purpose of this study is to assess rainfall erosivity in Europe in the form of the RUSLE R-factor, based on the best available datasets. Data have been collected from 1541 precipitation stations in all European Union (EU) Member States and Switzerland, with temporal resolutions of 5 to 60 min. The R-factor values calculated from precipitation data of different temporal resolutions were normalised to R-factor values with temporal resolutions of 30 min using linear regression functions. Precipitation time series ranged from a minimum of 5 years to a maximum of 40 years. The average time series per precipitation station is around 17.1 years, the most datasets including the first decade of the 21st century. Gaussian Process Regression (GPR) has been used to interpolate the R-factor station values to a European rainfall erosivity map at 1 km resolution. The covariates used for the R-factor interpolation were climatic data (total precipitation, seasonal precipitation, precipitation of driest/wettest months, average temperature), elevation and latitude/longitude. The mean R-factor for the EU plus Switzerland is 722 MJ mm ha(-1) h(-1) yr(-1), with the highest values (>1000 MJ mm ha(-1) h(-1) yr(-1)) in the Mediterranean and alpine regions and the lowest (<500 MJ mm ha(-1) h(-1) yr(-1)) in the Nordic countries. The erosivity density (erosivity normalised to annual precipitation amounts) was also the highest in Mediterranean regions which implies high risk for erosive events and floods. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Quantification of HSV-1-mediated expression of the ferritin MRI reporter in the mouse brain

PubMed Central

Iordanova, B; Goins, WF; Clawson, DS; Hitchens, TK; Ahrens, ET

2017-01-01

The development of effective strategies for gene therapy has been hampered by difficulties verifying transgene delivery in vivo and quantifying gene expression non-invasively. Magnetic resonance imaging (MRI) offers high spatial resolution and three-dimensional views, without tissue depth limitations. The iron-storage protein ferritin is a prototype MRI gene reporter. Ferritin forms a paramagnetic ferrihydrite core that can be detected by MRI via its effect on the local magnetic field experienced by water protons. In an effort to better characterize the ferritin reporter for central nervous system applications, we expressed ferritin in the mouse brain in vivo using a neurotropic herpes simplex virus type 1 (HSV-1). We computed three-dimensional maps of MRI transverse relaxation rates in the mouse brain with ascending doses of ferritin-expressing HSV-1. We established that the transverse relaxation rates correlate significantly to the number of inoculated infectious particles. Our results are potentially useful for quantitatively assessing limitations of ferritin reporters for gene therapy applications. PMID:22996196

Major Shifts in Glial Regional Identity Are a Transcriptional Hallmark of Human Brain Aging.

PubMed

Soreq, Lilach; Rose, Jamie; Soreq, Eyal; Hardy, John; Trabzuni, Daniah; Cookson, Mark R; Smith, Colin; Ryten, Mina; Patani, Rickie; Ule, Jernej

2017-01-10

Gene expression studies suggest that aging of the human brain is determined by a complex interplay of molecular events, although both its region- and cell-type-specific consequences remain poorly understood. Here, we extensively characterized aging-altered gene expression changes across ten human brain regions from 480 individuals ranging in age from 16 to 106 years. We show that astrocyte- and oligodendrocyte-specific genes, but not neuron-specific genes, shift their regional expression patterns upon aging, particularly in the hippocampus and substantia nigra, while the expression of microglia- and endothelial-specific genes increase in all brain regions. In line with these changes, high-resolution immunohistochemistry demonstrated decreased numbers of oligodendrocytes and of neuronal subpopulations in the aging brain cortex. Finally, glial-specific genes predict age with greater precision than neuron-specific genes, thus highlighting the need for greater mechanistic understanding of neuron-glia interactions in aging and late-life diseases. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Extracellular IL-33 cytokine, but not endogenous nuclear IL-33, regulates protein expression in endothelial cells.

PubMed

Gautier, Violette; Cayrol, Corinne; Farache, Dorian; Roga, Stéphane; Monsarrat, Bernard; Burlet-Schiltz, Odile; Gonzalez de Peredo, Anne; Girard, Jean-Philippe

2016-10-03

IL-33 is a nuclear cytokine from the IL-1 family that plays important roles in health and disease. Extracellular IL-33 activates a growing number of target cells, including group 2 innate lymphoid cells, mast cells and regulatory T cells, but it remains unclear whether intracellular nuclear IL-33 has additional functions in the nucleus. Here, we used a global proteomic approach based on high-resolution mass spectrometry to compare the extracellular and intracellular roles of IL-33 in primary human endothelial cells, a major source of IL-33 protein in human tissues. We found that exogenous extracellular IL-33 cytokine induced expression of a distinct set of proteins associated with inflammatory responses in endothelial cells. In contrast, knockdown of endogenous nuclear IL-33 expression using two independent RNA silencing strategies had no reproducible effect on the endothelial cell proteome. These results suggest that IL-33 acts as a cytokine but not as a nuclear factor regulating gene expression in endothelial cells.

The formation of the light-sensing compartment of cone photoreceptors coincides with a transcriptional switch

PubMed Central

Daum, Janine M; Keles, Özkan; Holwerda, Sjoerd JB; Kohler, Hubertus; Rijli, Filippo M

2017-01-01

High-resolution daylight vision is mediated by cone photoreceptors. The molecular program responsible for the formation of their light sensor, the outer segment, is not well understood. We correlated daily changes in ultrastructure and gene expression in postmitotic mouse cones, between birth and eye opening, using serial block-face electron microscopy (EM) and RNA sequencing. Outer segments appeared rapidly at postnatal day six and their appearance coincided with a switch in gene expression. The switch affected over 14% of all expressed genes. Genes that switched off were rich in transcription factors and neurogenic genes. Those that switched on contained genes relevant for cone function. Chromatin rearrangements in enhancer regions occurred before the switch was completed, but not after. We provide a resource comprised of correlated EM, RNAseq, and ATACseq data, showing that the growth of a key compartment of a postmitotic cell involves an extensive switch in gene expression and chromatin accessibility. PMID:29106373

A resolution expressing support for the people of Tibet.

THOMAS, 112th Congress

Sen. Feinstein, Dianne [D-CA

2012-01-30

Senate - 03/29/2012 Resolution agreed to in Senate without amendment and an amended preamble by Voice Vote. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

Distinct contributions of replication and transcription to mutation rate variation of human genomes.

PubMed

Cui, Peng; Ding, Feng; Lin, Qiang; Zhang, Lingfang; Li, Ang; Zhang, Zhang; Hu, Songnian; Yu, Jun

2012-02-01

Here, we evaluate the contribution of two major biological processes--DNA replication and transcription--to mutation rate variation in human genomes. Based on analysis of the public human tissue transcriptomics data, high-resolution replicating map of Hela cells and dbSNP data, we present significant correlations between expression breadth, replication time in local regions and SNP density. SNP density of tissue-specific (TS) genes is significantly higher than that of housekeeping (HK) genes. TS genes tend to locate in late-replicating genomic regions and genes in such regions have a higher SNP density compared to those in early-replication regions. In addition, SNP density is found to be positively correlated with expression level among HK genes. We conclude that the process of DNA replication generates stronger mutational pressure than transcription-associated biological processes do, resulting in an increase of mutation rate in TS genes while having weaker effects on HK genes. In contrast, transcription-associated processes are mainly responsible for the accumulation of mutations in highly-expressed HK genes. Copyright © 2012 Beijing Genomics Institute. Published by Elsevier Ltd. All rights reserved.

Atomic resolution mechanistic studies of ribocil: A highly selective unnatural ligand mimic of the E. coli FMN riboswitch

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

Howe, John A.; Xiao, Li; Fischmann, Thierry O.

2016-08-02

Bacterial riboswitches are non-coding RNA structural elements that direct gene expression in numerous metabolic pathways. The key regulatory roles of riboswitches, and the urgent need for new classes of antibiotics to treat multi-drug resistant bacteria, has led to efforts to develop small-molecules that mimic natural riboswitch ligands to inhibit metabolic pathways and bacterial growth. Recently, we reported the results of a phenotypic screen targeting the riboflavin biosynthesis pathway in the Gram-negative bacteria Escherichia coli that led to the identification of ribocil, a small molecule inhibitor of the flavin mononucleotide (FMN) riboswitch controlling expression of this biosynthetic pathway. Although ribocil ismore » structurally distinct from FMN, ribocil functions as a potent and highly selective synthetic mimic of the natural ligand to repress riboswitch-mediated ribB gene expression and inhibit bacterial growth both in vitro and in vivo. Herein, we expand our analysis of ribocil; including mode of binding in the FMN binding pocket of the riboswitch, mechanisms of resistance and structure-activity relationship guided efforts to generate more potent analogs.« less

Population transcriptomics with single-cell resolution: a new field made possible by microfluidics: a technology for high throughput transcript counting and data-driven definition of cell types.

PubMed

Plessy, Charles; Desbois, Linda; Fujii, Teruo; Carninci, Piero

2013-02-01

Tissues contain complex populations of cells. Like countries, which are comprised of mixed populations of people, tissues are not homogeneous. Gene expression studies that analyze entire populations of cells from tissues as a mixture are blind to this diversity. Thus, critical information is lost when studying samples rich in specialized but diverse cells such as tumors, iPS colonies, or brain tissue. High throughput methods are needed to address, model and understand the constitutive and stochastic differences between individual cells. Here, we describe microfluidics technologies that utilize a combination of molecular biology and miniaturized labs on chips to study gene expression at the single cell level. We discuss how the characterization of the transcriptome of each cell in a sample will open a new field in gene expression analysis, population transcriptomics, that will change the academic and biomedical analysis of complex samples by defining them as quantified populations of single cells. Copyright © 2013 WILEY Periodicals, Inc.

From Airy to Abbe: quantifying the effects of wide-angle focusing for scalar spherical waves

NASA Astrophysics Data System (ADS)

Calm, Yitzi M.; Merlo, Juan M.; Burns, Michael J.; Naughton, Michael J.

2017-10-01

Recent advances in optical microscopy have enabled imaging with spatial resolution beyond the diffraction limit. This limit is sometimes taken as one of several different criteria according to different conventions, including Rayleigh’s 0.61λ /NA, Abbe’s 0.5λ /NA, and Sparrow’s 0.47λ /NA. In this paper, we perform a parametric study, numerically integrating the scalar Kirchhoff diffraction integrals, and we propose new functional forms for the resolution limits derived from scalar focusing. The new expressions remain accurate under wide angle focusing, up to 90^\\circ . Our results could materially impact the design of high intensity focused ultrasound systems, and can be used as a qualitative guideline for the design of a particular type of planar optical element: the flat lens metasurface.

Multiplexed 3D FRET imaging in deep tissue of live embryos

PubMed Central

Zhao, Ming; Wan, Xiaoyang; Li, Yu; Zhou, Weibin; Peng, Leilei

2015-01-01

Current deep tissue microscopy techniques are mostly restricted to intensity mapping of fluorophores, which significantly limit their applications in investigating biochemical processes in vivo. We present a deep tissue multiplexed functional imaging method that probes multiple Förster resonant energy transfer (FRET) sensors in live embryos with high spatial resolution. The method simultaneously images fluorescence lifetimes in 3D with multiple excitation lasers. Through quantitative analysis of triple-channel intensity and lifetime images, we demonstrated that Ca2+ and cAMP levels of live embryos expressing dual FRET sensors can be monitored simultaneously at microscopic resolution. The method is compatible with a broad range of FRET sensors currently available for probing various cellular biochemical functions. It opens the door to imaging complex cellular circuitries in whole live organisms. PMID:26387920

Polynomial coefficients for calculating O2 Schumann-Runge cross sections at 0.5/cm resolution

NASA Technical Reports Server (NTRS)

Minschwaner, K.; Anderson, G. P.; Hall, L. A.; Yoshino, K.

1992-01-01

O2 cross sections from 49,000 to 57,000/cm have been fitted with temperature dependent polynomial expressions, providing an accurate and efficient means of determining Schumann-Runge band cross sections for temperatures between 130 and 500 K. The least squares fits were carried out on a 0.5/cm spectral grid, using cross sections obtained from a Schumann-Runge line-by-line model that incorporates the most recent spectroscopic data. The O2 cross sections do not include the underlying Herzberg continuum, but they do contain contributions from the temperature dependent Schumann-Runge continuum. The cross sections are suitable for use in UV transmission calculations at high spectral resolution. They should also prove useful for updating existing parameterizations of ultraviolet transmission and O2 photolysis.

[Locus of control and self-concept in interpersonal conflict resolution approaches].

PubMed

Hisli Sahin, Nesrin; Basim, H Nejat; Cetin, Fatih

2009-01-01

The purpose of this study was to investigate the relationship between self-concept and locus of control in interpersonal conflict resolution approaches and to determine the predictors of conflict resolution approach choices. The study included 345 students aged between 18 and 28 years that were studying at universities in Ankara. Data were collected using the Interpersonal Conflict Resolution Approaches Scale to measure conflict resolution approaches, the Social Comparison Scale to measure self-concept, and the Internal-External Locus of Control Scale to measure locus of control. It was observed that confrontation approach to interpersonal conflict was predicted by self-concept (beta = 0.396, P < 0.001) Moreover, self-concept was related to self-disclosure (beta = 0.180, P < 0.01) and emotional expression (beta = 0.196, P < 0.001) approaches. Locus of control played a role in the choice of all resolution approaches. In addition to these findings, it was observed that females used self-disclosure (beta = -0.163, P < 0.01) and emotional expression (beta = -0.219, P < 0.001), while males used approach (beta = 0.395, P < 0.001) and public behavior (beta = 0.270, P < 0.001) approaches in the resolution processes. Self-concept and locus of control were related to the behaviors adopted in the interpersonal conflict resolution process. Individuals with a positive self-concept and an internal locus of control adopted solutions to interpersonal conflict resolution that were more effective and constructive.

High-resolution profiling of linear B-cell epitopes from mucin-associated surface proteins (MASPs) of Trypanosoma cruzi during human infections

PubMed Central

Durante, Ignacio M.; La Spina, Pablo E.; Carmona, Santiago J.; Agüero, Fernán

2017-01-01

Background The Trypanosoma cruzi genome bears a huge family of genes and pseudogenes coding for Mucin-Associated Surface Proteins (MASPs). MASP molecules display a ‘mosaic’ structure, with highly conserved flanking regions and a strikingly variable central and mature domain made up of different combinations of a large repertoire of short sequence motifs. MASP molecules are highly expressed in mammal-dwelling stages of T. cruzi and may be involved in parasite-host interactions and/or in diverting the immune response. Methods/Principle findings High-density microarrays composed of fully overlapped 15mer peptides spanning the entire sequences of 232 non-redundant MASPs (~25% of the total MASP content) were screened with chronic Chagasic sera. This strategy led to the identification of 86 antigenic motifs, each one likely representing a single linear B-cell epitope, which were mapped to 69 different MASPs. These motifs could be further grouped into 31 clusters of structurally- and likely antigenically-related sequences, and fully characterized. In contrast to previous reports, we show that MASP antigenic motifs are restricted to the central and mature region of MASP polypeptides, consistent with their intracellular processing. The antigenicity of these motifs displayed significant positive correlation with their genome dosage and their relative position within the MASP polypeptide. In addition, we verified the biased genetic co-occurrence of certain antigenic motifs within MASP polypeptides, compatible with proposed intra-family recombination events underlying the evolution of their coding genes. Sequences spanning 7 MASP antigenic motifs were further evaluated using distinct synthesis/display approaches and a large panel of serum samples. Overall, the serological recognition of MASP antigenic motifs exhibited a remarkable non normal distribution among the T. cruzi seropositive population, thus reducing their applicability in conventional serodiagnosis. As previously observed in in vitro and animal infection models, immune signatures supported the concurrent expression of several MASPs during human infection. Conclusions/Significance In spite of their conspicuous expression and potential roles in parasite biology, this study constitutes the first unbiased, high-resolution profiling of linear B-cell epitopes from T. cruzi MASPs during human infection. PMID:28961244

Maternal Gametic Transmission of Translocations or Inversions of Human Chromosome 11p15.5 Results in Regional DNA Hypermethylation and Downregulation of CDKN1C Expression

PubMed Central

Smith, Adam C.; Suzuki, Masako; Thompson, Reid; Choufani, Sanaa; Higgins, Michael J.; Chiu, Idy W.; Squire, Jeremy A.; Greally, John M.; Weksberg, Rosanna

2015-01-01

Beckwith-Wiedemann syndrome (BWS) is an overgrowth syndrome associated with genetic or epigenetic alterations in one of two imprinted domains on chromosome 11p15.5. Rarely, chromosomal translocations or inversions of chromosome 11p15.5 are associated with BWS but the molecular pathophysiology in such cases is not understood. In our series of 3 translocation and 2 inversion patients with BWS, the chromosome 11p15.5 breakpoints map within the centromeric imprinted domain, 2. We hypothesized that either microdeletions/microduplications adjacent to the breakpoints could disrupt genomic sequences important for imprinted gene regulation. An alternate hypothesis was that epigenetic alterations of as yet unknown regulatory DNA sequences, result in the BWS phenotype. A high resolution Nimblegen custom microarray was designed representing all non-repetitive sequences in the telomeric 33 MB of the short arm of human chromosome 11. For the BWS-associated chromosome 11p15.5 translocations and inversions, we found no evidence of microdeletions/microduplications. DNA methylation was also tested on this microarray using the HpaII tiny fragment enrichment by ligation-mediated PCR (HELP) assay. This high-resolution DNA methylation microarray analysis revealed a gain of DNA methylation in the translocation/inversion patients affecting the p-ter segment of chromosome 11p15, including both imprinted domains. BWS patients that inherited a maternal translocation or inversion also demonstrated reduced expression of the growth suppressing imprinted gene, CDKN1C in Domain 2. In summary, our data demonstrate that translocations and inversions involving imprinted domain 2 on chromosome 11p15.5, alter regional DNA methylation patterns and imprinted gene expression in cis, suggesting that these epigenetic alterations are generated by an alteration in “chromatin context”. PMID:22079941

Three gangliogliomas: results of GTG-banding, SKY, genome-wide high resolution SNP-array, gene expression and review of the literature.

PubMed

Xu, Li-Xin; Holland, Heidrun; Kirsten, Holger; Ahnert, Peter; Krupp, Wolfgang; Bauer, Manfred; Schober, Ralf; Mueller, Wolf; Fritzsch, Dominik; Meixensberger, Jürgen; Koschny, Ronald

2015-04-01

According to the World Health Organization gangliogliomas are classified as well-differentiated and slowly growing neuroepithelial tumors, composed of neoplastic mature ganglion and glial cells. It is the most frequent tumor entity observed in patients with long-term epilepsy. Comprehensive cytogenetic and molecular cytogenetic data including high-resolution genomic profiling (single nucleotide polymorphism (SNP)-array) of gangliogliomas are scarce but necessary for a better oncological understanding of this tumor entity. For a detailed characterization at the single cell and cell population levels, we analyzed genomic alterations of three gangliogliomas using trypsin-Giemsa banding (GTG-banding) and by spectral karyotyping (SKY) in combination with SNP-array and gene expression array experiments. By GTG and SKY, we could confirm frequently detected chromosomal aberrations (losses within chromosomes 10, 13 and 22; gains within chromosomes 5, 7, 8 and 12), and identify so far unknown genetic aberrations like the unbalanced non-reciprocal translocation t(1;18)(q21;q21). Interestingly, we report on the second so far detected ganglioglioma with ring chromosome 1. Analyses of SNP-array data from two of the tumors and respective germline DNA (peripheral blood) identified few small gains and losses and a number of copy-neutral regions with loss of heterozygosity (LOH) in germline and in tumor tissue. In comparison to germline DNA, tumor tissues did not show substantial regions with significant loss or gain or with newly developed LOH. Gene expression analyses of tumor-specific genes revealed similarities in the profile of the analyzed samples regarding different relevant pathways. Taken together, we describe overlapping but also distinct and novel genetic aberrations of three gangliogliomas. © 2014 Japanese Society of Neuropathology.

General and specific responsiveness of the amygdala during explicit emotion recognition in females and males.

PubMed

Derntl, Birgit; Habel, Ute; Windischberger, Christian; Robinson, Simon; Kryspin-Exner, Ilse; Gur, Ruben C; Moser, Ewald

2009-08-04

The ability to recognize emotions in facial expressions relies on an extensive neural network with the amygdala as the key node as has typically been demonstrated for the processing of fearful stimuli. A sufficient characterization of the factors influencing and modulating amygdala function, however, has not been reached now. Due to lacking or diverging results on its involvement in recognizing all or only certain negative emotions, the influence of gender or ethnicity is still under debate. This high-resolution fMRI study addresses some of the relevant parameters, such as emotional valence, gender and poser ethnicity on amygdala activation during facial emotion recognition in 50 Caucasian subjects. Stimuli were color photographs of emotional Caucasian and African American faces. Bilateral amygdala activation was obtained to all emotional expressions (anger, disgust, fear, happy, and sad) and neutral faces across all subjects. However, only in males a significant correlation of amygdala activation and behavioral response to fearful stimuli was observed, indicating higher amygdala responses with better fear recognition, thus pointing to subtle gender differences. No significant influence of poser ethnicity on amygdala activation occurred, but analysis of recognition accuracy revealed a significant impact of poser ethnicity that was emotion-dependent. Applying high-resolution fMRI while subjects were performing an explicit emotion recognition task revealed bilateral amygdala activation to all emotions presented and neutral expressions. This mechanism seems to operate similarly in healthy females and males and for both in-group and out-group ethnicities. Our results support the assumption that an intact amygdala response is fundamental in the processing of these salient stimuli due to its relevance detecting function.

Methylation detection oligonucleotide microarray analysis: a high-resolution method for detection of CpG island methylation

PubMed Central

Kamalakaran, Sitharthan; Kendall, Jude; Zhao, Xiaoyue; Tang, Chunlao; Khan, Sohail; Ravi, Kandasamy; Auletta, Theresa; Riggs, Michael; Wang, Yun; Helland, Åslaug; Naume, Bjørn; Dimitrova, Nevenka; Børresen-Dale, Anne-Lise; Hicks, Jim; Lucito, Robert

2009-01-01

Methylation of CpG islands associated with genes can affect the expression of the proximal gene, and methylation of non-associated CpG islands correlates to genomic instability. This epigenetic modification has been shown to be important in many pathologies, from development and disease to cancer. We report the development of a novel high-resolution microarray that detects the methylation status of over 25 000 CpG islands in the human genome. Experiments were performed to demonstrate low system noise in the methodology and that the array probes have a high signal to noise ratio. Methylation measurements between different cell lines were validated demonstrating the accuracy of measurement. We then identified alterations in CpG islands, both those associated with gene promoters, as well as non-promoter-associated islands in a set of breast and ovarian tumors. We demonstrate that this methodology accurately identifies methylation profiles in cancer and in principle it can differentiate any CpG methylation alterations and can be adapted to analyze other species. PMID:19474344

Molecular characterization of phytoplankton dissolved organic matter (DOM) and sulfur components using high resolution Orbitrap mass spectrometry.

PubMed

Mangal, Vaughn; Stock, Naomi L; Guéguen, Celine

2016-03-01

Orbitrap high resolution mass spectrometry (HRMS) with electrospray ionization in both positive and negative polarity was conducted on Suwannee River fulvic acid (SRFA), Pony Lake fulvic acid (PLFA) standards, and dissolved organic matter (DOM) released by freshwater phytoplankton (Scenedesmus obliquus, Euglena mutabilis, and Euglena gracilis). Three-dimensional van Krevelen diagrams expressing various oxygenation states of sulfur molecules and abundance plots of sulfur-containing species were constructed. Orbitrap HRMS analysis of SRFA found a high density of peaks in the lignin region (77 %) and low density of protein material (6.53 %), whereas for PLFA, 25 % of the total peaks were lignin related compared to 56 % of peaks in protein regions, comparable with other HRMS studies. Phytoplankton-derived DOM of S. obliquus, E. mutabilis, and E. gracilis was dominated by protein molecules at respective percentages of 36, 46, and 49 %, and is consistent with previous experiments examining phytoplankton-derived DOM composition. The normalized percentage of SO-containing compounds was determined among the three phytoplankton to be 56 % for Scenedesmus, 54 % for E. mutabilis, and 47 % for E. gracilis, suggesting variation between sulfur content in phytoplankton-derived DOM and differences in metal binding capacities. These results suggest the level of resolution by Orbitrap mass spectrometry is sufficient for preliminary characterization of phytoplankton DOM at an affordable cost relative to other HRMS techniques.

The development of functional mapping by three sex-related loci on the third whorl of different sex types of Carica papaya L.

PubMed Central

Lin, Hui-Jun; Viswanath, Kotapati Kasi; Lin, Chih-Peng; Chang, Bill Chia-Han; Chiu, Pei-Hsun; Chiu, Chan-Tai; Wang, Ren-Huang; Chin, Shih-Wen; Chen, Fure-Chyi

2018-01-01

Carica papaya L. is an important economic crop worldwide and is used as a model plant for sex-determination research. To study the different flower sex types, we screened sex-related genes using alternative splicing sequences (AS-seqs) from a transcriptome database of the three flower sex types, i.e., males, females, and hermaphrodites, established at 28 days before flowering using 15 bacterial artificial chromosomes (BACs) of C. papaya L. After screening, the cDNA regions of the three sex-related loci, including short vegetative phase-like (CpSVPL), the chromatin assembly factor 1 subunit A-like (CpCAF1AL), and the somatic embryogenesis receptor kinase (CpSERK), which contained eight sex-related single-nucleotide polymorphisms (SNPs) from the different sex types of C. papaya L., were genotyped using high-resolution melting (HRM). The three loci were examined regarding the profiles of the third whorl, as described below. CpSVPL, which had one SNP associated with the three sex genotypes, was highly expressed in the male and female sterile flowers (abnormal hermaphrodite flowers) that lacked the fourth whorl structure. CpCAF1AL, which had three SNPs associated with the male genotype, was highly expressed in male and normal hermaphrodite flowers, and had no AS-seqs, whereas it exhibited low expression and an AS-seqs in intron 11 in abnormal hermaphrodite flowers. Conversely, carpellate flowers (abnormal hermaphrodite flowers) showed low expression of CpSVPL and AS-seqs in introns 5, 6, and 7 of CpSERK, which contained four SNPs associated with the female genotype. Specifically, the CpSERK and CpCAF1AL loci exhibited no AS-seq expression in the third whorl of the male and normal hermaphrodite flowers, respectively, and variance in the AS-seq expression of all other types of flowers. Functional mapping of the third whorl of normal hermaphrodites indicated no AS-seq expression in CpSERK, low CpSVPL expression, and, for CpCAF1AL, high expression and no AS-seq expression on XYh-type chromosomes. PMID:29566053

Cis-regulatory changes in Kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans

PubMed Central

Miller, Craig T.; Beleza, Sandra; Pollen, Alex A.; Schluter, Dolph; Kittles, Rick A.; Shriver, Mark D.; Kingsley, David M.

2010-01-01

SUMMARY Dramatic pigmentation changes have evolved within most vertebrate groups, including fish and humans. Here we use genetic crosses in sticklebacks to investigate the parallel origin of pigmentation changes in natural populations. High-resolution mapping and expression experiments show that light gills and light ventrums map to a divergent regulatory allele of the Kit ligand (Kitlg) gene. The divergent allele reduces expression in gill and skin tissue, and is shared by multiple derived freshwater populations with reduced pigmentation. In humans, Europeans and East Asians also share derived alleles at the KITLG locus. Strong signatures of selection map to regulatory regions surrounding the gene, and admixture mapping shows that the KITLG genomic region has a significant effect on human skin color. These experiments suggest that regulatory changes in Kitlg contribute to natural variation in vertebrate pigmentation, and that similar genetic mechanisms may underlie rapid evolutionary change in fish and humans. PMID:18083106

Degenerate R-S perturbation theory

NASA Technical Reports Server (NTRS)

Hirschfelder, J. O.; Certain, P. R.

1973-01-01

A concise, systematic procedure is given for determining the Rayleigh-Schrodinger energies and wave functions of degenerate states to arbitrarily high orders even when the degeneracies of the various states are resolved in arbitrary orders. The procedure is expressed in terms of an iterative cycle in which the energy through the (2n+1)st order is expressed in terms of the partially determined wave function through the n-th order. Both a direct and an operator derivation are given. The two approaches are equivalent and can be transcribed into each other. The direct approach deals with the wave functions (without the use of formal operators) and has the advantage that it resembles the usual treatment of nondegenerate perturbations and maintains close contact with the basic physics. In the operator approach, the wave functions are expressed in terms of infinite order operators which are determined by the successive resolution of the space of the zeroth order functions.

Non-invasive imaging using reporter genes altering cellular water permeability

NASA Astrophysics Data System (ADS)

Mukherjee, Arnab; Wu, Di; Davis, Hunter C.; Shapiro, Mikhail G.

2016-12-01

Non-invasive imaging of gene expression in live, optically opaque animals is important for multiple applications, including monitoring of genetic circuits and tracking of cell-based therapeutics. Magnetic resonance imaging (MRI) could enable such monitoring with high spatiotemporal resolution. However, existing MRI reporter genes based on metalloproteins or chemical exchange probes are limited by their reliance on metals or relatively low sensitivity. Here we introduce a new class of MRI reporters based on the human water channel aquaporin 1. We show that aquaporin overexpression produces contrast in diffusion-weighted MRI by increasing tissue water diffusivity without affecting viability. Low aquaporin levels or mixed populations comprising as few as 10% aquaporin-expressing cells are sufficient to produce MRI contrast. We characterize this new contrast mechanism through experiments and simulations, and demonstrate its utility in vivo by imaging gene expression in tumours. Our results establish an alternative class of sensitive, metal-free reporter genes for non-invasive imaging.

A multiplexable TALE-based binary expression system for in vivo cellular interaction studies.

PubMed

Toegel, Markus; Azzam, Ghows; Lee, Eunice Y; Knapp, David J H F; Tan, Ying; Fa, Ming; Fulga, Tudor A

2017-11-21

Binary expression systems have revolutionised genetic research by enabling delivery of loss-of-function and gain-of-function transgenes with precise spatial-temporal resolution in vivo. However, at present, each existing platform relies on a defined exogenous transcription activator capable of binding a unique recognition sequence. Consequently, none of these technologies alone can be used to simultaneously target different tissues or cell types in the same organism. Here, we report a modular system based on programmable transcription activator-like effector (TALE) proteins, which enables parallel expression of multiple transgenes in spatially distinct tissues in vivo. Using endogenous enhancers coupled to TALE drivers, we demonstrate multiplexed orthogonal activation of several transgenes carrying cognate variable activating sequences (VAS) in distinct neighbouring cell types of the Drosophila central nervous system. Since the number of combinatorial TALE-VAS pairs is virtually unlimited, this platform provides an experimental framework for highly complex genetic manipulation studies in vivo.

Degenerate RS perturbation theory. [Rayleigh-Schroedinger energies and wave functions

NASA Technical Reports Server (NTRS)

Hirschfelder, J. O.; Certain, P. R.

1974-01-01

A concise, systematic procedure is given for determining the Rayleigh-Schroedinger energies and wave functions of degenerate states to arbitrarily high orders even when the degeneracies of the various states are resolved in arbitrary orders. The procedure is expressed in terms of an iterative cycle in which the energy through the (2n + 1)-th order is expressed in terms of the partially determined wave function through the n-th order. Both a direct and an operator derivation are given. The two approaches are equivalent and can be transcribed into each other. The direct approach deals with the wave functions (without the use of formal operators) and has the advantage that it resembles the usual treatment of nondegenerate perturbations and maintains close contact with the basic physics. In the operator approach, the wave functions are expressed in terms of infinite-order operators which are determined by the successive resolution of the space of the zeroth-order functions.

Single-Image Super-Resolution Based on Rational Fractal Interpolation.

PubMed

Zhang, Yunfeng; Fan, Qinglan; Bao, Fangxun; Liu, Yifang; Zhang, Caiming

2018-08-01

This paper presents a novel single-image super-resolution (SR) procedure, which upscales a given low-resolution (LR) input image to a high-resolution image while preserving the textural and structural information. First, we construct a new type of bivariate rational fractal interpolation model and investigate its analytical properties. This model has different forms of expression with various values of the scaling factors and shape parameters; thus, it can be employed to better describe image features than current interpolation schemes. Furthermore, this model combines the advantages of rational interpolation and fractal interpolation, and its effectiveness is validated through theoretical analysis. Second, we develop a single-image SR algorithm based on the proposed model. The LR input image is divided into texture and non-texture regions, and then, the image is interpolated according to the characteristics of the local structure. Specifically, in the texture region, the scaling factor calculation is the critical step. We present a method to accurately calculate scaling factors based on local fractal analysis. Extensive experiments and comparisons with the other state-of-the-art methods show that our algorithm achieves competitive performance, with finer details and sharper edges.

Super-resolution method for face recognition using nonlinear mappings on coherent features.

PubMed

Huang, Hua; He, Huiting

2011-01-01

Low-resolution (LR) of face images significantly decreases the performance of face recognition. To address this problem, we present a super-resolution method that uses nonlinear mappings to infer coherent features that favor higher recognition of the nearest neighbor (NN) classifiers for recognition of single LR face image. Canonical correlation analysis is applied to establish the coherent subspaces between the principal component analysis (PCA) based features of high-resolution (HR) and LR face images. Then, a nonlinear mapping between HR/LR features can be built by radial basis functions (RBFs) with lower regression errors in the coherent feature space than in the PCA feature space. Thus, we can compute super-resolved coherent features corresponding to an input LR image according to the trained RBF model efficiently and accurately. And, face identity can be obtained by feeding these super-resolved features to a simple NN classifier. Extensive experiments on the Facial Recognition Technology, University of Manchester Institute of Science and Technology, and Olivetti Research Laboratory databases show that the proposed method outperforms the state-of-the-art face recognition algorithms for single LR image in terms of both recognition rate and robustness to facial variations of pose and expression.

Modeling photo-bleaching kinetics to map local variations in rod rhodopsin density

NASA Astrophysics Data System (ADS)

Ehler, M.; Dobrosotskaya, J.; King, E. J.; Czaja, W.; Bonner, R. F.

2011-03-01

Localized rod photoreceptor and rhodopsin losses have been observed in post mortem histology both in normal aging and in age-related maculopathy. We propose to noninvasively map local rod rhodopsin density through analysis of the brightening of the underlying lipofuscin autofluorescence (LAF) in confocal scanning laser ophthalmoscopy (cSLO) imaging sequences starting in the dark adapted eye. The detected LAF increases as rhodopsin is bleached (time constant ~ 25sec) by the average retinal irradiance of the cSLO 488nm laser beam. We fit parameters of analytical expressions for the kinetics of rhodopsin bleaching that Lamb validated using electroretinogram recordings in human. By performing localized (~ 100μm) kinetic analysis, we create high resolution maps of the rhodopsin density. This new noninvasive imaging and analysis approach appears well-suited for measuring localized changes in the rod photoreceptors and correlating them at high spatial resolution with localized pathological changes of the retinal pigment epithelium (RPE) seen in steady-state LAF images.

A Sparse Bayesian Approach for Forward-Looking Superresolution Radar Imaging

PubMed Central

Zhang, Yin; Zhang, Yongchao; Huang, Yulin; Yang, Jianyu

2017-01-01

This paper presents a sparse superresolution approach for high cross-range resolution imaging of forward-looking scanning radar based on the Bayesian criterion. First, a novel forward-looking signal model is established as the product of the measurement matrix and the cross-range target distribution, which is more accurate than the conventional convolution model. Then, based on the Bayesian criterion, the widely-used sparse regularization is considered as the penalty term to recover the target distribution. The derivation of the cost function is described, and finally, an iterative expression for minimizing this function is presented. Alternatively, this paper discusses how to estimate the single parameter of Gaussian noise. With the advantage of a more accurate model, the proposed sparse Bayesian approach enjoys a lower model error. Meanwhile, when compared with the conventional superresolution methods, the proposed approach shows high cross-range resolution and small location error. The superresolution results for the simulated point target, scene data, and real measured data are presented to demonstrate the superior performance of the proposed approach. PMID:28604583

Reconstructive correction of aberrations in nuclear particle spectrographs

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

Berz, M.; Joh, K.; Nolen, J.A.

A method is presented that allows the reconstruction of trajectories in particle spectrographs and the reconstructive correction of residual aberrations that otherwise limit the resolution. Using a computed or fitted high order transfer map that describes the uncorrected aberrations of the spectrograph, it is possible to calculate a map via an analytic recursion relation that allows the computation of the corrected data of interest such as reaction energy and scattering angle as well as the reconstructed trajectories in terms of position measurements in two planes near the focal plane. The technique is only limited by the accuracy of the positionmore » measurements, the incoherent spot sizes, and the accuracy of the transfer map. In practice the method can be expressed as an inversion of a nonlinear map and implemented in the differential algebraic framework. The method is applied to correct residual aberrations in the S800 spectrograph which is under construction at the National Superconducting Cyclotron Laboratory at Michigan State University and to two other high resolution spectrographs.« less

Analytical estimates of the PP-algorithm at low number of Doppler periods per pulse length

NASA Technical Reports Server (NTRS)

Angelova, M. D.; Stoykova, E. V.; Stoyanov, D. V.

1992-01-01

When discussing the Doppler velocity estimators, it is of significant interest to analyze their behavior at a low number of Doppler periods n(sub D) = 2v(sub r)t(sub s)/lambda is approximately equal to 1 within the resolution cell t(sub s) (v(sub 4) is the radial velocity, lambda is the wavelength). Obviously, at n(sub D) is approximately less than 1 the velocity error is essentially increased. The problem of low n(sub D) arises in the planetary boundary layer (PBL), where higher resolutions are usually required but the signal-to-noise ratio (SNR) is relatively high. In this work analytical expression for the relative root mean square (RMS) error of the PP Doppler estimator at low number of periods for a narrowband Doppler signal and arbitrary model of the noise correlation function is obtained. The results are correct at relatively high SNR. The analysis is supported by computer simulations at various SNR's.

Dissecting non-coding RNA mechanisms in cellulo by single-molecule high-resolution localization and counting

PubMed Central

Pitchiaya, Sethuramasundaram; Krishnan, Vishalakshi; Custer, Thomas C.; Walter, Nils G.

2013-01-01

Non-coding RNAs (ncRNAs) recently were discovered to outnumber their protein-coding counterparts, yet their diverse functions are still poorly understood. Here we report on a method for the intracellular Single-molecule High Resolution Localization and Counting (iSHiRLoC) of microRNAs (miRNAs), a conserved, ubiquitous class of regulatory ncRNAs that controls the expression of over 60% of all mammalian protein coding genes post-transcriptionally, by a mechanism shrouded by seemingly contradictory observations. We present protocols to execute single particle tracking (SPT) and single-molecule counting of functional microinjected, fluorophore-labeled miRNAs and thereby extract diffusion coefficients and molecular stoichiometries of micro-ribonucleoprotein (miRNP) complexes from living and fixed cells, respectively. This probing of miRNAs at the single molecule level sheds new light on the intracellular assembly/disassembly of miRNPs, thus beginning to unravel the dynamic nature of this important gene regulatory pathway and facilitating the development of a parsimonious model for their obscured mechanism of action. PMID:23820309

Analysis of high accuracy, quantitative proteomics data in the MaxQB database.

PubMed

Schaab, Christoph; Geiger, Tamar; Stoehr, Gabriele; Cox, Juergen; Mann, Matthias

2012-03-01

MS-based proteomics generates rapidly increasing amounts of precise and quantitative information. Analysis of individual proteomic experiments has made great strides, but the crucial ability to compare and store information across different proteome measurements still presents many challenges. For example, it has been difficult to avoid contamination of databases with low quality peptide identifications, to control for the inflation in false positive identifications when combining data sets, and to integrate quantitative data. Although, for example, the contamination with low quality identifications has been addressed by joint analysis of deposited raw data in some public repositories, we reasoned that there should be a role for a database specifically designed for high resolution and quantitative data. Here we describe a novel database termed MaxQB that stores and displays collections of large proteomics projects and allows joint analysis and comparison. We demonstrate the analysis tools of MaxQB using proteome data of 11 different human cell lines and 28 mouse tissues. The database-wide false discovery rate is controlled by adjusting the project specific cutoff scores for the combined data sets. The 11 cell line proteomes together identify proteins expressed from more than half of all human genes. For each protein of interest, expression levels estimated by label-free quantification can be visualized across the cell lines. Similarly, the expression rank order and estimated amount of each protein within each proteome are plotted. We used MaxQB to calculate the signal reproducibility of the detected peptides for the same proteins across different proteomes. Spearman rank correlation between peptide intensity and detection probability of identified proteins was greater than 0.8 for 64% of the proteome, whereas a minority of proteins have negative correlation. This information can be used to pinpoint false protein identifications, independently of peptide database scores. The information contained in MaxQB, including high resolution fragment spectra, is accessible to the community via a user-friendly web interface at http://www.biochem.mpg.de/maxqb.

SU-E-T-296: Dosimetric Analysis of Small Animal Image-Guided Irradiator Using High Resolution Optical CT Imaging of 3D Dosimeters

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

Na, Y; Qian, X; Wuu, C

Purpose: To verify the dosimetric characteristics of a small animal image-guided irradiator using a high-resolution of optical CT imaging of 3D dosimeters. Methods: PRESAEGE 3D dosimeters were used to determine dosimetric characteristics of a small animal image-guided irradiator and compared with EBT2 films. Cylindrical PRESAGE dosimeters with 7cm height and 6cm diameter were placed along the central axis of the beam. The films were positioned between 6×6cm{sup 2} cubed plastic water phantoms perpendicular to the beam direction with multiple depths. PRESAGE dosimeters and EBT2 films were then irradiated with the irradiator beams at 220kVp and 13mA. Each of irradiated PRESAGEmore » dosimeters named PA1, PA2, PB1, and PB2, was independently scanned using a high-resolution single laser beam optical CT scanner. The transverse images were reconstructed with a 0.1mm high-resolution pixel. A commercial Epson Expression 10000XL flatbed scanner was used for readout of irradiated EBT2 films at a 0.4mm pixel resolution. PDD curves and beam profiles were measured for the irradiated PRESAGE dosimeters and EBT2 films. Results: The PDD agreements between the irradiated PRESAGE dosimeter PA1, PA2, PB1, PB2 and the EB2 films were 1.7, 2.3, 1.9, and 1.9% for the multiple depths at 1, 5, 10, 15, 20, 30, 40 and 50mm, respectively. The FWHM measurements for each PRESAEGE dosimeter and film agreed with 0.5, 1.1, 0.4, and 1.7%, respectively, at 30mm depth. Both PDD and FWHM measurements for the PRESAGE dosimeters and the films agreed overall within 2%. The 20%–80% penumbral widths of each PRESAGE dosimeter and the film at a given depth were respectively found to be 0.97, 0.91, 0.79, 0.88, and 0.37mm. Conclusion: Dosimetric characteristics of a small animal image-guided irradiator have been demonstrated with the measurements of PRESAGE dosimeter and EB2 film. With the high resolution and accuracy obtained from this 3D dosimetry system, precise targeting small animal irradiation can be achieved.« less

Improving dust emission characterization in dust models using dynamic high-resolution geomorphic erodibility map

NASA Astrophysics Data System (ADS)

Parajuli, S. P.; Yang, Z.; Kocurek, G.

2013-12-01

Dust is known to affect the earth radiation budget, biogeochemical cycle, precipitation, human health and visibility. Despite the increased research effort, dust emission modeling remains challenging because dust emission is affected by complex geomorphological processes. Existing dust models overestimate dust emission and rely on tuning and a static erodibility factor in order to make simulated results comparable to remote sensing and ground-based observations. In most of current models, dust emission is expressed in terms of threshold friction speed, which ultimately depends mainly upon the percentage clay content and soil moisture. Unfortunately, due to the unavailability of accurate and high resolution input data of the clay content and soil moisture, estimated threshold friction speed commonly does not represent the variability in field condition. In this work, we attempt to improve dust emission characterization by developing a high resolution geomorphic map of the Middle East and North Africa (MENA), which is responsible for more than 50% of global dust emission. We develop this geomorphic map by visually examining high resolution satellite images obtained from Google Earth Pro and ESRI base map. Albeit subjective, our technique is more reliable compared to automatic image classification technique because we incorporate knowledge of geological/geographical setting in identifying dust sources. We hypothesize that the erodibility is unique for different geomorphic landforms and that it can be quantified by the correlation between observed wind speed and satellite retrieved aerosol optical depth (AOD). We classify the study area into several key geomorphological categories with respect to their dust emission potential. Then we quantify their dust emission potential using the correlation between observed wind speed and satellite retrieved AOD. The dynamic, high-resolution geomorphic erodibility map thus prepared will help to reduce the uncertainty in current dust models associated with poor characterization of dust sources. The baseline dust scheme used in this study is the Dust Entrainment and Deposition (DEAD) model, which is also a component of the community land model (CLM). Proposed improvements in the dust emission representation will help to better understand the accurate effect of dust on climate processes.

Expression, purification and crystallization of pecan (Carya illinoinensis) vicilin.

PubMed

Lee, BoRam; Zhang, Renhao; Du, Wen-Xian; Grauke, Larry J; McHugh, Tara H; Zhang, Yu-Zhu

2014-08-01

Tree nuts are responsible for many cases of severe food allergies. The 7S seed storage protein vicilin has been identified as a food allergen in many kinds of tree nuts. The vicilin protein consists of an N-terminal low-complexity region with antimicrobial activity and a C-terminal domain that forms a trimeric structure that belongs to the cupin superfamily. In this study, vicilin from pecan (Carya illinoinensis) was isolated and was expressed in bacteria for the first time. The cupin structural core of the protein, residues 369-792, was purified by metal-affinity and gel-filtration chromatography to high purity. Vicilin crystals were obtained and the best crystal diffracted to 2.65 Å resolution in space group P212121.

Expression, purification and crystallization of pecan (Carya illinoinensis) vicilin

PubMed Central

Lee, BoRam; Zhang, Renhao; Du, Wen-Xian; Grauke, Larry J.; McHugh, Tara H.; Zhang, Yu-Zhu

2014-01-01

Tree nuts are responsible for many cases of severe food allergies. The 7S seed storage protein vicilin has been identified as a food allergen in many kinds of tree nuts. The vicilin protein consists of an N-terminal low-complexity region with antimicrobial activity and a C-terminal domain that forms a trimeric structure that belongs to the cupin superfamily. In this study, vicilin from pecan (Carya illinoinensis) was isolated and was expressed in bacteria for the first time. The cupin structural core of the protein, residues 369–792, was purified by metal-affinity and gel-filtration chromatography to high purity. Vicilin crystals were obtained and the best crystal diffracted to 2.65 Å resolution in space group P212121. PMID:25084379

High resolution solar observations from first principles to applications

NASA Astrophysics Data System (ADS)

Verdoni, Angelo P.

2009-10-01

The expression "high-resolution observations" in Solar Physics refers to the spatial, temporal and spectral domains in their entirety. High-resolution observations of solar fine structure are a necessity to answer many of the intriguing questions related to solar activity. However, a researcher building instruments for high-resolution observations has to cope with the fact that these three domains often have diametrically opposed boundary conditions. Many factors have to be considered in the design of a successful instrument. Modern post-focus instruments are more closely linked with the solar telescopes that they serve than in past. In principle, the quest for high-resolution observations already starts with the selection of the observatory site. The site survey of the Advanced Technology Solar Telescope (ATST) under the stewardship of the National Solar Observatory (NSO) has identified Big Bear Solar Observatory (BBSO) as one of the best sites for solar observations. In a first step, the seeing characteristics at BBSO based on the data collected for the ATST site survey are described. The analysis will aid in the scheduling of high-resolution observations at BBSO as well as provide useful information concerning the design and implementation of a thermal control system for the New Solar Telescope (NST). NST is an off-axis open-structure Gregorian-style telescope with a 1.6 m aperture. NST will be housed in a newly constructed 5/8-sphere ventilated dome. With optics exposed to the surrounding air, NST's open-structure design makes it particularly vulnerable to the effects of enclosure-related seeing. In an effort to mitigate these effects, the initial design of a thermal control system for the NST dome is presented. The goal is to remediate thermal related seeing effects present within the dome interior. The THermal Control System (THCS) is an essential component for the open-telescope design of NST to work. Following these tasks, a calibration routine for the polarization optics for the Visible-light Imaging Magnetograph (VIM) is presented. VIM uses a set of two Liquid Crystal Variable Retarders (LCVRs) as the main components of its Stokes analyzer. Calibration of these components is a crucial step in providing reliable polarimetric measurements of the Sun using VIM. On 2007 July 15, using the Dunn Solar Telescope (DST) at the National Solar Observatory at Sacramento Peak (NSO/SP), New Mexico, the first polarimetric measurements using VIM were made. As a final step, illustrating an application of high-resolution solar observations, the results of a two-dimensional time-series acquired on 2006 June 11, using the DST at NSOP is presented. The data is used in a study of upflow events that are observed to occur in the Halpha 656.3 nm and Na D2 589.0 nm chromospheric absorption lines.

Distinct Protein Expression Profiles of Solid-Pseudopapillary Neoplasms of the Pancreas.

PubMed

Park, Minhee; Lim, Jong-Sun; Lee, Hyoung-Joo; Na, Keun; Lee, Min Jung; Kang, Chang Moo; Paik, Young-Ki; Kim, Hoguen

2015-08-07

Solid-pseudopapillary neoplasm (SPN) is an uncommon pancreatic tumor with mutation in CTNNB1 and distinct clinical and pathological features. We compared the proteomic profiles of SPN to mRNA expression. Pooled SPNs and pooled non-neoplastic pancreatic tissues were examined with high-resolution mass spectrometry. We identified 329 (150 up-regulated and 179 down-regulated) differentially expressed proteins in SPN. We identified 191 proteins (58.1% of the 329 dysregulated proteins) with the same expression tendencies in SPN based on mRNA data. Many overexpressed proteins were related to signaling pathways known to be activated in SPNs. We found that several proteins involved in Wnt signaling, including DKK4 and β-catenin, and proteins that bind β-catenin, such as FUS and NONO, were up-regulated in SPNs. Molecules involved in glycolysis, including PKM2, ENO2, and HK1, were overexpressed in accordance to their mRNA levels. In summary, SPN showed (1) distinct protein expression changes that correlated with mRNA expression, (2) overexpression of Wnt signaling proteins and proteins that bind directly to β-catenin, and (3) overexpression of proteins involved in metabolism. These findings may help develop early diagnostic biomarkers and molecular targets.

A resolution expressing support for designation of a "Welcome Home Vietnam Veterans Day".

THOMAS, 112th Congress

Sen. Burr, Richard [R-NC

2011-02-16

Senate - 03/07/2011 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution expressing support for designation of a "Welcome Home Vietnam Veterans Day".

THOMAS, 111th Congress

Sen. Burr, Richard [R-NC

2010-03-11

Senate - 03/19/2010 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

The imaging performance of the SRC on Mars Express

USGS Publications Warehouse

Oberst, J.; Schwarz, G.; Behnke, T.; Hoffmann, H.; Matz, K.-D.; Flohrer, J.; Hirsch, H.; Roatsch, T.; Scholten, F.; Hauber, E.; Brinkmann, B.; Jaumann, R.; Williams, D.; Kirk, R.; Duxbury, T.; Leu, C.; Neukum, G.

2008-01-01

The Mars Express spacecraft carries the pushbroom scanner high-resolution stereo camera (HRSC) and its added imaging subsystem super resolution channel (SRC). The SRC is equipped with its own optical system and a 1024??1024 framing sensor. SRC produces snapshots with 2.3 m ground pixel size from the nominal spacecraft pericenter height of 250 km, which are typically embedded in the central part of the large HRSC scenes. The salient features of the SRC are its light-weight optics, a reliable CCD detector, and high-speed read-out electronics. The quality and effective visibility of details in the SRC images unfortunately falls short of what has been expected. In cases where thermal balance cannot be reached, artifacts, such as blurring and "ghost features" are observed in the images. In addition, images show large numbers of blemish pixels and are plagued by electronic noise. As a consequence, we have developed various image improving algorithms, which are discussed in this paper. While results are encouraging, further studies of image restoration by dedicated processing appear worthwhile. The SRC has obtained more than 6940 images at the time of writing (1 September 2007), which often show fascinating details in surface morphology. SRC images are highly useful for a variety of applications in planetary geology, for studies of the Mars atmosphere, and for astrometric observations of the Martian satellites. This paper will give a full account of the design philosophy, technical concept, calibration, operation, integration with HRSC, and performance, as well as science accomplishments of the SRC. ?? 2007 Elsevier Ltd. All rights reserved.

New validated high-performance liquid chromatographic method for simultaneous analysis of ten flavonoid aglycones in plant extracts using a C18 fused-core column and acetonitrile-tetrahydrofuran gradient.

PubMed

Olszewska, Monika A

2012-09-01

An HPLC method of high resolution has been developed and validated for the simultaneous determination of ten prominent flavonoid aglycones in plant materials using a fused-core C18-silica column (Ascentis® Express, 4.6 mm × 150 mm, 2.7 μm). The separation was accomplished with an acetonitrile-tetrahydrofuran gradient elution at a flow rate of 1 mL/min and temperature of 30°C. UV spectrophotometric detection was employed at 370 nm for flavonols (quercetin [QU], myricetin [MY], isorhamnetin [IS], kaempferol [KA], sexangularetin [SX], and limocitrin [LM]) and 340 nm for flavones (apigenin [AP], acacetin [AC], chrysoeriol [CH], and luteolin [LU]). The high resolution of critical pairs QU/LU (10.50), QU/CH (3.40), AP/CH (2.51), SX/LM (2.30), and IS/KA (2.70) was achieved within 30.3 min. The observed column back pressure was less than 4300 psi, thus acceptable for conventional HPLC equipment. The method was sensitive enough having LODs of 0.115-0.525 ng and good linearity (r > 0.9999) over the test range. The precision values, expressed as RSD values, were <7.5%, and the accuracy was in the range of 95.3-100.2% for all analytes except MY (73.8%). The method was successfully employed for the determination of flavonoids in several medicinal plants, such as Ginkgo biloba, Betula pendula, and a variety of Sorbus species. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

New Researches and Application Progress of Commonly Used Optical Molecular Imaging Technology

PubMed Central

Chen, Zhi-Yi; Yang, Feng; Lin, Yan; Zhou, Qiu-Lan; Liao, Yang-Ying

2014-01-01

Optical molecular imaging, a new medical imaging technique, is developed based on genomics, proteomics and modern optical imaging technique, characterized by non-invasiveness, non-radiativity, high cost-effectiveness, high resolution, high sensitivity and simple operation in comparison with conventional imaging modalities. Currently, it has become one of the most widely used molecular imaging techniques and has been applied in gene expression regulation and activity detection, biological development and cytological detection, drug research and development, pathogenesis research, pharmaceutical effect evaluation and therapeutic effect evaluation, and so forth, This paper will review the latest researches and application progresses of commonly used optical molecular imaging techniques such as bioluminescence imaging and fluorescence molecular imaging. PMID:24696850

Gingival tissue transcriptomes in experimental gingivitis

PubMed Central

Jönsson, Daniel; Ramberg, Per; Demmer, Ryan T.; Kebschull, Moritz; Dahlén, Gunnar; Papapanou, Panos N.

2012-01-01

Aims We investigated the sequential gene expression in the gingiva during the induction and resolution of experimental gingivitis. Methods Twenty periodontally and systemically healthy non-smoking volunteers participated in a 3-week experimental gingivitis protocol, followed by debridement and 2-week regular plaque control. We recorded clinical indices and harvested gingival tissue samples from 4 interproximal palatal sites in half of the participants at baseline, Day 7, 14 and 21 (‘induction phase’), and at day 21, 25, 30 and 35 in the other half (‘resolution phase’). RNA was extracted, amplified, reversed transcribed, amplified, labeled and hybridized with Affymetrix Human Genome U133Plus2.0 microarrays. Paired t-tests compared gene expression changes between consecutive time points. Gene ontology analyses summarized the expression patterns into biologically relevant categories. Results The median gingival index was 0 at baseline, 2 at Day 21 and 1 at Day 35. Differential gene regulation peaked during the third week of induction and the first four days of resolution. Leukocyte transmigration, cell adhesion and antigen processing/presentation were the top differentially regulated pathways. Conclusions Transcriptomic studies enhance our understanding of the pathobiology of the reversible inflammatory gingival lesion and provide a detailed account of the dynamic tissue responses during induction and resolution of experimental gingivitis. PMID:21501207

Analysis of specific RNA in cultured cells through quantitative integration of q-PCR and N-SIM single cell FISH images: Application to hormonal stimulation of StAR transcription.

PubMed

Lee, Jinwoo; Foong, Yee Hoon; Musaitif, Ibrahim; Tong, Tiegang; Jefcoate, Colin

2016-07-05

The steroidogenic acute regulatory protein (StAR) has been proposed to serve as the switch that can turn on/off steroidogenesis. We investigated the events that facilitate dynamic StAR transcription in response to cAMP stimulation in MA-10 Leydig cells, focusing on splicing anomalies at StAR gene loci. We used 3' reverse primers in a single reaction to respectively quantify StAR primary (p-RNA), spliced (sp-RNA/mRNA), and extended 3' untranslated region (UTR) transcripts, which were quantitatively imaged by high-resolution fluorescence in situ hybridization (FISH). This approach delivers spatio-temporal resolution of initiation and splicing at single StAR loci, and transfers individual mRNA molecules to cytoplasmic sites. Gene expression was biphasic, initially showing slow splicing, transitioning to concerted splicing. The alternative 3.5-kb mRNAs were distinguished through the use of extended 3'UTR probes, which exhibited distinctive mitochondrial distribution. Combining quantitative PCR and FISH enables imaging of localization of RNA expression and analysis of RNA processing rates. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

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

Assenberg, René; Delmas, Olivier; Graham, Stephen C.

The expression, purification and crystallization of the full-length matrix protein from three lyssaviruses is described. The matrix (M) proteins of lyssaviruses (family Rhabdoviridae) are crucial to viral morphogenesis as well as in modulating replication and transcription of the viral genome. To date, no high-resolution structural information has been obtained for full-length rhabdovirus M. Here, the cloning, expression and purification of the matrix proteins from three lyssaviruses, Lagos bat virus (LAG), Mokola virus and Thailand dog virus, are described. Crystals have been obtained for the full-length M protein from Lagos bat virus (LAG M). Successful crystallization depended on a number ofmore » factors, in particular the addition of an N-terminal SUMO fusion tag to increase protein solubility. Diffraction data have been recorded from crystals of native and selenomethionine-labelled LAG M to 2.75 and 3.0 Å resolution, respectively. Preliminary analysis indicates that these crystals belong to space group P6{sub 1}22 or P6{sub 5}22, with unit-cell parameters a = b = 56.9–57.2, c = 187.9–188.6 Å, consistent with the presence of one molecule per asymmetric unit, and structure determination is currently in progress.« less

Local Lunar Gravity Field Analysis over the South Pole-aitken Basin from SELENE Farside Tracking Data

NASA Technical Reports Server (NTRS)

Goossens, Sander Johannes; Ishihara, Yoshiaki; Matsumoto, Koji; Sasaki, Sho

2012-01-01

We present a method with which we determined the local lunar gravity field model over the South Pole-Aitken (SPA) basin on the farside of the Moon by estimating adjustments to a global lunar gravity field model using SELENE tracking data. Our adjustments are expressed in localized functions concentrated over the SPA region in a spherical cap with a radius of 45deg centered at (191.1 deg E, 53.2 deg S), and the resolution is equivalent to a 150th degree and order spherical harmonics expansion. The new solution over SPA was used in several applications of geophysical analysis. It shows an increased correlation with high-resolution lunar topography in the frequency band l = 40-70, and admittance values are slightly different and more leveled when compared to other, global gravity field models using the same data. The adjustments expressed in free-air anomalies and differences in Bouguer anomalies between the local solution and the a priori global solution correlate with topographic surface features. The Moho structure beneath the SPA basin is slightly modified in our solution, most notably at the southern rim of the Apollo basin and around the Zeeman crater

Multiple resolution chirp reflectometry for fault localization and diagnosis in a high voltage cable in automotive electronics

NASA Astrophysics Data System (ADS)

Chang, Seung Jin; Lee, Chun Ku; Shin, Yong-June; Park, Jin Bae

2016-12-01

A multiple chirp reflectometry system with a fault estimation process is proposed to obtain multiple resolution and to measure the degree of fault in a target cable. A multiple resolution algorithm has the ability to localize faults, regardless of fault location. The time delay information, which is derived from the normalized cross-correlation between the incident signal and bandpass filtered reflected signals, is converted to a fault location and cable length. The in-phase and quadrature components are obtained by lowpass filtering of the mixed signal of the incident signal and the reflected signal. Based on in-phase and quadrature components, the reflection coefficient is estimated by the proposed fault estimation process including the mixing and filtering procedure. Also, the measurement uncertainty for this experiment is analyzed according to the Guide to the Expression of Uncertainty in Measurement. To verify the performance of the proposed method, we conduct comparative experiments to detect and measure faults under different conditions. Considering the installation environment of the high voltage cable used in an actual vehicle, target cable length and fault position are designed. To simulate the degree of fault, the variety of termination impedance (10 Ω , 30 Ω , 50 Ω , and 1 \\text{k} Ω ) are used and estimated by the proposed method in this experiment. The proposed method demonstrates advantages in that it has multiple resolution to overcome the blind spot problem, and can assess the state of the fault.

3D Cryo-Imaging: A Very High-Resolution View of the Whole Mouse

PubMed Central

Roy, Debashish; Steyer, Grant J.; Gargesha, Madhusudhana; Stone, Meredith E.; Wilson, David L.

2009-01-01

We developed the Case Cryo-imaging system that provides information rich, very high-resolution, color brightfield, and molecular fluorescence images of a whole mouse using a section-and-image block-face imaging technology. The system consists of a mouse-sized, motorized cryo-microtome with special features for imaging, a modified, brightfield/ fluorescence microscope, and a robotic xyz imaging system positioner, all of which is fully automated by a control system. Using the robotic system, we acquired microscopic tiled images at a pixel size of 15.6 µm over the block face of a whole mouse sectioned at 40 µm, with a total data volume of 55 GB. Viewing 2D images at multiple resolutions, we identified small structures such as cardiac vessels, muscle layers, villi of the small intestine, the optic nerve, and layers of the eye. Cryo-imaging was also suitable for imaging embryo mutants in 3D. A mouse, in which enhanced green fluorescent protein was expressed under gamma actin promoter in smooth muscle cells, gave clear 3D views of smooth muscle in the urogenital and gastrointestinal tracts. With cryo-imaging, we could obtain 3D vasculature down to 10 µm, over very large regions of mouse brain. Software is fully automated with fully programmable imaging/sectioning protocols, email notifications, and automatic volume visualization. With a unique combination of field-of-view, depth of field, contrast, and resolution, the Case Cryo-imaging system fills the gap between whole animal in vivo imaging and histology. PMID:19248166

The employment of weather satellite imagery in an effort to identify and locate the forest-tundra ecotone in Canada

NASA Technical Reports Server (NTRS)

Aldrich, S. A.; Aldrich, F. T.; Rudd, R. D.

1969-01-01

Weather satellite imagery provides the only routinely available orbital imagery depicting the high latitudes. Although resolution is low on this imagery, it is believed that a major natural feature, notably linear in expression, should be mappable on it. The transition zone from forest to tundra, the ecotone, is such a feature. Locational correlation is herein established between a linear signature on the imagery and several ground truth positions of the ecotone in Canada.

A Green-Light-Responsive System for the Control of Transgene Expression in Mammalian and Plant Cells.

PubMed

Chatelle, Claire; Ochoa-Fernandez, Rocio; Engesser, Raphael; Schneider, Nils; Beyer, Hannes M; Jones, Alex R; Timmer, Jens; Zurbriggen, Matias D; Weber, Wilfried

2018-05-18

The ever-increasing complexity of synthetic gene networks and applications of synthetic biology requires precise and orthogonal gene expression systems. Of particular interest are systems responsive to light as they enable the control of gene expression dynamics with unprecedented resolution in space and time. While broadly used in mammalian backgrounds, however, optogenetic approaches in plant cells are still limited due to interference of the activating light with endogenous photoreceptors. Here, we describe the development of the first synthetic light-responsive system for the targeted control of gene expression in mammalian and plant cells that responds to the green range of the light spectrum in which plant photoreceptors have minimal activity. We first engineered a system based on the light-sensitive bacterial transcription factor CarH and its cognate DNA operator sequence CarO from Thermus thermophilus to control gene expression in mammalian cells. The system was functional in various mammalian cell lines, showing high induction (up to 350-fold) along with low leakiness, as well as high reversibility. We quantitatively described the systems characteristics by the development and experimental validation of a mathematical model. Finally, we transferred the system into A. thaliana protoplasts and demonstrated gene repression in response to green light. We expect that this system will provide new opportunities in applications based on synthetic gene networks and will open up perspectives for optogenetic studies in mammalian and plant cells.

Human CD68 promoter GFP transgenic mice allow analysis of monocyte to macrophage differentiation in vivo

PubMed Central

Iqbal, Asif J.; McNeill, Eileen; Kapellos, Theodore S.; Regan-Komito, Daniel; Norman, Sophie; Burd, Sarah; Smart, Nicola; Machemer, Daniel E. W.; Stylianou, Elena; McShane, Helen; Channon, Keith M.; Chawla, Ajay

2014-01-01

The recruitment of monocytes and their differentiation into macrophages at sites of inflammation are key events in determining the outcome of the inflammatory response and initiating the return to tissue homeostasis. To study monocyte trafficking and macrophage differentiation in vivo, we have generated a novel transgenic reporter mouse expressing a green fluorescent protein (GFP) under the control of the human CD68 promoter. CD68-GFP mice express high levels of GFP in both monocyte and embryo-derived tissue resident macrophages in adult animals. The human CD68 promoter drives GFP expression in all CD115+ monocytes of adult blood, spleen, and bone marrow; we took advantage of this to directly compare the trafficking of bone marrow–derived CD68-GFP monocytes to that of CX3CR1GFP monocytes in vivo using a sterile zymosan peritonitis model. Unlike CX3CR1GFP monocytes, which downregulate GFP expression on differentiation into macrophages in this model, CD68-GFP monocytes retain high-level GFP expression for 72 hours after differentiation into macrophages, allowing continued cell tracking during resolution of inflammation. In summary, this novel CD68-GFP transgenic reporter mouse line represents a powerful resource for analyzing monocyte mobilization and monocyte trafficking as well as studying the fate of recruited monocytes in models of acute and chronic inflammation. PMID:25030063

Human CD68 promoter GFP transgenic mice allow analysis of monocyte to macrophage differentiation in vivo.

PubMed

Iqbal, Asif J; McNeill, Eileen; Kapellos, Theodore S; Regan-Komito, Daniel; Norman, Sophie; Burd, Sarah; Smart, Nicola; Machemer, Daniel E W; Stylianou, Elena; McShane, Helen; Channon, Keith M; Chawla, Ajay; Greaves, David R

2014-10-09

The recruitment of monocytes and their differentiation into macrophages at sites of inflammation are key events in determining the outcome of the inflammatory response and initiating the return to tissue homeostasis. To study monocyte trafficking and macrophage differentiation in vivo, we have generated a novel transgenic reporter mouse expressing a green fluorescent protein (GFP) under the control of the human CD68 promoter. CD68-GFP mice express high levels of GFP in both monocyte and embryo-derived tissue resident macrophages in adult animals. The human CD68 promoter drives GFP expression in all CD115(+) monocytes of adult blood, spleen, and bone marrow; we took advantage of this to directly compare the trafficking of bone marrow-derived CD68-GFP monocytes to that of CX3CR1(GFP) monocytes in vivo using a sterile zymosan peritonitis model. Unlike CX3CR1(GFP) monocytes, which downregulate GFP expression on differentiation into macrophages in this model, CD68-GFP monocytes retain high-level GFP expression for 72 hours after differentiation into macrophages, allowing continued cell tracking during resolution of inflammation. In summary, this novel CD68-GFP transgenic reporter mouse line represents a powerful resource for analyzing monocyte mobilization and monocyte trafficking as well as studying the fate of recruited monocytes in models of acute and chronic inflammation. © 2014 by The American Society of Hematology.

HRSCview: a web-based data exploration system for the Mars Express HRSC instrument

NASA Astrophysics Data System (ADS)

Michael, G.; Walter, S.; Neukum, G.

2007-08-01

The High Resolution Stereo Camera (HRSC) on the ESA Mars Express spacecraft has been orbiting Mars since January 2004. By spring 2007 it had returned around 2 terabytes of image data, covering around 35% of the Martian surface in stereo and colour at a resolu-tion of 10-20 m/pixel. HRSCview provides a rapid means to explore these images up to their full resolu-tion with the data-subsetting, sub-sampling, stretching and compositing being carried out on-the-fly by the image server. It is a joint website of the Free University of Berlin and the German Aerospace Center (DLR). The system operates by on-the-fly processing of the six HRSC level-4 image products: the map-projected ortho-rectified nadir pan-chromatic and four colour channels, and the stereo-derived DTM (digital terrain model). The user generates a request via the web-page for an image with several parameters: the centre of the view in surface coordinates, the image resolution in metres/pixel, the image dimensions, and one of several colour modes. If there is HRSC coverage at the given location, the necessary segments are extracted from the full orbit images, resampled to the required resolution, and composited according to the user's choice. In all modes the nadir channel, which has the highest resolu-tion, is included in the composite so that the maximum detail is always retained. The images are stretched ac-cording to the current view: this applies to the eleva-tion colour scale, as well as the nadir brightness and the colour channels. There are modes for raw colour, stretched colour, enhanced colour (exaggerated colour differences), and a synthetic 'Mars-like' colour stretch. A colour ratio mode is given as an alternative way to examine colour differences (R=IR/R, G=R/G and B=G/B). The final image is packaged as a JPEG file and returned to the user over the web. Each request requires approximately 1 second to process. A link is provided from each view to a data product page, where header items describing the full map-projected science data product are displayed, and a direct link to the archived data products on the ESA Planetary Science Archive (PSA) is provided. At pre-sent the majority of the elevation composites are de-rived from the HRSC Preliminary 200m DTMs gener-ated at the German Aerospace Center (DLR), which will not be available as separately downloadable data products. These DTMs are being progressively super-seded by systematically generated higher resolution archival DTMs, also from DLR, which will become available for download through the PSA, and be simi-larly accessible via HRSCview. At the time of writing this abstract (May 2007), four such high resolution DTMs are available for download via the HRSCview data product pages (for images from orbits 0572, 0905, 1004, and 2039).

Hypothyroidism leads to increased collagen-based stiffness and re-expression of large cardiac titin isoforms with high compliance.

PubMed

Wu, Yiming; Peng, Jun; Campbell, Kenneth B; Labeit, Siegfried; Granzier, Henk

2007-01-01

Because long-term hypothyroidism results in diastolic dysfunction, we investigated myocardial passive stiffness in hypothyroidism and focused on the possible role of titin, an important determinant of diastolic stiffness. A rat model of hypothyroidism was used, obtained by administering propylthiouracil (PTU) for times that varied from 1 month (short-term) to 4 months (long-term). Titin expression was determined by transcript analysis, gel electrophoresis and immunoelectron microscopy. Diastolic function was measured at the isolated heart, skinned muscle, and cardiac myocyte levels. We found that hypothyroidism resulted in expression of a large titin isoform, the abundance of which gradually increased with time to become the most dominant isoform in long-term hypothyroid rats. This isoform co-migrates on high-resolution gels with fetal cardiac titin. Transcript analysis on myocardium of long-term PTU rats, provided evidence for expression of additional PEVK and Ig domain exons, similar to what has been described in fetal myocardium. Consistent with the expression of a large titin isoform, titin-based restoring and passive forces were significantly reduced in single cardiac myocytes and muscle strips of long-term hypothyroid rats. Overall muscle stiffness and LV diastolic wall stiffness were increased, however, due to increased collagen-based stiffness. We conclude that long term hypothyroidism triggers expression of a large cardiac titin isoform and that the ensuing reduction in titin-based passive stiffness functions as a compensatory mechanism to reduce LV wall stiffness.

Optical-sectioning microscopy of protoporphyrin IX fluorescence in human gliomas: standardization and quantitative comparison with histology

NASA Astrophysics Data System (ADS)

Wei, Linpeng; Chen, Ye; Yin, Chengbo; Borwege, Sabine; Sanai, Nader; Liu, Jonathan T. C.

2017-04-01

Systemic delivery of 5-aminolevulinic acid leads to enhanced fluorescence image contrast in many tumors due to the increased accumulation of protoporphyrin IX (PpIX), a fluorescent porphyrin that is associated with tumor burden and proliferation. The value of PpIX-guided resection of malignant gliomas has been demonstrated in prospective randomized clinical studies in which a twofold greater extent of resection and improved progression-free survival have been observed. In low-grade gliomas and at the diffuse infiltrative margins of all gliomas, PpIX fluorescence is often too weak to be detected with current low-resolution surgical microscopes that are used in operating rooms. However, it has been demonstrated that high-resolution optical-sectioning microscopes are capable of detecting the sparse and punctate accumulations of PpIX that are undetectable via conventional low-power surgical fluorescence microscopes. To standardize the performance of high-resolution optical-sectioning devices for future clinical use, we have developed an imaging phantom and methods to ensure that the imaging of PpIX-expressing brain tissues can be performed reproducibly. Ex vivo imaging studies with a dual-axis confocal microscope demonstrate that these methods enable the acquisition of images from unsectioned human brain tissues that quantitatively and consistently correlate with images of histologically processed tissue sections.

Fluctuations in Species-Level Protein Expression Occur during Element and Nutrient Cycling in the Subsurface

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

Wilkins, Michael J.; Wrighton, Kelly C.; Nicora, Carrie D.

2013-03-05

While microbial activities in environmental systems play a key role in the utilization and cycling of essential elements and compounds, microbial activity and growth frequently fluctuates in response to environmental stimuli and perturbations. To investigate these fluctuations within a saturated aquifer system, we monitored a carbon-stimulated in situ Geobacter population while iron reduction was occurring, using 16S rRNA abundances and high-resolution tandem mass spectrometry proteome measurements. Following carbon amendment, 16S rRNA analysis of temporally separated samples revealed the rapid enrichment of Geobacter-like environmental strains with strong similarity to G. bemidjiensis. Tandem mass spectrometry proteomics measurements suggest high carbon flux throughmore » Geobacter respiratory pathways, and the synthesis of anapleurotic four carbon compounds from acetyl-CoA via pyruvate ferredoxin oxidoreductase activity. Across a 40-day period where Fe(III) reduction was occurring, fluctuations in protein expression reflected changes in anabolic versus catabolic reactions, with increased levels of biosynthesis occurring soon after acetate arrival in the aquifer. In addition, localized shifts in nutrient limitation were inferred based on expression of nitrogenase enzymes and phosphate uptake proteins. These temporal data offer the first example of differing microbial protein expression associated with changing geochemical conditions in a subsurface environment.« less

Comparative Proteomic Analysis of Yak Follicular Fluid during Estrus

PubMed Central

Guo, Xian; Pei, Jie; Ding, Xuezhi; Chu, Min; Bao, Pengjia; Wu, Xiaoyun; Liang, Chunnian; Yan, Ping

2016-01-01

The breeding of yaks is highly seasonal, there are many crucial proteins involved in the reproduction control program, especially in follicular development. In order to isolate differential proteins between mature and immature follicular fluid (FF) of yak, the FF from yak follicles with different sizes were sampled respectively, and two-dimensional gel electrophoresis (2-DE) of the proteins was carried out. After silver staining, the Image Master 2D platinum software was used for protein analysis and matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) was performed for differential protein identification. The expression level of transferrin and enolase superfamily member 1 (ENOSF1) was determined by Western blotting for verification analysis. The results showed that 2-DE obtained an electrophoresis map of proteins from mature and immature yak FF with high resolution and repeatability. A comparison of protein profiles identified 12 differently expressed proteins, out of which 10 of them were upregulated while 2 were downregulated. Western blotting showed that the expression of transferrin and ENOSF1 was enhanced with follicular development. Both the obtained protein profiles and the differently expressed proteins identified in this study provided experimental data related to follicular development during yak breeding seasons. This study also laid the foundation for understanding the microenvironment during oocyte development. PMID:26954118

Microvascular pericytes express platelet-derived growth factor-beta receptors in human healing wounds and colorectal adenocarcinoma.

PubMed Central

Sundberg, C.; Ljungström, M.; Lindmark, G.; Gerdin, B.; Rubin, K.

1993-01-01

The expression of platelet-derived growth factor- beta (PDGF-beta) receptors in the microvasculature of human healing wounds and colorectal adenocarcinoma was investigated. Frozen sections were subjected to double immunofluorescence staining using monoclonal antibodies (MAbs) specific for pericytes (MAb 225.28 recognizing the high-molecular weight-melanoma-associated antigen, expressed by activated pericytes during angiogenesis), endothelial cells (MAb PAL-E), laminin, as well as PDGF-beta receptors (MAb PDGFR-B2) and its ligand PDGF-B chain (MAb PDGF 007). Stained sections were analyzed by computer-aided imaging processing that allowed for a numerical quantification of the degree of colocalization of the investigated antigens. An apparent background colocalization, varying between 23 and 35%, between markers for cells not expected to co-localize was recorded. This background could be due to limitations of camera resolution, to out-of-focus fluorescence, and to interdigitations of the investigated structures. In all six tumor specimens, co-localization of PDGF-beta receptors and PAL-E was not different from the background co-localization, whereas that of PDGF-beta receptors and high-molecular weight-melanoma-associated antigen was significantly higher with mean values between 57 and 71%. Qualitatively, the same pattern was obtained in the two investigated healing wounds. PDGF-B chain did not co-localize with either PAL-E or high-molecular weight-melanoma-associated antigen, but PDGF-B chain-expressing cells were, however, frequently found juxtaposed to the microvasculature. The expression of PDGF-beta receptors on pericytes in activated microvessels and the presence of PDGF-B chain-expressing cells in close proximity to the microvasculature of healing wounds and colorectal adenocarcinoma is compatible with a role for PDGF in the physiology of the microvasculature in these conditions. Images Figure 1 p1381-a Figure 3 Figure 4 PMID:8238254

A resolution to express the sense of the Senate on international parental child abduction.

THOMAS, 112th Congress

Sen. Boxer, Barbara [D-CA

2012-08-02

Senate - 12/04/2012 Resolution agreed to in Senate with an amendment and an amended preamble by Voice Vote. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution expressing the sense of the Senate on religious minorities in Iraq.

THOMAS, 111th Congress

Sen. Levin, Carl [D-MI

2009-10-26

Senate - 08/05/2010 Resolution agreed to in Senate with an amendment and an amended preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution to express the sense of the Senate regarding the importance of public diplomacy.

THOMAS, 111th Congress

Sen. Lugar, Richard G. [R-IN

2009-02-13

Senate - 05/19/2009 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

Attenuation tomography of the main volcanic regions of the Campanian Plain.

NASA Astrophysics Data System (ADS)

de Siena, Luca; Del Pezzo, Edoardo; Bianco, Francesca

2010-05-01

Passive, high resolution attenuation tomography is used to image the geological structure in the first upper 4 km of shallow crust beneath the Campanian Plain. Images were produced by two separate attenuation tomography studies of the main volcanic regions of the Campanian Plain, Southern Italy, Mt. Vesuvius volcano and Campi Flegrei caldera. The three-dimensional S wave attenuation tomography of Mt. Vesuvius has been obtained with multiple measurements of coda-normalized S-wave spectra of local small magnitude earthquakes. P-wave attenuation tomography was performed using classical spectral methods. The images were obtained inverting the spectral data with a multiple resolution approach expressively designed for attenuation tomography. This allowed to obtain a robust attenuation image of the volumes under the central cone at a maximum resolution of 300 m. The same approach was applied to a data set recorded in the Campi Flegrei area during the 1982-1984 seismic crisis. Inversion ensures a minimum cell size resolution of 500 meters in the zones with sufficient ray coverage, and 1000 meters outside these zones. The study of the resolution matrix as well as the synthetic tests guarantee an optimal reproduction of the input anomalies in the center of the caldera, between 0 and 3.5 km in depth. Results allowed an unprecedented view of several features of the medium, like the residual part of solidified magma from the last eruption, under the central cone of Mt. Vesuvius, and the feeding systems and top of the carbonate basement, 3 km depth below both volcanic areas. Vertical Q contrast image important fault zones, such as the La Starza fault, as well as high attenuation structures that correspond to gas or fluid reservoirs, and reveal the upper part of gas bearing conduits connecting these high attenuation volumes with the magma sill revealed at about 7 km in depth by passive travel-time tomography under the whole Campanian Plain.

Mix & match electron beam & scanning probe lithography for high throughput sub-10 nm lithography

NASA Astrophysics Data System (ADS)

Kaestner, Marcus; Hofer, Manuel; Rangelow, Ivo W.

2013-03-01

The prosperous demonstration of a technique able to produce features with single nanometer (SN) resolution could guide the semiconductor industry into the desired beyond CMOS era. In the lithographic community immense efforts are being made to develop extreme ultra-violet lithography (EUVL) and multiple-e-beam direct-write systems as possible successor for next generation lithography (NGL). However, patterning below 20 nm resolution and sub-10 nm overlay alignment accuracy becomes an extremely challenging quest. Herein, the combination of electron beam lithography (EBL) or EUVL with the outstanding capabilities of closed-loop scanning proximal probe nanolithography (SPL) reveals a promising way to improve both patterning resolution and reproducibility in combination with excellent overlay and placement accuracy. In particular, the imaging and lithographic resolution capabilities provided by scanning probe microscopy (SPM) methods touches the atomic level, which expresses the theoretical limit of constructing nanoelectronic devices. Furthermore, the symbiosis between EBL (EUVL) and SPL expands the process window of EBL (EUVL) far beyond state-of-the-art allowing SPL-based pre- and post-patterning of EBL (EUVL) written features at critical dimension level with theoretically nanometer precise pattern overlay alignment. Moreover, we can modify the EBL (EUVL) pattern before as well as after the development step. In this paper we demonstrate proof of concept using the ultra-high resolution molecular glass resist calixarene. Therefor we applied Gaussian E-beam lithography system operating at 10 keV and a home-developed SPL set-up. The introduced Mix and Match lithography strategy enables a powerful use of our SPL set-up especially as post-patterning tool for inspection and repair functions below the sub-10 nm critical dimension level.

A preliminary neutron diffraction study of rasburicase, a recombinant urate oxidase enzyme, complexed with 8-azaxanthin

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

Budayova-Spano, Monika, E-mail: spano@embl-grenoble.fr; Institut Laue-Langevin, 6 Rue Jules Horowitz, BP 156, 38042 Grenoble; Bonneté, Françoise

2006-03-01

Neutron diffraction data of hydrogenated recombinant urate oxidase enzyme (Rasburicase), complexed with a purine-type inhibitor 8-azaxanthin, was collected to 2.1 Å resolution from a crystal grown in D{sub 2}O by careful control and optimization of crystallization conditions via knowledge of the phase diagram. Deuterium atoms were clearly seen in the neutron-scattering density map. Crystallization and preliminary neutron diffraction measurements of rasburicase, a recombinant urate oxidase enzyme expressed by a genetically modified Saccharomyces cerevisiae strain, complexed with a purine-type inhibitor (8-azaxanthin) are reported. Neutron Laue diffraction data were collected to 2.1 Å resolution using the LADI instrument from a crystal (grownmore » in D{sub 2}O) with volume 1.8 mm{sup 3}. The aim of this neutron diffraction study is to determine the protonation states of the inhibitor and residues within the active site. This will lead to improved comprehension of the enzymatic mechanism of this important enzyme, which is used as a protein drug to reduce toxic uric acid accumulation during chemotherapy. This paper illustrates the high quality of the neutron diffraction data collected, which are suitable for high-resolution structural analysis. In comparison with other neutron protein crystallography studies to date in which a hydrogenated protein has been used, the volume of the crystal was relatively small and yet the data still extend to high resolution. Furthermore, urate oxidase has one of the largest primitive unit-cell volumes (space group I222, unit-cell parameters a = 80, b = 96, c = 106 Å) and molecular weights (135 kDa for the homotetramer) so far successfully studied with neutrons.« less

A resolution expressing the sense of the Senate with respect to ongoing violations of the territorial integrity and sovereignty of Georgia and the importance of a peaceful and just resolution to the conflict within Georgia's internationally recognized borders.

THOMAS, 112th Congress

Sen. Shaheen, Jeanne [D-NH

2011-05-10

Senate - 07/29/2011 Resolution agreed to in Senate without amendment and with a preamble by Voice Vote. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

X-ray detection capability of a BaCl{sub 2} single crystal scintillator

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

Koshimizu, Masanori; CREST, Japan Science and Technology Agency, Sanbancho, Chiyoda-ku, Tokyo 102-0075; Onodera, Kazuya

2012-01-15

The x-ray detection capability of a scintillation detector equipped with a BaCl{sub 2} single crystal was evaluated. The scintillation decay kinetics can be expressed by a sum of two exponential decay components. The fast and slow components have lifetimes of 1.5 and 85 ns, respectively. The total light output is 5% that of YAP:Ce. A subnanosecond timing resolution was obtained. The detection efficiency of a 67.41 keV x-ray is 87% for a detector equipped with a BaCl{sub 2} crystal 6-mm thick. Thus, excellent timing resolution and high detection efficiency can be simultaneously achieved. Additionally, luminescence decay characteristics under vacuum ultravioletmore » excitation have been investigated. Radiative decay of self-trapped excitons is thought to be responsible for the fast scintillation component.« less

Over-expression and purification strategies for recombinant multi-protein oligomers: a case study of Mycobacterium tuberculosis σ/anti-σ factor protein complexes.

PubMed

Thakur, Krishan Gopal; Jaiswal, Ravi Kumar; Shukla, Jinal K; Praveena, T; Gopal, B

2010-12-01

The function of a protein in a cell often involves coordinated interactions with one or several regulatory partners. It is thus imperative to characterize a protein both in isolation as well as in the context of its complex with an interacting partner. High resolution structural information determined by X-ray crystallography and Nuclear Magnetic Resonance offer the best route to characterize protein complexes. These techniques, however, require highly purified and homogenous protein samples at high concentration. This requirement often presents a major hurdle for structural studies. Here we present a strategy based on co-expression and co-purification to obtain recombinant multi-protein complexes in the quantity and concentration range that can enable hitherto intractable structural projects. The feasibility of this strategy was examined using the σ factor/anti-σ factor protein complexes from Mycobacterium tuberculosis. The approach was successful across a wide range of σ factors and their cognate interacting partners. It thus appears likely that the analysis of these complexes based on variations in expression constructs and procedures for the purification and characterization of these recombinant protein samples would be widely applicable for other multi-protein systems. Copyright © 2010 Elsevier Inc. All rights reserved.

Genome-wide analysis of alternative splicing during human heart development

NASA Astrophysics Data System (ADS)

Wang, He; Chen, Yanmei; Li, Xinzhong; Chen, Guojun; Zhong, Lintao; Chen, Gangbing; Liao, Yulin; Liao, Wangjun; Bin, Jianping

2016-10-01

Alternative splicing (AS) drives determinative changes during mouse heart development. Recent high-throughput technological advancements have facilitated genome-wide AS, while its analysis in human foetal heart transition to the adult stage has not been reported. Here, we present a high-resolution global analysis of AS transitions between human foetal and adult hearts. RNA-sequencing data showed extensive AS transitions occurred between human foetal and adult hearts, and AS events occurred more frequently in protein-coding genes than in long non-coding RNA (lncRNA). A significant difference of AS patterns was found between foetal and adult hearts. The predicted difference in AS events was further confirmed using quantitative reverse transcription-polymerase chain reaction analysis of human heart samples. Functional foetal-specific AS event analysis showed enrichment associated with cell proliferation-related pathways including cell cycle, whereas adult-specific AS events were associated with protein synthesis. Furthermore, 42.6% of foetal-specific AS events showed significant changes in gene expression levels between foetal and adult hearts. Genes exhibiting both foetal-specific AS and differential expression were highly enriched in cell cycle-associated functions. In conclusion, we provided a genome-wide profiling of AS transitions between foetal and adult hearts and proposed that AS transitions and deferential gene expression may play determinative roles in human heart development.

A resolution expressing support for the victims of the typhoon in the Philippines and the surrounding region.

THOMAS, 113th Congress

Sen. Schatz, Brian [D-HI

2013-11-13

Senate - 11/14/2013 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution expressing support for designation of October 7, 2010, as "Jumpstart's Read for the Record Day".

THOMAS, 111th Congress

Sen. Murray, Patty [D-WA

2010-07-22

Senate - 09/21/2010 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

Improving the quantitative accuracy of optical-emission computed tomography by incorporating an attenuation correction: application to HIF1 imaging

NASA Astrophysics Data System (ADS)

Kim, E.; Bowsher, J.; Thomas, A. S.; Sakhalkar, H.; Dewhirst, M.; Oldham, M.

2008-10-01

Optical computed tomography (optical-CT) and optical-emission computed tomography (optical-ECT) are new techniques for imaging the 3D structure and function (including gene expression) of whole unsectioned tissue samples. This work presents a method of improving the quantitative accuracy of optical-ECT by correcting for the 'self'-attenuation of photons emitted within the sample. The correction is analogous to a method commonly applied in single-photon-emission computed tomography reconstruction. The performance of the correction method was investigated by application to a transparent cylindrical gelatin phantom, containing a known distribution of attenuation (a central ink-doped gelatine core) and a known distribution of fluorescing fibres. Attenuation corrected and uncorrected optical-ECT images were reconstructed on the phantom to enable an evaluation of the effectiveness of the correction. Significant attenuation artefacts were observed in the uncorrected images where the central fibre appeared ~24% less intense due to greater attenuation from the surrounding ink-doped gelatin. This artefact was almost completely removed in the attenuation-corrected image, where the central fibre was within ~4% of the others. The successful phantom test enabled application of attenuation correction to optical-ECT images of an unsectioned human breast xenograft tumour grown subcutaneously on the hind leg of a nude mouse. This tumour cell line had been genetically labelled (pre-implantation) with fluorescent reporter genes such that all viable tumour cells expressed constitutive red fluorescent protein and hypoxia-inducible factor 1 transcription-produced green fluorescent protein. In addition to the fluorescent reporter labelling of gene expression, the tumour microvasculature was labelled by a light-absorbing vasculature contrast agent delivered in vivo by tail-vein injection. Optical-CT transmission images yielded high-resolution 3D images of the absorbing contrast agent, and revealed highly inhomogeneous vasculature perfusion within the tumour. Optical-ECT emission images yielded high-resolution 3D images of the fluorescent protein distribution in the tumour. Attenuation-uncorrected optical-ECT images showed clear loss of signal in regions of high attenuation, including regions of high perfusion, where attenuation is increased by increased vascular ink stain. Application of attenuation correction showed significant changes in an apparent expression of fluorescent proteins, confirming the importance of the attenuation correction. In conclusion, this work presents the first development and application of an attenuation correction for optical-ECT imaging. The results suggest that successful attenuation correction for optical-ECT is feasible and is essential for quantitatively accurate optical-ECT imaging.

Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing

PubMed Central

2012-01-01

Background RNA sequencing (RNA-Seq) has emerged as a powerful approach for the detection of differential gene expression with both high-throughput and high resolution capabilities possible depending upon the experimental design chosen. Multiplex experimental designs are now readily available, these can be utilised to increase the numbers of samples or replicates profiled at the cost of decreased sequencing depth generated per sample. These strategies impact on the power of the approach to accurately identify differential expression. This study presents a detailed analysis of the power to detect differential expression in a range of scenarios including simulated null and differential expression distributions with varying numbers of biological or technical replicates, sequencing depths and analysis methods. Results Differential and non-differential expression datasets were simulated using a combination of negative binomial and exponential distributions derived from real RNA-Seq data. These datasets were used to evaluate the performance of three commonly used differential expression analysis algorithms and to quantify the changes in power with respect to true and false positive rates when simulating variations in sequencing depth, biological replication and multiplex experimental design choices. Conclusions This work quantitatively explores comparisons between contemporary analysis tools and experimental design choices for the detection of differential expression using RNA-Seq. We found that the DESeq algorithm performs more conservatively than edgeR and NBPSeq. With regard to testing of various experimental designs, this work strongly suggests that greater power is gained through the use of biological replicates relative to library (technical) replicates and sequencing depth. Strikingly, sequencing depth could be reduced as low as 15% without substantial impacts on false positive or true positive rates. PMID:22985019

Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing.

PubMed

Robles, José A; Qureshi, Sumaira E; Stephen, Stuart J; Wilson, Susan R; Burden, Conrad J; Taylor, Jennifer M

2012-09-17

RNA sequencing (RNA-Seq) has emerged as a powerful approach for the detection of differential gene expression with both high-throughput and high resolution capabilities possible depending upon the experimental design chosen. Multiplex experimental designs are now readily available, these can be utilised to increase the numbers of samples or replicates profiled at the cost of decreased sequencing depth generated per sample. These strategies impact on the power of the approach to accurately identify differential expression. This study presents a detailed analysis of the power to detect differential expression in a range of scenarios including simulated null and differential expression distributions with varying numbers of biological or technical replicates, sequencing depths and analysis methods. Differential and non-differential expression datasets were simulated using a combination of negative binomial and exponential distributions derived from real RNA-Seq data. These datasets were used to evaluate the performance of three commonly used differential expression analysis algorithms and to quantify the changes in power with respect to true and false positive rates when simulating variations in sequencing depth, biological replication and multiplex experimental design choices. This work quantitatively explores comparisons between contemporary analysis tools and experimental design choices for the detection of differential expression using RNA-Seq. We found that the DESeq algorithm performs more conservatively than edgeR and NBPSeq. With regard to testing of various experimental designs, this work strongly suggests that greater power is gained through the use of biological replicates relative to library (technical) replicates and sequencing depth. Strikingly, sequencing depth could be reduced as low as 15% without substantial impacts on false positive or true positive rates.

Efficient conditioned pain modulation despite pain persistence in painful diabetic neuropathy.

PubMed

Granovsky, Yelena; Nahman-Averbuch, Hadas; Khamaisi, Mogher; Granot, Michal

2017-05-01

Alleviation of pain, by either medical or surgical therapy, is accompanied by transition from less efficient, or pro-nociceptive, to efficient conditioned pain modulation (CPM). Spontaneous decrease or resolution of pain with disease progression is reported for some patients with painful diabetic neuropathy (PDN). To explore whether CPM changes similarly in parallel to spontaneous resolution of pain in PDN patients. In this cross-sectional study, thirty-three patients with PDN underwent psychophysical assessment of pain modulation on the forearm, remote from the clinical pain. Pain duration was not correlated with neuropathic pain intensity, yet, it correlated with CPM efficiency; patients with longer pain duration had same pain level, but more efficient CPM than those with short-pain duration (ρ = -0.417; P = 0.025, Spearman correlation). Patients with pain more than 2 years (median split) expressed efficient CPM that was not different from that of healthy controls. These patients also had lower temporal summation of pain than the short-pain duration patients group ( P < 0.05). The 2 patient groups did not differ in clinical pain characteristics or use of analgesics. Pro-nociception, expressed by less efficient CPM and high temporal summation that usually accompanies clinical painful conditions, seems to "normalize" with chronicity of the pain syndrome. This is despite continuing pain, suggesting that pro-nociceptivity in pain syndromes is multifactorial. Because the pain modulation profile affects success of therapy, this suggests that different drugs might express different efficacy pending on duration of the pain in patients with PDN.

Investigation of FANCA gene in Fanconi anaemia patients in Iran

PubMed Central

Saffar Moghadam, Ali Akbar; Mahjoubi, Frouzandeh; Reisi, Nahid; Vosough, Parvaneh

2016-01-01

Background & objectives: Fanconi anaemia (FA) is a syndrome with a predisposition to bone marrow failure, congenital anomalies and malignancies. It is characterized by cellular hypersensitivity to cross-linking agents such as mitomycin C (MMC). In the present study, a new approach was selected to investigate FANCA (Fanconi anaemia complementation group A) gene in patients clinically diagnosed with cellular hypersensitivity to DNA cross-linking agent MMC. Methods: Chromosomal breakage analysis was performed to prove the diagnosis of Fanconi anaemia in 318 families. Of these, 70 families had a positive result. Forty families agreed to molecular genetic testing. In total, there were 27 patients with unknown complementary types. Genomic DNA was extracted and total RNA was isolated from fresh whole blood of the patients. The first-strand cDNA was synthesized and the cDNA of each patient was then tested with 21 pairs of overlapping primers. High resolution melting curve analysis was used to screen FANCA, and LinReg software version 1.7 was utilized for analysis of expression. Results: In total, six sequence alterations were identified, which included two stop codons, two frames-shift mutations, one large deletion and one amino acid exchange. FANCA expression was downregulated in patients who had sequence alterations. Interpretation & conclusions: The results of the present study show that high resolution melting (HRM) curve analysis may be useful in the detection of sequence alteration. It is simpler and more costeffective than the multiplex ligation-dependent probe amplification (MLPA) procedure. PMID:27121516

Investigation of FANCA gene in Fanconi anaemia patients in Iran.

PubMed

Moghadam, Ali Akbar Saffar; Mahjoubi, Frouzandeh; Reisi, Nahid; Vosough, Parvaneh

2016-02-01

Fanconi anaemia (FA) is a syndrome with a predisposition to bone marrow failure, congenital anomalies and malignancies. It is characterized by cellular hypersensitivity to cross-linking agents such as mitomycin C (MMC). In the present study, a new approach was selected to investigate FANCA (Fanconi anaemia complementation group A) gene in patients clinically diagnosed with cellular hypersensitivity to DNA cross-linking agent MMC. Chromosomal breakage analysis was performed to prove the diagnosis of Fanconi anaemia in 318 families. Of these, 70 families had a positive result. Forty families agreed to molecular genetic testing. In total, there were 27 patients with unknown complementary types. Genomic DNA was extracted and total RNA was isolated from fresh whole blood of the patients. The first-strand cDNA was synthesized and the cDNA of each patient was then tested with 21 pairs of overlapping primers. High resolution melting curve analysis was used to screen FANCA, and LinReg software version 1.7 was utilized for analysis of expression. In total, six sequence alterations were identified, which included two stop codons, two frames-shift mutations, one large deletion and one amino acid exchange. FANCA expression was downregulated in patients who had sequence alterations. The results of the present study show that high resolution melting (HRM) curve analysis may be useful in the detection of sequence alteration. It is simpler and more cost-effective than the multiplex ligation-dependent probe amplification (MLPA) procedure.

Orbitrap mass spectrometry characterization of hybrid chondroitin/dermatan sulfate hexasaccharide domains expressed in brain.

PubMed

Robu, Adrian C; Popescu, Laurentiu; Munteanu, Cristian V A; Seidler, Daniela G; Zamfir, Alina D

2015-09-15

In the central nervous system, chondroitin/dermatan sulfate (CS/DS) glycosaminoglycans (GAGs) modulate neurotrophic effects and glial cell maturation during brain development. Previous reports revealed that GAG composition could be responsible for CS/DS activities in brain. In this work, for the structural characterization of DS- and CS-rich domains in hybrid GAG chains extracted from neural tissue, we have developed an advanced approach based on high-resolution mass spectrometry (MS) using nanoelectrospray ionization Orbitrap in the negative ion mode. Our high-resolution MS and multistage MS approach was developed and applied to hexasaccharides obtained from 4- and 14-week-old mouse brains by GAG digestion with chondroitin B and in parallel with AC I lyase. The expression of DS- and CS-rich domains in the two tissues was assessed comparatively. The analyses indicated an age-related structural variability of the CS/DS motifs. The older brain was found to contain more structures and a higher sulfation of DS-rich regions, whereas the younger brain was found to be characterized by a higher sulfation of CS-rich regions. By multistage MS using collision-induced dissociation, we also demonstrated the incidence in mouse brain of an atypical [4,5-Δ-GlcAGalNAc(IdoAGalNAc)2], presenting a bisulfated CS disaccharide formed by 3-O-sulfate-4,5-Δ-GlcA and 6-O-sulfate-GalNAc moieties. Copyright © 2015 Elsevier Inc. All rights reserved.

Functional high-resolution time-course expression analysis of human embryonic stem cells undergoing cardiac induction.

PubMed

Piccini, Ilaria; Araúzo-Bravo, Marcos; Seebohm, Guiscard; Greber, Boris

2016-12-01

Cardiac induction of human embryonic stem cells (hESCs) is a process bearing increasing medical relevance, yet it is poorly understood from a developmental biology perspective. Anticipated technological progress in deriving stably expandable cardiac precursor cells or in advancing cardiac subtype specification protocols will likely require deeper insights into this fascinating system. Recent improvements in controlling hESC differentiation now enable a near-homogeneous induction of the cardiac lineage. This is based on an optimized initial stimulation of mesoderm-inducing signaling pathways such as Activin and/or FGF, BMP, and WNT, followed by WNT inhibition as a secondary requirement. Here, we describe a comprehensive data set based on varying hESC differentiation conditions in a systematic manner and recording high-resolution differentiation time-courses analyzed by genome-wide expression profiling (GEO accession number GSE67154). As a baseline, hESCs were differentiated into cardiomyocytes under optimal conditions. Moreover, in additional time-series, individual signaling factors were withdrawn from the initial stimulation cocktail to reveal their specific roles via comparison to the standard condition. Hence, this data set presents a rich resource for hypothesis generation in studying human cardiac induction, as we reveal numbers of known as well as uncharacterized genes prominently marking distinct intermediate stages in the process. These data will also be useful for identifying putative cardiac master regulators in the human system as well as for characterizing expandable cardiac stem cells.

Precise Detection of IDH1/2 and BRAF Hotspot Mutations in Clinical Glioma Tissues by a Differential Calculus Analysis of High-Resolution Melting Data

PubMed Central

Hatae, Ryusuke; Yoshimoto, Koji; Kuga, Daisuke; Akagi, Yojiro; Murata, Hideki; Suzuki, Satoshi O.; Mizoguchi, Masahiro; Iihara, Koji

2016-01-01

High resolution melting (HRM) is a simple and rapid method for screening mutations. It offers various advantages for clinical diagnostic applications. Conventional HRM analysis often yields equivocal results, especially for surgically obtained tissues. We attempted to improve HRM analyses for more effective applications to clinical diagnostics. HRM analyses were performed for IDH1R132 and IDH2R172 mutations in 192 clinical glioma samples in duplicate and these results were compared with sequencing results. BRAFV600E mutations were analyzed in 52 additional brain tumor samples. The melting profiles were used for differential calculus analyses. Negative second derivative plots revealed additional peaks derived from heteroduplexes in PCR products that contained mutations; this enabled unequivocal visual discrimination of the mutations. We further developed a numerical expression, the HRM-mutation index (MI), to quantify the heteroduplex-derived peak of the mutational curves. Using this expression, all IDH1 mutation statuses matched those ascertained by sequencing, with the exception of three samples. These discordant results were all derived from the misinterpretation of sequencing data. The effectiveness of our approach was further validated by analyses of IDH2R172 and BRAFV600E mutations. The present analytical method enabled an unequivocal and objective HRM analysis and is suitable for reliable mutation scanning in surgically obtained glioma tissues. This approach could facilitate molecular diagnostics in clinical environments. PMID:27529619

ErbB4 signaling stimulates pro-inflammatory macrophage apoptosis and limits colonic inflammation

PubMed Central

Schumacher, Michael A; Hedl, Matija; Abraham, Clara; Bernard, Jessica K; Lozano, Patricia R; Hsieh, Jonathan J; Almohazey, Dana; Bucar, Edie B; Punit, Shivesh; Dempsey, Peter J; Frey, Mark R

2017-01-01

Efficient clearance of pro-inflammatory macrophages from tissues after resolution of a challenge is critical to prevent prolonged inflammation. Defects in clearance can contribute to conditions such as inflammatory bowel disease, and thus may be therapeutically targetable. However, the signaling pathways that induce termination of pro-inflammatory macrophages are incompletely defined. We tested whether the ErbB4 receptor tyrosine kinase, previously not known to have role in macrophage biology, is involved in this process. In vitro, pro-inflammatory activation of cultured murine and human macrophages induced ErbB4 expression; in contrast, other ErbB family members were not induced in pro-inflammatory cells, and other innate immune lineages (dendritic cells, neutrophils) did not express detectable ErbB4 levels. Treatment of activated pro-inflammatory macrophages with the ErbB4 ligand neuregulin-4 (NRG4) induced apoptosis. ErbB4 localized to the mitochondria in these cells. Apoptosis was accompanied by loss of mitochondrial membrane potential, and was dependent upon the proteases that generate the cleaved ErbB4 intracellular domain fragment, suggesting a requirement for this fragment and mitochondrial pathway apoptosis. In vivo, ErbB4 was highly expressed on pro-inflammatory macrophages but not neutrophils during experimental DSS colitis in C57Bl/6 mice. Active inflammation in this model suppressed NRG4 expression, which may allow for macrophage persistence and ongoing inflammation. Consistent with this notion, NRG4 levels rebounded during the recovery phase, and administration of exogenous NRG4 during colitis reduced colonic macrophage numbers and ameliorated inflammation. These data define a novel role for ErbB4 in macrophage apoptosis, and outline a mechanism of feedback inhibition that may promote resolution of colitis. PMID:28230865

A Contextual Approach to the Study of Discourse Anaphoric Expressions: On the Probabilistic Nature of Theoretical Predictions

ERIC Educational Resources Information Center

Madhkhan, Mozhgan; Mousavi, Mojtaba

2017-01-01

Anaphoric expressions are among the most frequent language forms which depend on context for their resolution. Among efforts made in theorizing referential choice, distance approaches take into account how accessibility/continuity is reflected by choice of referring expressions. The thing is that individual's choices are made under major and minor…

The HRSC on Mars Express: Mert Davies' Involvement in a Novel Planetary Cartography Experiment

NASA Astrophysics Data System (ADS)

Oberst, J.; Waehlisch, M.; Giese, B.; Scholten, F.; Hoffmann, H.; Jaumann, R.; Neukum, G.

2002-12-01

Mert Davies was a team member of the HRSC (High Resolution Stereo Camera) imaging experiment (PI: Gerhard Neukum) on ESA's Mars Express mission. This pushbroom camera is equipped with 9 forward- and backward-looking CCD lines, 5184 samples each, mounted in parallel, perpendicular to the spacecraft velocity vector. Flight image data with resolutions of up to 10m/pix (from an altitude of 250 km) will be acquired line by line as the spacecraft moves. This acquisition strategy will result in 9 separate almost completely overlapping image strips, each of them having more than 27,000 image lines, typically. [HRSC is also equipped with a superresolution channel for imaging of selected targets at up to 2.3 m/pixel]. The combined operation of the nadir and off-nadir CCD lines (+18.9°, 0°, -18.9°) gives HRSC a triple-stereo capability for precision mapping of surface topography and for modelling of spacecraft orbit- and camera pointing errors. The goals of the camera are to obtain accurate control point networks, Digital Elevation Models (DEMs) in Mars-fixed coordinates, and color orthoimages at global (100% of the surface will be covered with resolutions better than 30m/pixel) and local scales. With his long experience in all aspects of planetary geodesy and cartography, Mert Davies was involved in the preparations of this novel Mars imaging experiment which included: (a) development of a ground data system for the analysis of triple-stereo images, (b) camera testing during airborne imaging campaigns, (c) re-analysis of the Mars control point network, and generation of global topographic orthoimage maps on the basis of MOC images and MOLA data, (d) definition of the quadrangle scheme for a new topographic image map series 1:200K, (e) simulation of synthetic HRSC imaging sequences and their photogrammetric analysis. Mars Express is scheduled for launch in May of 2003. We miss Mert very much!

Are X-rays the key to integrated computational materials engineering?

DOE PAGES

Ice, Gene E.

2015-11-01

The ultimate dream of materials science is to predict materials behavior from composition and processing history. Owing to the growing power of computers, this long-time dream has recently found expression through worldwide excitement in a number of computation-based thrusts: integrated computational materials engineering, materials by design, computational materials design, three-dimensional materials physics and mesoscale physics. However, real materials have important crystallographic structures at multiple length scales, which evolve during processing and in service. Moreover, real materials properties can depend on the extreme tails in their structural and chemical distributions. This makes it critical to map structural distributions with sufficient resolutionmore » to resolve small structures and with sufficient statistics to capture the tails of distributions. For two-dimensional materials, there are high-resolution nondestructive probes of surface and near-surface structures with atomic or near-atomic resolution that can provide detailed structural, chemical and functional distributions over important length scales. Furthermore, there are no nondestructive three-dimensional probes with atomic resolution over the multiple length scales needed to understand most materials.« less

Venusian tectonics: Convective coupling to the lithosphere?

NASA Technical Reports Server (NTRS)

Phillips, R. J.

1987-01-01

The relationship between the dominant global heat loss mechanism and planetary size has motivated the search for tectonic style on Venus. Prior to the American and Soviet mapping missions of the past eight years, it was thought that terrestrial style plate tectonics was operative on Venus because this planet is approximately the size of the Earth and is conjectured to have about the same heat source content per unit mass. However, surface topography mapped by the altimeter of the Pioneer Venus spacecraft did not show any physiographic expression of terrestrial style spreading ridges, trenches, volcanic arcs or transform faults, although the horizontal resolution was questionable for detection of at least some of these features. The Venera 15 and 16 radar missions mapped the northern latitudes of Venus at 1 to 2 km resolution and showed that there are significant geographic areas of deformation seemingly created by large horizontal stresses. These same high resolution images show no evidence for plate tectonic features. Thus a fundamental problem for venusian tectonics is the origin of large horizontal stresses near the surface in the apparent absence of plate tectonics.

Molecular regulators of resolution of inflammation: potential therapeutic targets in the reproductive system.

PubMed

Hutchinson, James L; Rajagopal, Shalini P; Sales, Kurt J; Jabbour, Henry N

2011-07-01

Inflammatory processes are central to reproductive events including ovulation, menstruation, implantation and labour, while inflammatory dysregulation is a feature of numerous reproductive pathologies. In recent years, there has been much research into the endogenous mechanisms by which inflammatory reactions are terminated and tissue homoeostasis is restored, a process termed resolution. The identification and characterisation of naturally occurring pro-resolution mediators including lipoxins and annexin A1 has prompted a shift in the field of anti-inflammation whereby resolution is now observed as an active process, triggered as part of a normal inflammatory response. This review will address the process of resolution, discuss available evidence for expression of pro-resolution factors in the reproductive tract and explore possible roles for resolution in physiological reproductive processes and associated pathologies.

A resolution honoring the life of Manute Bol and expressing the condolences of the Senate on his passing.

THOMAS, 111th Congress

Sen. Brownback, Sam [R-KS

2010-07-13

Senate - 08/05/2010 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution expressing support for the designation of November 16, 2011, as National Information and Referral Services Day.

THOMAS, 112th Congress

Sen. Menendez, Robert [D-NJ

2011-07-27

Senate - 11/15/2011 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution expressing the sense of the Senate on the 10-year anniversary of NATO Allied Command Transformation.

THOMAS, 113th Congress

Sen. Warner, Mark R. [D-VA

2013-05-23

Senate - 07/31/2013 Resolution agreed to in Senate with an amendment and an amended preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution to express the sense of the Senate in support of reducing its budget by at least 5 percent.

THOMAS, 112th Congress

Sen. Wicker, Roger F. [R-MS

2011-03-08

Senate - 03/16/2011 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution expressing support for improvement in the collection, processing, and consumption of recyclable materials throughout the United States.

THOMAS, 112th Congress

Sen. Carper, Thomas R. [D-DE

2011-08-02

Senate - 11/16/2011 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution expressing the sense of the Senate on empowering and strengthening the United States Agency for International Development (USAID).

THOMAS, 111th Congress

Sen. Dodd, Christopher J. [D-CT

2009-10-13

Senate - 11/09/2009 Resolution agreed to in Senate with an amendment and an amended preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution condemning the downing of Malaysia Airlines Flight 17 and expressing condolences to the families of the victims.

THOMAS, 113th Congress

Sen. Murphy, Christopher [D-CT

2014-07-24

Senate - 07/31/2014 Resolution agreed to in Senate without amendment and an amended preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution honoring the life, accomplishments, and legacy of Billy Frank, Jr., and expressing condolences on his passing.

THOMAS, 113th Congress

Sen. Murray, Patty [D-WA

2014-05-22

Senate - 06/04/2014 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

Model Building to Facilitate Understanding of Holliday Junction and Heteroduplex Formation, and Holliday Junction Resolution

ERIC Educational Resources Information Center

Selvarajah, Geeta; Selvarajah, Susila

2016-01-01

Students frequently expressed difficulty in understanding the molecular mechanisms involved in chromosomal recombination. Therefore, we explored alternative methods for presenting the two concepts of the double-strand break model: Holliday junction and heteroduplex formation, and Holliday junction resolution. In addition to a lecture and…

A resolution expressing appreciation for Foreign Service and Civil Service professionals who represent the United States around the globe.

THOMAS, 112th Congress

Sen. Whitehouse, Sheldon [D-RI

2012-03-21

Senate - 09/13/2012 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

Mass spectrometric imaging as a high-spatial resolution tool for functional genomics: Tissue-specific gene expression of TT7 inferred from heterogeneous distribution of metabolites in Arabidopsis flowers

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

Korte, Andrew R.; Song, Zhihong; Nikolau, Basil J.

Laser desorption/ionization (LDI) mass spectrometry imaging (MSI) was used to acquire chemical images of flavonoid metabolites on the surface of wild-type and mutant (tt7) Arabidopsis thaliana flowers. Flavonoids were localized to the petals and carpels of flowers, with tissue heterogeneity in the petals. Specifically, kaempferol and/or its glycosides were abundant in the distal region of petals and quercetin and its downstream flavonoids were highly enriched in the more proximal region of petals. As a result of a mutation in the TT7 gene which blocks the conversion of dihydrokaempferol to dihydroquercetin, the downstream metabolites, quercetin, isohamnetin, and their glycosides, were notmore » observed in the mutant flowers. Instead, the metabolites in an alternative pathway, kaempferol and/or its glycosides, were as highly abundant on the proximal region of the petals as in the distal region. In addition, the combined flavonoid amounts on the proximal region of petals in the wild-type are almost equivalent to the amounts of kaempferol and/or its glycosides in the mutant. This strongly suggests that the expression of the TT7 gene is localized on the proximal part of the petal while the other genes in the upper stream pathway are evenly expressed throughout the petal. Most importantly, this work demonstrates MSI of metabolites can be utilized for the localization of gene expression.« less

Characterization of alterations in diabetic myocardial tissue using high resolution MRI.

PubMed

Loganathan, Rajaprasad; Bilgen, Mehmet; Al-Hafez, Baraa; Smirnova, Irina V

2006-02-01

Cardiovascular complications, including diabetic cardiomyopathy, are the major cause of fatalities in diabetes. Diabetic cardiomyopathy is expressed in part through fibrosis and left ventricular hypertrophy, increasing myocardial stiffness leading to heart failure. In order to search for curative interventions, precise evaluation of the diabetic heart pathology is extremely important. Magnetic resonance imaging (MRI) is ideally suited for the assessment of heart disorders due to its high resolution, three-dimensional properties and dimensional accuracy. In this study streptozotocin injected Sprague-Dawley rats were used as a model of type 1 diabetes to characterize abnormalities in the diabetic left ventricle (LV). High resolution MRI using a 9.4 T horizontal bore scanner was performed on control and 7 weeks diabetic rats. In the diabetic rats as compared to controls, we found increased LV wall volume to body weight ratio, suggestive of LV hypertrophy; increased LV wall mean pixel intensity, and decreased T2 relaxation time, both suggestive of changes in the diabetic tissue properties, perhaps due to presence of fibrosis which was detected through increase in the collagen fractional area. In addition, changes in the LV cavity area were observed and quantified in post-mortem diabetic hearts indicative of stiffer and less resilient LV myocardial tissue with diabetes. Together the data suggest that LV hypertrophy and fibrosis may be a major factor underlying structural and functional abnormalities in the diabetic heart, and MRI is a valuable tool to non-invasively monitor the pathological changes in diabetic cardiomyopathy.

All-optical optoacoustic microscopy system based on probe beam deflection technique

NASA Astrophysics Data System (ADS)

Maswadi, Saher M.; Tsyboulskic, Dmitri; Roth, Caleb C.; Glickman, Randolph D.; Beier, Hope T.; Oraevsky, Alexander A.; Ibey, Bennett L.

2016-03-01

It is difficult to achieve sub-micron resolution in backward mode OA microscopy using conventional piezoelectric detectors, because of wavefront distortions caused by components placed in the optical path, between the sample and the objective lens, that are required to separate the acoustic wave from the optical beam. As an alternate approach, an optoacoustic microscope (OAM) was constructed using the probe beam deflection technique (PBDT) to detect laserinduced acoustic signals. The all-optical OAM detects laser-generated pressure waves using a probe beam passing through a coupling medium, such as water, filling the space between the microscope objective lens and sample. The acoustic waves generated in the sample propagate through the coupling medium, causing transient changes in the refractive index that deflect the probe beam. These deflections are measured with a high-speed, balanced photodiode position detector. The deflection amplitude is directly proportional to the magnitude of the acoustic pressure wave, and provides the data required for image reconstruction. The sensitivity of the PBDT detector expressed as noise equivalent pressure was 12 Pa, comparable to that of existing high-performance ultrasound detectors. Because of the unimpeded working distance, a high numerical aperture objective lens, i.e. NA = 1, was employed in the OAM to achieve near diffraction-limited lateral resolution of 0.5 μm at 532nm. The all-optical OAM provides several benefits over current piezoelectric detector-based systems, such as increased lateral and axial resolution, higher sensitivity, robustness, and potentially more compatibility with multimodal instruments.

Determination of lattice parameters, strain state and composition in semipolar III-nitrides using high resolution X-ray diffraction

NASA Astrophysics Data System (ADS)

Frentrup, Martin; Hatui, Nirupam; Wernicke, Tim; Stellmach, Joachim; Bhattacharya, Arnab; Kneissl, Michael

2013-12-01

In group-III-nitride heterostructures with semipolar or nonpolar crystal orientation, anisotropic lattice and thermal mismatch with the buffer or substrate lead to a complex distortion of the unit cells, e.g., by shearing of the lattice. This makes an accurate determination of lattice parameters, composition, and strain state under assumption of the hexagonal symmetry impossible. In this work, we present a procedure to accurately determine the lattice constants, strain state, and composition of semipolar heterostructures using high resolution X-ray diffraction. An analysis of the unit cell distortion shows that four independent lattice parameters are sufficient to describe this distortion. Assuming only small deviations from an ideal hexagonal structure, a linear expression for the interplanar distances dhkl is derived. It is used to determine the lattice parameters from high resolution X-ray diffraction 2ϑ-ω-scans of multiple on- and off-axis reflections via a weighted least-square fit. The strain and composition of ternary alloys are then evaluated by transforming the elastic parameters (using Hooke's law) from the natural crystal-fixed coordinate system to a layer-based system, given by the in-plane directions and the growth direction. We illustrate our procedure taking an example of (112¯2) AlκGa1-κN epilayers with Al-contents over the entire composition range. We separately identify the in-plane and out-of-plane strains and discuss origins for the observed anisotropy.

The 18 kDa Translocator Protein (Peripheral Benzodiazepine Receptor) Expression in the Bone of Normal, Osteoprotegerin or Low Calcium Diet Treated Mice

PubMed Central

Kam, Winnie Wai-Ying; Meikle, Steven R.; Dunstan, Colin R.; Banati, Richard B.

2012-01-01

The presence of the translocator protein (TSPO), previously named as the mitochondrial or peripheral benzodiazepine receptor, in bone cells was studied in vitro and in situ using RT-qPCR, and receptor autoradiography using the selective TSPO ligand PK11195. In vitro, the TSPO is highly expressed in osteoblastic and osteoclastic cells. In situ, constitutive expression of TSPO is found in bone marrow and trabecular bone, e.g., spongiosa. Mice with a reduction of bone turnover induced by a 4-day treatment of osteoprotegerin reduces [3H]PK11195 binding in the spongiosa (320±128 Bq.mg−1, 499±106 Bq.mg−1 in saline-treated controls). In contrast, mice with an increase in bone turnover caused by a 4-day low calcium diet increases [3H]PK11195 binding in the spongiosa (615±90 Bq.mg−1). Further, our study includes technical feasibility data on [18F]fluoride microPET imaging of rodent bone with altered turnover. Despite [18F]fluoride having high uptake, the in vivo signal differences were small. Using a phantom model, we describe the spillover effect and partial volume loss that affect the quantitative microPET imaging of the small bone structures in experimental mouse models. In summary, we demonstrate the expression of TSPO in small rodent bone tissues, including osteoblasts and osteoclasts. A trend increase in TSPO expression was observed in the spongiosa from low to high bone turnover conditions. However, despite the potential utility of TSPO expression as an in vivo biomarker of bone turnover in experimental rodent models, our small animal PET imaging data using [18F]fluoride show that even under the condition of a good biological signal-to-noise ratio and high tracer uptake, the currently achievable instrument sensitivity and spatial resolution is unlikely to be sufficient to detect subtle differences in small structures, such as mouse bone. PMID:22295097

Purification, crystallization and preliminary X-ray analysis of the IgV domain of human nectin-4.

PubMed

Xu, Xiang; Zhang, Xiaoai; Lu, Guangwen; Cai, Yongping

2012-08-01

Nectin-4 belongs to a family of immunoglobulin-like cell adhesion molecules and is highly expressed in cancer cells. Recently, nectin-4 was found to be a receptor of measles virus and the IgV domain sustains strong binding to measles virus H protein. In this study, the successful expression and purification of human nectin-4 V domain (nectin-4v) is reported. The purified protein was crystallized using the sitting-drop vapour-diffusion method. The crystals diffracted to 1.8 Å resolution and belonged to space group P2(1), with unit-cell parameters a = 33.1, b = 51.7, c = 56.9 Å, β = 94.7°. Preliminary analysis of the diffraction data was also performed.

Purification, crystallization and preliminary X-ray analysis of the IgV domain of human nectin-4

PubMed Central

Xu, Xiang; Zhang, Xiaoai; Lu, Guangwen; Cai, Yongping

2012-01-01

Nectin-4 belongs to a family of immunoglobulin-like cell adhesion molecules and is highly expressed in cancer cells. Recently, nectin-4 was found to be a receptor of measles virus and the IgV domain sustains strong binding to measles virus H protein. In this study, the successful expression and purification of human nectin-4 V domain (nectin-4v) is reported. The purified protein was crystallized using the sitting-drop vapour-diffusion method. The crystals diffracted to 1.8 Å resolution and belonged to space group P21, with unit-cell parameters a = 33.1, b = 51.7, c = 56.9 Å, β = 94.7°. Preliminary analysis of the diffraction data was also performed. PMID:22869128

Expression profile of HSP genes during different seasons in goats (Capra hircus).

PubMed

Dangi, Satyaveer Singh; Gupta, Mahesh; Maurya, Divakar; Yadav, Vijay Prakash; Panda, Rudra Prasanna; Singh, Gyanendra; Mohan, Nitai Haridas; Bhure, Sanjeev Kumar; Das, Bikash Chandra; Bag, Sadhan; Mahapatra, Ramkrishna; Taru Sharma, Guttalu; Sarkar, Mihir

2012-12-01

The present study has demonstrated the expression of HSP60, HSP70, HSP90, and UBQ in peripheral blood mononuclear cells (PBMCs) during different seasons in three different age groups (Groups I, II, and III with age of 0-2, 2-5, and >5 years, respectively) of goats of tropical and temperate regions. Real-time polymerase chain reaction was applied to investigate mRNA expression of examined factors. Specificity of the desired products was documented using analysis of the melting temperature and high-resolution gel electrophoresis to verify that the transcripts are of the exact molecular size predicted. The mRNA expression of HSP60, HSP90, and UBQ was significantly higher (P < 0.05) in all age groups during peak summer season as compared with peak winter season in both tropical and temperate region goats. HSP70 mRNA expression was significantly higher (P < 0.05) during summer season as compared with winter season in tropical region goats. However, in the temperate region, in goats from all the three age groups studied, a non-significant difference of HSP70 expression between summer and winter seasons was noticed. In conclusion, results demonstrate that (1) HSP genes are expressed in caprine PBMCs and (2) higher expression of HSPs during thermal stress suggest possible involvement of them to ameliorate deleterious effect of thermal stress so as to maintain cellular integrity and homeostasis in goats.

Sheep skeletal muscle transcriptome analysis reveals muscle growth regulatory lncRNAs.

PubMed

Chao, Tianle; Ji, Zhibin; Hou, Lei; Wang, Jin; Zhang, Chunlan; Wang, Guizhi; Wang, Jianmin

2018-01-01

As widely distributed domestic animals, sheep are an important species and the source of mutton. In this study, we aimed to evaluate the regulatory lncRNAs associated with muscle growth and development between high production mutton sheep (Dorper sheep and Qianhua Mutton Merino sheep) and low production mutton sheep (Small-tailed Han sheep). In total, 39 lncRNAs were found to be differentially expressed. Using co-expression analysis and functional annotation, 1,206 co-expression interactions were found between 32 lncRNAs and 369 genes, and 29 of these lncRNAs were found to be associated with muscle development, metabolism, cell proliferation and apoptosis. lncRNA-mRNA interactions revealed 6 lncRNAs as hub lncRNAs. Moreover, three lncRNAs and their associated co-expressed genes were demonstrated by cis-regulatory gene analyses, and we also found a potential regulatory relationship between the pseudogene lncRNA LOC101121401 and its parent gene FTH1. This study provides a genome-wide resolution of lncRNA and mRNA regulation in muscles from mutton sheep.

Expression of Terminal Effector Genes in Mammalian Neurons Is Maintained by a Dynamic Relay of Transient Enhancers.

PubMed

Rhee, Ho Sung; Closser, Michael; Guo, Yuchun; Bashkirova, Elizaveta V; Tan, G Christopher; Gifford, David K; Wichterle, Hynek

2016-12-21

Generic spinal motor neuron identity is established by cooperative binding of programming transcription factors (TFs), Isl1 and Lhx3, to motor-neuron-specific enhancers. How expression of effector genes is maintained following downregulation of programming TFs in maturing neurons remains unknown. High-resolution exonuclease (ChIP-exo) mapping revealed that the majority of enhancers established by programming TFs are rapidly deactivated following Lhx3 downregulation in stem-cell-derived hypaxial motor neurons. Isl1 is released from nascent motor neuron enhancers and recruited to new enhancers bound by clusters of Onecut1 in maturing neurons. Synthetic enhancer reporter assays revealed that Isl1 operates as an integrator factor, translating the density of Lhx3 or Onecut1 binding sites into transient enhancer activity. Importantly, independent Isl1/Lhx3- and Isl1/Onecut1-bound enhancers contribute to sustained expression of motor neuron effector genes, demonstrating that outwardly stable expression of terminal effector genes in postmitotic neurons is controlled by a dynamic relay of stage-specific enhancers. Copyright © 2016 Elsevier Inc. All rights reserved.

Structural study of the membrane protein MscL using cell-free expression and solid-state NMR

NASA Astrophysics Data System (ADS)

Abdine, Alaa; Verhoeven, Michiel A.; Park, Kyu-Ho; Ghazi, Alexandre; Guittet, Eric; Berrier, Catherine; Van Heijenoort, Carine; Warschawski, Dror E.

2010-05-01

High-resolution structures of membrane proteins have so far been obtained mostly by X-ray crystallography, on samples where the protein is surrounded by detergent. Recent developments of solid-state NMR have opened the way to a new approach for the study of integral membrane proteins inside a membrane. At the same time, the extension of cell-free expression to the production of membrane proteins allows for the production of proteins tailor made for NMR. We present here an in situ solid-state NMR study of a membrane protein selectively labeled through the use of cell-free expression. The sample consists of MscL (mechano-sensitive channel of large conductance), a 75 kDa pentameric α-helical ion channel from Escherichia coli, reconstituted in a hydrated lipid bilayer. Compared to a uniformly labeled protein sample, the spectral crowding is greatly reduced in the cell-free expressed protein sample. This approach may be a decisive step required for spectral assignment and structure determination of membrane proteins by solid-state NMR.

Synthesis of a probe for monitoring HSV1-tk reporter gene expression using chemical exchange saturation transfer MRI

PubMed Central

Bar-Shir, Amnon; Liu, Guanshu; Greenberg, Marc M; Bulte, Jeff W M; Gilad, Assaf A

2013-01-01

In experiments involving transgenic animals or animals treated with transgenic cells, it is important to have a method to monitor the expression of the relevant genes longitudinally and noninvasively. An MRI-based reporter gene enables monitoring of gene expression in the deep tissues of living subjects. This information can be co-registered with detailed high-resolution anatomical and functional information. We describe here the synthesis of the reporter probe, 5-methyl-5,6-dihydrothymidine (5-MDHT), which can be used for imaging of the herpes simplex virus type 1 thymidine kinase (HSV1-tk) reporter gene expression in rodents by MRI. The protocol also includes data acquisition and data processing routines customized for chemical exchange saturation transfer (CEST) contrast mechanisms. The dihydropyrimidine 5-MDHT is synthesized through a catalytic hydrogenation of the 5,6-double bond of thymidine to yield 5,6-dihydrothymidine, which is methylated on the C-5 position of the resulting saturated pyrimidine ring. The synthesis of 5-MDHT can be completed within 5 d, and the compound is stable for more than 1 year. PMID:24177294

Sheep skeletal muscle transcriptome analysis reveals muscle growth regulatory lncRNAs

PubMed Central

Chao, Tianle; Ji, Zhibin; Hou, Lei; Wang, Jin; Zhang, Chunlan

2018-01-01

As widely distributed domestic animals, sheep are an important species and the source of mutton. In this study, we aimed to evaluate the regulatory lncRNAs associated with muscle growth and development between high production mutton sheep (Dorper sheep and Qianhua Mutton Merino sheep) and low production mutton sheep (Small-tailed Han sheep). In total, 39 lncRNAs were found to be differentially expressed. Using co-expression analysis and functional annotation, 1,206 co-expression interactions were found between 32 lncRNAs and 369 genes, and 29 of these lncRNAs were found to be associated with muscle development, metabolism, cell proliferation and apoptosis. lncRNA–mRNA interactions revealed 6 lncRNAs as hub lncRNAs. Moreover, three lncRNAs and their associated co-expressed genes were demonstrated by cis-regulatory gene analyses, and we also found a potential regulatory relationship between the pseudogene lncRNA LOC101121401 and its parent gene FTH1. This study provides a genome-wide resolution of lncRNA and mRNA regulation in muscles from mutton sheep. PMID:29666768

The HRSC Experiment on Mars Express: First Imaging Results from the Commissioning Phase

NASA Astrophysics Data System (ADS)

Oberst, J.; Neukum, G.; Hoffmann, H.; Jaumann, R.; Hauber, E.; Albertz, J.; McCord, T. B.; Markiewicz, W. J.

2004-12-01

The ESA Mars Express spacecraft was launched from Baikonur on June 2, 2003, entered Mars orbit on December 25, 2003, and reached the nominal mapping orbit on January 28, 2004. Observing conditions were favorable early on for the HRSC (High Resolution Stereo Camera), designed for the mapping of the Martian surface in 3-D. The HRSC is a pushbroom scanner with 9 CCD line detectors mounted in parallel and perpendicular to the direction of flight on the focal plane. The camera can obtain images at high resolution (10 m/pix), in triple stereo (20 m/pix), in four colors, and at five different phase angles near-simultaneously. An additional Super-Resolution Channel (SRC) yields nested-in images at 2.3 m/pix for detailed photogeologic studies. Even for nominal spacecraft trajectory and camera pointing data from the commissioning phase, solid stereo image reconstructions are feasible. More yet, the three-line stereo data allow us to identify and correct errors in navigation data. We find that > 99% of the stereo rays intersect within a sphere of radius < 20m after orbit and pointing data correction. From the HRSC images we have produced Digital Terrain Models (DTMs) with pixel sizes of 200 m, some of them better. HRSC stereo models and data obtained by the MOLA (Mars Orbiting Laser Altimeter) show good qualitative agreement. Differences in absolute elevations are within 50 m, but may reach several 100 m in lateral positioning (mostly in the spacecraft along-track direction). After correction of these offsets, the HRSC topographic data conveniently fill the gaps between the MOLA tracks and reveal hitherto unrecognized morphologic detail. At the time of writing, the HRSC has covered approx. 22.5 million square kilometers of the Martian surface. In addition, data from 5 Phobos flybys from May through August 2004 were obtained. The HRSC is beginning to make major contributions to geoscience, atmospheric science, photogrammetry, and cartography of Mars (papers submitted to Nature).

Restoration Of MEX SRC Images For Improved Topography: A New Image Product

NASA Astrophysics Data System (ADS)

Duxbury, T. C.

2012-12-01

Surface topography is an important constraint when investigating the evolution of solar system bodies. Topography is typically obtained from stereo photogrammetric or photometric (shape from shading) analyses of overlapping / stereo images and from laser / radar altimetry data. The ESA Mars Express Mission [1] carries a Super Resolution Channel (SRC) as part of the High Resolution Stereo Camera (HRSC) [2]. The SRC can build up overlapping / stereo coverage of Mars, Phobos and Deimos by viewing the surfaces from different orbits. The derivation of high precision topography data from the SRC raw images is degraded because the camera is out of focus. The point spread function (PSF) is multi-peaked, covering tens of pixels. After registering and co-adding hundreds of star images, an accurate SRC PSF was reconstructed and is being used to restore the SRC images to near blur free quality. The restored images offer a factor of about 3 in improved geometric accuracy as well as identifying the smallest of features to significantly improve the stereo photogrammetric accuracy in producing digital elevation models. The difference between blurred and restored images provides a new derived image product that can provide improved feature recognition to increase spatial resolution and topographic accuracy of derived elevation models. Acknowledgements: This research was funded by the NASA Mars Express Participating Scientist Program. [1] Chicarro, et al., ESA SP 1291(2009) [2] Neukum, et al., ESA SP 1291 (2009). A raw SRC image (h4235.003) of a Martian crater within Gale crater (the MSL landing site) is shown in the upper left and the restored image is shown in the lower left. A raw image (h0715.004) of Phobos is shown in the upper right and the difference between the raw and restored images, a new derived image data product, is shown in the lower right. The lower images, resulting from an image restoration process, significantly improve feature recognition for improved derived topographic accuracy.

Single-Cell Mass Spectrometry Reveals Changes in Lipid and Metabolite Expression in RAW 264.7 Cells upon Lipopolysaccharide Stimulation

NASA Astrophysics Data System (ADS)

Yang, Bo; Patterson, Nathan Heath; Tsui, Tina; Caprioli, Richard M.; Norris, Jeremy L.

2018-05-01

It has been widely recognized that individual cells that exist within a large population of cells, even if they are genetically identical, can have divergent molecular makeups resulting from a variety of factors, including local environmental factors and stochastic processes within each cell. Presently, numerous approaches have been described that permit the resolution of these single-cell expression differences for RNA and protein; however, relatively few techniques exist for the study of lipids and metabolites in this manner. This study presents a methodology for the analysis of metabolite and lipid expression at the level of a single cell through the use of imaging mass spectrometry on a high-performance Fourier transform ion cyclotron resonance mass spectrometer. This report provides a detailed description of the overall experimental approach, including sample preparation as well as the data acquisition and analysis strategy for single cells. Applying this approach to the study of cultured RAW264.7 cells, we demonstrate that this method can be used to study the variation in molecular expression with cell populations and is sensitive to alterations in that expression that occurs upon lipopolysaccharide stimulation. [Figure not available: see fulltext.

Single-Cell Mass Spectrometry Reveals Changes in Lipid and Metabolite Expression in RAW 264.7 Cells upon Lipopolysaccharide Stimulation

NASA Astrophysics Data System (ADS)

Yang, Bo; Patterson, Nathan Heath; Tsui, Tina; Caprioli, Richard M.; Norris, Jeremy L.

2018-03-01

It has been widely recognized that individual cells that exist within a large population of cells, even if they are genetically identical, can have divergent molecular makeups resulting from a variety of factors, including local environmental factors and stochastic processes within each cell. Presently, numerous approaches have been described that permit the resolution of these single-cell expression differences for RNA and protein; however, relatively few techniques exist for the study of lipids and metabolites in this manner. This study presents a methodology for the analysis of metabolite and lipid expression at the level of a single cell through the use of imaging mass spectrometry on a high-performance Fourier transform ion cyclotron resonance mass spectrometer. This report provides a detailed description of the overall experimental approach, including sample preparation as well as the data acquisition and analysis strategy for single cells. Applying this approach to the study of cultured RAW264.7 cells, we demonstrate that this method can be used to study the variation in molecular expression with cell populations and is sensitive to alterations in that expression that occurs upon lipopolysaccharide stimulation. [Figure not available: see fulltext.

Shotgun Bisulfite Sequencing of the Betula platyphylla Genome Reveals the Tree’s DNA Methylation Patterning

PubMed Central

Su, Chang; Wang, Chao; He, Lin; Yang, Chuanping; Wang, Yucheng

2014-01-01

DNA methylation plays a critical role in the regulation of gene expression. Most studies of DNA methylation have been performed in herbaceous plants, and little is known about the methylation patterns in tree genomes. In the present study, we generated a map of methylated cytosines at single base pair resolution for Betula platyphylla (white birch) by bisulfite sequencing combined with transcriptomics to analyze DNA methylation and its effects on gene expression. We obtained a detailed view of the function of DNA methylation sequence composition and distribution in the genome of B. platyphylla. There are 34,460 genes in the whole genome of birch, and 31,297 genes are methylated. Conservatively, we estimated that 14.29% of genomic cytosines are methylcytosines in birch. Among the methylation sites, the CHH context accounts for 48.86%, and is the largest proportion. Combined transcriptome and methylation analysis showed that the genes with moderate methylation levels had higher expression levels than genes with high and low methylation. In addition, methylated genes are highly enriched for the GO subcategories of binding activities, catalytic activities, cellular processes, response to stimulus and cell death, suggesting that methylation mediates these pathways in birch trees. PMID:25514241

An anatomically comprehensive atlas of the adult human brain transcriptome

PubMed Central

Guillozet-Bongaarts, Angela L.; Shen, Elaine H.; Ng, Lydia; Miller, Jeremy A.; van de Lagemaat, Louie N.; Smith, Kimberly A.; Ebbert, Amanda; Riley, Zackery L.; Abajian, Chris; Beckmann, Christian F.; Bernard, Amy; Bertagnolli, Darren; Boe, Andrew F.; Cartagena, Preston M.; Chakravarty, M. Mallar; Chapin, Mike; Chong, Jimmy; Dalley, Rachel A.; David Daly, Barry; Dang, Chinh; Datta, Suvro; Dee, Nick; Dolbeare, Tim A.; Faber, Vance; Feng, David; Fowler, David R.; Goldy, Jeff; Gregor, Benjamin W.; Haradon, Zeb; Haynor, David R.; Hohmann, John G.; Horvath, Steve; Howard, Robert E.; Jeromin, Andreas; Jochim, Jayson M.; Kinnunen, Marty; Lau, Christopher; Lazarz, Evan T.; Lee, Changkyu; Lemon, Tracy A.; Li, Ling; Li, Yang; Morris, John A.; Overly, Caroline C.; Parker, Patrick D.; Parry, Sheana E.; Reding, Melissa; Royall, Joshua J.; Schulkin, Jay; Sequeira, Pedro Adolfo; Slaughterbeck, Clifford R.; Smith, Simon C.; Sodt, Andy J.; Sunkin, Susan M.; Swanson, Beryl E.; Vawter, Marquis P.; Williams, Derric; Wohnoutka, Paul; Zielke, H. Ronald; Geschwind, Daniel H.; Hof, Patrick R.; Smith, Stephen M.; Koch, Christof; Grant, Seth G. N.; Jones, Allan R.

2014-01-01

Neuroanatomically precise, genome-wide maps of transcript distributions are critical resources to complement genomic sequence data and to correlate functional and genetic brain architecture. Here we describe the generation and analysis of a transcriptional atlas of the adult human brain, comprising extensive histological analysis and comprehensive microarray profiling of ~900 neuroanatomically precise subdivisions in two individuals. Transcriptional regulation varies enormously by anatomical location, with different regions and their constituent cell types displaying robust molecular signatures that are highly conserved between individuals. Analysis of differential gene expression and gene co-expression relationships demonstrates that brain-wide variation strongly reflects the distributions of major cell classes such as neurons, oligodendrocytes, astrocytes and microglia. Local neighbourhood relationships between fine anatomical subdivisions are associated with discrete neuronal subtypes and genes involved with synaptic transmission. The neocortex displays a relatively homogeneous transcriptional pattern, but with distinct features associated selectively with primary sensorimotor cortices and with enriched frontal lobe expression. Notably, the spatial topography of the neocortex is strongly reflected in its molecular topography— the closer two cortical regions, the more similar their transcriptomes. This freely accessible online data resource forms a high-resolution transcriptional baseline for neurogenetic studies of normal and abnormal human brain function. PMID:22996553

Cloning and heterologous expression of the entire gene clusters for PD 116740 from Streptomyces strain WP 4669 and tetrangulol and tetrangomycin from Streptomyces rimosus NRRL 3016.

PubMed Central

Hong, S T; Carney, J R; Gould, S J

1997-01-01

The genes for the complete pathways for two polycyclic aromatic polyketides of the angucyclinone class have been cloned and heterologously expressed. Genomic DNAs of Streptomyces rimosus NRRL 3016 and Streptomyces strain WP 4669 were partially digested with MboI, and libraries (ca. 40-kb fragments) in Escherichia coli XL1-Blue MR were prepared with the cosmid vector pOJ446. Hybridization with the actI probe from the actinorhodin polyketide synthase genes identified two clusters of polyketide genes from each organism. After transfer of the four clusters to Streptomyces lividans TK24, expression of one cluster from each organism was established through the identification of pathway-specific products by high-performance liquid chromatography with photodiode array detection. Peaks were identified from the S. rimosus cluster (pksRIM-1) for tetrangulol, tetrangomycin, and fridamycin E. Peaks were identified from the WP 4669 cluster (pksWP-2) for tetrangulol, 19-hydroxytetrangulol, 8-O-methyltetrangulol, 19-hydroxy-8-O-methyltetrangulol, and PD 116740. Structures were confirmed by 1H nuclear magnetic resonance spectroscopy and high-resolution mass spectrometry. PMID:8990300

Cloning and heterologous expression of the entire gene clusters for PD 116740 from Streptomyces strain WP 4669 and tetrangulol and tetrangomycin from Streptomyces rimosus NRRL 3016.

PubMed

Hong, S T; Carney, J R; Gould, S J

1997-01-01

The genes for the complete pathways for two polycyclic aromatic polyketides of the angucyclinone class have been cloned and heterologously expressed. Genomic DNAs of Streptomyces rimosus NRRL 3016 and Streptomyces strain WP 4669 were partially digested with MboI, and libraries (ca. 40-kb fragments) in Escherichia coli XL1-Blue MR were prepared with the cosmid vector pOJ446. Hybridization with the actI probe from the actinorhodin polyketide synthase genes identified two clusters of polyketide genes from each organism. After transfer of the four clusters to Streptomyces lividans TK24, expression of one cluster from each organism was established through the identification of pathway-specific products by high-performance liquid chromatography with photodiode array detection. Peaks were identified from the S. rimosus cluster (pksRIM-1) for tetrangulol, tetrangomycin, and fridamycin E. Peaks were identified from the WP 4669 cluster (pksWP-2) for tetrangulol, 19-hydroxytetrangulol, 8-O-methyltetrangulol, 19-hydroxy-8-O-methyltetrangulol, and PD 116740. Structures were confirmed by 1H nuclear magnetic resonance spectroscopy and high-resolution mass spectrometry.

High resolution digital elevation modelling from TLS and UAV campaign reveals structural complexity at the 2014/15 Holuhraun eruption site, Iceland

NASA Astrophysics Data System (ADS)

Müller, Daniel; Walter, Thomas R.; Schöpa, Anne; Witt, Tanja; Steinke, Bastian; Gudmundsson, Magnús T.; Dürig, Tobias

2017-07-01

Fissure eruptions are commonly linked to magma dikes at depth, associated with elastic and anelastic surface deformation. Elastic deformation is well described by subsidence above, uplift and lateral widening perpendicular to the dike plane. The anelastic part is associated with the formation of a graben, bordered by graben parallel faults that might express as sets of fractures at the surface. Additionally secondary structures, like push ups, bends and step overs yield information about the deforming domain. The formation of such structures associated with fissure eruptions, however, is barely preserved in nature because of the rapid erosion or sediment coverage. Therefore, simple normal fault displacements are commonly assumed at dikes. At the 2014/2015 Holuhraun eruption sites (Iceland), evidence is increasing that the developing fractures are showing variations in their displacement modes. In an attempt to investigate these variations, a fieldwork mapping project combining Terrestrial Laser Scanning (TLS) and Unmanned Aerial Vehicle (UAV) based aerophoto analysis was realized. From this data, we generated locally high resolution Digital Elevation Models (DEMs) and a structural map that allows for identification of kinematic indicators and assessing particularities of the observed structures. We identified 315 fracture segments from satellite data. For single segments we measured strike directions including the amount of opening and opening angles, indicating that many of the measured fractures show transtensional dislocations. Out of these, 81 % are showing significant left-lateral slip, only 17% right-lateral slip and 2% pure tensile opening. We show that local complexities in the fracture traces and geometries are closely related to variations in the transtensional opening direction. Moreover, we identified local changes in fracture azimuths and offsets close to eruption sites, which we speculate to be associated with geometrical changes in the magma feeder itself. Results highlight that opening of fractures associated with an erupting fissure commonly show transtensional modes having both, left-lateral and right-lateral slip, with important implications for interpreting the expression of surface structures at rift zones elsewhere. Results further highlight the great value of UAV based high resolution data to contribute to the integrity of observations of structural complexities at local geologic events.

Nuclear Heat Shock Response and Novel Nuclear Domain 10 Reorganization in Respiratory Syncytial Virus-Infected A549 Cells Identified by High-Resolution Two-Dimensional Gel Electrophoresis

PubMed Central

Brasier, Allan R.; Spratt, Heidi; Wu, Zheng; Boldogh, Istvan; Zhang, Yuhong; Garofalo, Roberto P.; Casola, Antonella; Pashmi, Jawad; Haag, Anthony; Luxon, Bruce; Kurosky, Alexander

2004-01-01

The pneumovirus respiratory syncytial virus (RSV) is a leading cause of epidemic respiratory tract infection. Upon entry, RSV replicates in the epithelial cytoplasm, initiating compensatory changes in cellular gene expression. In this study, we have investigated RSV-induced changes in the nuclear proteome of A549 alveolar type II-like epithelial cells by high-resolution two-dimensional gel electrophoresis (2DE). Replicate 2D gels from uninfected and RSV-infected nuclei were compared for changes in protein expression. We identified 24 different proteins by peptide mass fingerprinting after matrix-assisted laser desorption ionization-time of flight mass spectrometry (MS), whose average normalized spot intensity was statistically significant and differed by ±2-fold. Notable among the proteins identified were the cytoskeletal cytokeratins, RNA helicases, oxidant-antioxidant enzymes, the TAR DNA binding protein (a protein that associates with nuclear domain 10 [ND10] structures), and heat shock protein 70- and 60-kDa isoforms (Hsp70 and Hsp60, respectively). The identification of Hsp70 was also validated by liquid chromatography quadropole-TOF tandem MS (LC-MS/MS). Separate experiments using immunofluorescence microscopy revealed that RSV induced cytoplasmic Hsp70 aggregation and nuclear accumulation. Data mining of a genomic database showed that RSV replication induced coordinate changes in Hsp family proteins, including the 70, 70-2, 90, 40, and 40-3 isoforms. Because the TAR DNA binding protein associates with ND10s, we examined the effect of RSV infection on ND10 organization. RSV induced a striking dissolution of ND10 structures with redistribution of the component promyelocytic leukemia (PML) and speckled 100-kDa (Sp100) proteins into the cytoplasm, as well as inducing their synthesis. Our findings suggest that cytoplasmic RSV replication induces a nuclear heat shock response, causes ND10 disruption, and redistributes PML and Sp100 to the cytoplasm. Thus, a high-resolution proteomics approach, combined with immunofluorescence localization and coupled with genomic response data, yielded unexpected novel insights into compensatory nuclear responses to RSV infection. PMID:15479789

Quantitative Proteomics of Sleep-Deprived Mouse Brains Reveals Global Changes in Mitochondrial Proteins

PubMed Central

Li, Tie-Mei; Zhang, Ju-en; Lin, Rui; Chen, She; Luo, Minmin; Dong, Meng-Qiu

2016-01-01

Sleep is a ubiquitous, tightly regulated, and evolutionarily conserved behavior observed in almost all animals. Prolonged sleep deprivation can be fatal, indicating that sleep is a physiological necessity. However, little is known about its core function. To gain insight into this mystery, we used advanced quantitative proteomics technology to survey the global changes in brain protein abundance. Aiming to gain a comprehensive profile, our proteomics workflow included filter-aided sample preparation (FASP), which increased the coverage of membrane proteins; tandem mass tag (TMT) labeling, for relative quantitation; and high resolution, high mass accuracy, high throughput mass spectrometry (MS). In total, we obtained the relative abundance ratios of 9888 proteins encoded by 6070 genes. Interestingly, we observed significant enrichment for mitochondrial proteins among the differentially expressed proteins. This finding suggests that sleep deprivation strongly affects signaling pathways that govern either energy metabolism or responses to mitochondrial stress. Additionally, the differentially-expressed proteins are enriched in pathways implicated in age-dependent neurodegenerative diseases, including Parkinson’s, Huntington’s, and Alzheimer’s, hinting at possible connections between sleep loss, mitochondrial stress, and neurodegeneration. PMID:27684481

A preliminary crystallographic analysis of the putative mevalonate diphosphate decarboxylase from Trypanosoma brucei

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

Byres, Emma; Martin, David M. A.; Hunter, William N., E-mail: w.n.hunter@dundee.ac.uk

2005-06-01

The gene encoding the putative mevalonate diphosphate decarboxylase, an enzyme from the mevalonate pathway of isoprenoid precursor biosynthesis, has been cloned from T. brucei. Recombinant protein has been expressed, purified and highly ordered crystals obtained and characterized to aid the structure–function analysis of this enzyme. Mevalonate diphosphate decarboxylase catalyses the last and least well characterized step in the mevalonate pathway for the biosynthesis of isopentenyl pyrophosphate, an isoprenoid precursor. A gene predicted to encode the enzyme from Trypanosoma brucei has been cloned, a highly efficient expression system established and a purification protocol determined. The enzyme gives monoclinic crystals in spacemore » group P2{sub 1}, with unit-cell parameters a = 51.5, b = 168.7, c = 54.9 Å, β = 118.8°. A Matthews coefficient V{sub M} of 2.5 Å{sup 3} Da{sup −1} corresponds to two monomers, each approximately 42 kDa (385 residues), in the asymmetric unit with 50% solvent content. These crystals are well ordered and data to high resolution have been recorded using synchrotron radiation.« less

Multi-scale imaging and informatics pipeline for in situ pluripotent stem cell analysis.

PubMed

Gorman, Bryan R; Lu, Junjie; Baccei, Anna; Lowry, Nathan C; Purvis, Jeremy E; Mangoubi, Rami S; Lerou, Paul H

2014-01-01

Human pluripotent stem (hPS) cells are a potential source of cells for medical therapy and an ideal system to study fate decisions in early development. However, hPS cells cultured in vitro exhibit a high degree of heterogeneity, presenting an obstacle to clinical translation. hPS cells grow in spatially patterned colony structures, necessitating quantitative single-cell image analysis. We offer a tool for analyzing the spatial population context of hPS cells that integrates automated fluorescent microscopy with an analysis pipeline. It enables high-throughput detection of colonies at low resolution, with single-cellular and sub-cellular analysis at high resolutions, generating seamless in situ maps of single-cellular data organized by colony. We demonstrate the tool's utility by analyzing inter- and intra-colony heterogeneity of hPS cell cycle regulation and pluripotency marker expression. We measured the heterogeneity within individual colonies by analyzing cell cycle as a function of distance. Cells loosely associated with the outside of the colony are more likely to be in G1, reflecting a less pluripotent state, while cells within the first pluripotent layer are more likely to be in G2, possibly reflecting a G2/M block. Our multi-scale analysis tool groups colony regions into density classes, and cells belonging to those classes have distinct distributions of pluripotency markers and respond differently to DNA damage induction. Lastly, we demonstrate that our pipeline can robustly handle high-content, high-resolution single molecular mRNA FISH data by using novel image processing techniques. Overall, the imaging informatics pipeline presented offers a novel approach to the analysis of hPS cells that includes not only single cell features but also colony wide, and more generally, multi-scale spatial configuration.

The 2010 Pakistan floods: high-resolution simulations with the WRF model

NASA Astrophysics Data System (ADS)

Viterbo, Francesca; Parodi, Antonio; Molini, Luca; Provenzale, Antonello; von Hardenberg, Jost; Palazzi, Elisa

2013-04-01

Estimating current and future water resources in high mountain regions with complex orography is a difficult but crucial task. In particular, the French-Italian project PAPRIKA is focused on two specific regions in the Hindu-Kush -- Himalaya -- Karakorum (HKKH)region: the Shigar basin in Pakistan, at the feet of K2, and the Khumbu valley in Nepal, at the feet of Mount Everest. In this framework, we use the WRF model to simulate precipitation and meteorological conditions with high resolution in areas with extreme orographic slopes, comparing the model output with station and satellite data. Once validated the model, we shall run a set of three future time-slices at very high spatial resolution, in the periods 2046-2050, 2071-2075 and 2096-2100, nested in different climate change scenarios (EXtreme PREcipitation and Hydrological climate Scenario Simulations -EXPRESS-Hydro project). As a prelude to this study, here we discuss the simulation of specific, high-intensity rainfall events in this area. In this paper we focus on the 2010 Pakistan floods which began in late July 2010, producing heavy monsoon rains in the Khyber Pakhtunkhwa, Sindh, Punjab and Balochistan regions of Pakistan and affecting the Indus River basin. Approximately one-fifth of Pakistan's total land area was underwater, with a death toll of about 2000 people. This event has been simulated with the WRF model (version 3.3.) in cloud-permitting mode (d01 14 km and d02 3.5 km): different convective closures and microphysics parameterization have been used. A deeper understanding of the processes responsible for this event has been gained through comparison with rainfall depth observations, radiosounding data and geostationary/polar satellite images.

Preclinical fluorescent mouse models of pancreatic cancer

NASA Astrophysics Data System (ADS)

Bouvet, Michael; Hoffman, Robert M.

2007-02-01

Here we describe our cumulative experience with the development and preclinical application of several highly fluorescent, clinically-relevant, metastatic orthotopic mouse models of pancreatic cancer. These models utilize the human pancreatic cancer cell lines which have been genetically engineered to selectively express high levels of the bioluminescent green fluorescent (GFP) or red fluorescent protein (RFP). Fluorescent tumors are established subcutaneously in nude mice, and tumor fragments are then surgically transplanted onto the pancreas. Locoregional tumor growth and distant metastasis of these orthotopic implants occurs spontaneously and rapidly throughout the abdomen in a manner consistent with clinical human disease. Highly specific, high-resolution, real-time visualization of tumor growth and metastasis may be achieved in vivo without the need for contrast agents, invasive techniques, or expensive imaging equipment. We have shown a high correlation between florescent optical imaging and magnetic resonance imaging in these models. Alternatively, transplantation of RFP-expressing tumor fragments onto the pancreas of GFP-expressing transgenic mice may be used to facilitate visualization of tumor-host interaction between the pancreatic tumor fragments and host-derived stroma and vasculature. Such in vivo models have enabled us to serially visualize and acquire images of the progression of pancreatic cancer in the live animal, and to demonstrate the real-time antitumor and antimetastatic effects of several novel therapeutic strategies on pancreatic malignancy. These fluorescent models are therefore powerful and reliable tools with which to investigate human pancreatic cancer and therapeutic strategies directed against it.

Subcellular localization of leptin and leptin receptor in breast cancer detected in an electron microscopic study.

PubMed

Al-Shibli, Saad M; Amjad, Nasser M; Al-Kubaisi, Muna K; Mizan, Shaikh

2017-01-22

Leptin (LEP) and leptin receptor (LEPR) have long been found associated with breast cancer. So far no high-resolution method such as electron microscopy has been used to investigate the subcellular localization of leptin and leptin receptor in breast cancer. We collected cancer and non-cancer breast tissues from 51 women with invasive ductal breast cancer. Leptin and leptin receptor in the tissues were estimated using immunohistochemistry (IHC). LEP and LEPR were localized at subcellular level by immunocytochemistry (ICC) using ultra-fine gold particle conjugated antibody, and visualized with transmission electron microscopy (TEM). IHC showed high presence of LEP and LEPR in 65% and 67% respectively of the breast cancer samples, 100% and 0% respectively of the adipose tissue samples, and no high presence in the non-cancer breast tissue samples. On TEM views both LEP and LEPR were found highly concentrated within the nucleus of the cancer cells, indicating that nucleus is the principal seat of action. However, presence of high concentration of LEP does not necessarily prove its over-expression, as often concluded, because LEP could be internalized from outside by LEPR in the cells. In contrast, LEPR is definitely over-expressed in the ductal breast cancer cells. Therefore, we hypothesize that over-expression of LEPR, rather than that of LEP has a fundamental role in breast carcinogenesis in particular, and probably for LEP-LEPR associated tumors in general. Copyright © 2016 Elsevier Inc. All rights reserved.

High resolution time interval meter

DOEpatents

Martin, A.D.

1986-05-09

Method and apparatus are provided for measuring the time interval between two events to a higher resolution than reliability available from conventional circuits and component. An internal clock pulse is provided at a frequency compatible with conventional component operating frequencies for reliable operation. Lumped constant delay circuits are provided for generating outputs at delay intervals corresponding to the desired high resolution. An initiation START pulse is input to generate first high resolution data. A termination STOP pulse is input to generate second high resolution data. Internal counters count at the low frequency internal clock pulse rate between the START and STOP pulses. The first and second high resolution data are logically combined to directly provide high resolution data to one counter and correct the count in the low resolution counter to obtain a high resolution time interval measurement.

Complementary analyses of hollow cylindrical unioriented permanent magnet (HCM) with high permeability external layer

NASA Astrophysics Data System (ADS)

Lobo, Carlos M. S.; Tosin, Giancarlo; Baader, Johann E.; Colnago, Luiz A.

2017-10-01

In this article, several studies based on analytical expressions and computational simulations on Hollow Cylindrical Magnets with an external soft ferromagnetic material (HCM magnets) are presented. Electromagnetic configurations, as well as permanent-magnet-based structures, are studied in terms of magnetic field strength and homogeneity. Permanent-magnet-based structures are further analyzed in terms of the anisotropy of the magnetic permeability. It was found that the HCM magnets produce a highly homogeneous magnetic field as long as the magnetic material is isotropic. The dependency of the magnetic field strength and homogeneity in terms of the anisotropy of the magnetic permeability is also explored here. These magnets can potentially be used in medium-resolution NMR spectrometers and high-field NMR spectrometers.

Resolution No. 43/121. Use of children in the illicit traffic in narcotic drugs and rehabilitation of drug-addicted minors, 8 December 1988.

PubMed

1988-01-01

This document contains the text of a 1988 UN Resolution on the use of children in the illicit traffic in narcotic drugs and rehabilitation of drug-addicted minors. In this Resolution, the General Assembly recalls previous resolutions adopted to fight illicit drugs, expresses alarm at the fact that drug dealers are using children to further their illicit activities and at the increasing number of drug-addicted children, and refers to the Declaration of the Rights of the Child and the upcoming Convention on the Rights of the Child. Based on this, the UN condemns all forms of drug trafficking, especially those which involve children; urges states to establish programs to protect children from drugs; invites member states with the most urgent problems to adopt additional measures; calls for suitably severe punishment of drug-trafficking crimes that involve children; urges all organizations to place high priority on the prevention and treatment of drug addiction in children; asks international agencies and the UN Fund for Drug Abuse Control to give financial support to such programs; and asks the UN Department of Pubic Information of the Secretariat to publish information designed to prevent drug use in children.

Integrating 4-d light-sheet imaging with interactive virtual reality to recapitulate developmental cardiac mechanics and physiology

NASA Astrophysics Data System (ADS)

Ding, Yichen; Yu, Jing; Abiri, Arash; Abiri, Parinaz; Lee, Juhyun; Chang, Chih-Chiang; Baek, Kyung In; Sevag Packard, René R.; Hsiai, Tzung K.

2018-02-01

There currently is a limited ability to interactively study developmental cardiac mechanics and physiology. We therefore combined light-sheet fluorescence microscopy (LSFM) with virtual reality (VR) to provide a hybrid platform for 3- dimensional (3-D) architecture and time-dependent cardiac contractile function characterization. By taking advantage of the rapid acquisition, high axial resolution, low phototoxicity, and high fidelity in 3-D and 4-D (3-D spatial + 1-D time or spectra), this VR-LSFM hybrid methodology enables interactive visualization and quantification otherwise not available by conventional methods such as routine optical microscopes. We hereby demonstrate multi-scale applicability of VR-LSFM to 1) interrogate skin fibroblasts interacting with a hyaluronic acid-based hydrogel, 2) navigate through the endocardial trabecular network during zebrafish development, and 3) localize gene therapy-mediated potassium channel expression in adult murine hearts. We further combined our batch intensity normalized segmentation (BINS) algorithm with deformable image registration (DIR) to interface a VR environment for the analysis of cardiac contraction. Thus, the VR-LSFM hybrid platform demonstrates an efficient and robust framework for creating a user-directed microenvironment in which we uncovered developmental cardiac mechanics and physiology with high spatiotemporal resolution.

The investigation of improved SHARAD profiles over Martian lobate debris aprons

NASA Astrophysics Data System (ADS)

Kim, J.; Baik, H. S.

2016-12-01

The Shallow Subsurface Radar (SHARAD), a radar sounding radar on the Mars Reconnaissance Orbiter has produced high valuable information concerning subsurface of Mars. It has been successfully used to observe complicate substructures of Mars such as polar deposit, pedestal crater and the other geomorphic features involving possible subsurface ice body. In this study, we summarized all SHARAD profiles over Martian Lobate debris aprons (LDAs) where significant arguments about their origins are undergoing. To make clear result, we used radon transformation for noise filtering. Also, we tried the clutter simulation on our target's Digital elevation model(DEM) produced by High Resolution Stereo Camera(HRSC) of Mars Express; As the comparison results between noise-removed SHARAD profile and clutter simulation, layers were able to be more clearly identified at many LDAs. We integrated our SHARAD profiles over all mid latitude LDAs into GIS. These will be demonstrated together with several radargram structures. However, it appeared the discontinuities over SHARAD profile result is not sufficient to be a clue of its origin. Thus the intensive interpretations employing thermal inertia, high resolution topographic profile with CTX and HiRISE stereo DTM altogether will be further conducted.

Integrating light-sheet imaging with virtual reality to recapitulate developmental cardiac mechanics.

PubMed

Ding, Yichen; Abiri, Arash; Abiri, Parinaz; Li, Shuoran; Chang, Chih-Chiang; Baek, Kyung In; Hsu, Jeffrey J; Sideris, Elias; Li, Yilei; Lee, Juhyun; Segura, Tatiana; Nguyen, Thao P; Bui, Alexander; Sevag Packard, René R; Fei, Peng; Hsiai, Tzung K

2017-11-16

Currently, there is a limited ability to interactively study developmental cardiac mechanics and physiology. We therefore combined light-sheet fluorescence microscopy (LSFM) with virtual reality (VR) to provide a hybrid platform for 3D architecture and time-dependent cardiac contractile function characterization. By taking advantage of the rapid acquisition, high axial resolution, low phototoxicity, and high fidelity in 3D and 4D (3D spatial + 1D time or spectra), this VR-LSFM hybrid methodology enables interactive visualization and quantification otherwise not available by conventional methods, such as routine optical microscopes. We hereby demonstrate multiscale applicability of VR-LSFM to (a) interrogate skin fibroblasts interacting with a hyaluronic acid-based hydrogel, (b) navigate through the endocardial trabecular network during zebrafish development, and (c) localize gene therapy-mediated potassium channel expression in adult murine hearts. We further combined our batch intensity normalized segmentation algorithm with deformable image registration to interface a VR environment with imaging computation for the analysis of cardiac contraction. Thus, the VR-LSFM hybrid platform demonstrates an efficient and robust framework for creating a user-directed microenvironment in which we uncovered developmental cardiac mechanics and physiology with high spatiotemporal resolution.

Integrating light-sheet imaging with virtual reality to recapitulate developmental cardiac mechanics

PubMed Central

Ding, Yichen; Abiri, Arash; Abiri, Parinaz; Li, Shuoran; Chang, Chih-Chiang; Hsu, Jeffrey J.; Sideris, Elias; Li, Yilei; Lee, Juhyun; Segura, Tatiana; Nguyen, Thao P.; Bui, Alexander; Sevag Packard, René R.; Hsiai, Tzung K.

2017-01-01

Currently, there is a limited ability to interactively study developmental cardiac mechanics and physiology. We therefore combined light-sheet fluorescence microscopy (LSFM) with virtual reality (VR) to provide a hybrid platform for 3D architecture and time-dependent cardiac contractile function characterization. By taking advantage of the rapid acquisition, high axial resolution, low phototoxicity, and high fidelity in 3D and 4D (3D spatial + 1D time or spectra), this VR-LSFM hybrid methodology enables interactive visualization and quantification otherwise not available by conventional methods, such as routine optical microscopes. We hereby demonstrate multiscale applicability of VR-LSFM to (a) interrogate skin fibroblasts interacting with a hyaluronic acid–based hydrogel, (b) navigate through the endocardial trabecular network during zebrafish development, and (c) localize gene therapy-mediated potassium channel expression in adult murine hearts. We further combined our batch intensity normalized segmentation algorithm with deformable image registration to interface a VR environment with imaging computation for the analysis of cardiac contraction. Thus, the VR-LSFM hybrid platform demonstrates an efficient and robust framework for creating a user-directed microenvironment in which we uncovered developmental cardiac mechanics and physiology with high spatiotemporal resolution. PMID:29202458

Preliminary interpretation of high resolution 3D seismic data from offshore Mt. Etna, Italy

NASA Astrophysics Data System (ADS)

Gross, F.; Krastel, S.; Chiocci, F. L.; Ridente, D.; Cukur, D.; Bialas, J.; Papenberg, C. A.; Crutchley, G.; Koch, S.

2013-12-01

In order to gain knowledge about subsurface structures and its correlation to seafloor expressions, a hydro-acoustic dataset was collected during RV Meteor Cruise M86/2 (December 2011/January 2012) in Messina Straits and offshore Mt. Etna. Especially offshore Mt. Etna, the data reveals an obvious connection between subsurface structures and previously known morphological features at the sea floor. Therefore a high resolution 3D seismic dataset was acquired between Riposto Ridge and Catania Canyon close to the shore of eastern Sicily. The study area is characterized by a major structural high, which hosts several ridge-like features at the seafloor. These features are connected to a SW-NE trending fault system. The ridges are bended in their NE-SW direction and host major escarpments at the seafloor. Furthermore they are located directly next to a massive amphitheater structure offshore Mt. Etna with slope gradients of up to 35°, which is interpreted as remnants of a massive submarine mass wasting event off Sicily. The new 3D seismic dataset allows an in depth analysis of the ongoing deformation of the east flank of Mt. Etna.

Comparison of Two Grid Refinement Approaches for High Resolution Regional Climate Modeling: MPAS vs WRF

NASA Astrophysics Data System (ADS)

Leung, L.; Hagos, S. M.; Rauscher, S.; Ringler, T.

2012-12-01

This study compares two grid refinement approaches using global variable resolution model and nesting for high-resolution regional climate modeling. The global variable resolution model, Model for Prediction Across Scales (MPAS), and the limited area model, Weather Research and Forecasting (WRF) model, are compared in an idealized aqua-planet context with a focus on the spatial and temporal characteristics of tropical precipitation simulated by the models using the same physics package from the Community Atmosphere Model (CAM4). For MPAS, simulations have been performed with a quasi-uniform resolution global domain at coarse (1 degree) and high (0.25 degree) resolution, and a variable resolution domain with a high-resolution region at 0.25 degree configured inside a coarse resolution global domain at 1 degree resolution. Similarly, WRF has been configured to run on a coarse (1 degree) and high (0.25 degree) resolution tropical channel domain as well as a nested domain with a high-resolution region at 0.25 degree nested two-way inside the coarse resolution (1 degree) tropical channel. The variable resolution or nested simulations are compared against the high-resolution simulations that serve as virtual reality. Both MPAS and WRF simulate 20-day Kelvin waves propagating through the high-resolution domains fairly unaffected by the change in resolution. In addition, both models respond to increased resolution with enhanced precipitation. Grid refinement induces zonal asymmetry in precipitation (heating), accompanied by zonal anomalous Walker like circulations and standing Rossby wave signals. However, there are important differences between the anomalous patterns in MPAS and WRF due to differences in the grid refinement approaches and sensitivity of model physics to grid resolution. This study highlights the need for "scale aware" parameterizations in variable resolution and nested regional models.

Tracking Single Cells in Live Animals Using a Photoconvertible Near-Infrared Cell Membrane Label

PubMed Central

Wu, Juwell; Runnels, Judith M.; Turcotte, Raphaël; Celso, Cristina Lo; Scadden, David T.; Strom, Terry B.; Lin, Charles P.

2013-01-01

We describe a novel photoconversion technique to track individual cells in vivo using a commercial lipophilic membrane dye, DiR. We show that DiR exhibits a permanent fluorescence emission shift (photoconversion) after light exposure and does not reacquire the original color over time. Ratiometric imaging can be used to distinguish photoconverted from non-converted cells with high sensitivity. Combining the use of this photoconvertible dye with intravital microscopy, we tracked the division of individual hematopoietic stem/progenitor cells within the calvarium bone marrow of live mice. We also studied the peripheral differentiation of individual T cells by tracking the gain or loss of FoxP3-GFP expression, a marker of the immune suppressive function of CD4+ T cells. With the near-infrared photoconvertible membrane dye, the entire visible spectral range is available for simultaneous use with other fluorescent proteins to monitor gene expression or to trace cell lineage commitment in vivo with high spatial and temporal resolution. PMID:23990881

Tracking single cells in live animals using a photoconvertible near-infrared cell membrane label.

PubMed

Carlson, Alicia L; Fujisaki, Joji; Wu, Juwell; Runnels, Judith M; Turcotte, Raphaël; Spencer, Joel A; Celso, Cristina Lo; Scadden, David T; Strom, Terry B; Lin, Charles P

2013-01-01

We describe a novel photoconversion technique to track individual cells in vivo using a commercial lipophilic membrane dye, DiR. We show that DiR exhibits a permanent fluorescence emission shift (photoconversion) after light exposure and does not reacquire the original color over time. Ratiometric imaging can be used to distinguish photoconverted from non-converted cells with high sensitivity. Combining the use of this photoconvertible dye with intravital microscopy, we tracked the division of individual hematopoietic stem/progenitor cells within the calvarium bone marrow of live mice. We also studied the peripheral differentiation of individual T cells by tracking the gain or loss of FoxP3-GFP expression, a marker of the immune suppressive function of CD4(+) T cells. With the near-infrared photoconvertible membrane dye, the entire visible spectral range is available for simultaneous use with other fluorescent proteins to monitor gene expression or to trace cell lineage commitment in vivo with high spatial and temporal resolution.

Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.

PubMed

Klein, Allon M; Mazutis, Linas; Akartuna, Ilke; Tallapragada, Naren; Veres, Adrian; Li, Victor; Peshkin, Leonid; Weitz, David A; Kirschner, Marc W

2015-05-21

It has long been the dream of biologists to map gene expression at the single-cell level. With such data one might track heterogeneous cell sub-populations, and infer regulatory relationships between genes and pathways. Recently, RNA sequencing has achieved single-cell resolution. What is limiting is an effective way to routinely isolate and process large numbers of individual cells for quantitative in-depth sequencing. We have developed a high-throughput droplet-microfluidic approach for barcoding the RNA from thousands of individual cells for subsequent analysis by next-generation sequencing. The method shows a surprisingly low noise profile and is readily adaptable to other sequencing-based assays. We analyzed mouse embryonic stem cells, revealing in detail the population structure and the heterogeneous onset of differentiation after leukemia inhibitory factor (LIF) withdrawal. The reproducibility of these high-throughput single-cell data allowed us to deconstruct cell populations and infer gene expression relationships. VIDEO ABSTRACT. Copyright © 2015 Elsevier Inc. All rights reserved.

Transcriptional landscape of the prenatal human brain.

PubMed

Miller, Jeremy A; Ding, Song-Lin; Sunkin, Susan M; Smith, Kimberly A; Ng, Lydia; Szafer, Aaron; Ebbert, Amanda; Riley, Zackery L; Royall, Joshua J; Aiona, Kaylynn; Arnold, James M; Bennet, Crissa; Bertagnolli, Darren; Brouner, Krissy; Butler, Stephanie; Caldejon, Shiella; Carey, Anita; Cuhaciyan, Christine; Dalley, Rachel A; Dee, Nick; Dolbeare, Tim A; Facer, Benjamin A C; Feng, David; Fliss, Tim P; Gee, Garrett; Goldy, Jeff; Gourley, Lindsey; Gregor, Benjamin W; Gu, Guangyu; Howard, Robert E; Jochim, Jayson M; Kuan, Chihchau L; Lau, Christopher; Lee, Chang-Kyu; Lee, Felix; Lemon, Tracy A; Lesnar, Phil; McMurray, Bergen; Mastan, Naveed; Mosqueda, Nerick; Naluai-Cecchini, Theresa; Ngo, Nhan-Kiet; Nyhus, Julie; Oldre, Aaron; Olson, Eric; Parente, Jody; Parker, Patrick D; Parry, Sheana E; Stevens, Allison; Pletikos, Mihovil; Reding, Melissa; Roll, Kate; Sandman, David; Sarreal, Melaine; Shapouri, Sheila; Shapovalova, Nadiya V; Shen, Elaine H; Sjoquist, Nathan; Slaughterbeck, Clifford R; Smith, Michael; Sodt, Andy J; Williams, Derric; Zöllei, Lilla; Fischl, Bruce; Gerstein, Mark B; Geschwind, Daniel H; Glass, Ian A; Hawrylycz, Michael J; Hevner, Robert F; Huang, Hao; Jones, Allan R; Knowles, James A; Levitt, Pat; Phillips, John W; Sestan, Nenad; Wohnoutka, Paul; Dang, Chinh; Bernard, Amy; Hohmann, John G; Lein, Ed S

2014-04-10

The anatomical and functional architecture of the human brain is mainly determined by prenatal transcriptional processes. We describe an anatomically comprehensive atlas of the mid-gestational human brain, including de novo reference atlases, in situ hybridization, ultra-high-resolution magnetic resonance imaging (MRI) and microarray analysis on highly discrete laser-microdissected brain regions. In developing cerebral cortex, transcriptional differences are found between different proliferative and post-mitotic layers, wherein laminar signatures reflect cellular composition and developmental processes. Cytoarchitectural differences between human and mouse have molecular correlates, including species differences in gene expression in subplate, although surprisingly we find minimal differences between the inner and outer subventricular zones even though the outer zone is expanded in humans. Both germinal and post-mitotic cortical layers exhibit fronto-temporal gradients, with particular enrichment in the frontal lobe. Finally, many neurodevelopmental disorder and human-evolution-related genes show patterned expression, potentially underlying unique features of human cortical formation. These data provide a rich, freely-accessible resource for understanding human brain development.

Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes

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

Hasin-Brumshtein, Yehudit; Khan, Arshad H.; Hormozdiari, Farhad

2016-09-13

Previous studies had shown that the integration of genome wide expression profiles, in metabolic tissues, with genetic and phenotypic variance, provided valuable insight into the underlying molecular mechanisms. We used RNA-Seq to characterize hypothalamic transcriptome in 99 inbred strains of mice from the Hybrid Mouse Diversity Panel (HMDP), a reference resource population for cardiovascular and metabolic traits. We report numerous novel transcripts supported by proteomic analyses, as well as novel non coding RNAs. High resolution genetic mapping of transcript levels in HMDP, reveals bothlocalandtransexpression Quantitative Trait Loci (eQTLs) demonstrating 2transeQTL 'hotspots' associated with expression of hundreds of genes. We alsomore » report thousands of alternative splicing events regulated by genetic variants. Finally, comparison with about 150 metabolic and cardiovascular traits revealed many highly significant associations. Our data provide a rich resource for understanding the many physiologic functions mediated by the hypothalamus and their genetic regulation.« less

Trait Differentiation within the Fungus-Feeding (Mycophagous) Bacterial Genus Collimonas

PubMed Central

Ballhausen, Max-Bernhard; Vandamme, Peter; de Boer, Wietse

2016-01-01

The genus Collimonas consists of facultative, fungus-feeding (mycophagous) bacteria. To date, 3 species (C. fungivorans, C. pratensis and C. arenae) have been described and over 100 strains have been isolated from different habitats. Functional traits of Collimonas bacteria that are potentially involved in interactions with soil fungi mostly negatively (fungal inhibition e.g.), but also positively (mineral weathering e.g.), affect fungal fitness. We hypothesized that variation in such traits between Collimonas strains leads to different mycophagous bacterial feeding patterns. We investigated a) whether phylogenetically closely related Collimonas strains possess similar traits, b) how far phylogenetic resolution influences the detection of phylogenetic signal (possession of similar traits by related strains) and c) if there is a pattern of co-occurrence among the studied traits. We measured genetically encoded (nifH genes, antifungal collimomycin gene cluster e.g.) as well as phenotypically expressed traits (chitinase- and siderophore production, fungal inhibition and others) and related those to a high-resolution phylogeny (MLSA), constructed by sequencing the housekeeping genes gyrB and rpoB and concatenating those with partial 16S rDNA sequences. Additionally, high-resolution and 16S rDNA derived phylogenies were compared. We show that MLSA is superior to 16SrDNA phylogeny when analyzing trait distribution and relating it to phylogeny at fine taxonomic resolution (a single bacterial genus). We observe that several traits involved in the interaction of collimonads and their host fungus (fungal inhibition e.g.) carry phylogenetic signal. Furthermore, we compare Collimonas trait possession with sister genera like Herbaspirillum and Janthinobacterium. PMID:27309848

Tuning donut profile for spatial resolution in stimulated emission depletion microscopy.

PubMed

Neupane, Bhanu; Chen, Fang; Sun, Wei; Chiu, Daniel T; Wang, Gufeng

2013-04-01

In stimulated emission depletion (STED)-based or up-conversion depletion-based super-resolution optical microscopy, the donut-shaped depletion beam profile is of critical importance to its resolution. In this study, we investigate the transformation of the donut-shaped depletion beam focused by a high numerical aperture (NA) microscope objective, and model STED point spread function (PSF) as a function of donut beam profile. We show experimentally that the intensity profile of the dark kernel of the donut can be approximated as a parabolic function, whose slope is determined by the donut beam size before the objective back aperture, or the effective NA. Based on this, we derive the mathematical expression for continuous wave (CW) STED PSF as a function of focal plane donut and excitation beam profiles, as well as dye properties. We find that the effective NA and the residual intensity at the center are critical factors for STED imaging quality and the resolution. The effective NA is critical for STED resolution in that it not only determines the donut shape but also the area the depletion laser power is dispersed. An improperly expanded depletion beam will have negligible improvement in resolution. The polarization of the depletion beam also plays an important role as it affects the residual intensity in the center of the donut. Finally, we construct a CW STED microscope operating at 488 nm excitation and 592 nm depletion with a resolution of 70 nm. Our study provides detailed insight to the property of donut beam, and parameters that are important for the optimal performance of STED microscopes. This paper will provide a useful guide for the construction and future development of STED microscopes.

Comparing long-term geomorphic model outcomes with sediment archives highlights the need for high-resolution Holocene land cover reconstructions

NASA Astrophysics Data System (ADS)

De Brue, Hanne; Verstraeten, Gert

2013-04-01

During the last decade, several global land cover reconstructions have been produced that enable to quantify human impact on the landscape since the introduction of agriculture. Application of these land cover maps in geomorphic models potentially allows to estimate the anthropogenic impact on sediment fluxes and thus to reconstruct changes in landscape morphology through time. However, current land cover reconstructions face some drawbacks. First of all, their low spatial resolution (i.e. 5 arc-minutes at best) questions their use in geomorphic models, as sub-catchment vegetation patterns play an important role in sediment dynamics. Existing global land cover reconstructions also do not differentiate the typology of human impact (cropland, grazing land, disturbed forests), although the susceptibility of different anthropogenic land uses towards erosion varies greatly. Finally, the various land cover reconstructions differ significantly regarding the estimated intensity of human impact for the preindustrial period. In this study, we assessed the performance of a spatially distributed erosion and sediment redistribution model that operates at high resolution (100 m) to the quality and spatial resolution of input land cover maps. This was done through a comparison of two sets of model runs. Firstly, low-resolution land cover (expressed as percentage of non-natural vegetation) maps were resampled to a spatial resolution of 100 m without differentiation of non-natural vegetation types. For the second set of model runs, estimated non-natural vegetation was differentiated in areas of cropland and grassland, and spatially allocated to a high-resolution grid (100 m) using a logistic model that relates contemporary land cover classes to slope, soil characteristics, landforms and distance to rivers. For both land cover maps, different scenarios for the ratio between cropland and grassland were simulated. Analyses were performed for several time periods throughout the Holocene, for the Scheldt River Basin (19,000 km2) in Belgium and northern France. Results indicate that low-resolution land cover information, regardless of the considered cropland/grassland ratio, leads to largely overestimated sediment fluxes when compared to field-based sediment budgets. Allocation of land cover to a higher spatial resolution yields far better results. Variations in model outcomes are related to differences in landscape connectivity between allocated and non-allocated land cover. These results point towards the need for higher-resolution land cover maps that incorporate the patchiness of vegetation at relevant scales regarding geomorphic processes. Also, model results with allocated and non-allocated land cover maps differ greatly for different cropland/grassland ratios. This indicates that there is not only a need for land cover reconstructions at high spatial resolution, but also that differentiation between cropland and grassland is essential for accurate geomorphic modeling. Further improvements in land cover reconstructions are thus needed before reliable quantitative estimates of anthropogenic impact on soil profiles and sediment redistribution can be simulated at continental scales. Detailed historic sediment budgets can provide an important tool not only for validating but also for reconstructing land cover histories.

Stabilization of Functional Recombinant Cannabinoid Receptor CB2 in Detergent Micelles and Lipid Bilayers

PubMed Central

Vukoti, Krishna; Kimura, Tomohiro; Macke, Laura; Gawrisch, Klaus; Yeliseev, Alexei

2012-01-01

Elucidation of the molecular mechanisms of activation of G protein-coupled receptors (GPCRs) is among the most challenging tasks for modern membrane biology. For studies by high resolution analytical methods, these integral membrane receptors have to be expressed in large quantities, solubilized from cell membranes and purified in detergent micelles, which may result in a severe destabilization and a loss of function. Here, we report insights into differential effects of detergents, lipids and cannabinoid ligands on stability of the recombinant cannabinoid receptor CB2, and provide guidelines for preparation and handling of the fully functional receptor suitable for a wide array of downstream applications. While we previously described the expression in Escherichia coli, purification and liposome-reconstitution of multi-milligram quantities of CB2, here we report an efficient stabilization of the recombinant receptor in micelles - crucial for functional and structural characterization. The effects of detergents, lipids and specific ligands on structural stability of CB2 were assessed by studying activation of G proteins by the purified receptor reconstituted into liposomes. Functional structure of the ligand binding pocket of the receptor was confirmed by binding of 2H-labeled ligand measured by solid-state NMR. We demonstrate that a concerted action of an anionic cholesterol derivative, cholesteryl hemisuccinate (CHS) and high affinity cannabinoid ligands CP-55,940 or SR-144,528 are required for efficient stabilization of the functional fold of CB2 in dodecyl maltoside (DDM)/CHAPS detergent solutions. Similar to CHS, the negatively charged phospholipids with the serine headgroup (PS) exerted significant stabilizing effects in micelles while uncharged phospholipids were not effective. The purified CB2 reconstituted into lipid bilayers retained functionality for up to several weeks enabling high resolution structural studies of this GPCR at physiologically relevant conditions. PMID:23056277

Metabolomics and proteomics technologies to explore the herbal preparation affecting metabolic disorders using high resolution mass spectrometry.

PubMed

Zhang, Aihua; Zhou, Xiaohang; Zhao, Hongwei; Zou, Shiyu; Ma, Chung Wah; Liu, Qi; Sun, Hui; Liu, Liang; Wang, Xijun

2017-01-31

An integrative metabolomics and proteomics approach can provide novel insights in the understanding of biological systems. We have integrated proteome and metabolome data sets for a holistic view of the molecular mechanisms in disease. Using quantitative iTRAQ-LC-MS/MS proteomics coupled with UPLC-Q-TOF-HDMS based metabolomics, we determined the protein and metabolite expression changes in the kidney-yang deficiency syndrome (KYDS) rat model and further investigated the intervention effects of the Jinkui Shenqi Pill (JSP). The VIP-plot of the orthogonal PLS-DA (OPLS-DA) was used for discovering the potential biomarkers to clarify the therapeutic mechanisms of JSP in treating KYDS. The results showed that JSP can alleviate the kidney impairment induced by KYDS. Sixty potential biomarkers, including 5-l-glutamyl-taurine, phenylacetaldehyde, 4,6-dihydroxyquinoline, and xanthurenic acid etc., were definitely up- or down-regulated. The regulatory effect of JSP on the disturbed metabolic pathways was proved by the established metabonomic method. Using pathway analyses, we identified the disturbed metabolic pathways such as taurine and hypotaurine metabolism, pyrimidine metabolism, tyrosine metabolism, tryptophan metabolism, histidine metabolism, steroid hormone biosynthesis, etc. Furthermore, using iTRAQ-based quantitative proteomics analysis, seventeen differential proteins were identified and significantly altered by the JSP treatment. These proteins appear to be involved in Wnt, chemokine, PPAR, and MAPK signaling pathways, etc. Functional pathway analysis revealed that most of the proteins were found to play a key role in the regulation of metabolism pathways. Bioinformatics analysis with the IPA software found that these differentially-expressed moleculars had a strong correlation with the α-adrenergic signaling, FGF signaling, etc. Our data indicate that high-throughput metabolomics and proteomics can provide an insight on the herbal preparations affecting the metabolic disorders using high resolution mass spectrometry.

Genistein promotes DNA demethylation of the steroidogenic factor 1 (SF-1) promoter in endometrial stromal cells

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

Matsukura, Hiroshi, E-mail: hmatsukura.epi@mri.tmd.ac.jp; Aisaki, Ken-ichi; Igarashi, Katsuhide

2011-08-26

Highlights: {yields} Genistein (GEN) is a phytoestrogen found in soy products. {yields} GEN demethylated/unsilenced the steroidogenic factor 1 gene in endometrial tissue. {yields} GEN thus altered mRNA expression in uteri of ovariectomized (OVX) mice. {yields} A high-resolution melting assay was used to screen for epigenetic change. {yields} We isolated an endometrial cell clone that was epigenetically modulated by GEN. -- Abstract: It has recently been demonstrated that genistein (GEN), a phytoestrogen in soy products, is an epigenetic modulator in various types of cells; but its effect on endometrium has not yet been determined. We investigated the effects of GEN onmore » mouse uterine cells, in vivo and in vitro. Oral administration of GEN for 1 week induced mild proliferation of the endometrium in ovariectomized (OVX) mice, which was accompanied by the induction of steroidogenic factor 1 (SF-1) gene expression. GEN administration induced demethylation of multiple CpG sites in the SF-1 promoter; these sites are extensively methylated and thus silenced in normal endometrium. The GEN-mediated promoter demethylation occurred predominantly on the luminal side, as opposed to myometrium side, indicating that the epigenetic change was mainly shown in regenerated cells. Primary cultures of endometrial stromal cell colonies were screened for GEN-mediated alterations of DNA methylation by a high-resolution melting (HRM) method. One out of 20 colony-forming cell clones showed GEN-induced demethylation of SF-1. This clone exhibited a high proliferation capacity with continuous colony formation activity through multiple serial clonings. We propose that only a portion of endometrial cells are capable of receiving epigenetic modulation by GEN.« less

A method for generating high resolution satellite image time series

NASA Astrophysics Data System (ADS)

Guo, Tao

2014-10-01

There is an increasing demand for satellite remote sensing data with both high spatial and temporal resolution in many applications. But it still is a challenge to simultaneously improve spatial resolution and temporal frequency due to the technical limits of current satellite observation systems. To this end, much R&D efforts have been ongoing for years and lead to some successes roughly in two aspects, one includes super resolution, pan-sharpen etc. methods which can effectively enhance the spatial resolution and generate good visual effects, but hardly preserve spectral signatures and result in inadequate analytical value, on the other hand, time interpolation is a straight forward method to increase temporal frequency, however it increase little informative contents in fact. In this paper we presented a novel method to simulate high resolution time series data by combing low resolution time series data and a very small number of high resolution data only. Our method starts with a pair of high and low resolution data set, and then a spatial registration is done by introducing LDA model to map high and low resolution pixels correspondingly. Afterwards, temporal change information is captured through a comparison of low resolution time series data, and then projected onto the high resolution data plane and assigned to each high resolution pixel according to the predefined temporal change patterns of each type of ground objects. Finally the simulated high resolution data is generated. A preliminary experiment shows that our method can simulate a high resolution data with a reasonable accuracy. The contribution of our method is to enable timely monitoring of temporal changes through analysis of time sequence of low resolution images only, and usage of costly high resolution data can be reduces as much as possible, and it presents a highly effective way to build up an economically operational monitoring solution for agriculture, forest, land use investigation, environment and etc. applications.

Fluorescence imaging of angiogenesis in green fluorescent protein-expressing tumors

NASA Astrophysics Data System (ADS)

Yang, Meng; Baranov, Eugene; Jiang, Ping; Li, Xiao-Ming; Wang, Jin W.; Li, Lingna; Yagi, Shigeo; Moossa, A. R.; Hoffman, Robert M.

2002-05-01

The development of therapeutics for the control of tumor angiogenesis requires a simple, reliable in vivo assay for tumor-induced vascularization. For this purpose, we have adapted the orthotopic implantation model of angiogenesis by using human and rodent tumors genetically tagged with Aequorea victoria green fluorescent protein (GFP) for grafting into nude mice. Genetically-fluorescent tumors can be readily imaged in vivo. The non-luminous induced capillaries are clearly visible against the bright tumor fluorescence examined either intravitally or by whole-body luminance in real time. Fluorescence shadowing replaces the laborious histological techniques for determining blood vessel density. High-level GFP-expressing tumor cell lines made it possible to acquire the high-resolution real-time fluorescent optical images of angiogenesis in both primary tumors and their metastatic lesions in various human and rodent tumor models by means of a light-based imaging system. Intravital images of angiogenesis onset and development were acquired and quantified from a GFP- expressing orthotopically-growing human prostate tumor over a 19-day period. Whole-body optical imaging visualized vessel density increasing linearly over a 20-week period in orthotopically-growing, GFP-expressing human breast tumor MDA-MB-435. Vessels in an orthotopically-growing GFP- expressing Lewis lung carcinoma tumor were visualized through the chest wall via a reversible skin flap. These clinically-relevant angiogenesis mouse models can be used for real-time in vivo evaluation of agents inhibiting or promoting tumor angiogenesis in physiological micro- environments.

Genome-wide dynamics of alternative polyadenylation in rice

PubMed Central

Fu, Haihui; Yang, Dewei; Su, Wenyue; Ma, Liuyin; Shen, Yingjia; Ji, Guoli; Ye, Xinfu; Wu, Xiaohui

2016-01-01

Alternative polyadenylation (APA), in which a transcript uses one of the poly(A) sites to define its 3′-end, is a common regulatory mechanism in eukaryotic gene expression. However, the potential of APA in determining crop agronomic traits remains elusive. This study systematically tallied poly(A) sites of 14 different rice tissues and developmental stages using the poly(A) tag sequencing (PAT-seq) approach. The results indicate significant involvement of APA in developmental and quantitative trait loci (QTL) gene expression. About 48% of all expressed genes use APA to generate transcriptomic and proteomic diversity. Some genes switch APA sites, allowing differentially expressed genes to use alternate 3′ UTRs. Interestingly, APA in mature pollen is distinct where differential expression levels of a set of poly(A) factors and different distributions of APA sites are found, indicating a unique mRNA 3′-end formation regulation during gametophyte development. Equally interesting, statistical analyses showed that QTL tends to use APA for regulation of gene expression of many agronomic traits, suggesting a potential important role of APA in rice production. These results provide thus far the most comprehensive and high-resolution resource for advanced analysis of APA in crops and shed light on how APA is associated with trait formation in eukaryotes. PMID:27733415

Spectral resolution of SU(3)-invariant solutions of the Yang-Baxter equation

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

Alishauskas, S.I.; Kulish, P.P.

1986-11-20

The spectral resolution of invariant R-matrices is computed on the basis of solution of the defining equation. Multiple representations in the Clebsch-Gordon series are considered by means of the classifying operator A: a linear combination of known operators of third and fourth degrees in the group generators. The matrix elements of A in a nonorthonormal basis are found. Explicit expressions are presented for the spectral resolutions for a number of representations.

Spectral resolution of SU(3)-invariant solutions of the Yang-Baxter equation

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

Alishavskas, S.I.; Kulish, P.P.

1986-11-01

The spectral resolution of invariant R-matrices is computed on the basis of solution of the defining equation. Multiple representations in the Clebsch-Gordon series are considered by means of the classifying operator A: a linear combination of known operators of third and fourth degrees in the group generators. The matrix elements of A in a nonorthonormal basis are found. Explicit expressions are presented for the spectral resolutions for a number of representations.

Automatic Detection of Changes on Mars Surface from High-Resolution Orbital Images

NASA Astrophysics Data System (ADS)

Sidiropoulos, Panagiotis; Muller, Jan-Peter

2017-04-01

Over the last 40 years Mars has been extensively mapped by several NASA and ESA orbital missions, generating a large image dataset comprised of approximately 500,000 high-resolution images (of <100m resolution). The overall area mapped from orbital imagery is approximately 6 times the overall surface of Mars [1]. The multi-temporal coverage of Martian surface allows a visual inspection of the surface to identify dynamic phenomena, i.e. surface features that change over time, such as slope streaks [2], recurring slope lineae [3], new impact craters [4], etc. However, visual inspection for change detection is a limited approach, since it requires extensive use of human resources, which is very difficult to achieve when dealing with a rapidly increasing volume of data. Although citizen science can be employed for training and verification it is unsuitable for planetwide systematic change detection. In this work, we introduce a novel approach in planetary image change detection, which involves a batch-mode automatic change detection pipeline that identifies regions that have changed. This is tested in anger, on tens of thousands of high-resolution images over the MC11 quadrangle [5], acquired by CTX, HRSC, THEMIS-VIS and MOC-NA instruments [1]. We will present results which indicate a substantial level of activity in this region of Mars, including instances of dynamic natural phenomena that haven't been cataloged in the planetary science literature before. We will demonstrate the potential and usefulness of such an automatic approach in planetary science change detection. Acknowledgments: The research leading to these results has received funding from the STFC "MSSL Consolidated Grant" ST/K000977/1 and partial support from the European Union's Seventh Framework Programme (FP7/2007-2013) under iMars grant agreement n° 607379. References: [1] P. Sidiropoulos and J. - P. Muller (2015) On the status of orbital high-resolution repeat imaging of Mars for the observation of dynamic surface processes. Planetary and Space Science, 117: 207-222. [2] O. Aharonson, et al. (2003) Slope streak formation and dust deposition rates on Mars. Journal of Geophysical Research: Planets, 108(E12):5138 [3] A. McEwen, et al. (2011) Seasonal flows on warm martian slopes. Science, 333 (6043): 740-743. [4] S. Byrne, et al. (2009) Distribution of mid-latitude ground ice on mars from new impact craters. Science, 325(5948):1674-1676. [5] K. Gwinner, et al (2016) The High Resolution Stereo Camera (HRSC) of Mars Express and its approach to science analysis and mapping for Mars and its satellites. Planetary and Space Science, 126: 93-138.

Chromosomal breaks at FRA18C: association with reduced DOK6 expression, altered oncogenic signaling and increased gastric cancer survival.

PubMed

Leong, Siew Hong; Lwin, Kyaw Myo; Lee, Sze Sing; Ng, Wai Har; Ng, Kia Min; Tan, Soo Yong; Ng, Bee Ling; Carter, Nigel P; Tang, Carol; Lian Kon, Oi

2017-01-01

Chromosomal rearrangements are common in cancer. More than 50% occur in common fragile sites and disrupt tumor suppressors. However, such rearrangements are not known in gastric cancer. Here we report recurrent 18q2 breakpoints in 6 of 17 gastric cancer cell lines. The rearranged chromosome 18, t(9;18), in MKN7 cells was flow sorted and identified by reverse chromosome painting. High-resolution tiling array hybridization mapped breakpoints to DOK6 (docking protein 6) intron 4 in FRA18C (18q22.2) and an intergenic region in 9q22.2. The same rearrangement was detected by FISH in 22% of 99 primary gastric cancers. Intron 4 truncation was associated with reduced DOK6 transcription. Analysis of The Cancer Genome Atlas stomach adenocarcinoma cohort showed significant correlation of DOK6 expression with histological and molecular phenotypes. Multiple oncogenic signaling pathways (gastrin-CREB, NGF-neurotrophin, PDGF, EGFR, ERK, ERBB4, FGFR1, RAS, VEGFR2 and RAF/MAP kinase) known to be active in aggressive gastric cancers were strikingly diminished in gastric cancers with low DOK6 expression. Median survival of patients with low DOK6 -expressing tumors was 2100 days compared with 533 days in patients with high DOK6 -expressing tumors (log-rank P  = 0.0027). The level of DOK6 expression in tumors predicted patient survival independent of TNM stage. These findings point to new functions of human DOK6 as an adaptor that interacts with diverse molecular components of signaling pathways. Our data suggest that DOK6 expression is an integrated biomarker of multiple oncogenic signals in gastric cancer and identify FRA18C as a new cancer-associated fragile site.

Information science team

NASA Technical Reports Server (NTRS)

Billingsley, F.

1982-01-01

Concerns are expressed about the data handling aspects of system design and about enabling technology for data handling and data analysis. The status, contributing factors, critical issues, and recommendations for investigations are listed for data handling, rectification and registration, and information extraction. Potential supports to individual P.I., research tasks, systematic data system design, and to system operation. The need for an airborne spectrometer class instrument for fundamental research in high spectral and spatial resolution is indicated. Geographic information system formatting and labelling techniques, very large scale integration, and methods for providing multitype data sets must also be developed.

Selected questions of topical interest in human bioclimatology

NASA Astrophysics Data System (ADS)

Jendritzky, G.

1991-09-01

This paper deals with the different effects of climate, and the likely impact of climatic change, on the human being, his health and well-being. Those effects follow from consideration of the human energy budget and air pollution, including photooxidants and radiation, the latter especially in the UV-range. The development of tools to produce bioclimate maps, i.e. maps expressed in physiologically significant terms, in different scales up to the high resolution necessary for the microscale urban climate, will be discussed. The most important questions in bioclimate research and its application will be considered.

Selected questions of topical interest in human bioclimatology.

PubMed

Jendritzky, G

1991-11-01

This paper deals with the different effects of climate, and the likely impact of climatic change, on the human being, his health and well-being. Those effects follow from consideration of the human energy budget and air pollution, including photooxidants and radiation, the latter especially in the UV-range. The development of tools to produce bioclimate maps, i.e. maps expressed in physiologically significant terms, in different scales up to the high resolution necessary for the microscale urban climate, will be discussed. The most important questions in bioclimate research and its application will be considered.

HIV envelope glycoprotein imaged at high resolution | Center for Cancer Research

Cancer.gov

The outer surface of the human immunodeficiency virus (HIV) is surrounded by an envelope studded with spike-shaped glycoproteins called Env that help the deadly virus identify, bind, and infect cells. When unbound, Env exists in a “closed” conformational state. Upon binding with target cells, such as CD4+ T cells, the protein transitions to an “open” configuration. Given that Env is the only viral protein expressed on HIV’s surface, knowing its detailed structure—especially in the unbound state—may be critical for designing antibodies and vaccines against HIV.

In vivo multiphoton imaging of a diverse array of fluorophores to investigate deep neurovascular structure

PubMed Central

Miller, David R.; Hassan, Ahmed M.; Jarrett, Jeremy W.; Medina, Flor A.; Perillo, Evan P.; Hagan, Kristen; Shams Kazmi, S. M.; Clark, Taylor A.; Sullender, Colin T.; Jones, Theresa A.; Zemelman, Boris V.; Dunn, Andrew K.

2017-01-01

We perform high-resolution, non-invasive, in vivo deep-tissue imaging of the mouse neocortex using multiphoton microscopy with a high repetition rate optical parametric amplifier laser source tunable between λ=1,100 and 1,400 nm. By combining the high repetition rate (511 kHz) and high pulse energy (400 nJ) of our amplifier laser system, we demonstrate imaging of vasculature labeled with Texas Red and Indocyanine Green, and neurons expressing tdTomato and yellow fluorescent protein. We measure the blood flow speed of a single capillary at a depth of 1.2 mm, and image vasculature to a depth of 1.53 mm with fine axial steps (5 μm) and reasonable acquisition times. The high image quality enabled analysis of vascular morphology at depths to 1.45 mm. PMID:28717582

Clinical applications of in vivo fluorescence confocal laser scanning microscopy

NASA Astrophysics Data System (ADS)

Oh, Chilhwan; Park, Sangyong; Kim, Junhyung; Ha, Seunghan; Park, Gyuman; Lee, Gunwoo; Lee, Onseok; Chun, Byungseon; Gweon, Daegab

2008-02-01

Living skin for basic and clinical research can be evaluated by Confocal Laser Scanning Microscope (CLSM) non-invasively. CLSM imaging system can achieve skin image its native state either "in vivo" or "fresh biopsy (ex vivo)" without fixation, sectioning and staining that is necessary for routine histology. This study examines the potential fluorescent CLSM with a various exogenous fluorescent contrast agent, to provide with more resolution images in skin. In addition, in vivo fluorescent CLSM researchers will be extended a range of potential clinical application. The prototype of our CLSM system has been developed by Prof. Gweon's group. The operating parameters are composed of some units, such as illuminated wavelength 488 nm, argon illumination power up to 20mW on the skin, objective lens, 0.9NA oil immersion, axial resolution 1.0μm, field of view 200μm x 100μm (lateral resolution , 0.3μm). In human volunteer, fluorescein sodium was administrated topically and intradermally. Animal studies were done in GFP transgenic mouse, IRC mouse and pig skin. For imaging of animal skin, fluorescein sodium, acridine orange, and curcumine were used for fluorescein contrast agent. We also used the GFP transgenic mouse for fluorescein CLSM imaging. In intact skin, absorption of fluorescein sodium by individual corneocyte and hair. Intradermal administrated the fluorescein sodium, distinct outline of keratinocyte cell border could be seen. Curcumin is a yellow food dye that has similar fluorescent properties to fluorescein sodium. Acridin Orange can be highlight nuclei in viable keratinocyte. In vivo CLSM of transgenic GFP mouse enable on in vivo, high resolution view of GFP expressing skin tissue. GFP signals are brightest in corneocyte, kertinocyte, hair and eccrine gland. In intact skin, absorption of fluorescein sodium by individual corneocyte and hair. Intradermal administrated the fluorescein sodium, distinct outline of keratinocyte cell border could be seen. In papillary dermis, fluorescein distribution is more homogeneous. Curcumin is a yellow food dye that has similar fluorescent properties to fluorescein sodium. In vivo CLSM of transgenic GFP mouse enable on in vivo, high resolution view of GFP expressing skin tissue. GFP signals are brightest in corneocyte, kertinocyte, skin appendage and blood vessels. In conclusion, this study demonstrates the usefulness of CLSM as technique for imaging skin in vivo. In addition, CLSM is non-invasive, the same tissue site may be imaged over a period of time to monitor the various change such as wound healing, severity of skin diseases and effect of therapeutic management.

Ultraperformance convergence chromatography-high resolution tandem mass spectrometry for lipid biomarker profiling and identification.

PubMed

Jones, Jace W; Carter, Claire L; Li, Fei; Yu, Jianshi; Pierzchalski, Keely; Jackson, Isabel L; Vujaskovic, Zeljko; Kane, Maureen A

2017-03-01

Lipids represent biologically ubiquitous and highly dynamic molecules in terms of abundance and structural diversity. Whereas the potential for lipids to inform on disease/injury is promising, their unique characteristics make detection and identification of lipids from biological samples analytically demanding. We report the use of ultraperformance convergence chromatography (UPC 2 ), a variant of supercritical fluid chromatography, coupled to high-resolution, data-independent tandem mass spectrometry for characterization of total lipid extracts from mouse lung tissue. The UPC 2 platform resulted in lipid class separation and when combined with orthogonal column chemistries yielded chromatographic separation of intra-class species based on acyl chain hydrophobicity. Moreover, the combined approach of using UPC 2 with orthogonal column chemistries, accurate mass measurements, time-aligned low- and high-collision energy total ion chromatograms, and positive and negative ion mode product ion spectra correlation allowed for confident lipid identification. Of great interest was the identification of differentially expressed ceramides that were elevated 24 h post whole thorax lung irradiation. The identification of lipids that were elevated 24 h post-irradiation signifies a unique opportunity to investigate early mechanisms of action prior to the onset of clinical symptoms in the whole thorax lung irradiation mouse model. Copyright © 2016 John Wiley & Sons, Ltd.

Calcium activates the light-dependent conductance in melanopsin-expressing photoreceptors of amphioxus.

PubMed

Peinado, Gabriel; Osorno, Tomás; Gomez, María del Pilar; Nasi, Enrico

2015-06-23

Melanopsin, the photopigment of the "circadian" receptors that regulate the biological clock and the pupillary reflex in mammals, is homologous to invertebrate rhodopsins. Evidence supporting the involvement of phosphoinositides in light-signaling has been garnered, but the downstream effectors that control the light-dependent conductance remain unknown. Microvillar photoreceptors of the primitive chordate amphioxus also express melanopsin and transduce light via phospholipase-C, apparently not acting through diacylglycerol. We therefore examined the role of calcium in activating the photoconductance, using simultaneous, high time-resolution measurements of membrane current and Ca(2+) fluorescence. The light-induced calcium rise precedes the onset of the photocurrent, making it a candidate in the activation chain. Moreover, photolysis of caged Ca elicits an inward current of similar size, time course and pharmacology as the physiological photoresponse, but with a much shorter latency. Internally released calcium thus emerges as a key messenger to trigger the opening of light-dependent channels in melanopsin-expressing microvillar photoreceptors of early chordates.

Expression and purification of functional PDGF receptor beta.

PubMed

Shang, Qingbin; Zhao, Liang; Wang, Xiaojing; Wang, Meimei; Sui, Sen-Fang; Mi, Li-Zhi

2017-07-29

Platelet Derived Growth Factor receptors (PDGFRs), members of receptor tyrosine kinase superfamily, play essential roles in early hematopoiesis, angiogenesis and organ development. Dysregulation of PDGF receptor signaling under pathological conditions associates with cancers, vascular diseases, and fibrotic diseases. Therefore, they are attractive targets in drug development. Like any other membrane proteins with a single-pass transmembrane domain, the high-resolution structural information of the full-length PDGF receptors is still not resolved. It is caused, at least in part, by the technical challenges in the expression and purification of the functional, full-length PDGF receptors. Herein, we reported our experimental details in expression and purification of the full-length PDGFRβ from mammalian cells. We found that purified PDGFRβ remained in two different oligomeric states, presumably the monomer and the dimer, with basal kinase activity in detergent micelles. Addition of PDGF-B promoted dimerization and elevated kinase activity of the receptor, suggesting that purified receptors were functional. Copyright © 2017 Elsevier Inc. All rights reserved.

A resolution expressing the sense of the Senate on the restitution of or compensation for property seized during the Nazi and Communist eras.

THOMAS, 111th Congress

Sen. Nelson, Bill [D-FL

2009-05-19

Senate - 06/18/2009 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution expressing support for the Ukrainian people in light of President Yanukovych's decision not to sign an Association Agreement with the European Union.

THOMAS, 113th Congress

Sen. Murphy, Christopher [D-CT

2013-12-12

Senate - 01/07/2014 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution condemning violence by the Government of Syria against journalists, and expressing the sense of the Senate on freedom of the press in Syria.

THOMAS, 112th Congress

Sen. Wyden, Ron [D-OR

2012-03-08

Senate - 03/29/2012 Resolution agreed to in Senate without amendment and an amended preamble by Voice Vote. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution expressing the regret of the Senate for the passage of discriminatory laws against the Chinese in America, including the Chinese Exclusion Act.

THOMAS, 112th Congress

Sen. Brown, Scott P. [R-MA

2011-05-26

Senate - 10/06/2011 Resolution agreed to in Senate with amendments and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

Characterization, Localization, Essentiality, and High-Resolution Crystal Structure of Glucosamine 6-Phosphate N-Acetyltransferase from Trypanosoma brucei ▿ ‡ §

PubMed Central

Mariño, Karina; Güther, M. Lucia Sampaio; Wernimont, Amy K.; Qiu, Wei; Hui, Raymond; Ferguson, Michael A. J.

2011-01-01

A gene predicted to encode Trypanosoma brucei glucosamine 6-phosphate N-acetyltransferase (TbGNA1; EC 2.3.1.4) was cloned and expressed in Escherichia coli. The recombinant protein was enzymatically active, and its high-resolution crystal structure was obtained at 1.86 Å. Endogenous TbGNA1 protein was localized to the peroxisome-like microbody, the glycosome. A bloodstream-form T. brucei GNA1 conditional null mutant was constructed and shown to be unable to sustain growth in vitro under nonpermissive conditions, demonstrating that there are no metabolic or nutritional routes to UDP-GlcNAc other than via GlcNAc-6-phosphate. Analysis of the protein glycosylation phenotype of the TbGNA1 mutant under nonpermissive conditions revealed that poly-N-acetyllactosamine structures were greatly reduced in the parasite and that the glycosylation profile of the principal parasite surface coat component, the variant surface glycoprotein (VSG), was modified. The significance of results and the potential of TbGNA1 as a novel drug target for African sleeping sickness are discussed. PMID:21531872

Influence of the Yukon River on the Bering Sea

NASA Technical Reports Server (NTRS)

Dean, K.; Mcroy, C. P.

1986-01-01

The relationships between the discharge of the Yukon River to the currents and biological productivity in the northern Bering Sea were studied. Specific objectives were: to develop thermal, sediment, and chlorophyll surface maps using Thematic Mapper (TM) data of the discharge of the Yukon River and the Alaskan Coastal Current during the ice free season; to develop a historical model of the distribution of the Yukon River discharge and the Alaskan Coastal Current using LANDSAT Multispectral band scanner (MSS) and NOAA satellite imagery; and to use high resolution TM data to define the surface dynamics of the front between the Alaskan Coastal Current and the Bering Shelf/Anadyr Current. LANDSAT MSS, TM, and Advanced Very High Resolution Radiometer (AVHRR) data were recorded during the 1985 ice free period. The data coincided with shipboard measurements acquired by Inner Shelf Transfer and Recycling (ISTAR) project scientists. An integrated model of the distribution of turbid water discharged from the Yukon River was compiled. A similar model is also being compiled for the Alaskan Coastal and Bering Shelf/Anadyr water masses based on their thermal expressions seen on AVHRR imagery.

Identification of a new fault and associated lineament features in Oregon's Summer Lake Valley using high-resolution LiDAR data

NASA Astrophysics Data System (ADS)

Bennett, L.; Madin, I.

2012-12-01

In 2012, the Oregon Department of Geology and Mineral Industries (DOGAMI) contracted WSI to co-acquire airborne Light Detecting and Ranging (LiDAR) and Thermal Infrared Imagery (TIR) data within the region surrounding Summer Lake, Oregon. The objective of this project was to detect surficial expressions of geothermal activity and associated geologic features. An analysis of the LiDAR data revealed one newly identified fault and several accompanying lineaments that strike northwest, similar to the trend of the Ana River, Brothers, and Eugene-Denio Fault Zones in Central Oregon. The age of the Ana River Fault Zone and Summer Lake bed is known to be within the Holocene epoch. Apparent scarp height observed from the LiDAR is up to 8 meters. While detailed analysis is ongoing, the data illustrated the effectiveness of using high resolution remote sensing data for surficial analysis of geologic displacement. This presentation will focus on direct visual detection of features in the Summer Lake, Oregon landscape using LiDAR data.

Long-term, high-resolution imaging in the mouse neocortex through a chronic cranial window

PubMed Central

Holtmaat, Anthony; Bonhoeffer, Tobias; Chow, David K; Chuckowree, Jyoti; De Paola, Vincenzo; Hofer, Sonja B; Hübener, Mark; Keck, Tara; Knott, Graham; Lee, Wei-Chung A; Mostany, Ricardo; Mrsic-Flogel, Tom D; Nedivi, Elly; Portera-Cailliau, Carlos; Svoboda, Karel; Trachtenberg, Joshua T; Wilbrecht, Linda

2011-01-01

To understand the cellular and circuit mechanisms of experience-dependent plasticity, neurons and their synapses need to be studied in the intact brain over extended periods of time. Two-photon excitation laser scanning microscopy (2PLSM), together with expression of fluorescent proteins, enables high-resolution imaging of neuronal structure in vivo. In this protocol we describe a chronic cranial window to obtain optical access to the mouse cerebral cortex for long-term imaging. A small bone flap is replaced with a coverglass, which is permanently sealed in place with dental acrylic, providing a clear imaging window with a large field of view (∼0.8–12 mm2). The surgical procedure can be completed within ∼1 h. The preparation allows imaging over time periods of months with arbitrary imaging intervals. The large size of the imaging window facilitates imaging of ongoing structural plasticity of small neuronal structures in mice, with low densities of labeled neurons. The entire dendritic and axonal arbor of individual neurons can be reconstructed. PMID:19617885

Ultrasound Biomicroscopy in Small Animal Research: Applications in Molecular and Preclinical Imaging

PubMed Central

Greco, A.; Mancini, M.; Gargiulo, S.; Gramanzini, M.; Claudio, P. P.; Brunetti, A.; Salvatore, M.

2012-01-01

Ultrasound biomicroscopy (UBM) is a noninvasive multimodality technique that allows high-resolution imaging in mice. It is affordable, widely available, and portable. When it is coupled to Doppler ultrasound with color and power Doppler, it can be used to quantify blood flow and to image microcirculation as well as the response of tumor blood supply to cancer therapy. Target contrast ultrasound combines ultrasound with novel molecular targeted contrast agent to assess biological processes at molecular level. UBM is useful to investigate the growth and differentiation of tumors as well as to detect early molecular expression of cancer-related biomarkers in vivo and to monitor the effects of cancer therapies. It can be also used to visualize the embryological development of mice in uterus or to examine their cardiovascular development. The availability of real-time imaging of mice anatomy allows performing aspiration procedures under ultrasound guidance as well as the microinjection of cells, viruses, or other agents into precise locations. This paper will describe some basic principles of high-resolution imaging equipment, and the most important applications in molecular and preclinical imaging in small animal research. PMID:22163379

Preliminary crystallographic analysis of avian infectious bronchitis virus main protease

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

Li, Jun; Shen, Wei; Liao, Ming, E-mail: mliao@scau.edu.cn

The avian infectious bronchitis virus main protease has been crystallized; crystals diffract to 2.7 Å resolution. Infectious bronchitis virus (IBV) is the prototype of the genus Coronavirus. It causes a highly contagious disease which affects the respiratory, reproductive, neurological and renal systems of chickens, resulting great economic losses in the poultry industry worldwide. The coronavirus (CoV) main protease (M{sup pro}), which plays a pivotal role in viral gene expression and replication through a highly complex cascade involving the proteolytic processing of replicase polyproteins, is an attractive target for antiviral drug design. In this study, IBV M{sup pro} was overexpressed inmore » Escherichia coli. Crystals suitable for X-ray crystallography have been obtained using microseeding techniques and belong to space group P6{sub 1}22. X-ray diffraction data were collected in-house to 2.7 Å resolution from a single crystal. The unit-cell parameters were a = b = 119.1, c = 270.7 Å, α = β = 90, γ = 120°. Three molecules were predicted to be present in the asymmetric unit from a calculated self-rotation function.« less

Recombinant production, crystallization and preliminary structural characterization of Schistosoma japonicum profilin

PubMed Central

Vervaet, Nele; Kallio, Juha Pekka; Meier, Susanne; Salmivaara, Emilia; Eberhardt, Maike; Zhang, Shuangmin; Sun, Xi; Wu, Zhongdao; Kursula, Petri; Kursula, Inari

2013-01-01

Helminthic parasites of the genus Schistosoma contain a tegumental membrane, which is of crucial importance for modulation of the host immune response and parasite survival. The actin cytoskeleton plays an important role in the function of the tegument. Profilins are among the most important proteins regulating actin dynamics. Schistosoma japonicum possesses one profilin-like protein, which has been characterized as a potential vaccine candidate. Notably, profilins are highly immunogenic molecules in many organisms. Here, the profilin from S. japonicum was expressed, purified and crystallized. A native data set to 1.91 Å resolution and a single-wavelength anomalous diffraction (SAD) data set to a resolution of 2.2 Å were collected. The crystals belonged to space group P212121, with unit-cell parameters a = 31.82, b = 52.17, c = 59.79 Å and a = 35.29, b = 52.15, c = 59.82 Å, respectively. PMID:24192365

Recombinant production, crystallization and preliminary structural characterization of Schistosoma japonicum profilin.

PubMed

Vervaet, Nele; Kallio, Juha Pekka; Meier, Susanne; Salmivaara, Emilia; Eberhardt, Maike; Zhang, Shuangmin; Sun, Xi; Wu, Zhongdao; Kursula, Petri; Kursula, Inari

2013-11-01

Helminthic parasites of the genus Schistosoma contain a tegumental membrane, which is of crucial importance for modulation of the host immune response and parasite survival. The actin cytoskeleton plays an important role in the function of the tegument. Profilins are among the most important proteins regulating actin dynamics. Schistosoma japonicum possesses one profilin-like protein, which has been characterized as a potential vaccine candidate. Notably, profilins are highly immunogenic molecules in many organisms. Here, the profilin from S. japonicum was expressed, purified and crystallized. A native data set to 1.91 Å resolution and a single-wavelength anomalous diffraction (SAD) data set to a resolution of 2.2 Å were collected. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 31.82, b = 52.17, c = 59.79 Å and a = 35.29, b = 52.15, c = 59.82 Å, respectively.

Alexnet Feature Extraction and Multi-Kernel Learning for Objectoriented Classification

NASA Astrophysics Data System (ADS)

Ding, L.; Li, H.; Hu, C.; Zhang, W.; Wang, S.

2018-04-01

In view of the fact that the deep convolutional neural network has stronger ability of feature learning and feature expression, an exploratory research is done on feature extraction and classification for high resolution remote sensing images. Taking the Google image with 0.3 meter spatial resolution in Ludian area of Yunnan Province as an example, the image segmentation object was taken as the basic unit, and the pre-trained AlexNet deep convolution neural network model was used for feature extraction. And the spectral features, AlexNet features and GLCM texture features are combined with multi-kernel learning and SVM classifier, finally the classification results were compared and analyzed. The results show that the deep convolution neural network can extract more accurate remote sensing image features, and significantly improve the overall accuracy of classification, and provide a reference value for earthquake disaster investigation and remote sensing disaster evaluation.

High resolution fate map of the zebrafish diencephalon.

PubMed

Russek-Blum, Niva; Nabel-Rosen, Helit; Levkowitz, Gil

2009-07-01

The diencephalon acts as an interactive site between the sensory, central, and endocrine systems and is one of the most elaborate structures in the vertebrate brain. To better understand the embryonic development and morphogenesis of the diencephalon, we developed an improved photoactivation (uncaging)-based lineage tracing strategy. To determine the exact position of a given diencephalic progenitor domain, we used a transgenic line driving green fluorescent protein (GFP) in cells expressing the proneural protein, Neurogenin1 (Neurog1), which was used as a visible neural plate landmark. This approach facilitated precise labeling of defined groups of cells in the prospective diencephalon of the zebrafish neural plate. In this manner, we labeled multiple overlapping areas of the diencephalon, thereby ensuring both accuracy and reproducibility of our lineage tracing regardless of the dynamic changes of the developing neural plate. We present a fate map of the zebrafish diencephalon at a higher spatial resolution than previously described. (c) 2009 Wiley-Liss, Inc.

A cellular perspective on brain energy metabolism and functional imaging.

PubMed

Magistretti, Pierre J; Allaman, Igor

2015-05-20

The energy demands of the brain are high: they account for at least 20% of the body's energy consumption. Evolutionary studies indicate that the emergence of higher cognitive functions in humans is associated with an increased glucose utilization and expression of energy metabolism genes. Functional brain imaging techniques such as fMRI and PET, which are widely used in human neuroscience studies, detect signals that monitor energy delivery and use in register with neuronal activity. Recent technological advances in metabolic studies with cellular resolution have afforded decisive insights into the understanding of the cellular and molecular bases of the coupling between neuronal activity and energy metabolism and point at a key role of neuron-astrocyte metabolic interactions. This article reviews some of the most salient features emerging from recent studies and aims at providing an integration of brain energy metabolism across resolution scales. Copyright © 2015 Elsevier Inc. All rights reserved.

Estimating the effective spatial resolution of an AVHRR time series

USGS Publications Warehouse

Meyer, D.J.

1996-01-01

A method is proposed to estimate the spatial degradation of geometrically rectified AVHRR data resulting from misregistration and off-nadir viewing, and to infer the cumulative effect of these degradations over time. Misregistrations are measured using high resolution imagery as a geometric reference, and pixel sizes are computed directly from satellite zenith angles. The influence or neighbouring features on a nominal 1 km by 1 km pixel over a given site is estimated from the above information, and expressed as a spatial distribution whose spatial frequency response is used to define an effective field-of-view (EFOV) for a time series. In a demonstration of the technique applied to images from the Conterminous U.S. AVHRR data set, an EFOV of 3·1km in the east-west dimension and 19 km in the north-south dimension was estimated for a time series accumulated over a grasslands test site.

3D fluorescence anisotropy imaging using selective plane illumination microscopy.

PubMed

Hedde, Per Niklas; Ranjit, Suman; Gratton, Enrico

2015-08-24

Fluorescence anisotropy imaging is a popular method to visualize changes in organization and conformation of biomolecules within cells and tissues. In such an experiment, depolarization effects resulting from differences in orientation, proximity and rotational mobility of fluorescently labeled molecules are probed with high spatial resolution. Fluorescence anisotropy is typically imaged using laser scanning and epifluorescence-based approaches. Unfortunately, those techniques are limited in either axial resolution, image acquisition speed, or by photobleaching. In the last decade, however, selective plane illumination microscopy has emerged as the preferred choice for three-dimensional time lapse imaging combining axial sectioning capability with fast, camera-based image acquisition, and minimal light exposure. We demonstrate how selective plane illumination microscopy can be utilized for three-dimensional fluorescence anisotropy imaging of live cells. We further examined the formation of focal adhesions by three-dimensional time lapse anisotropy imaging of CHO-K1 cells expressing an EGFP-paxillin fusion protein.

CD4+ T cell expression of MyD88 is essential for normal resolution of Chlamydia muridarum genital tract infection.

PubMed

Frazer, Lauren C; Sullivan, Jeanne E; Zurenski, Matthew A; Mintus, Margaret; Tomasak, Tammy E; Prantner, Daniel; Nagarajan, Uma M; Darville, Toni

2013-10-15

Resolution of Chlamydia genital tract infection is delayed in the absence of MyD88. In these studies, we first used bone marrow chimeras to demonstrate a requirement for MyD88 expression by hematopoietic cells in the presence of a wild-type epithelium. Using mixed bone marrow chimeras we then determined that MyD88 expression was specifically required in the adaptive immune compartment. Furthermore, adoptive transfer experiments revealed that CD4(+) T cell expression of MyD88 was necessary for normal resolution of genital tract infection. This requirement was associated with a reduced ability of MyD88(-/-)CD4(+) T cells to accumulate in the draining lymph nodes and genital tract when exposed to the same inflammatory milieu as wild-type CD4(+) T cells. We also demonstrated that the impaired infection control we observed in the absence of MyD88 could not be recapitulated by deficiencies in TLR or IL-1R signaling. In vitro, we detected an increased frequency of apoptotic MyD88(-/-)CD4(+) T cells upon activation in the absence of exogenous ligands for receptors upstream of MyD88. These data reveal an intrinsic requirement for MyD88 in CD4(+) T cells during Chlamydia infection and indicate that the importance of MyD88 extends beyond innate immune responses by directly influencing adaptive immunity.

Expression, purification and preliminary crystallographic analysis of Mycobacterium tuberculosis CysQ, a phosphatase involved in sulfur metabolism

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

Erickson, Anna I.; Sarsam, Reta D.; Fisher, Andrew J., E-mail: ajfisher@ucdavis.edu

The cysQ gene from Mycobacterium tuberculosis was cloned and the expressed protein, a 3′-phosphoadenosine-5′’-phosphatase, was purified and crystallized. X-ray diffraction data were collected to 1.7 Å resolution.

Laue Crystal Structure of Shewanella oneidensis Cytochrome c Nitrite Reductase from a High-yield Expression System

PubMed Central

Youngblut, Matthew; Judd, Evan T.; Srajer, Vukica; Sayyed, Bilal; Goelzer, Tyler; Elliott, Sean J.; Schmidt, Marius; Pacheco, A. Andrew

2012-01-01

The high-yield expression and purification of Shewanella oneidensis cytochrome c nitrite reductase (ccNiR), and its characterization by a variety of methods, notably Laue crystallography, is reported. A key component of the expression system is an artificial ccNiR gene in which the N-terminal signal peptide from the highly expressed S. oneidensis protein “Small Tetra-heme c” replaces the wild-type signal peptide. This gene, inserted into the plasmid pHSG298 and expressed in S. oneidensis TSP-1 strain, generated ~20 mg crude ccNiR/L culture, compared with 0.5–1 mg/L for untransformed cells. Purified ccNiR has nitrite and hydroxylamine reductase activities comparable to those previously reported for E. coli ccNiR, and is stable for over two weeks in pH 7 solution at 4° C. UV/Vis spectropotentiometric titrations and protein film voltammetry identified 5 independent 1-electron reduction processes. Global analysis of the spectropotentiometric data also allowed determination of the extinction coefficient spectra for the 5 reduced ccNiR species. The characteristics of the individual extinction coefficient spectra suggest that, within each reduced species, the electrons are distributed amongst the various hemes, rather than being localized on specific heme centers. The purified ccNiR yielded good quality crystals, with which the 2.59 Å resolution structure was solved at room temperature using the Laue diffraction method. The structure is similar to that of E. coli ccNiR, except in the region where the enzyme interacts with its physiological electron donor (CymA in the case of S. oneidensis ccNiR, NrfB in the case of the E. coli protein). PMID:22382353

Genetically expressed voltage sensor ArcLight for imaging large scale cortical activity in the anesthetized and awake mouse

PubMed Central

Borden, Peter Y.; Ortiz, Alex D.; Waiblinger, Christian; Sederberg, Audrey J.; Morrissette, Arthur E.; Forest, Craig R.; Jaeger, Dieter; Stanley, Garrett B.

2017-01-01

Abstract. With the recent breakthrough in genetically expressed voltage indicators (GEVIs), there has been a tremendous demand to determine the capabilities of these sensors in vivo. Novel voltage sensitive fluorescent proteins allow for direct measurement of neuron membrane potential changes through changes in fluorescence. Here, we utilized ArcLight, a recently developed GEVI, and examined the functional characteristics in the widely used mouse somatosensory whisker pathway. We measured the resulting evoked fluorescence using a wide-field microscope and a CCD camera at 200 Hz, which enabled voltage recordings over the entire cortical region with high temporal resolution. We found that ArcLight produced a fluorescent response in the S1 barrel cortex during sensory stimulation at single whisker resolution. During wide-field cortical imaging, we encountered substantial hemodynamic noise that required additional post hoc processing through noise subtraction techniques. Over a period of 28 days, we found clear and consistent ArcLight fluorescence responses to a simple sensory input. Finally, we demonstrated the use of ArcLight to resolve cortical S1 sensory responses in the awake mouse. Taken together, our results demonstrate the feasibility of ArcLight as a measurement tool for mesoscopic, chronic imaging. PMID:28491905

Expression of terrain and surface geology in high-resolution helicopter-borne gravity gradient (AGG) data: examples from Great Sand Dunes National Park, Rio Grande Rift, Colorado

USGS Publications Warehouse

Drenth, Benjamin J.

2013-01-01

Airborne gravity gradient (AGG) data are rapidly becoming standard components of geophysical mapping programs, due to their advantages in cost, access, and resolution advantages over measurements of the gravity field on the ground. Unlike conventional techniques that measure the gravity field, AGG methods measure derivatives of the gravity field. This means that effects of terrain and near-surface geology are amplified in AGG data, and that proper terrain corrections are critically important for AGG data processing. However, terrain corrections require reasonable estimates of density for the rocks and sediments that make up the terrain. A recommended philosophical approach is to use the terrain and surface geology, with their strong expression in AGG data, to the interpreter’s advantage. An example of such an approach is presented here for an area with very difficult ground access and little ground gravity data. Nettleton-style profiling is used with AGG data to estimate the densities of the sand dunefield and adjacent Precambrian rocks from the area of Great Sand Dunes National Park in southern Colorado. Processing of the AGG data using the density estimate for the dunefield allows buried structures, including a hypothesized buried basement bench, to be mapped beneath the sand dunes.

Consistent integration of experimental and ab initio data into molecular and coarse-grained models

NASA Astrophysics Data System (ADS)

Vlcek, Lukas

As computer simulations are increasingly used to complement or replace experiments, highly accurate descriptions of physical systems at different time and length scales are required to achieve realistic predictions. The questions of how to objectively measure model quality in relation to reference experimental or ab initio data, and how to transition seamlessly between different levels of resolution are therefore of prime interest. To address these issues, we use the concept of statistical distance to define a measure of similarity between statistical mechanical systems, i.e., a model and its target, and show that its minimization leads to general convergence of the systems' measurable properties. Through systematic coarse-graining, we arrive at appropriate expressions for optimization loss functions consistently incorporating microscopic ab initio data as well as macroscopic experimental data. The design of coarse-grained and multiscale models is then based on factoring the model system partition function into terms describing the system at different resolution levels. The optimization algorithm takes advantage of thermodynamic perturbation expressions for fast exploration of the model parameter space, enabling us to scan millions of parameter combinations per hour on a single CPU. The robustness and generality of the new model optimization framework and its efficient implementation are illustrated on selected examples including aqueous solutions, magnetic systems, and metal alloys.

omega-Amino acid:pyruvate transaminase from Alcaligenes denitrificans Y2k-2: a new catalyst for kinetic resolution of beta-amino acids and amines.

PubMed

Yun, Hyungdon; Lim, Seongyop; Cho, Byung-Kwan; Kim, Byung-Gee

2004-04-01

Alcaligenes denitrificans Y2k-2 was obtained by selective enrichment followed by screening from soil samples, which showed omega-amino acid:pyruvate transaminase activity, to kinetically resolve aliphatic beta-amino acid, and the corresponding structural gene (aptA) was cloned. The gene was functionally expressed in Escherichia coli BL21 by using an isopropyl-beta-D-thiogalactopyranoside (IPTG)-inducible pET expression system (9.6 U/mg), and the recombinant AptA was purified to show a specific activity of 77.2 U/mg for L-beta-amino-n-butyric acid (L-beta-ABA). The enzyme converts various beta-amino acids and amines to the corresponding beta-keto acids and ketones by using pyruvate as an amine acceptor. The apparent K(m) and V(max) for L-beta-ABA were 56 mM and 500 U/mg, respectively, in the presence of 10 mM pyruvate. In the presence of 10 mM L-beta-ABA, the apparent K(m) and V(max) for pyruvate were 11 mM and 370 U/mg, respectively. The enzyme exhibits high stereoselectivity (E > 80) in the kinetic resolution of 50 mM D,L-beta-ABA, producing optically pure D-beta-ABA (99% enantiomeric excess) with 53% conversion.

ω-Amino Acid:Pyruvate Transaminase from Alcaligenes denitrificans Y2k-2: a New Catalyst for Kinetic Resolution of β-Amino Acids and Amines

PubMed Central

Yun, Hyungdon; Lim, Seongyop; Cho, Byung-Kwan; Kim, Byung-Gee

2004-01-01

Alcaligenes denitrificans Y2k-2 was obtained by selective enrichment followed by screening from soil samples, which showed ω-amino acid:pyruvate transaminase activity, to kinetically resolve aliphatic β-amino acid, and the corresponding structural gene (aptA) was cloned. The gene was functionally expressed in Escherichia coli BL21 by using an isopropyl-β-d-thiogalactopyranoside (IPTG)-inducible pET expression system (9.6 U/mg), and the recombinant AptA was purified to show a specific activity of 77.2 U/mg for l-β-amino-n-butyric acid (l-β-ABA). The enzyme converts various β-amino acids and amines to the corresponding β-keto acids and ketones by using pyruvate as an amine acceptor. The apparent Km and Vmax for l-β-ABA were 56 mM and 500 U/mg, respectively, in the presence of 10 mM pyruvate. In the presence of 10 mM l-β-ABA, the apparent Km and Vmax for pyruvate were 11 mM and 370 U/mg, respectively. The enzyme exhibits high stereoselectivity (E > 80) in the kinetic resolution of 50 mM d,l-β-ABA, producing optically pure d-β-ABA (99% enantiomeric excess) with 53% conversion. PMID:15066855

Eye evolution and its functional basis.

PubMed

Nilsson, Dan-E

2013-03-01

Eye evolution is driven by the evolution of visually guided behavior. Accumulation of gradually more demanding behaviors have continuously increased the performance requirements on the photoreceptor organs. Starting with nondirectional photoreception, I argue for an evolutionary sequence continuing with directional photoreception, low-resolution vision, and finally, high-resolution vision. Calculations of the physical requirements for these four sensory tasks show that they correlate with major innovations in eye evolution and thus work as a relevant classification for a functional analysis of eye evolution. Together with existing molecular and morphological data, the functional analysis suggests that urbilateria had a simple set of rhabdomeric and ciliary receptors used for directional photoreception, and that organ duplications, positional shifts and functional shifts account for the diverse patterns of eyes and photoreceptors seen in extant animals. The analysis also suggests that directional photoreception evolved independently at least twice before the last common ancestor of bilateria and proceeded several times independently to true vision in different bilaterian and cnidarian groups. This scenario is compatible with Pax-gene expression in eye development in the different animal groups. The whole process from the first opsin to high-resolution vision took about 170 million years and was largely completed by the onset of the Cambrian, about 530 million years ago. Evolution from shadow detectors to multiple directional photoreceptors has further led to secondary cases of eye evolution in bivalves, fan worms, and chitons.

Expression and functional analysis of the lysine decarboxylase and copper amine oxidase genes from the endophytic fungus Colletotrichum gloeosporioides ES026.

PubMed

Zhang, Xiangmei; Wang, Zhangqian; Jan, Saad; Yang, Qian; Wang, Mo

2017-06-05

Huperzine A (HupA) isolated from Huperzia serrata is an important compound used to treat Alzheimer's disease (AD). Recently, HupA was reported in various endophytic fungi, with Colletotrichum gloeosporioides ES026 previously isolated from H. serrata shown to produce HupA. In this study, we performed next-generation sequencing and de novo RNA sequencing of C. gloeosporioides ES026 to elucidate the molecular functions, biological processes, and biochemical pathways of these unique sequences. Gene ontology and Kyoto Encyclopedia of Genes and Genomes assignments allowed annotation of lysine decarboxylase (LDC) and copper amine oxidase (CAO) for their conversion of L-lysine to 5-aminopentanal during HupA biosynthesis. Additionally, we constructed a stable, high-yielding HupA-expression system resulting from the overexpression of CgLDC and CgCAO from the HupA-producing endophytic fungus C. gloeosporioides ES026 in Escherichia coli. Quantitative reverse transcription polymerase chain reaction analysis confirmed CgLDC and CgCAO expression, and quantitative determination of HupA levels was assessed by liquid chromatography high-resolution mass spectrometry, which revealed that elevated expression of CgLDC and CgCAO produced higher yields of HupA than those derived from C. gloeosporioides ES026. These results revealed CgLDC and CgCAO involvement in HupA biosynthesis and their key role in regulating HupA content in C. gloeosporioides ES026.

Ultra-High Resolution Spectroscopic Remote Sensing: A Microscope on Planetary Atmospheres

NASA Technical Reports Server (NTRS)

Kostiuk, Theodor

2010-01-01

Remote sensing of planetary atmospheres is not complete without studies of all levels of the atmosphere, including the dense cloudy- and haze filled troposphere, relatively clear and important stratosphere and the upper atmosphere, which are the first levels to experience the effects of solar radiation. High-resolution spectroscopy can provide valuable information on these regions of the atmosphere. Ultra-high spectral resolution studies can directly measure atmospheric winds, composition, temperature and non-thermal phenomena, which describe the physics and chemistry of the atmosphere. Spectroscopy in the middle to long infrared wavelengths can also probe levels where dust of haze limit measurements at shorter wavelength or can provide ambiguous results on atmospheric species abundances or winds. A spectroscopic technique in the middle infrared wavelengths analogous to a radio receiver. infrared heterodyne spectroscopy [1], will be describe and used to illustrate the detailed study of atmospheric phenomena not readily possible with other methods. The heterodyne spectral resolution with resolving power greater than 1,000.000 measures the true line shapes of emission and absorption lines in planetary atmospheres. The information on the region of line formation is contained in the line shapes. The absolute frequency of the lines can be measured to I part in 100 ,000,000 and can be used to accurately measure the Doppler frequency shift of the lines, directly measuring the line-of-sight velocity of the gas to --Im/s precision (winds). The technical and analytical methods developed and used to measure and analyze infrared heterodyne measurements will be described. Examples of studies on Titan, Venus, Mars, Earth, and Jupiter will be presented. 'These include atmospheric dynamics on slowly rotating bodies (Titan [2] and Venus [3] and temperature, composition and chemistry on Mars 141, Venus and Earth. The discovery and studies of unique atmospheric phenomena will also be described, such as non-thermal and lasing phenomena on Mars and Venus, mid-infrared aurora on Jupiter [5], and results of small body impacts on Jupiter [6]. The heterodyne technique can also be applied for detailed study of the Earth's stratosphere and mesosphere by measuring trace constituent abundances and temporal and spatial variability as well as winds, which provide information of transport. All ground-based measurements will be described as complementary and supporting studies for on-going and future space missions [7] (Mars Express, Venus Express, Cassini Huygens, JUNO, ExoMars Trace Gas Orbiter, and the Europa Jupiter System Mission, an Earth Science Venture Class missions), Proposed instrument and technology development for a space flight infrared heterodyne spectrometer will be described.

A Leveraged Signal-to-Noise Ratio (LSTNR) Method to Extract Differentially Expressed Genes and Multivariate Patterns of Expression From Noisy and Low-Replication RNAseq Data

PubMed Central

Lozoya, Oswaldo A.; Santos, Janine H.; Woychik, Richard P.

2018-01-01

To life scientists, one important feature offered by RNAseq, a next-generation sequencing tool used to estimate changes in gene expression levels, lies in its unprecedented resolution. It can score countable differences in transcript numbers among thousands of genes and between experimental groups, all at once. However, its high cost limits experimental designs to very small sample sizes, usually N = 3, which often results in statistically underpowered analysis and poor reproducibility. All these issues are compounded by the presence of experimental noise, which is harder to distinguish from instrumental error when sample sizes are limiting (e.g., small-budget pilot tests), experimental populations exhibit biologically heterogeneous or diffuse expression phenotypes (e.g., patient samples), or when discriminating among transcriptional signatures of closely related experimental conditions (e.g., toxicological modes of action, or MOAs). Here, we present a leveraged signal-to-noise ratio (LSTNR) thresholding method, founded on generalized linear modeling (GLM) of aligned read detection limits to extract differentially expressed genes (DEGs) from noisy low-replication RNAseq data. The LSTNR method uses an agnostic independent filtering strategy to define the dynamic range of detected aggregate read counts per gene, and assigns statistical weights that prioritize genes with better sequencing resolution in differential expression analyses. To assess its performance, we implemented the LSTNR method to analyze three separate datasets: first, using a systematically noisy in silico dataset, we demonstrated that LSTNR can extract pre-designed patterns of expression and discriminate between “noise” and “true” differentially expressed pseudogenes at a 100% success rate; then, we illustrated how the LSTNR method can assign patient-derived breast cancer specimens correctly to one out of their four reported molecular subtypes (luminal A, luminal B, Her2-enriched and basal-like); and last, we showed the ability to retrieve five different modes of action (MOA) elicited in livers of rats exposed to three toxicants under three nutritional routes by using the LSTNR method. By combining differential measurements with resolving power to detect DEGs, the LSTNR method offers an alternative approach to interrogate noisy and low-replication RNAseq datasets, which handles multiple biological conditions at once, and defines benchmarks to validate RNAseq experiments with standard benchtop assays. PMID:29868123

Resolving anaphoras for the extraction of drug-drug interactions in pharmacological documents

PubMed Central

2010-01-01

Background Drug-drug interactions are frequently reported in the increasing amount of biomedical literature. Information Extraction (IE) techniques have been devised as a useful instrument to manage this knowledge. Nevertheless, IE at the sentence level has a limited effect because of the frequent references to previous entities in the discourse, a phenomenon known as 'anaphora'. DrugNerAR, a drug anaphora resolution system is presented to address the problem of co-referring expressions in pharmacological literature. This development is part of a larger and innovative study about automatic drug-drug interaction extraction. Methods The system uses a set of linguistic rules drawn by Centering Theory over the analysis provided by a biomedical syntactic parser. Semantic information provided by the Unified Medical Language System (UMLS) is also integrated in order to improve the recognition and the resolution of nominal drug anaphors. Besides, a corpus has been developed in order to analyze the phenomena and evaluate the current approach. Each possible case of anaphoric expression was looked into to determine the most effective way of resolution. Results An F-score of 0.76 in anaphora resolution was achieved, outperforming significantly the baseline by almost 73%. This ad-hoc reference line was developed to check the results as there is no previous work on anaphora resolution in pharmalogical documents. The obtained results resemble those found in related-semantic domains. Conclusions The present approach shows very promising results in the challenge of accounting for anaphoric expressions in pharmacological texts. DrugNerAr obtains similar results to other approaches dealing with anaphora resolution in the biomedical domain, but, unlike these approaches, it focuses on documents reflecting drug interactions. The Centering Theory has proved being effective at the selection of antecedents in anaphora resolution. A key component in the success of this framework is the analysis provided by the MMTx program and the DrugNer system that allows to deal with the complexity of the pharmacological language. It is expected that the positive results of the resolver increases performance of our future drug-drug interaction extraction system. PMID:20406499

Music Therapy with Bereaved Youth: Expressing Grief and Feeling Better

ERIC Educational Resources Information Center

McFerran, Katrina

2011-01-01

Music therapy is a promising intervention with bereaved youth. In comparison to other programs, it appears particularly effective for promoting the resolution of grief-related feelings; providing opportunities to express and release feelings through musical participation. Descriptions from music therapy participants are supported by research…

Single sensor processing to obtain high resolution color component signals

NASA Technical Reports Server (NTRS)

Glenn, William E. (Inventor)

2010-01-01

A method for generating color video signals representative of color images of a scene includes the following steps: focusing light from the scene on an electronic image sensor via a filter having a tri-color filter pattern; producing, from outputs of the sensor, first and second relatively low resolution luminance signals; producing, from outputs of the sensor, a relatively high resolution luminance signal; producing, from a ratio of the relatively high resolution luminance signal to the first relatively low resolution luminance signal, a high band luminance component signal; producing, from outputs of the sensor, relatively low resolution color component signals; and combining each of the relatively low resolution color component signals with the high band luminance component signal to obtain relatively high resolution color component signals.

Electron momentum density and Compton profile by a semi-empirical approach

NASA Astrophysics Data System (ADS)

Aguiar, Julio C.; Mitnik, Darío; Di Rocco, Héctor O.

2015-08-01

Here we propose a semi-empirical approach to describe with good accuracy the electron momentum densities and Compton profiles for a wide range of pure crystalline metals. In the present approach, we use an experimental Compton profile to fit an analytical expression for the momentum densities of the valence electrons. This expression is similar to a Fermi-Dirac distribution function with two parameters, one of which coincides with the ground state kinetic energy of the free-electron gas and the other resembles the electron-electron interaction energy. In the proposed scheme conduction electrons are neither completely free nor completely bound to the atomic nucleus. This procedure allows us to include correlation effects. We tested the approach for all metals with Z=3-50 and showed the results for three representative elements: Li, Be and Al from high-resolution experiments.

Soluble Alpha-APP (sAPPalpha) Regulates CDK5 Expression and Activity in Neurons

PubMed Central

Hartl, Daniela; Klatt, Stephan; Roch, Manfred; Konthur, Zoltan; Klose, Joachim; Willnow, Thomas E.; Rohe, Michael

2013-01-01

A growing body of evidence suggests a role for soluble alpha-amyloid precursor protein (sAPPalpha) in pathomechanisms of Alzheimer disease (AD). This cleavage product of APP was identified to have neurotrophic properties. However, it remained enigmatic what proteins, targeted by sAPPalpha, might be involved in such neuroprotective actions. Here, we used high-resolution two-dimensional polyacrylamide gel electrophoresis to analyze proteome changes downstream of sAPPalpha in neurons. We present evidence that sAPPalpha regulates expression and activity of CDK5, a kinase that plays an important role in AD pathology. We also identified the cytoprotective chaperone ORP150 to be induced by sAPPalpha as part of this protective response. Finally, we present functional evidence that the sAPPalpha receptor SORLA is essential to mediate such molecular functions of sAPPalpha in neurons. PMID:23776568

Efficient conditioned pain modulation despite pain persistence in painful diabetic neuropathy

PubMed Central

Granovsky, Yelena; Nahman-Averbuch, Hadas; Khamaisi, Mogher; Granot, Michal

2017-01-01

Abstract Introduction: Alleviation of pain, by either medical or surgical therapy, is accompanied by transition from less efficient, or pro-nociceptive, to efficient conditioned pain modulation (CPM). Spontaneous decrease or resolution of pain with disease progression is reported for some patients with painful diabetic neuropathy (PDN). Objectives: To explore whether CPM changes similarly in parallel to spontaneous resolution of pain in PDN patients. Methods: In this cross-sectional study, thirty-three patients with PDN underwent psychophysical assessment of pain modulation on the forearm, remote from the clinical pain. Results: Pain duration was not correlated with neuropathic pain intensity, yet, it correlated with CPM efficiency; patients with longer pain duration had same pain level, but more efficient CPM than those with short-pain duration (ρ = −0.417; P = 0.025, Spearman correlation). Patients with pain more than 2 years (median split) expressed efficient CPM that was not different from that of healthy controls. These patients also had lower temporal summation of pain than the short-pain duration patients group (P < 0.05). The 2 patient groups did not differ in clinical pain characteristics or use of analgesics. Conclusion: Pro-nociception, expressed by less efficient CPM and high temporal summation that usually accompanies clinical painful conditions, seems to “normalize” with chronicity of the pain syndrome. This is despite continuing pain, suggesting that pro-nociceptivity in pain syndromes is multifactorial. Because the pain modulation profile affects success of therapy, this suggests that different drugs might express different efficacy pending on duration of the pain in patients with PDN. PMID:29392208

Rapid, scalable and highly automated HLA genotyping using next-generation sequencing: a transition from research to diagnostics

PubMed Central

2013-01-01

Background Human leukocyte antigen matching at allelic resolution is proven clinically significant in hematopoietic stem cell transplantation, lowering the risk of graft-versus-host disease and mortality. However, due to the ever growing HLA allele database, tissue typing laboratories face substantial challenges. In light of the complexity and the high degree of allelic diversity, it has become increasingly difficult to define the classical transplantation antigens at high-resolution by using well-tried methods. Thus, next-generation sequencing is entering into diagnostic laboratories at the perfect time and serving as a promising tool to overcome intrinsic HLA typing problems. Therefore, we have developed and validated a scalable automated HLA class I and class II typing approach suitable for diagnostic use. Results A validation panel of 173 clinical and proficiency testing samples was analysed, demonstrating 100% concordance to the reference method. From a total of 1,273 loci we were able to generate 1,241 (97.3%) initial successful typings. The mean ambiguity reduction for the analysed loci was 93.5%. Allele assignment including intronic sequences showed an improved resolution (99.2%) of non-expressed HLA alleles. Conclusion We provide a powerful HLA typing protocol offering a short turnaround time of only two days, a fully integrated workflow and most importantly a high degree of typing reliability. The presented automated assay is flexible and can be scaled by specific primer compilations and the use of different 454 sequencing systems. The workflow was successfully validated according to the policies of the European Federation for Immunogenetics. Next-generation sequencing seems to become one of the new methods in the field of Histocompatibility. PMID:23557197

Assessing very high resolution UAV imagery for monitoring forest health during a simulated disease outbreak

NASA Astrophysics Data System (ADS)

Dash, Jonathan P.; Watt, Michael S.; Pearse, Grant D.; Heaphy, Marie; Dungey, Heidi S.

2017-09-01

Research into remote sensing tools for monitoring physiological stress caused by biotic and abiotic factors is critical for maintaining healthy and highly-productive plantation forests. Significant research has focussed on assessing forest health using remotely sensed data from satellites and manned aircraft. Unmanned aerial vehicles (UAVs) may provide new tools for improved forest health monitoring by providing data with very high temporal and spatial resolutions. These platforms also pose unique challenges and methods for health assessments must be validated before use. In this research, we simulated a disease outbreak in mature Pinus radiata D. Don trees using targeted application of herbicide. The objective was to acquire a time-series simulated disease expression dataset to develop methods for monitoring physiological stress from a UAV platform. Time-series multi-spectral imagery was acquired using a UAV flown over a trial at regular intervals. Traditional field-based health assessments of crown health (density) and needle health (discolouration) were carried out simultaneously by experienced forest health experts. Our results showed that multi-spectral imagery collected from a UAV is useful for identifying physiological stress in mature plantation trees even during the early stages of tree stress. We found that physiological stress could be detected earliest in data from the red edge and near infra-red bands. In contrast to previous findings, red edge data did not offer earlier detection of physiological stress than the near infra-red data. A non-parametric approach was used to model physiological stress based on spectral indices and was found to provide good classification accuracy (weighted kappa = 0.694). This model can be used to map physiological stress based on high-resolution multi-spectral data.

A resolution expressing the sense of the Senate that public servants should be commended for their dedication and continued service to the United States during Public Service Recognition week.

THOMAS, 112th Congress

Sen. Akaka, Daniel K. [D-HI

2012-04-17

Senate - 04/26/2012 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution expressing the sense of the Senate that ambush marketing adversely affects the United States Olympic and Paralympic teams.

THOMAS, 113th Congress

Sen. Begich, Mark [D-AK

2013-11-07

Senate - 02/06/2014 Resolution agreed to in Senate with an amendment and an amendment to the Title and an amended preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution expressing support for designation of 2011 as "World Veterinary Year" to bring attention to and show appreciation for the veterinary profession on its 250th anniversary.

THOMAS, 111th Congress

Sen. Ensign, John [R-NV

2010-07-15

Senate - 09/23/2010 Resolution agreed to in Senate with an amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution expressing profound concern, deepest sympathies, and solidarity on behalf of the people of the United States to the people and Government of Chile following the massive earthquake.

THOMAS, 111th Congress

Sen. Lugar, Richard G. [R-IN

2010-03-03

Senate - 03/04/2010 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution recognizing May 16, 2012, as Hereditary Angioedema Awareness Day and expressing the sense of the Senate that more research and treatments are needed for Hereditary Angioedema.

THOMAS, 112th Congress

Sen. Inouye, Daniel K. [D-HI

2011-10-05

Senate - 01/31/2012 Resolution agreed to in Senate with an amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution expressing the sense of the Senate that Village Voice Media Holdings, LLC should eliminate the "adult entertainment" section of the classified advertising website Backpage.com.

THOMAS, 112th Congress

Sen. Blumenthal, Richard [D-CT

2012-04-25

Senate - 12/20/2012 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution expressing the sense of the Senate with respect to enhanced relations with the Republic of Moldova and support for the Republic of Moldova's territorial integrity.

THOMAS, 113th Congress

Sen. Shaheen, Jeanne [D-NH

2014-07-10

Senate - 07/23/2014 Resolution agreed to in Senate without amendment and with a preamble by Voice Vote. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution expressing the sense of Congress relating to the commemoration of the 180th anniversary of diplomatic relations between the United States and the Kingdom of Thailand.

THOMAS, 113th Congress

Sen. Menendez, Robert [D-NJ

2013-03-18

Senate - 04/09/2013 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution expressing the sense of the Senate supporting the U.S.-Africa Leaders Summit to be held in Washington, D.C., from August 4 through 6, 2014.

THOMAS, 113th Congress

Sen. Coons, Christopher A. [D-DE

2014-07-24

Senate - 07/31/2014 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution expressing the sense of the Senate on the recovery, rehabilitation, and rebuilding of Haiti following the humanitarian crisis caused by the January 12, 2010, earthquake in Haiti.

THOMAS, 111th Congress

Sen. Kerry, John F. [D-MA

2010-02-09

Senate - 03/04/2010 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution expressing the sense of the Senate that the Government of Libya should apologize for the welcome home ceremony held to celebrate the release of convicted Lockerbie bomber Abdel Baset al-Megrahi.

THOMAS, 111th Congress

Sen. Schumer, Charles E. [D-NY

2009-09-08

Senate - 09/23/2009 Resolution agreed to in Senate without amendment by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution expressing the sense of the Senate regarding the critical need for political dialogue in Bangladesh, and for other purposes.

THOMAS, 113th Congress

Sen. Durbin, Richard J. [D-IL

2013-12-11

Senate - 01/07/2014 Resolution agreed to in Senate without amendment and an amendment to the Title and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution expressing the sense of the Senate regarding the Fifth Summit of the Americas, held in Port of Spain, Trinidad and Tobago, April 17, 18, and 19, 2009.

THOMAS, 111th Congress

Sen. Kerry, John F. [D-MA

2009-03-30

Senate - 04/03/2009 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

Image resolution enhancement via image restoration using neural network

NASA Astrophysics Data System (ADS)

Zhang, Shuangteng; Lu, Yihong

2011-04-01

Image super-resolution aims to obtain a high-quality image at a resolution that is higher than that of the original coarse one. This paper presents a new neural network-based method for image super-resolution. In this technique, the super-resolution is considered as an inverse problem. An observation model that closely follows the physical image acquisition process is established to solve the problem. Based on this model, a cost function is created and minimized by a Hopfield neural network to produce high-resolution images from the corresponding low-resolution ones. Not like some other single frame super-resolution techniques, this technique takes into consideration point spread function blurring as well as additive noise and therefore generates high-resolution images with more preserved or restored image details. Experimental results demonstrate that the high-resolution images obtained by this technique have a very high quality in terms of PSNR and visually look more pleasant.

Nucleosome positioning from tiling microarray data.

PubMed

Yassour, Moran; Kaplan, Tommy; Jaimovich, Ariel; Friedman, Nir

2008-07-01

The packaging of DNA around nucleosomes in eukaryotic cells plays a crucial role in regulation of gene expression, and other DNA-related processes. To better understand the regulatory role of nucleosomes, it is important to pinpoint their position in a high (5-10 bp) resolution. Toward this end, several recent works used dense tiling arrays to map nucleosomes in a high-throughput manner. These data were then parsed and hand-curated, and the positions of nucleosomes were assessed. In this manuscript, we present a fully automated algorithm to analyze such data and predict the exact location of nucleosomes. We introduce a method, based on a probabilistic graphical model, to increase the resolution of our predictions even beyond that of the microarray used. We show how to build such a model and how to compile it into a simple Hidden Markov Model, allowing for a fast and accurate inference of nucleosome positions. We applied our model to nucleosomal data from mid-log yeast cells reported by Yuan et al. and compared our predictions to those of the original paper; to a more recent method that uses five times denser tiling arrays as explained by Lee et al.; and to a curated set of literature-based nucleosome positions. Our results suggest that by applying our algorithm to the same data used by Yuan et al. our fully automated model traced 13% more nucleosomes, and increased the overall accuracy by about 20%. We believe that such an improvement opens the way for a better understanding of the regulatory mechanisms controlling gene expression, and how they are encoded in the DNA.

ANALYSIS OF DIOXINS IN CONTAMINATED SOILS WITH THE CALUX AND CAFLUX BIOASSAYS, AN IMMUNOASSAY, AND GAS CHROMATOGRAPHY/HIGH-RESOLUTION MASS SPECTROMETRY

PubMed Central

Nording, Malin; Denison, Michael S.; Baston, David; Persson, Ylva; Spinnel, Erik; Haglund, Peter

2010-01-01

The chemically activated luciferase expression assay, the chemically activated fluorescence expression assay, and the enzyme-linked immunosorbent assay (ELISA) are all bioanalytical methods that have been used for the detection and quantification of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/Fs). However, no comparisons of the results obtained by these three methods have been published analyzing identical replicates of purified sample extracts. Therefore, we have evaluated the performance of each of these methods for analyzing PCDD/Fs in aliquots of extracts from aged-contaminated soil samples and compared the results with those obtained by gas chromatography/high-resolution mass spectrometry (GC/HRMS). The quantitative performance was assessed and the effects of sample purification and data interpretation on the quality of the bioassay results were investigated. Results from the bioanalytical techniques were, in principle, not significantly different from each other or from the GC/HRMS data (p = 0.05). Furthermore, properly used, all of the bioanalytical techniques examined were found to be sufficiently sensitive, selective, and accurate to be used in connection with soil remediation activities when aiming at the remediation goal recommended by the U.S. Environmental Protection Agency (i.e., < 1,000 pg toxic equivalency/g). However, a site-specific correction factor should be applied with the use of the ELISA to account for differences between the toxic equivalency factors and the ELISA cross-reactivities of the various PCDD/F congeners, which otherwise might significantly underestimate the PCDD/F content. PMID:17571676

Freedom of Expression, the University, and the Media.

ERIC Educational Resources Information Center

Dennis, Everette E.

1992-01-01

Discusses the University of Oregon's long and proud tradition of protecting freedom of speech in light of the current controversy over freedom of expression on U.S. campuses and in the community at large. Discusses multiculturalism and political correctness on campus, and advocates more dispute resolution through public discussion. (SR)

Complementary analyses of hollow cylindrical unioriented permanent magnet (HCM) with high permeability external layer.

PubMed

Lobo, Carlos M S; Tosin, Giancarlo; Baader, Johann E; Colnago, Luiz A

2017-10-01

In this article, several studies based on analytical expressions and computational simulations on Hollow Cylindrical Magnets with an external soft ferromagnetic material (HCM magnets) are presented. Electromagnetic configurations, as well as permanent-magnet-based structures, are studied in terms of magnetic field strength and homogeneity. Permanent-magnet-based structures are further analyzed in terms of the anisotropy of the magnetic permeability. It was found that the HCM magnets produce a highly homogeneous magnetic field as long as the magnetic material is isotropic. The dependency of the magnetic field strength and homogeneity in terms of the anisotropy of the magnetic permeability is also explored here. These magnets can potentially be used in medium-resolution NMR spectrometers and high-field NMR spectrometers. Copyright © 2017 Elsevier Inc. All rights reserved.

Construction of mutant TKGFP for real-time imaging of temporal dynamics of HIF-1 signal transduction activity mediated by hypoxia and reoxygenation in tumors in living mice.

PubMed

Hsieh, Chia-Hung; Kuo, Jung-Wen; Lee, Yi-Jang; Chang, Chi-Wei; Gelovani, Juri G; Liu, Ren-Shyan

2009-12-01

The herpes simplex virus type 1 thymidine kinase (HSV1-tk)/green fluorescent protein (TKGFP) dual-reporter gene and a multimodality imaging approach play a critical role in monitoring therapeutic gene expression, immune cell trafficking, and protein-protein interactions in translational molecular-genetic imaging. However, the cytotoxicity and low temporal resolution of TKGFP limits its application in studies that require a rapid turnover of the reporter. The purpose of this study was to construct a novel mutant TKGFP fusion reporter gene with low cytotoxicity and high temporal resolution for use in the real-time monitoring of temporal dynamics and spatial heterogeneity of hypoxia-inducible factor 1 (HIF-1) signal transduction activity mediated by hypoxia and reoxygenation in vitro and in vivo. Destabilized TKGFP was produced by inserting the nuclear export signal (NES) sequence at the N terminus and fusing the degradation domain of mouse ornithine decarboxylase (dMODC) at the C terminus. The stability of TKGFP in living NG4TL4 cells was determined by Western blot analysis, HSV1-tk enzyme activity assay, and flow cytometric analysis. The suitability of NESTKGFP:dMODC as a transcription reporter was investigated by linking it to a promoter consisting of 8 copies of hypoxia-responsive elements, whose activities depend on HIF-1. The dynamic transcriptional events mediated by hypoxia and reoxygenation were monitored by NESTKGFP:dMODC or TKGFP and determined by optical imaging and PET. Unlike TKGFP, NESTKGFP:dMODC was unstable in the presence of cycloheximide and showed a short half-life of protein and enzyme activity. Rapid turnover of NESTKGFP:dMODC occurred in a 26S proteasome-dependent manner. Furthermore, NESTKGFP:dMODC showed an upregulated expression and low cytotoxicity in living cells. Studies of hypoxia-responsive TKGFP and NESTKGFP:dMODC expression showed that NESTKGFP:dMODC as a reporter gene had better temporal resolution than did TKGFP for monitoring the dynamic transcriptional events mediated by hypoxia and reoxygenation; the TKGFP expression level was not optimal for the purpose of monitoring. In translational molecular-genetic imaging, NESTKGFP:dMODC as a reporter gene, together with optical imaging and PET, allows the direct monitoring of transcription induction and easy determination of its association with other biochemical changes.

Impact of high resolution land surface initialization in Indian summer monsoon simulation using a regional climate model

NASA Astrophysics Data System (ADS)

Unnikrishnan, C. K.; Rajeevan, M.; Rao, S. Vijaya Bhaskara

2016-06-01

The direct impact of high resolution land surface initialization on the forecast bias in a regional climate model in recent years over Indian summer monsoon region is investigated. Two sets of regional climate model simulations are performed, one with a coarse resolution land surface initial conditions and second one used a high resolution land surface data for initial condition. The results show that all monsoon years respond differently to the high resolution land surface initialization. The drought monsoon year 2009 and extended break periods were more sensitive to the high resolution land surface initialization. These results suggest that the drought monsoon year predictions can be improved with high resolution land surface initialization. Result also shows that there are differences in the response to the land surface initialization within the monsoon season. Case studies of heat wave and a monsoon depression simulation show that, the model biases were also improved with high resolution land surface initialization. These results show the need for a better land surface initialization strategy in high resolution regional models for monsoon forecasting.

Building quantitative, three-dimensional atlases of gene expression and morphology at cellular resolution.

PubMed

Knowles, David W; Biggin, Mark D

2013-01-01

Animals comprise dynamic three-dimensional arrays of cells that express gene products in intricate spatial and temporal patterns that determine cellular differentiation and morphogenesis. A rigorous understanding of these developmental processes requires automated methods that quantitatively record and analyze complex morphologies and their associated patterns of gene expression at cellular resolution. Here we summarize light microscopy-based approaches to establish permanent, quantitative datasets-atlases-that record this information. We focus on experiments that capture data for whole embryos or large areas of tissue in three dimensions, often at multiple time points. We compare and contrast the advantages and limitations of different methods and highlight some of the discoveries made. We emphasize the need for interdisciplinary collaborations and integrated experimental pipelines that link sample preparation, image acquisition, image analysis, database design, visualization, and quantitative analysis. Copyright © 2013 Wiley Periodicals, Inc.

Protein preparation and preliminary X-ray crystallographic analysis of a putative glucosamine 6-phosphate deaminase from Streptococcus mutants

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

Hu, Guan-Jing; Li, Lan-Fen; Li, Dan

2007-09-01

A glucosamine 6-phosphate deaminase homologue from S. mutans was expressed, purified and crystallized. Diffraction data have been collected to 2.4 Å resolution. The SMU.636 protein from Streptococcus mutans is a putative glucosamine 6-phosphate deaminase with 233 residues. The smu.636 gene was PCR-amplified from S. mutans genomic DNA and cloned into the expression vector pET-28a(+). The resultant His-tagged fusion protein was expressed in Escherichia coli and purified to homogeneity in two steps. Crystals of the fusion protein were obtained by the hanging-drop vapour-diffusion method. The crystals diffracted to 2.4 Å resolution and belong to space group P2{sub 1}2{sub 1}2{sub 1}, withmore » unit-cell parameters a = 53.83, b = 82.13, c = 134.70 Å.« less

High resolution array CGH and gene expression profiling of alveolar soft part sarcoma

PubMed Central

Selvarajah, Shamini; Pyne, Saumyadipta; Chen, Eleanor; Sompallae, Ramakrishna; Ligon, Azra H.; Nielsen, Gunnlaugur P.; Dranoff, Glenn; Stack, Edward; Loda, Massimo; Flavin, Richard

2014-01-01

Purpose Alveolar soft part sarcoma (ASPS) is a soft tissue sarcoma with poor prognosis, and little molecular evidence for its origin, initiation and progression. The aim of this study was to elucidate candidate molecular pathways involved in tumor pathogenesis. Experimental Design We employed high-throughput array comparative genomic hybridization and cDNA-Mediated Annealing, Selection, Ligation, and Extension Assay to profile the genomic and expression signatures of primary and metastatic ASPS from 17 tumors derived from 11 patients. We used an integrative bioinformatics approach to elucidate the molecular pathways associated with ASPS progression. Fluorescence in situ hybridization was performed to validate the presence of the t(X;17)(p11.2;q25) ASPL-TFE3 fusion and hence confirm the aCGH observations. Results FISH analysis identified the ASPL-TFE3 fusion in all cases. ArrayCGH revealed a higher number of numerical aberrations in metastatic tumors relative to primaries, but failed to identify consistent alterations in either group. Gene expression analysis highlighted 1,063 genes which were differentially expressed between the two groups. Gene set enrichment analysis identified 16 enriched gene sets (p < 0.1) associated with differentially expressed genes. Notable among these were several stem cell gene expression signatures and pathways related to differentiation. In particular, the paired box transcription factor PAX6 was up-regulated in the primary tumors, along with several genes whose mouse orthologs have previously been implicated in Pax6-DNA binding during neural stem cell differentiation. Conclusion In addition to suggesting a tentative neural line of differentiation for ASPS, these results implicate transcriptional deregulation from fusion genes in the pathogenesis of ASPS. PMID:24493828

Simultaneous Quantification of Viral Antigen Expression Kinetics Using Data-Independent (DIA) Mass Spectrometry*

PubMed Central

Croft, Nathan P.; de Verteuil, Danielle A.; Smith, Stewart A.; Wong, Yik Chun; Schittenhelm, Ralf B.; Tscharke, David C.; Purcell, Anthony W.

2015-01-01

The generation of antigen-specific reagents is a significant bottleneck in the study of complex pathogens that express many hundreds to thousands of different proteins or to emerging or new strains of viruses that display potential pandemic qualities and therefore require rapid investigation. In these instances the development of antibodies for example can be prohibitively expensive to cover the full pathogen proteome, or the lead time may be unacceptably long in urgent cases where new highly pathogenic viral strains may emerge. Because genomic information on such pathogens can be rapidly acquired this opens up avenues using mass spectrometric approaches to study pathogen antigen expression, host responses and for screening the utility of therapeutics. In particular, data-independent acquisition (DIA) modalities on high-resolution mass spectrometers generate spectral information on all components of a complex sample providing depth of coverage hitherto only seen in genomic deep sequencing. The spectral information generated by DIA can be iteratively interrogated for potentially any protein of interest providing both evidence of protein expression and quantitation. Here we apply a solely DIA mass spectrometry based methodology to profile the viral antigen expression in cells infected with vaccinia virus up to 9 h post infection without the need for antigen specific antibodies or other reagents. We demonstrate deep coverage of the vaccinia virus proteome using a SWATH-MS acquisition approach, extracting quantitative kinetics of 100 virus proteins within a single experiment. The results highlight the complexity of vaccinia protein expression, complementing what is known at the transcriptomic level, and provide a valuable resource and technique for future studies of viral infection and replication kinetics. Furthermore, they highlight the utility of DIA and mass spectrometry in the dissection of host-pathogen interactions. PMID:25755296

High Resolution Stereo Camera (HRSC) on Mars Express - a decade of PR/EO activities at Freie Universität Berlin

NASA Astrophysics Data System (ADS)

Balthasar, Heike; Dumke, Alexander; van Gasselt, Stephan; Gross, Christoph; Michael, Gregory; Musiol, Stefanie; Neu, Dominik; Platz, Thomas; Rosenberg, Heike; Schreiner, Björn; Walter, Sebastian

2014-05-01

Since 2003 the High Resolution Stereo Camera (HRSC) experiment on the Mars Express mission is in orbit around Mars. First images were sent to Earth on January 14th, 2004. The goal-oriented HRSC data dissemination and the transparent representation of the associated work and results are the main aspects that contributed to the success in the public perception of the experiment. The Planetary Sciences and Remote Sensing Group at Freie Universität Berlin (FUB) offers both, an interactive web based data access, and browse/download options for HRSC press products [www.fu-berlin.de/planets]. Close collaborations with exhibitors as well as print and digital media representatives allows for regular and directed dissemination of, e.g., conventional imagery, orbital/synthetic surface epipolar images, video footage, and high-resolution displays. On a monthly basis we prepare press releases in close collaboration with the European Space Agency (ESA) and the German Aerospace Center (DLR) [http://www.geo.fu-berlin.de/en/geol/fachrichtungen/planet/press/index.html]. A release comprises panchromatic, colour, anaglyph, and perspective views of a scene taken from an HRSC image of the Martian surface. In addition, a context map and descriptive texts in English and German are provided. More sophisticated press releases include elaborate animations and simulated flights over the Martian surface, perspective views of stereo data combined with colour and high resolution, mosaics, and perspective views of data mosaics. Altogether 970 high quality PR products and 15 movies were created at FUB during the last decade and published via FUB/DLR/ESA platforms. We support educational outreach events, as well as permanent and special exhibitions. Examples for that are the yearly "Science Fair", where special programs for kids are offered, and the exhibition "Mars Mission and Vision" which is on tour until 2015 through 20 German towns, showing 3-D movies, surface models, and images of the HRSC camera experiment. Press and media appearances of group members, and talks to school classes and interested communities also contribute to the public outreach. For HRSC data dissemination we use digital platforms. Since 2007 HRSC image data can be viewed and accessed via the online interface HRSCview [http://hrscview.fu-berlin.de] which was built in cooperation with the DLR Institute for Planetary Research. Additionally HRSC ortho images (level 4) are presented in a modern MapServer setup in GIS-read format since 2013 [http://www.geo.fu-berlin.de/en/geol/fachrichtungen/planet/projects/marsexpress/level4downloads/index.html]. All of these offers ensured the accessibility of HRSC data and products to the science community as well as to the general public for the last ten years and will do so also in the future, taking advantage of modern and user-optimized applications and networks.

High Resolution Image Reconstruction from Projection of Low Resolution Images DIffering in Subpixel Shifts

NASA Technical Reports Server (NTRS)

Mareboyana, Manohar; Le Moigne-Stewart, Jacqueline; Bennett, Jerome

2016-01-01

In this paper, we demonstrate a simple algorithm that projects low resolution (LR) images differing in subpixel shifts on a high resolution (HR) also called super resolution (SR) grid. The algorithm is very effective in accuracy as well as time efficiency. A number of spatial interpolation techniques using nearest neighbor, inverse-distance weighted averages, Radial Basis Functions (RBF) etc. used in projection yield comparable results. For best accuracy of reconstructing SR image by a factor of two requires four LR images differing in four independent subpixel shifts. The algorithm has two steps: i) registration of low resolution images and (ii) shifting the low resolution images to align with reference image and projecting them on high resolution grid based on the shifts of each low resolution image using different interpolation techniques. Experiments are conducted by simulating low resolution images by subpixel shifts and subsampling of original high resolution image and the reconstructing the high resolution images from the simulated low resolution images. The results of accuracy of reconstruction are compared by using mean squared error measure between original high resolution image and reconstructed image. The algorithm was tested on remote sensing images and found to outperform previously proposed techniques such as Iterative Back Projection algorithm (IBP), Maximum Likelihood (ML), and Maximum a posterior (MAP) algorithms. The algorithm is robust and is not overly sensitive to the registration inaccuracies.

The Dyadic Construction of Romantic Conflict Recovery Sabotage

PubMed Central

Haydon, Katherine C.; Jonestrask, Cassandra; Guhn-Knight, Haley; Salvatore, Jessica E.

2017-01-01

This longitudinal study of 100 couples assessed individual and dyadic processes associated with romantic conflict recovery, or how couples behave in the moments following conflict. Couples completed measures of attachment anxiety and avoidance; a conflict discussion during which affect, behavior, and conflict resolution were coded; a cool-down discussion during which post-conflict behavior was coded; and measures of relationship satisfaction and stability one year later. Recovery sabotage (negative behavior and perseveration on conflict in the moments following conflict) was associated with high attachment anxiety and low avoidance. Recovery sabotage was unrelated to affect expressed during conflict and was instead tied to whether partners aired or suppressed grievances. Consistent with the demand-withdraw conflict pattern, recovery sabotage was associated with lower actor conflict avoidance but higher partner conflict avoidance. These effects were independent of conflict resolution, which was not significantly associated with recovery sabotage when other features of conflict were controlled. Recovery sabotage and conflict resolution also differentially predicted satisfaction and stability one year later. Findings suggest recovery sabotage is a distinct, developmentally organized relationship process tied to attachment history and behavioral, rather than affective, transactions between partners during conflict. PMID:29398761

Synergetic Use of Sentinel-1 and Sentinel-2 Data for Soil Moisture Mapping at 100 m Resolution.

PubMed

Gao, Qi; Zribi, Mehrez; Escorihuela, Maria Jose; Baghdadi, Nicolas

2017-08-26

The recent deployment of ESA's Sentinel operational satellites has established a new paradigm for remote sensing applications. In this context, Sentinel-1 radar images have made it possible to retrieve surface soil moisture with a high spatial and temporal resolution. This paper presents two methodologies for the retrieval of soil moisture from remotely-sensed SAR images, with a spatial resolution of 100 m. These algorithms are based on the interpretation of Sentinel-1 data recorded in the VV polarization, which is combined with Sentinel-2 optical data for the analysis of vegetation effects over a site in Urgell (Catalunya, Spain). The first algorithm has already been applied to observations in West Africa by Zribi et al., 2008, using low spatial resolution ERS scatterometer data, and is based on change detection approach. In the present study, this approach is applied to Sentinel-1 data and optimizes the inversion process by taking advantage of the high repeat frequency of the Sentinel observations. The second algorithm relies on a new method, based on the difference between backscattered Sentinel-1 radar signals observed on two consecutive days, expressed as a function of NDVI optical index. Both methods are applied to almost 1.5 years of satellite data (July 2015-November 2016), and are validated using field data acquired at a study site. This leads to an RMS error in volumetric moisture of approximately 0.087 m³/m³ and 0.059 m³/m³ for the first and second methods, respectively. No site calibrations are needed with these techniques, and they can be applied to any vegetation-covered area for which time series of SAR data have been recorded.

Synergetic Use of Sentinel-1 and Sentinel-2 Data for Soil Moisture Mapping at 100 m Resolution

PubMed Central

Gao, Qi; Zribi, Mehrez

2017-01-01

The recent deployment of ESA’s Sentinel operational satellites has established a new paradigm for remote sensing applications. In this context, Sentinel-1 radar images have made it possible to retrieve surface soil moisture with a high spatial and temporal resolution. This paper presents two methodologies for the retrieval of soil moisture from remotely-sensed SAR images, with a spatial resolution of 100 m. These algorithms are based on the interpretation of Sentinel-1 data recorded in the VV polarization, which is combined with Sentinel-2 optical data for the analysis of vegetation effects over a site in Urgell (Catalunya, Spain). The first algorithm has already been applied to observations in West Africa by Zribi et al., 2008, using low spatial resolution ERS scatterometer data, and is based on change detection approach. In the present study, this approach is applied to Sentinel-1 data and optimizes the inversion process by taking advantage of the high repeat frequency of the Sentinel observations. The second algorithm relies on a new method, based on the difference between backscattered Sentinel-1 radar signals observed on two consecutive days, expressed as a function of NDVI optical index. Both methods are applied to almost 1.5 years of satellite data (July 2015–November 2016), and are validated using field data acquired at a study site. This leads to an RMS error in volumetric moisture of approximately 0.087 m3/m3 and 0.059 m3/m3 for the first and second methods, respectively. No site calibrations are needed with these techniques, and they can be applied to any vegetation-covered area for which time series of SAR data have been recorded. PMID:28846601

Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple.

PubMed

Wai, Ching M; VanBuren, Robert; Zhang, Jisen; Huang, Lixian; Miao, Wenjing; Edger, Patrick P; Yim, Won C; Priest, Henry D; Meyers, Blake C; Mockler, Todd; Smith, J Andrew C; Cushman, John C; Ming, Ray

2017-10-01

The altered carbon assimilation pathway of crassulacean acid metabolism (CAM) photosynthesis results in an up to 80% higher water-use efficiency than C 3 photosynthesis in plants making it a potentially useful pathway for engineering crop plants with improved drought tolerance. Here we surveyed detailed temporal (diel time course) and spatial (across a leaf gradient) gene and microRNA (miRNA) expression patterns in the obligate CAM plant pineapple [Ananas comosus (L.) Merr.]. The high-resolution transcriptome atlas allowed us to distinguish between CAM-related and non-CAM gene copies. A differential gene co-expression network across green and white leaf diel datasets identified genes with circadian oscillation, CAM-related functions, and source-sink relations. Gene co-expression clusters containing CAM pathway genes are enriched with clock-associated cis-elements, suggesting circadian regulation of CAM. About 20% of pineapple microRNAs have diel expression patterns, with several that target key CAM-related genes. Expression and physiology data provide a model for CAM-specific carbohydrate flux and long-distance hexose transport. Together these resources provide a list of candidate genes for targeted engineering of CAM into C 3 photosynthesis crop species. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Arctic storms simulated in atmospheric general circulation models under uniform high, uniform low, and variable resolutions

NASA Astrophysics Data System (ADS)

Roesler, E. L.; Bosler, P. A.; Taylor, M.

2016-12-01

The impact of strong extratropical storms on coastal communities is large, and the extent to which storms will change with a warming Arctic is unknown. Understanding storms in reanalysis and in climate models is important for future predictions. We know that the number of detected Arctic storms in reanalysis is sensitive to grid resolution. To understand Arctic storm sensitivity to resolution in climate models, we describe simulations designed to identify and compare Arctic storms at uniform low resolution (1 degree), at uniform high resolution (1/8 degree), and at variable resolution (1 degree to 1/8 degree). High-resolution simulations resolve more fine-scale structure and extremes, such as storms, in the atmosphere than a uniform low-resolution simulation. However, the computational cost of running a globally uniform high-resolution simulation is often prohibitive. The variable resolution tool in atmospheric general circulation models permits regional high-resolution solutions at a fraction of the computational cost. The storms are identified using the open-source search algorithm, Stride Search. The uniform high-resolution simulation has over 50% more storms than the uniform low-resolution and over 25% more storms than the variable resolution simulations. Storm statistics from each of the simulations is presented and compared with reanalysis. We propose variable resolution as a cost-effective means of investigating physics/dynamics coupling in the Arctic environment. Future work will include comparisons with observed storms to investigate tuning parameters for high resolution models. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. SAND2016-7402 A

A Small System—High-Resolution Study of Metabolic Adaptation in the Central Metabolic Pathway to Temperate Climates in Drosophila melanogaster

PubMed Central

Lavington, Erik; Cogni, Rodrigo; Kuczynski, Caitlin; Koury, Spencer; Behrman, Emily L.; O’Brien, Katherine R.; Schmidt, Paul S.; Eanes, Walter F.

2014-01-01

In this article, we couple the geographic variation in 127 single-nucleotide polymorphism (SNP) frequencies in genes of 46 enzymes of central metabolism with their associated cis-expression variation to predict latitudinal or climatic-driven gene expression changes in the metabolic architecture of Drosophila melanogaster. Forty-two percent of the SNPs in 65% of the genes show statistically significant clines in frequency with latitude across the 20 local population samples collected from southern Florida to Ontario. A number of SNPs in the screened genes are also associated with significant expression variation within the Raleigh population from North Carolina. A principal component analysis of the full variance–covariance matrix of latitudinal changes in SNP-associated standardized gene expression allows us to identify those major genes in the pathway and its associated branches that are likely targets of natural selection. When embedded in a central metabolic context, we show that these apparent targets are concentrated in the genes of the upper glycolytic pathway and pentose shunt, those controlling glycerol shuttle activity, and finally those enzymes associated with the utilization of glutamate and pyruvate. These metabolites possess high connectivity and thus may be the points where flux balance can be best shifted. We also propose that these points are conserved points associated with coupling energy homeostasis and energy sensing in mammals. We speculate that the modulation of gene expression at specific points in central metabolism that are associated with shifting flux balance or possibly energy-state sensing plays a role in adaptation to climatic variation. PMID:24770333

Water transport by Na+-coupled cotransporters of glucose (SGLT1) and of iodide (NIS). The dependence of substrate size studied at high resolution

PubMed Central

Zeuthen*, Thomas; Belhage, Bo; Zeuthen, Emil

2006-01-01

The relation between substrate and water transport was studied in Na+-coupled cotransporters of glucose (SGLT1) and of iodide (NIS) expressed in Xenopus oocytes. The water transport was monitored from changes in oocyte volume at a resolution of 20 pl, more than one order of magnitude better than previous investigations. The rate of cotransport was monitored as the clamp current obtained from two-electrode voltage clamp. The high resolution data demonstrated a fixed ratio between the turn-over of the cotransporter and the rate of water transport. This applied to experiments in which the rate of cotransport was changed by isosmotic application of substrate, by rapid changes in clamp voltage, or by poisoning. Transport of larger substrates gave rise to less water transport. For the rabbit SGLT1, 378 ± 20 (n = 18 oocytes) water molecules were cotransported along with the 2 Na+ ions and the glucose-analogue α-MDG (MW 194); using the larger sugar arbutin (MW 272) this number was reduced by a factor of at least 0.86 ± 0.03 (15). For the human SGLT1 the respective numbers were 234 ± 12 (18) and 0.85 ± 0.8 (7). For NIS, 253 ± 16 (12) water molecules were cotransported for each 2 Na+ and 1 thiocyanate (SCN−, MW 58), with I− as anion (MW 127) only 162 ± 11 (19) water molecules were cotransported. The effect of substrate size suggests a molecular mechanism for water cotransport and is opposite to what would be expected from unstirred layer effects. Data were analysed by a model which combined cotransport and osmosis at the membrane with diffusion in the cytoplasm. The combination of high resolution measurements and precise modelling showed that water transport across the membrane can be explained by cotransport of water in the membrane proteins and that intracellular unstirred layers effects are minute. PMID:16322051

Nano-Mole Scale Side-Chain Signal Assignment by 1H-Detected Protein Solid-State NMR by Ultra-Fast Magic-Angle Spinning and Stereo-Array Isotope Labeling

PubMed Central

Nishiyama, Yusuke; Endo, Yuki; Nemoto, Takahiro; Yamauchi, Kazuo; Asakura, Tetsuo; Takeda, Mitsuhiro; Terauchi, Tsutomu; Kainosho, Masatsune; Ishii, Yoshitaka

2015-01-01

We present a general approach in 1H-detected 13C solid-state NMR (SSNMR) for side-chain signal assignments of 10-50 nmol quantities of proteins using a combination of a high magnetic field, ultra-fast magic-angle spinning (MAS) at ~80 kHz, and stereo-array-isotope-labeled (SAIL) proteins [Kainosho M. et al., Nature 440, 52–57, 2006]. First, we demonstrate that 1H indirect detection improves the sensitivity and resolution of 13C SSNMR of SAIL proteins for side-chain assignments in the ultra-fast MAS condition. 1H-detected SSNMR was performed for micro-crystalline ubiquitin (~55 nmol or ~0.5mg) that was SAIL-labeled at seven isoleucine (Ile) residues. Sensitivity was dramatically improved by 1H-detected 2D 1H/13C SSNMR by factors of 5.4-9.7 and 2.1-5.0, respectively, over 13C-detected 2D 1H/13C SSNMR and 1D 13C CPMAS, demonstrating that 2D 1H-detected SSNMR offers not only additional resolution but also sensitivity advantage over 1D 13C detection for the first time. High 1H resolution for the SAIL-labeled side-chain residues offered reasonable resolution even in the 2D data. A 1H-detected 3D 13C/13C/1H experiment on SAIL-ubiquitin provided nearly complete 1H and 13C assignments for seven Ile residues only within ~2.5 h. The results demonstrate the feasibility of side-chain signal assignment in this approach for as little as 10 nmol of a protein sample within ~3 days. The approach is likely applicable to a variety of proteins of biological interest without any requirements of highly efficient protein expression systems. PMID:25856081

Advances in Using Fiber-Optic Distributed Temperature Sensing to Identify the Mixing of Waters

NASA Astrophysics Data System (ADS)

Briggs, M. A.; Day-Lewis, F. D.; Rosenberry, D. O.; Harvey, J. W.; Lane, J. W., Jr.; Hare, D. K.; Boutt, D. F.; Voytek, E. B.; Buckley, S.

2014-12-01

Fiber-optic distributed temperature sensing (FO-DTS) provides thermal data through space and time along linear cables. When installed along a streambed, FO-DTS can capture the influence of upwelling groundwater (GW) as thermal anomalies. The planning of labor-intensive physical measurements can make use of FO-DTS data to target areas of focused GW discharge that can disproportionately affect surface-water (SW) quality and temperature. Typical longitudinal FO-DTS spatial resolution ranges 0.25 to1.0 m, and cannot resolve small-scale water-column mixing or sub-surface diurnal fluctuations. However, configurations where the cable is wrapped around rods can improve the effective vertical resolution to sub-centimeter scales, and the pipes can be actively heated to induce a thermal tracer. Longitudinal streambed and high-resolution vertical arrays were deployed at the upper Delaware River (PA, USA) and the Quashnet River (MA, USA) for aquatic habitat studies. The resultant datasets exemplify the varied uses of FO-DTS. Cold anomalies found along the Delaware River steambed coincide with zones of known mussel populations, and high-resolution vertical array data showed relatively stable in-channel thermal refugia. Cold anomalies at the Quashnet River identified in 2013 were found to persist in 2014, and seepage measurements and water samples at these locations showed high GW flux with distinctive chemistry. Cable location is paramount to seepage identification, particularly in faster flowing deep streams such as the Quashnet and Delaware Rivers where steambed FO-DTS identified many seepage zones with no surface expression. The temporal characterization of seepage dynamics are unique to FO-DTS. However, data from Tidmarsh Farms, a cranberry bog restoration site in MA, USA indicate that in slower flowing shallow steams GW inflow affects surface temperature; therefore infrared imaging can provide seepage location information similar to FO-DTS with substantially less effort.

Linking Automated Data Analysis and Visualization with Applications in Developmental Biology and High-Energy Physics

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

Ruebel, Oliver

2009-11-20

Knowledge discovery from large and complex collections of today's scientific datasets is a challenging task. With the ability to measure and simulate more processes at increasingly finer spatial and temporal scales, the increasing number of data dimensions and data objects is presenting tremendous challenges for data analysis and effective data exploration methods and tools. Researchers are overwhelmed with data and standard tools are often insufficient to enable effective data analysis and knowledge discovery. The main objective of this thesis is to provide important new capabilities to accelerate scientific knowledge discovery form large, complex, and multivariate scientific data. The research coveredmore » in this thesis addresses these scientific challenges using a combination of scientific visualization, information visualization, automated data analysis, and other enabling technologies, such as efficient data management. The effectiveness of the proposed analysis methods is demonstrated via applications in two distinct scientific research fields, namely developmental biology and high-energy physics.Advances in microscopy, image analysis, and embryo registration enable for the first time measurement of gene expression at cellular resolution for entire organisms. Analysis of high-dimensional spatial gene expression datasets is a challenging task. By integrating data clustering and visualization, analysis of complex, time-varying, spatial gene expression patterns and their formation becomes possible. The analysis framework MATLAB and the visualization have been integrated, making advanced analysis tools accessible to biologist and enabling bioinformatic researchers to directly integrate their analysis with the visualization. Laser wakefield particle accelerators (LWFAs) promise to be a new compact source of high-energy particles and radiation, with wide applications ranging from medicine to physics. To gain insight into the complex physical processes of particle acceleration, physicists model LWFAs computationally. The datasets produced by LWFA simulations are (i) extremely large, (ii) of varying spatial and temporal resolution, (iii) heterogeneous, and (iv) high-dimensional, making analysis and knowledge discovery from complex LWFA simulation data a challenging task. To address these challenges this thesis describes the integration of the visualization system VisIt and the state-of-the-art index/query system FastBit, enabling interactive visual exploration of extremely large three-dimensional particle datasets. Researchers are especially interested in beams of high-energy particles formed during the course of a simulation. This thesis describes novel methods for automatic detection and analysis of particle beams enabling a more accurate and efficient data analysis process. By integrating these automated analysis methods with visualization, this research enables more accurate, efficient, and effective analysis of LWFA simulation data than previously possible.« less

VisANT 3.0: new modules for pathway visualization, editing, prediction and construction.

PubMed

Hu, Zhenjun; Ng, David M; Yamada, Takuji; Chen, Chunnuan; Kawashima, Shuichi; Mellor, Joe; Linghu, Bolan; Kanehisa, Minoru; Stuart, Joshua M; DeLisi, Charles

2007-07-01

With the integration of the KEGG and Predictome databases as well as two search engines for coexpressed genes/proteins using data sets obtained from the Stanford Microarray Database (SMD) and Gene Expression Omnibus (GEO) database, VisANT 3.0 supports exploratory pathway analysis, which includes multi-scale visualization of multiple pathways, editing and annotating pathways using a KEGG compatible visual notation and visualization of expression data in the context of pathways. Expression levels are represented either by color intensity or by nodes with an embedded expression profile. Multiple experiments can be navigated or animated. Known KEGG pathways can be enriched by querying either coexpressed components of known pathway members or proteins with known physical interactions. Predicted pathways for genes/proteins with unknown functions can be inferred from coexpression or physical interaction data. Pathways produced in VisANT can be saved as computer-readable XML format (VisML), graphic images or high-resolution Scalable Vector Graphics (SVG). Pathways in the format of VisML can be securely shared within an interested group or published online using a simple Web link. VisANT is freely available at http://visant.bu.edu.